Epidemiologic information is key when interpreting whole genome sequence data – lessons learned from the genomic analysis of the largest German Legionella pneumophila outbreak (Warstein, 2013)

Whole genome sequencing (WGS) is increasingly being used in outbreak investigations of Legionnaires’ disease (LD). WGS offers a higher resolution for the analysis of endemic strains compared to sequence-based typing, the gold standard typing method for L. pneumophila. Recently, a gene-by-gene typing approach of 1,521 core genes called core genome multilocus sequence typing (cgMLST) was described that enables a robust and standardised typing of L. pneumophila. We applied this cgMLST scheme to isolates obtained during the largest outbreak of LD reported in Germany. This outbreak had a unique characteristic since the epidemic clone ST345 was isolated from four different environmental sources. In total forty-two clinical and environmental isolates were typed. Epidemiologically unrelated ST345 isolates were clearly distinguishable from the epidemic clone. Remarkably, epidemic isolates from both, clinical and environmental samples, split up into two distinct clusters, ST345 A and ST345 B, exhibiting a difference of 40 alleles, located in two neighbouring genomic regions. Additional analysis supported horizontal gene transfer of two regions of about 42 and 26 kb size, respectively. Both regions comprise virulence genes and have been reported earlier to be involved in recombination events. This corroborates the notion that genomic outbreak investigation should always take epidemiological information into consideration when making inferences. Overall, cgMLST was instrumental in disentangling the complex genomic epidemiology of this large outbreak that involved two clusters of one epidemic clone.

全基因组测序（Whole Genome Sequencing, WGS）正日益应用于军团菌病（Legionnaires’ Disease, LD）的暴发调查研究。相较于嗜肺军团菌（Legionella pneumophila, L. pneumophila）的金标准分型方法——基于序列的分型（sequence-based typing），全基因组测序为地方性流行菌株的分析提供了更高的分辨率。近期，一项针对1521个核心基因的逐基因分型方法被提出，即核心基因组多位点序列分型（Core Genome Multilocus Sequence Typing, cgMLST），该方法可实现嗜肺军团菌的稳健且标准化分型。我们将该cgMLST分型方案应用于德国报告的最大规模军团菌病暴发事件中获取的分离株。此次暴发存在独特特征：疫情克隆ST345从四类不同的环境来源中被分离获得。总计42株临床与环境分离株完成分型。流行病学上无关联的ST345分离株可与本次疫情克隆清晰区分。值得注意的是，来自临床与环境样本的疫情分离株均分为两个独立的聚类群——ST345 A与ST345 B，二者存在40个等位基因的差异，且位于两个相邻的基因组区域内。额外分析证实，两段分别约42kb与26kb的区域发生了水平基因转移（horizontal gene transfer）。这两段区域均包含毒力基因（virulence genes），此前已有研究报道其参与重组事件。这一结果佐证了“基因组暴发调查在进行推论时应始终结合流行病学信息”这一观点。总体而言，cgMLST在解析此次涉及单个疫情克隆的两个聚类群的大规模暴发的复杂基因组流行病学特征中发挥了关键作用。