Hwang Sang Mee, Cho Hee Won, Kim Tae Yeul, Park Jeong Su, Jung Jongtak, Song Kyoung-Ho, Lee Hyunju, Kim Eu Suk, Kim Hong Bin, Park Kyoung Un
Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea.
College of Medicine, Seoul National University, Seoul 03080, Korea.
Diagnostics (Basel). 2021 Jan 29;11(2):201. doi: 10.3390/diagnostics11020201.
Carbapenem-resistant (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 isolates, three clonal lineages were identified from the outbreak. The coexistence of and with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.
医院环境中耐碳青霉烯类鲍曼不动杆菌（CRAB）暴发对患者治疗和感染控制构成挑战。了解临床分离株的相关性对于区分暴发分离株和散发病例很重要。本研究通过全基因组测序（WGS）对一家医院暴发中的11株CRAB分离株进行了调查，并利用各种生物信息学工具进行暴发分析。比较了通过基于网络的工具进行的多位点序列分型（MLST）、单核苷酸多态性（SNP）分析和WGS系统发育树分析的结果，并进行了重复元件聚合酶链反应（rep-PCR）分型。通过对11株分离株的WGS，从此次暴发中鉴定出三个克隆谱系。在所有分离株中均鉴定出blaOXA-23和blaOXA-51以及其他预计赋予多重耐药性的氨基糖苷类失活酶的共存。MLST牛津方案鉴定出三种类型（ST191、ST369和ST451），并且通过全基因组MLST和全基因组SNP分析，发现在MLST类型中存在不同的克隆。wgSNP在分离株之间显示出最高的鉴别力和最低的相似性。使用各种用于WGS的生物信息学工具，CRAB暴发分析是适用的，并鉴定出三个离散的簇，区分了分离株之间不同的流行病学关系。
