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EIT Pathogena launched!

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.

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Infection Inspection

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.

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News Talks Tuberculosis

Talk on Kafka and tuberculosis

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.

You can watch the talk for free here

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News

MMM at the Westgate Shopping Centre

The annual Oxford Biomedical Research Centre (BRC) Open Day was held on Thursday 30 May 2024 in the Westgate Shopping Centre in Oxford; this year is was jointly held with the Oxford Health BRC.

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.

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News

Who should own data about you?

We ran a session at the Philosophy in Pubs Oxford group in April 2024, discussing where the moral lines can and should be drawn around the use of data about us. Who does the data really belong to? What are legitimate uses of it? What are the factors that make people uncomfortable? And are they justified? We had a very interesting discussion with around 16 people from the local Oxfordshire area, covering questions such as “Does the idea of the public good ever outweigh an individual’s right to control how their data is used?”, “Is it correct that any data that is “about” us also “belongs” to us, even if we did not create it, nor have any use for it ourselves?”, and “Does it change things if the data is completely anonymised or is there still a general rule about self determination that applies?”

It was really interesting to hear how different people viewed these questions very differently, not just in the field of healthcare data but also more generally. You can find out more about Philosophy in Pubs Oxford events here.

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We need you!

We are looking for new members to join our existing patient and public group and work with us to make sure that public views on how we run our research are heard and acted on.

For more information, please click here.

If you are interested, please return the application form available through the link above by 5pm on Thursday 21 March 2024.

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News

Infection Inspection in New Scientist!

You can read all about our latest Zooniverse project, InfectionInspection, in New Scientist (15 March 2023 issue).

This citizen science project is part of a larger project developing a new way of diagnosing infections resistant to antibiotics and brings together researchers from Medical Sciences, Physics and Oxford University Hospitals NHS Trust and is funded by the Oxford Martin School.

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News

Science Together in Oxford

Science Together is a series of workshops and events being held at the Oxford Museum of Natural History on Tue 7 June 2022. Events start at 10.30am and run until 5pm.

From 5-7pm you can find out more about some of the projects through Science on the Sofa where Oli Moore will talk to some of scientists behind the different public engagement projects on display during the day, including our very own Carla Wright and Emma Pritchard!

You can register to attend in person, or follow the livestream, via this link.

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BashTheBug on the Zooniverse News

BashTheBug paper out!

Read the first scientific paper published in eLife. Anyone can go to the website and read it, there is no paywall.

Each image is looked at by up to 17 different citizen scientists — in this paper we show that taking the median of these classifications is both reproducible and accurate.

In fact, if you apply the criteria defined by the relevant ISO standard their results are sufficient accurate but not quite reproducible enough to qualify as an Antibiotic Susceptibility Testing device.

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News

Listen to Sarah Walker talk about the ONS Covid population survey

Professor Sarah Walker has been Principal Investigator of the ONS Covid Infection Survey since it started in April 2020. By regularly testing random samples of the UK population for infection and Covid antibodies, this has provided hugely valuable information as the Covid pandemic has progressed and has helped inform public health policy.

You can listen to her talk about the survey in the first episode of the new Statistically Speaking podcast by the Office of National Statistics (ONS), along with other people heavily involved in the survey.