Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia.
Antimicrob Resist Infect Control. 2021 May 10;10(1):79. doi: 10.1186/s13756-021-00941-8.
The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. bla genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that bla-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated bla and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements.
A total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, bla genes were categorized as either chromosomal or plasmid-borne.
WGS-based genotyping identified 58 AMR genes, including four bla alleles (i.e., bla, bla, bla, and bla). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of bla genes. Out of 45 bla gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal bla was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles.
Our study revealed the co-occurrence of ISEcp1-bla and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species.
超广谱β-内酰胺酶（ESBLs）的流行病学发生了巨大变化，CTX-M 型酶超过其他类型占据主导地位。bla 基因，编码 CTX-M 型 ESBLs，通常存在于质粒上，但染色体定位也越来越常见。由于 bla 携带菌株通常表现出多重耐药（MDR），因此研究染色体整合的 bla 与其他抗菌药物耐药（AMR）基因的存在之间的关联，以及鉴定其他相关遗传元件非常重要。
对来自赞比亚的 46 株头孢他啶耐药肠杆菌科（1 株阴沟肠杆菌、9 株肺炎克雷伯菌和 36 株大肠埃希菌）进行全基因组测序（WGS），使用 MiSeq 和 MinION。通过重建近完整基因组，将 bla 基因分为染色体或质粒携带。
基于 WGS 的基因分型鉴定了 58 个 AMR 基因，包括 4 个 bla 等位基因（即 blaCTX-M-15、blaCTX-M-27、blaCTX-M-14 和 blaCTX-M-55）。使用选定的表型和基因型特征进行层次聚类表明 bla 基因的克隆传播。在 45 个 bla 基因携带菌株中，有 7 个菌株的染色体上携带该基因。在 1 株阴沟肠杆菌和 3 株大肠埃希菌菌株中，染色体 bla 位于长度超过 10 kb 的插入物上。这些插入物的一端被 ISEcp1 包围，与先前报道的质粒具有高度的核苷酸序列同源性，并携带与表型 AMR 谱相对应的多个 AMR 基因。
本研究揭示了 ISEcp1-bla 和多个 AMR 基因在阴沟肠杆菌和大肠埃希菌染色体插入物中的共存，表明 ISEcp1 可能负责将不同的 AMR 基因从质粒转移到染色体上。这些插入物在染色体上的稳定保留可能有助于这些肠杆菌科物种中 MDR 克隆的成功传播。
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