Complete Genome Sequence of Leptospira alstonii Serovar Room22 Strain GWTS #1

Nally, Jarlath E.; Bayles, Darrell O.; Hurley, Daniel; Fanning, Séamus; McMahon, Barry J.; Arent, Zbigniew

doi:10.1128/genomea.01230-16

Cited by 9 publications

(8 citation statements)

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“…For example, strain GWTS assigned to pathogen L . alstonii based on the 16S rRNA and secY genes [63, 64] did not cluster with the L . alstonii reference strain and formed a distinct branch in our phylogenetic tree (S2 Fig).…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2019

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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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Section: Resultsmentioning

confidence: 99%

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

et al. 2019

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“…The complete genome sequences of the 90 strains described in this study were compared to the previously published genome sequences from the already known Leptospira species and strain GWTS#1, that was wrongly assigned to the species Leptospira alstonii [33, 34] (S1 Table). As a note, we sequenced the genome of L .…”

Section: Resultsmentioning

confidence: 99%

“…nov.) which was previously wrongly assigned to L . alstonii (strain GWTS#1 T ) based on the 16S rRNA and secY genes [33, 34]. Only one representative strain of each of the 64 Leptospira species was retained for further analysis.…”

Section: Resultsmentioning

confidence: 99%

“…Previously assigned to L . alstonii [33, 34], this strain belongs to the subclade P1. Genome Accession Number is GCA_001729245.1.…”

Section: Resultsmentioning

confidence: 99%

“…alstoni and L . tipperaryensis which were isolated from amphibians in China [47] and shrews in Ireland [33, 34], respectively. Although these other species are in the P1 subclade, they failed to induce disease or colonization in animal models like other Leptospira species tested in the P2, S1 and S2 subclades [15].…”

Section: Discussionmentioning

confidence: 99%

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Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics

et al. 2019

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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 worldwide and we have redefined the classification of species in the genus. The implication of several new potentially infectious Leptospira species for human and animal health remains to be determined but our data also provide new insights into the emergence of virulence in the pathogenic species.

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

Grillová

Picardeau

2020

Methods in Molecular Biology

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With the advent of whole-genome sequencing (WGS), comparative analysis has led to the use of core genome MLST (cgMLST) schemes for the 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 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, clades, clonal groups and sequence types. We show several examples 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 in order to facilitate international collaborations and support the global surveillance of leptospirosis.

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Complete Genome Sequence of Leptospira alstonii Serovar Room22 Strain GWTS #1

Abstract: We report here the complete genome sequence of Leptospira alstonii serovar Room22 strain GWTS #1. This is the first isolate of L. alstonii to be cultured from a mammal and in western Europe, and it represents a new serovar of pathogenic leptospires.

Cited by 9 publications

References 8 publications

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

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

Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics

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

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