I am so excited by todays’ guest blog post. I’ve been so eagerly awaiting sharing it with you all. I don’t have any tattoos myself but it is something that is common amongst my friendship group, and I get asked about tattoo related infections A LOT. Partly as I was involved in some of the investigations when there was an issue some time back. So, a post that could help address some of the risk assessment and best practices linked to this art form felt very necessary, even though I didn’t feel I was best placed to write one. Then I saw this great article from Julie Russell on LinkedIn and I just had to reach out and see if she fancies writing a guest blog for me, and thankfully she said yes!
I first met Julie as Head of Culture Collection at Public Health England, that has since changed it’s name to the UK Health Security Agency. She was an inspiring microbiologist, who just had so much knowledge, and she became a great phone a friend. Since then she has moved on to work in a really different area where she still gets to put her microbiology and infection prevention and control knowledge to good use, as the director of a tattoo/art studio in Muswell Hill. No one is better placed therefore to answer the questions that I always get asked and have not felt best placed to answer.
Blog post from Julie Russell
After years in NHS microbiology laboratories, I joined the Public Health Laboratory Service, where I provided external quality assessment schemes and reference materials to laboratories worldwide. After that, I decided to do something completely different. I now co-own and manage Old Marine Arts Group, a tattoo studio in Muswell Hill, London.
It hadn’t occurred to me that tattooing, one of the oldest art forms in the world, essentially creates controlled wounds on people to decorate their bodies. I’ve had tattoos since my 20s – my first done in a legalised squat by a friend who’d never tattooed anyone in his life before. There was no personal protective equipment (PPE) involved; it healed beautifully, and I didn’t think about it anymore.
Many thousands of people across the UK have similar stories with no ill effects. Yet infections linked to tattooing have been recognised since the 19th century, and the government quite reasonably seeks to minimise such risks.
Tattooing, Skin, and Infection Risk
Bear in mind that the skin has a rich, diverse microbiome consisting of millions of microorganisms, some of which can cause infections if the skin is broken. Tattooing involves puncturing the skin with needles thousands of times, to a depth of approximately 1.5-2 mm, to place pigment into the dermis, creating a permanent design. Invariably, the tattoo process causes some bleeding, and after it’s finished, short-term redness, swelling and scabbing are normal. Resisting the urge to scratch is essential to minimise the risk of infection.
A July 2024 YouGov1 poll suggests 28% of UK adults – around 15 million people – now have tattoos. The UK Health Security Agency (UKHSA) notes that the true prevalence of tattoo-associated infections is unknown. There are no statutory notification procedures in place for infections specifically caused by tattooing, and no indication that such infections significantly burden the NHS. Various estimates suggest that approximately 1-3% of tattoos become infected in the UK. Most infections are mild local skin infections that can be treated with a single course of antibiotics; severe infections remain rare.
Interpreting the Evidence
Publications on tattoo-related infections must be read with caution. A December 2024 paper in The Lancet Microbe2, “Microbiology of tattoo-associated infections since 1820”, highlights rare severe cases such as necrotising fasciitis, leprosy and atypical mycobacteria outbreaks. The authors state that, “Despite advancements in public health policies and increased awareness of tattoo-related risks, a notable rise in both the number and diversity of microbial infections has been observed with an increase in the population opting for tattoos, particularly since 2000”. However, they provide no population-level denominators and conflate expected irritation, redness and swelling with true microbial infections. The authors fail to note that severe cases are overrepresented in the literature precisely because they are unusual. The paper may be a useful clinical catalogue, but it is not an incidence study.
A Brief History of Safety
Tattooists and clinicians have long recognised infection risks in tattooing. In the late 1800s, some artists infamously spat into powdered ink and sucked the needles during the tattooing process. Meanwhile, London-based artists in the early 1900s, such as Alfred South, promoted “the most perfect antiseptic treatment, painless and absolutely harmless”, whilst Tom Riley warned: “Caution to Ladies and Gentlemen thinking of being tattooed – First see the work of two or three tattooists then make choice {sic}. See that a complete set of new needles are {sic} used at each sitting as well as antiseptics”. Some early tattooists even wore white coats to convey a clinical level of cleanliness.
Legal regulation, however, arrived much later. It was still legal to tattoo children in the UK until the Tattooing of Minors Act 1969. Some aristocratic families reportedly tattooed babies for identification – in case, for example, their children were hospitalised or kidnapped.
Modern Regulation
Mandatory licensing changed the landscape. Under the Local Government (Miscellaneous Provisions) Act 1982, tattoo studios need to be registered. More recently, there is the British Standard BS EN 17169:2020, which covers safe and hygienic practice, although not many councils use it as a benchmark. This standard covers workplace preparation, equipment sterilisation, PPE, client consultation and aftercare. It requires studio owners to implement a comprehensive hygiene protocol to protect clients and staff, and tattoo artists to provide evidence of continued professional development.
Wales now requires tattooists to complete and pass a regulated Level 2 Infection Prevention and Control Award. Requirements in England and Scotland are less specific. Barnet Council licenses my studio; their Code of Practice 13 details the specific requirements for tattooing activities, in addition to those laid down in the Regulations applicable to all special treatment licensed premises. It notes that tattoo artists who are unable to demonstrate hygiene competence may be asked to complete a Level 2 hygiene certificate.
Reducing the Risk
Infection risk can be reduced through:
Good personal hygiene (artist and client)
Effective cleaning
Separating clean and dirty materials
Correct sterilisation or disposable equipment
Artists must assess clients for skin issues (including rashes, moles and scarring), alcohol or drug use, and relevant health risks (e.g. allergies, immunosuppression, pregnancy). Artists must be vaccinated against Hepatitis B.
Tattoo stations should be treated as clinical areas. Equipment must be protected from contamination; inks must be decanted into disposable cups; distilled water used for dilution of ink and ‘green soap’ (a vegetable-oil-based surgical soap used in the tattoo industry) or for washing the needles between colours.
Dressings applied afterwards are usually transparent, self-adhesive, polyurethane film (known as second skin in the industry), similar to those used for burns and post-operative incisions, or cling film attached to the skin with surgical tape. Clear aftercare guidance should be provided verbally and in writing about how to care for the tattoo whilst it heals (no swimming, spa pools, sunbathing, perfumed soaps or scratching).
Unlicensed Tattooing
Although it is illegal to tattoo in unlicensed premises, this is rarely enforced. Anyone can buy machines and inks online and tattoo friends at home, often with limited knowledge of hygiene.
Inspections across the UK vary, with some councils inspecting only once when the studio opens, while others do so more regularly. Licensing rules differ widely outside the UK. Excellent tattoo studios can be found abroad, but so too can be deplorable hygiene. Getting a tattoo may be a more permanent souvenir of a fun holiday than a fridge magnet, but it can be risky, and alcohol and sunshine don’t help healing.
Final Thoughts
Tattooing in the UK, when performed by licensed professionals, carries a low risk of infection. I believe the demand for tattoos will grow, and I support nationally enforceable, pragmatic safety standards.
Takeaway messages:
Tattooing by licensed professionals in the UK is low risk
Nationally recognised training and regulation are likely to emerge
A tattoo is a controlled wound—so please, as I once observed, don’t let your dog lick it
Kondakala, Sandeep et al. Microbiology of tattoo-associated infections since 1820 The Lancet Microbe, Volume 6, Issue 4, 101005
Training For Aspiring Tattoo Artists:
After two years in the tattoo industry, I now work with licensed tattoo artist, TomCatTatt, to provide introductory training for aspiring tattoo artists, covering the basics in safety and hygiene, legislation and licensing, and an introduction to tattooing techniques. Contact me for more information: julieru13@hotmail.com.
I am currently in the middle of secret project, which I hope to announce more about in late August/early September. I’m really excited about it but it’s taking a bunch of my time. I’m hoping that you will be just as excited when I can share more details. The wonderful Dr Claire Walker is helping me deliver my passion project by curating the Girlymicrobiologist blog for a few weeks. This means that I hope you all enjoy getting some great guest blogs from a range of topics. Girlymicrobiologist is a community, and all of the wonderful authors stepping up, sharing their thoughts and projects, to support me in mine means the world. I hope you enjoy this guest blog series. Drop me a line if you too would be interested in joining this community by writing a guest blog.
Callum is a disciple of the biomedical sciences, current master’s student creating a more authentic lab experience for those after me, aspiring consultant microbiologist (the best discipline, sorry Claire – you see he understands, like me, that micro will always trump immunology).
Callum is supervised by Dr Walker who is a paid up member of the Dream Team since 2013, token immunologist and occasional defector from the Immunology Mafia. Registered Clinical Scientist in Immunology with a background in genetics (PhD), microbiology and immunology (MSc), biological sciences (mBiolSci), education (PgCert) and indecisiveness (everything else). Now a Senior Lecturer in Immunology at University of Lincoln. She has previously written many great guest blogs for the Girlymicrobiologist, including Exome Sequencing and the Hunt for New Genetic Diseases.
Blog by Callum Barnes
Hello again everyone! It certainly feels weird to be writing another one of these, but my supervisor the lovely Dr Claire Walker thought it would be a great idea considering the outcome of my research that I discussed here.
A small recap for those that don’t want to read two blogposts – I am an Mbio Biomedical Science student at the University of Lincoln and completed my portfolio on a placement year in a local microbiology lab. It was great and I became so much more confident in both my practical and theoretical work, which really showed me the value of clinical placements. The problem is that these placements are too few and too competitive nationwide, and only a fraction of those that want to join the biomedical workforce get to experience them despite their value. Long story short, we created a clinical simulation that was as authentic to a real pathology lab as possible, with patient request cards and a functioning (front-end) LIMS, both seen below:
Can you believe no one got the Star Trek references? Anyway. The results were honestly incredible, with basically everyone that participated getting value out of it. I can’t share too much as we are yet to publish, but here are some quotes that really highlight how the clinical simulation increased confidence and was effective as a learning tool.
“Getting hands on experience in the lab. It gave me the confidence to continue in the lab setting.”
“Overall, the lab practicals have been helpful. I think my lab skills have drastically improved, especially my microscopy skills and interpreting my lab results.”
“I like the opportunity we had to practice new skills and learn about it in the contrast of a case study.”
These results were really good, but during my background research I came to realise that other medical disciplines are ahead of us in utilising learning tools to teach university students – like really ahead. Trainee doctors have actors, manikins, and in the last decade have extensively integrated VR/AR/XR technologies into their teachings. We are left with a couple of practical sessions per discipline to cover the hundreds of different diagnostic processes that biomedical scientists go through. And this is almost entirely down to cost, practicals cost a fortune after all. They take setting up, and time, which staff don’t have enough of as is. Which brings us back to virtual reality…
Virtual reality (can be) cheap, accessible, and most importantly repeatable. Other medical disciplines have already identified this, and there is good data to back up the use of VR in those disciplines. But none in biomedical science, because clinical simulation is only just being recognised as a worthy endeavour.
And so, this is going to be my goal. I am going to develop software to train biomedical scientists in virtual reality. It’s going to be tough, but I do truly believe that this is a sorely neglected part of training the next generation of pathologists here in the UK, and honestly hopefully the world too. And if everything goes well (and even if it doesn’t), I’ll be back here in a year to let you all know how it went.
Following on from the wonderful fungal post on fungal toxins (mycotoxins) last week from Dr Sam Watkin, I wanted to follow up with a post on the latest fungi of interest from a clinical perspective, Candidozyma auris. This fungi is getting more and more coverage, as well as becoming more important in healthcare, so I thought I would take a moment to talk about what it is, what it does, how to find it, and what to do when you do.
In a pre-pandemic world, which feels like a long time ago, Professor Lena Ciric was working at a media fellowship, and as part of that work wrote an article for the BBC on Candida auris, which has subsequently been renamed to Candidozyma auris.
This article came out in 2019, so maybe C. auris is not so new but in terms of the numbers of cases we are seeing within the NHS, and the changing prevalence out in healthcare systems more widely, it is definitely more of a feature and a concern than it was back then. Reflecting this change the UKHSA guidance Candidozyma auris (formerly Candida auris): guidance for acute healthcare settings which was originally published in 2016, has been updated recently (19th March 2025). It feels timely therefore to put something out in order to raise awareness of this organism and the unique challenges it presents.
NB I can neither spell nor pronounce Candidozyma auris and so we’re sticking to C. auris from this point out.
Yeast are a type of fungus, and Candida species are often associated with colonisation (present without causing infection or symptoms) on skin, in the mouth or within the vagina. If they grow up to high levels they can cause an infection called candidiasis, which often causes symptoms like itching or discharge. Common infections include Thrush and nappy rash. Candida albicans is one of the most common yeast infections seen within the healthcare setting, and in this kind of environment more serious infections can be seen, especially those linked to the blood stream, and occasionally serious organ infections.
C. auris was originally believed to be a relatively new species of genus Candida, as it often behaves in a similar way to the other Candida species. The reason for the name change to Candidozyma auris, was because, although in many ways it behaves similarly to its Candida cousins, it does have some differences in the way it behaves. These include features such as intrinsic antifungal resistance and growth conditions, that make it useful to characterise in a way that acknowledges it as a novel genus in its own right.
What is the difference between C. auris and the other Candida species that you know?
Many Candida species can cause severe infections within specific settings, however C. auris has been known to not only cause a wide variety of infections (bloodstream, intra-abdominal, bone and cerebrospinal fluid (CSF) infections), but ones which lead to significant mortality rates, with an estimated rate of 30 – 72% in severe infection reported in the literature.
Infections can occur in any patient group, although UK outbreaks have been most frequent associated with adult settings. Augmented care settings (such as intensive care and transplant settings) are at highest risk due to the vulnerable, long stay nature of many of their patients. Management of any infection occurring is complicated by the fact that C. auris has developed resistance to many available classes of antifungals, with emergence of pan-resistant strains, which add to the mortality risk.
C. auris also appears able to both easily transmit and colonise the skin of patients, with most patients being colonised before they go on to develop any subsequent infection. These colonised patients can then contaminate their healthcare environments, and unlike other yeast species, C. auris is able to survive and represent a continued risk within the environment for prolonged periods, all of which contributes to outbreak risk.
It was first identified in the ear canal of a patient in Japan in 2009, but has since been found globally, and is now separated into six genetically distinct clades:
Clade I = the South Asian clade, first detected in India and Pakistan
Clade II = the East Asian clade, first detected in Japan
Clade III = the South African clade, first detected in South Africa
Clade IV = the South American clade, first detected in Venezuela
Within the UK from January 2013 – December 2024, 637 C. auris isolates were reported through laboratory surveillance in England, with 59 (9.3%) isolated from blood culture specimens. It should be noted that not all labs report, and for some time many labs could not accurately identify C. auris, or actively screened for it, and so this may represent under reporting. A routine whole genome sequencing service is not currently available for typing, although it can be undertaken linked to specific outbreaks. Hopefully this will be up and running soon to better understand how the different clades discussed above are represented in the UK, and whether any of them are linked to more challenging outcomes than others.
Due to its global distribution, overseas patients may also be at increased risk of introducing C. auris into UK healthcare settings, with one centre reported 1.6% of their overseas admission detected as colonised, with patients coming from the Middle East, India and Pakistan, showing higher levels of recovery.
UKHSA guidance suggests we should screen any patient who has had an overnight stay in a healthcare facility outside of the UK in the previous year, as well as patients patients coming from affected units in the UK. This sounds relatively straight forward, but it can be challenging to identify patients who have had an overnight stay overseas on admission if they are not being admitted from overseas. It also relies on clear communication from other centres that they have an issue, if we are to screen patients from impacted units. Many centres have therefore decided to screen all patients on high-risk wards, such as intensive care, to address some of this unknown risk.
Risk factors for developing C. auris colonisation or infection should be considered when deciding on screening strategies and the list within the UKHSA guidance includes patients who have experience:
healthcare abroad, including repatriations or international patient transfers to UK hospitals for medical care, especially from countries with ongoing transmissions
recent surgery, including vascular surgery within 30 days
prolonged stay in critical care
severe underlying disease with immunosuppression, such as HIV and bone marrow transplantation
corticosteroid therapy
neutropenia
malignancy
chronic kidney disease or diabetes mellitus
mechanical ventilation
presence of a central-venous catheter or urinary catheter
extra-ventricular CSF drainage device
prolonged exposure to broad-spectrum antibiotic or antifungal use
Screening is undertaken by taking swabs from the axilla (armpit), groin and nose, although different patient groups may require additional screening. Patient surveillance is important for two reasons:
1) to understand which patients are colonised in order to introduce additional precautions to limit risk of transmission to other patients or the environment
2) to support improved patient management but allowing patients to be put on the most effective antifungal if they go on to develop any signs of yeast infection, in order to improve outcomes
If a patient is detected as positive, other screening sites can help manage individual patients and so UKHSA say additional site screening should be considered:
urine (especially if there is a urinary catheter in-situ, including intermittent self-catheterisation)
throat swab
perineal swab
rectal swab (in paediatrics we would consider a stool sample instead)
low vaginal swab
sputum or endotracheal secretions
drain fluid (abdominal, pelvic or mediastinal)
vascular access sites
wounds or broken skin
ear
umbilical area (neonates)
Swabs should ideally be processed on chromogenic media (colour changing agar plates) and fungal colonies confirmed using MALDI ToF or a validated PCR (my previous post on PCR may help with this). It can also be helpful to incubate plates at 40oC, as C. auris can grow as much higher temperatures than its Candida cousins, which can help with identification. If grown then the yeast should be stored in case you need them for future typing to help in understanding transmissions or outbreaks.
Why should we care about it?
Due to the high mortality rates for patients who develop infections, and the issues with choosing antifungals that work, it is really important that we know when we have patients who are colonised with C. auris. Controlling spread, even if patients don’t become infected, is incredibly important for the individual. This is because if a patient is detected as positive they won’t be de-alerted (have IPC precautions stopped) at any point and so it will impact them for months, if not years. These IPC precautions include isolation (keeping separate from other patients), and sometimes only being nursed by specific members of staff. These patient and staff impacts are so significant they’ve even been acknowledged in popular media, with a three episode arch covering C. auris in The Resident on Netflix (season three, episodes 18, 19 and 20).
Are there differences in how you might treat?
As I’ve already said, C. auris is pretty resistant to treatment compared to its Candida cousins. UK data indicates that isolates are resistant (don’t respond to) to the normal first line treatment of fluconazole, and often to other antifungals within the azole class. Some isolates have been resistant to other commonly used antifungals, such as amphotericin B (20%) and echinocandins (10%). Resistance to other antifungals can also occur whilst infections are being treated, and so it is important to monitor sensitivities (whether the drug works) and send to reference labs in order to understand the most appropriate therapy. Its resistance profile is one of the reasons the WHO have highlighted C. auris as a priority fungal pathogen for further research and to highlight clinical risk.
Its not just antifungals that are important however, antimicrobial stewardship is important in general, as prolonged exposure to broad-spectrum antibiotics and antifungal agents are risk factors for both C. auris colonisation and infection (again this links back to the high risk patient groups impacted). Therefore, doing a better job of monitoring and controlling antimicrobials in general is likely to have a beneficial impact on C. auris risk.
Challenges with environmental control
One of the many things I love about the new C. auris guidance is its focus on multidisciplinary input ‘Healthcare workers are encouraged to work in multi-disciplinary teams, including Clinical Infection Specialists and IPC teams, to risk assess and support the management of patients infected or colonised with C. auris‘. I think this is so important, especially with an organism that is so challenging and can present such a high risk.
Environmental control is a particular issue for C. auris as we know it’s ability to survive and can grow at higher temperatures than many other fungi, means that it is likely to survive well in the environment. It also has the ability to form environmental biofilms, which can mean it is difficult to impact effectively using standard cleaning techniques, and once within the environment has been been detected for 4 weeks.
Within the UKHSA documentation, environmental contamination for C. auris has been found on the following surfaces during outbreaks:
beds, bedside equipment, bedding materials including mattresses, bed sheets and pillows
ventilation grilles and air conditioning units
radiators
windowsills and other horizontal surfaces
hand wash basins, sink drains and taps
floors
bathrooms doors and walls
disposable and reusable equipment such as ventilators, skin-surface temperature probes, blood pressure cuffs, electrocardiogram leads, stethoscopes, pulse oximeters and cloth lanyards
Basically most of your healthcare environment, whether fixed or movable features. In order to help stop the transfer from patients to the environment, via staff, the use of personal protective equipment is really important. Therefore the use of gowns and gloves is suggested. Single use and disposable equipment should also be used whenever possible, and patients should be kept in single, ensuite rooms, to minimise the risk of C. auris escaping from within the bed space to adjacent clinical environments. Any items within the space should either be cleanable with a disinfectant, or disposed of after a patient leaves. One thousand ppm of available chlorine should be used for cleaning, but needs to be used in concert with an appropriate contact time if it is to be effective.
WHO fungal priority pathogens list to guide research, development and public health action 2022
Outbreaks
Most detections of C. auris cases detected are colonisation rather than infection (though colonisations can lead to subsequent infections). Within the UK there have been 5 significant outbreak of C. auris, each with over 50 cases, in addition to many sporadic introductions of single cases, frequently from overseas. Many of these have been in London or the South of England, and have resulted in considerable disruption to services over a prolonged period of time. This disruption can, in itself, be a risk to patients as it can result in delayed access to care. Outbreaks are also financially significant, with outbreaks reported as costing over £1 million for a service impacted for 7 months.
Although outbreak numbers are currently small, they are becoming more frequent, and even if infrequent have significant impacts. The need to control this risk before it becomes endemic within the UK health system is therefore significant. It is crucial therefore to collect more data and understand transmission routes of C. auris better.
Despite probable under reporting, it is clear that C. auris is becoming more common within UK healthcare settings, and has the ability to both cause significant issues for both individual patients and for services, due to outbreak impacts. Although fairly new on the scene there is increasing recognition of how C. auris could change fungal risks within healthcare, and even long stay residential settings. If we are going to adjust approaches in order to react to the new risks C. auris represents we need to both update our current practices, and invest in research, in order to learn how to do things even better. This is the reason that it feels important to share a post that is a little more technical than normal, both to help myself by learning more, but also to ensure that we are having conversations about an organism that has the ability to impact us all.
Dr Claire Walker has been a paid up member of the Dream Team since 2013, token immunologist and occasional defector from the Immunology Mafia. Registered Clinical Scientist in Immunology with a background in genetics (PhD), microbiology and immunology (MSc), biological sciences (mBiolSci), education (PgCert) and indecisiveness (everything else). Now a Senior Lecturer in Immunology at University of Lincoln. She has previously written many great guest blogs for The Girlymicrobiologist, including one on turning criticism into a catalyst for change.
What may be less well known, even to regular readers of this blog, is that she did her PhD on finding genetic diseases, and as this ties in so well with the recent blog series I’ve been doing on DNA I thought having a guest blog from Claire might be the cherry on top of this particular ice cream sunday!
If you’ve missed any of the blog series of posts, especially if you want a refresher on how DNA works before reading about Claire’s work, I’ve included links to all the posts the below:
Having spent some time covering what is however, I thought I would follow up with a couple of book reviews that focus on how the world of DNA, DNA editing and DNA interpretation could change the lives of everyone involved.
When I was 26 I finished my Clinical Scientist training and was offered a full-time position at the hospital I trained in, with a good pay increase and a view to becoming a laboratory manager in the next few years. It was a great gig with a lovely team, good earning potential and support to further my clinical training. Unfortunately for them, I had just completed a secondment to a famous children’s hospital and had my mind absolutely blown. I had seen how immunology was being influenced by the study of human genetics, at the forefront of the field with cutting edge techniques which seemed, frankly, indistinguishable from magic. Suddenly, working in adult rheumatology and learning how to manage NHS laboratory budgets just didn’t seem so interesting anymore. So I turned down the job, went home, looked my husband in the eye, and said the words he’d been quietly dreading ever since I’d first jumped from environmental microbiology to human immunology: ‘I think I want to retrain… again.’
I applied for a PhD in genetics and immunology at University College London Institute of Child Health. Specifically, I focused on children with rare syndromes that didn’t have a clear diagnosis often called “syndromes without a name.” These kids and their families had often been on a long and frustrating diagnostic journey, seeing specialist after specialist, with no real answers. That’s where exome sequencing came in. By reading the protein-coding parts of the genome — the exome — we hoped to find clues hidden deep in their DNA that could point to the cause of their symptoms. Think of it like a high-stakes game of genetic detective work. Each patient’s exome was a puzzle, and sometimes, we’d find that one variant that explained it all. Other times, we discovered new candidate genes that had never been linked to disease before. Conversely, we found that some quite well-known genetic diseases could have highly unusual presentations – what we call expanding the clinical phenotype of a condition.
The disease I was assigned to work on was the oh-so-easy to pronounce and explain, Haemophagocytic Lymphohistiocytosis (HLH). HLH is a rare but serious condition where the immune system goes into overdrive and won’t switch off. Instead of protecting the body, it causes severe inflammation and can damage organs including the liver, brain, and bone marrow. It can look like a really bad infection, but it’s actually the immune system attacking the body from within. Some cases are triggered by infections or cancer, but others are caused by inherited defects in genes like UNC13D or PRF1. The children in my student were amongst the big chunk of patients where none of the usual suspects showed up on molecular testing.
But finding a genetic change through exome sequencing was only the beginning — I still had to figure out if it actually meant anything. Not all changes in our DNA cause disease, so we looked for the presence of the mutation in healthy controls and used predictive software like PolyPhen2 to solve the first clue: what would this mutation do to the protein the gene encoded? Then came the hard part — proving it. I had to design and run experiments to test how the genetic fault affected the protein’s job in the immune system, and whether that could explain the symptoms we were seeing in the child.
The hard work paid off, in my study we found: one case that was UNC13D protein defective HLH, but only affected the brain; one that turned out to be a totally different (and very rare) immune disorder; and one that revealed a brand-new genetic disease caused by defects in DNaseII resulting in something akin to HLH and another inflammatory condition. In all of these cases what this really gave us was the opportunity to get these kids an answer and onto treatment that could actually work for them.
Figure 3. Defects in DNaseII sit downstream of defects known to cause HLH. Image credit – Claire Walker, thesis.
For me what’s really fascinating about genetics is that what took me years of research is fast becoming a routine test – an incredible reminder of how quickly genetic technologies can evolve. What was once a complex puzzle of genetic mysteries is now providing families with the answers they’ve long needed, turning uncertainty into hope and paving the way for more personalized, effective care in the future. I think that alone was worth putting my husband through yet another ‘re-training’ episode, who knows what I’ll come up with next?
I hope this addition has given you an insight into why working to learn more about how our genes impact us is so important, but also how needed specialists like Claire are for us to do this safely and make the difference we want to make. Sometimes all patients need is an answer, a name to put to what they are going through, something that can provide a route forward even if it doesn’t provide a complete fix. Something so simple can be so difficult to achieve, but just because something is hard doesn’t mean that we shouldn’t try.
This month I’ve been honouring of World DNA day 2025 by publishing a number of posts linked to what DNA is, how we look for it, and what it means to send it away.
Today I’m talking about Upgrade by Blake Crouch. In the story explored in this world, DNA based technology, although very obviously rooted in present day science, has evolved and so has the impact and access to this technology for both individuals and society. In this post I thought it might be interesting to explore ow much of this book is science, and how much of it is fiction? Before I get onto that however, here’s a reminder of the other posts that have been available in the DNA blog series:
One of the reasons I picked Upgrade for the final book review is that I thought it would be interesting, after discussing the current usage of DNA for testing and therapies in previous posts, to explore a book that covers a slightly further future, based in 2060, and what impact the use of DNA technologies could have on humanity in the future.
‘You are the next step in human evolution . . .’
What if you were capable of more?
Your concentration was better, you could multitask quicker, read faster, memorize more, sleep deeper.
For Logan Ramsay, it’s happening. He’s beginning to see the world around him, even those he loves the most, in whole new ways.
He knows that it’s not natural, that his genes have been hacked. He has been targeted for an upgrade.
Logan’s family legacy is one he has been trying to escape for decades and it has left him vulnerable to attack. But with a terrifying plan in place to replicate his upgrade throughout the world’s population, he may be the only person capable of stopping what has already been set in motion.
To win this war against humanity Logan will now have to become something other than himself . . .
In this world, DNA based technology, although very obviously rooted in present day science, has evolved and so has the impact and access to this technology for both individuals and society. It raises some interesting questions about what it means to be human. In this post I thought I would explore some of the science that is included, and what questions the use of this science brings into play.
Are visions of a world where DNA controls our lives unique?
Before I get into the science of the book however, I wanted to flag that visions of a world where the use of DNA testing, evaluation or modification, are not new. GATTACA (did you see what they did there……they are all DNA bases) have been around since the 90’s, when the technology we use clinically now was only in its infancy. Fear of how science could be used in the future is a pretty constant feature of this type of creative content, as it provides a safe way to explore these fears and ethical challenges. I suppose what I’m saying is that just because something is included in these kinds of visioning pieces does not make it bad, wrong or scary. It just means that we also need to think and reflect on what checks and balances are included as part of their introduction in order to make sure the world we create and influence based upon them is the one that we are aiming for, and we have taken steps that include the law of unexpected consequences rather than ignoring it. DNA editing is an amazing, technically complex and powerful tool that has the potential to be positively life changing, so please keep that in mind when you read the rest of this post.
The world of upgrade
In the world of Upgrade the impacts of climate change have really been felt. Entire cities have been flooded as the seas rise and access to food has become a real issue for vast portions of the worlds population. Logan, our protagonist is the son of a genius, a woman changing the face of science. Being the child of a world famous geneticist makes Logan feel the reality of being a normal person surrounding by an extraordinary vision.
I had extraordinary dreams but had been gifted only an ordinary mind
Sadly, as is often the case in these tales, his mothers (Miriam Ramsay) drive for change comes with a fair amount of hubris. In an attempt to address the food shortages Miriam, with Logan supporting as a junior scientist, develops a new gene editing tool called Scythe in an attempt to genetically enhance rice crops. The process goes wrong, and results in The Great Starvation that leads to the deaths of 200 million people.
As a result of the mass deaths, genetic manipulation using Scythe or related tools originating from CRISPR, are outlawed and their use results in a mandatory 30 year minimum jail term. Thus making the field of genetics either outlawed or suspect, and to the birth of the Gene Protection Agency, a police force which aims to track down those undertaking illegal manipulations or research.
Logan ends up going to prison for his work with his mother’s research, and his mother commits suicide. After serving his time Logan is released and joins the very agency that has been set up to prevent a repeat of the genetic manipulation that changed the world. At the start of the book Logan is investigating a scene where an explosion happens, his body is hit by shards of ice, and his life changes again…..forever.
My mother had tried to edit a few rice paddies and ended up killing two hundred million people. What havoc could she wreak—intentionally or through unintended consequences—by attempting to change something as fundamental as how Homo sapiens think?
So, what is gene editing?
I’ve already mentioned CRISPR but I’ve not described what it or gene editing actually are. Gene editing as defined by the World Health Organisation is:
A method for making specific changes to the DNA of a cell or organism. It can be used to add, remove or alter DNA in the genome. Human genome editing technologies can be used on somatic cells (non-heritable), germline cells (not for reproduction) and germline cells (for reproduction).
Before I go further I should probably talk about how CRISPR works and what it is used for. Tools like CRISPR/Cas9 are tools for gene editing, and are the present day origins behind the futuristic tools present in Upgrade. Emmanuelle Charpentier and Jennifer Doudna were awarded the Nobel Prize in Chemistry in 2020 for the development of CRISPR, commonly referred to as genetic scissors.
CRISPR allows you to design a targeted way of manipulating a gene section that you are interested in, and in some cases then replace it with an alternative gene section, which enables the gene to function in a different way. Being able to target and replace, or inactivate genes, in this way opens up a whole new world of possibilities, from health to industrial applications. There are three main approaches to gene manipulation:
Replacing a disease-causing gene with a healthy copy of the gene
Inactivating a disease-causing gene that is not functioning properly
Introducing a new or modified gene into the body to help treat a disease
Now, wearing my geek credentials on my sleeve, I wanted to share with you a music video that describes how CRISPR works. It’s set to the music of ‘Mr Sandman, bring me a dream’ and is retitled ‘CRISPR/Cas9 bring me a gene’. I love this as it I think it describes the history of the process really well. I will tell you now though, that when I made Mr Girlymicro watch this for the 5th time he could not get out the room fast enough, so this may just be a me thing.
Where is the science rooted in the present?
Having talked about the fact that gene editing isn’t the work of science fiction, I thought it would be useful to talk about how and where it is actually being used right now.
According to the Federal Drug Administration there are a variety of types of gene therapy products, i.e. products that manipulate genes, currently available:
Plasmid DNA: Circular DNA molecules can be genetically engineered to carry therapeutic genes into human cells.
Viral vectors: Viruses have a natural ability to deliver genetic material into cells, and therefore some gene therapy products are derived from viruses. Once viruses have been modified to remove their ability to cause infectious disease, these modified viruses can be used as vectors (vehicles) to carry therapeutic genes into human cells.
Bacterial vectors: Bacteria can be modified to prevent them from causing infectious disease and then used as vectors (vehicles) to carry therapeutic genes into human tissues.
Human gene editing technology: The goals of gene editing are to disrupt harmful genes or to repair mutated genes.
Patient-derived cellular gene therapy products: Cells are removed from the patient, genetically modified (often using a viral vector) and then returned to the patient.
There are a number of ways that gene therapy products are already being used for the clinical management of patients, including for patients with conditions such as HIV and sickle-cell disease. One big change that has occured during my clinical career is the use of CAR-T cell therapy for tackling some types of cancer. CAR-T cell therapy is a type of immunotherapy where a patients own T cells (type of white blood cell) are taken from a patient who has cancer, and the cells are then modified in order to better recognise and attack cancer cells within the patients body when they are then given back. So gene editing is already saving lives and in every day use, even if its roll out is currently limited.
Having established that gene editing is very much the next frontier for expansion in healthcare, it’s probably important to consider how stable these changes will be within the wider the gene pool. It’s worth noting that the human genome editing techniques that are being introduced in healthcare are linked to somatic cells, where changes would be non-heritable, rather than within germline cells, which are involved in reproduction, where any changes would be inherited by future generations. Most of the changes that are currently being targeted for gene therapy would not therefore cause the changes to be established within the gene pool. There is a question about whether the target genes, even for somatic changes, may become more established as some of those carrying them may not have previously survived to reproductive age, but to be honest this feels like the impact will be minimal and a price worth paying as a society for improving both quality and length of life in those impacted. Changing future generations of children is however a whole different ball game.
The technology discussed within Upgrade has moved on somewhat from CRISPR. It retains some features of current technology however, as the delivery of Scythe is via viral vector. The interesting thing about this form of delivery is that, in the world of Upgrade, the viruses have been modified and use their standard invasion routes to deliver the genetic material into cells, but, unlike the way that this is being undertaken as part of gene therapy in current healthcare, the viruses do not appear to have been fully modified to remove their ability to cause infectious disease. Some of the plot, therefore, is driven by the fact that it is possible to undertake wide spread indiscriminate gene editing within the human population. The modified viral cells retain their transmissibility alongside their gene editing functionality, and so a gene manipulation can spread in a similar way to any respiratory viral infection. The R0 within Upgrade is 8, which means that every person infected will infect, on average, 8 other people, which means the potential for spread within the population is massive. (If you want to know more about what an R0 is, I’ve covered it in a previous post here). It is not clear to me whether the gene targets within Upgrade are targeting just somatic changes, or a combination of somatic and germ line, but when you can spread so widely so quickly that is probably not the main consideration.
What questions does Upgrade raise?
Within the world of Upgrade, the gene editing doesn’t just target a single gene, but a whole suite of different genes for large scale changed. The problem with using gene manipulation that changes multiple gene targets, that are non-personalised to the condition/individual, and are highly transmissible, is that it is highly likely that the changes won’t work for everyone’s genome. There are going to be side effects or potentially significant impacts. Within Upgrade these are seen through errors that then occur in the brain due to protein mis-folding, very similar to how prion diseases work. The change in some people is catastrophic and there is no intervention available to reverse it. Using indiscriminate gene manipulation has the power to create mass disruption and change societies. It is this power for change that is the jeopardy that drives the novel. Is the cost worth the outcome, and who gets to decide? How much collateral damage would we be prepared to accept, even if the wider benefit to society is a positive one?
Prion diseases: A rare group of neurodegenerative disorders October 2022 In book: Viral, Parasitic, Bacterial, and Fungal Infections Antimicrobial, Host Defense, and Therapeutic Strategies (pp.651-662) Edition:1 Chapter: 53 Publisher: Elsevier: Academic Press
What does it mean to be human?
As part of this risk/benefit consideration, Upgrade asks a lot of questions of the reader, the main one of which, for me, is what does it actually mean to be human?
There is a genetic definition of what it means to be human, but the gene modifications within humans causes our protagonist Logan to ask some very valid questions about what it actually means to be human. Is it just about genetics? How much can we change not only our genes, but our outlook/perceptions, as people and still remain human?
The ‘upgrades’ received cause different characters in the book to judge humanity in general, and other human beings, in very different ways. Do genetic changes make you superior? Does being intellectually smarter permit you to make decisions for others for their benefit, as determined by the smarter individual? In many ways this brought to mind, for me, the old approach to clinical decision making, which was very paternalistic and the role of the person/people impacted was highly passive. I’d like to think we are now moving towards a much more patient focus decision making process, but this book made me think about what would happen if this model was used, not just for one to one interactions, but for the future of humanity.
The question about decision making is an interesting one however. There is plenty of data that demonstrates improved decision making in small groups, and if time is of the essence how would you engage with enough people for a decision to be valid? Especially a global decision? How many people would you need to interact with for a choice about changing the DNA of your species to be valid? How would you manage a lack of consensus? Would you let the world burn whilst the choice was being made, or would you accept that at some point someone would need to step in and lead the way forward? It’s the uncomfortable space between ethics and pragmatism, and definitely not something that is easy to answer, even conceptually.
Is intelligence the problem?
As discussed above, a lot of the plot driven by the counter to our protagonist in Upgrade, is based on the concept that if humans were smarter they would make better decisions. Therefore, by improving how people think and removing some of the emotional component the human race would be improved and therefore ‘saved’. This is especially important in the world of Upgrade, as because of the damage that is being done linked to climate change and other damage caused by humanity, the clock is ticking and Logan is very aware in his upgraded state that there is only 100 years left to save mankind.
The problem, as it plays out to me, is that it is very much not about intellect however, it’s about the ability of individual humans to care enough for others. For one person to make decisions that costs them rather than benefits them for the sake of someone that they do not know well if at all. This is especially true for problems that are going to impact future generations, like climate change, where the people most impacted have yet to be born. By the time we ‘meet’ those who will be most affected it will be too late to save them. Even for a present day context it raises questions, we all think of ourselves as having empathy and caring for others, so why does that not play out and allow us to care for the migrants that are dying trying to join us and share in our safety? Why is our compassion so limited?
One of the reasons for this has nothing to do with intellect, and would in no way be altered no matter how smart we become. It’s based on a theory known as the Dunbar number, which predicts that we can only empathise with a maximum number of 150 people, the number of people that would likely to have been the maximum size of our primate tribe. More than this, we can only truly care, to the point we may want to sacrifice, about a much smaller number of people. The book therefore postulates that we aren’t held back due to a lack of intelligence or innovation, we’re held back by a lack of compassion and the ability to truly care about people we don’t know and will never meet. If we are to change anything about ourselves in order to save mankind therefore, it’s not intellect we need more of, we need to find a way to increase our capacity for compassion and therefore change our Dunbar number, to adapt for the world we now find ourselves in. So maybe the answer to the problem is to become more ‘human’ rather than less.
Where do all of these questions leave today’s gene editing technology?
Gene editing technologies are making massive strides, saving lives, and positively helping people who have serious health conditions.
Somatic gene editing is well established, and has been developed over the last 20 years so that regulation is in place, and it being more and more routine rolled out in countries that have access to advanced scientific technologies. The problem is just that however, these interventions are technologically challenging and incredibly expensive, and therefore not universally available. This means that they also do not necessarily take into account the diversity of the human genetic population or the lived experience within different cultural communities. Regulation is also not present universally, with some people forced to access these therapies through the use of rogue clinics, or by undertaking medical tourism, which brings with it increased risk. There is also the potential for illegal, unregistered, unethical or unsafe research and other activities, including the offer of unproven so-called therapeutic interventions, as with any emergent technologies. Ensuring equity of access and appropriate regulation will be essential to ensure a safe global adoption of these therapies.
Germline gene editing is however in a very different place, as this would lead to the editing of DNA in a way that may be heritable across generations. There is an intense debate linked to its use as the the future generations that would be impacted would have no capacity to consent to the changes, and or risks, that are being made. There could be possible risks and consequences for offspring and for society in general, and once that genie is released it will not be possible to put it back in the bottle. Discussing what circumstances it would ever be appropriate to undertake these changes requires us all to be actively engaged in these discussions.
I hope you’ve enjoyed these series of blogs linked World DNA Day and taken some to celebrate the miraculous nature of just being you. I’ve really enjoying sharing some of the technical information, but also diving into some fictional worlds and discussing the thoughts that they provoke. With summer coming up I hope you may even pick up a copy of these great novels and dive into their worlds yourself. If you find any others in your reading adventures, return the favour and let me know. I may even include them in a future review. Happy reading.
Friday just gone, 25th April, was World DNA Day. I’ve had a series of blogs that I’ve been playing around with linked to what DNA is, how we look for and investigate it and how we are exploring DNA in our everyday lives. Linked to this I’ve also got two book reviews coming where the world changes because of genetic testing and genetic manipulation. So this is the first of four part DNA bonanza.
I thought I would write these posts, because as much as artificial intelligence could change the way we live and is frequently discussed, we are all accessing DNA based testing more and more, with many of us not really thinking about how this too is changing the world in which we live.
I remember really clearly the first time I actively came across the concept of DNA, DNA testing and DNA manipulation. It was in Jurassic Park, when Mr DNA pops up at the start of the film to talk you through how they used DNA and cloning in order to make the dinosaurs. This film came out in 1993, I was 13 and I just remember how all of my class were queuing up to get tickets. It was the first film I really remember there being hype about, well that and Aladdin which was a different kind of seminal moment. It was the first film I remember watching and thinking just how cool science and scientists were.
In fact I talk about Mr DNA so much that the wonderful Mr Girlymicro brought me a Mr DNA Funko pop which lives on my desk at work and reminds me that the impression we make on people stays with them.
What does all this have to do with how we use DNA now? Well, in 1990 when Jurassic Park came out, the routine use of DNA, even in research, was still pretty much science fiction. The structure of DNA had only been described in 1953. Polymerase Chain Reaction (PCR), which is the main way we investigate DNA, had only been developed in 1983, and was only starting to become more widely available in the 1990’s. When I started working within healthcare in 2004, we were only really just starting to move from PCR being something that was used in research to something that was common place in clinical diagnostics. The leap from there, to a world where thousands of us can swab ourselves at home and post samples off to be diagnosed with SARS CoV2 during the pandemic, or to get information on our genetic heritage, would have sounded like something that would only occur in a science fiction novel if you’d mentioned to me back theb.
Just a flag, this part one post has a lot of the technical stuff linked to what DNA is and how we investigate it. You may want to skip this post and head directly for part two if you don’t want to be reminded of secondary school science, but if you can bear with me I think it will help some of the context.
What is DNA?
DNA, or to give it its full name Deoxyribonucleic acid, is commonly referred to as the building block of life. The structure of DNA consists of a double-stranded helix held together by complementary base pairs. The nucleotides that form the base pairs are adenine, thymine, guanine or cytosine. These nucleotides act to link the two strands together via hydrogen bonds, with thymine always pairing with adenine (T-A) and guanine always pairing with cytosine (G-C).
Sections of DNA then combine together together to code for genes, which are sections of DNA that work together in order to code for proteins, that then permits the expression of our DNA in physical form.
Genes are organised into chromosomes or packages of DNA. Each chromosome is formed from a single, enormously long DNA molecule that contains a strand of many genes, with the human genome containing 3.2 × 109 DNA (3,200,000,000) nucleotide pairs, divided into 46 chromosomes formed from 23 pairs (22 pairs of different autosomes and a pair sex chromosomes).
So how do we get from DNA to proteins? The specific sequences of nucleotides that form our DNA are arranged in triplets (groups of three). To turn DNA into protein, it gets transcribed into RNA (ribonucleic acid) within cells, with each of these triplets coding (translating) into an amino acid, which then get combined together to form proteins. The amino acids combined dictate what form and function the resulting proteins takes. Proteins then serve as structural support, biochemical catalysts, hormones, enzymes, and building blocks for all the processes we need to survive as humans.
Long and short, everything comes from your DNA, it’s super important, and is unique to you, but it’s structure is complex and there’s a lot of it in each of us.
How do we investigate DNA?
Now that we know about what DNA is, and how important it is for life, not just for humans but for all living things, it makes sense why so much time and energy has been deployed into understanding more about what it means for us as a species, as well as for us as individuals.
I’ve mentioned that PCR was first developed in the 80’s but didn’t really come into routine clinical testing until the 2000’s. What is PCR though and how does it work?
I often describe PCR as a way to look for DNA that is similar to looking for a needle in a 25 story block of flats sized haystack. The human genome is 3.2 billion base pairs, and we are often looking for a fragment of DNA about 150 base pairs in length, 1/21 millionth of the genome. It’s quite the technical challenge and you can see why it took quite a while to be able to move from theoretically possible to every day use. What makes it even more complicated is that you need to know what that 150 nucleotide fragment is likely to contain or where it is likely to be positioned within those 3.2 billion base pairs to really do it well. The human genome was not fully sequenced, and therefore available to us to design against, until the year before I started my training at GOSH, 2003. The progress therefore in the last 20 years has been extraordinary, and I can only imagine what will happen in the next 20 years. Hence the book reviews that will be coming as parts 3 and 4 of this blog.
So, how does PCR work? Well the first thing to say is that there are actually a number of different types of PCR, although the basic principles are the same. For example, there are some types of PCR that target RNA. There are also types of PCR that are used more frequently within clinical settings for things like SARS CoV2 testing, that are called Real Time PCR, called that as results become available in real time rather than waiting for the end of the process. It is for Real Time PCR that the small ~150 nucleotide fragment length is an issue. So all of these processes have their own pros and cons. Like many things in science, you have to use the right process to answer the right question.
The basic principles shared between types of PCR are as follows:
Designing your primers:
Primers are the pieces of DNA that you design and make that will stick to your target piece of DNA you are interested in. The reason this works is because of the fact that the nucleotides that make up DNA are complimentary and so A binds to T, C binds to G. As DNA is double stranded you can design your primers (your equivalent to the magnets to find you needle in your haystack) so that they will bind to your specific target (the piece of DNA you are interest in). If you want to have your primer stick to a piece of DNA sequence that reads AAG CTC TTG, you would design a primer that ran TTC GAG AAC using the complementary bases, make sense?
You design one set of primers for one strand, this is called your forward primer (moving from 5′ to 3′), and then you design your reverse primer at the other end of your target for the opposite DNA strand (moving from 3′ to 5′). Doing it this way means that when you start your PCR process you end up with complete copies of your target. You will then successfully have pulled the needle from your haystack using you targeted magnets.
Undertaking the PCR:
Once you’ve got your primers (which you can just order in once designed) you can then get onto the process of the PCR itself. You combine your sample that you think might contain the DNA target you are looking for (be that human, bacterial, environmental etc) with the reagents (chemicals) that you need to make the process work all in a single small tube. This tends to be a delicate process that needs to be undertaken at controlled temperatures as the protein that runs the process (Taq polymerase) is delicate and expensive. To do this we combine:
DNA Template: This is the sample that contains the DNA target you want to amplify
DNA Polymerase: Almost always this is Taq polymerase which is used due to its heat-stability as it originates from a bacteria that lives it deep sea vents. This allows it to function at the high temperatures required for PCR and is used to make the new DNA copies
Primers: These are the short, synthetic DNA sequences that you design to attach to either end of your target DNA region. These then allow the DNA polymerase to add nucleotides to create the new DNA strands
Nucleotides (dNTPs): These are single nucleotides (bases) that are then used to build the new DNA strands (adenine, thymine, guanine, and cytosine)
Buffer Solution: This solution provides the optimal conditions (pH, salt concentration) for the enzyme to function properly
Once you have your reagents you then put them on a platform that heats and cools for different steps to allow the enzymes to work and for the new DNA strands to be created:
Denaturation: The double-stranded DNA template is heated (typically to 95°C) to separate it into two single strands. This step ensures that the primers can access the DNA sequence of interest
Annealing: The temperature is lowered (typically to 50-60°C) to allow primers to bind to their complementary sequences on the single-stranded DNA. This is the step where your magnets find their needle
Extension: The temperature is raised again (usually to somewhere around 72°C, the optimal temperature for Taq polymerase activity). Taq polymerase extends the primers by adding complementary nucleotides based on the DNA sequence to create new copies of the original DNA target
These three stages are repeated in cycles, typically 20-40 times, which results in thousands and thousands of copies of the original target to be created, so that eventually your 25 storey haystack is made up of more needles than it is hay, and therefore it is easy to find what you are looking for.
Interpreting your results:
At the end of your PCR step, if you are using traditional PCR, you run what is now called your PCR product or amplicon (the things you’ve made) through something called a gel. This is just a flat jelly made of agarose (or seaweed) which also contains a dye that binds to DNA and allows to separate your DNA based on size. This allows you pick out where you have samples that have the massive amplification you are looking for, as you can see it as a band within the gel. If a band is there and the right size (as you know how big your target was supposed to be) this is a PCR positive.
If you need to know more detail than whether something is present or absent, for instance if you need to know not just that a gene is there but which variant of a gene is present, you need to be able to tell what the nucleotides that were added between your two primers actually were. To do this, you will follow up PCR with a process called sequencing.
You take your target PCR’d section and then put it through a process to work out what the nucleotides added were. This involves doing the PCR process again, to make even more copies, but the nucleotides added into the reagent mix have fluorescence attached so you can tell which ones have been added during the PCR process. G’s often produce a black colour when hit by light, A’s green, T’s red and C’s blue.
For our original sequence we talked about, AAG CTC TTG, the sequence would read Green, Green, Black then Blue, Red, Blue followed by Red Red Black. Colours are then back interpreted into a DNA sequence (a series of letters) and there you have it, you know what the DNA is between your primers and you can then interpret your sequencing result. If you have large fragments of DNA you are interested in, you may have to do this in overlapping segments and put it back together, something like a jigsaw, before you can get your answer, but the basic process is the same.
What can DNA tell us?
As I’ve said, the search for DNA and specific genes has become an increasingly normal part of providing diagnostics in healthcare. Most of us will have sent off a swab for a PCR at least once during the COVID-19 pandemic. PCRs are frequently used in my world of infectious diseases to see if a bacteria is present or absent. They are also used so that I am able to see if a bacteria will respond to an antibiotic, by seeing if they carry antibiotic resistance genes, which can be crucial to getting patients on the right treatment at the right time.
Looking for specific variants of genes is also key to making sure that the treatments we give also don’t cause any unexpected consequences. A good example of this is when we use PCR and sequencing to look at genetic variants of a gene called MT-RNR1. A specific variant in this gene, m.1555A>G, is known to increase the risk of aminoglycoside-induced hearing loss. Aminoglycosides are a crucial antibiotic class that are used pretty widely, but especially in management of some conditions such as cystic fibrosis and certain types of cancers. A small number of people have a gene that makes them prone to something called ototoxicity as a result of taking these antibiotics, resulting in hearing loss. If we know a patient has this gene variant we can then choose to use different antibiotics, improving patient outcomes and avoiding a life long hearing impact.
Outside of screening linked to patients presenting with specific conditions, the use of DNA sequencing is being utilised more widely to look for genes or conditions before they even present with symptoms, in order to reduce time to diagnosis, and hopefully to be able to find patients and start management before they’re impacted or even present as unwell. A great example of this is the newborn screening programme that started last year. This screens newborns using the heel pricks of blood taken at birth so that rare diseases that could take months or years to diagnose by traditional means are picked up early in life, therefore allowing appropriate treatment to start earlier and hopefully saving lives.
DNA is fascinating and I love knowing about it. It’s not just me though. In recent years there has been an increasing trend for people to send off their DNA for other purposes than to hospitals for clinical testing. I’m not going to say too much about this in part one, but it was this that really inspired me to write these posts in the first place and is the main focus of part two of this blog series.
Just a quick google however provides a wide number of different companies offering a variety of DNA testing services outside of the NHS (NB I don’t advocate for any of them):
Crystal Health Group: Operates a network of DNA testing clinics, offering relationship testing and other services.
23andMe: Provides DNA testing for health, ancestry, and other personal insights.
Living DNA: Focuses on both ancestry and wellbeing-related DNA testing.
MyHeritage: Provides DNA testing, particularly for ancestry research.
AncestryDNA: Company specialising in DNA testing for ancestry discovery.
The complication with all of this type of provision of testing is that outside of the clinical world in the UK, where testing should be undertaken in accredited laboratories and reporting of the results must meet certain standards, sending off DNA to private companies is much less monitored.
I hope you can see by some of the technical descriptions just how complicated these DNA processes can be. How time consuming, and how expensive to get right. There is also a lot of nuance about the different types of PCR, sequencing, gene targets, and results analysis that can be offered under the umbrella of ‘DNA testing’. Without the right people involved to make sure that there is embedded quality assurance challenges could arise, depending on what kind of testing is undertaken.
As stated in a recent Independent article:
As they’re based on estimates, I suggest treating home DNA tests as a fun investigation to get to know your family history a little better rather than a to-the-letter representation of everything that’s ever happened in your gene pool – Ella Duggan Friday 28 March 2025
The devil for all of these things really is in the detail, and we’ll get into that detail much more in part two! For those of you interested in learning more about the history of DNA testing, I’ve included a talk below. Happy World DNA Day
I’ve been finding myself in a bit of a hole recently where my first response to anything, and the first words out of my mouth, are always an instinctive ‘I’m sorry’. Whether I have done something wrong or not, whether someone is accusing me of something or not, I just can’t get the words ‘I’m sorry’ not to be the first ones that immediately leap to my lips. Now, owning when you need to apologise is a really important thing. The thing is, that there are a lot of consequences to unnecessary and anxious apologising that I don’t think we necessarily recognise. After all, what does it matter if we say sorry too much? No one is hurt by the words ‘I’m sorry’. Is that true though? After a particularly anxious weekend last week I spent some time thinking about how apologising too much can actually be a leadership issue, and what steps you can take to reduce the downsides if this is something you are impacted by, like me.
It can make you come across as weak
Leadership can be challenging at the best of times, but in a resource limited setting with competing pressures, it can feel more challenging than ever. Those you are leading need to feel secure in your direction of travel and protected in your leadership.
Despite authenticity being important, being an anxious apologiser can come over as weakness and something that can be exploited by others. It can come over as not owning your time, boundaries, responsibilities, or actions. Worse than that, it can also make those you lead feel more uncertain, depending on the context of the apology. Owning up to mistakes and proportionate apologies are great, inappropriate ones, very much less so.
Makes setting boundaries more challenging
One of the things that I am super aware of is that my anxious apologies make boundary setting less easy. I am allowed to take time off sick or to be on holiday, I should not feel the need to apologise for it. Doing so makes others feel less able to also take the time they are owed. I am an emotional person. I wear my heart on my sleeve. In many ways, I believe that makes me a better leader. I, therefore, need to stop apologising for trying to be myself rather than attempting to fit some predetermined mould. If I don’t feel I can be authentic, it makes me a lesser leader and means others will also feel like they need to hide who they are.
You may accept culpability even when you don’t
Another thing about anxious apologise is that your immediate response can end up making it look like you are taking responsibility for something which you actually aren’t. A recurrent example of this one, for me, is when someone takes action and ignores advice/guidance, and I end up apologising for not providing sufficient clarity. In reality, it was up to the individual to seek additional clarity if required, not for me to be psychic and try to predict their actions. Just one example of an easy trap to fall into.
It can make genuine apologies feel less authentic
This is a big one for me. If you apologise all the time, as an auto response, it can make those moments when you choose to do so consciously feel like it has less impact for the person receiving it. Making sure those moments where you need to own your actions and learning are undertaken with sufficient thoroughness helps, but avoiding using apologies as punctuation is a longer-term change.
You may end being annoying to be around
Speaking as someone who does this a lot, I hear from many of my friends just how annoying it is. A favourite quote of Mr Girlymicro to me when I get in a particular space where I constantly need to be told it’s OK is ‘stop apologising, it’s a sign of weakness’ from the film Little Miss Sunshine. It makes me laugh every time and reminds me of how much the required back and forth is an energy drain on everyone involved. Take a deep breath and step away from the spiral, and acknowledge the costs you are placing in others.
May make your leadership confusing
Another way that anxious apologies can make your leadership confusing it that they can work to actively derail trains of thought. They can end up de-railing conversations, so they become all about a single thing rather than the original focus of the discussion. They can make your communication less clear and end up meaning that key points are obscured, or worst of all, forgotten by all involved. As clear communication is a key foundation of good leadership, this is good for no one.
Conversations that are not about you can pivot
I had a moment last week when I got hit from out of the blue with an emotional response to a conversation. This meant that a conversation that should have been about me offering support, guidance, and clarity, became all about the people involved comforting me. This is a disastrous thing to have happen. My immediate response is then to apologise more for letting it occur, but this then drives the cycle. Stepping away from it. Knowing you should do better and reflecting with yourself why it occurred is the only real remedy you can offer.
So, how can we do things differently?
Acknowledging that this is not a healthy habit or coping strategy is a start, but what we actually do about it in order to do it less or limit the impacts on our leadership?
Listen to your frequency
One of the primary actions is to be aware of the frequency of your anxious apologies. For me, at least, this isn’t an always-on/always-off thing. It comes in waves depending on other things that are happening and my general levels of anxiety or confidence dips. Knowing when you are going through a bad patch enables you to focus some resource on reduction, especially in risky or high stakes moments. Doing the constant apologising at home may be annoying. Doing it in the wrong situation at work could have much bigger consequences.
Be aware, especially during high stakes moments
There are moments, for both you and your leadership, where being perceived as weak or accepting ownership when you don’t, can have significant impacts. In these moments it’s crucial to be aware of where your head is at and your tendency to undertake this behaviour. These high stakes moments tend to also be high risk moments, so if you apologise as a stress response, you are even more likely to fall into an apology during these encounters.
In order to help with this, one of the main things I try to do is just take a beat before I open my mouth. Those of you who know me probably know this isn’t my strongest skill. Mouth open, should be shut. At times like these, though, it is so important. That breath allows me to sense check my response and remove the work ‘sorry’ from my automatic vocabulary. It allows me a moment to try and re-phrase my immediate thoughts or dialogue to make it more in line with my core meaning. It helps me avoid throwing myself and others into an unnecessary bear pit.
Don’t let others take advantage
It is also worth remembering that it is not just you that notices this behaviour. In the past I had a colleague, who was perhaps not my biggest fan, who I realise in hind sight would almost set me up in scenarios to take advantage of my tendency to accept responsibility readily. If your apologies do come across as a sign of weakness, and you work in a high competition environment, then this is a risk. Taking time to understand how others respond to your anxiety trait (irritated, sympathetic, exploitative, etc) is an important part of learning how to manage your own behaviour. Know when to bite your tongue and stay silent despite all of your instincts telling you otherwise.
Try to embed change
One of the easiest ways (although still far from easy) to manage this tendency is to try to find other ways to respond. Ways that still allow you to feel you have responded but that are less likely to be interpreted as you taking ownership all the time. Embedding these changes consistently, even if you are going through a particularly bad spell, can make it easier. Language is a learnt response, and much of it is based on habit. Getting into a space where you only apologise consciously for things that actually require it is a habit worth gaining.
I’m still not good at this. I think it’s an area of constant improvement. I have found it is easier to try and embed this shift in written communication first, and then it comes a little easier with verbal reinforcement later. Just take it one conversation at a time and see what works best for you.
Find trusted friends
For me, one of the best ways I have to manage this is to find my people, my trusted friends. There are two main reasons for this. One, Mr Girlymicro loves me enough to cope with me apologising, me talking about apologising, and me agonising about whether I need to apologise, for the hours it sometimes takes to get me to work through what is going on, and to then move past it. I also have some key people in my life who I know I can text and be ‘this happened, do I need to worry’, and who I 100% trust in their response to guide my actions. The second area where I find these people really useful in my life is that they will flag to me, when I lack the self awareness to notice, when I’m starting to increase my anxious apologising, so that I can be more aware of my own emotional state and the impact it is having. Knowing that others have your back, and can support you, even when you are not aware that you need support, is a real gift in this life and if you have access to those people make sure you hear what they have to say.
Be OK with not always getting it right
You are not going to get this right all the time. There are times in my life when I don’t manage to get it right even most of the time. Treat yourself with the grace that you would give to others. Anxious apologising is driven by, guess what, anxiety. Don’t drive your anxiety further by diving deeper into the rabbit hole and stressing about things you can’t control. It happened. You may be able to fix it, you may not. Nothing is to be gained by stressing about it, and the best cure for some of that anxiety is to take action if you calmly decide there is an action to be taken. The irony of me writing these words is in no way lost on me, as I can never stop the resulting panic, that doesn’t mean that the logical part of my brain does not acknowledge that it is the right move however. Try choosing grace over guilt whenever possible, as you will be a better person as a result.
Invest your energy based on circumstance
Having acknowledged that you won’t get it right all the time, a key thing is to know when you MUST get it right, or when to invest energy in order to bring your best self. We’ve talked about being aware of your high risk moments, and if you only have a certain level of energy resource to invest, then this is where to choose to spend what you have. When I’m working through a significant anxious period I can’t keep it together at all times, I just don’t have that level of cognitive resource. I have to have my safe people who I can spend time with, so I have periods where I can just let myself be and work through how I’m feeling. I also tend to stay away from people or situations who I don’t need to interact with at that time and tend to make me feel less safe/triggered, in order to not fuel the situation I find myself in. No matter what is going on, trying to be self aware enough that you make good decisions to help yourself through is definitely worth the resource requirement.
Don’t forget to deal with the underlying drivers
At the end of the day, however, it’s important to remember that anxious apologising is a symptom and not the cause. It’s really easy to focus on the symptom that is taking up you energy and cognitive space, when really we need to be stepping back and seeing what is driving the current situation. In my case, it’s often when I’ve not recognised that my health is not great and anxiety is often secondary to flares, lack of sleep and generalised discomfort. That said, I am also of an age where being peri-menopausal is definitely a thing, and my hormones are definitely writing their own story right now, with little input from me. Whatever the reason, making sure that you try to understand what is driving you means that you can start to focus on the root cause of the problem, not just react to the moment, giving you both actionable intel and hopefully a way out of the way you are feeling. None of this stuff is easy, but know that you are not alone in managing it or finding a way forward. If you need one, I’m always happy to be your safe space.
Norovirus is estimated to cause more than 21 million cases every year worldwide and to cost the NHS over £100 million every year. Because of its impacts, there’s been a fair amount in the news related to Norovirus recently as the numbers have been up this year. I thought the timing might be good, therefore, to talk about this clever and tricky virus, and why we should care about it even if it is not likely to result in significant harm to most people.
In their recent blog post the UK Health Security Agency (UKHSA) have listed a number of reasons why levels might be higher at the end of 2024 than in recent years:
Post-pandemic changes in population immunity
Changes in diagnostic testing capabilities
Changes in reporting to national surveillance
A true rise in norovirus transmission due to the emergence of GII.17
I’ve written a post before about food poisoning and food borne outbreaks, but as Noro (Norovirus) is the queen of this particular court, I thought it was high time I gave her the recognition she deserves and explain some of the reasons they’ve listed in more detail so that the reasons might become clearer.
What is Norovirus?
So, let’s start by talking some virology. Feel free to skip this section if the technical stuff doesn’t really appeal to you, I’ll try to include plenty of context in the other sections so they still make sense.
Norovirus is a single-stranded positive sense non-enveloped RNA virus, but what is that, and what does it mean?
RNA (ribonucleic acid) – We talk about DNA being the building blocks of life but viruses act a little different as they are able to take over the mechanics of the cell/host they invade. This means they dont have to have DNA to function. Their genomes (the code for what they are) can be made from RNA alone.
RNA molecules range widely in length and are often less stable than DNA. RNA carries information that can then be used to help cells build proteins using the machinery in the host, which are essential for replication and other steps
Single stranded – RNA is frequently single stranded, versus DNA, which is normally double stranded (there are however examples of single stranded DNA viruses, such as Parvovirus)
Positive sense – Noroviruses use their own genome as messenger RNA (mRNA). This means the virus can be directly translated (tell the cell what to do) into viral proteins by the host cell’s ribosomes (cell machinery) without an intermediate step
Non-enveloped – This refers to a virus that lacks the lipid bilayer that surrounds enveloped viruses, meaning that they are sometimes called ‘naked’. These viruses are more resistant to heat, dryness, extreme pH, harsh treatment conditions, detergents, and simple disinfectants than enveloped viruses.
Noro is part of the family Caliciviridae, and human Norovirus used to be commonly referred to as Norwalk virus. As genetic information has become more available, it is now known that there are 7 common genogroups or G types of norovirus (GI – GVII), only some of which can infect humans (GI, GII and GIV).
Representative virus strains and their known carbohydrate ligands are shown in orange. Data are adapted from PLoS ONE 2009, 4, e5058.
Within these main genogroups, GI and GII contain a number of different genotypes, which will circulate at different amounts across different years and cause most of the infection we see in the population. You can also probably see that, although we use numbers to talk circulating strains, they also commonly have names, often based on the city or area where they were found. This can make everything a bit confusing, so I’ll mainly just use numbers here. This year, as talked about by UKHSA, the primary culprit is a rise in GII.17.
Symptoms/presentation
Noro is interesting as it frequently presents as something known as ‘Gastric flu’. This means that initial symptoms are often linked to a headache and feeling generally unwell, potentially with a fever. So, not just the diarrhoea and vomiting that people often think of associated with this virus.
That said, you also get the perfectly well to sudden projectile vomiting type of presentation, which is what people think of. Norovirus is the reason I once sat at a train station and vomited on my own shoes, as it just came out of nowhere. There is often a very short, intense spike in temperature, and then it is upon you. This form of intense and sudden presentation is just one of the reasons for the transmissibility of this particular virus. The lack of warning means that it is almost impossible to get away from others, and you won’t have ‘taken to your bed’ before the acute symptoms start.
It is worth noting that as well as these differences in adult presentations, presentations in young children are often also different, with more diarrhoea rather than vomiting. This means that Noro in young children can slide under the radar until adults caring for them then start to feel unwell.
The incubation period is pretty short (a couple of days), and so transmission windows in close quarters can be pretty intense. The duration of illness in most people is also pretty short, although symptoms tend to come in waves, and so it can be difficult for individuals to predict in some cases when it will finally be over. All of this is true for your standard healthy immunocompetent adult, but it is worth remembering that in both children and immunosuppressed adults, presentations, severity of illness, and length of infectivity can be very different.
Diagnosis
Most diagnoses of Norovirus within the community are going to be based on symptoms and presentation, as in most cases, any management is going to be symptom relief by maintaining fluid balance, etc. More specific diagnostics therefore only tend to be undertaken within healthcare environments, where it is important to know viral details to help inform risk assessment linked to transmission, as well as to monitor recover and inform epidemiology (what strains are spreading and if any of them are cause more severe disease).
There are many possible ways to diagnose Norovirus in the lab, from routine diagnostics using molecular methods and immunoassays, to how people are looking to diagnose using Norovirus in areas like care homes in the future using smart phones and other novel methods.
Maja A. Zaczek-Moczydlowska, Azadeh Beizaei, Michael Dillon, Katrina Campbell. Current state-of-the-art diagnostics for Norovirus detection: Model approaches for point-of-care analysis. Trends in Food Science & Technology, Volume 114, 2021, Pages 684-695
In terms of immunoassays, there are a couple of commonly used tests. The first are lateral flow assays (LFA), which most of us will be familiar with in terms of the lateral flow assays used for SARS CoV2, and the principles are similar. Enzyme immunoassays (EIAs) follow similar principles but are usually undertaken in the lab with many samples being processed at the same time, allowing much more widespread testing to be undertaken.
Which diagnostic test is most appropriate depends on how frequent cases are. In outbreak or high prevalence settings, then EIA has sufficient sensitivity to detect most cases. If circulating levels are not very high, i.e. outside of the standard season or outbreaks, or in high risk settings where missing cases could have severe patient impacts, such as some healthcare settings, then most publications suggest molecular methods are the most appropriate way to test.
The molecular methods listed include isothermal amplification, with Loop-mediated isothermal amplification (LAMP) being a common method that was recognised during the pandemic for detecting SARS CoV2, and can be used outside of the traditional lab environment. I, in fact, validated a LAMP test for Noro when I was a trainee, so it’s been around for a while. The other listed is high throughput sequencing (HTS), which is a much more demanding technique requiring specialist skills and equipment, but also gains you all kinds of info, including that linked to strain and transmission data.
The most common molecular diagnostic test for Norovirus in high-risk settings is actually via polymerase chain reaction (PCR). This will usually target roughly a 130 base pair section of the Norovirus RNA genome out of the (on average) total 7500 base pairs of the virus, roughly 1.7% of the genome. This target area will usually enable differentiation between the common GI and GII species, which helps with monitoring and is chosen based on being present in all of those types in order to maximise sensitivity. Further differentiation into genogroups requires HTS but is often not needed outside of outbreaks and public health level epidemiology.
Norovirus is traditionally thought to be spread via what is known as the ‘faecal-oral’ route. That means that bits of poo and diarrhoea end up being swallowed by the person who then gets infected. This is because if someone has diarrhoea and goes to the bathroom, they will have up to 100,000,000 copies of the virus. This can then land in the area of the toilet, especially if the toilet seat isn’t closed on flushing, contaminating the surrounding area for anyone who goes into the bathroom and uses it afterwards. If someone then enters that bathroom and is susceptible to the virus, it is thought you then only need to swallow 10 – 100 copies of those 100,000,000 to become infected, and so only a very little is needed to spread the virus onward.
This isn’t the only route however. One of the issues with the acute vomiting phase of Noro is that someone vomiting can also vomit 30,000,000 copies of Noro. As the vomiting can be projectile, and come with a lot of force, this is ejected at high speed and can form what is known as an aerosol. This means the invisible vomit ‘cloud’ can hang around in the air for some time after the original vomit, meaning that anyone walking into the room where the vomit occurred for some time afterwards, or is present when it happens, can breath in the virus, and thus get infected that way.
As people can be infectious for some time after they’ve had acute infection (at least 48 hours) or when they have initial gastric virus symptoms before becoming acutely unwell, spread can commonly occur due to contamination of food products prepared by those infected. The common example is self catered events, such as weddings and birthday parties, where someone made a load of food on the morning and didn’t start to feel unwell until later in the day. 24 – 48 hours later a lot of the guests then suddenly start to feel unwell. This is a route via which lots of people can get sick from a single event and is known as a point source. Hand hygiene is always key, especially so when dealing with food, but the viral loading of people who are unwell with Norovirus means that avoiding being involved with food may be the only option, as there may just be too much virus present on hands etc to remove all of it easily.
The final route to consider is indirect spread. All of the circulating virus that’s in the air or in water droplets from the toilet flush, then will eventually come down and land on surfaces. Therefore those surfaces end up having a lot of virus upon them, and the virus, as non-enveloped, can survive on surfaces for some days. This means that then interacting with those surfaces can be a transmission risk, and so cleaning, and again hand hygiene, is really key to stopping ongoin spread.
Outbreaks
As those infected can be become unwell suddenly and spread lots of virus in a short period of time, Norovirus can be difficult to contain. Once an event occurs, all of the various transmission routes mean that Norovirus outbreaks can be difficult to control, and management is based upon rapid identification of cases and, if in hospital or even on a cruise ship, restricting contact to other people in order to reduce risk of spread.
The biggest issues occur in the kind of areas where lots of people get together, high densities of people in physically confined areas. Everywhere from military training camps to schools and nurseries can be affected. As mentioned before, centres where people may present in atypical ways due to age or underlying condition can also make it more complex to contain infections and prevent spread. Hospitals have high population densities with restricted space for movement, combined with patients that are high risk as they already have conditions that impact immune function or make them more vulnerable.
Outside of traditional health and residential areas, such as care homes, cruise ships are at high risk as passengers can feel fine when they get on board and then experience symptoms in a confined space, with little room to spread out.
Even once recovered from symptoms, some of the passengers are also likely to continue to shed the virus (one adult study suggested for 182 days) and therefore some of those who get sick early on and recover may continue to be a silent source and risk for other passengers if they don’t have good general hygiene practices.
It can also be a challenge to decontaminate some of the surfaces, as they are often predominated by soft furnishing where it can be difficult to use cleaning agents with sufficient activity as Noro can be resistant to disinfection and present in such high loads it can be hard to remove. This has led to the surfaces in cruise ships being a continued risk even when all of the original passengers have departed and a completed fresh set has boarded.
Seasonality
Norovirus outbreaks are seasonal, with the peak occurring in the winter months. This is partly because, as humans, we tend to spend more time indoors in close quarters with each other during the colder months. We get together for the festive season, and because the nights draw in earlier. This means that we tend to spend more time in higher density interactions than in the summer, where we might be out eating alfresco or going for evening walks, or in my case, cocktails. We also tend to travel to other households and cook for each other as part of the seasonal festivities, which means the food borne route definitely comes into play. Finally, as temperature and humidity impact on the indirect surface route, environmental conditions mean that the viruses survival on surfaces at this time of year is probably more prolonged. Norovirus never really goes away, but the number of cases definitely spikes during the winter.
Strain variance/immunity
The UKHSA mentioned that one of the reasons that there may be more Norovirus cases around now is because one of the current predominant strains is GII.17. The chart below is linked to circulating Norovirus in China, so not the UK, but you can see, even over a few years, how the levels of different circulating strains changes, and that within years there are normally a few strains that co-circulate with a predominate strain type.
Cao, R., Ma, X. & Pan, M. Molecular characteristics of norovirus in sporadic and outbreak cases of acute gastroenteritis and in sewage in Sichuan, China. Virol J 19, 180 (2022)
GII.17 is a less common strain and so many people will not have experienced it recently, if at all. If you haven’t had GII.17 before you won’t have immunity and therefore are susceptible to infection. Even if you have had GII.17 before, one of the reasons control of Norovirus is hard is that immunity is short lived. Even if you have experiences GII.17 before, therefore, the data shows that immunity lasts for anywhere from 6 months to 4 years, and therefore only relatively recent infection is protective. Finally, there is no cross strain immunity, so if there are three circulating strains of Norovirus in a season, unless you have experienced each of them in the relatively recent timeframe, it is possible to get multiple episodes, 1 from each strain, in a short period of time.
Prevention/Actions
Norovirus particles retain infectivity on surfaces and are resistant to a variety of disinfectants. This means that not only direct transmission routes (such as person to person) but indirect transmission via surfaces can be important. Interventions therefore need to take into account all of these different routes. Some common recommendations include:
Hand hygiene with soap and water (alcohol gel is less effective as Noro is a non-enveloped virus)
Staying away from other people until 48 hours after symptoms have ceased (as you often get a second wave of symptoms which increases risk of spread)
Avoid cooking or preparing meals for other people until at least 48 hours after symptoms have ceased, and ensure good hand hygiene when you re-commence
Cleaning with disinfectants (bleach etc at home) may be required, and multiple cleans may be needed due to the amount of virus present
Time cleaning so there is enough time for any virus in the air to settle on the surface, so a re-cleaning after 2 hours will probably be needed
Avoid going into a space where someone has vomited for 2 hours if possible to reduce the risk of inhaling virus
Ensure you are aware that Noro can present with gastric flu type symptoms, headache and temperature, before gastric symptoms start, and so be weary of seeing high risk individuals if you have any symptoms present (especially those in hospitals or immunocompromised)
Due to the challenges with short lived immunity and high viral loading, you won’t be able to avoid getting Norovirus into confined areas and high risk settings, so rapidly identifying when you have cases and making sure that your interventions enable you to stop secondary spread is key. If you get sick, stay home, ensure you keep hydrated, and don’t let the virus fool you into thinking it’s done when you are feeling that little bit better on day 2, it’s Noro’s way of tricking you into going back out into the world an spreading it further. The queen of the gastric viruses is super clever and so we need to be even smarter to prevent her spread.
This post was supposed to be something quite different. It was supposed to be about One Heath and a great podcast created by Beckman Coulter I was involved with in 2024, alongside some really inspiring people. In some ways it still is that, but because of the cruel reality of life it is actually also something quite different.
”Going Macro on Micro” is a podcast that Dr Simon Doherty and I were involved with that explores emerging themes and pressing issues in the world of microbiology. As the host, Dr Lough, says the podcast covers everything from investigating the global challenges of infection control to unveiling the future of diagnostic technologies.
The week the final episode of the podcast dropped, before Christmas, I got some pretty devastating news. Sadly Simon has passed away. Now, I didn’t know Simon well. We’d emailed since doing the podcase together and I kept an eye on the awards he received and his really interesting posts. In this limited contact though, he still managed to inspire. Recording the series with him was such a privilege. He was kind, open and funny. More than that he was so knowledgeable and I came away feeling like I’d learnt so much. I am so sad that I won’t be able to build on the foundation we laid to continue to learn from him and talk about the challenges/opportunities that face us in the fascinating world we both inhabited. I thought about not sharing these episodes when I heard the news, but then decided that I don’t want you to lose out on the honour I had of learning from him direct. I hope that you will hear both his wisdom and his challenge, and also aspire to do better, as I do, as a result. Thank you Simon.
I’ve decided to keep the focus on Simon and just put some graphics and links here that might supporting learning more about antimicrobial resistance and One Health. At some point when the loss of Simon has had a little more time to be processed I will think about writing something in a little more depth reflecting on his comments and the overlap between human health and veterinary medicine. Until then, the links to the episodes are below:
Ahmad Nayeem , Joji Ronni Mol , Shahid Mohammad. (2023). Evolution and implementation of One Health to control the dissemination of antibiotic-resistant bacteria and resistance genes: A review. Frontiers in Cellular and Infection Microbiology
Episode One
Rhouma, M., Soufi, L., Cenatus, S., Archambault, M., & Butaye, P. (2022). Current Insights Regarding the Role of Farm Animals in the Spread of Antimicrobial Resistance from a One Health Perspective. Veterinary Sciences, 9(9), 480. https://doi.org/10.3390/vetsci9090480
Episode Two
Sanseverino, Isabella & Navarro, Anna & Loos, Robert & Marinov, Dimitar & Lettieri, Teresa. (2018). State of the Art on the Contribution of Water to Antimicrobial Resistance. 10.2760/771124
Episode Three
Sanseverino, Isabella & Navarro, Anna & Loos, Robert & Marinov, Dimitar & Lettieri, Teresa. (2018). State of the Art on the Contribution of Water to Antimicrobial Resistance. 10.2760/771124
Episode Four
Sanseverino, Isabella & Navarro, Anna & Loos, Robert & Marinov, Dimitar & Lettieri, Teresa. (2018). State of the Art on the Contribution of Water to Antimicrobial Resistance. 10.2760/771124
Episode Five
Sanseverino, Isabella & Navarro, Anna & Loos, Robert & Marinov, Dimitar & Lettieri, Teresa. (2018). State of the Art on the Contribution of Water to Antimicrobial Resistance. 10.2760/771124
Episode Six
Sanseverino, Isabella & Navarro, Anna & Loos, Robert & Marinov, Dimitar & Lettieri, Teresa. (2018). State of the Art on the Contribution of Water to Antimicrobial Resistance. 10.2760/771124
For regular readers of this blog, the fact that I adore Christmas probably comes as no surprise. It contains everything I love, time with people I care about, movies, heaps of romance, and an excuse to indulge in lots of lovely food and drink. I’m not religious. I embrace the shamelessly commercial, and I dive right in. I make Christmas puddings the week after Halloween. My Christmas tree gets delivered on the last weekend in November, and from that point on I’m full blown carols and Christmas cheer for as long as I can get away with. So, in this, my last post before Christmas, I wanted to share all of the reasons why I love it and explain, even as someone who won’t be at church on Christmas Eve, all of the benefits I think the season can provide!
Time for reflection
Number one on my list (that’s definitely not hierarchical) is the fact that this time of year encourages me to spend some time on active reflection. I spend so much of my working life in responsive mode and fire fighting, that it can feel like I achieve nothing and go no where. When looking at what I need to close off before the end of 2024, I am also trying to take some time to actively reflect. What did I actually achieve? What went well? What have I learnt, especially from the things that didn’t go so well? What do I want to take with me in terms of life lessons and priorities into 2025? Almost more important, what do I need to let go off? What baggage am I leaving in 2024 in order to leave me with room for grow moving forward? This is the time when I review what’s happened, take both the learning and the good, and leave the rest in the frozen tundra so it doesn’t start to define me or weigh me down.
Time to review progress
As the nights draw in, I, like most of us, desperately try to close off some of my outstanding work list. I am, therefore, almost forced to give some of my focus into what that list will look like going into the next year. The thing that I’ve tried to do is to review whether things that are going to roll into 2025 are a) still needed or b) still serve me in my direction of travel. There are always going to be jobs that are still needed and not optional (so many apologies for not getting these done in 2024), but there are other goals, such as writing an environmental IPC textbook, were worthy of review to see if they were still something I wanted. If you are wondering the answer is yes to both the textbook and the book of this blog, both of which fell by the wayside due to limitations in capacity in 2024. I refer to this period of activity as my Christmas mental cleansing, and I find it both a helpful and comforting process that can be undertaken under a blanket with a warm cup of tea. This is also the time where I make an active choice to celebrate my successes and forgive myself for everything else.
Time for joy
Another of my favourite things at this time of year is to give myself permission to make time for joy. It’s probably no surprise to anyone that my life is pretty work heavy and there isn’t a lot of space for downtime. At this time of year I have a list of things that bring me joy that I actively schedule in and am determined to find time for. Christmas movies make up a lot of this. Watching a Muppet Christmas Carol, either on Christmas Eve or when decorating the tree. Sobbing to Love Actually and Serendipity as I take a moment to remember happy times with my sister. Indulging in the delights of spending time with my husband whilst watching Die Hard, which is a Christmas movie, on Christmas Eve. Carols whilst cooking and sitting together to highlight the Christmas Radio Times. There is never enough time to do all that I would wish, but these stolen moments make my soul feel lighter and instil every day with an extra level of joy that means I value every single single hour in the run up to the main event.
Time to indulge
OK OK, I acknowledge we all need to be healthier. I’m aware that I do not ‘need’ another cocktail, piece of chocolate, or an extra roast potato, but I am a lover of all things food and sparkling, so what’s a girl to do. Don’t get me wrong, I don’t just indulge in edibles, I also indulge in Christmas experiences, like theatre shows and more shopping than is probably good for my bank balance. I usually don’t like crowds or areas with lots of people, Christmas is the exception. I love the buzz, the feel of the atmosphere and lights whilst carols play in the background. For me, even the provision of time to shop that isn’t time restricted and just has plenty of browsing time without any time pressure built in is an indulgence. It’s a time where I allow myself to prioritise enjoyment and experiences, not just tasks. For me it’s about, for a short while, experiencing the joy of living in the moment and what it feels like to live a life without a deadline.
Time for family
It shouldn’t count as an indulgence, but sadly sometimes I am aware that I can be so focused on work and task that I forget to make room for the most important thing in my world, my family. I’m aware that I am really fortunate to have such a great relationship with my family, but I also include here the family we have by choice, not just by blood. In general my family put up with a lot; lateness, lack of focus, even the odd missed event. At this time of the year, despite the fact that it should be all year, I really do try to ensure that my priorities are in order and that they come first. It’s one of the reasons that the indulgence part is important to me, as it also involves making room and time for those indulgences and experiences to be shared. To build new memories together and to celebrate both each other and each others company. I’ve lost too many people I love in recent years to not realise what a precious gift this is and would encourage us all to take the time to slow down and smell the poinsettia.
Time to remember
My sister and I felt the same way about Christmas. It was always important to us, as well as to mummy and Mr Girlymicro. So much so that when life at Christmas meant that we had too much on and couldn’t celebrate ‘Goosemas’ together we have been known to celebrate Christmas in September, or actually at many other times of year, when we could still get together and cook a goose in each others company. You see, fundamentally, it isn’t about the date for us, it’s about the company and the time spent together. Now she’s gone we keep my sisters memory alive by watching the movies we always used to watch together, like Serendipity. This one was so much a feature of our Christmas celebrations that when Mr Girlymicro and I got married, our wedding present from my sister was to spend 3 nights at the Waldorf Astoria in New York, purely so we could re-create the lift scene from the start of the film, and visit Serendipity 3. Unlike the couple in the movie, Mr Girlymicro and I both picked the same floor (our wedding date) and manage to move direct to our happy ever after. I cry buckets every time I watch these films, but making space to remember the loved ones we’ve lost along the way, and to remember the joy they brought, is an important part of my Christmas experience.
Time to take a break
One of the reasons that any of this is possible is because this is the time of year where I always prioritise taking a break. It feels easier to do as many people are doing the same, so the addition to the email mountain is never quite as much as when you are the only one fleeing with an out of office on. It is also important for me as I know that I am going to find the months from January to March really hard. I work in a windowless converted toilet cubicle as my office, I love it, but it means that in the darker months I barely see sunlight, and after a while it gets to influence my mood. Having this little bump of joy is the foundation I use to get me through till when the flowers start to bloom and my heart starts to lift again. It’s like I’m creating a festive battery to serve until that time.
Time to reconnect
The very act of having a period of days off, when other people are often more available, means that there is an opportunity to really reconnect with people. I have very patient friends and family. I am lucky to have people in my life who I may not see for months, or even years, and yet once we hear from each other it’s like no time has passed. These people are both precious and rare in life, and so I try to ensure that this is the time that I at least reach out, even if I can’t meet up as time is short and we are geographically far away. Time is the resource that I have least of, so using it at Christmas is actually the most valuable gift I can give.
Time to feel re-inspired
A side consequence of taking a break and doing some processing is that I genuinely always come out of this time so re-invigorated and inspired. I feel like I have permission to have conversations with others about what I still want to achieve, and these very conversations give my brain all kinds of ideas. It’s so nice to have time to bounce ideas around, and feel like you are truly having time to have dialogue, rather than the sometimes perfunctory task based thinking that is all there is normally time for. The excitement that comes from these conversations really does fuel me and these things can’t happen without space and connection, and so inspiration really is a gift I give myself at this time of year.
Time to show gratitude
It’s so easy to take people for granted. I do it all the time, even though I really don’t want to. Life is run at pace, and in that rush it is easy to believe we acknowledge and thank others more than we really do, and more than they may have time to hear. My life functions because of Mr Girlymicro. He makes untold sacrifices so that I have time to sit here on the sofa writing, rather than partaking in my share of chores. Mummy Girlymicro does not get the devoted daughter she deserves, as I’m always focusing on too many things at once. This is before you bring me onto colleagues, that cover so I can undertake teaching and research, or my other friends and family, who put up with cancellations either due to work or exhaustion. I owe so many thanks to so many people. They really do make my life a blessed existence. This time of year I hope that I shout my thank you’ s loud enough to be heard and recognised, and that I put down the laptop down for long enough that, for once, I am the one taking care of others, rather than the other way around. I also want to say thank you for reading this blog. It’s come to mean so much to me, and I know that everyone has so many other options about what to do with their time. So thank you. Thank you for reading. Thank you for commenting. Thank you for liking. Thank you for coming on this journey with me.
Time to look to the future
All of which brings me to my final point. The things this season provides enables me to lift myself up and look to the future. It enables me to do so free of the baggage that has built up in the previous 12 months. It lets me do so with a focus born of reflection as to what I want and what needs to be done. It grounds me in connection and means that I remember the core values that drive me. It supports me in entering 2025 in an inspired mindset, which acts as a spring board for everything else. So I will enter my future with optimism, a clear sense of direction and the certainty that I will not be travelling alone as I move forward.
Who doesn’t love a Christmas game!
Now, if as Mr Girlymicro has stated, that was a little motivational speaker, lets bring it back to the real spirit of Christmas, festive games!!! I, being a gamer, love a festive game and so here is a fun one to kick off your day.
All opinions in this blog are my own
I know that not everyone loves this time of year or finds it easy. Please don’t feel alone and reach out for any support you need to make it through the season.
I’m off to the Federation of Infection Societies (FIS) conference this week. I’m involved in 3 sessions over 2 days, and in many ways, these types of events are a complete highlight for me. I get to be inspired by hearing new science, I get to catch up with wonderful colleagues who I don’t get time to see very often, and I get to immerse myself in all things microbiology without the distraction.
There is another side to this coin, however, and that is both the anxiety that builds before I go, and that can last throughout the whole event. The ever-present spirals of ‘do I know anything?’, ‘will I say something stupid?’, ‘will I know anyone?’, and the classic ‘do any of these people actually like me?’.
The combination of this social anxiety with the, sometimes long, very peopley days, can mean that I hit spirals pretty easily and the lack of solo recovery time means that I can find it pretty exhausting by the end.
Now, I’m obviously not talking about extreme cases of social anxiety that may require informed medical or long-term support. I’m talking about situational anxiety that most of us may find ourselves in from time to time.
Just in case there is anyone out there in a similar boat, I thought I might put together some things I’ve learnt along the way that help manage some of my anxiety traits and enable me to actually enjoy the experience rather than dreading it.
Do your prep work ahead of time
The first thing I’ve had to learn is that I can’t just pretend that doesn’t happen. I can’t wish it away. What I can do is be prepared and make sure that I have made the process as trigger free as possible.
For me, this is about simple things, like getting a hotel as close to the venue as possible. It means that if I just need a 30-minute alone break, I can take one. It removes anxiety about getting lost or forgetting something crucial and not having time to go back for it, which, although minor, can be the final straw. It’s also about making sure that I have pre-found all the rooms I need to locate ahead of time, so I know where I’m going, and that ahead of multi-day meetings I have a plan for which sessions I’m going to before I even travel to the event.
Know your triggers
I know that I have a few things that really lead to anxiety, but perhaps more unique to me, is the fear that I was have an auto immune attack and won’t be with people who understand what is needed. I learnt early that the best way to cover this one off is that I very rarely travel alone, especially over seas. I often travel with my mum or one of a very small list of truly trusted people, who I know would understand how to get me help if required.
Something that is more likely to strike a cord with others, is that I am also the girl who has walked into conference rooms, spent 15 minutes and walked out, as I knew no one and was just overwhelmed. I’m not proud of these moments, but I think it’s important to acknowledge that they have occurred. Although, to be honest, when they’ve happened, I mostly felt invisible, so I doubt anyone noticed.
I have discovered that I need to know that the space is one where I feel welcome for me to perform at my best. This sense of welcome can be either intellectual, because of the topics covered, or because of feeling a sense of community, as the room contains people within my field or in strong alignment with my values. I’ve found the overwhelming feeling hits most strongly when I’ve been in very large political or strategic sessions, where I felt out of my comfort zone on both intellectual and community counts.
That said, I’m not too bad in the sessions themselves, I’m there to learn something new, and learning excites me even now. It’s the breaks that are my nemesis, especially when large groups all surge into a space at the same time, and the weight of expectation that you must now network lands. The seconds that feel like hours of desperately searching for faces you recognise and being forced to face the fact that yes, you really should go up and speak to that absolute stranger, as it’s the right thing to do. It’s these moments that can cause me to bolt for the nearest bathroom.
Carve out time for yourself
One of the key mechanisms I’ve identified to help with my triggers is that I make sure I have enough time to myself, be that eating food away from the venue so I feel more certain what it contains and less at risk, to making sure I have evenings to myself to process and unwind.
I usually come over as really social, and really into spending time with people, and I am both of those things. I also only have a limited amount of social battery, and so in order to maintain that extrovert part of myself I have to have recharge time. I love talking to people about this blog, I love hearing about and responding to other peoples work, but at a certain point I need to sit down with an audio book and a cup of tea in order to do it well. This means that when I go through the brochure ahead of time, and plan my sessions, I make sure that I have enough blocks of time to enable me to be my best self when I’m in the space with others. Sometimes all you need is a walk to a local coffee shop and back to give you the perspective you need.
The wonderful thing about having hit my 20th year as a Healthcare Scientist, is that I now also know quite a few people, some of whom I’ve known for well over a decade. This means that at most events, there are also people who I count not only as colleagues but as friends. People that I can just go and spend time with that doesn’t include social commitment. Those friends you have that you can just be in the same space without any demands being made. If I’m at an event where these people are also attending, then I know that I have someone I can just excuse myself to catch up with if I’m having a moment. It’s also the great thing about ensuring that you have a hotel room nearby. Your safe bolt hole is only minutes away.
Make an agreement with yourself about how much is enough
The fact that you have social anxiety does not provide a free pass to escape one of the fundamental purposes of attending conferences, networking. It’s key to your career, it’s key to your development, it needs to happen. The thing is that there are varying degrees of what networking can be, and before you’re in the space, you need to decide what level you are aiming for and will therefore achieve. For me, my deal is that I will, on each day, speak to one person I don’t know. I am not allowed to finish my day without this happening, but once I have had that one daily interaction, then any further moments are a bonus. Once that one challenging moment is over with the pressure is off, and then I almost always over achieve on my goal.
Be realistic about how much you can expect of yourself
The key thing I’ve learnt is that I have to realistic when I’m making that deal with myself and deciding on achievable targets. For me, there is not point is saying I will speak to five people I haven’t met before, as I’ll just be setting myself up for failure. You will also find that I rarely sign up for conference dinners, as I have over the years found that if I’m in a space with other people from 08:00 – 18:00 I will really struggle to then spend yet more time with other people, no matter how lovely or interesting those people are. All I will want at that point is room service, tea, and a movie in my room.
Everyone will have their own tolerances and lines. The important thing is to have enough self reflection to know what yours are. Otherwise, you just add guilt into the anxiety mix, which is not much fun for anyone.
Learn how to work a room using tools you are comfortable with
One of the other things that I’ve learnt about myself, is that although I get super anxious standing in a room trying to approach someone at the coffee table, I am much much more comfortable moving around the exhibitor stands. The guys at the exhibitor stands are motivated to speak to those who approach, and there are usually science based discussions that I am eager to have. This, for me, is a match made in heaven, as it breaks me into the speaking to people I don’t know in a very gentle way. If I’m lucky, I will also meet others when I’m wandering around, which will allow me to tick my ‘speak to one stranger box’ as exhibitors do not count on that front. The added bonus is that I also often manage to find cool new stuff I’m interested in or develop collaborations whilst this is happening, so it’s a no lose scenario for me.
The other thing that having worked for 20 years has given me is the opportunity to be asked to be involved with sessions. For this girl with social anxiety, this is actually a great thing, despite the fact that it sounds like it should be stressful. I’ve never minded public speaking in the same way as I worry about 1:1 interactions. When I speak, all I can do is put my best foot forward and hope that others will be interested in what I have to say. For the most part, if people don’t engage they will just leave and not give it another thought. On the positive side though, if people find what you say interesting enough to want to speak to you afterwards, this a great way to tick the ‘speak to one person you don’t know box’ and as they are approaching you all you have to do is respond. I find this so rewarding, but I also appreciate how fortunate I am to have this type of opportunity and how much it helps me manage to get the most out of events.
Prepare your exit strategy
One of the important things to bear in mind, and which I often forget, is that others do not necessarily feel the same way about social requirements. I struggle when people arrange evening meals at meetings when you’re already booked to spend a full day together. I understand the purpose, it’s lovely to build bonds and memories, and logistically it’s easier. I rarely, if ever, hit the end of the meeting day and wish to spend the few hours downtime I have with others, over reading in the bath however. There are frequently times I can’t opt out of these moments, but where I can, I will often have a pre planned reason to excuse myself. Often, this is work related, as I will always genuinely need to do some email catch up, and doing this after dinner means working till midnight. I don’t lie but I may pre-plan my rationale for not being available to support both my work load and my mental well being. I will never not pre-inform, as that is rude. People will have budgeted and made arrangements, so I will never last minute drop, but if the option arises I may flag unavailability at the planning stage.
Don’t succumb to expectations and pressure
People are amazing and much more welcoming than you expect. I’m always counting myself as so fortunate is be asked to unexpected drinks, meals and catch ups at conferences. I have learnt that I need to not get caught up in the moment and end up crossing the carefully curated boundaries I have put together, in order to ensure that I can last the social distance of the conference. I’m a planner for a reason and I don’t riff off the plan well. I also struggle with saying no. This means that there have been multiple times when I’ve said yes to that dinner, or those drinks, and have then suffered the consequences afterwards. Now, I work hard to keep to my boundaries so that I don’t make life harder for myself. This can be surprisingly difficult as all these invites are inclusive and well intended, I just have to remind myself to make the sensible choice to enjoy the entire event, rather than burning out after a single evening.
Know that this is an essential part of the job, so invest in coping strategies early in your career
The truth is that networking and attending these kinds of events is essential. They are a fundamental way of hearing the latest science and expanding your knowledge. They are also key for collaboration and building your networks, as well as dissemination of your work. No matter what anyone says, I have found that science fields tend not to be meritocracies, there’s plenty of ‘who you know’ involved, and the only way to address that is to get yourself out there. So you will need to learn how to navigate these settings, and the earlier in your career you manage that, the more rewards you will reap.
I’ve talked about some of my own pitfalls and things that I’ve implemented to help me, but you will have your own triggers, and each response will need to be customised to yoi and your needs. What is true for all of us is that you are not alone, and if you are in need of someone to speak to during the horror of a break, then I am always happy to be your person. This is what I look like and I will never turn you away.
Know that it gets easier
The longer you hang on in there, the easier it gets, honestly. I haven’t walked out on an event in a decade, although the toilet hiding is still a little more frequent 🤣
Pre manage your expectations of yourself and make sure they are reasonable
Book with a group or a friend if you can to take the edge of socialising with strangers
Join a social network, as you can use it to find like-minded people, and it can give you a virtual introduction rather than the cold approach
Similarly, join a society. Societies often have small meet-ups either before events or at meetings, and so you can make connections in a smaller, less intimidating space
Submit work. It’s much less intimidating if people come and speak to you rather than the other way around
Know it’s absolutely OK to need to tap out and have your own space, but make sure this is pre-planned so you don’t miss the reason you came to the event
Right, well, having talked about the need to be prepared. I haven’t even packed yet, so I’d better get on that. If any of you are Liverpool bound, make sure you come and say hi. I’m there Wednesday and Thursday.
All opinions in this blog are my own
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It has not been a great week for science, with many of us being concerned about how the presence of a vaccine denier on the successful ticket to the white house will impact public health initiatives and the quality of science communication in general. I’ve been thinking a lot about how we got here and how, even more than previously, embedding good science into mediums that are routinely accessed by the majority, will be crucial in ensuring the reach of accurate science communication when some of the more standard public health routes are bound to suffer in the coming years.
I think it will be a surprise to none of you that I am a bit of a lover of TV and movies, we’ve also covered a number of book reviews linked to this blog, and I like nothing better than snuggling down with a good book and a cup of Darjeeling. What does any of this have to do with anything? Infection, infection control, and science in general is a huge chunk of my every day, but this isn’t the case for everyone, or even most people. Many people are passive absorbers, meaning that they may not search out information but take on board when they encounter it when going about their lives. This means that the quality of what they encounter may be hugely variable, depending on how and where this happens. I’ve previously talked about the quality of the science in some of the books I enjoy, including the News Flesh series, as well as posting last week about how infection control is represented the Alien movies for Halloween. These are fun posts to do, but it made me think of the most popular movies that are linked to infection out there. How good is the science they represent? and by doing this better, could we support science literacy in general?
IMDB list of Top 25 Virus/Pandemic/Epidemic/Infection Movies
In order to think about this more detail I hit the Internet Movie Database (IMDB) which contains all kinds of lists, including a top 25 of Virus/Pandemic/Epidemic/Infection Movies (https://www.imdb.com/list/ls094715071/)
A Quiet Place (2018) (Girlymicro comment – I don’t know that this should count as it’s an alien invasion film)
Bird Box (2018) (Girlymicro comment – I don’t know that this should count as it’s an unknown enemy film that does not appear to be linked to infection)
Now, I have only seen 16/25 of these, Mr Girlymicro has seen 22/25, so between us we have most of these, so hopefully I’ll be to comment from a position of knowledge on a fair few of these. Before we even start however, as you can see from my commentary on this list, the poor science starts early during the classification of some of these as infection movies, even before we start to talk about the science content of the movie/show itself. Firstly, let’s look at the name of the list = Top 25 Virus/Pandemic/Epidemic/Infection Movies and how it related to the actual definition.
An increase, often sudden, in the number of cases of a disease above what is normally expected in a specific population and area.
An outbreak, which carries the same definition as an epidemic, but is often used for a more limited geographic area.
The CDC suggests epidemics occur when an agent and susceptible hosts are present in adequate numbers, and the agent can be effectively conveyed from a source to the susceptible hosts. Whereas a pandemic refers to an epidemic that has spread over several countries or continents, usually affecting a large number of people. The starting epidemic is usually due to a combination of factors including:
A recent increase in amount or virulence of the agent,
The recent introduction of the agent into a setting where it has not been before,
An enhanced mode of transmission so that more susceptible persons are exposed,
A change in the susceptibility of the host response to the agent, and/or
Factors that increase host exposure or involve introduction through new portals of entry
So you can see from the above that a number of movies on this list don’t actually count under the terms linked with to the title. Some of them are alien invasion, some of them are climate change related, and one is even on the topic of bioremediation. Yet there they are on the list.
For some of the others, I’ve already covered their concept during my Zombie post, so I’m not going to go through these in this blog, but focus instead on the ones that fulfill the epidemic based criteria. That said, give me a shout if you’d like a more in-depth zombie comparison post as Train to Busan is an awesome movie, and I’ll accept any excuse to re-watch it.
Let’s start at the very beginning
The first film on the list is Outbreak, a film that came out in 1995, with a description of ‘A team of Army doctors struggle to find a cure for the deadly Motaba virus that was transported from Africa to North America by a white-headed Capuchin monkey and is now spreading quickly throughout a small California town.’
This movie has an amazing cast, but I have to say I don’t want any of them in my team if it came to trying to lock down a high risk infection from an unknown source (vector). In terms of the escape monkey component. You’d think that it is far fetched, and if you’d asked me yesterday I would have said just that, but just today on BBC News there was a story on 43 escaped monkeys from a research lab in the US. So far fetched it may be, but not unheard of, in the case of vector escape.
Even if the vector component may not be quite as unlikely as I’d previously thought, I’d like to say that the rest of the practice in this is highly suspect at times. That said, I do have to admit, that I once went to a talk by a scientist who was looking for viral transmission sources of haemorrhagic fevers in Africa. They showed pictures of the table where they performed autopsies on found deceased animals in the jungle, under the same canopy as the table where they then sat down for dinner. So, as much as the way that high consequence infectious diseases (Ebola etc) are not portrayed as accurately as I’d like, maybe this is a movie of its time, as was that lecture. I really want to enjoy this movie, as it so defined how many of us had our first introduction to outbreaks and what they could mean, but almost 30 years on I don’t think I could recommend the scientific accuracy it portrays. The fact that this is still the top rated movie does not bode well for our scientific literacy hopes.
What a difference a decade makes
Almost 15 years after Outbreak, Contagion was released in 2011. This was the first of the infection movies on this list that I saw after I’d started working within Infection Prevention and Control. Contagion is described as ‘Healthcare professionals, government officials and everyday people find themselves in the midst of a pandemic as the CDC works to find a cure.’ I remember going to see this with a scientist friend and whooping out loud at the explanation of an R0, it gave me so much joy I was shushed by someone else in the cinema, to my ongoing shame.
The CDC defines an R0 as ‘The basic reproduction number (R 0), also called the basic reproduction ratio or rate or the basic reproductive rate, is an epidemiological metric used to describe the contagiousness or transmissibility of infectious agents.’ So, see if you share my joy at how the movie explains what this is, in a way that is so much more approachable than the CDC definition:
This film is not perfect, I clearly remember losing my mind about the glove use at one point, and SPOILER ALERT, it was that poor glove use that meant I was OK with one of the characters dying, but the underlying science is well explained and some of the approaches to containment and vaccination are definitely well routed in evidence. The differences in the quality of embedded science between Outbreak and Contagion are highly noticeable. Part of me wonders if some of the drivers for this heightened quality is linked to awareness of the topic due to the 2009 Swine Flu pandemic, or whether this was part of a wider shift towards improved factual grounding in these kinds of movies.
When talking to Mr Girlymicro about this movie, whilst writing this post, he has pointed out that despite my enjoyment he found it an act of ultimate depression which he will not be watching again, and that was when he watched it before the pandemic. It may therefore be, something that triggered my science joy may, in fact, be too depressing or triggering for other reasons to equate to true enjoyment for the general public. This may be an example of something that could risk being dis-engaging by being too close to the truth, despite being second on the IMDB list. Especially in a post pandemic world, this is a line that may prove difficult to walk and prove to be a barrier to movies and TV on this topic being commissioned in the short to medium term.
A completely different movie about primates
Still on viruses and re-visiting our primate theme from Outbreak comes Rise of the Planet of the Apes , which was also a 2011 release. It came out the same year as Contagion, and in the same discussion as Mr Girlymicro stated he would not re-watch that movie, for all the accuracy of it’s science, he would watch Rise repeatedly, and I can testify that in fact he has. Rise has the following description ‘A substance designed to help the brain repair itself gives advanced intelligence to a chimpanzee who leads an ape uprising.’ This is a really interesting addition to the category, as the pandemic aspects of it are mainly actually addressed in the closing credits which demonstrate how a pandemic can spread across the globe, with the film very much focused on the human (and primate) story behind the build up.
This film utilises a viral vector to try to address and revert brain abnormalities linked to Alzheimer’s, with a scientist desperately trying to find a cure for his father, whilst undertaking clinical trials on primates. Now, the clinical trial aspects of this film could not be further from the reality, and any scientist caught undertaking clinical trials and then sneaking the medication to treat their father would at best be fired and at worst been imprisoned. Somehow, because of the focus on the relationships rather than the science, the bad science in this movie bothers me significantly less than that represented in Outbreak, possibly because it feels deliberately portrayed as more like science fiction than science fact. There are some aspects of science to this one that I find interesting and like. The idea of a vaccine or medication behaving differently across species barriers is something that is interesting and could be deeply seated in evidence based plot-lines. I am aware, in this age of post truth and vaccine denial, having a film that focuses on how a vaccine or treatment could end life as we know it may not play into the goals I’m wishing to achieve using popular culture.
Let’s not forget about fungi
In recent years there’s been a rise in the quality of TV and the amount of choice has exploded, especially on streaming and other services. The switch to being able to film big budget TV over shorter film equivalents has provided storytellers with the capacity to really explore bigger and more complex tales that may not have been possible in under 3 hours.
This is last and most recent entry onto the IMDB list and is also the only TV entrant. It is our first step away from the world of viruses, into the world of mycology and all things fungal. The Last of Us came out in 2023, although it’s based on a computer game that was released in 2013. The series is set ‘after a global pandemic destroys civilization, a hardened survivor takes charge of a 14-year-old girl who may be humanity’s last hope.’ This is therefore a great combination of the way different mediums impact popular culture. The plot asks big questions about how far you would go to get a cure for the world, how much is one persons life versus the possible saving of mankind. It’s a real homage to the power that vaccination could hold to impact the world, and how when one isn’t available how desperately people might act in the search for a cure. This is the only entry on the list that came about post pandemic, and I think it is because of that (despite being a parallel to the game) that really resonates on where that desperation comes from, and despite the current vaccine back lash, shows how different outcomes could be.
The very first scenes of the series are a flashback interview from before the pandemic where a scientist talks about what they think the next bit pandemic will be, and I have to say the whole scene brings me unacceptable levels of science joy.
Anyway, this one played so much into my particular ball park that I worked with Liv Gaskill at ID Transmission on a series of articles that talked about the science behind both the Last of Us computer game and the resulting TV series, which pretty closely followed the same plot. This four part series was a real joy to be involved with and so I’m hoping that you might enjoy them too:
I wonder if fungi will be increasingly represented in this genre a) due to the success of The Last of Us and b) as viruses feel a little too close to home these days and so the fungal world might feel like a safer sand box to play around in. This could provide a safe way to have accurate science portrayal, alongside entertainment, as the real prospect of a fungal pandemic is thankfully pretty small.
A shocking oversight
We’ve reached the end of the list, but not the end of the blog post as I want to address an appalling over sight on the IMDB list, and that is the omission of The Strain on the list. This is also a TV series, where season 1 was released in 2014, covered a series of 3 books, and ran for 4 seasons. The series is described as ‘A mysterious viral outbreak with hallmarks of an ancient and evil strain of vampirism ravages the city of New York.’
The strain – episode one, season one
There are many reasons why I love this series (and at some point I should do a vampirism and infection blog to include things like Ultraviolet) is that some of the main characters are epidemiologists linked to the CDC and so some of the science exposition as part of the job based discussions is very pleasing. The other reason I like this series is there is a definite bait and switch, in terms of the causative agent, with all the initial dialogue being linked to your standard viral outbreak, with a gradual reveal that the culprit is actually a parasite. This adds a layer of interest as the approaches to dealing with transmission really start to reflect this, and provide an interesting change as the characters are also forced to pivot and discuss the differences. So, the use of a non-viral infection is not as unique as some of the coverage of The Last of Us may imply. That said, the general science outside of the epidemiology in this definitely becomes more to serve the horror plot than feasibility as time progresses.
Where are the bacteria?
You’ve survived ~3000 words of outbreak talk, covering viruses, fungi and even parasites. You may however be struck by the lack of bacterial cause in any of these listings. I’ve been thinking about this whilst I’ve been writing this blog and I’ve come up with a few thoughts as to why this might be the case:
Too close to home – many people have experienced bacterial infections themselves in their loved ones, sometimes with tragic consequences. It may be hard to therefore suspend belief enough to enjoy the offering. I wonder if this will be true to an extent for viruses now, or whether popular culture will be a safe way to explore collective trauma linked to the pandemic
Too slow – one of the features of many of the scenarios in these movies and shows is that the impact to fast and significant. This an important aspect of making events have real risk and in raising tensions. If accurately portrayed bacterial infections may be too slow in their impact OR the deterioration is so quick there is insufficient time for viewer engagement
Not dramatic enough – bacterial transmission (as described by R0) are not going to be as dramatic as their viral counterparts, so if you subscribe to ‘go big or go home’ this transmission route is probably not the one to drive a sprawling plot-line forward
Too commonly encountered – there are 101 medical shows which have bacterial infections and their consequences featured and so they may be too close to a different genre
The science is pretty hard to get right – as people are more familiar with the topic the less story flexibility there is and the greater the need to not be too jarring for those you are trying to engage. At least in the UK, many people will have been taught about Typhoid Mary and the John Snow Cholera outbreak, and so may have some familiarity. It may also be that these also make people think of the past, and this is not the feel many of these properties are trying to evoke.
So maybe bacteria are a harder sell, although I’d be intrigued to throw a little antibiotic resistance into the mix, or some bacterial toxin related drama and then see what cool things could be done as a result. Maybe that might be my future project 🙂 Let me know if you think that there is a bacterial based film/series that I’ve missed.
This month is the start of a painful re-entry into normal life. Normal life in terms of work demands, normal life in terms of commuting and normal life in terms of getting back to not eating party food and leftovers for at least 50% of our meals. Now, mummy Girlymicro, Mr Girlymicro, and I have done our fair share of celebrating over the last few weeks, including eating out at large catered events and throwing our own parties for friends. Clinically, norovirus is now giving us its cyclical peak, and there was also a lot of food related outbreak news over the holidays. I thought, therefore, that I would start this years IPC related posts with one on foodborne outbreaks and the kinds of organisms involved.
Food related sickness and outbreaks can be caused by a number of different microorganisms and through a few different routes. The two main routes are infection and intoxication, and these are related to the organisms that tend to be the causative agents. The foods that are linked to these routes are also different, and if investigating can give you an idea of what you might be looking for, especially when combined with presentation, both in terms of clinical symptoms and speed.
Infection vs intoxication
Intoxication based food poisoning is usually linked to rapid onset symptoms following the ingestion of the food i.e. a matter of hours. This is because the symptoms aren’t related to an infection based process, where symptoms are linked to the invasion and replication process of the organism. There are two main types of toxins, heat stable and heat labile toxins. Heat stable toxins can be problematic, as once present in food these cannot be removed purely by re-heating to an appropriate temperature. Heat stable toxins, such as those produced by Bacillus cereus, are produced when the bacteria are present, hitting the right temperatures then kills the bacteria but the toxins remain. This process can be exacerbated when foods are not rapidly chilled or are left at a temperature where the bacteria could grown, there is therefore a prolonged period when toxins could be produced. Toxin related food poisoning (intoxication) can be caused by both bacteria and fungi.
Infection based food poisoning is linked to the ingestion of the organism itself, and presentations are therefore usually delayed as the organism needs to infect the gut mucosa. Many organisms that produce toxins can also cause infection related symptoms if present in high enough loads, and if suitable temperatures for bacterial kill are not met. Infection based food poisoning can be due to viruses, such as norovirus, parasites, such as E. histolytica, as well as bacteria, and the risks are often related to food hygiene efficiency as well as production factors.
Patient management
Most food related illness self resolves and management is mainly focussed on maintaining hydration and electrolyte balance. There is usually a requirement to undertake a minimum isolation period of 48 hours post symptoms in order to prevent any ongoing risk of person to person transmission, even if the original acquisition is thought to be via a food related source. Isolation may need to be prolonged in relation to certain groups because of the risk of ongoing to spread to others, either through personal hygiene awareness or through work based activity.
Recommendations for the Public Health Management of Gastrointestinal Infections 2019: Principles and Practice has a lot more detail on the main organisms associated with foodborne illnesses and some of these requirements for isolation. I’ve attached a copy below, but the link is also here in case it’s useful.
If symptoms continue for period of a week or are especially severe it may be necessary to take samples in order to identify a causative organism in order to support patient management. When taking a patient history it’s important to capture any patient specific risk factors (see below section on risk groups), travel history, recent event attendance history and details of hobbies (such as preserving) that may impact of food ingestion patterns. Additional individual management options can include antimicrobials (antiparasitic or antibacterial) and for non-bloody diarrhoea without fever antidiarrheal agents.
How do these organisms get into food?
Organisms can get into food from numerous sources. They can be present in the environment in which the food comes from, such as manure that is used to fertilise salad plants can contain organisms, like E. coli, even more so if human waste is used. Food, such as oysters, can be contaminated as part of their life cycle as filter feeders if they are growing in an environment where they are exposed to animal or human waste, and so can harbour organisms like norovirus and become highly loaded. Food can also become contaminated as part of the production or manufacturing process, contaminated from other items that are produced in the same facility, contaminated from the processes, such as the water or preservatives utilised, or from failures in the preservation process that would normally have removed organisms that are naturally present linked to food.
Organisms can also come from the humans involved in the process. Those manufacturing or handling the food may be carrying or infected with organisms, whether symptomatic or not. A Staphylococcus aureus colonised person making sandwiches may contaminated the food they are making. An asymptomatic norovirus infected canteen worker could expose those being served food by unwittingly contaminating food and/or serving implements. In the case of bacteria, low level contamination from those producing the food may then be able to grow up to levels where ingestion results in symptoms if the processes are not well enough controlled.
Food processing and manufacturing
Most food preserving techniques aim to ensure that if contamination occurs during production or manufacturing it is not able to replicate to the point where the organism would cause symptoms in those who ingest them. Many preserving techniques aim to control organism survival or replication/loading via either temperature, cell lysis/resource availability or both. There are two main groups of techniques, either physical or chemical.
Some of these processes are more prone to risk of failure than others, both depending on the process and where is it being undertaken. When undertaken in food manufacturing, these techniques are usually undertaken under highly controlled conditions using the HACCP process in order to manage some of this risk variance:
Food preparation in the home
Obviously, none of us are following HACCP processes when we are preparing food at home, that doesn’t mean that there isn’t any risk to home cooking. One of the hazards linked to cooking at home can be the home environment itself. I’m still aware of people who wash out chicken or turkey cavities in their kitchen sink, unaware of the droplets that are produced and how they can then deposit on other surfaces, which are now contaminated whilst appearing visibly clean. Other hazards can link to the fact that most of us don’t have access to rapid (blast) cooling, and therefore when cooking big batches of food and putting in the fridge, the cooling process may not be fast enough to prevent bacterial growth. Also, in terms of equipment, I work in IPC and I’m a bit of a control freak so I possess things like meat thermometers, in order to ensure that meat has reached appropriate safe temperatures. I am aware that not everyone lives in this particular world, and so may not have some of these pieces of kit lying around.
Most of the time if you end up preparing food less well at home the consequences are non-ideal but not massively serious, however, if you have an ‘at risk’ member of your household or visiting then it becomes more important to focus on controlling these risk, both through the food that is brought and how it is prepared.
Food preparation (catering)
We’ve already talked a little about the HACCP processes that are put in place to control risk in formal settings. Catering can be a tricky area of risk, even if undertaken by professionals. It is one thing to undertake catering in your restaurant or a space you work in all the time. Catering however, is often undertaken in sites that are not the ‘home’ of either the professional or the average person. Catering equipment can be hired to serve food in church halls, for weddings or other special events. It can also be undertaken on beaches, in forests and other remote locations with variable levels of power to support refrigeration. This can mean that control processes, such temperature control, are undertaken in atypical ways, such as temperature control using ice packs, which will have variable efficiency depending on external factors, such as ambient temperature.
Home catering for parties also brings risks. I love to throw an afternoon tea party for charity, but that means that I am suddenly trying to put waaaaaay more in the fridge than I normally would. Food may be out on a table for a number of hours. Some of the food may also be high risk, such as cheese or smoked fish, and it will be next to less high risk foods. Also, if you are not used to prepping food for large groups, you may inadvertently increase risks by the order in which food it prepped. That is without the risk of people bringing food to contribute to yours which you don’t know the origins of, or people picking up food with fingers and therefore increasing risk of spread if they have anything onboard.
Food storage
Once all of that catering is done, you are then left with a decision, what do you do with all the food that is left? Do you then try and shove it all in your fridge or freezer? Do you give it people to take home in Tupperware pots? How much have you taken into account the length of time that food has been non-temperature controlled? What does that do to the use by? Is everyone aware of any re-heating requirements or the dangers irrespective of re-heating of intoxication?
Issues with food storage are true not just for party catering, but also for batch cooking, something a lot of us are doing more and more of now the weather is colder and because food it more expensive. Foods like stews and rice dishes, which are high risk for intoxication, are also the kinds of foods that fulfil a lot of batch cooking requirements. It is really important to bear these risks in mind, ensuring rapid cooling and that temperature is monitored appropriately.
This also extends to ensuring that even dry goods are stored appropriately. We’ve all been there when we’ve found the pack of spice that 15 years old. Spices, canned goods and other preserved food have been identified as the source of outbreaks, and even when originally in good condition can become a risk if not well maintained, such as dented cans or if moisture has gotten into packets.
What kind of incidences are we talking about?
Over the Christmas period there have been two well publicised food related outbreaks, one linked to E.coli in cheese and one linked Cronobacter sakazakii (previously Enterobacter sakazakii) in infant formula.
BBC News – One dead after E. coli outbreak linked to cheese
This outbreak was linked to the presence of STEC toxin producing strain of E. coli. This leads to an intoxication that can impact of kidney function. Although not stated, elsewhere it was reported that the cheese may have been made from unpasteurised milk, removing one of the stages used to control organism risk in food production.
Advice for individuals from UKHSA included:
“Washing your hands with soap and warm water and using bleach-based products to clean surfaces will help stop infections from spreading. Don’t prepare food for others if you have symptoms or for 48 hours after symptoms stop.
“Do not return to work or school once term restarts until 48 hours after your symptoms have stopped.”
The other recent recall was linked to possible contamination of infant formula detected at manufacturing. Formula feed outbreaks linked to Cronobacter sakazakii have been noted in the past, with a large outbreak in France being the last large scale event. Infection does not just lead to GI symptoms but is associated in some patients with presentations such as blood stream infection and/or meningitis.
The formula included in this recall is mostly used in healthcare or is prescribed to individuals. This makes it critical as it is likely to have been given to an ‘at risk’ population. Milk related contamination is particularly challenging as heating impacts the nutritional content of the milk and so use of thermal risk reduction is not straight forward. Some hospitals, such as the one where I work, undertake an additional step, pasteurisation, for any formula feeds due to be given to high risk infants because of this well acknowledged risk in order to support infection risk reduction.
BBC News – Baby formula recalled over bacteria contamination fears
Current and Future Perspectives on the Role of Probiotics, Prebiotics, and Synbiotics in Controlling Pathogenic Cronobacter Spp. in Infants October 2021 Frontiers in Microbiology 12
There are obviously multiple examples every year of foodborne risks linked to contamination at source or HACCP failure, but these are the ones that have been most recently featured in the national press.
Are any groups at higher risk?
Although food related infection or intoxication can impact anyone, certain groups are more at risk of significant symptoms requiring treatment or are more at risk linked to certain organisms in terms of presentation. These groups are your very young, very old, the immunosuppressed and pregnant women. The very young and very old are more likely to need support linked to dehydration, and all 4 groups are likely to be less able to mount immune responses to invasive infection. The immunosuppressed and pregnant women have specific guidance linked to avoiding high-risk food groups because of severity of impact if infection occurs.
One particular organism linked with significant infection risk for pregnant women and the immunosuppressed is Listeria monocytogenes.
Microorganisms 2022, 10(8), 1522
Listeria crosses the gut wall at locations known as Peyer’s patches, and from there invades lymph nodes and blood. Once in the bloodstream, it can progress to cause meningitis/encephalitis by infecting the brain. In pregnant women it can also cross over into the placenta, where it can cause infection in the foetus/unborn child. Foodborne listeria outbreaks have been associated with a wide variety of foods, but are often linked to preserved foods and cheese.
There are a number of stages to investigating foodborne outbreaks. Initially, there will need to be some sort of flag to suggest an outbreak event. This is usually a number of people attending GPs or A&E linked to a single event, an uptick in samples positive for a specific organisms that is noted through lab reporting, or any cases of specific reportable organisms which will then get followed up.
Depending on the circumstances, a combination of the following steps will be undertaken:
Patient questionnaire (case)
Questionnaire of those who attended the same event but did not get sick (control)
Sampling and microbiological testing of possible implicated food, if still available
Sampling of the production environment, such as factories or restaurant kitchens
Investigation needs to be undertaken to identify the target food or batch as most production facilities will make more than one kind of food and will have multiple batches. If the outbreak is linked to a specific event, multiple types of party or other food is likely to have been available. Getting more information about what those who got sick ate vs the others enables you to narrow down what the culprit might be.
Once you have your questionnaires, it’s time for a little bit of stats. This enables you to calculate something called the relative risk for the cohort. The cohort being all those people who were at the same event, ate at the same restaurant, brought food from the same factory etc. This will include those who became unwell and those who did not. For each type of food or batch you can calculate a ratio of the risk of disease (infection/intoxication) in people who have been exposed (ate that food) compared to those unexposed (decided that food was not for them).
You then get a list of risks for different food types eaten. So if the following food was available at our event you can then undertake the calculation:
pigs in blankets
mini fish and chips
turkey and stuffing roulade
mini pavlova (with cream)
cheese pinwheels
If the number if >1 then it indicates and increased risk, if RR = 1 then it doesn’t impact on risk, and if RR <1 then there is a risk reduction. So in the case of our party food:
pigs in blankets RR = 1
mini fish and chips = 0.98
turkey and stuffing roulade = 1.73
mini pavlova (with cream) = 1.1
cheese pinwheels = 0.99
In conclusion………the turkey probably did it!
I hope that’s helpful, I know there’s loads more that could be covered, and if you are interested in anything in particular drop me a comment and I’ll see if I can post a follow up. The main take away is that there are multiple organisms that can cause foodborne infection/intoxication, and whether it’s home or out and about we can all be impacted. For most of us, it’s an unpleasant but low consequence event, but there are are people and populations where the outcomes can be much more severe. So, if you’re ever asked to complete a questionnaire please do so, and don’t ignore those news articles that tell you to throw an item away as it’s not a risk worth taking.
I adore Christmas, it’s one of my favourite times of the year. I meant to get this one out before Christmas, but to be honest, I was too busy having family time. For those of us working or looking for some fun reading between Christmas and New Year I thought this one might still be of interest.
Every year the British Medical Journal have a wonderful tradition. They post some free to access journal article. Now, these aren’t just any journal articles. They apply serious scientific processes to brilliant topics, such as the disappearance rates hard vs soft centred chocolates in ward environments presented as an observational study.
These articles always bring a smile to my face, and if you’re looking at an entertaining way to learn more about scientific processes or scientific writing these are a great place to start. I hope you’ll feel the same when you have a read of some of the ones linked to below, and know that there are more out there if you want to journey down this particular rabbit hole.
Merry Christmas, and thank you so much for spending another year in the company of the Girlymicro blog!
Objectives To determine the overall rate of loss of workplace teaspoons and whether attrition and displacement are correlated with the relative value of the teaspoons or type of tearoom. Design Longitudinal cohort study. Setting Research institute employing about 140 people. Subjects 70 discreetly numbered teaspoons placed in tearooms around the institute and observed weekly over five months. Main outcome measures Incidence of teaspoon loss per 100 teaspoon years and teaspoon half life.
Results 56 (80%) of the 70 teaspoons disappeared during the study. The half life of the teaspoons was 81 days. The half life of teaspoons in communal tearooms (42 days) was significantly shorter than for those in rooms associated with particular research groups (77 days). The rate of loss was not influenced by the teaspoons’ value. The incidence of teaspoon loss over the period of observation was 360.62 per 100 teaspoon years. At this rate, an estimated 250 teaspoons would need to be purchased annually to maintain a practical institute-wide population of 70 teaspoons.
Conclusions The loss of workplace teaspoons was rapid, showing that their availability, and hence office culture in general, is constantly threatened.
Objective To investigate whether sleep deprived people are perceived as less healthy, less attractive, and more tired than after a normal night’s sleep. Design Experimental study. Setting Sleep laboratory in Stockholm, Sweden. Participants 23 healthy, sleep deprived adults (age 18-31) who were photographed and 65 untrained observers (age 18-61) who rated the photographs. Intervention Participants were photographed after a normal night’s sleep (eight hours) and after sleep deprivation (31 hours of wakefulness after a night of reduced sleep). The photographs were presented in a randomised order and rated by untrained observers. Main outcome measure Difference in observer ratings of perceived health, attractiveness, and tiredness between sleep deprived and well rested participants using a visual analogue scale (100 mm).
Results Sleep deprived people were rated as less healthy (visual analogue scale scores, mean 63 (SE 2) v 68 (SE 2), P<0.001), more tired (53 (SE 3) v 44 (SE 3), P<0.001), and less attractive (38 (SE 2) v 40 (SE 2), P<0.001) than after a normal night’s sleep. The decrease in rated health was associated with ratings of increased tiredness and decreased attractiveness.
Conclusion Our findings show that sleep deprived people appear less healthy, less attractive, and more tired compared with when they are well rested. This suggests that humans are sensitive to sleep related facial cues, with potential implications for social and clinical judgments and behaviour. Studies are warranted for understanding how these effects may affect clinical decision making and can add knowledge with direct implications in a medical context.
Objective To quantify the consumption of chocolates in a hospital ward environment. Design Multicentre, prospective, covert observational study. Setting Four wards at three hospitals (where the authors worked) within the United Kingdom. Participants Boxes of Quality Street (Nestlé) and Roses (Cadbury) on the ward and anyone eating these chocolates. Intervention Observers covertly placed two 350 g boxes of Quality Street and Roses chocolates on each ward (eight boxes were used in the study containing a total of 258 individual chocolates). These boxes were kept under continuous covert surveillance, with the time recorded when each chocolate was eaten. Main outcome measure Median survival time of a chocolate.
Results 191 out of 258 (74%) chocolates were observed being eaten. The mean total observation period was 254 minutes (95% confidence interval 179 to 329). The median survival time of a chocolate was 51 minutes (39 to 63). The model of chocolate consumption was non-linear, with an initial rapid rate of consumption that slowed with time. An exponential decay model best fitted these findings (model R2=0.844, P<0.001), with a survival half life (time taken for 50% of the chocolates to be eaten) of 99 minutes. The mean time taken to open a box of chocolates from first appearance on the ward was 12 minutes (95% confidence interval 0 to 24). Quality Street chocolates survived longer than Roses chocolates (hazard ratio for survival of Roses v Quality Street 0.70, 95% confidence interval 0.53 to 0.93, P=0.014). The highest percentages of chocolates were consumed by healthcare assistants (28%) and nurses (28%), followed by doctors (15%).
Conclusions From our observational study, chocolate survival in a hospital ward was relatively short, and was modelled well by an exponential decay model. Roses chocolates were preferentially consumed to Quality Street chocolates in a ward setting. Chocolates were consumed primarily by healthcare assistants and nurses, followed by doctors. Further practical studies are needed.
Objective To detect and localise the Christmas spirit in the human brain. Design Single blinded, cross cultural group study with functional magnetic resonance imaging (fMRI). Setting Functional imaging unit and department of clinical physiology, nuclear medicine and PET in Denmark. Participants 10 healthy people from the Copenhagen area who routinely celebrate Christmas and 10 healthy people living in the same area who have no Christmas traditions. Main outcome measures Brain activation unique to the group with Christmas traditions during visual stimulation with images with a Christmas theme.
Methods Functional brain scans optimised for detection of the blood oxygen level dependent (BOLD) response were performed while participants viewed a series of images with Christmas themes interleaved with neutral images having similar characteristics but containing nothing that symbolises Christmas. After scanning, participants answered a questionnaire about their Christmas traditions and the associations they have with Christmas. Brain activation maps from scanning were analysed for Christmas related activation in the “Christmas” and “non-Christmas” groups individually. Subsequently, differences between the two groups were calculated to determine Christmas specific brain activation.
Results Significant clusters of increased BOLD activation in the sensory motor cortex, the premotor and primary motor cortex, and the parietal lobule (inferior and superior) were found in scans of people who celebrate Christmas with positive associations compared with scans in a group having no Christmas traditions and neutral associations. These cerebral areas have been associated with spirituality, somatic senses, and recognition of facial emotion among many other functions.
Conclusions There is a “Christmas spirit network” in the human brain comprising several cortical areas. This network had a significantly higher activation in a people who celebrate Christmas with positive associations as opposed to a people who have no Christmas traditions and neutral associations. Further research is necessary to understand this and other potential holiday circuits in the brain. Although merry and intriguing, these findings should be interpreted with caution.
Objective To determine whether artificial intelligence (AI) can generate plausible and engaging titles for potential Christmas research articles in The BMJ. Design Observational study. Setting Europe, Australia, and Africa. Participants 1 AI technology (Generative Pre-trained Transformer 3, GPT-3) and 25 humans. Main outcome measures Plausibility, attractiveness, enjoyability, and educational value of titles for potential Christmas research articles in The BMJ generated by GPT-3 compared with historical controls.
Results AI generated titles were rated at least as enjoyable (159/250 responses (64%) v 346/500 responses (69%); odds ratio 0.9, 95% confidence interval 0.7 to 1.2) and attractive (176/250 (70%) v 342/500 (68%); 1.1, 0.8 to 1.4) as real control titles, although the real titles were rated as more plausible (182/250 (73%) v 238/500 (48%); 3.1, 2.3 to 4.1). The AI generated titles overall were rated as having less scientific or educational merit than the real controls (146/250 (58%) v 193/500 (39%); 2.0, 1.5 to 2.6); this difference, however, became non-significant when humans curated the AI output (146/250 (58%) v 123/250 (49%); 1.3, 1.0 to 1.8). Of the AI generated titles, the most plausible was “The association between belief in conspiracy theories and the willingness to receive vaccinations,” and the highest rated was “The effects of free gourmet coffee on emergency department waiting times: an observational study.”
Conclusions AI can generate plausible, entertaining, and scientifically interesting titles for potential Christmas research articles in The BMJ; as in other areas of medicine, performance was enhanced by human intervention.
Objective To examine the effect of a (fictional) doctor working during the festive period on population health. Design Natural experiment. Setting England, Wales, and the UK.
Main outcome measures Age standardised annual mortality rates in England, Wales, and the UK from 1963, when the BBC first broadcast Doctor Who, a fictional programme with a character called the Doctor who fights villains and intervenes to save others while travelling through space and time. Mortality rates were modelled in a time series analysis accounting for non-linear trends over time, and associations were estimated in relation to a new Doctor Who episode broadcast during the previous festive period, 24 December to 1 January. An interrupted time series analysis modelled the shift in mortality rates from 2005, when festive episodes of Doctor Who could be classed as a yearly Christmas intervention.
Results 31 festive periods from 1963 have featured a new Doctor Who episode, including 14 broadcast on Christmas Day. In time series analyses, an association was found between broadcasts during the festive period and subsequent lower annual mortality rates. In particular, episodes shown on Christmas Day were associated with 0.60 fewer deaths per 1000 person years (95% confidence interval 0.21 to 0.99; P=0.003) in England and Wales and 0.40 fewer deaths per 1000 person years (0.08 to 0.73; P=0.02) in the UK. The interrupted time series analysis showed a strong shift (reduction) in mortality rates from 2005 onwards in association with the Doctor Who Christmas intervention, with a mean 0.73 fewer deaths per 1000 person years (0.21 to 1.26; P=0.01) in England and Wales and a mean 0.62 fewer deaths per 1000 person years (0.16 to 1.09; P=0.01) in the UK.
Conclusions A new Doctor Who episode shown every festive period, especially on Christmas Day, was associated with reduced mortality rates in England, Wales, and the UK, suggesting that a doctor working over the festive period could lower mortality rates. This finding reinforces why healthcare provision should not be taken for granted and may prompt the BBC and Disney+ to televise new episodes of Doctor Who every festive period, ideally on Christmas Day.
Objectives To identify Barbie brand dolls that had medicine and science themed professions in comparison with other career dolls and to determine their accuracy in meeting clinical and laboratory safety standards. Design Descriptive quantitative study. Setting Visual and data analysis of web searches.
Main outcome measures To identify the kinds of medical and scientific subspecialties that the Barbie dolls (and a comparison doll group) worked in; and to determine whether these medical professional and scientist dolls met laboratory and clinical safety standards. Additional data about doll demographics (ie, age, ethnic group, and sex) were also collected.
Participants 92 Barbie brand dolls were analyzed: doctor (n=53), scientist (n=10), science educator (n=2), nurse (n=15), dentist (n=11), and paramedic (n=1). 65 non-Barbie brand dolls were also analyzed for comparison purposes: doctor (n=26), scientist (n=27), nurse (n=7), dentist (n=2), engineer (n=2), and magnetic resonance imaging (MRI) technician (n=1) dolls.
Results Barbie brand medical professional dolls (n=80) largely treated children (66%, n=53/80), with only three (4%) medical professional dolls being directly depicted working with adults. Of the 12 scientist Barbie brand dolls, none met all proper personal protective equipment requirements related to hair and clothing. Barbie brand dolls often came with items, such as laboratory coats, microscopes, stethoscopes, and glasses, that children stereotypically associate with doctors and scientists. While comparison dolls offered a wider range of age and ethnic groups than the Barbie doll group did, the dolls similarly struggled to portray a wide range of medical and scientific subfields and most comparison dolls did not wear proper personal protective equipment.
Conclusions Medicine and science themed dolls help to inspire tomorrow’s medical professionals and scientists. All toy companies should ensure that future medical professional and scientist dolls meet clinical and laboratory safety standards and diversify the types of medical and scientific professions represented (especially among male dominated fields). For young girls’ sakes as much as her own, Barbie must keep shattering glass ceilings.
I was fortunate enough to be asked to record a podcast last week with the absolutely awesome Betty Adamou for her series Tales of Female Badassery. Just as we were prepping to record I was struck with a moment of panic. I didn’t know whether I was a Badass. I didn’t know if I’d every done anything that would make me a Badass. I called one my girls in a state of panic, she responded with ‘don’t be so ridiculous, you’re not only a badass, you’re one of the most badass people I know’.
It got me to thinking. I am super fortunate to be really close to my family and to have the wonderful Mr Girlymicro as my constant companion. In more recent years I have, however, also become aware of how wonderful it is to have a small tight knit group of women in my life. These are the people who understand if I don’t call them for months. The ones who know me well enough to know when to challenge and when to comfort. The ones who I can sit and watch bad movies with in pyjamas and who would never judge me for the state of my house. Some of them I have known for decades, others more like 5 years, but time doesn’t really matter. They are my girls. They get me, and this post is dedicated to them and why you should consider finding your own equivalents.
Constructive challenge
Not everyone has a Mr Girlymicro in their lives and to be honest we all need someone to call us on our BS sometimes. Having a small cicle that you trust completely, which have the ability to stop you in your tracks when you’re going down a cognitive rabbit hole is so valuable.
I suspect we’ve all been there, sounded off about X or Y, when suddenly someone trusts calls us out on what we are doing that could trigger that behaviour, or pushes us to understand why we are so triggered. This calling out opens up a whole new vehicle to understanding or route for a response that would not have been available to us otherwise.
In my case, my girls often join forces with Mr and mummy Girlymicro in asking me why? Why have I decided to take on yet another thing? Why do I think it’s needed? What extra will it add? What will I drop to enable me to take on the shiny new? What does it mean for them? Will they see even less of me now? Will I be even more distracted and do even less at home? These conversations can lead to me walking back commitments, or at least force me to articulate my thought process and gain a better understanding of where I actually am with my workload.
Unconditional support
The reason that constructive challenge can happen is because I know these guys are 100% on my side. They are unwavering. They know all the bad in me and choose me anyway. They can, therefore, be brutal about the truth when needed, as they are also around for the rebuilding that is sometimes required after being faced with a harsh truth.
This also means that I hear what they say. If they tell me someone is out of line and validate my feelings, I hear it more because I also know they would tell me if the opposite was true and I was the one who’d acted badly. To me, unconditional support isn’t about just giving me what I want to hear. It’s giving me what I need to hear in terms of the truth/reality check. They tell me both that I’m not superwoman, but also that I’m a god damn queen who can achieve anything she puts her mind to. Just not simultaneously.
Shared experiences
Not through any deliberate endeavour, but just because of how life has worked out, my girls all happen to be kick ass women who either work in STEM (science, technology, engineering and maths) or are STEM qualified. In fact, they are all coincidentally PhD qualified. I didn’t meet them all through science however. For instance, Diane, I met my first day at uni and has been keeping me sane for over 20 years. Claire (known as Dr Claire, as she was the first Claire with a PhD) I met because she was dating a friend of my future husband, the boyfriend exited the picture and we stayed friends. Claire (Captain Claire, due to our shared appreciation of Captain Jean Luc Picard) and I met over several bottles of wine when we were both doing our PhDs and have continued on the wine trajectory ever since. This means we have both a bunch of shared and different experiences.
Our shared experiences, linked to being women in science, mean that they can sometimes help me see challenges coming in a way I wouldn’t have anticipated. They can also share what did and did not work for them when they encountered something similar. We can, on occasion, also just rage about the injustice of it all in a way that enables us to put our feelings in a box and carry on regardless.
A different view of the world
I have some wonderful women in my world who I count as dear friends but whom I still work with. These wonderful women are often my go-to for support and guidance as they are emersed in my world. The difference between them and this group of girls is that we don’t work together, and have never worked together in the same department. This means that we took different paths through both work and life. We don’t just reinforce each others perceptions and bias therefore through having pre-established knowledge of the other people in each others lives or work. We have a bunch of shared experiences, but a lot of our progress has led us to very different places. Some of us have kids, some don’t, some of us still work academically or in science, some don’t. This breadth of experiences mean that they can sometimes offer a very different view to mine. They can point out nuance I would have missed or when my previous experience is biasing me to a current situation.
We also have very different ideas of what constitutes a good time. I’m a book, fire, sofa and afternoon tea kind of girl. Whereas the Claires would way prefer to be with their animals (chickens, wallabies, etc) and Diane would happily be walking through the Scottish countryside. This is also helpful. It has always pushed me to try things I wouldn’t have. Once it pushed me to try camping. This was a mistake. Camping was a step too far. They love me anyway.
Parachute provision
I’ve written before about my tendency to shame spiral. I’m not alone. Captain Claire and I are known to call each other up mid shame spiral and offer each other a parachute outta there. We talk through what we’ve done, talk through the possible consequences, and how we might act or handle things differently next time, in a space of acceptance without judgement. It’s this last piece that is key. We’re not trying to ‘fix’ each other, just support each other by providing a safe space for verbal reflection and to articulate our fears, whether rational or not. From my perspective, this often permits an early exit from the spiral combined with some centering and learning. What more could a girl ask for?
Sometimes, we all cry
That same space of zero judgement is also important as it provides a space where you have licence to just feel. Sometimes, I have to ride the wave of emotions to process them and get through to the other side. It’s no secret to the readers of this blog that there have been some tough times in the last few years. Having a space where you can just have freedom to express that you are angry or upset by the state of the world or the way you have been treated professionally is so special. I have this with Mr and mummy Girlymicro as well, but it helps them to be able to share the load, especially when things can go through intense periods. Sometimes, I just need to cry and say that things are unfair, and then I get it out of my system and find the emotional band width to remember my why and can get back on with the fight.
Borrowed courage
When I phoned up Dr Claire and declared ‘I’m just not a badass’, her first response of ‘hell yes you are’ gave me courage. It made me brave enough to go ahead and record something I was hesitant about. This is what my girls do. They loan me courage when mine fails me. When my imposter syndrome or my fear tells me I can’t, they are always there to tell me I can. When I receive awards or recognition and I ask ‘why me’, they respond ‘because’. They see me when I cannot see myself. They will tell me to ignore the fear and just get on with it. They will challenge me when I’m avoiding things because I’m not brave enough and loan me the courage I need to do what is needed. When required, they bring out the bad ass warrior in me.
Courageous authenticity
The validation I am lucky enough to receive from my family and my girls is important for another reason. They make me feel like it’s OK for me to be myself, not some projected version of myself. I’m pretty open in this blog about who I am, how I feel, and how I respond to challenges. I’m also (I hope) pretty honest about my personal flaws and areas that I’m trying to grow and improve around. This blog wouldn’t be possible without having people around who not only validate that that message is OK, but that it is actually important and helpful to talk about these things.
There are days for all of us where we can’t love ourselves. Days where all we can see are our flaws and none of our strengths. Days when we compare and we just don’t stack up. Having people in your world who also see and acknowledge these weaknesses, love you anyway, and tell you you have value even in their presence is one of the greatest gifts we can receive from another person. It enables you to still be who you are even when that may be the last thing you want to be. To continue to work on being unapologetically authentically you.
Mutual appreciation society
One of the best things about these relationships is that they are bi-directional. Most of the time, when one of us is having a bad time, the other is doing OK and can be there to lift the other up. On the occasions where we are both just going through it, then a shared pit of despair can still provide comfort. (We’ve decked ours our with pillows, blankets, and everything). I think these ladies rock it. I trust them completely. I trust them to call me out and challenge me, which means when they validate my other feelings, I believe that too. I love them and consider myself blessed to have them in my life. I also hope that I am there for them as much as they are there for me.
My girls and I aren’t in competition with each other. We’re all on different paths. We value different things, and that’s not only OK but joyous! It doesn’t matter who is achieving what. It doesn’t matter if that’s getting the kids to school on time, or getting out of bed and just making it to work when we’re having a bad time and just wish to hide from the world. All of it is valid and worth celebrating. When they were having kids and I was finding it hard as I was still working through my own situation, they were always mindful but still knew that I was genuinely happy for them. One thing does not obliviate the other.
Distilled awesome
So, to end, I want to say thank you. Thank you to the women out there supporting other women. Thank you to the ladies who straighten my crown even when I don’t realise it’s crooked. Thank you to my girls, the one’s who I cry, scream and cheer with. You are distilled awesome and I will never be able to truly describe the difference you’ve made to my life and how grateful I am to have you on this journey with me. I may be absent for months, I may be a special kind of crazy, but know I am always here for you!
Girlymicro 