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Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance

Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at t...

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Autores principales: Guglielmini, Julien, Bourhy, Pascale, Schiettekatte, Olivier, Zinini, Farida, Brisse, Sylvain, Picardeau, Mathieu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513109/
https://www.ncbi.nlm.nih.gov/pubmed/31026256
http://dx.doi.org/10.1371/journal.pntd.0007374
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author Guglielmini, Julien
Bourhy, Pascale
Schiettekatte, Olivier
Zinini, Farida
Brisse, Sylvain
Picardeau, Mathieu
author_facet Guglielmini, Julien
Bourhy, Pascale
Schiettekatte, Olivier
Zinini, Farida
Brisse, Sylvain
Picardeau, Mathieu
author_sort Guglielmini, Julien
collection PubMed
description Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.
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spelling pubmed-65131092019-05-31 Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance Guglielmini, Julien Bourhy, Pascale Schiettekatte, Olivier Zinini, Farida Brisse, Sylvain Picardeau, Mathieu PLoS Negl Trop Dis Research Article Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen. Public Library of Science 2019-04-26 /pmc/articles/PMC6513109/ /pubmed/31026256 http://dx.doi.org/10.1371/journal.pntd.0007374 Text en © 2019 Guglielmini et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Guglielmini, Julien
Bourhy, Pascale
Schiettekatte, Olivier
Zinini, Farida
Brisse, Sylvain
Picardeau, Mathieu
Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance
title Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance
title_full Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance
title_fullStr Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance
title_full_unstemmed Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance
title_short Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance
title_sort genus-wide leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513109/
https://www.ncbi.nlm.nih.gov/pubmed/31026256
http://dx.doi.org/10.1371/journal.pntd.0007374
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