With funding from the Government of Canada's Genomics Research and Development Initiative (GRDI) researchers at the Canadian Food Inspection Agency (CFIA) are working to understand whether bacteria in the foods we eat—even the harmless bacteria—may play a role in the transmission of antimicrobial resistance (AMR) to humans.
"Could AMR genes in the harmless bacteria we consume be contributing to the development of AMR in dangerous bacteria? We just don't know yet—but genomics technologies give us the tools we need to answer those kinds of questions."
The CFIA investigators, led by research scientist Dr. Catherine Carrillo, are funded as part of the larger GRDI‑AMR research project. The 5‑year project, launched in 2016, involves scientists from 5 federal departments and agencies collaborating on a series of closely linked projects aimed at understanding how antibiotics used in food production may be contributing to an increase in AMR in people.
Adding the genomics advantage
At the CFIA, Dr. Carrillo says GRDI funding has given the Agency the capacity to include the detection of genes associated with AMR in its genomic analysis of priority pathogens found in food, such as disease‑causing types of E. coli and Salmonella. "This is really a value‑added proposition," says Dr. Carrillo. "In the past, we've used lab testing to see whether a pathogenic bacteria had any kind antibiotic resistance, but those tests were fairly limited in the amount of information they provided. Now, with whole genome sequencing, we can see exactly which genes are responsible for the AMR we may find in a particular sample of bacteria."
By comparing those findings with the AMR genes found in bacteria that collaborators in other departments are collecting from cattle, poultry and pork operations, the environment and from sick people in hospitals, researchers can begin to see how AMR circulates—and start to look at ways to reduce the risk.
Do "harmless" bacteria pose a risk?
A key part of Dr. Carrillo's research, in collaboration with researchers at Health Canada, involves studying whether the harmless bacteria found in foods may play a role in transmitting AMR to humans.
"Bacteria considered harmless can also have AMR, and the genes that provide resistance move easily from one species of bacteria to another," explains Dr. Carrillo. "Could AMR genes in the harmless bacteria we consume be contributing to the development of AMR in dangerous bacteria? We just don't know yet—but genomics technologies give us the tools we need to answer those kinds of questions."
Dr. Carrillo points out that harmless bacteria can pose a risk in other ways. "Should one of these bacteria escape from our digestive system and, for example, enter the bloodstream, the urinary tract, or be transmitted to someone with a compromised immune system, it could be very harmful—causing an infection that must be treated with antibiotics or other antimicrobials. If that so‑called harmless bacteria happens to be AMR, treating it successfully can be very difficult."
Collaboration helps to accelerate progress
"The development of new genomics tools and techniques is just one example…through the GRDI, we're able to share information about new tools in the development stage, so the customization that allows it to meet the needs of multiple departments can be built in from the beginning."
Thanks to the cross‑government collaboration enabled by the GRDI, our understanding of how AMR may be circulating through food production, the environment and humans is growing rapidly.
"It's hard to put a value on the importance of collaboration among departments in this project. Sharing information is a huge part of that, of course, but there's much more to it," says Dr. Carrillo. "The development of new genomics tools and techniques is just one example. In the past, someone in another department might develop a new research tool that we could use, but since it was designed for a particular purpose in that other department, we would have to spend time and money adapting it to our needs. Now, through the GRDI, we're able to share information about new tools in the development stage, so the customization that allows it to meet the needs of multiple departments can be built in from the beginning."
Informing evidence-based policy
As a major part of the Federal Action Plan on Antimicrobial Resistance and Use in Canada, the findings of the research led by Dr. Carrillo and others engaged in the GRDI‑AMR project will play a key role in determining the next steps in addressing AMR. "This is what our research at the CFIA and the entire GRDI‑AMR project is about," says Dr. Carrillo. "It's not up to us as researchers to decide Canada's response to AMR—but it is our job to make sure the people who make those decisions are basing them on the very best science we can provide.