"Antibiotic use is common in beef and dairy production, as well as in the poultry and swine industries, and that inevitably leads to bacteria that develop AMR…these bacteria with genes that provide AMR are shed in the manure of these animals. What we want to know is whether these AMR bacteria pose any risk to humans when that manure is used as fertilizer."
Research funded by the Government of Canada's Genomics Research and Development Initiative (GRDI) has revealed that while antimicrobial resistance—AMR—may be transmitted to humans by food crops grown in fields fertilized with manure, technologies already available can reduce the risk.
As part of the 5‑year GRDI‑AMR project—a unique collaboration among scientists from 5 federal departments and agencies working on interlocking AMR‑related research projects—Dr. Ed Topp of Agriculture and Agri‑Food Canada is leading an investigation into AMR in agroecosystems.
Low tech meets high tech
"Antibiotic use is common in beef and dairy production, as well as in the poultry and swine industries, and that inevitably leads to bacteria that develop AMR—and we know that these bacteria with genes that provide AMR are shed in the manure of these animals," says Dr. Topp. "What we want to know is whether these AMR bacteria pose any risk to humans when that manure is used as fertilizer. To do that, we fertilize a field with manure, and plant a crop such as vegetables—that's the low‑tech part. After we harvest the vegetables, we do the high‑tech part—using the genomics technology we've acquired with GRDI funding to analyse the plants to see if any of the AMR bacteria present in the manure ends up on the vegetables."
Dr. Topp says the research to date shows that this is exactly what is happening: using manure from animals treated with antibiotics as fertilizer increases the risk that AMR bacteria that may be in the manure will find their way onto vegetables grown in the soil. This, in turn, indicates that the bacteria—and the AMR genes they carry—can be transmitted to humans through the consumption of uncooked or unwashed vegetables.
Reducing the risk
"…composting manure before applying it as fertilizer significantly reduces the bacteria, including AMR bacteria, in the manure," says Dr. Topp. "Therefore there's a lower chance that bacteria will end up on the food crop, and a smaller risk that the AMR will be transmitted to humans."
Fortunately, the research being carried on by Dr. Topp and his 10‑member team suggests that reducing the risk of AMR being transmitted to humans in this way may be relatively simple, and may even provide additional economic and environmental benefits.
"We've been working exclusively with manure from dairy cattle, but it appears that composting manure before applying it as fertilizer significantly reduces the bacteria, including AMR bacteria, in the manure," says Dr. Topp. "Therefore there's a lower chance that bacteria will end up on the food crop, and a smaller risk that the AMR will be transmitted to humans."
Potential for additional benefits
"We wanted to look at ways to reduce the risk of AMR transmission from manure to humans that could be implemented fairly quickly and at relatively low cost."
Dr. Topp's team has also been examining the potential of anaerobic digestion to reduce or even eliminate AMR bacteria from manure to be used as fertilizer. "This involves sealing the manure in a large, airtight container, pumping out the oxygen and letting the manure ferment," says Dr. Topp. "Of course, in addition to the possibility that this treatment may reduce AMR bacteria, it also produces hydrogen and methane—clean fuels that benefit our environment, and at the same time offer the possibility of a new income stream for producers."
As a further benefit, Dr. Topp notes that both methods are already commercially available, pointing out that including them in the research was a strategic decision. "We wanted to look at ways to reduce the risk of AMR transmission from manure to humans that could be implemented fairly quickly and at relatively low cost," explains Dr. Topp. "Composting manure is pretty straightforward, and doesn't necessarily have to involve a large investment. An anaerobic digestion system does involve a larger up‑front cost, but it is a fairly simple system once it's up‑and‑running—and again, it does come with other benefits."
International impact
Halfway through the GRDI‑AMR project, the work being done by Dr. Topp and his team, along with that of other researchers involved in the overall project, is already attracting attention beyond Canada. Among others, the United Nations Food and Agriculture Organization—the FAO—has asked GRDI‑AMR researchers about what they are finding in terms of reducing the risk of AMR transmission from food production to humans for inclusion in its Codex Alimentarius—the FAO's international guidebook for producing food safely.