Molecular Epidemiology of Photobacterium damselae subsp. damselae Outbreaks in Marine Rainbow Trout Farms Reveals Extensive Horizontal Gene Transfer and High Genetic Diversity

Abstract

The marine bacterium Photobacterium damselae subsp. damselae is a pathogen for a variety of marine animals, as well as for humans, and is nowadays considered an emerging pathogen for fish of importance in marine aquaculture. Recent studies have suggested that outbreaks in fish farms are caused by multiclonal populations of this subspecies that exist in the environment. Here, we report the study of a collection of 31 strains isolated during the course of disease outbreaks in marine rainbow trout farms in Denmark in 1994, 1995, and 2006, respectively. A phylogenetic analysis based on the toxR gene sequence, and the screening of virulence-related genes uncovered a high genetic heterogeneity, even among strains isolated from the same fish farm at the same time. Moreover, comparative analysis of the whole genome sequences of four selected strains revealed a large number of differentially occurring genes, which included virulence genes, pPHDD1 plasmid, polysaccharide synthesis gene clusters, CRISPR-Cas systems and putative new mobile genetic elements. This study provides sound evidence that P. damselae subsp. damselae outbreaks in Danish rainbow trout farms were caused by multiclonal populations and that horizontal gene transfer constitutes a strong driving force in the generation of intraspecific diversity in this pathogen.

Genotypic diversity, and molecular and pathogenic characterization of Photobacterium damselae subsp. piscicida isolated from different fish species in Taiwan

“…Phylogenetic analysis based on the ToxR gene alone has demonstrated a multiclonal population of P. damselae subsp. damselae isolates that caused disease outbreaks in rainbow trout ( Oncorhynchus mykiss ) in Denmark from different years (Terceti et al, 2018). Interestingly, the strains clustered together using ToxR gene sequencing analysis shared the same biotypes as described in previous study (Pedersen, Dalsgaard, & Larsen, 1997).…”

Diverse Horizontally-Acquired Gene Clusters Confer Sucrose Utilization to Different Lineages of the Marine Pathogen Photobacterium damselae subsp. damselae

“…An extensive study that analyzed 71 Pdd isolates from fish in Spain, reported that 4% were sucrose-fermenters [28]. In another study with Pdd strains from disease outbreaks in marine rainbow trout, one isolate out of 31 tested positive for sucrose fermentation [24]. A study reported the simultaneous isolation on a TCBS agar plate of yellow and green Pdd colonies from different organs of the same fish [29].…”

“…In this study, 8 Pdd strains contained a scr gene cluster. Of these, six were isolated from European seabass in the Black Sea [30], one from diseased rainbow trout in Denmark [24,37] and one from gilthead seabream from unknown geographical origin (Table 1). In order to ascertain whether the sucrose positive strains conform a clonal entity or whether the scr clusters have been acquired by different genetic lineages of Pdd, we carried out a comparative analysis of 23 complete Pdd genomes.…”

“…Moreover, it can cause opportunistic infections in humans that may evolve into a fatal outcome [23]. Pdd is considered a genetically diverse subspecies, and horizontal gene transfer largely contributes to the generation of such diversity [22,[24][25][26]. Pdd typically forms green colonies on TCBS medium, but early studies pointed out that 5% of the isolates produced yellow colonies on TCBS [27].…”

“…Pdd typically forms green colonies on TCBS medium, but early studies pointed out that 5% of the isolates produced yellow colonies on TCBS [27]. Since then, a number of studies have described Pdd strains that produce yellow colonies on TCBS [24,[28][29][30][31], but the genetic basis of such phenotypic variability remains uncharacterized.…”