Core Genome Multi-Locus Sequence Typing Analyses of Leptospira spp. Using the Bacterial Isolate Genome Sequence Database.

With the advent of whole-genome sequencing (WGS), comparative genomic analyses have enabled the development of core genome multilocus sequence typing (cgMLST) schemes for high-resolution, reproducible typing of bacterial isolates. In cgMLST, hundreds of loci are used for gene-by-gene comparisons of assembled genomes for studying the genetic diversity of isolates, including clinically important pathogens. Combination of the cgMLST data and metadata of the isolates is useful for epidemiological investigations.Here we present a cgMLST scheme for the high-resolution typing of isolates from the whole Leptospira genus, enabling identification at the level of species, clonal groups, and sequence types. We show several examples of how the cgMLST Leptospira database, which is a publicly available web-based database, can be used for the analyses of WGS data of Leptospira isolates. This effort was undertaken to facilitate international collaborations and support the global surveillance of leptospirosis.