Genome sequencing links persistent outbreak of legionellosis in Sydney to an emerging clone ofLegionella pneumophilaST211

The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and bring the outbreak to a close we examined the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks. A total of 48 isolates from patients and cooling towers were sequenced and compared using SNP-based, core-genome MLST and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (March and May) and Suburb 1. These isolates were designated “Main cluster” and consisted of isolates from two patients from the CBD March outbreak, one patient and one tower isolate from Suburb 1 and isolates from two cooling towers and three patients from the CDB May outbreak. All main cluster isolates were sequence type ST211 which has only ever been reported in Canada. Significantly, pangenome analysis identified mobile genetic elements containing a unique T4ASS that was specific to the main cluster and co-circulating clinical strains, suggesting a potential mechanism for increased fitness and persistence of the outbreak clone. Genome sequencing was key in deciphering the environmental sources of infection among the spatially and temporally coinciding cases of legionellosis in this highly populated urban setting. Further, the discovery of a unique T4ASS emphasises the potential contribution of genome recombination in the emergence of successful Lp1 clones.