Legionella pneumophila subsp. pneumophila Raw sequence reads

Legionella pneumophila serogroup 1 (Lpn-SG1) is an aquatic, environmental bacterium that opportunistically causes outbreaks of a severe pneumonia called Legionnaires disease. Epidemics are typically associated with aerosolized contaminated warm water sources. Genomics is increasingly being used to support epidemiological investigations and implicate sources of contamination. Here, we undertook a 21-year (1994-2014) retrospective comparative genomic investigation of 170 Lpn-SG1 respiratory clinical isolates; a time frame that spanned eight outbreaks, including the Melbourne Aquarium outbreak involving 125 cases. We applied Bayesian and multivariate analyses to explore the relationship between genotype and isolate origin. The population structure was represented by six diverse genotypes (50,000 SNP median pairwise difference), but was dominated by a single genotype (sequence type 30) shared by 68% of isolates with a median core SNP distance of only five SNPs across 21 years. Despite the high conservation within ST30, genome analysis using a complete ST30 reference genome uncovered previously unrecognized isolate heterogeneity within outbreak clusters, including four distinct ST30 subtypes within the large Melbourne Aquarium outbreak. These data indicate that a specific Lpn-SG1 genotype has contributed to the majority of disease in Melbourne since at least 1994. The lack of genetic diversity in this clone suggests a reservoir of slowly replicating or latent-state bacteria sporadically seeding warm water sources. A deep understanding of local Legionella pneumophila population structure (both clinical and environmental) will be required, as the combination of extreme genomic monomorphism combined with outbreaks caused by mixed pathogen populations could lead to erroneous conclusions regarding source attribution.