Epidemiologic information is key when interpreting whole genome sequence data – lessons learned from the genomic analysis of the largest German Legionella pneumophila outbreak (Warstein, 2013). Legionella Warstein outbreak 2013

Whole genome sequencing (WGS) is increasingly being used in outbreak investigations of Legionnaires’ disease (LD). WGS offers a higher resolution for the analysis of endemic strains compared to sequence-based typing, the gold standard typing method for L. pneumophila. Recently, a gene-by-gene typing approach of 1,521 core genes called core genome multilocus sequence typing (cgMLST) was described that enables a robust and standardised typing of L. pneumophila. We applied this cgMLST scheme to isolates obtained during the largest outbreak of LD reported in Germany. This outbreak had a unique characteristic since the epidemic clone ST345 was isolated from four different environmental sources. In total forty-two clinical and environmental isolates were typed. Epidemiologically unrelated ST345 isolates were clearly distinguishable from the epidemic clone. Remarkably, epidemic isolates from both, clinical and environmental samples, split up into two distinct clusters, ST345 A and ST345 B, exhibiting a difference of 40 alleles, located in two neighbouring genomic regions. Additional analysis supported horizontal gene transfer of two regions of about 42 and 26 kb size, respectively. Both regions comprise virulence genes and have been reported earlier to be involved in recombination events. This corroborates the notion that genomic outbreak investigation should always take epidemiological information into consideration when making inferences. Overall, cgMLST was instrumental in disentangling the complex genomic epidemiology of this large outbreak that involved two clusters of one epidemic clone.