Miller Hilary, Harte David, Khokryakova Irina, Jordan Ronan, Bradshaw Amy, Wang Jing, Winter David
New Zealand Institute for Public Health and Forensic Science, Porirua, New Zealand.
Microb Genom. 2025 Sep;11(9). doi: 10.1099/mgen.0.001467.
is a pathogen of global health importance due to its role in causing Legionnaires' disease (LD), a severe form of community-acquired pneumonia. Throughout the USA and Europe, is often identified as the primary cause of LD, but in countries such as New Zealand and Australia, where testing for non- species is employed systematically, high rates of are reported. Development of genomic tools to track outbreaks and identify infection sources for has lagged behind that of . This study addresses this deficit through the development of a core-genome multilocus sequence typing (cgMLST) scheme for . Using all 7 publicly available complete genomes and 89 draft genomes, we developed a schema with 2,608 loci at the 95% presence threshold. The schema was validated using 192 isolates, representing both serogroups and all publicly available isolates available as of July 2024. All isolates had 98% or more of the gene targets, indicating the schema is well defined and representative of the breadth of diversity of sequenced to date. Comparison with core-genome SNP analysis showed high concordance between clusters identified with cgMLST and SNP typing, but cgMLST had higher resolution than SNP typing due to the large number of SNPs in recombinant regions that were removed from the analysis. The cgMLST schema will improve the ability of public health laboratories to perform whole genome sequencing-based surveillance of and thus improve our understanding of the global diversity of this pathogen.
由于其在引起军团病（LD）（一种严重的社区获得性肺炎形式）中所起的作用，它是一种具有全球健康重要性的病原体。在美国和欧洲各地，它常被确定为军团病的主要病因，但在新西兰和澳大利亚等国家，那里系统地对非该物种进行检测，报告显示其感染率很高。用于追踪该病原体爆发和确定感染源的基因组工具的开发落后于其他病原体。本研究通过开发一种针对该病原体的核心基因组多位点序列分型（cgMLST）方案来解决这一不足。利用所有7个公开可用的完整基因组和89个草图基因组，我们开发了一个在95%存在阈值下有2608个位点的方案。该方案使用192个分离株进行了验证，这些分离株代表了血清群以及截至2024年7月所有公开可用的分离株。所有分离株都有98%或更多的基因靶点，这表明该方案定义明确，代表了迄今为止测序的该病原体多样性的广度。与核心基因组SNP分析的比较表明，cgMLST鉴定的簇与SNP分型之间具有高度一致性，但由于从分析中去除了重组区域中的大量SNP，cgMLST的分辨率高于SNP分型。cgMLST方案将提高公共卫生实验室对该病原体进行基于全基因组测序监测的能力，从而增进我们对这种病原体全球多样性的理解。
