RESEARCH ARTICLE Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance Julien Guglielmini1☯, Pascale Bourhy2☯, Olivier Schiettekatte2,3, Farida Zinini2, 4³ 2³ Sylvain Brisse *, Mathieu PicardeauID * 1 Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France, 2 Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France, 3 Universite Paris Diderot, Ecole Doctorale BioSPC, Paris, France, 4 Institut Pasteur, Biodiversity and Epidemiology of a1111111111 Bacterial Pathogens, Paris, France a1111111111 a1111111111 ☯ These authors contributed equally to this work. a1111111111 ³ These authors are joint senior authors on this work. a1111111111 *
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[email protected] (MP) Abstract OPEN ACCESS Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolu- Citation: Guglielmini J, Bourhy P, Schiettekatte O, tionary lineages and >300 serovars. The causative agents of leptospirosis are responsible Zinini F, Brisse S, Picardeau M (2019) Genus-wide of an emerging zoonotic disease worldwide. To advance our understanding of the biodiver- Leptospira core genome multilocus sequence sity of Leptospira strains at the global level, we evaluated the performance of whole-genome typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 13(4): e0007374. https://doi. sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we pro- org/10.1371/journal.pntd.0007374 pose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping Editor: Tao Lin, Baylor College of Medicine, scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evalu- UNITED STATES ation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly Received: December 13, 2018 sequenced genomes, from diverse species, sources and geographical locations.