Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN.
Division of Clinical Microbiology, Mayo Clinic, Rochester, MN.
Diagn Microbiol Infect Dis. 2020 May;97(1):114996. doi: 10.1016/j.diagmicrobio.2020.114996. Epub 2020 Jan 21.
Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.
全基因组测序（WGS）正在取代传统的微生物学分型方法，用于临床环境中暴发的调查。在这里，我们使用临床微生物学实验室核心基因组多位点序列分型（cgMLST）工作流程来分析 40 株肺炎克雷伯菌的分离株，这些分离株是抗菌药物耐药性领导组（ARLG）分离株收集的一部分，同时还分析了 10 株梅奥诊所的肺炎克雷伯菌分离株，将结果与脉冲场凝胶电泳（PFGE）进行比较。此外，我们还使用 WGS 数据来预测表型抗菌药物敏感性（AST）。40 株 ARLG 肺炎克雷伯菌分离株中有 31 株属于同一 PFGE 型，所有这些分离株以及 3 株不同 PFGE 型的分离株通过 cgMLST 形成了一个大的聚类。PFGE 和 cgMLST 对于 10 株梅奥诊所的肺炎克雷伯菌分离株完全一致。对于 AST 预测，表型 AST 和基因型预测之间的总体一致性为 95.6%。
