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.
A well-assembled bacterial genome put together by a long-read assembler. Note how the long-read assembly is circular, as bacterial chromosomes should be.A poorly put-together bacterial genome,by a hybrid assembler
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!
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.
This has been a long time coming but last month, the Ellison Institute of Technology launched EIT Pathogena. This is a website where anyone anywhere in the world can work out what species of Mycobacteria are in a sample and, if it is Mycobacterium tuberculosis, which, as the name suggests, is the causative agent of tuberculosis, also work out which antibiotics are likely to be effective. Lastly it also tells you if the genome of that sample is sufficiently similar to any other samples you’ve uploaded that they could be part of the same outbreak.
So how does it do this? Well you have to have put your Mycobacterial sample through a genetic sequencing machine — this gives you two output files (called FASTQ files) which contain lots of short stretches of DNA found in the sample which will have come from the patient, other bacteria, the odd virus and probably some Mycobacteria. Historically sifting through these files and working out what is what and then seeing if you can build a genome from some of the short stretches (a bit like a really big jigsaw, just one where the pieces overlap and some have mistakes) is the job of a Bioinformatician and is difficult.
EIT Pathogena makes that simple; all you have to do is drag and drop the FASTQ files onto the web portal and it will upload them, then automatically remove and forget any bits of human DNA (as these could be used to identify the patient in theory) before working out what species are present etc.
We have written all the computer code that handles all the short stretches of DNA. Much of the software used to predict which antibiotic is likely to work was originally written as part of our earlier CRyPTIC project but has been rewritten by our Research Software Engineers (RSE) to bring it inline with modern software engineering practices.
If you like looking at code, head over to GitHub and check out gnomonicus which in turn uses gumpy and piezo. All of these are written in Python3 — Jeremy Westhead who is one of our RSEs noticed that we could speed up this part of the pipeline significantly by rewriting gumpy in Rust. He called this new version grumpy of course! All of this software has a license allowing anyone to use it for research but prohibits using it for commercial purposes.
When we test a sample taken from a patient to see which antibiotics will work (and which will not) we test many thousands of bacteria all at once; if the antibiotic kills most of them we say it is susceptible. But in some cases that isn’t good enough: the few that are left (because they are resistant) can grow and multiply so all you’ve done is buy a little time.
What if instead you could look at the effects of an antibiotic on a single bacterium?
That, in essence, is what the interdisciplinary team drawn from both the Department of Physics and the John Radcliffe hospital in Oxford did with this project. Using fluorescent staining and super-resolution microscopy they can image individual bacteria and ones which are resistant to an antibiotic “look different”, providing you’ve stained the right parts of the bug.
Humans, of course, are really good at looking at photographs and so they also set up a Citizen Science project on the Zooniverse called, you guessed it, Infection Inspection. They asked volunteers to classify of E. coli which had been fluorescently stained and then treated with an antibiotic as either resistant or susceptible.
If you want to read more about this please go and read their paper.
To mark the centenary of Franz Kafka’s death from laryngeal tuberculosis at the age of 40 in June 1924, the University of Oxford ran a series of events, including talks, an exhibition and a public reading of the Metamorphosis in the Sheldonian Theatre.
It is believe he lived with tuberculosis for the last 7 years of his life and it likely affected his writings, including works such as The Hunger Artist. In recognition there was a public talk on 5 June 2024 entitled “Tuberculosis: vaccines, diagnostics and experience” with contributions on vaccines by Professor Helen McShane and diagnostics by one of our Unit, Dr Philip Fowler.
The highlight however was hearing the experience of someone who had been diagnosed with tuberculosis about 20 years and how, despite, surviving this ancient disease, it has profoundly affected how she lives day to day.
Join Our Microbe Drawing Competition and Win a Cuddly Toy! 🦠🎨
We are thrilled to announce an exciting opportunity for budding young scientists and artists alike! Our Microbe Drawing Competition is now open, and we are inviting participants of all ages to get creative and learn about the fascinating world of microbiology. Hosted by our team at Oxford University’s Modernising Medical Microbiology, this competition offers a fun and educational way to engage with science.
How to Enter: To participate, simply draw a microbe or design your own imaginative version! Once your masterpiece is ready, send it along with your name/initials, the microbe’s name, and your age to @bashthebug on Instagram or email us at crookpm@ndm.ox.ac.uk. Make sure to submit your entries by June 30th, 2024.
Quick Facts About Our Bugs Up for Grabs 🦠🔍:
Pseudomonas aeruginosa: This microbe is known for its striking blue or green color under the microscope!
Escherichia coli: While some strains can cause food poisoning, most E. coli are harmless and live in your intestines, helping with digestion.
MRSA: This germ is so resistant to antibiotics it is considered a ‘superbug’ (hence the cape!).
This competition is a fantastic way to spark interest in microbiology and science. Whether you’re a parent looking for a fun educational activity for your child or a teacher seeking engaging science content for your students, this drawing competition is the perfect opportunity.
We can’t wait to see all the creative and colorful entries! Your support and participation mean the world to us, and we look forward to sharing the wonderful artwork with our community.
Stay tuned for more updates, and don’t forget to follow us on Instagram, Facebook and X (@bashthebug) for the latest news and announcements.
It was half-term for schools in Oxfordshire so lots of children, parents and grandparents were in town. The Dance Mat, demonstrating how mutations always creep in when you try an copy something, was very popular as always! We had a pipetting game where you could try out pipetting into a 96-well plate (with giant couscous) as well as an investigation with clues and a public poll on how antibiotics should be improved.
We’d designed and ordered some squishy antibiotics and some (much cuter) green Mycobacterium tuberculosis bacteria and managed to hand out over 90 to interested people over the course of the day.
My name is Teresa Street and I’m a senior postdoctoral scientist in the Modernising Medical Microbiology (MMM) research group, part of the Nuffield Department of Medicine at the University of Oxford, UK. MMM aims to transform how we analyse and treat infections so we can improve patient care. For the last few years, we’ve worked on studies that try to develop better ways of detecting bacterial infections and predicting antibiotic resistance using DNA sequencing.
Our latest study focused on detecting gonorrhoea in patient samples. Gonorrhoea is a common sexually transmitted infection, caused by the bacteria Neisseria gonorrhoeae. It is usually successfully treated with a combination of two antibiotics. Increasingly, there are more cases arising where these two antibiotics are no longer effective at treating gonorrhoea, as the bacteria has developed resistance to them. This resistance has been detected globally, making gonorrhoea a significant public health risk.
To tackle this problem, we need to be able to identify and treat infections quickly: early detection and faster treatment will help control the spread of antibiotic-resistant strains. Gonorrhoea is usually detected by collecting urine or a swab sample from patients and then growing any bacteria contained within the samples in a laboratory. If bacteria do grow, further tests can be done to identify which antibiotics will successfully kill them. Scientists also do molecular tests (PCR), which involve trying to detect DNA from the gonorrhoea bacteria. It can take a while to get the results back from all of these tests as often bacteria can take a few days to grow. A single test that could be done much faster, and which would identify both whether a gonorrhoea infection is present and which antibiotics would treat it best would allow the correct treatment for each patient to be started sooner. This, in turn, would reduce the onward transmission of gonorrhoea. This is particularly important in those cases where the bacteria is resistant to multiple antibiotics.
Recently, a molecular method called Metagenomic Sequencing, or mNGS, has shown potential as a new diagnostic test. It utilises next generation sequencing (NGS) technologies to identify DNA from bacteria directly from patient samples, without needing to grow the bacteria in a laboratory first. The bacterial DNA can be identified by comparing it to a database of many known bacterial sequences, and this helps to identify the bacteria causing an infection. If we can extract enough bacterial DNA from a sample, not only can mNGS work out which type of bacteria is causing the infection, but it can also identify specific parts of its DNA that we know lead to antibiotic resistance (AMR). mNGS can also be faster than current tests, often detecting the cause of an infection and which treatments will work within a few hours. In this way we have the potential for a single test that both identifies the cause of infection and gives us information about which antibiotics will (or won’t) treat it much faster than current methods.
In a previous study we tested the ability of mNGS to detect N. gonorrhoeae directly from urine samples. We were able to detect gonorrhoea and in some cases also see some AMR determinants. mNGS can, however, sometimes be hampered by high levels of host contamination: DNA extracted from a clinical sample will contain DNA from the patient as well as from any bacteria. This limits the detection of bacterial DNA in our sequence data and makes it more difficult to identify AMR determinants. We observed this in our previous work, and so our latest study tested a method to enrich for gonorrhoea before sequencing.
We used a technique called Target Enrichment to capture any gonorrhoea DNA in our extracts before sequencing. This involves designing probes – short sequences of RNA that are complementary to specific regions of the target DNA. In this case our target DNA was the N. gonorrhoeae genome and we also focussed on known AMR determinants, including probes that match to these known sequences. By mixing the probes with DNA extracted from patient samples they will selectively hybridize, or bind, to their complementary gonorrhoea target sequences. Subsequent steps remove the unbound DNA (which we hoped would be human and any other bacterial DNA), increasing the relative abundance of the gonorrhoea DNA compared to non-target DNA in the sample. In this way we should be able to enrich for gonorrhoea over the human DNA.
We tested this enrichment method for gonorrhoea-positive urine and urethral swab samples. Our results demonstrated a substantial improvement in the proportion of DNA sequences classified as N. gonorrhoeae in comparison to the same sample without enrichment. This enhanced genome coverage enabled detection of AMR determinants in chromosomal genes that are known to confer resistance, and we were able to predict the resistance seen by the laboratory to certain antibiotics in our samples. We also tested the feasibility of multiplexing, where multiple samples were pooled, enriched and sequenced simultaneously, to improve efficiency and reduce the costs associated with enrichment and sequencing. We obtained enough genome coverage to detect AMR determinants in these samples, too.
We hope our results have shown the usefulness of enrichment for detecting gonorrhoea directly from patient samples without needing to culture it in the laboratory first. We were even able to detect an AMR determinant in a sample which did not grow in the laboratory and so didn’t have a recommendation for which antibiotic would be best to kill it. We think this really highlights the utility of mNGS for looking at infections where bacteria are difficult to grow in a laboratory.
In October 2023 I travelled to Harare, in Zimbabwe, to teach a team of scientists how to genome sequence SARS-CoV-2 using Oxford Nanopore Technologies sequencing. The team were taking part in a study to observe COVID infections in Zimbabwe and had a collection of over 600 samples they were keen to sequence.
I spent a week at Professor Tariro Makadzange’s Infectious Diseases Research Laboratory (part of the Charles River Medical Group), teaching the team how to prepare samples and analyse data using the Global Pathogen Analysis Service (GPAS).
Hard at work preparing samples for sequencingCelebrating starting the first SARS-CoV-2 sequencing run
I’m so grateful I got to experience scientific research outside the UK, and I couldn’t have spent the week with a friendlier, more welcoming group of people. My time in Harare also really made me appreciate the facilities we have and the things we take for granted. We don’t have thunder and lightning storms so powerful they regularly knock out our power for hours at a time; nor do we have labs that leak under the sheer volume of rain that falls. We also take our superfast Wi-Fi for granted: trying to download software and upload data at 2Mb/sec is frustrating, to say the least!
The lab (in what used to be a peanut butter factory!)
This collaboration would have seriously struggled to achieve all it did in such a short space of time without the help of Bede Constantinides. He made himself available from back home for the whole week to hold our hands through setting up the computing and guiding us through the analysis, so that I could leave the team fully self-sufficient for all their future work.
I’m pleased to report the team have now finished sequencing their 600+ sample collection and are now using ONT sequencing for other studies.
Zimbabwe is an incredible country with fantastic people, and I really hope I have the opportunity to visit again one day!
Imire Lodge Rhino and Wildlife Conservation Reserve
