Host distribution of intra- and inter-cellular mobile genetic elements in complex microbial communities

细菌中抗菌素耐药性(AMR)的日益流行是一个全球性的健康危机。动物微生物区系是AMR基因水平基因转移(HGT)的一个公认热点，因为它既包括敏感的和耐药的共生菌，也包括各种潜在的致病物种。了解动物微生物区系中移动AMR决定因素的演变和持久性，对于解决AMR在One Health框架中的传播问题，为有效缓解AMR出现的政策提供信息，以及评估减少抗菌剂使用将如何影响取消选择后已建立的移动AMR决定因素的持久性，是当务之急。尽管非治疗性抗菌剂在农业中的使用受到限制，但AMR仍将是一个令人关切的问题，因为几十年来已经建立了高水平的抗药性，而且将继续有必要治疗性使用抗生素，以确保生产动物的健康和人道待遇。AMR基因在病原菌中的出现有两种不同的移动机制--细菌细胞内基因组位置之间的移动和两个不同细菌之间的转移。通常，以前未知的AMR基因首先与细胞内移动遗传元件(MGE)相关，该元件可以促进移动到原始细菌基因组中的不同位置。通过这些运动，抗性基因可以被动员到更大的细胞间MGE中，例如质粒，这可以促进转移到新的细菌宿主。这些事件通常起源于共生或环境细菌，接触抗菌剂会促使选择含有AMR基因的菌株。持续的选择压力导致扩散到不同的分类群，并有利于出现更成功的MGE-AMR组合，多药耐药质粒的日益流行证明了这一点。我的研究计划旨在确定复杂微生物群落中细胞内和细胞间MGES的宿主分布，并确定MGE的传播途径，以帮助预测AMR的出现。我将使用培养丰富的元基因组学和邻近连接测序来检查MGES的分布，由于AMR的已知流行和与猪肉行业的相关性，我将重点研究猪的肠道群落。我还将为元基因组数据开发一个统一的MGE本体和分类管道，并开发测试尚未实验表征的新型MGES的流动性的方法。我将使用这些方法来鉴定和分类猪肠道中的MGES，并随后测量这些MGES在使用抗菌剂时丰度和扩散的变化。这项研究采用社区的方法来了解猪的微生物区系中的HGT以及在农业系统中抗生素选择下发生的进化变化。

The increasing prevalence of antimicrobial resistance (AMR) in bacteria is a global health crisis. The animal microbiota is a recognized hot spot of horizontal gene transfer (HGT) of AMR genes as it includes both susceptible and antimicrobial resistant commensal bacteria as well as diverse potentially pathogenic species. Understanding the evolution and persistence of mobile AMR determinants within the animal microbiota is imperative to address the dissemination of AMR in a One Health framework, inform policies to effectively mitigate AMR emergence, and evaluate how reducing antimicrobial use will impact persistence of established mobile AMR determinants after selection is removed. Although the use of non-therapeutic antimicrobials has been restricted in agriculture, AMR will continue to be a concern since high levels of resistance have been established over several decades, and therapeutic use of antibiotics will continue to be necessary in order to ensure the health and humane treatment of production animals. Emergence of AMR genes in pathogenic bacteria occurs by two different mechanisms of mobility - movement between genomic locations within a bacterial cell and transfer between two different bacteria. Typically, a previously unknown AMR gene first becomes associated with an intra-cellular mobile genetic element (MGE) that can facilitate movement to different sites within the original bacterial genome. Through these movements, the resistance gene can get mobilized into a larger inter-cellular MGE, such as a plasmid, which can facilitate transfer to a new bacterial host. These events commonly originate in commensal or environmental bacteria and exposure to antimicrobials drives the selection of strains harboring the AMR gene. Continued selection pressure results in dissemination to diverse taxa and favors the emergence of more successful MGE-AMR combinations as evidenced by the increasing prevalence of multi-drug resistant plasmids. My research program aims to identify the host distribution of both intra-cellular and inter-cellular MGEs in complex microbial communities and identify pathways of MGE dissemination that can help predict AMR emergence. I will use culture-enriched metagenomics and proximity ligation sequencing to examine the distribution of MGEs, focusing on swine gut communities due to the known prevalence of AMR and relevance to the pork industry. I will also develop a unified MGE ontology and classification pipeline for metagenomic data and develop methods for testing the mobility of novel MGEs that have yet to be experimentally characterized. I will use these methods to identify and classify MGEs in the swine gut and subsequently to measure changes in the abundance and dissemination of these MGEs in response to antimicrobial use. This research takes a community approach to understanding HGT within the swine microbiota and the evolutionary changes that occur under antibiotic selection in agricultural systems.