December 15, 2022

 

Scientists explore livestock systems' role in antimicrobial resistant bacteria that may affect human health

 

 

Scientists from the International Livestock Research Institute (ILRI), the University of Liverpool, the University of Edinburgh and elsewhere have traced how livestock systems act as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise people.

 

This study sheds light on the factors influencing AMR at the intersection of multiple species and the One-Health sector. The study, undertaken in Nairobi, Kenya, recently appeared in BMC Medicine, and helps detail how to avoid and manage the development of drug resistance in bacteria.

 

Alexander Fleming, who discovered the world's first antibiotic, penicillin, warned that misusing antibiotics could lead to AMR. He showed that bacteria, viruses, fungi and parasites evolve when exposed to antibiotic drugs and eventually no longer respond to those medicines. As a result of drug resistance, antibiotics and other antimicrobial medicines become ineffective and infections become increasingly difficult or impossible to treat.

 

One path by which AMR is hypothesised to develop is through the large amount of antibiotics used in the livestock industry, where bacteria develop resistance and then spread to people. Quantifiable information addressing this has thus far been insufficient. Today's study used genomics, epidemiology and ecology to look into the patterns of AMR gene carriage in an exemplar organism, E. coli.

 

As part of a controlled epidemiological assessment of 99 households in Nairobi, scientists sequenced the whole genomes of bacteria isolated from 311 human, 606 cattle and 399 wildlife excrement samples. Using statistical models, they looked at the prevalence of AMR carriage and described the diversity and structure of the AMR genes in distinct host populations around the city. They also investigated conditions that could lead to the spread of AMR genes from humans to sympatric animals at the household level.

 

In animal and human isolates, the team found 13-point mutations and 56 acquired genes that are known to confer resistance to nine different antibiotic classes. They discovered that the makeup of the AMR gene community is not related to the host species, but that AMR genes were frequently co-located, possibly on plasmids, suggesting that multi-drug resistance could be acquired and spread in a single step. The risk for AMR transmission across human-livestock interfaces is greatest when manure is improperly disposed of, and in larger households.

 

Two policy implications flow from the study. The first is to highlight the importance of ecosystem-wide surveillance of AMR.

 

"Doctors should not just be thinking about the rise of AMR in humans, but in livestock and the broader environment, because what we're seeing is that wildlife collect and move around with what they acquire from the environment," said Dishon Muloi, the study’s lead scientist and research fellow at ILRI and former PhD student at the University of Edinburgh.

 

The study's findings of widespread carriage of clinically relevant AMR mechanisms in human and animal populations, especially in wildlife that move long-distances, underline the importance of evidence-based surveillance to combat antimicrobial resistance on a worldwide scale.

 

"This study shows how easily antimicrobial resistance genes move between humans and livestock in a crowded urban environment, underlining that if we are to beat the resistance problem we will need a coordinated response across the medical and veterinary sectors," said Mark Woolhouse, professor and chair of infectious disease epidemiology at the University of Edinburgh.

 

The second policy implication is the issue of manure disposal, which may seem mundane, but is essential.

 

"If you drive around Nairobi, you see heaps of manure by the road," said Muloi. "We haven't traditionally thought of manure as a problem and even if we look at our policies, which are similar to those in many other countries, manure is not seen as a risk. But it's clear we need to do a much better job of cleaning up the environment, for the sake of good public health."

 

The study is part of an overall project called the Urban Zoo, or more formally known as the "Epidemiology, ecology and socio-economics of disease emergence in Nairobi." It is funded by the Medical Research Council (UK)-coordinated programme on the Environmental and Social Ecology of Human Infectious Diseases.

 

The objective of the study — according to study lead Eric Fèvre, professor of veterinary infectious diseases at the Institute of Infection, Veterinary and Ecological Sciences (University of Liverpool) and jointly appointed principal scientist at ILRI — is to understand the mechanisms leading to the introduction and spread of pathogens into urban populations.

 

"Here, we see that we need to take a holistic approach, which includes humans, animals, their waste and the shared environment," said Fèvre.

 

- International Livestock Research Institute