Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy

Abstract

Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). L1 comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. L2 is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is related to the aquaculture industry. L3 is also linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. Lastly, L4 and L5 include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. Based on these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name “piscis.”

Adaptation to host in Vibrio vulnificus, a zoonotic pathogen that causes septicemia in fish and humans

“…vep07 was present together with ftbp not only in pv. piscis but also in recent isolates of V. vulnificus from other phylogenetic lineages not previously linked to disease in fish (Roig et al ., ), as well as in the plasmid of one V. harveyi strain isolated from diseased seabass. Interestingly, two main groups were established on the basis of vep07 variability, one group with all the pv.…”

“…A recent phylogenomic study classified V. vulnificus into five phylogenetic lineages plus one pathovar (pv. piscis), which includes all the strains harbouring a fish virulence plasmid (pVvBt2) (Roig et al, 2018). This pathovar is further subdivided into three serovar-related subgroups, one of which, serovar E, constitutes a zoonotic clonal-complex (Sanjuán et al, 2011;Roig et al, 2018).…”

“…piscis), which includes all the strains harbouring a fish virulence plasmid (pVvBt2) (Roig et al, 2018). This pathovar is further subdivided into three serovar-related subgroups, one of which, serovar E, constitutes a zoonotic clonal-complex (Sanjuán et al, 2011;Roig et al, 2018). Currently, the zoonotic clonal-complex is present worldwide and includes strains isolated over a 40-year period from humans, diseased/healthy animals and water-samples (Roig et al, 2018).…”

“…This pathovar is further subdivided into three serovar-related subgroups, one of which, serovar E, constitutes a zoonotic clonal-complex (Sanjuán et al, 2011;Roig et al, 2018). Currently, the zoonotic clonal-complex is present worldwide and includes strains isolated over a 40-year period from humans, diseased/healthy animals and water-samples (Roig et al, 2018). The most relevant virulence factors described in the zoonotic clonal-complex are the RtxA1 toxin, involved in invasion and death by sepsis (Jeong and Satchell, 2012;Lee et al, 2013;Callol et al, 2015;Murciano et al, 2017), a capsule, involved in resistance to human serum, and the O-antigen, conferring resistance to eel serum (Amaro et al, 1994;Amaro et al, 1997).…”

Potentially human‐virulentVibrio vulnificusisolates from diseased great pompano (Trachinotus goodei)

“…A recent phylogenomic study proposed a subdivision into five lineages plus one pathovar (pv. piscis ) (Roig et al, ). This pathovar includes all the strains that able to infect fish, regardless of lineage.…”