Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics.
The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity...
Published in: | PLOS Neglected Tropical Diseases |
---|---|
Main Authors: | , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2019
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pntd.0007270 https://doaj.org/article/c19955a4a0094b5ab36b6f3f216e55b6 |
id |
ftdoajarticles:oai:doaj.org/article:c19955a4a0094b5ab36b6f3f216e55b6 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:c19955a4a0094b5ab36b6f3f216e55b6 2024-09-09T19:28:06+00:00 Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. Antony T Vincent Olivier Schiettekatte Cyrille Goarant Vasantha Kumari Neela Eve Bernet Roman Thibeaux Nabilah Ismail Mohd Khairul Nizam Mohd Khalid Fairuz Amran Toshiyuki Masuzawa Ryo Nakao Anissa Amara Korba Pascale Bourhy Frederic J Veyrier Mathieu Picardeau 2019-05-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0007270 https://doaj.org/article/c19955a4a0094b5ab36b6f3f216e55b6 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0007270 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007270 https://doaj.org/article/c19955a4a0094b5ab36b6f3f216e55b6 PLoS Neglected Tropical Diseases, Vol 13, Iss 5, p e0007270 (2019) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2019 ftdoajarticles https://doi.org/10.1371/journal.pntd.0007270 2024-08-05T17:48:54Z The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity of non-pathogenic Leptospira and species for which the virulence status is not clearly established. The genus Leptospira is currently divided into 35 species classified into three phylogenetic clusters, which supposedly correlate with the virulence of the bacteria. In this study, a total of 90 Leptospira strains isolated from different environments worldwide including Japan, Malaysia, New Caledonia, Algeria, mainland France, and the island of Mayotte in the Indian Ocean were sequenced. A comparison of average nucleotide identity (ANI) values of genomes of the 90 isolates and representative genomes of known species revealed 30 new Leptospira species. These data also supported the existence of two clades and 4 subclades. To avoid classification that strongly implies assumption on the virulence status of the lineages, we called them P1, P2, S1, S2. One of these subclades has not yet been described and is composed of Leptospira idonii and 4 novel species that are phylogenetically related to the saprophytes. We then investigated genome diversity and evolutionary relationships among members of the genus Leptospira by studying the pangenome and core gene sets. Our data enable the identification of genome features, genes and domains that are important for each subclade, thereby laying the foundation for refining the classification of this complex bacterial genus. We also shed light on atypical genomic features of a group of species that includes the species often associated with human infection, suggesting a specific and ongoing evolution of this group of species that will require more attention. In conclusion, we have uncovered a massive species diversity and revealed a novel subclade in environmental samples collected ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Indian PLOS Neglected Tropical Diseases 13 5 e0007270 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Antony T Vincent Olivier Schiettekatte Cyrille Goarant Vasantha Kumari Neela Eve Bernet Roman Thibeaux Nabilah Ismail Mohd Khairul Nizam Mohd Khalid Fairuz Amran Toshiyuki Masuzawa Ryo Nakao Anissa Amara Korba Pascale Bourhy Frederic J Veyrier Mathieu Picardeau Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity of non-pathogenic Leptospira and species for which the virulence status is not clearly established. The genus Leptospira is currently divided into 35 species classified into three phylogenetic clusters, which supposedly correlate with the virulence of the bacteria. In this study, a total of 90 Leptospira strains isolated from different environments worldwide including Japan, Malaysia, New Caledonia, Algeria, mainland France, and the island of Mayotte in the Indian Ocean were sequenced. A comparison of average nucleotide identity (ANI) values of genomes of the 90 isolates and representative genomes of known species revealed 30 new Leptospira species. These data also supported the existence of two clades and 4 subclades. To avoid classification that strongly implies assumption on the virulence status of the lineages, we called them P1, P2, S1, S2. One of these subclades has not yet been described and is composed of Leptospira idonii and 4 novel species that are phylogenetically related to the saprophytes. We then investigated genome diversity and evolutionary relationships among members of the genus Leptospira by studying the pangenome and core gene sets. Our data enable the identification of genome features, genes and domains that are important for each subclade, thereby laying the foundation for refining the classification of this complex bacterial genus. We also shed light on atypical genomic features of a group of species that includes the species often associated with human infection, suggesting a specific and ongoing evolution of this group of species that will require more attention. In conclusion, we have uncovered a massive species diversity and revealed a novel subclade in environmental samples collected ... |
format |
Article in Journal/Newspaper |
author |
Antony T Vincent Olivier Schiettekatte Cyrille Goarant Vasantha Kumari Neela Eve Bernet Roman Thibeaux Nabilah Ismail Mohd Khairul Nizam Mohd Khalid Fairuz Amran Toshiyuki Masuzawa Ryo Nakao Anissa Amara Korba Pascale Bourhy Frederic J Veyrier Mathieu Picardeau |
author_facet |
Antony T Vincent Olivier Schiettekatte Cyrille Goarant Vasantha Kumari Neela Eve Bernet Roman Thibeaux Nabilah Ismail Mohd Khairul Nizam Mohd Khalid Fairuz Amran Toshiyuki Masuzawa Ryo Nakao Anissa Amara Korba Pascale Bourhy Frederic J Veyrier Mathieu Picardeau |
author_sort |
Antony T Vincent |
title |
Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. |
title_short |
Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. |
title_full |
Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. |
title_fullStr |
Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. |
title_full_unstemmed |
Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. |
title_sort |
revisiting the taxonomy and evolution of pathogenicity of the genus leptospira through the prism of genomics. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pntd.0007270 https://doaj.org/article/c19955a4a0094b5ab36b6f3f216e55b6 |
geographic |
Arctic Indian |
geographic_facet |
Arctic Indian |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 13, Iss 5, p e0007270 (2019) |
op_relation |
https://doi.org/10.1371/journal.pntd.0007270 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007270 https://doaj.org/article/c19955a4a0094b5ab36b6f3f216e55b6 |
op_doi |
https://doi.org/10.1371/journal.pntd.0007270 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
13 |
container_issue |
5 |
container_start_page |
e0007270 |
_version_ |
1809897379258695680 |