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布了一份联合文件，称抗菌素耐药性（AMR）是一种全球流行病。细菌可以携带一种遗传物质，称为移动的遗传元件，它可以水平转移到其他细菌。移动的遗传元件运输基因，并且这些基因中的一些可能使细菌对抗微生物剂具有抗性。全基因组测序可用于评价细菌的遗传相关性、其移动的遗传元件和其抗微生物剂抗性基因。细菌分离株和它们的移动的遗传因子的相关性，再加上它们的地理分布和取样来源的信息，提供了关于移动的遗传因子传播的见解。这也提供了关于随着时间的推移，细菌群落中AMR细菌的维持的信息。 这项研究的目的是： 1)应用全基因组测序和生物信息学，更好地了解从许多来源分离的指示细菌（大肠杆菌）的遗传相关性，这些来源包括家禽谷仓、零售禽肉（当地采购）、井水（来自同一农场）、地表水（来自同一流域）和废水（同一流域上游）; 2)应用长读段测序以更好地表征抗性分离物的移动的遗传元件中的抗性遗传基础; 3)评价和比较E.从肠道和环境来源的大肠杆菌作为耐药性传播宿主的能力;和 4)描述各种来源的耐药决定因素的模式和频率，并评估遗传结果与潜在耐药决定因素和/或风险因素之间的关联。这些信息还将用于模拟AMR遗传决定因素在家禽生产链中的传播，沿着。 本研究将进一步加深对E.大肠杆菌、它们的移动的遗传分离物和它们的抗性基因，分离自不同来源。 我们也将更好地了解之间的相似性和差异性的水源和家禽来源的E。大肠杆菌分离株，有助于阐明水源细菌在人类、动物和其他来源之间传播移动的遗传因子方面的作用。 移动的元件之间的密切相关性可能表明细菌之间移动的遗传元件和编码AMR的基因的传递。使用全基因组测序的监测可以快速发现高耐药菌株的出现和传播，从而可以迅速启动控制和预防策略。总体而言，这项研究将提供可用于完善监测系统的信息，并为侧重于人类、动物和/或环境战略的缓解和生物安保计划提供信息。

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.