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

复杂微生物群落中细胞内和细胞间移动遗传元件的宿主分布

• 批准号: RGPIN-2022-03455
• 负责人: Ricker, Nicole
• 金额: $ 2.26万
• 依托单位: University of Guelph
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=761928
• 关键词: Host; distribution; intra; inter; cellular

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.

细菌中抗菌素耐药性（AMR）的日益普遍是一场全球性的健康危机。动物微生物群是AMR基因水平基因转移（HGT）的公认热点，因为它包括敏感和抗微生物药物耐药的肠道细菌以及各种潜在的致病物种。了解动物微生物群中移动的AMR决定因素的演变和持续性对于在一个健康框架中解决AMR的传播，为有效缓解AMR出现的政策提供信息，以及评估减少抗生素使用将如何影响选择被删除后已建立的移动的AMR决定因素的持续性至关重要。尽管非治疗性抗菌剂在农业中的使用受到限制，但AMR仍将是一个令人担忧的问题，因为几十年来已经建立了高水平的耐药性，为了确保生产动物的健康和人道待遇，抗生素的治疗性使用仍将是必要的。 病原菌中AMR基因的出现是通过两种不同的移动机制发生的-细菌细胞内基因组位置之间的移动和两种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的遗传元件（MGE）相关联，该元件可以促进移动到原始细菌基因组内的不同位点。通过这些移动，抗性基因可以被移动到更大的细胞间MGE中，例如质粒，其可以促进转移到新的细菌宿主。这些事件通常起源于肠道或环境细菌，暴露于抗菌剂会促使选择携带AMR基因的菌株。持续的选择压力导致传播到不同的类群，并有利于出现更成功的MGE-AMR组合，如多药耐药质粒的流行率增加所证明的。我的研究项目旨在确定复杂微生物群落中细胞内和细胞间MGE的宿主分布，并确定MGE传播的途径，以帮助预测AMR的出现。我将使用培养物富集宏基因组学和邻近连接测序来检查MGE的分布，由于已知AMR的流行和与猪肉行业的相关性，重点关注猪肠群落。我还将为宏基因组数据开发一个统一的MGE本体和分类管道，并开发用于测试尚未通过实验表征的新型MGE的移动性的方法。我将使用这些方法来识别和分类猪肠道中的MGE，并随后测量这些MGE的丰度和传播的变化，以响应抗菌剂的使用。这项研究采用社区方法来了解猪微生物群中的HGT以及农业系统中抗生素选择下发生的进化变化。