Antimicrobial resistant organisms in imported foods: exploring an under-appreciated source of resistance in the food supply

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Antibiotics are arguably the most important medical advance of the 20th century. Before the introduction of penicillin in the early 1940's, physicians and veterinarians were largely powerless to stop infections. Unfortunately, the extraordinary ability of bacteria to adapt led to the emergence of antibiotic resistance, and untreatable infections are increasingly encountered. The use of antibiotics in agriculture is recognized as one of the contributing drivers of antimicrobial resistance; surveillance programs targeting food animals and retail meats have therefore been implemented. In Canada, the Public Health Agency conducts resistance surveillance focusing on domestically produced beef, pork and poultry targeting potential pathogens such as Salmonella or E. coli. While this strategy is very effective within its mandate, it fails to recognize the presence of resistance in other agricultural species, imported foods or non-pathogens. The ability of bacteria to acquire DNA from other bacteria or the environment is remarkable, resistance conferring genes harboured by any organism (the community resistome) are therefore potentially available to other bacteria. The importance of the resistome is apparent when we consider the mobilization of resistance genes from non-pathogenic, environmental organisms into pathogens as has been seen in the case of the CTX-M -lactamases and qnr type fluoroquinolone resistance genes. There is a profound research and publication bias towards pathogens; consequently vast swaths of the resistome have been largely overlooked. The missed opportunity to detect novel resistance genes, or progenitors to recognized genes and therefore improve our understanding of the biology of resistance is a corollary of this bias. We hypothesize that antimicrobial resistant, non-pathogenic bacteria, including those possessing novel resistance genes will be found in food associated microbial communities. In pilot studies we have identified multi-drug resistant bacteria (both pathogenic and non-pathogenic) not possessing recognized resistance genes which would explain their phenotypes. In the proposed research program we will expand upon this work, screening additional food products to identify antimicrobial resistant organisms to our isolate collection, and identifying the genetic basis of resistance using whole genome sequencing. The innovative approaches proposed to interrogate the resistome, will contribute to a transformation of our understanding of the biology of resistance including the role of non-pathogens and novel resistance genes. Our results will be directly applicable by the Public Health Agency of Canada and other domestic and international regulatory agencies in improving their resistance surveillance programs.