Chukamnerd Arnon, Singkhamanan Kamonnut, Chongsuvivatwong Virasakdi, Palittapongarnpim Prasit, Doi Yohei, Pomwised Rattanaruji, Sakunrang Chanida, Jeenkeawpiam Kongpop, Yingkajorn Mingkwan, Chusri Sarunyou, Surachat Komwit
Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
Comput Struct Biotechnol J. 2022 Jan 6;20:545-558. doi: 10.1016/j.csbj.2021.12.038. eCollection 2022.
The worldwide spread of carbapenem-resistant (CRAB) has become a healthcare challenge for some decades. To understand its molecular epidemiology in Southern Thailand, we conducted whole-genome sequencing (WGS) of 221 CRAB clinical isolates. A comprehensive bioinformatics analysis was performed using several tools to assemble, annotate, and identify sequence types (STs), antimicrobial resistance (AMR) genes, mobile genetic elements (MGEs), and virulence genes. ST2 was the most prevalent ST in the CRAB isolates. For the detection of AMR genes, almost all CRAB isolates carried the gene, while certain isolates harbored the or genes. Also, various AMR genes were observed in these CRAB isolates, particularly aminoglycoside resistance genes (e.g., , , and ), fosfomycin resistance gene (), and tetracycline resistance genes ((B) and (39)). For plasmid replicon typing, RepAci1 and RepAci7 were the predominant replicons found in the CRAB isolates. Many genes encoding for virulence factors such as the , , , , and genes were also identified in all CRAB isolates. In conclusion, most CRAB isolates contained a mixture of AMR genes, MGEs, and virulence genes. This study provides significant information about the genetic determinants of CRAB clinical isolates that could assist the development of strategies for improved control and treatment of these infections.
耐碳青霉烯类鲍曼不动杆菌（CRAB）在全球范围内的传播在过去几十年里一直是医疗保健领域面临的一项挑战。为了解其在泰国南部的分子流行病学情况，我们对221株CRAB临床分离株进行了全基因组测序（WGS）。使用多种工具进行了全面的生物信息学分析，以组装、注释并鉴定序列类型（STs）、抗菌药物耐药性（AMR）基因、移动遗传元件（MGEs）和毒力基因。ST2是CRAB分离株中最常见的序列类型。对于AMR基因的检测，几乎所有CRAB分离株都携带了 基因，而某些分离株则含有 或 基因。此外，在这些CRAB分离株中还观察到了各种AMR基因，特别是氨基糖苷类耐药基因（如 、 和 ）、磷霉素耐药基因（ ）以及四环素耐药基因（（B）和（39））。对于质粒复制子分型，RepAci1和RepAci7是在CRAB分离株中发现的主要复制子。在所有CRAB分离株中还鉴定出了许多编码毒力因子的基因，如 、 、 、 和 基因。总之，大多数CRAB分离株都含有AMR基因、MGEs和毒力基因的混合物。本研究提供了有关CRAB临床分离株遗传决定因素的重要信息，这有助于制定改善这些感染控制和治疗策略。
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