Multilocus sequence typing reveals high genetic diversity and epidemic population structure for the fish pathogen <i>Yersinia ruckeri</i>

Yersinia ruckeri is the etiological agent of enteric redmouth (ERM) disease of farmed salmonids. Enteric redmouth disease is traditionally associated with rainbow trout (Oncorhynchus mykiss, Walbaum), but its incidence in Atlantic salmon (Salmo salar) is increasing. Yersinia ruckeri isolates recovered from diseased Atlantic salmon have been poorly characterized, and very little is known about the relationship of the isolates associated with these two species. Phenotypic approaches were used to characterize 109 Y. ruckeri isolates recovered over a 14-year period from infected Atlantic salmon in Scotland; 26 isolates from infected rainbow trout were also characterized. Biotyping, serotyping, and comparison of outer membrane protein profiles identified 19 Y. ruckeri clones associated with Atlantic salmon but only five associated with rainbow trout; none of the Atlantic salmon clones occurred in rainbow trout and vice versa. These findings suggest that distinct subpopulations of Y. ruckeri are associated with each species. A new O serotype (designated O8) was identified in 56 biotype 1 Atlantic salmon isolates and was the most common serotype identified from 2006 to 2011 and in 2014, suggesting an increased prevalence during the time period sampled. Rainbow trout isolates were represented almost exclusively by the same biotype 2, serotype O1 clone that has been responsible for the majority of ERM outbreaks in this species within the United Kingdom since the 1980s. However, the identification of two biotype 2, serotype O8 isolates in rainbow trout suggests that vaccines containing serotypes O1 and O8 should be evaluated in both rainbow trout and Atlantic salmon for application in Scotland. IMPORTANCEVaccination plays an important role in protecting Atlantic salmon against the bacterial pathogen Yersinia ruckeri, but, in recent years, there has been an increasing incidence of vaccine breakdown in salmon. This is largely because current vaccines are aimed at rainbow trout and are based on serotypes specific for this species. A wider range of serotypes is responsible for infection in Atlantic salmon, but very little is known about the diversity of these strains and their relationships to those recovered from rainbow trout. In the present study, we demonstrate that Y. ruckeri isolates recovered from diseased Atlantic salmon in Scotland are more diverse than those from rainbow trout; furthermore, isolates from the two species represent distinct subpopulations. In addition, a new O serotype was identified that is responsible for a significant proportion of the disease in Atlantic salmon. Our findings are likely to have important implications for the development of improved vaccines against Y. ruckeri. The Gram-negative bacterium Yersinia ruckeri is the etiological agent of enteric redmouth (ERM) disease of cultured salmonids and causes significant economic losses to the fish-farming industry. Yersinia ruckeri was first isolated in 1956 from diseased rainbow trout (Oncorhynchus mykiss, Walbaum) in the Hagerman Valle...

Section: Discussionsupporting

confidence: 79%

“…Previous comparative studies of Y. ruckeri strain diversity have included only small numbers of isolates recovered from Atlantic salmon (19,24,30,(32)(33)(34). Surprisingly, few investigations have focused exclusively, or predominantly, on isolates associated with yersiniosis of this species (9,12).…”

mentioning

confidence: 99%

Yersinia ruckeri Isolates Recovered from Diseased Atlantic Salmon (Salmo salar) in Scotland Are More Diverse than Those from Rainbow Trout (Oncorhynchus mykiss) and Represent Distinct Subpopulations

Ormsby

Caws

Burchmore

et al. 2016

“…This situation is in sharp contrast to that in F. psychrophilum (59,62,63), R. salmoninarium (61), and Y. ruckeri (60), for which the sequence data unambiguously revealed transcontinental dissemination linked to the international trade of broodfish and eggs. Furthermore, as a result of preferential dissemination routes or of adaptive niche specificity, the large clonal complexes detected in F. psychrophilum tended to be strongly associated with particular host fish species (59,62,64).…”

Section: Distribution and Evolution Of Fish Pathogenicity In The Genuscontrasting

confidence: 70%

Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

Habib

Houel

Lunazzi

et al. 2014

130

The genus Tenacibaculum, a member of the family Flavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogen Tenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the species T. maritimum constitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoring Tenacibaculum infections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related to T. dicentrarchi, a recently described species.

“…Multilocus sequence typing (MLST) is a robust, reproducible, and established technique to identify and characterize the strain diversity of human and animal bacterial pathogens (21, 22), including those affecting fish (23)(24)(25)(26)(27). MLST is based on the sequencing of, typically, 7 housekeeping gene loci, whereby an isolate is characterized by the allele types (ATs) found at the loci.…”

Section: Importancementioning

confidence: 99%

“…A number of molecular biology-based assays have been employed to study the genetic diversity of F. psychrophilum in an attempt to define its host specificity, geographical associations, and virulence (15-18). However, despite these concerted efforts, the lack of standardized, reproducible, and comparable assays (18)(19)(20) left the intraspecific heterogeneity of F. psychrophilum as it relates to distribution and transmission routes incompletely understood.Multilocus sequence typing (MLST) is a robust, reproducible, and established technique to identify and characterize the strain diversity of human and animal bacterial pathogens (21, 22), including those affecting fish (23)(24)(25)(26)(27). MLST is based on the sequencing of, typically, 7 housekeeping gene loci, whereby an isolate is characterized by the allele types (ATs) found at the loci.…”

mentioning

confidence: 99%

Genetic Diversity of Flavobacterium psychrophilum Isolates from Three Oncorhynchus spp. in the United States, as Revealed by Multilocus Sequence Typing

Vliet

Wiens

Loch

et al. 2016

The use of a multilocus sequence typing (MLST) technique has identified the intraspecific genetic diversity of U.S. Flavobacterium psychrophilum, an important pathogen of salmonids worldwide. Prior to this analysis, little U.S. F. psychrophilum genetic information was known; this is of importance when considering targeted control strategies, including vaccine development. Herein, MLST was used to investigate the genetic diversity of 96 F. psychrophilum isolates recovered from rainbow trout (Oncorhynchus mykiss), coho salmon (Oncorhynchus kisutch), and Chinook salmon (Oncorhynchus tshawytscha) that originated from nine U.S. states. The isolates fell into 34 distinct sequence types (STs) that clustered in 5 clonal complexes (CCs) (n ‫؍‬ 63) or were singletons (n ‫؍‬ 33). The distribution of STs varied spatially, by host species, and in association with mortality events. Several STs (i.e., ST9, ST10, ST30, and ST78) were found in multiple states, whereas the remaining STs were localized to single states. With the exception of ST256, which was recovered from rainbow trout and Chinook salmon, all STs were found to infect a single host species. Isolates that were collected during bacterial cold water disease outbreaks most frequently belonged to CC-ST10 (e.g., ST10 and ST78). Collectively, the results of this study clearly demonstrate the genetic diversity of F. psychrophilum within the United States and identify STs of clinical significance. Although the majority of STs described herein were novel, some (e.g., ST9, ST10, ST13, ST30, and ST31) were previously recovered on other continents, which demonstrates the transcontinental distribution of F. psychrophilum genotypes. IMPORTANCEFlavobacterium psychrophilum is the causative agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS) and is an important bacterial pathogen of wild and farmed salmonids worldwide. These infections are responsible for large economic losses globally, yet the genetic diversity of this pathogen remains to be fully investigated. Previous studies have identified the genetic diversity of this pathogen in other main aquaculture regions; however, little effort has been focused on the United States. In this context, this study aims to examine the genetic diversity of F. psychrophilum from the United States, as this region remains important in salmonid aquaculture.T he causative agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS), Flavobacterium psychrophilum, is an important bacterial pathogen of wild and farmed salmonids worldwide (1). In addition to horizontal transmission, F. psychrophilum is suspected of being vertically transmitted (2-5) and appears to resist standard povidone-iodine treatment during egg disinfection (4, 6, 7), which make efforts to control this bacterium particularly problematic. Since the initial isolation of F. psychrophilum in North America (8), F. psychrophilum infections have been reported in Europe, South America, Asia, and Australia (9-11) and from all of...