产酸克雷伯菌核心基因组多位点序列分型方案

A core genome multilocus sequence typing scheme for Klebsiella oxytoca

目的对产酸克雷伯菌进行核心基因组多位点序列分型(cgMLST)并探索产酸克雷伯菌克隆群(clonal groups,CGs)在国家或地区层面上的遗传多样性。方法chewBBACA被用作GbG(gene-by-gene)分析的生物信息学管道,从整个物种的基因组序列中进行集群识别,以构建和验证产酸克雷伯菌的cgMLST方案。公开获得的21个完整的产酸克雷伯菌基因组序列用于cgMLST方案的创建,386个不完整的产酸克雷伯菌基因组序列用于cgMLST方案的验证。结果建立了一个针对3356个核心基因的cgMLST(简称3356-cgMLST)方案。提出的3356-cgMLST方案实现了针对98%以上(400/407)的产酸克雷伯菌分离株基因组序列的分型。根据提出的3356-cgMLST方案,最终纳入分型的400株产酸克雷伯菌基因组序列中共确定了130个CGs。基于3356-cgMLST方案获得的CGs分布情况可以看出产酸克雷伯菌呈现出明显的多国家多地区传播现象。结论本研究为产酸克雷伯菌提供一个公开的3356-cgMLST方案,并揭示产酸克雷伯菌基因组序列呈现高度的遗传多样性,CG26为优势克隆群。

Core genome multilocus sequence typing(cgMLST)of Klebsiella oxytoca was performed,and the genetic diversity of clonal groups(CGs)of K.oxytoca was explored at the national and regional levels.The chewBBACA bioinformatics pipeline was used for gene-by-gene(GbG)analyses to construct and verify the cgMLST scheme of K.oxytoca,and identify possible clusters from all K.oxytoca samples.All 21 publicly available complete K.oxytoca genomes were used to create the cgMLST scheme,and 386 incomplete(contig,chromosome and scaffold)genomes were used for validation of the cgMLST scheme.Accordingly,we established a cgMLST scheme targeting 3356 genes(3356-cgMLST).The proposed 3356-cgMLST for K.oxytoca typed more than 98%(400/407)of the available isolates.A total of 130 CGs were identified from 400 strains of K.oxytoca through 3356-cgMLST,and CG26 was the dominant clonal group.The CGs obtained through the 3356-cgMLST scheme showed clear multi-country and multi-regional spread of K.oxytoca.Overall,our study provides a publicly accessible 3356-cgMLST scheme for K.oxytoca and reveals high genetic diversity among K.oxytoca genome sequences,with CG26 being the dominant clone group.