Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America.
PLoS One. 2018 Oct 18;13(10):e0206110. doi: 10.1371/journal.pone.0206110. eCollection 2018.
Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations.
嗜肺军团菌属是一种严重细菌性肺炎的病原体，称为军团病（LD）。在某些情况下，当前的遗传亚型方法无法解决由常见、潜在地方性嗜肺军团菌（Lp）序列型（ST）引起的 LD 爆发，这使得实验室调查和环境源归因复杂化。在美国（US），ST1 是最常见的临床和环境 Lp 序列型。为了描述 ST1 群体，我们对来自美国的 289 例爆发和非爆发相关的临床和环境 ST1 以及 ST1 变体 Lp 菌株进行了测序，并与国际分离株序列一起，探索了它们的遗传和地理多样性。ST1 群体在核苷酸水平上高度保守；98%的核心核苷酸位置不变，与人类疾病无关的环境分离株（n = 99）比临床散发性（n = 139）或爆发相关（n = 28）ST1 亚组包含约 65%更多的核苷酸多样性。环境分离株的辅助泛基因组也比其他亚组大 30-60%，并且富含转位和共轭转移相关元件。高达约 10%的美国 ST1 遗传变异可以用地理起源来解释，但从地理位置遥远的州和不同年代分离的菌株之间存在相当大的遗传保守性。这些发现为 ST1 群体结构提供了新的见解，并为解释 ST1 菌株之间的遗传关系奠定了基础；这些数据也可能为改进爆发调查的未来分析提供信息。
