Antibiotic resistance genes in the meat industry

Genomics can track antibiotic resistance during beef production
23 March 2016

Interview with 

Noelle Noyes, Colorado State University




Antibiotic resistance has been highlighted as a major medical risk facing the global population. And as bugs become increasingly difficult to treat, antimicrobial drug pipelines are ironically almost empty. One source of drug resistance might be the meat industry where antibiotics are administered to animals to keep them healthy and to encourage them to grow rapidly. But what risk does this pose? Colorado State University's Noelle Noyes has been following the food chain, as she explained to Chris Smith...

Noelle - The meat that we eat could potentially harbour different organisms or different antimicrobial resistance genes that we could ingest and then could make us ill. But other way that this can happen is the fact that we’re all connected environmentally in some way or another, and to some degree or another. So, these animal production facilities are part of our environment and things that happen in these different animal production facilities can be dispersed into the environment through different pathways.

Chris - How then were you trying to find out what the likely traffic is for these antibiotic resistant elements between the agricultural setting and the human world?

Noelle - The thing that we would love to do, the ideal study would be to take a group of animals and to track them throughout their entire lives, all the way from the time they're born on a farm until they reach your dinner plate. That’s incredibly difficult to do given the livestock production system. So in this study, we tracked pens of cattle from the time they enter the feedlot through the time they exit at the feedlot then their transport through the slaughterhouse. And then we actually followed the animals into the slaughterhouse and then the carcass was disassembled and we actually sampled the final product right before it was packaged for distribution into the retail chain.

Chris - What source of specimens were you collecting at each stage and how did you analyse those specimens?

Noelle - We collected faecal samples from the pen floor, soil from the pen floor, and then we collected drinking water samples. When they were unloaded at the slaughterhouse, we went into the trucks and we swabbed the inside walls of the truck. The cattle then go through the slaughter process and at the end of that, we swabbed the conveyor belt.

Chris - How did you analyse these things? were you trying to culture microorganisms? Were you using genetic techniques to look what was in there?

Noelle - We don’t use culture and we don’t use PCR. We basically extract all of the DNA that are in all those samples that I just described and we fragment that DNA into small pieces and then we sequence it.

Chris - And you can then match that up with a database so you know what bugs are there and potentially, what antibiotics they have the ability to fend off.

Noelle - Yes. So we take those short fragments of DNA and we basically just try to match the pattern to known resistance gene DNA sequences that are available publicly.

Chris - What did this reveal to you when you did it? What did you find?

Noelle - The first finding that surprised us initially was that when we took those samples at the very end of that production system and we did this method, we actually didn’t identify any resistance genes. So that was a surprising finding. And then the other finding was what was happening during the feedlot period. So that’s when antibiotics tend to be used more frequently in cattle production. During that time, we found a decrease in the diversity of the different resistance genes. The genes that tended to persist during the feeding period were resistance genes to antibiotics that were used in the cattle so that made sense to us.

Chris - That reflects a sort of selection within the animals for bugs that are endowed with that resistance so they can enrich in those animals because you're giving those animals those antibiotics.

Noelle - Yes. So, that’s the theory. Of course, a lot more work needs to be done to figure out if that is really what's happening. But the hypothesis at this point is that the antibiotics that were being used were creating a selection pressure that through natural selection favoured the bacteria that were able to defend against those antibiotics. And so, we saw those resistance genes persisting in the bacterial population throughout the feeding period.

Chris - Late in 2015, there was a study. It was published in one of the Lancet journals showing that in China, there was a significant co-occurrence of resistance against one class of antibiotic. This was colistin where large amounts of it were being used and it was cropping in the meat but also patients in hospitals. So how does that discovery sit alongside your work?

Noelle - Yeah. It speaks to the same point which we talk about in the paper which is that we really need to perhaps not shift focus but maybe expand focus to looking at these potential environmental routes of transfer. So, we have very robust systems right now, surveillance and monitoring systems, as well as food safety systems that sort of deal with that food chain transmission route. But we have much less clarity around the environmental exposure route. And so, I think that that paper that you just described as well as our work suggests that perhaps we should expand our focus to include some of these potential environmental pathways.


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