摘要
      抗微生物耐药性（AMR）被认为是对公共健康的严重威胁，以高通量分析序列数据为特征的基因组/宏基因组研究越来越普遍和重要。我们之前介绍了MEGARes，这是一个具有非循环分层注释结构的综合AMR数据库，有助于高通量计算分析，以及AMR++，这是专门设计用于高通量分析的定制生物信息学管道，用于表征宏基因组序列数据中的AMR基因（ARG）。在这里，我们介绍了MEGARes v3.0，这是一个已发表的抗微生物药物、杀生物剂和金属的ARG序列的综合数据库，以及AMR++v3.0，我们定制的用于宏基因组数据高通量分析的生物信息学管道的更新（可在MEGLab.org上获得）。数据库注释已经扩展，包括关于单核苷酸多态性（SNPs）和插入和/或缺失（indel）的特定基因组位置的信息，当特定ARG需要抗性表达时，并且更新的AMR++管道使用该信息来检查宏基因组测序读数中是否存在赋予抗性的遗传变异。这一新信息包括337个ARG，其赋予抗性的变体以前无法以这种方式得到证实。在MEGARes 3.0中，非循环层次本体的节点包括4种抗微生物化合物类型、59个抗性类别、233种机制和1448个基因组，这些基因组对8733份材料进行了分类。
Abstract
Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common and important. We previously introduced MEGARes, a comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates high-throughput computational analysis, as well as AMR++, a customized bioinformatic pipeline specifically designed to use MEGARes in high-throughput analysis for characterizing AMR genes (ARGs) in metagenomic sequence data. Here, we present MEGARes v3.0, a comprehensive database of published ARG sequences for antimicrobial drugs, biocides, and metals, and AMR++ v3.0, an update to our customized bioinformatic pipeline for high-throughput analysis of metagenomic data (available at MEGLab.org). Database annotations have been expanded to include information regarding specific genomic locations for single-nucleotide polymorphisms (SNPs) and insertions and/or deletions (indels) when required by specific ARGs for resistance expression, and the updated AMR++ pipeline uses this information to check for presence of resistance-conferring genetic variants in metagenomic sequenced reads. This new information encompasses 337 ARGs, whose resistance-conferring variants could not previously be confirmed in such a manner. In MEGARes 3.0, the nodes of the acyclic hierarchical ontology include 4 antimicrobial compound types, 59 resistance classes, 233 mechanisms and 1448 gene groups that classify the 8733 accessions.

https://academic.oup.com/nar/article/51/D1/D744/6830666?login=false