14 August 2019

National genomics project needed to track resistant bugs

Genetics Research

Australia should lift its game on antimicrobial resistance by establishing a national pathogen genomics program like those in the US and UK – but GPs and pathology laboratories also have a role to play.

Writing in the Medical Journal of Australia, Deborah Williamson and colleagues from Melbourne University’s Doherty Institute and the University of Queensland, say the insights provided by genomic analysis are crucial to understanding the origins and movement of resistant pathogens, given our increasing global interconnectedness. Factors such as population growth, geopolitical instability, climate change and food insecurity have also contributed to the problem.

“With pathogen genomics, instead of just looking at tiny little bit of the bacterial or viral genome, we can look at every single nucleotide within them,” Professor Williamson told TMR.

“This gives us an unprecedented level of resolution and remarkable insights into how related different bacteria or viruses are to each other, and about transmission of resistant pathogens between hospitals and across sectors – not just humans, but animals and the environment.

“It also allows us to characterise resistance genes and the bits of DNA that they travel on with a far greater degree of clarity.

“A number of laboratories in Australia are doing this, but what hasn’t happened is joining the dots between states and harnessing the technology at a national level.”

The paper gives four examples of bugs whose provenance has been tracked through genomics: carbapenemase-producing Enterobacteriales and Candida auris in hospital settings, and community-acquired ceftriaxone-resistant Neisseria gonorrhoeae and extensively drug-resistant Salmonella enterica serotype Typhi from Pakistan.

Professor Williamson said pathogen genomics had been able to show that antibiotic resistance genes tended not to be embedded in a microbe’s chromosomes but in plasmids, and that in the absence of the selective pressure created by antibiotics they disappear, since they impose a metabolic cost on the organism.

In the case of gonorrhoea – whose notifications in Australia doubled between 2014 and last year – Professor Williamson said genomics had allowed researchers to track transmission across different populations and how the resistance genes were spreading.

GPs are involved in antimicrobial resistance monitoring at the level of statutory notifications, Professor Williamson said, but could also help by taking more bacterial samples for culturing.

“Often, particularly for STIs, the test is taken and sent to the lab and the patient gets a yes/no result. But you don’t find out if it’s a resistant infection because the sample for bacterial culture simply wasn’t taken in the first place. That’s something that definitely could be improved through primary care.

“Another thing that GPs may be seeing more of is multi-resistant Shigella, which is really an emerging public health problem. The laboratory may only do a PCR test to see whether the pathogen is present or not. And from a GP’s perspective, that’s not helpful because they’ve got no way of guiding their antibiotic treatment.”

States have their own projects, such as NSW Health’s Public Health Genomics Partnership.

But one of the pillars of the expiring National Antimicrobial Resistance Strategy is nationally coordinated One Health surveillance of resistance, and this is impeded by the lack of a national mechanism for rapid sharing and analysis of resistance-related genomic and epidemiological data across jurisdictions, the paper says.

“There’s a lot of good will among different laboratories, but it requires central coordination and resourcing by the Department of Health,” Professor Williamson said.

MJA, 5 August