Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii. Defining a cgMLST scheme for A. baumannii

Objectives: We have employed whole genome sequencing to define and evaluate a core genome multilocus sequence typing (cgMLST) scheme for Acinetobacter baumannii. Methods: To define a core genome we downloaded a total of 1,573 putative A. baumannii genomes from NCBI as well as representative isolates belonging to the eight previously described international A. baumannii clonal lineages. The core genome was then employed against a total of fifty-three carbapenem-resistant A. baumannii isolates that were previously typed by PFGE and linked to hospital outbreaks in eight German cities. Results: We defined a core genome of 2,390 genes of which an average 98.4% were called successfully from 1,339 A. baumannii genomes, while Acinetobacter nosocomialis, Acinetobacter pittii, and Acinetobacter calcoaceticus resulted in 71.2%, 33.3%, and 23.2% good targets, respectively. When tested against the previously identified outbreak strains, we found good correlation between PFGE and cgMLST clustering, with 0-8 allelic differences within a pulsotype, and 40-2,166 differences between pulsotypes. The highest number of allelic differences was between the isolates representing the international clones. Conclusions: This typing scheme was highly discriminatory and identified separate A. baumannii outbreaks. Moreover, because a standardised cgMLST nomenclature is used, the system will allow inter-laboratory exchange of data.

研究目的：本研究采用全基因组测序技术，定义并评估鲍氏不动杆菌（Acinetobacter baumannii）的核心基因组多位点序列分型（core genome multilocus sequence typing, cgMLST）方案。
研究方法：为确定核心基因组范围，本研究从美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）下载了共计1573株推定的鲍氏不动杆菌基因组，以及此前已报道的8种国际鲍氏不动杆菌克隆进化枝的代表性分离株。随后，利用该核心基因组对共计53株此前通过脉冲场凝胶电泳（pulsed field gel electrophoresis, PFGE）分型、且与德国8座城市医院暴发疫情相关的碳青霉烯类耐药鲍氏不动杆菌分离株进行分型分析。
研究结果：本研究确定的核心基因组包含2390个基因，在1339株鲍氏不动杆菌基因组中，平均98.4%的基因可成功完成分型。针对诺科莫不动杆菌（Acinetobacter nosocomialis）、皮氏不动杆菌（Acinetobacter pittii）以及钙透明不动杆菌（Acinetobacter calcoaceticus），其有效靶标比例分别为71.2%、33.3%与23.2%。将该分型方案应用于此前已鉴定的暴发菌株时，结果显示脉冲场凝胶电泳分型与cgMLST聚类结果具有良好的相关性：同一脉冲型内的等位基因差异数为0~8，不同脉冲型间的等位基因差异数为40~2166。其中，代表国际克隆株的分离株之间的等位基因差异数最高。
结论：本研究建立的分型方案具备优异的鉴别能力，可有效区分不同的鲍氏不动杆菌暴发疫情。此外，由于该系统采用标准化的cgMLST命名规则，能够实现不同实验室间的数据交流与共享。