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

世界卫生组织、世界贸易组织和世界知识产权组织发表了一份联合文件，称抗菌素耐药性（AMR）是一种全球流行病。细菌可以携带一种被称为移动遗传元素的遗传物质，它可以水平转移到其他细菌身上。可移动的遗传元件运输基因，其中一些基因可能使细菌对抗菌素具有耐药性。全基因组测序可用于评价细菌的遗传亲缘关系、细菌的移动遗传元件和细菌的耐药基因。细菌分离物及其移动遗传元件的相关性，以及它们的地理分布和采样来源信息，提供了有关移动遗传元件传播的见解。这也提供了关于细菌群落中具有AMR的细菌随时间的维持的信息。本研究的目标是：1)应用全基因组测序和生物信息学来更好地了解从众多来源分离的指示细菌（大肠杆菌）的遗传相关性，包括家禽饲养场、零售禽肉（来自当地）、井水（来自同一农场）、地表水（来自同一流域）和废水（来自同一流域上游）；2)利用长读测序技术更好地表征耐药菌株移动遗传元件的耐药遗传基础；3)评估和比较肠道和环境来源的大肠杆菌作为耐药性传播宿主的能力；4)描述各种来源的抗性决定因素的模式和频率，并评估遗传结果与潜在抗性决定因素和/或风险因素之间的关联。这一信息还将用于模拟抗菌素耐药性遗传决定因素在家禽生产链中的传播。本研究将提高我们对不同来源的大肠杆菌、它们的移动遗传分离株和它们的抗性基因的遗传亲缘关系的认识。我们还将更好地了解水源和家禽来源的大肠杆菌分离株之间的异同，有助于阐明水源细菌在人类、动物和其他来源之间传播可移动遗传元素的作用。移动元件之间的密切关系可能表明细菌之间的移动遗传元件和AMR编码基因的传播。利用全基因组测序进行监测可以迅速发现高耐药菌株的出现和传播，从而迅速启动控制和预防战略。总的来说，这项研究将提供可用于完善监测系统的信息，并为缓解和生物安全计划提供信息，以关注人类、动物和/或环境战略。

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.