Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits

Type Article
Date 2013-10
Language English
Author(s) Goudenege David1, Labreuche Yannick1, Krin Evelyne2, 3, Ansquer Dominique4, Mangenot Sophie5, Calteau Alexandra5, 6, Medigue Claudine5, 6, Mazel Didier2, 3, Polz Martin F.7, Le Roux Frederique1
Affiliation(s) 1 : Equipe Emergente Ifremer UPMC Genom Vibrio, F-29688 Roscoff, France.
2 : Inst Pasteur, Dept Genomes & Genet, Unite Plast Genome Bacterien, Paris, France.
3 : CNRS, UMR3525, Paris, France.
4 : IFREMER, Dept Lagons Ecosyst & Aquaculture Durable Nouvell, Noumea, New Caledonia.
5 : CEA, Inst Genom, Evry, France.
6 : CNRS, UMR8030, Lab Genom Comparat, Evry, France.
7 : MIT, Parsons Lab Environm Sci & Engn, Cambridge, MA 02139 USA.
Source Isme Journal (1751-7362) (Nature Publishing Group), 2013-10 , Vol. 7 , N. 10 , P. 1985-1996
DOI 10.1038/ismej.2013.90
WOS© Times Cited 20
Keyword(s) horizontal gene transfer, nigritoxin, phylogeny, shrimp, virulence, vibrio
Abstract Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
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Goudenege David, Labreuche Yannick, Krin Evelyne, Ansquer Dominique, Mangenot Sophie, Calteau Alexandra, Medigue Claudine, Mazel Didier, Polz Martin F., Le Roux Frederique (2013). Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits. Isme Journal, 7(10), 1985-1996. Publisher's official version : https://doi.org/10.1038/ismej.2013.90 , Open Access version : https://archimer.ifremer.fr/doc/00160/27117/