摘要
抗生素耐药性是一个与人类健康相关的问题，需要全面的方法来深入了解人类细菌病原体中获取，稳定和耐药性传播过程。由于自然（非临床）生态系统是抗性基因的储存库，抗生素抗性流行病学的健康综合研究需要对这些生态系统进行探索，以确定它们在抗生素耐药性的选择，进化和传播中可能发挥的作用基因，涉及所谓的抵抗mobilome。高通量测序技术为描述给定微生物群的遗传组成提供了前所未有的机会，而无需对存在于内部的有机体进行继代培养。然而，用于分析这些大量数据的生物信息学方法，主要是关于将每个抗性基因与寄存它的生物体区分开的方法，仍处于初期阶段。在这里，我们讨论目前的基因组方法如何可以用来分析抗性mobilome及其与不同的细菌基因组和宏基因组的联系。此外，我们描述了目前用于分析电阻移动芯片的方法的缺陷，主要是在复杂微生物的情况下，并讨论实施新工具以改进我们目前的宏基因组工具箱的可能性。

Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health‐integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so‐called resistance mobilome. High‐throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox.

https://nyaspubs.onlinelibrary.wiley.com/doi/full/10.1111/nyas.13282