Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.

抗菌素耐药性是一个主要的全球性公共卫生问题，当病原体主要通过普通微生物和病原微生物之间的基因重组而获得抗菌素耐药基因（ARG）时，就会出现这种情况。电阻组是所有ARG的集合。在微生物中，获取ARG的主要方法是水平基因转移（HGT）。因此，了解和鉴定HGT可以提供对抗菌素耐药性传播和传播机制的深入了解。高通量测序技术的使用使ARG序列的分析变得可行且可访问。尤其是，宏基因组学方法已促进了基于社区的抗菌素耐药性的鉴定。这种方法很有用，因为它允许访问环境样品中的基因组数据，而无需在分析之前分离和培养微生物。在这里，我们旨在反思在研究抗菌素耐药性的三种主要方法中分析宏基因组学数据所面临的挑战：（i）微生物多样性分析，（ii）功能基因分析，以及（iii）搜索最完整和最相关的电阻组数据库。