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What can genomics tell us about AMR?

Dr Estee Torok details how her novel research into using whole-genome sequencing in real-time so that AMR can be tracked and future medical provisions
I have with me here Estee Torok, who’s going to be telling us about her research into how genome sequencing can be useful for medical microbiology. So, Estee, tell us about your research. Hello, Josie. As you know, I’m a Consultant in Infectious Diseases and Medical Microbiology at Addenbrooke’s Hospital in Cambridge. And I spend most of my time in research. My research involves using microbial genomics to investigate outbreaks of infection in hospital, and also to rapidly diagnose drug-resistant infections. And this can be very helpful, because it can inform infection control teams and advise them as to whether to escalate or de-escalate infection control procedures. And in terms of patient management, it can help us to target antibiotic therapy.
Currently, how are bacterial infections tested for drug resistance? So, what we normally do in the diagnostic laboratory is we plate the organisms onto agar plates. And then we put antibiotic discs onto the agar plates and incubate them overnight. And if the organism is sensitive to the antibiotics, you get a zone of clearance around the antibiotic disc. But if the organism is resistant, then the organisms grow up towards the antibiotic disc. So, it’s a method that is cheap and relatively straightforward, but can take 24 to 48 hours to give us a result. What can genomics offer over these traditional laboratory methods?
So, in addition to giving us antibiotics susceptibility data, one of the advantages is that the rapid methods can do this much more quickly. So, within a few hours, rather than within 24 to 48 hours. In addition to the antibiotic susceptibility or resistance data, it can give us organism identity, and information about virulence factors, such as toxin genes. So, are you using these genomic methods routinely at Addenbrooke’s Hospital? We’re not quite. This is something that we’ve been trying to do for a little while. And we’re in the process. We’ve done a number of proof-of-concept studies. But at the moment, we’re not able to do this in real time.
However, there is a project that’s about start at Addenbrooke’s in the new year, which will aim to do this in real time. And obviously, within Public Health England, it’s being done for organisms such as tuberculosis. So it’s not quite in everyday clinical practise, but it’s on its way. So what are the challenges associated with using these methods routinely in a health care setting? OK, so, there are a number of challenges. First of all, not every diagnostic microbiology laboratory has sequencing machine, because they’re quite expensive. Secondly, people need to be trained to use them. Thirdly, we need to have expertise to analyse the genome sequence data and report it back to clinical, and people. So, there are a number of challenges.
First of all, cost, secondly, expertise, and thirdly, availability. And things are being changed at the moment. So, bioinformatic pipelines are being developed that will become more automated, and will enable us to use this in clinical practice. And is it expensive? To buy a machine is, I think, about £80,000. So it’s too expensive for most laboratories to afford them by themselves. The costs of the actual tests, I think you can sequence a bacterial genome for between £50 and £100, depending on economies of scale. Thank you very much, Estee. My pleasure, Josie.

Dr Estee Torok is conducting pioneering research into using whole-genome sequencing in real-time so that AMR can be tracked and the results used to inform treatment. Watch the interview to learn how she does it, and her predictions on how these tools will be used in the future.

Estee explains that microbial genomics techniques could improve routine healthcare in the NHS in England. She also highlights three challenges – what are these? In the comments area, share what you think these three challenges are.

Suggest ways that these challenges can be met in the UK and in your own context?

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Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

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