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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Acknowledgements
We acknowledge Dr Eliane Chung and Iony Manitra Razanajatovo for providing the strains isolated in Madagascar, Sophie Le Panse for the transmission electron microscopy analysis, the staff of the station Ifremer Nouvelle Calédonie, the ABIMS and LABGeM plateform for technical support, Dr Simonetta Gribaldo, Otto Cordero and Dr Cyrille Goarant for fruitful discussions and Dr Brigid Davis for critical reading of the manuscript. The present study has been supported by the Genoscope (appel d’offre 2007 and 2011) Region Bretagne (SAD Vibrigen 6633), the Institut Pasteur, the CNRS (UMR3525), the ANR blanc (11-BSV7-023-01 ‘VIBRIOGEN’) and Ifremer (DG post doctoral funding).
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Goudenège, D., Labreuche, Y., Krin, E. et al. Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits. ISME J 7, 1985–1996 (2013). https://doi.org/10.1038/ismej.2013.90
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DOI: https://doi.org/10.1038/ismej.2013.90
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