PRJNA423272
Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1
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. Recent reports demonstrate the value of whole-genome sequencing (WGS) for improving discrimination of Legionella isolates during outbreak investigations, therefore we sequenced 288 ST1 and ST1-variant Lp strains from the US, and together with international isolate sequences, explored their genetic and geographic diversity, and tested methods for increasing LD cluster resolution. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant. However, environmental isolates unassociated with human disease contained ~65% more nucleotide diversity compared to clinical-sporadic or outbreak-associated 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 structure could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and across multiple decades. We also identified a subset of highly variable genomic loci to aid in discriminating ST1 isolates through a simplified molecular subtyping scheme, similar to sequence-based typing.