Molecular epidemiology of antimicrobial resistance in poultry, poultry products, and the environment.

点击翻译按钮获取中文摘要

The World Health Organization, World Trade Organization and World Intellectual Property Organization released a joint paper calling antimicrobial resistance (AMR) a global epidemic. Bacteria can carry a type of genetic material, called a mobile genetic element, which can transfer horizontally to other bacteria. Mobile genetic elements transport genes, and some of these genes may make the bacteria resistant to antimicrobial agents. Whole genome sequencing can be used to evaluate genetic relatedness of bacteria, their mobile genetic elements and their antimicrobial resistance genes. The relatedness of bacterial isolates and their mobile genetic elements, paired with information about their geographical distribution and sampling sources, provides insight concerning transmission of mobile genetic elements. This also provides information about the maintenance, over time, of bacteria with AMR, within bacterial communities. The objectives of this research are to: 1) apply whole genome sequencing and bioinformatics to better understand genetic relatedness of indicator bacteria (Escherichia coli) that were isolated from numerous sources, including poultry barns, retail poultry meats (sourced locally), well water (from the same farms), surface water (from the same watershed) and wastewater (upstream in the same watershed); 2) apply long read sequencing to better characterize the genetic basis of resistance in mobile genetic elements of resistant isolates; 3) assess and compare E. coli from enteric and environmental sources with respect to their ability to act as reservoirs in resistance transmission; and 4) describe the patterns and frequency of resistance determinants across the sources, and assess associations between genetic outcomes and potential resistance determinants and/or risk factors. This information will also be used to model transmission of  genetic determinants of AMR along the poultry production chain. This research will improve our understanding of the genetic relatedness of E. coli, their mobile genetic isolates, and their resistant genes, isolated from different sources. We will also better understand the similarities and differences between water-sourced and poultry-sourced E. coli isolates, helping shed light on the role of water-sourced bacteria in transmission of mobile genetic elements between humans, animals and other sources.  Close relatedness between mobile elements may suggest transmission of mobile genetic elements and genes coding for AMR between bacteria. Surveillance using whole genome sequencing could rapidly detect emergence and dissemination of highly resistant bacterial strains so control and prevention strategies could be rapidly initiated. Overall, this research will provide information which can be used to refine surveillance systems and inform mitigation and biosecurity plans to focus on humans, animals and/or the environment strategies.