Development and validation of a core-genome multilocus sequence typing scheme for Legionella longbeachae

Legionella longbeachae is a pathogen of global health importance due to its role in causing Legionnaires' disease (LD), a severe form of community-acquired pneumonia. Throughout the USA and Europe, Legionella pneumophila is often identified as the primary cause of LD, but in countries such as New Zealand and Australia, where testing for non-pneumophila Legionella species is employed systematically, high rates of L. longbeachae are reported. Development of genomic tools to track outbreaks and identify infection sources for L. longbeachae has lagged behind that of L. pneumophila. This study addresses this deficit through the development of a core-genome multilocus sequence typing (cgMLST) scheme for L. longbeachae. Using all 7 publicly available complete genomes and 89 draft genomes, we developed a schema with 2,608 loci at the 95% presence threshold. The schema was validated using 192 isolates, representing both serogroups and all publicly available isolates available as of July 2024. All isolates had 98% or more of the gene targets, indicating the schema is well defined and representative of the breadth of diversity of L. longbeachae sequenced to date. Comparison with core-genome SNP analysis showed high concordance between clusters identified with cgMLST and SNP typing, but cgMLST had higher resolution than SNP typing due to the large number of SNPs in recombinant regions that were removed from the analysis. The cgMLST schema will improve the ability of public health laboratories to perform whole genome sequencing-based surveillance of L. longbeachae and thus improve our understanding of the global diversity of this pathogen.