出身背景
对抗微生物耐药性基因（ARGs）和细菌的监测是预防和控制抗微生物耐药性（AMR）的一种关键方法。下一代测序（NGS）是监测ARGs和耐药细菌出现和传播的有力工具。质粒介导的ARGs在宿主细菌之间的水平转移在NGS耐药性监测中是一个挑战，因为短读测序很难产生完整的质粒基因组序列，并且ARGs和质粒之间的相关性也很难确定。
方法
从NCBI数据库中收集455个携带mcr的质粒（pMCRs）的完整基因组序列及其宿主细菌和分离区的数据。对每个质粒搜索Inc型和ARG基因。通过泛基因组聚类和基因组比对分析了这些质粒的基因组相似性。
后果
在这些pMCR中共鉴定出52种Inc型，包括多种包含2种或更多Inc型的融合质粒，并由复杂宿主菌携带。pMCRs中普遍观察到ARGs的共现，每个质粒平均有3.9个ARGs。通过泛基因组聚类鉴定出22个序列和基因组成一致或高度相似的聚类，其特征是每个聚类中不同国家/地区、年份或宿主细菌的分布。
讨论
根据完整的质粒序列，可以明确地揭示mcr基因在不同Inc型质粒中的分布，它们与其他AMR的共存，以及一个pMCR跨区域和宿主细菌的传播。完整的质粒基因组和实验室网络中的比较对于携带ARG的质粒的传播追踪和AMR监测中的风险评估是必要的。
Background
The surveillance of antimicrobial resistance genes (ARGs) and bacteria is one critical approach to prevent and control antimicrobial resistance (AMR). Next-generation sequencing (NGS) is a powerful tool in monitoring the emergence and spread of ARGs and resistant bacteria. The horizontal transfer of ARGs across host bacteria mediated by plasmids is a challenge in NGS surveillance for resistance because short-read sequencing can hardly generate the complete plasmid genome sequence, and the correlation between ARGs and plasmids are difficult to determine.

Methods
The complete genome sequences of 455 mcr-carrying plasmids (pMCRs), and the data of their host bacteria and isolation regions were collected from the NCBI database. Genes of Inc types and ARGs were searched for each plasmid. The genome similarity of these plasmids was analyzed by pangenome clustering and genome alignment.

Results
A total of 52 Inc types, including a variety of fusion plasmids containing 2 or more Inc types were identified in these pMCRs and carried by complex host bacteria. The cooccurrence of ARGs in pMCRs was generally observed, with an average of 3.9 ARGs per plasmid. Twenty-two clusters with consistent or highly similar sequences and gene compositions were identified by the pangenome clustering, which were characterized with distributions in different countries/regions, years or host bacteria in each cluster.

Discussion
Based on the complete plasmid sequences, distribution of mcr genes in different Inc type plasmids, their co-existence with other AMRs, and transmission of one pMCR across regions and host bacteria can be revealed definitively. Complete plasmid genomes and comparisons in the laboratory network are necessary for spread tracing of ARG-carrying plasmids and risk assessment in AMR surveillance.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9005491/