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

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.

Actin activates Pseudomonas aeruginosa ExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins

“…6a). For this, we selected the ExoY-like module from the MARTX toxin encoded by the virulence-associated plasmid pA SFn1 from V. nigripulchritudo 1633, an emerging marine pathogen infecting farmed shrimps. The multidomain MARTX toxin is processed inside host cells into individual effector domains by an inbuilt cysteine protein domain34.…”

Dynamics of phytoplankton communities in eutrophying tropical shrimp ponds affected by vibriosis

“…During the warm and cold seasons, two types of vibriosis induce shrimp mortalities in growing ponds, threatening the economic viability of the industry. Epidemiological studies have revealed that the first type of vibriosis results from the highly pathogenic (HP) Vibrio nigripulchritudo (Vn) strain and that the colonization of the shrimp pond ecosystem by this particular pathogenic cluster occurs at the onset of the disease outbreak (Goarant et al, 2006a(Goarant et al, , 2006bReynaud et al, 2008;Le Roux et al, 2010;Goudenège et al, 2013). Known as "Summer Syndrome", this disease is currently restricted to one particular area of New Caledonia (St Vincent Bay).…”

Actin activatesPseudomonas aeruginosaExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins

“…7a). For this, we selected the ExoY-like module from the MARTX toxin encoded by the virulence-associated plasmid pAs Fn1 from Vibrio nigripulchritudo 13, 31 , an emerging marine pathogen infecting farmed shrimps. The multidomain MARTX toxin is processed inside host cells by an inbuilt cysteine protein domain (CPD), into individual effector domains 32 .…”