Population genomics of Legionella longbeachae linked to growing media samples reveals hidden complexities of source attribution

Legionella longbeachae is the primary cause of legionellosis in Australasia and South East Asia, and an emerging pathogen in Europe and the USA. Our understanding of the population diversity of L. longbeachae from patient and environmental sources is very limited. In this study we analyzed the genomes of 70 L. longbeachae isolates, including 29 from a cluster of legionellosis cases linked to commercial growing media in Scotland in 2013, and 41 from non-outbreak isolates from Scotland and other countries. We identified extensive genetic diversity across the L. longbeachae species associated with intra- and interspecies gene flow, and a wide geographic distribution of closely related genotypes. Importantly, we observed a highly diverse pool of L. longbeachae genotypes within compost samples, which precluded the genetic establishment of an infection source. These data represent a view of the genomic diversity of the emerging pathogen L. longbeachae that will inform strategies for investigating future outbreaks.