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%.

中文翻译：

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使用临床上适合的工作流程进行核心基因组MLST和肺炎克雷伯菌的耐药组分析。

全基因组测序（WGS）正在取代传统的微生物分型方法，以研究临床环境中的疾病暴发。在这里，我们使用了临床微生物学实验室核心基因组多基因座序列分型（cgMLST）工作流程，分析了40株肺炎克雷伯菌的分离株，它们是抗菌素耐药性领导小组（ARLG）分离株集合的一部分，另外还有10个梅奥诊所肺炎克雷伯菌分离株，比较结果与脉冲场凝胶电泳（PFGE）的结果相同。此外，我们使用WGS数据来预测表型抗药性（AST）。40个ARLG肺炎克雷伯菌分离株中有31个属于同一PFGE类型，所有这些菌株与3个不同PFGE类型的分离株一起通过cgMLST形成了一个大簇。PFGE和cgMLST与10个梅奥诊所的肺炎克雷伯菌分离株完全一致。