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Work experience: what have we been up to?

Throughout the past three days doing work experience at MMM we’ve learnt about the different roles within the department, their responsibilities and contributions to research. After being briefed about a potential deadly outbreak in the MMM labs we were tasked with trying to identify the offending pathogen. Swabbing high contact points and warm areas such as our shoes, lab doors and keyboards we set about trying to culture the bacteria. Next we learnt how to use the streaking method to transfer the bacteria to our agar plates and create single colonies that we could later analyse. Examining the plates the next day, the coffee machine proved to be the incubator for the infection, the plates were crawling with enterococcus, coliforms and even a particularly large fungus. Luckily, Kate’s keyboard and Tree’s phone proved to be relatively clean.

We then took our sample to the OUH labs to try to figure out what groups the bacteria came from. Gram staining helped us with this, and so we doused our samples with purple, then orange then clear before finally red liquid. Examining them under the microscope allowed us to ascertain not only whether the bacteria were gram positive or gram negative, as illustrated by their purple or red colour, but also whether they were bacillus or cocci (rods or circles).

Throughout our placement we got a sense about the daily runnings of a lab, sitting in on a group talk on public engagement as well as hosting a journal club and recipient individual talks from different members of the team. Helen spoke to us about project management and her role within Oxford University, as well as the time she got invited to the American ambassadors 4th of July party! Though, she did assure us that this isn’t typical of a role in management. Ali talked to us about the green initiatives the lab is taking to try to improve their environmental sustainability such as recycling loops and pipette tips, and how they managed to achieve a silver in the green impact award and are now aiming for gold. Carlos talked to us about the computing side to the research and how the group works together so that everyone can do the roles their best at.

Highlights of our time at MMM included developing the dance mat game with Jo and Hieu, creating a new level for a local primary school that they are visiting soon, and creating agar art with Cat and Eloise, making some beautiful flowers!

We really enjoyed our time at MMM and can’t wait to join them some day!

Iris, Lori, Jess

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Green Impact Silver Award!

This year, our group has achieved Silver in the Green Impact award – a sustainability scheme which supports teams who want to improve their sustainability efforts. As part of the scheme, you are given a toolkit with lots of different activities to complete which encourages people to think more about their environmental impact. Each task is assigned a point value, and you need to collect a specific number of points to achieve Bronze, Silver, Gold and Beyond Gold. Check out our other blog posts about our plant-based potluck, and recycling contaminated lab plastics to see some of the things we’ve been up to!

I really enjoyed completing the green impact award this year, some of the tasks really make you think outside of the box – like the biodiversity monitoring activities! I also appreciated that many of the activities are quite group oriented, giving us the added wellbeing benefit of team building as well as encouraging greener practices. 

There were plenty of tasks we couldn’t complete this year – we’ll definitely be taking part in 2026 and aiming for Gold!

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Recycling Lab Plastics 

Easily the biggest source of waste in our lab is single-use plastics – pipette tips, plastic loops, bottles, tubes… the list goes on. It’s estimated that the biosciences sector alone produces 5.5 million tonnes of plastic waste every year, which is roughly equivalent to the carbon footprint of over one million UK citizens!

As advocates for the environment, it can be pretty demoralising to see just how much plastic you go through in your day-to-day lab work – it sometimes makes other efforts feel a bit pointless.

Because we work with biological samples, getting rid of contaminated plastics in an environmentally friendly way is no easy task, but our Lab Manager, Ali, was determined to find a solution. She came across a company called RecycleLab, which takes contaminated lab plastics and breaks them down to be turned into something new. The only thing we need to do first is to de contaminate them.

After some initial meetings, a visit to the RecycleLab site and some major updates to our SOPs, we now have a functioning lab plastic recycling system. So far, we’ve diverted 700 litres of our lab’s used plastics from the traditional non-recycling waste stream!

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MMM at the Westgate Shopping Centre (2025)

This is the third year that the NIHR Oxford Biomedical Research Centre (BRC) held its Showcase at the popular Westgate Shopping Centre in the centre of Oxford. Like last year it was held jointly with the NIHR Oxford Health BRC.

Our research software engineers had redesigned and rewritten our dance mat game so now you took on the role of a doctor firing different coloured antibiotics at incoming bacteria. So far so easy: over time, however, the bacteria get resistant to one or more of the antibiotics (denoted by a coloured shape appearing on them) meaning a lot of foot stamping is required to keep changing to the right colour antibiotic!

The game starts nice and slowly but the difficulty increases rapidly. On the day a few people scored over a hundred but anything more than that was too challenging…

It was half-term which was great as it meant lots of parents, grandparents and children stopped by and talked to us about our research. By the end of day we’d spoken to 130 people; half of them had heard about the Showcase beforehand, three members of our PPIEP committee and some ex-members of MMM dropped in to say hi, the Deputy Head of Mabel Prichard School (whose school we visited earlier in the year) and finally we spoke to one person who was halfway through a 10km run!

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Plant-Based Potluck 

In our efforts to encourage sustainable habits, the Green Team hosted our first-ever plant-based potluck lunch! The idea was simple: everyone brings along a plant-based dish, snack, or dessert (homemade or shop bought!) for people to try. It was a fun way to show just how varied and delicious a plant-based diet can be, and hopefully inspire a few new go-to recipes.

We had some very tasty contributions, like vegan sausage rolls, beetroot hummus, chocolate-covered strawberries, peanut butter filled dates, and loads more!

The feedback was really positive – people enjoyed the chance to catch up over food and try new things, and for our plant-based colleagues, it was especially nice to be able to join in without having to worry about the ingredients. We loved it so much, it’s now a monthly occurrence!

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The importance of hand-washing

Three of our researchers visited Mabel Prichard School in Oxford on Thursday 6 February and ran a session showing the children the importance of handwashing. You can see a photo and read more about it on Instagram here.

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The rise of superbugs (video)

For World Antibiotic Awareness Week some of the MMM Unit created an old-skool stop motion video to tell the story of how overuse of antibiotics leads to superbugs. Check out the cape…

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Putting 2 and 2 together: Using long-read bacterial genome assembly for public health surveillance

What is the problem?

Studying the genetic code of bacteria (DNA) can give us vital information like the genes they carry and how they are related. This can help us detect outbreaks and track how antimicrobial resistance genes spread, so we can contain them better. Putting the whole genome together gives us a clearer story than just looking at the short DNA fragments that come out of a sequencer, just like binding a book tells a clearer story than looking at the scattered pages. We can be more certain of where certain genes are, which can indicate whether it was borrowed from another bacteria, for example. 


Traditionally, the most accurate way to put together, or assemble, a bacterial genome into the correct sequence of the A, T, C and G nucleotide ‘rungs’ of the DNA ladder, has been to use a combination of two different technologies in a ‘hybrid’ method: highly accurate but hard-to-assemble short-read Illumina sequences, and error-prone but easy to put together long-reads. Long read sequences make it easier to get the overall structure right- a bit like doing a 1000-piece instead of a 500,000-piece jigsaw puzzle of a modern art painting. The bigger ‘jigsaw’ pieces are more likely to include a unique part that helps orientate where you fit in the overall picture. The highly-accurate illumina short-reads then swoop in to spell-check everything. The problem with using both methods in this way is that it is expensive to run two different experiments for a single sample, and this acts as a barrier to using bacterial whole genome sequencing on a larger scale in public health surveillance. 

Luckily, continued improvements in long-read sequencing utilising powerful computers and the latest machine learning techniques have driven down the error-rates of this technology.

What did we do?

To test this out, we assembled the genomes of 96 bacteria, taken from human bloodstream infections across England, using both hybrid and long-read only methods. We found that whilst both methods allowed us to create very high-quality genomes, the long-read only method was actually better than some of the hybrid methods at putting the genomes together.

So what?

This is great news for public health professionals! It means that creating complete and accurate bacterial genomes is now much more cost-effective than it was before, and takes us one step closer to integrating this into our routine surveillance of disease-causing bacteria. It could help us detect outbreaks earlier and pinpoint where they came from more accurately, especially when different bacteria start swapping smaller bits of DNA with each other and may not be linked to an outbreak with our current methods. Ultimately, looking at whole bacterial genomes better enables us to track their spread at a higher resolution compared to the more fragmented genomes from short-read sequencing, and will allow us to more effectively prevent people from getting infected.

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Microbes vs Medicine: A Bash the Bug Art Competition

Methicillin-resistant Staphylococcus aureus (MRSA) fighting a punchbag representing antibiotics by a previous winner, Marni (age 9)


This week is World Antimicrobial Awareness Week (18th–24th November)! To celebrate and raise awareness, we invite you to participate in our exciting art competition, Microbes vs Medicine. Open to all ages, this competition highlights the fascinating interplay between the invisible world of microbes and the power of medicine while addressing the critical issue of antimicrobial resistance.

Why Antimicrobial Awareness Matters

Antimicrobial resistance (AMR) is a growing global concern where bacteria, viruses, fungi, and parasites develop resistance to the medicines designed to combat them. This means life-saving treatments like antibiotics may become less effective, putting millions of lives at risk. Through this competition, part of World Antimicrobial Awareness Week, we aim to spread knowledge about AMR and inspire action toward its responsible management.

We want to see your creative interpretation of the relationship between microbes and medicine. Your artwork could depict the battle, harmony, or interplay between these forces, emphasizing the importance of understanding and combating AMR.


About the Competition

This art competition is proudly hosted by the Modernising Medical Microbiology group at the University of Oxford as part of our public engagement project, Bash the Bug. Dedicated to raising awareness of antimicrobial resistance through education and community involvement, Bash the Bug invites you to explore science through art!

This initiative is inspired by a previous winner, Marni (age 9), who created the imaginative depiction of Methicillin-resistant Staphylococcus aureus (MRSA) fighting a punchbag representing antibiotics shown above. This artwork exemplifies how creativity can make complex issues like AMR accessible and engaging.


Prizes and Recognition

Winning entries will receive special prizes and will be featured in our online gallery for all to admire.


How to Enter

Submit your artwork by 20th December to bashthebug@gmail.com with your name and age.


We can’t wait to see how your creativity brings Microbes vs Medicine to life. Let’s spread awareness and inspire change together!

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Major five-year project awarded

One side of research that isn’t seen much but is hugely important is securing the funding to do the research. We work very closely with the National Institutes for Health Research (NIHR) and, for example, lead the Modernising Medical Microbiology and Big Infection Diagnostics theme in the NIHR Oxford Biomedical Research Centre.

The NIHR recently announced £80 million of funding for a series of five-year initiatives, called Health Protection Research Units (HPRUs). Each HPRU focusses on a specific important health problem and works closely with UKHSA to carry out research and implement recommendations to improve patient outcomes in the UK.

In collaboration with both UKHSA and a number of other UK universities we have been awarded nearly £11 million to come up with new ways to reduce healthcare associated infections and antimicrobial resistance, in particular in hospitals and other healthcare settings. The HPRU will be led by Professor Sarah Walker who is experienced at managing large research projects, having, amongst other things, led the Office for National Statistics Covid-19 Infection Survey during the pandemic.