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Skip to 0 minutes and 6 seconds So this is Nick Thomson whose lab does research on the genomics of AMR. What is Antimicrobial Resistance? So we use antimicrobials therapeutically to kill and to treat infections. And when a microbe or bacteria is no longer sensitive, it’s no longer killed by an antibiotic, by definition, it’s resistant to the antibiotic. Why do bacteria become resistant to antibiotics? It’s because we are reliant on antibiotics to treat infections, therefore we use lots of them. They’re used all over the world. There are multiple different types, and we don’t always tailor the amount of antibiotic we take to the size of person. For example, everyone gets a standard dose.

Skip to 1 minute and 1 second And so just by sheer size, the doses of the antibiotic that circulate within our body are different. When you take an antibiotic for a specific infection, the antibiotic can even be sweated in your skin. So everything every bacteria in your guts, on your skin, everywhere is exposed to the antibiotic regardless of whether that’s the bacterium causing the infection or not. So the reason that we get resistance is through exposure. We take antibiotics we expose bacteria to antibiotics. Those that are resistant survive. Those that are sensitive don’t. And so we select for resistant. We hear about AMR all the time on the news. Why should we be worried about it? It’s a problem, because antibiotics are very important for treatment.

Skip to 1 minute and 50 seconds And reverting or going back to a time where we had no antibiotics mean that very common illnesses become real life threatening. And it’s not just through infections. It’s everything where we break the skin barrier. So for operations, for hip, knee operations, anything where bacteria can enter the body and cause an infection, if we don’t have antibiotics to treat those infections, then those infections can become life threatening. Is this a problem all over the world? It’s a problem all over the world. Resistance is spreading. So these resistant bacteria are able to spread not just locally, nationally, but globally. We carry them on our skin. And so there are many ways for them to spread and within our bodies.

Skip to 2 minutes and 40 seconds And so anywhere where we’ve overused antibiotics or that resistance has developed, it’s a problem and that, at the moment, because of our reliance on antibiotics is most of the world. So what can genomics do to help us tackle the problem of AMR? So that we know there are different ways to become resistant. You can be naturally truly resistant. You can acquire genes that confer, allow you to be resistant, a bacterium that is. And we also have bacteria which we know are more resistant than others. And so genomics allows us to identify all of those possibilities. It allows us to look at highly-resistant bacteria and how they’re spreading.

Skip to 3 minutes and 26 seconds It allows us to understand whether that gene is able to spread to other bacteria or is confined to that single bacterium, or whether the mechanism of resistance is a threat in terms of other bacteria. It could spread to other bacteria and confer resistance more broadly. So really what it does is to allow us to estimate the risk of not only the bacteria that is resistant but the genes that confer resistance pose to human health. So could you give us an example from your research where you’ve used genomics in the context of AMR to help us understand more about it? We had a very unusual example of disease in Africa. It was a bacteria that’s familiar to many, salmonella, Salmonella typhimurium.

Skip to 4 minutes and 17 seconds In the UK, for example, where I’m based, you would mostly associate salmonella food with food poisoning, so with food. In Africa, it wasn’t associated with food at all. And it also didn’t necessarily generate the symptoms that we’d be familiar with here, so diarrhoea. It caused a fever, so an invasive illness that led to a fever, a very high fever. It was life threatening and treated with antibiotics. The recommended antibiotic for Salmonella in that setting wasn’t working. And so when we sequenced the bug, the first thing we found out was that these were a very specialised form of the Salmonella that we would have in the UK, but different and that explained why they were causing a fever, an invasive disease.

Skip to 5 minutes and 9 seconds We also found that they carried the genes not just for one antibiotic, but for five different antibiotics that conferred resistance to those antibiotics, which explained why treatment was failing to limit the severity of the infection. And in actual fact, as a result, there was extremely high mortality rate. And so we were able to not only define this organism and its resistance, we were able to say how far that had spread. And it actually spread right across Africa. And so therefore, you can alert anyone who wants to treat these types of infections to the presence of an organism that will not respond to the recommended antimicrobials. OK. Thank you very much, Nick.

Present day danger of antimicrobial resistance

In this video, Josie interviews Professor Nick Thomson for his perspective about the risks of antimicrobial resistance. We will hear about the scale of the threat, as well as the promise of whole genome sequencing to better understand and treat outbreaks.

In the comments area, share your thoughts on how research on the genomes of infectious diseases can help to inform public health and medical services?

Can you share one example from where you live of how genomic research is being used to help control the rise in antimicrobial resistance?

Or can you Identify any opportunities and/or barriers to integrating the use of whole genome sequencing to inform public health and medical services in your community?

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This video is from the free online course:

Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

Wellcome Genome Campus Advanced Courses and Scientific Conferences