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

抗生素可以说是20世纪最重要的医学进步。在20世纪40年代初S引入青霉素之前，医生和兽医在很大程度上无力阻止感染。不幸的是，细菌非凡的适应能力导致了抗生素耐药性的出现，无法治愈的感染越来越多地出现。 在农业中使用抗生素被认为是造成抗菌素耐药性的原因之一；因此已经实施了针对食用动物和零售肉类的监测方案。在加拿大，公共卫生局进行耐药性监测，重点是国内生产的牛肉、猪肉和家禽，目标是潜在的病原体，如沙门氏菌或大肠杆菌。虽然这一战略在其任务范围内非常有效，但它没有认识到其他农业物种、进口食品或非病原体中存在抗药性。细菌从其他细菌或环境中获得DNA的能力是显著的，因此任何有机体(群落抵抗体)所蕴含的抗药性基因可能对其他细菌可用。当我们考虑将非致病性环境生物的耐药基因动员到病原体中时，耐药组的重要性是显而易见的，就像CTX-Mü-内酰胺酶和qnr型氟喹诺酮耐药基因的情况一样。 对病原体存在着深刻的研究和出版偏见；因此，大片的耐药组在很大程度上被忽视了。错过了发现新的抗性基因或已识别基因的祖先并因此提高我们对抗性生物学的理解的机会是这种偏见的必然结果。我们假设，在与食品相关的微生物群落中将发现具有抗菌素耐药性的非致病细菌，包括那些拥有新的耐药性基因的细菌。 在初步研究中，我们发现了多重耐药细菌(包括致病和非致病)，它们不具有公认的耐药基因，这可以解释它们的表型。在拟议的研究计划中，我们将扩展这项工作，筛选更多的食品，以识别我们分离的抗菌素耐药生物体，并使用全基因组测序确定抗药性的遗传基础。提出的询问耐药组的创新方法，将有助于转变我们对抗性生物学的理解，包括非病原体的作用和新的抗性基因。我们的结果将直接应用于加拿大公共卫生局和其他国内和国际监管机构，以改进他们的耐药性监测计划。

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 ß-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.