This week is results week, many people will have been receiving A-level, T-level, and BTEC results, and making some pretty big life choices as a result, often feeling a lot of pressure to get them right as, for some, it can feel like a point of no return.
I’ve previously written about this from my point of view:
All that being said, I graduated university over twenty years ago, and if I was an academic paper reference you’d discount me for being out of date. I was thrilled therefore when Megan volunteered to write a guest blog on her experience of entering the field of Healthcare Science.
Megan has just successfully completed a BSc at the University of Lincoln and navigated the process to apply for, and be accepted onto, the national scientific training programme (STP) in audiology and is due to start in 2026. Megan had initially thought medicine was the only way into a career in the NHS and I hope that by sharing her experiences it can help others navigate, what can be, a complex landscape into a wonderful career pathway.
Guest blog by Megan Baines
Like many people working in healthcare science, my path wasn’t quite as straightforward as I once imagined.
Looking back, I’ve always been academically minded. As a child, I was the one who preferred curling up with a book rather than running around outside. I enjoyed classroom lessons far more than active lessons (forever hopeless at PE), and I found genuine excitement in learning new things. While my interests changed over the years, one subject consistently stood out above the rest: science. From a young age, science fascinated me. I knew that I wanted to pursue a career where science was at the heart of what I did. I didn’t yet know exactly what that career would look like, but I knew it would involve science and hopefully a hospital.
As I approached the end of sixth form, I encountered something that many aspiring healthcare professionals experience. When you tell a careers adviser, teacher, or family member that you’re interested in healthcare, the conversation almost inevitably turns to medicine or nursing. Both are incredibly rewarding professions, and the dedication of those working within them cannot be overstated. However, they are far from the only careers that make a meaningful difference to patients.
At the time, though, I wasn’t aware of the breadth of opportunities available. Like many students, I assumed medicine was the obvious route. So, I applied to four medical schools, with Biomedical Science as my fifth UCAS choice, thinking of it simply as a backup plan if I was rejected. In my mind, I had mapped out my future: I would study medicine, become a doctor, and that would be that.
However, as I attended university open days, rather than becoming more excited, I found myself feeling increasingly uncertain with each visit leaving me with an uncomfortable sense of dread. It wasn’t that medicine wasn’t interesting (it absolutely was) but I realised I couldn’t picture myself enjoying the course or the career in the way I had hoped. The more I reflected on it, the more I recognised that I had been pursuing an idea of what I thought I should do, rather than what genuinely inspired me.
Though, everything changed during my final open day at the University of Lincoln.
Walking around the Biomedical Science department, speaking with staff and students, and learning more about the course, I felt something I hadn’t experienced during any of the medical school visits: genuine excitement. The programme combined everything I loved about science with the opportunity to contribute directly to healthcare through research, diagnostics, and laboratory medicine. It immediately felt like the right fit.
Making the decision to withdraw my medical school offers wasn’t easy. After years of working towards what I believed was my dream, changing direction felt daunting. But it was also one of the best decisions I have ever made. I accepted my offer to study Biomedical Science at the University of Lincoln, and I have never looked back.
The three years I spent there were some of the most rewarding of my life. I was fortunate to be part of an incredibly supportive cohort, many of whom remain close friends today. My lecturers were not only excellent teachers but accomplished scientists whose enthusiasm for their work was infectious. They demonstrated that there are countless ways to make a meaningful impact within healthcare beyond the roles most people immediately think of and often had meandering paths into their dream careers.
One lecturer, in particular, had previously completed the Scientist Training Programme (STP). Through her teaching and conversations about her own career, I was introduced to the STP for the first time. Until then, I had never even heard of it. Like many students, I had been completely unaware that such a pathway existed. Discovering the STP opened my eyes to an entirely different career that perfectly combined my love of science with patient care.
Perhaps that’s a rather long-winded way of saying that careers are rarely as linear as we expect them to be. When I first started university, if you had told me that one day I would be training to become an audiologist, I probably wouldn’t have believed you. Like many Biomedical Science students, I assumed my future would lie in pathology, research, or another laboratory-based discipline. Audiology wasn’t even on my radar.
Yet that’s exactly where I found myself. Looking back, from choosing Biomedical Science over medicine, to discovering the Scientist Training Programme, to ultimately finding my place in audiology has led me to a career that genuinely excites me. I feel more motivated than I ever have before.
It’s funny how the opportunities you never knew existed can end up being the ones that suit you best. That’s one of the reasons I wanted to start writing. I remember how little I knew about healthcare science careers when I was applying to university, and if sharing my experiences helps even one person discover a path they hadn’t considered then I’ve done something right. It’s truly a privilege to now be writing for a blog that I have long enjoyed reading, while also beginning a blogging journey of my own.
When I started training, TB was around but in most areas was at pretty low levels and drug resistant TB, which makes it very hard to treat, was not a thing. Times have changed however, multi-drug and extremely drug resistant TB are increasingly common. TB itself, which is a disease strongly correlated with social deprivation, is something we see with increasing regularity. All of this means that TB is definitely not a disease of the past, it is having a resurgence within the UK (13.6% case increase from 2023 to 2024). So I was super happy that Dr Eleanor Senior offered to write me a guest blog linked to a book on the topic that offers a non-Eurocentric narrative on the disease.
Eleanor got in touch after I posted on LinkedIn a few weeks ago with a call for anyone who wanted to try their hand at blog writing, she volunteered to contribute a guest blog. If you are reading this and interested in giving it a go too then please email me on elaine@girlymicrobiologist.com.
I really want to use the platform I have to give opportunities to others, as I have been fortunate enough to benefit from those opportunities myself. Writing a guest blog can be useful if you are putting together training portfolios, or just want to try and develop your writing style. So, if you’re interested send me a 300 word pitch about what you’d like to write a blog on and I’ll see whether it is something I can support you with.
Eleanor is a Clinical Scientist in Microbiology at the Countess of Chester Hospital. She has a background in Infection and Global Health (PhD), Clinical Microbiology (MSc) and Biological Sciences (MSci).
Guest blog by Dr Eleanor Senior
Tuberculosis has been entwined with humanity for millennia. Once romanticized as a malady of poets, today tuberculosis is a disease of poverty that walks the trails of injustice and inequity we blazed for it
The book
I was first introduced to this book, surprisingly, by my sister-in law. She isn’t a scientist, she a writer, and usually doesn’t have much interest in microbiology. However, when she said ‘I had to read it’ I knew it was going to be an interesting read.
The book mainly centres around the narrative of ‘Henry’s story’, a young boy from Sierra Leone who the author John Green meets. Henry develops TB at age 6, which then becomes multi-drug resistant. He goes through several course of treatment, including at Lakka Government hospital. The book focuses of key barriers for people, such as Henry, to effective treatment. This includes inaccessibility of treatment centres, financial cost of treatment, mistrust of the medical community and general racism. For instance, TB was at one time considered to be a ‘White man’s plague’ as black people ‘weren’t smart enough’ to catch it. TB still continues to be a stigmatised disease in many communities, leading to suffers being shunned. This stigma can lead to people not seeking out treatment or follow-up care. A key message of this book is that TB, broadly speaking, is treatable and the main barriers to its eradication are societal and based on health inequalities.
It also shows how the impact of TB can be seen everywhere in modern day life. For example, Pasadena, in California was a TB treatment hub, and TB ‘tourism’ led to increases in its economy. Additionally, Adirondack chairs were designed for patients in sanitoriums.
What is TB?
Tuberculosis is a highly infectious disease. It is an ancient disease and has been estimated to have killed 1 in 7 of all people who have ever lived. It has been around for thousands of years, killing numerous people including John Keats, Chopin, Anne Bronte, Henry VII and Eleanor Roosevelt. Evidence has also been found as the cause of death in Egyptian mummies (2400 BC) and in the Neolithic period (5800BC).
It is caused by a bacterium called Mycobacterium tuberculosis and spread through the air by the coughs and sneezes of infected people. There are 2 forms of the disease: active and latent. Active TB can cause a variety of symptoms, including a chronic cough, night sweats and weight loss. In this way it was often known as ‘consumption’ or ‘wasting disease’. Latent TB does not cause symptoms and is not infectious, but the bacteria are still present.
Multi-drug resistant TB (MDR-TB)
TB is typically treated with a cocktail of several antibiotics for several months. For the microbiology/pharmacy nerds it is usually a cocktail of Rifampicin, Isoniazid, Pyrazinamide and Ethambutol (RIPE).
However, due to several reasons, including mismanagement of TB treatment, some strains of TB are becoming resistant to this treatment. This means that the normal treatment will not work and longer, more complex, courses of different antibiotics (sometimes 18-months or longer) are required. These can have cost implications and can have a variety of side effects. The complexity of cost of this can then lead to more people not completing their treatment, further compounding the issues.
Estimated number of people who developed MDR/RR-TB (incident cases) in 2023, for countries with at least 1000 incident cases (World Health Organisation)
Health inequalities
Henry’s story shows that the chances of survival from this disease are often based on where a person lives. As mentioned, TB was considered a ‘white person’s disease’ and so it was able to be rife in non-white communities. However, it was later decided that it was a ‘black disease’ and one reason to prevent the abolition of slavery was because it would increase the spread of TB.
The cure for TB is here, however, due to issues with healthcare and economic systems, the treatments and assistance are not provided equitably to the societies that need them most. A range of socioeconomic factors can increase risk for TB, including poverty, language barriers and limited access to health care and housing.
Even now, TB disproportionately affects racial and ethnic minorities. In 2023 it was estimated that 90.1% of TB cases occurred amongst minorities (https://www.cdc.gov/tb/health-equity/index.html). Currently, there are many different initiatives to attempt to remove these barriers, including communication and outreach events, policies to identify ‘at risk’ groups, highlighting personal stories and collaborations between different international bodies, such as the CDC.
Conclusion
TB is a highly interesting disease; it has been around since history began and has shaped out modern world. Even know, it continues to be a challenge for healthcare professionals around the globe. Finally eradicating this disease will require a multifaceted approach, including effective drug regimens, education and removing barriers to equitable treatment.
I posted on LinkedIn a few weeks ago a call for anyone who wanted to try their hand at blog writing to contribute a guest blog to The Girlymicrobiologist. I’ve been lucky to have a few responses, and if you are reading this and interested in giving it a go then please email me on elaine@girlymicrobiologist.com. I really want to use the platform I have to give opportunities to others, as I have been fortunate enough to benefit from those opportunities myself. Writing a guest blog can be useful if you are putting together training portfolios, or just want to try and develop your writing style. So, if you’re interested send me a 300 word pitch about what you’d like to write a blog on and I’ll see whether it is something I can support you with. At the same time as putting out the call, I’ve reached out to some great friends and colleagues to see if they have anything they would think would help others, and this week I am lucky enough to share a guest blog from Professor Lena Ciric, Professor of Built Environment Microbiology at UCL Civil, Environmental and Geomatic Engineering.
Lena completed her first degree in Biological Sciences at the University of Oxford in 2000. She then went on to work as a research assistant at the NERC Centre for Ecology and Hydrology (CEH) in Oxford, where she also completed a CASE PhD Studentship hosted at Napier University Edinburgh investigating the bacterial community dynamics in diesel degrading groundwater consortia in 2006. Lena moved to the UCL Eastman Dental Institute in 2007 and worked on two EU funded postdoctoral projects investigating novel antimicrobials and antimicrobial resistance. Lena took up a permanent post at UCL CEGE in October 2012 and leads the Healthy Infrastructure Research Group there.
Lena and I have known and worked together for over a decade, we even made Professor together in the same year. We have shared both the highs, and lows, of academic life and grant funding. One of the things that has always inspired me about Lena is her ability to communicate, to talk through complicated or challenging topics from a place of authenticity. I am super privileged to be able to share this post from her today about the drivers that guide our approaches to work and life, and how things that can serve us in some stages of our lives end up causing us issues as life progresses. I hope her reflections help us as much as they have aided me.
Blog by Professor Lena Ciric
Last weekend I transitioned from my mid- to my late forties. I don’t feel any sort of way about it. Over the last few years, both work life and home life have presented me with some challenges, and I have been working hard to overcome these. I am much clearer on where I want to go, who I want to be and more accepting of who I am.
But getting to this place has not been easy and is very much a work in progress. A major obstacle that I have had to overcome in recent years has been learning how to ask for what I need from my colleagues. I have also had to stop shying away from difficult conversations.
But why were these obstacles there in the first place? I’ve done some soul searching and come up with some answers. These are numerous, complex and some go back many decades.
Looking at the past to understand the present
Firstly, I have never felt good enough. I am a child of socialism, born in Belgrade on the eve of the 80s, the only child of two university educated parents who were brough up in the post-war socialist state – one that prioritised education among other things. I was bright, worked hard and always did well in school. But my efforts were rarely acknowledged or rewarded. There was always a feeling that I could try harder and do better – that I was not good enough.
Secondly, I was taught from an early age that a woman should make her own money and not depend on anyone else. My mother, who had been a journalist, had to give up work when we moved to the Netherlands in the late 80s and then never worked again. Up until then, she had worked all her life and had always told me that a woman should have independent means. From an early age, I knew that I would have a career and that I would have to be ambitious.
Thirdly, I am a woman in a mostly male world. Or I certainly was. I had a natural talent for maths and the sciences. The STEM (science, technology, engineering and maths) subjects came easily to me and I enjoyed them, but I was conscious of the fact that I was often among a minority of girls in the class. This improved a little as I moved through university and my PhD. I am a life scientist by training, and the life and medical sciences tend to have more equal gender representation. Having said that, as one rises through the ranks of academia, the leadership roles are mostly populated by men, so while things have changed for the better, we still have a way to go.
Finally, in the early years of my research career, I learned that I am good at getting stuck in and working things out for myself. Practicing and trying again if things don’t work until they do. I learned not to depend too much on any one individual. My supervisors were often busy, and I did not get to see them very often, so I just had to get on with it and figure out my own way forward.
All the above have contributed to a belief that you can always do more and try harder and that you shouldn’t rely on others. And this belief stayed with me for a long time. Too long. I thought that if I needed something done, I would have to do it myself. It’s a philosophy that took me through my PhD, my postdocs and into my academic career first as a Lecturer and then an Associate Professor – through my 20s and 30s, and into the start of my 40s. It’s a philosophy that got me where I am now – a professor in one of the best universities in the UK, and in the world. But one that no longer serves me.
Nobody told me how the job would change
At some stage when I wasn’t looking, my job became less about doing things myself, and more about asking others to do things. My career had provided me with the skills and experience to be able to see the bigger picture and think more strategically. My job description had changed, but I was still doing what I had always done – trying to do it all myself.
To see the bigger picture and be strategic, you cannot be bogged down in the detail. You need bandwidth to step back, observe and reflect. You need headspace to appreciate what those you work with need from you. In academia, our jobs change as we rise through the ranks, but this is never explicitly acknowledged. Nor are we trained in how to make these adjustments. At some stage you go from doing it all yourself to asking others to do it for you, but nobody ever tells you how you make this transition.
I found myself in my mid-forties feeling uncomfortable in the place I had arrived – the place I had strived to be for decades. I was a fish out of water. I couldn’t do what I had always done – doing it all myself – because there was simply too much to do. But I was also uncomfortable with asking for help. Something had to give…
Never stop adapting and evolving
I had to learn to ask for help. And to anticipate when I would need it. I had to learn to resource my projects properly. I had to learn to relay on others – people who could do things that I couldn’t. And together, our whole was greater than the sum of its parts.
To get to this point, I have had to learn to ask for what I need and be explicit about my expectations. I have had to relinquish some responsibility and control. This was initially hard for me, but in the end, it has been liberating and beneficial for my colleagues.
I have also had to learn to tell colleagues when they are not meeting expectations. These conversations are uncomfortable for most of us, but without them, we miss out on the opportunity for growth – on both sides. And, from experience, I have found that they provide both sides with the opportunity to talk openly, listen, and find common ground. Leading to better relationships in the long run and a better understanding of each other as people.
Academia is a funny profession. Academics are, by our nature, competitive. We have had to compete to get funding, we have had to compete to publish our research. We are judged on these metrics. We are encouraged to compete – it preys on our insecurities. There is always more to do and never enough hours in the day. We are reduced to the sum of the grant funding we have won and our h-index…
We must remember we are so much more than that. We are humans each trying to find our way in the world. We might feel that we are pitted against each other, but in reality, we are much stronger together. There is joy in appreciating other’s differences and the things that make others tick. There is joy in helping each other navigate the complexities of our careers.
Last week I wrote about the challenges of the current Ebola virus outbreak, talking about some details linked to the virus itself, and also some challenges that mean this outbreak may be more challenging to manage. I was involved in previous outbreaks, but definitely in a peripheral support capacity, because of my underlying autoimmune condition I did not travel to Sierra Leone. Context and learning from previous events is important however, so I tapped my good friend and colleague Ant De Souza, who was directly involved in supporting diagnostics, to write me a guest blog of his experiences.
Anthony De Souza is an award-winning Healthcare Science educator with over a decade of experience as Biomedical Scientist in microbiology. He was the first Healthcare Scientist to gain a permanent Practice Educator post, a post he has only continued to develop and expand since its inception. Ant’s transition into strategic education leadership has empowered the Healthcare Science workforce to improve patient outcomes based on his approach; which links strengthening multidisciplinary collaboration, expanding clinical capabilities, and elevating the profile of the healthcare science workforce to ensure they are invited to have a seat at the table. The impact of this has been recognised not just by me, but by him being named on The Pathologist’s Power List for his outstanding contributions to the field.
Ebola Deployment, Sierra Leone – A Personal Reflection
In 2015, when an urgent appeal was issued by Public Health England (now UKHSA) for scientists to support the Ebola crisis in West Africa, I didn’t hesitate—I knew I had to go.
In the past, I’d seen similar calls for volunteers and questioned whether my skills were enough to make a meaningful contribution. The last thing I would ever want was to become a burden on a mission of such importance. But this time felt different. For the first time, my experience, confidence, and mindset aligned with what was needed. I was working as a Band 6 Biomedical Scientist at Watford General Hospital, in a busy microbiology department delivering a 24/7 service. I was used to working under pressure, and I felt ready to contribute.
Before committing, I spoke with my colleagues. A five-week deployment would mean they would take on additional workload, and it was important to me that I had their full support. With their encouragement, I signed up.
Preparation and training
Preparation for deployment was thorough and, at times, intense. I travelled to Porton Down in Salisbury for specialist training, where we learned how to work safely with high-risk pathogens such as Ebola. This included simulation exercises in a laboratory environment designed to mirror the Kerrytown facility, where we practised managing realistic scenarios, including equipment failures and power outages.
We also completed security awareness and hostage survival training, alongside a series of vaccinations for diseases such as yellow fever, cholera, and typhoid. Anti-malarial medication was essential. The preparation highlighted not only the scientific challenges ahead, but also the environmental and personal risks we would face.
The journey
Getting to Sierra Leone was a journey in itself. We travelled by plane, transferred in Morocco, then boarded another flight to Freetown. From there, the journey continued by minibus to a port, a boat crossing, and finally another minibus to the site.
It was a strange experience travelling with a group of people I had never met—yet over the course of five weeks, these individuals would become a close-knit team.
Arrival and first impressions
On arrival, small behavioural changes immediately became part of daily life. Handshakes were replaced with elbow taps, a simple but important measure to reduce transmission risk. Regular temperature checks became routine, particularly at checkpoints when travelling to and from the treatment centre.
We were based at the Ebola Treatment Centre (ETC) in Kerrytown, outside of Freetown—a facility built by the British Army Royal Engineers and funded by the Department for International Development. The scale of the operation was impressive, and there was a strong sense of shared purpose. People from different organisations and backgrounds worked together with a single goal.
The ETC was divided into zones based on risk, from green (low-risk areas) to red (high-risk patient areas). Full personal protective equipment (PPE) was mandatory in higher-risk areas.
Working in the laboratory
Our laboratory was located centrally within the site, shared with the Ministry of Defence. After donning PPE, we met the outgoing team and received a rapid but essential handover. For a few days, we worked alongside them before taking full responsibility.
Our role was to test blood and swab samples from individuals suspected of having Ebola. We operated six days a week, with two teams of six covering shifts from 06:00 to 22:00.
Many samples came from community settings, including remote villages. A significant proportion were post-mortem samples, taken to determine whether Ebola had caused the death. The high number of samples from children and infants was particularly difficult to process emotionally.
Specimen reception took place outside the lab. Samples were placed into chlorine solution for decontamination before being handled further. Wearing full PPE in the heat of the sun was physically exhausting, and the need for constant vigilance—checking for incorrectly packaged samples or hidden sharps—added to the pressure.
Inside the lab, resources were basic but functional. The space had sealed cement benches, limited air conditioning, and no negative pressure system. Testing was carried out using PCR techniques for Ebola, alongside POCT testing for malaria. A flexible film isolator was used to safely inactivate the virus before analysis.
Life beyond the lab
Outside of the laboratory, the scale of the public health response was visible everywhere. Posters, radio messages, and community outreach efforts aimed to educate people about Ebola transmission, safe burial practices, and how to protect themselves.
Strict measures were in place:
Large gatherings were prohibited
Schools and religious services were disrupted
Curfews were enforced
Checkpoints monitored movement and health status
Movement restrictions between districts
Daily life, as it once was, had largely come to a standstill.
Cultural challenges and adaptation
One of the most striking aspects of the outbreak was its impact on traditional burial practices.
In Sierra Leone, burial rituals are deeply rooted in cultural and religious beliefs. Traditionally, families wash, dress, and physically say goodbye to loved ones. However, in the context of Ebola, these practices posed a significant risk, as the virus remains highly infectious after death.
To reduce transmission, specially trained burial teams were introduced. These teams worked closely with communities and religious leaders to adapt traditions safely. While physical contact was removed, efforts were made to preserve dignity—allowing families to view the body from a distance, limiting attendees, and involving community leaders in the process.
This collaboration was essential. Without it, there was a real risk that families would carry out burials in secret, increasing the spread of the virus.
Reflections
There is much I could say about my time in Sierra Leone—far more than can fit into a single blog. The work was challenging, both physically and emotionally. There were moments of exhaustion, uncertainty, and sadness.
But above all, what stays with me is the resilience of the people.
In the face of immense hardship, communities adapted their traditions, supported one another, and worked alongside international teams to combat the outbreak. It was a powerful reminder that effective public health is not just about science or medicine—it is about trust, collaboration, and cultural understanding.
This experience reshaped my perspective on global health, teamwork, and the role we each play in times of crisis. It remains one of the most challenging and meaningful periods of my career.
Everywhere I look at the moment people are talking about ChatGPT and artificial intelligence (AI). On LinkedIn this week everyone was sporting ChatGPT produced images, and I have to say I felt completely out of things as I’d have no idea where to even start. The challenge is, the same cannot be said for our students. As an external examiner I see how the AI creep is really beginning to impact on assessments, so I reached out to my great friend and educationalist Dr Claire Walker, who is actively working to think about how we can respond to the AI challenge when it comes to our assessments.
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 Dr Claire Walker
So, there’s a new problem in higher education. The elephant in the room that we’re all talking about, or sometimes pretending doesn’t really exist: our chatty friend, generative AI. When I first encountered it, I suspected the impact might be overstated. Students do not come to university simply to cheat; they come for authentic learning experiences and to gain transferable skills. I mean, they want real jobs eventually, right?! But the reality facing educators is more complicated. Alongside the rise of AI, we are also facing another persistent challenge: do more with less. Larger cohorts, less time, fewer staff and an increasing pressure to design assessments that genuinely measure skills rather than copy-paste ability. Many of our classic approaches to assessment – lab reports, literature reviews, and even theses can be generated with just a few of the right kind of prompts.
Our chatty friend or the nemesis of lecturers everywhere
So how can we create authentic learning experiences that are difficult to outsource to AI while still being practical to run and mark? At the University of Lincoln in our Genetics and Bioethics module, we have developed one approach: AI-supported patient roleplay combined with pedigree analysis and ethical reflection. One of the long-standing challenges in genetics education is giving students meaningful practice in family history taking and pedigree construction. Traditional simulated patient encounters are highly effective but expensive and logistically demanding, often requiring trained actors and significant coordination. As a result, many students learn pedigree analysis primarily through static textbook cases. I can’t say this isn’t useful, but it’s pretty far removed from the realities of genuine clinical conversations.
Our solution was to create interactive patient roleplay scenarios in which students interview a simulated patient using Claude.AI during a live teaching session. The students interact with a “patient” presenting with features of the genetic condition hereditary haemochromatosis. They gather the relevant family history by asking structured clinical questions of our AI bot pre-programmed with a real clinical case. The information they need does not exist in advance as a written case study; it emerges through the interaction, requiring students to listen carefully, probe appropriately, and adapt their questioning strategy in real time. This immediately changes the learning dynamic. Students are no longer passively interpreting a pre-constructed pedigree; they must build the dataset themselves by asking the right questions. Mistakes become learning opportunities, and repeated questioning helps them to refine both clinical reasoning and communication skills. Following the roleplay session, students translate the collected information into a formal pedigree diagram using a clinical pedigree-drawing software fortunately available for free online. This requires them to apply standardized genetic notation accurately while organizing complex family information into a clear visual representation that can be assessed objectively, and delightfully quickly. Most importantly – right now ChatGPT can’t draw this from a script. Maybe one day, but for today this assessment is one step ahead.
A medical family history drawing tool from Health Education England
The assessment does not stop at technical skills. Students are also asked to reflect on the family scenario and the issues raised during the session to consider a realistic counselling question: would they personally choose to undergo testing for a variably penetrant mutation associated with hereditary haemochromatosis? The genetic test used in the module looks for two common changes in the HFE gene known as C282Y andH63D. In simple terms, the test examines a person’s DNA to see whether they carry gene variants that can affect how the body regulates iron absorption. Certain combinations, particularly inheriting two copies of the C282Y variant, increase the likelihood of developing iron overload, but they do not guarantee disease. Many individuals with these genetic results remain healthy, illustrating the concept of variable penetrance; genetic changes that influence risk rather than determine destiny. Environmental and lifestyle factors such as diet, alcohol intake, blood donation habits, and biological sex also affect whether symptoms develop and how severe they become. Students are therefore encouraged to reflect on how genetic risk, environmental influences, and personal values shape decisions about predictive testing taking into account what they learnt from their virtual patient experience. At the end of the module, they are offered the opportunity, within the academic teaching setting, to undergo testing themselves so they can engage directly with the ethical, psychological, and practical considerations that accompany real-world genetic screening decisions.
Instructions to Claude.Ai for how to behave as a patient and a excerpt of the transcript of the interview
An additional advantage of this approach is assessment authenticity. Because the key information is generated dynamically during a live interaction, the task cannot easily be completed using generative AI alone. Students must attend, participate, and apply lecture knowledge in context, meaning the assessment evaluates what we actually want to measure: their ability to gather relevant genetic information, interpret it, and think critically about its implications. Equally important, the approach remains scalable and low-cost. No actor recruitment is required, sessions can be delivered across large cohorts, and students can practice interviewing skills in a structured but flexible environment. What once required substantial logistical planning can now be implemented with minimal additional resources. Moreover, all modules must have some laboratory component, and this one falls into a middle of our usual price point.
I’m not offering a complete solution to this huge challenge facing higher education, but it is a step toward something we increasingly need: assessments that measure real skills, encourage real engagement, and prepare students for the complex clinical and ethical conversations they will eventually have with real patients.
TL/DR – If AI can take the assessment, change the assessment.
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.
It’s the most wonderful time of the year! It’s time for the annual Environment Network meeting, where we get together to talk all things environmental microbiology; sharing new research and experience to improve practice. And your guide for the conference this year, live blogging the morning session, is the token immunologist in the group, Dr Claire Walker.
What is the environment network?
Before we get onto todays’ content, a little introduction to what the Environment Network is.
The Environment Network works to support people in clinical, engineering and scientific roles who are interested in environmental infection prevention and control (IPC) and/or the built environment
Do you want to know more about what to do with your water screening and air sampling results? Are you keen to understand the evidence behind equipment cleaning and the role of the environment in healthcare associated infection?
Then welcome to the Environment Network!
This is a network for people in clinical/scientific/engineering roles within the NHS and other associated organisations who are interested in the role of environmental infection prevention and control in preventing infection.
The aim of the network is to support infection prevention and control professionals involved in commissioning, environmental audit, water, air and surface testing within their Trusts. By working together we can share best practice between Trusts; as well as circulating the latest evidence and discussing personal experiences.
What are the aims of the network?
To support the development of member networks
To provide events where shared learning can be supported
To permit sharing of experiences and best practice to improve clinical interventions
To support and share research in order to achieve improvements in evidence based practice
What is our remit?
Environmental testing and monitoring within healthcare environments
On to today. First up we have Gavin Wood, an authorising engineer for water who acts as an independent advisor to Trusts. He is covering the fascinating topic of water associate outbreaks and what we can ask of our water safety groups during an outbreak. There should always be a policy which covers how to organise the estates teams and the water safety groups – covering who is responsible for each area during the outbreak. Regular outbreaks are caused by organisms like Legionella and Pseudomonas, but might include non-tuberculosis causing mycobacteria. Detection of these organisms during routine screening is reported to the water safety group to assess potential risk. Most pathogens that we look at will grow within a certain temperature range, so maintaining cold water as cold, and hot water as hot is essential. What we really don’t want is warm water stagnating in the system as the pathogens can thrive in it. On top of this, we need chemical control of organisms – mostly silver and copper ion systems. Stagnant areas of warm water are pockets where the pathogens might thrive so flushing the system and chemical controls are key in maintaining a healthy water supply in hospitals. Controls that are effective for indicator organisms that we routinely test for, like legionella, tend to be effective for any other outbreak organisms. In an outbreak situation the first port of call is the Legionella risk assessment which considers the efficacy of temperature and chemical control. After this, in line with guidance, all trusts should refer to their Water Safety Plan which is contains the detail on actions to take when results are outside the expected limits. Most of the time the authorised engineer already has the answers because the system is repeatedly routinely tested.
Like any system in a hospital, it is vital that the risk assessment and training is up to date. As Gavin says if we haven’t covered everything in the risk assessment, and if the water policy hasn’t been recently reviewed then the whole system is vulnerable. External audit by authorise engineers ensures the system remains optimal. Investigation of an outbreak focuses on the patient pathway – where has the visitor or patient been on their journey through the hospital. This process finds the clues to identify the source of the environmental outbreak. Surprisingly one of the main pieces of evidence comes from review of training and competence records, is everyone appropriately trained and acting in accordance with policy. If in doubt, going an witnessing monitoring and maintenance tasks can provide essential information in a high pressure outbreak situation. Gavin drives home how important practice is in this – we need this information as much on a random rainy Tuesday as much as we need it during a Legionella outbreak!
Our next talk comes from Karren Staniforth from UKHSA. She is a clinical scientist and UKHSA IPC specialist adviser, and is talking to us about the pros and cons of different outbreak investigation techniques. Karren invites us to imagine painting a busy ward in different colour 10cm squares, every single surface with a cotton tip swab. Imagine how long that could take and just how many squares you would end up with! Even if you took 200 samples, how many squares have you failed to test? Usually we can only take 20-40 samples…. So even if they all come back negative, it doesn’t necessarily mean there isn’t an organism there – its just that the sampling didn’t find it. The chances of going in and finding nothing is quite high, but if you put a patient in that room for a week, they will almost certainly find that organism (not that we recommend that as a testing method!).
Karren reminds us that reading environmental plates is quite an art and different from clinical samples, it’s a different skill and guidance from experts is essential. Clinical diagnostic laboratories aren’t accredited to process environmental samples and the staff aren’t trained to process and analyse this work. Commercial companies can come and do testing for you, and they are extremely good at routine work. Bespoke work is harder to commission, and that’s where knowing the network can really help! So if you have an outbreak of something unusual, it’s hard to find the information on what level of environmental organisms – like aspergillus – are ok, and what constitutes a danger to patients.
The questions becomes, what type of samples do we want to take and why? We need to understand basal levels of indicator organisms to work out when to act. Building on what Gavin has shared this morning, you need to look – really look- at what is happening in your environment. Karren reflects on how useful an audit can be but we don’t go into an outbreak with the information already in front of you, so your audit probably won’t ask exactly the right questions. Epidemiology provides the answers – which organisms and then which patients are affected, where and when? Identifying common exposures can be easy when infections match case distribution e.g. sequential patients with the same infection in the same room. However some are less obvious like laundry delivered to multiple sites causing infection clusters which are miles apart or commercial products that might only impact high risk patients in very low numbers, but at multiple sites across countries. This can be exceptionally difficult to trace. Though remember not every exposure results in colonisation and infection, and even if exposure is universal some patient groups are more likely to develop infections than others.
Knowing what kind of sample to take is essential, especially when sample numbers are limited. Negative results can be just as useful as positive results – and identifying the source of the outbreak is as much detective work as it is learning to read plates! Karren reminds us – ‘You don’t always need sampling, somethings are just WRONG!’.
To close the first session, we have Louise Clarke who knows everything there is to know about proper ventilation. Ventilation is essential the movement of air within a system. The law tells us we must provide ventilation under the Healthy and Safety at Work Act, and building regulations set a minimum standard for ventilation. The main reason for good ventilation is to have a safe and comfortable environment; to remove odours, to control temperature and importantly to protect from harmful organisms and toxic substances. We have natural ventilation (like opening a window!), mechanical ventilation which pushes air around the building and a mixed mode – a combination of the two. The preferred method for ventilating a hospital remains natural ventilation, something which really shocked the group. It might work well on a windy day but it certainly doesn’t cover all areas and some times of year, like winter, it’s really no good at all.
Like Lou says, simple is best. When we talk about ventilation, we need to ask what is the issue we are looking at? Human elements are usually a key element to understanding problems in ventilation – you need to think about when the issue arose and who was involved? Often there is a significant time lag between the problem starting and it’s detection in real time. You can be left scrabbling around for details long after the issue began. Lou walked us through the potential information sources to considering during an outbreak, including design records. Which tend to be a little less useful than you would imagine, considering they often tell you the purpose the room was designed for 30 years ago – perhaps not so relevant now! Echoing the sentiments of Karren earlier, one of the most important things you can do is go physically and take a look – not an audit, just turn up and use all your senses!
To kick off the session after a much needed cup of tea (Earl Grey, hot!) we have Dr Mariyam Mirfenderesky who is talking about the challenges of managing fungal outbreaks. Candidozyma auris (note the new name!) is probably one of the most difficult outbreak causing organism to manage. To help with this a Clinical Expert Reference Group was established in March 2025. Candida species are the dominating fungal pathogens of invasive fungal disease and account for >85% of fungaemia in Europe and the United States. Candidozyma auris was first identified in 2009 from a Japanese patient with ear discharge, and is a critical WHO priority fungal pathogen. It is fluconazole resistant and has a propensity to cause healthcare associated infection outbreaks. There are 6 independent clades, with clade 1 dominating in England. Mariyam walked us through the identification of the first neonatal case of C.auris from an eye swab – it was found in two infants, five weeks apart with no direct contact between the children. Fortunately both were colonisation with the fungus only. She then discussed the safety measures that should be in place to manage this difficult pathogen – particularly focusing on why the current cleaning protocols are insufficient to manage this threat. Her final points considered how to act when you detect C.auris – you must be decisive and act!
If you’d like to know more about C. auris, check out this blog post from earlier this year:
Next we have Dr John Hartley who is talking to us about investigating environmental surface mediated outbreaks – what you can’t see may still hurt you. Using the classic movie ‘the fiend without a face’ as a metaphor for IPC, John introduced the idea of modes of transmission between individuals. It feels like a simple problem, its just cleaning and handwashing after all! But we see there is a complex person-organism-environment dynamic system, and as John says, there is always a well known solution to every human problem – neat, plausible and wrong! John highlights the importance of continual surveillance and knowing ‘where the fiend is’. The controls are based on a four pronged approach – clean, replace, destroy or rebuild.
By way of a case study, John told us about his experience of managing adenovirus outbreaks in a paediatric BMT ward. This is a very common virus causing 5-10% of febrile illness in early childhood. Almost everyone has had it, and it can establish latency which can reactivate during BMT. More often it causes severe morbidity and mortality in these patients who can develop hepatitis. What you can’t tell is if the child caught adenovirus from the environment or if it has reactivated post latency. However, whole genome sequencing (WGS) can resolve 1-3 SNPs across genomes – its not like looking for a needle in a haystack, its rather like looking for a needle in the whole of Texas. But WGS can be used to confirm or refute cross infection events.
Of course the next question is, what can be done? Visual assessment is not a reliable indicator of surface cleanliness, John described the varied methods which can be used to detect adenovirus. Then we need to develop the right tools to manage it – including development of environmental PCR as a measure of cleaning efficacy by GirlyMicro herself! Finishing on a Dr Who reference to delight a crowd of scientists is always a win – even if it is comparing adenovirus to the scariest episode, the weeping angels! Of course, when monitoring adenovirus, the most important advice is ‘Don’t Blink’.
To close the morning session we have Dr Sam Watkin discussing research tools to help predict the future of outbreaks. Sam began acknowledging the current challenges facing preventing transmission of environmental organisms. In his PhD he aimed to identify how microbes disseminate through the clinical space, if the starting contamination site determined how is was disseminated and if the usage of space influenced microbial transmission risk. IPC is often retrospective to the aim was to develop research tools to allow the development of prospective knowledge. Sam used cauliflower mosaic virus DNA markers as a surrogate for pathogens, and followed its movement around two different units. It was shocking to see how far this benign organism could spread in such a short time.
I think if we take away anything this morning it’s that nobody likes the new name for C.auris, and death, death to recirculating air conditioning units!
The morning was followed in the afternoon by a series of case discussions in order to help implement the learning from the morning, help everyone get to know each other, and support the sharing of peer to peer learning. The case discussions this year included:
Case discussion one (Facilitated by Dr John Hartley):
Seek and remove: approaches to source control for environmental surface mediated outbreaks
Case discussion two (Facilitated by Professor Elaine Cloutman-Green):
How to implement a multi-disciplinary approach to investigation of water borne outbreaks
Case discussion three (Facilitated by Louise Clarke):
Interpretation of ventilation data and applying it to ventilation risk assessments
Case discussion four (Facilitated by Dr Sam Watkin):
Determining the role of equipment in outbreaks: how do you investigate?
Case discussion five (Facilitated by Karren Staniforth):
Introducing new cleaning process: what should you consider?
Case discussion six (Facilitated by Dr Claire Walker):
Choosing new equipment and furnishings: what questions should you ask?
It was truly inspiring to hear the buzz in the room that all of the discussion created. Thank you to Mr Girlymicro (Jon Cloutman-Green) for being in charge of photography, and to all of our speakers and facilitators for making the day happen. Also, massive shout out to Ant De Souza for pulling the day together, Angela McGee for making sure we all turned up to the right place at the right time, Mummy Girlymicro for running the reception desk, and to Richard Axell for supporting all of the tech on the day.
Now it is all over, the only thing to do is to tap our feet until we all get to meet again in 2026, although the presentations and discussion sheets should go up some time during 2025. Until then however, if you want to know more either head to the Environment Network website to look at info from previous years, or read some of the other blog posts linked to environmental IPC down below.
I must admit I shed a bit of a happy tear when this arrived unsolicited in my inbox, it’s been a bit of a week. My next thought was that there is no way I could share it, as it would be the epitome of self promotion, and that’s never considered to be a good look. Then I sat and thought, what would I advise a friend to do if they were in the same situation and I decided something. I decided to be proud of what I’d achieved. To be proud of the hours spent to achieve the output earned, and to be proud to have someone so invested they would take the time to write an unsolicited review for this blog. I know that is what I would advise and hope that all of you would do, and so this is my moment I decided to model the advice I would give. We all have the right to own our achievements and not make ourselves small to avoid the commentary of others.
Dr Walker 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 one on turning criticism into a catalyst for change.
Full disclosure: I wasn’t invited to write this review, I insisted. I also haven’t been paid for it; quite the opposite, in fact. I went out and bought two copies of Professor Elaine Cloutman-Green’s book with my own money: one for me and one for my PhD students to share (or squabble over). And yes, I did get her to sign them. What can I say? I’m a lifelong fangirl.
Professor Cloutman-Green’s It Shouldn’t Happen to a PhD Student is a rare gem in academic literature a compassionate, wise, and profoundly practical guide that feels like a conversation with the mentor every research student wishes they had. Written with warmth, humour, and candour, the book demystifies the PhD journey from start to finish, transforming what can often be an isolating experience into one filled with clarity, community, and hope.
Elaine, known affectionately as my favourite Professor or the GirlyMicrobiologist, draws upon two decades of experience as both scientist and supervisor to craft a guide that balances rigour with humanity. Structured in three accessible sections; getting onto a PhD programme, surviving and thriving during it, and using it as a springboard for the future. The book serves as both a roadmap and a reassuring companion. Each chapter blends actionable advice with reflections that acknowledge the emotional highs and lows of research life, creating a tone that is both authoritative and deeply empathetic.
From the very first chapter, “Knowing Your Why,” Elaine invites readers to pause and reflect on their motivations, an exercise that sets the tone for the entire book. Rather than treating doctoral study as a mechanical career step, she frames it as a personal journey of purpose and growth. As she writes, “A PhD should be a step towards delivering on your aspirations, not just a title to put in front of your name.” It’s a line that perfectly encapsulates her philosophy that research is not about prestige, but about purpose.
What truly elevates this book above other graduate-school guides is its inclusivity and warmth. Elaine writes as a mentor who has seen it all: the sleepless nights, the imposter syndrome, the joy of a successful experiment, and the power of perseverance. Her anecdotes and checklists are peppered with practical wisdom not the vague “work harder” platitudes found elsewhere, but concrete steps to manage deadlines, develop professional skills, and build meaningful academic networks. The inclusion of “Top Tips” sections at the end of each stage provides digestible summaries that make the book easy to dip in and out of throughout the PhD journey.
And it’s not just students who need this book. Supervisors – myself included – will find plenty here that resonates. Elaine reminds us, gently but firmly, that supervisors are people too: flawed, human, and still learning alongside our students. Her reflections on empathy, communication, and shared growth are as valuable for those guiding PhDs as for those undertaking them. Every research group could benefit from having this guide on their shelf, it’s as much a manual for mentorship as it is for PhD survival.
Of course I must acknowledge my own bias, Elaine was my mentor during my own PhD, and many of the insights in this book feel like familiar echoes of the advice that got me through my hardest days. She taught me so much about science but more importantly that research, like life, is all about surrounding yourself with people who lift you up when you falter. It Shouldn’t Happen to a PhD Student captures that same generous spirit, showing that the best kind of academic success is shared success: when mentors and students grow together, celebrate each other’s wins, and keep curiosity at the heart of everything they do. Everyone deserves a mentor like Elaine someone who reminds you that with compassion, courage, and community, the PhD journey can be one of the most transformative experiences of your life. Oh, and she provides the most excellent of snacks, the occasional much needed gin and tonic, and a rousing rendition of ‘Drop it like it’s hot!’… but that’s a story for another time.
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.
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 The Clinical Academic Path – From the Lab to the Lectern.
This weeks blog post is from Dr Shayda Karimi, who is a medical doctor and self published author, discussing how important creativity is in science.
Blog by Shayda Karimi
Hello! My name is Shayda.
I’m a medical doctor, specialising in anaesthesia and pre-hospital emergency care. Medicine has always been considered one of the ‘softer’ sciences, but never the less is more of a science than a humanity, and the subject takes pride in adhering to evidence based practice. Creativity lies at the heart of problem solving, and problem solving is key to providing high quality, innovative medical care, especially in dynamic specialities like emergency care. For example, I was recently faced with the dilemma of a man impaled on a large segment of aluminium ladder. The metal couldn’t be removed without a CT scan to determine which structures it had damaged, and due to the angle of penetration, the patient couldn’t fit through the scanner with it in place. The creative solution was to put a 999 call out to the fire service, who with specialist cutting equipment were able to reduce the size on the metal segment. The patient safely had his scan.
Creativity in science should be encouraged. Through my time at medical school, opportunities to be creative were very limited- most lectures were on never changing topics- anatomy and physiology. I took a student component module called ‘medicine in literature’- even that was factual. To resolve this gap in my undergraduate education, in my F3 year (a common point for junior doctors to take a year out of training, having completed two foundation years and before commencing higher specialist training) I decided to complete a masters degree in creative writing. I was the only person on my course with a ‘science’ background.
The dissertation for this course was a long piece of writing. Which for the first time in my post primary school life, could be completely and utterly false. This dissertation turned into my first novel. Writing fiction develops problem solving skills- characters must resolve the obstacles put into their path, and this must be believable with the rules they are living in. I learned about how language can be used to invoke emotions and atmosphere- this is of vital importance when speaking to patients and colleagues. Or even when writing emails! I developed an appreciation that though creativity is not fact- it can also be to a certain degree taught and developed.
The dissertation turned into my first published novel ‘Heirs’, set in a future dystopian London, conjoined twins are born next in line to the throne. They end up separated and in a fight for power. This was fun experience; taking the science I knew as fact, and adding a whole load of fiction to turn it into a familiar but bizarre future.
Creativity and science go hand in hand. We should all endeavour to leave the cold hard world of facts every once in a while and dive into something purely imaginative; an art class or high fantasy novel.
“The true sign of intelligence is not knowledge, but imagination” – Albert Einstein
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.
Dr Walker 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 Simulating Success – Enhancing Biomedical Science Education through Clinical Simulation. This blog was written by a group of her final year students on their experiences of trying to teach differently.
Blog by Yvana, Nicole and Ellie
We were a small group of three final-year Biomedical students—Yvana, Nicole, and Ellie who were brought together by a shared goal to create something useful for other students by us students. In our final year at the University of Lincoln, we were offered the opportunity to work on a collaborative project focused on improving on how ELISA (enzyme-linked immunosorbent assay) is taught to students- a commonly used technique in the immunology department to quantify and detect biological molecules.
Meet the Team
Yvana
Hello, I’m Yvana – Three years ago, I began my journey as a Biomedical Science student at the University of Lincoln. Like many, I was unsure of the exact career path I wanted to follow, but I knew one thing for certain, I was deeply fascinated by diagnostics and disease. Over time, that interest developed into a love for laboratory work, especially when I had the opportunity to experience clinical simulation sessions led by Dr Claire Walker which stood out to me as they offered a taste of what a real-life clinical lab feels like beyond university.
One of the highlights of my third year was engaging in a unique series of laboratory-based activities known as Laboratory Skills, coordinated by Dr Andy Gilbert. These sessions were designed to strengthen our core technical abilities and confidence in the lab through a series of activities covering microbiology to biochemistry!. After completing 6 weeks of lab skills, Dr Andy Gilbert approached me with an exciting opportunity to collaborate with two other students, Nicole and Elle, also led by Dr Claire Walker on a co-creation lab skills project. Our task? To design a step-by-step resource that would deconstruct one of the most widely used techniques in immunology, ELISA – making it easier for students to understand and perform.
Ellie
Hi everyone, my name’s Ellie! I’m 1/3 of the amazing group that have carried out the ELISA workshop, led by students, for students. During my years at the University of Lincoln, I’ve grown to love the fascinating world of microbiology and I’m even going back this September to do a Microbiology Masters! I have really enjoyed my time at Lincoln and part of that is thanks to Andy Gilbert for putting on his extra lab skills sessions, which allowed me and other students to gain that vital extra laboratory knowledge and practice important techniques.
I’ve just finished the final year of my undergraduate Biomedical Science degree and throughout this year I was able to create something incredible. I, Yvana and Nicole, were given the opportunity to collaborate and develop a practical booklet as a building point of the skills needed to carry out an ELISA. The main reason I agreed to take part in this task is that we, as students, do not get many chances to have such a hands-on experience with many complex techniques, like an ELISA, during this degree. Because of this amazing opportunity, we were able to give students across all years at Lincoln the chance to gain more knowledge and extra practice in learning this crucial technique!
Nicole
Hi, I’m Nicole – one of the final-year Biomedical Science students behind this project. Starting at the University of Lincoln, I wasn’t entirely sure which direction I wanted to take within biomedical science. As the course progressed, I enjoyed the hands-on lab work, particularly how it transformed theoretical knowledge into practical application. This became evident in my second year during Laboratory Skills sessions led by Dr. Andy Gilbert. These weekly sessions focused on core techniques like centrifugation, microscopy, and microbiology.
Co-creating the ELISA workshop booklet felt like more than just a project; it was an opportunity to make lab-based learning more accessible and less intimidating. Since ELISA is a technique, we limited experience with as students, developing this protocol felt was crucial. Working with Ellie and Yvana to bring our ideas together was fulfilling. My favourite part was seeing the complete protocol, knowing it would support students to tackle the ELISA confidentially.
Figure depicting how ELISA works step-by-step
Building the booklet
This project was a collaborative effort and not something we did alone- we brought our own strengths together to create the now called ELISA Team (given by Claire Walker herself!). We spent countless hours in the lab, testing and refining each activity to make sure it worked as intended and delivered the essential skills students would need to confidently complete an ELISA in real time. We held regular meetings, worked on it during lectures (sorry Claire and Andy!), and genuinely had a lot of fun creating something meaningful that we hope will support future students just like us.
Under the guidance of Dr Claire Walker and Dr Andy Gilbert, we set out to create a resource that would feel practical, and genuinely useful for students. We didn’t want a booklet created from a lecturer’s perspective of what students might find helpful. We wanted to build something we would have found helpful when we first encountered ELISA, a step-by-step walkthrough from a student’s perspective.
Overview of ELISA (Enzyme-Linked Immunosorbent Assay) booklet use to educate students
The booklet breaks down ELISA into its fundamental components, from how to properly use a multichannel pipette (which was a nightmare to handle!) to interpreting results and avoiding common mistakes students might fall for. For instance, one key focus was on the washing stages, an often-overlooked step that if done incorrectly, can lead to high background noise and inaccurate results, which in a diagnostic lab can be the difference between a patient receiving an accurate diagnosis or potentially missing one altogether.
What made this project especially rewarding was the opportunity to run our session with real students from first year undergraduates in Biomedical Science to postgraduates in Biotechnology. The feedback we received was overwhelmingly positive. Many said the booklet helped them better understand ELISA both in theory and in practice. We focused heavily on visual learning using diagrams, photos, and annotated guides because we knew from our own experience that clarity and visual support were essential when learning complex lab techniques.
Initial plate setup demonstrating serial dilutions and pipette accuracy during the first activity, comparing multichannel versus single-channel pipetting.
Our final thoughts
Our co-creation project not only gave us a chance to give back to the large community of students, but we were able to bridge a gap that many lectures hadn’t quite managed before, true co-creation between students and lecturers. Together, we created something that students appreciated and benefited from which was entirely made by their peers through mutual experience.
Looking back, we are incredibly proud of what we achieved as a team. It showed us how impactful student-led projects can be when they’re supported by passionate educators and built around supporting the educational needs of the community.
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.
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.
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 Microbial Culture: An Immunologist’s Side Project Gone Wild.
This weeks blog post continues this months fungal theme (all things yeast) and is from the absolutely amazing Kate Rennie. Kate is a born microbiologist, even if she was diverted by the world of nursing and has gone on to become a cracking Infection Prevention and Control nurse. Her curiosity and willingness to learn and expand her skill sets, makes it no surprise to me that when she decided to expand her hobbies, she decided to go down a route that touches on all things micro.
Before we get into the sour dough however, let’s start by talking what coeliac disease (the condition that leads to the requirement for gluten free bread) as written for us by Dr Claire Walker, our in-house immunologist:
Coeliac disease is a serious autoimmune condition where eating gluten, a protein in wheat, barley, and rye, triggers the immune system to attack an enzyme in the gut called tissue transglutaminase. This damages the villi, tiny structures in the small intestine that absorb nutrients. The result? Symptoms like bloating, diarrhoea, fatigue, and iron deficiency. But it doesn’t stop at the gut. Some people develop dermatitis herpetiformis, an intensely itchy, blistering skin rash. Others experience neurological symptoms such as brain fog, headaches, and numbness or tingling in the limbs. It’s often misdiagnosed or missed entirely.
Around 1 in 100 people in the UK have coeliac disease, but most remain undiagnosed. Diagnosis usually starts with blood tests (like the tTG-IgA), followed by a small bowel biopsy to confirm intestinal damage. These tests only work if you’re currently eating gluten. So if someone’s already gone gluten-free and are feeling better, they need to reintroduce it for several weeks which can cause symptoms to reappear and puts many people off testing.
There’s no cure and the only treatment is a strict, lifelong gluten-free diet. That means no “cheat days” as even tiny amounts can cause damage. It takes serious commitment: careful label reading, avoiding cross-contamination, and asking awkward questions when eating out. But for most, removing gluten thankfully leads to major improvements in symptoms and overall wellbeing.
Blog by Kate Rennie
What am I growing in my kitchen… a gluten free sourdough journey through the eyes of an IPC nurse
I’m Kate, I’m an infection control nurse at GOSH. I’ve worked in infection control since 2020 (1.5 years in primary care, 9 months in community/mental health and I’ve been at GOSH since April 2022). I was diagnosed with Coeliac disease in 2013 and decided 2025 would be the year of new hobbies and I am bored of gluten free bread that resembles cardboard.
I decided to embark on my sourdough journey (albeit slightly late to the party as I know this was a lockdown thing). I didn’t actually know what I was getting into with making sourdough, I read the first few steps and thought it sounded pretty simple, flour and water in a jar.
My flour and water sat on my kitchen side in a jar for 2 weeks (gross), and I named it Marilyn (Mondough)… I nurtured her and fed her daily, for those who may remember Tamagotchi’s, this is how I can describe it and as a previous Tamagotchi owner, I loved it.
Part of me was obsessed with what have created and look forward to waking up each morning to see how it’s looking (highlight of your late 20s) but the infection control nurse in me is slightly grossed out by it. I’ve read a bit more and learnt a lot, she just needed a little bit of extra love and care (troubleshooting) at a few days old.
HOOCH – I’ve only ever known hooch as this from my late teens/early 20s.
Fast forward to my late 20s, this is a sign that your sourdough starter is hungry, it’s eaten all its nutrients, and you must feed it more frequently. I was reluctant to throw her away and start fresh so I added teff flour in the hope she would perk up and SHE DID.
But she smelt disgusting… A familiar reminder of my 16 year old, pre-nurse self, having my long acrylic nails removed in the salon. ACETONE?? Apparently, it’s a byproduct of fermentation…
So, I wondered if this was actually safe to have something fermenting in my kitchen with absolutely 0 knowledge and thinking I’m probably going to poison myself. After a bit of research, I learnt this is normal and how to fix it, yet again, she’s hungry and I’m a rubbish mother.
Whatever is happening inside that jar is creating its own yeast to make it grow which is quite cool! I’m not sure how many people have actually gone this deep into the thought of a sourdough starter, but my IPC brain is fascinated yet disgusted and I want to know more. Do I want to culture it in the lab? Probably not. Am I going to eat it? Most definitely.
Fast forward 2 weeks… My sourdough journey ended abruptly after my first loaf. I felt disheartened that it didn’t turn out like the GF loaves I’d spent too much time obsessing over on Tik Tok. The perfectionist I am wanted the perfect loaf to happen first time, so I abandoned sourdough and ventured into making non-sourdough gluten free bread. I popped Marilyn in the fridge for when I decided to revisit sourdough making and there she stayed for a good 3 months. Apparently, this puts it to sleep, and you can later revive it… but after pulling it out the fridge and seeing a layer of black liquid on top of the starter, my IPC brain got the better of me and I decided with my limited knowledge of sourdough and fermentation at home, it probably was best that I didn’t consume this and decided to throw it in the bin and I spared a brief thought for what Marilyn was and could have been if I had more patience.
I’d hoped this would be a success story about my gluten free sourdough rather than a failure but basically, sourdough isn’t easy and gluten free sourdough, really isn’t easy. It truly is a science.
Gluten free bread making in general is a delicate science because it lacks the key protein—gluten—that gives traditional bread its structure, elasticity, and chew. In wheat-based breads, gluten forms a stretchy network that traps gas bubbles from yeast, allowing the dough to rise and hold its shape. Without gluten, you have to rely on a blend of alternative flours—like rice, sorghum, or buckwheat—each contributing unique properties such as starch, protein, or flavour. Binding agents like psyllium husk are also essential to mimic gluten’s elasticity. No single gluten-free flour can replicate all the functions of wheat flour, which is why crafting a successful gluten-free loaf requires a carefully balanced mix rather than just throwing in a single substitute flour and hoping for the best.
I have been successful on a few occasions in making non-sourdough gluten free bread which has still been a real insight into science in everyday life.
To all life’s problems there are solutions if only we are curious and passionate enough to see them and change direction in order to maximise our successes. It appears Kates’ experience with sour dough as part of her coeliac journey is no different.
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.
Previous mycology posts have covered how fungal mycotoxins can cause us harm, and how the new yeast on the block, C. auris, is causing problems in healthcare, but the next two posts will talk about how beneficial fungi can be in our every day lives.
The blog posts will look at how certain yeasts can be used in something that brings me a lot of joy, bread. Many of you will know I’m dairy free, and although I know I should cut down on carbs, you can take my bread from my cold dead hands. It’s one of the few things I can eat without fear and makes me happy. In celebration of this oft overlooked area of microbiology we shall be talking all things baking over the next two weeks.
The first of these posts is written 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.
Before I hand over to Claire though, I thought I would talk a little about baking and fermentation. About 50% of all the PhD students I speak to have dreamt at some point of throwing their research out the window, running away and starting a bakery. This may be because baking has a surprising amount of science within it when compared to some other forms of cooking, hence the need to closely align to a recipe. A lot of this is actually because you are working with yeast, a living organism, hence the fact that we are talking about this on the Girlymicro blog, as micro is just cool in so many ways
Fermentation is an anaerobic (occurs without the presence of oxygen) process where microorganisms, like bacteria and yeast, convert sugars into energy and various byproducts, like acids, gases, or alcohol. In baking, it causes yeast and bacteria to convert sugars into carbon dioxide, among other things. This is what causes the dough to rise, as well as adding flavour, and is therefore essential to all things yummy and bread related. The most commonly used yeast is Saccharomyces cerevisiae, and this is one of the reason baking can behave so variably on times of the day or seasons, as both temperature and pH can impact on how well the fermentation process works. It can also mean, if you are impatient like me, you add water at far too high a temperature and effectively kill off your yeast so it doesn’t work at all. Fermentation, and its use in food production, is one of the many examples of how microbiology and microbes impact our every day lives, and of how much poorer our lives would be without them. So I hope you’ll enjoy the next couple of blogs about how baking has both microbiological and immunological links.
Blog by Dr Claire Walker
As I’ve confessed on this blog before,I am, what I like to call, a ‘failed microbiologist’. Many moons ago I completed a master’s qualification in environmental microbiology and dreamed of a career tracking pathogens through our water systems guaranteeing safe water for all. However, I graduated during a recession and started applying for any job that would have me. As luck would have it, I ended up on the immunology clinical scientist training scheme (the story of that fateful application I will save for a later date), and the rest is history. However, I’ve always loved a bit of microbiology and my fascination with all things fermented has taken me on many adventures. Including baking afternoon tea for a GirlyMicro special event!
My treat for finishing my marking this year was a fermentation course at the Welbeck School of Artisanal food learning all about the transformation of food by microorganisms. The word fermentation comes from the Latin fervere meaning ‘to boil’ after Romans watched the bubbles forming when they fermented grapes into wine. Name a scientist who doesn’t love a bit of Latin? There are several biological processes occurring when we ferment foods like grapes, but essentially it is a process by which large chains of molecules are broken down by enzymes into their smaller, tastier, more nutritious, and more easily digestible parts.
The area of fermentation about which I am really passionate is sourdough. Yes, I lived in East London for many years, and yes, I owned a banneton before it was cool. Sourdough doesn’t just indulge my microbiology side project; it became unexpectedly personal. After picking up a particularly unpleasant microbe while travelling in India, I developed amoebic dysentery, and my gut never fully bounced back. I couldn’t tolerate shop-bought bread or much of anything, really. It wasn’t until I began incorporating fermented foods, especially sourdough, into my diet that I noticed slow but steady improvement. (Though let me be clear: this is my experience, not medical advice – if you’re unwell, definitely speak to your clinician!)
For the uninitiated, a sourdough mother, or starter, is a living culture of wild yeast and lactic acid bacteria that needs regular feeding with flour and water to stay active. As a failed microbiologist, I found something oddly fulfilling about sustaining a microbial ecosystem especially one that produces bread with real health benefits. What’s not to love about a culture that feeds you back?
Of course, I’m a dyed in the wool clinical immunologist so I can’t finish up this post without waxing lyrical about the immunology of sourdough. What makes sourdough really special, from an immunologists perspective, is how it supports our gut, which is home to about 70% of our immune cells. By encouraging a healthy mix of gut bacteria, sourdough helps produce bioactive compounds that keep our immune system balanced, strengthening our defenses without overreacting. This means it can help protect us from infections while calming down low-grade chronic inflammation that might otherwise cause problems. So, sourdough isn’t just tasty, it’s a simple, natural way to support a well-regulated immune response. Of course, sourdough isn’t for everyone, especially not for coeliacs. After all, even the most dedicated immunologist moonlighting as a microbiologist hasn’t yet figured out how to turn gluten into something completely safe. Guess some mysteries are still off the menu!
I’m so excited by this weeks guest blog post. I’m a massive murder mystery fan, and from Agatha Christie onwards there have been multiple books where mushrooms and mushroom toxins (mycotoxins) have been used, either deliberately or accidently, as a pivotal component of the plot. In recent months however, mycotoxins have been in the news in a real world sense, as the case of Erin Patterson has been heard and the jury are deliberating as I write. Erin Patterson is accused of 3 charges of murder, and one of attempted murder, linked to feeding guests a poisonous dish of Beef Wellington at a dinner party.
This led me to speak to my go to guy for mushroom (mycological) based questions. Sam is in love with all things shroom, and even has a mushroom foraging based Instagram. Who better to go to with a request to write a blog post on mycotoxins and to learn more about this intriguing topic?
Blog by Dr Sam Watkin
Hello Girlymicro blog readers! I’m Sam, a previous PhD student of Elaine’s with research focused on investigating trends in microbial dissemination in hospitals. I’m taking the blog astray from the world of IPC however with this post, and instead will focus in on one of my other interests. As people who know me have probably come to realise, I’m a big fan of mushroom foraging. There is something so rewarding to me about finding excellent edible mushrooms that you just can’t buy in shops and exploring the different flavours they can add to food. My partner had to put up with me having a Cauliflower fungus (Sparassis crispa) the size of a football in our freezer for well over a year. We would break bits off and make fantastic soups and stew bases with it – it has a really unique nutty flavour. More than just the pursuit of a free dinner though, I find it very enjoyable finding fungi that I haven’t seen before, or that are particularly rare. I imagine it is similar to the enjoyment a twitcher gets from sighting a rare bird, although mushrooms tend to stay put so there is less pressure on being constantly focussed. Having said that, searching for fungi does often devolve into a game of looking at the brown forest floor trying to spot the slightly-different-brown mushroom. More than once have I run over to a promising shade of brown or yellow, only to be disappointed by a frustratingly deceptive leaf. It is nevertheless a pursuit I thoroughly enjoy, despite the frequent soakings in rain showers and occasional run-ins with brambles.
One aspect of foraging (and indeed looking to identify fungi) is being aware of what ones you can eat and what ones are to be avoided. The old adage “All fungi are edible, some fungi are only edible once” absolutely holds true. While my professional life involves researching microbial transmission and how best to prevent infection, I am fascinated by the toxic nature of fungi. I did consider becoming a toxicologist in my teens, but rapidly realised that the amount of chemistry required was simply not my idea of joy. I do find it very interesting however how fungi are capable of producing some of the most unpleasant, and also strangest, toxins that can be found in the natural world (or at least I think so). So here I am going to run through a few of the fungi that I find most fascinating when it comes to their chemical makeup and the influence they have had on humans through history.
A fairytale classic – Amanita muscaria
Few fungi are more iconic than A. muscaria (known in English as the Fly Agaric). Their characteristic red caps and white flakes are often illustrated in children’s books and are probably what comes to mind when one pictures a ‘toadstool’. They are in every respect the archetypal fungus. This being said; however, you absolutely would not want to eat one. If someone were unfortunate enough to eat a specimen on A. muscaria, they would most likely experience a range of unpleasant neurological symptoms. Confusion, dizziness, ataxia, hallucinations, muscle twitching are often reported, as well as nausea and vomiting. In severe cases, a loss of consciousness and dangerous decreases in blood pressure can occur. These unpleasant effects are due to the makeup of alkaloids present in the fungus, with ibotenic acid and muscimol being predominantly responsible for these effects. Muscimol has a similar molecular structure to GABA-A – the most abundant inhibitory neurotransmitter in the human brain. Ingesting a chemical which mimics such an important neurotransmitter as part of your supper is unlikely to be good news. It acts as an agonist for GABA-A receptors, causing a reduction in the excitability of neurons, causing the range of neurological symptoms. Muscimol is by no means alone here however – A. muscaria also contains ibotenic acid which further acts as an agonist of a host of neurotransmitter receptors (for instance metabotropic glutamate receptors – another widespread neurotransmitter receptor class. Oh, and ibotenic acid is metabolically converted to muscimol in the body. More fun to go around!
It’s not only the alkaloid balance or popular culture appearance of A. muscaria that makes it interesting however – it has had significant historical and cultural influences. It has been traditionally consumed by shaman in northern Europe as a part of winter solstice celebrations. This is due to the intoxicating effects of consumption, where the experience was likened to flying. Part of the rituals would involve the fungi being collected while wearing ceremonial red robes. The fungi were also often fed to reindeer before ingestion to metabolise out some of the more toxic components, with the hallucinatory agents collected in the reindeer’s urine which was then consumed. I’ll pass. But, an association with winter and red robes, feelings of flying and reindeer… these rituals have indeed been credited as a potential origin of the popular imagery of Santa Claus. I guess everything must start somewhere!
An explosive pufferfish – Gyromitra esculenta
I find this to be one of the most fascinating fungi in existence. Partly fuelled by the fact that I still am yet to find this species growing wild (one day my persistence will pay off) and partly by how unique these fungi are both in shape, cultural perceptions and toxicity. Looking like mini brains, they can be found under pine trees on sandy soil in autumn (or so I’m told… maybe they are deliberately avoiding me). They are found in Europe and certain parts of North America, and are called False Morels due to their relation and similarity to the delicious Morels.
Despite being well known as a poisonous fungus their name would suggest otherwise, with “esculenta” being Latin for “edible”. And these fungi are indeed eaten in large quantities! When prepared correctly. As such, they have been likened to the pufferfish of the fungal world, which is quite the title! Appropriately prepared they are supposed to be a delicacy – I can’t speak from experience on this one, my adventures into free fungal food doesn’t quite stretch this far – however raw or improperly cooked they can be fatal. This toxicity is down to the presence of a volatile toxin called gyromitrin. When ingested, gyromitrin is metabolised to monomethyl hydrazine. This goes on to wreak havoc on a wide range of enzymes and processes, inhibiting cytochrome P450, amine oxidases and preventing the formation of pyridoxal 5-phosphate. This compound is a key cofactor in the synthesis of our old friend GABA. This causes a reduction of GABA present, preventing neuronal inhibition and causing to a prolonged excitatory state in the brain – almost the opposite of the effect seen in A. muscaria. This is still not good news however, with symptoms including severe gastrointestinal distress, kidney and liver damage and seizures and death in severe cases. Interestingly, the toxic metabolite produced here is used amongst other chemicals as a rocket propellant. I can’t but help imagine a future where we have spacecraft fuelled by fungi (albeit from a poisonous metabolite of a mycotoxin). Somehow, I doubt it.
Building up to it – Paxillus involutus
Following on from the theme of the last fungus, P. involutus is no stranger to gastronomic controversies. This very common, fairly non-descript fungus is a rather boring shade of brown (sorry if this is your favourite fungus!), although its cap does have a uniquely rolled-over rim (hence the imaginative English name – Brown Roll-Rim). It has historically been considered to be an edible mushroom, with many guidebooks simply stating that once cooked, it was safe to consume. Needless to say, these guidebooks are now firmly out of date and it is now recognised as a deadly poisonous fungus. Unlike the previous two fungi I’ve described here, this fungus does not contain any psychoactive alkaloids or toxic rocket fuel precursors. Instead, this species contains some rather unpleasant irritants which, upon consumption of raw specimens, result in severe gastroenteritis. These toxins however are degraded on heating, hence why it used to be considered edible after cooking. No, the real toxins are much more sinister in this fungus.
True to the weird nature of fungi, this species rebels against the “only edible once” saying quoted earlier. This fungus can actually be edible quite a few times before it poisons you. Unlike other toxins which you may expect to have a rapid onset after consumption (maybe a few days after ingestion at the most), the compounds responsible for the fatal poisonings attributed to P. involutus can take months to manifest. This is because the toxic effects often become apparent after repeated exposure, usually through the repeated consumption of the fungus. This is because the toxic compound here is in fact an antigen, which the body becomes sensitised to over time. Once enough meals of P. involutus have been eaten, the antigen present stimulates a rare autoimmune response where the body produces antibodies which attach to and disrupt red blood cells (autoimmune haemolytic anaemia). This causes life-threatening reductions in red blood cell counts, kidney damage and multi-organ failure. There is no antidote. If in doubt…
So, there are three of the fungi that I find most interesting in terms of their toxicity. This only scratches the surface of the wild world that is mycotoxins – there are hundreds of others. From St Anthony’s Fire (a range of medieval diseases attributed to Ergot (Claviceps purpurea) to the near-certain fatality after consumption of Amanita phalloides or Amanita virosa (named the Death Cap and Destroying Angel respectively – foreboding!), mycotoxins are truly fascinating. These show the massive variety of toxins out there and how they influence both our health but our culture and relationship with wild foods. From a foraging perspective, the range of dangerous fungi out there clearly shows the importance of only foraging with an experienced guide and only collecting what you can identify with 100% confidence. If in doubt, leave it out!
NB from Girlymicro – Whilst we’re delving into some mycological (fungal) joy over a couple of blog posts I thought I would take the opportunity to re-share this four part article series on the fungi of The Last of Us, which was a real joy to be involved with, and a clinical article that may surprise you:
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.
I’m back from a lovely week away at Disneyland Paris, celebrating Christmas and escaping reality (a post on Disney and denial as a coping mechanism is on its way). Whilst I am still struggling with the return to reality this weeks blog post is supplied by the wonderful Callum Barnes. 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 Claire 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 one on turning criticism into a catalyst for change.
Two years ago, I began a placement year in the microbiology department of a pathology lab, unsure of what was to come, and unsure of myself and my skillset as a scientist. As I think every scientist feels at some point, I was mostly concerned that I would be a hinderance to all the wonderful staff that were just trying to get on with their jobs. Everyone was amazing though and helped me develop the skills and confidence I needed to successfully complete my IBMS portfolio verification. Returning back to university for my final year, I found the lab-based work so much easier than in my second year with my experience, but… something was different. This wasn’t the same stuff I just spent the last year working on, where was the LIMS? The booking in of the samples, the investigative process and the, frankly, the occasional chaos were missing. That’s not to say the labs weren’t good – they were great – and the staff that developed and ran them miles better, but something felt like it was missing. And that’s when my now supervisor Dr Claire Walker came to me with a project for my Mbio year.
Claire and I both have experience in the NHS, herself a lot more than me, but we have both felt and experienced the environment that a pathology lab has. It has a very unique feel to it, slightly alive in my opinion. This is not a very common experience to have in academia though as most academics have a research background, which means that the practical pathology side of things can sometimes get lost when students do their practical work. As such, Claire and I have been working on creating a lab experience that is as authentic to an NHS pathology lab as possible.
But why even bother? The students are learning the same things, just in a different way, so does it really matter? Well in fact, yes, it does! As Claire has said previously, the pilot study she did had very good results, so the data is there to back up our work. But imagine for just a second that you are looking at applying for medicine, and you have two offers. One university offers a fully simulated experience using manikins and actors – the whole shebang. And the other university teaches mostly through theory and shadowing – no practical experience is offered. I know which course I would enjoy and learn the most from. Medical schools know this too and is why most of them offer simulated teaching – it makes for better doctors too.
So, we should really ask, why isn’t this offered for biomedical scientists? Maybe it’s cost, maybe there isn’t the associated prestige. Whatever it is, I am sure that our work will guarantee a truly authentic clinical laboratory experience here on the iBMS accredited course at the University of Lincoln – something I know will provide the right skills for the pathologists of tomorrow.
I’m off for some much needed leave enjoying being a Disney adult this week, it’s really needed as between COVID and a broken foot the start of 2024 has not been kind. I’ve called upon a great friend therefore to help me out and write this weeks blog post, so I can focus on drinking cocktails and braving the Tower of Terror. I hope you enjoy reading it as much as I did.
Dr Walker 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 one on turning criticism into a catalyst for change.
I’ve written before on this blog about how inspired I was by the work of Professor Ian Davies and Aimee Pinnington on the introduction of clinical simulation to biomedical science education. Clinical simulation is used widely across medical training but to date, has largely been overlooked in biomedical science education. I signed off my last post on this subject with the intentions to build this into my own immunology module on the iBMS accredited course at the University of Lincoln. We are fortunate to have many Health and Care Professional Council registered members of staff across a wide range of disciplines teaching on our course, as well as a very active iBMS liaison committee with links to local laboratories. So I had many wonderful people to pester endlessly with my ideas for how to integrate more clinical simulation across our course. We already do a brilliant job of incorporating our own experiences as healthcare professions into our teaching through both use of case studies and work with simulated patients. My feeling is that enhancing this work with additional clinical simulation practical sessions can only further benefit our students here.
Immunology, in particular, as a discipline lends itself beautifully to clinical simulation as a learning technique. Students often view immunology as challenging due to its complex and multi-faceted nature. It can be seen as dry because we ask them to develop an understanding of abstract concepts and use a diverse array of terminology which often are difficult to pronounce and even harder to remember. I often remind students that though immunologists are quite brilliant, but we probably shouldn’t have been allowed to name our own findings – especially given how frequently we tend to rename molecules. Furthermore, immunology is a notoriously difficult discipline to find placement opportunities in, thus it is essential for students to have authentic learning experiences in this field whilst at university. As such, using clinical simulation to create realistic scenarios which foster active learning and emotional engagement can only help students with this dry, dusty old subject.
I might love Immunology so much I own the teacup, but it isn’t for everyone. Perhaps Clinical Simulation can change this.
One of the most significant barriers to the introduction of clinical simulation to immunology is the frankly exorbitant cost of the commercial reagents to laboratory practicals. Fortunately, my students here at the University of Lincoln have a dry, dusty old teacher (me!) who remembers the days when we made, rather than bought, all of our kit in the clinical laboratory. To that end, with the help of my favourite histologist Dr Issam Hussain and my delightful mBio student, we have been making ANCA slides and using antibodies to manufacture patient samples for clinical simulation. For those of you who haven’t come across ANCA testing before, this is the preparation of ethanol-fixed neutrophil slides which we use in the clinical laboratory to run immunofluorescence staining to help diagnose patients with autoimmune vasculitis. This is a particularly serious condition which often presents as a clinical emergency and is probably the most urgent test run in the immunology laboratory. The results can be highly subjective and difficult to interpret, with extensive follow-on testing required. The clinical decision is often made based solely on the patient presentation and this single immunology test. Thus, the reporting of these urgent results can be nerve wracking for the most experienced of healthcare scientists. The opportunity to practice this skill in a risk-free environment with a range of clinical scenarios offers the ideal space for students to make mistakes and learn from them without putting a patient at risk. Simulation of this work can help to build confidence and competence, and introduces our students to the concepts of clinical judgment and decision-making.
Figure depicting the production of ANCA slides, their staining and visualisation with a immunofluorescence microscope.
Before and after the simulation lab session we ran anonymous surveys to evaluate what our students thought of the learning experience. I was delighted to see in our preliminary review of the data that more than 95% of the students felt the simulation improved their understanding of both the techniques and the diagnostic process, and 98% felt that clinical simulation was a good learning experience. With a really significant number of responses, and so few negative comments, I feel my view point on simulation has been reaffirmed. Watch this space. I am now fully committed to the idea that we can really enhance the training of our future workforce of biomedical scientists through this powerful teaching strategy. And thank goodness the students enjoy it too.
An example of weak ANCA staining seen down the microscope during for a simulated patient. Students are asked to identify the staining pattern, and with some additional clinical information, make a decision about whether to report urgently or wait for further tests.
As I continue the slow road to feeling more like myself again I thought it might be nice to have a guest blog from the wonderful Sam Walker on some of the things that have been happening in the research Girlymicro world, so you know I haven’t been entirely resting on my laurels and eating copious amounts of chocolate. One of my favourite papers ever is based on the release of cauliflower mosaic virus DNA into a ward space, to support prospective tracking of where organisms go, instead of trying to guess based solely on where we find them without origin data. Due to a number of technical factors this approach to improving environmental transmission pathways hasn’t widely been repeated………..until now!
Sam is a Doctoral Research Student whose research focusses on the development for environmental surface monitoring protocols to inform clinical risk assessments and infection control procedures. His project aims to develop an evidence base for the presence of nosocomial pathogens in the hospital environment, as well as model the transmission of pathogens in clinical spaces. He obtained an MBiol degree from Aston University in 2020, with projects focusing on C. difficile spore germination.
Infection Control Research
“I imagine the swabbing part will be easy, it’s the data processing I’m worried about”. I think I said this about a month before the largest, and final, sample collection campaign in my PhD project. Famous last words.
A little bit about me – my name’s Sam and I’m one of Elaine’s PhD students. I’m finishing off my third year now (crunch time!). My project focusses on developing evidence-based surface sampling guidance to inform infection prevention and control practice. Practically, this involves collecting a range of samples from different clinical spaces and seeing that they can tell us in terms of microbial communities and microorganism dissemination, then using this information to target guidance for designing the most effective surface sampling protocols. In order to best inform this, we designed a study which looks at the movement of microbial surrogate markers through several different wards at Great Ormond Street Hospital. This involved a lot of preparation and many evenings swabbing sites across four wards. As of last week, all this sampling work has finished and I thought I’d share a few reflections on what the experience of conducting research in an active clinical space was like.
Working across settings is amazing!
For many projects focusing on clinical practice, particularly ones relating to IPC, working in collaboration with a clinical institution is absolutely essential. As my project involves collecting evidence from clinical settings to then process and develop into guidance, in my case this work wouldn’t be possible without this collaborative approach. As the end goal of my project is guidance that will inform clinical practice, not only is it important that the evidence is gathered from clinical settings, but it’s essential we understand the routine challenges faced by IPC teams. We can design the best set of guidance with all the technical detail in the world, but if we don’t take into account every day IPC challenges and what implementing this guidance will actually look like, then in a way it would fall flat. Being in the clinical space also opens up the possibility for conversations with the people who live and breathe IPC all day – the hospital staff! Informal discussions we have had over the course of this most recent sampling project have given me completely new insights and ways to view the work we’re undertaking which I never would have thought of otherwise! Getting this insight from working in clinical settings will ultimately improve both the quality and utility of the work we produce.
Stepping out of my comfort zone
As a lot of project is lab-based, the trips outside of this setting into clinical environments can be a bit of a shock to the system. I’m used to, and probably most at home in, a quiet laboratory space with a few other people at the most, maybe the odd visitor and the trusty PCR machines. The majority of the time I make the journey from UCL to GOSH, it’s to meet either with Elaine or other members of the IPC team, or maybe to pick something up from the microbiology labs there. When it’s time to collect samples however, this is a completely different experience.
The units we looked at in this most recent piece of work we did were two outpatient and two inpatient wards, serving different patient populations. One of the first things I really noticed was just how different these wards all were. I knew that there would be some big differences, for example I knew that the cardiac intensive care unit would be a very different experience to the oncology day care unit. What I didn’t necessarily expect however, was just how different the two outpatient wards would be from each other, and how different the same ward could be on different days.
With these differences came a different way to approach the research at hand. For the outpatient units, that often meant waiting until all the bed spaces were free so we could go in and collect the samples from the environment. This wasn’t always possible though, and sometimes we just had to accept that we weren’t going to get all of the samples we set out to gather. This took quite a while to get used to – my inner laboratory scientist was wincing at the thought of lost data points. Being able to put this to one side and carry on was a skill that took a while to master, particularly when sampling with a team. No-one will thank you when you’ve been on the ward for an hour and a half and you propose “just waiting a few more minutes” to see if a bed space will become free. Having that skill to just move on however turned out to be very useful when collecting the data, as it meant we could focus more effort in the areas we could collect samples from.
All this boils down to how the space is used completely differently. The hospital is first and foremost for providing care to patients, and as a researcher I have to acknowledge that I am a guest in the space. Understanding and accepting that we won’t always be able to collect all of the 65 or so samples we planned to on a given day is just part of the process when conducting sampling in the real-world hospital setting. At first, I remember feeling like this may be frustrating when it came to analyzing the data, and that it would make interpreting my results harder due to data gaps. However, looking back on it now, I actually feel it makes understanding the story the data tells easier, and much more insightful. Being able to relate the information we gathered to how the space was used at the time of collection, even where samples could not be obtained, just makes the story all the more applicable to real clinical practice and, in this case, how microbes could move through the clinical space under all sorts of conditions.
Anticipate the challenges
While embracing the dynamic environment of the clinical space is really important for putting data gathered in these settings into context, it doesn’t mean that there isn’t a fair share of challenges with it. Before I began the sampling campaigns, both my supervisors absolutely insisted that I pre-planned every tiny detail. Down to the exact number of extra swabs I would take for each day. And I cannot think of better advice when it comes to performing this sort of work. Planning is absolutely everything. One of the reasons missing some data points during collection didn’t impact the overall quality of the data was because we anticipated that we may miss some points each day, so planned to take extra to account for this. We planned a detailed sampling sheet, so we could not only check off samples as we took them, but could make notes as we went around the ward on the environment to help with the downstream analysis. I cannot stress it enough; thorough planning made the whole experience so much better.
One challenge of conducting this piece of work was the intensity of the settings. I have a very much academic background, having done my MBiol degree and gone straight into my PhD. In other words, I have no clinical training whatsoever. This wasn’t so much of a problem in wards which were not high dependency, however I really noticed this lack of clinical exposure when we did the sampling in the cardiac intensive care unit. I knew it may be a difficult experience, given the nature of the ward we were going in to, but it still was a shock the first day of sampling there. I’m incredibly grateful for the team I did this part of the work with, who had the experience to navigate the space as well as make sure I was alright being in the setting. I think that this support, alongside taking some time to reflect on the overall experience, was invaluable for this particular component of the work.
This leads me on to the other absolutely key point for doing this sort of research – having the right people with you. As academics, we often won’t have been trained in clinical practice. This can not only make some clinical spaces quite intimidating, but also can make them hard to read. For example, without a clinical understanding of what is going on in a bed space, it can be hard to know whether to ask if it’s alright to take a swab of the bed rail quickly, or if you should leave the space and move on. Having people with you who can help read these situations is so important, both for help with collecting the data but also for supporting the researcher. Another massive benefit I noticed was the links formed between me, the researcher, and the ward staff. Having someone involved who has experience in both worlds can really help break down any barriers on entering the space and help everyone understand the work that is being done, and how it relates to the ward.
Top tips for laboratory researchers gathering samples from clinical spaces
So, having said all that, my top tips on performing research in clinical spaces as an academic are:
Planning is everything!
Anticipate and embrace the unique challenges of this sort of research
Have a good team who can support you in the clinical space
And finally, get involved! Undertaking research in clinical settings is very rewarding and I would highly recommend it wherever possible!
As summer draws to a close, results come in and we all think about what our next steps might look like it felt like now would be a good time to share a guest blog that has been written to help inspire what some of those options might look like.
Joanna Ward is a prize winning MBio student based at the University of Lincoln. She has recently completed her MBio and been accepted into a prestigious PhD programme, continuing under her MBio supervisors Professor Claire Hills and Professor Paul Squires.
A year in the life of an MBio student
As I come to the end of my degree, I have been reflecting upon my experience at the University of Lincoln, but in particular, my master’s year which I have just completed. As an MBio student, my degree consisted of a three-year BSc Biomedical Science course, before an additional ‘masters’ year in which I was fortunate enough to join the University of Lincoln Renal Group. Supervised by Prof Claire Hills and Prof Paul Squires, the group has research interests in diabetes, chronic kidney disease and cardiovascular disease. Specifically, they study the underlying mechanisms which drive disease progression, to better understand how we can intervene clinically and improve patient outcomes. I love these areas of research which aim to bridge bench to bedside– it epitomises everything I have ever wanted to do and I am driven everyday by the possibility of our research being beneficial to so many people.
After a disrupted undergraduate degree as a result of COVID, going into my master’s year I had very little lab experience and the thought of completing a lab-based project was quite a daunting prospect, but I was incredibly fortunate to be part of a team where there’s no such thing as a silly question and support is always at hand. I soon realised that I loved being in the lab and the research absolutely fascinated me.
Being part of a very active research group meant I spent a lot of time at the bench, conducting experiments and analysing data. My typical day in the lab would involve firstly checking on my cells; tissue culture forms a huge part of our research so getting to grips with the techniques behind it was a key part of being able to run the experiments. I used human kidney cells to create an in vitro model of chronic kidney disease which then allowed us to determine whether the drugs we were treating our cells with were having a protective effect. After this, I would run multiple different experiments throughout the day, these could involve techniques that include Western blotting, PCR and several different laboratory assays. Having a lab-based year through completing the MBio gave me the opportunity to develop so many different lab skills, something which I am hugely grateful for.
Aside from lab work, this year I have also developed multiple skills important to a career in science. One of these is keeping up with the literature surrounding our research topics, this is both essential but also difficult since papers are published so frequently and knowledge around specific subject areas can develop quickly. Creating a system which enabled me to keep up with this early on was something which made my life a lot easier as the year progressed so I absolutely cannot recommend this enough! Science communication forms a huge part of research, and through being lucky enough to attend the Diabetes UK professional conference, regularly presenting at lab meetings, research showcases and poster presentations, I have developed more confidence in public speaking. Importantly I have developed a greater appreciation for the ability to communicate our research to people in other disciplines.
I have had the most incredible year and have grown on both a personal and professional level, but this absolutely hasn’t happened by chance. I have been incredibly fortunate to be guided into the world of science by the most wonderful supervisors who have not only given me so many incredible opportunities but have also encouraged and supported me every step of the way. They have believed in me when I didn’t believe in myself and have made me realise a career in research is exactly what I want to do with my life. They are also incredible scientists who I look up to enormously- as an early career researcher you absolutely need mentors who are supportive and whom you trust, so having supervisors like this has been an absolute privilege. I have also been blessed with the most wonderful lab mates who have become some of my best friends and make every day full of laughter and fun. They have taught me more than they will ever know and couldn’t have been more supportive, reassuring, and hilarious. I look forward to every single day I spend with them!
My master’s has been an absolute joy, I would tell anyone considering doing an MBio to give it everything that you have, go above and beyond, be a team player and make the most out of every opportunity you are given. I am incredibly excited to see where my path in science and research takes me next and will forever be thankful to team Renal for providing the very best start in this.
I am currently away enduring the heat of Houston, Texas, at the American Society of Microbiology annual conference. Hopefully, I will find lots of lovely inspiration whilst I’m here to share with you all. In the meantime, and whilst jet lag is kicking my ass, the wonderful Dr Claire Walker has swooped in and saved me by writing another awesome guest blog.
Dr Walker 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 one on the transition from lab to academia.
So, the other night before a conference @girlymicro and I were sat in a hotel bar, drinking martinis and listening to me bemoan some fairly harsh feedback I recently received anonymously from a student in the form of the oft dreaded ‘Module evaluation feedback form’. The conversation went a little like the Deep Space 9 meme of Julian and Garek that’s doing the rounds – you know the one….
I love the internet. Meme generators entertain me no end.
Back to the story, I was complaining and @girlymicro, quite rightly, reminded me of two important facts. One, all constructive feedback is always useful even if we don’t particularly like hearing it. And two, not everyone is going to love us even if we really, really want them to.
I went to bed reflecting on this conversation and my poor feedback. Constructive critical feedback is a powerful tool for growth, yes it stings a little at the time, but when we take time to reflect can we see why we received it? This particular individual found me to be blunt and rude, and in honesty, in this specific instance I would say they aren’t totally wrong. This year, my decision to support University College Union strike action prevented me from giving the first lecture of my module. I use this lecture not only to introduce myself and describe the content of the module, but to set the expectations for behaviour in my classroom. I’m what has been described by my friends and colleagues as ‘old school’, and this makes me something of a marmite individual for students. I want to provide a safe space for discussions, and I cover a lot of triggering subjects. I have no time for disruptive behaviour that detracts from the groups collective learning experiences, and I have a low threshold for calling students out on this. Am I blunt? Probably. Could it be perceived as rude? Absolutely. Without these early conversations the students this year weren’t aware of my expectations and thus my behaviour had no context. Does this make the feedback fair? Possibly. In my honest opinion when you come to a place of learning you put your phone down and respect the teacher as well as your fellow students, and at University level teaching you shouldn’t need to be reminded of this. However, what I’ve learnt is just how important those conversations are, and I will be having them come hell or high water next year.
Girlymicro’s second point also gave me pause for thought. Not everyone is going to adore me. My teaching style isn’t guaranteed to work for everyone. So after finishing my martinis I returned to my feedback and applied the Pareto Principle. The Pareto principle asserts that 80% of outcomes result from 20% of causes. When I view negative feedback through the lens of the Pareto principle, I see that a significant proportion of this feedback comes from a small percentage of students. And the same is true of the positive feedback. Understanding this principle lets me focus on how I can direct my efforts to addressing their concerns specifically and prioritise improvements across my teaching to make meaningful change. However, it’s also crucial to recognise the silent majority the 80% who are, apparently, content enough not to provide an evaluation of the module. A major overhaul probably isn’t necessary, but there are tweaks to be made to make the content work for everyone.
Finally, I reflect on the words of wisdom from the great Obi Wan Kenobi himself:
“ You’re going to find that many of the truths we cling to depend greatly on our own point of view.” / “The truth is often what we make of it; you heard what you wanted to hear, believed what you wanted to believe.”
My ‘truth’, my point of view has been that my teaching style is interactive and engaging, and certainly some of my students share this opinion. But this isn’t everyone’s point of view and through receiving feedback I am able to see the opinions of those individuals that differ from my own. I often say that teaching is an iterative process, dependent on a cycle of reflection and growth. I may enjoy a particular style of lecture but if it’s not working for the majority, I have to put it down and build something new. Based on both the negative and positive comments, I have been able to introduce more lab sessions, simulated clinical experiences and data analysis workshops to my modules, and move away from traditional didactic teaching. Yes, it’s more work over the summer but hopefully this will lead to a significant improvement in the learning experience of my students. Who knows? Hopefully that quiet 80% like the changes. Either way I’ll await my next critique and take it from there.
TLDR: You can’t win ‘em all. But you can have a lot of fun with meme generators.
Girlymicro 