Epidemiological characteristics and molecular features of carbapenem-resistant <i>Enterobacter</i> strains in China: a multicenter genomic study

Epidemiological characteristics and molecular features of carbapenem-resistant <i>Enterobacter</i> (CR-<i>Ent</i>) species remain unclear in China. In this study, we performed a genomic study on 92 isolates from <i>Enterobacter</i>-caused infections from a multicenter study in China. Whole genome sequencing (WGS) was used to determine the genome sequence of 92 non-duplicated CR-<i>Ent</i> strains collected from multiple tertiary health centres. The precise species of <i>Enterobacter</i> strains were identified by average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH). Molecular features of high-risk CR-<i>Ent</i> sequence type (ST) lineages and carbapenemase-encoding plasmids were determined. The result revealed that the most common human-source CR-<i>Ent</i> species in China was <i>E. xiangfangensis</i> (66/92, 71.93%), and the proportion of carbapenemase-producing <i>Enterobacter</i> (CP-<i>Ent</i>) in CR-<i>Ent</i> was high (72/92, 78.26%) in comparison to other global regions. Furthermore, ST171 and ST116 <i>E. xiangfangensis</i> were the major lineages of CP-<i>Ent</i> strains, and ST171 <i>E. xiangfangensis</i> was more likely to cause infections in older patients. Genomic analysis also highlighted the likelihood of intra-hospital/inter-hospital clonal transmission of ST171 and ST116 <i>E. xiangfangensis</i>. In addition, the <i>bla</i>_NDM-harbouring IncX3-type plasmid was identified as the prevalent carbapenemase-encoding plasmid carried by CR-<i>Ent</i> strains, and was experimentally confirmed to be able to self-transfer with high frequency. This study detailed the genomic and clinical characteristics of CR-<i>Ent</i> in China in the form of multicenter for the first time. The high risk of carbapenemase-producing ST171 and ST116 <i>E. xiangfangensis</i>, and the <i>bla</i>_NDM-harbouring IncX3-type plasmid were detected and emphasized.

中国地区碳青霉烯类耐药肠杆菌属（carbapenem-resistant Enterobacter, CR-Ent）的流行病学特征与分子特性目前仍未明确。本研究依托中国多中心研究队列，对92株分离自肠杆菌属感染病例的菌株开展基因组学分析。研究采用全基因组测序（whole genome sequencing, WGS）对采集自多家三级医疗机构的92株非重复CR-Ent菌株进行全基因组测序；通过平均核苷酸同源性（average nucleotide identity, ANI）与数字化DNA-DNA杂交（in silico DNA–DNA hybridization, isDDH）精准鉴定肠杆菌属菌株的物种分类，并解析高风险CR-Ent序列型（sequence type, ST）谱系与碳青霉烯酶编码质粒的分子特征。结果显示，中国临床分离的CR-Ent最常见物种为香坊肠杆菌（E. xiangfangensis），共计66株，占比达71.93%；且产碳青霉烯酶肠杆菌属（carbapenemase-producing Enterobacter, CP-Ent）在CR-Ent中的占比为78.26%（72/92），显著高于全球其他地区的报道水平。进一步分析表明，ST171与ST116型香坊肠杆菌是CP-Ent菌株的主要流行谱系，其中ST171型香坊肠杆菌更易引发老年患者感染。基因组学分析还提示，ST171与ST116型香坊肠杆菌存在医院内乃至医院间的克隆传播风险。此外，本研究鉴定出携带bla_NDM基因的IncX3型质粒是CR-Ent菌株携带的主要碳青霉烯酶编码质粒，并通过实验证实该质粒可实现高频自主转移。本研究首次以多中心研究形式，系统阐明了中国地区CR-Ent的基因组学与临床特征，重点揭示了ST171、ST116型香坊肠杆菌及携带bla_NDM的IncX3型质粒的高传播与感染风险。

搜集汇总

背景与挑战

背景概述

该数据集基于中国多中心收集的92个耐碳青霉烯类肠杆菌（CR-Ent）菌株的全基因组测序数据，首次系统分析了中国CR-Ent的流行病学和分子特征。研究发现，E. xiangfangensis是最常见物种，碳青霉烯酶产生菌株比例高，ST171和ST116为主要高风险谱系，且blaNDM-harbouring IncX3型质粒是主要传播载体，具有高频率自我转移能力。