Wang Lan, Zhu Mei, Yan Chunxia, Zhang Yanfang, He Xuying, Wu Lin, Xu Jiefeng, Lu Junwan, Bao Qiyu, Hu Yunliang, Xu Teng, Liang Jialei
Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China.
Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China.
Front Microbiol. 2023 Mar 6;14:985102. doi: 10.3389/fmicb.2023.985102. eCollection 2023.
The emergence of highly drug-resistant , has become a major public health challenge. In this work, we aim to investigate the diversity of species and sequence types (STs) of clinical isolates and to characterize the prevalence and structure of class 1 integrons.
Based on the whole genome sequencing, species identification was performed by 16S rRNA gene homology and average nucleotide identity (ANI) analysis. STs were determined in accordance with the international MLST schemes for and . Integron characterization and comparative genomic analysis were performed using various bioinformatic tools.
Species identification showed that the 167 isolates belonged to four species: , subsp. , and . Thirty-six known and 5 novel STs were identified in , and 10 novel STs were identified in subsp. . Class 1 integrons were found in 57.49% (96/167) of the isolates, and a total of 169 resistance gene cassettes encoding 19 types of resistance genes, including carbapenem resistance gene ( ) and class D β-lactamases gene ( and ), were identified. Among the 17 complete genomes, 29 class 1 integrons from 12 groups were found, only 1 group was encoded on chromosomes. Interestingly, one plasmid (pKP167-261) carrying two copies of approximately 19-kb IS-Int1 complex resistance region that contains an integron and a multidrug resistance gene fragment.
The results of this work demonstrated that the species and STs of the clinical isolates were more complex by the whole genome sequence analysis than by the traditional laboratory methods. Finding of the new structure of MGEs related to the resistance genes indicates the great importance of deeply exploring the molecular mechanisms of bacterial multidrug resistance.
高耐药性的出现已成为一项重大的公共卫生挑战。在本研究中，我们旨在调查临床分离株的物种多样性和序列类型（STs），并表征1类整合子的流行情况和结构。
基于全基因组测序，通过16S rRNA基因同源性和平均核苷酸同一性（ANI）分析进行物种鉴定。根据针对[具体物种1]和[具体物种2]的国际多位点序列分型（MLST）方案确定STs。使用各种生物信息学工具进行整合子表征和比较基因组分析。
物种鉴定表明，167株分离株属于四个物种：[物种1]、[物种2]亚种、[物种3]和[物种4]。在[物种1]中鉴定出36种已知的和5种新的STs，在[物种2]亚种中鉴定出10种新的STs。在57.49%（96/167）的分离株中发现了1类整合子，共鉴定出169个编码19种耐药基因的耐药基因盒，包括碳青霉烯耐药基因（[具体基因名称1]）和D类β-内酰胺酶基因（[具体基因名称2]和[具体基因名称3]）。在17个完整基因组中，发现了来自12个组的29个1类整合子，只有1组编码在染色体上。有趣的是，一个质粒（pKP167 - 261）携带两个拷贝的约19 kb的IS-Int1复合耐药区域，该区域包含一个整合子和一个多药耐药基因片段。
本研究结果表明，通过全基因组序列分析，临床[相关细菌]分离株的物种和STs比传统实验室方法更为复杂。与耐药基因相关的移动遗传元件（MGEs）新结构的发现表明深入探索细菌多药耐药分子机制具有重要意义。
