Abstract
The pathogen Flavobacterium psychrophilum is a major problem for the expanding salmonid fish farming industry in Sweden as well as worldwide. A better understanding of the phylogeography and infection routes of F. psychrophilum outbreaks could help to improve aquaculture profitability and the welfare of farmed fish while reducing the need for antibiotics. In the present study, high-throughput genome sequencing was applied to a collection of F. psychrophilum isolates (n=38) from outbreaks on fish farms in different regions of Sweden between 1988 and 2016. Antibiotic susceptibility tests were applied to a subset of the isolates and the results correlated to the presence of genetic resistance markers. We show that F. psychrophilum clones are not regionally biased and that new clones with a higher degree of antibiotic resistance have emerged nationwide during the study period. This supports previous theories of the importance of live fish and egg trade as a route of infection. Continuous monitoring of recovered isolates by high-throughput sequencing techniques in the future could facilitate tracing of clones within and between countries, as well as the detection of emergent virulent or antibiotic-resistant clones. This article contains data hosted by Microreact.
Highlights
Fish farming is a rapidly growing and profitable industry in Sweden
The newly assigned sequence type (ST)-337 was consistent with an allocation to CC-ST236, while the newly assigned ST-338 differed by a single locus each from ST-132 and ST-237 in the PubMLST database, creating a new CC (CC-ST338)
F. psychrophilum is currently endemic in Sweden and has been shown to colonize various wild salmonid and non-salmonid fish species, with or without causing signs of disease [2]
Summary
Fish farming is a rapidly growing and profitable industry in Sweden. Salmonid fish dominate the production output; the most common species farmed is rainbow trout (Oncorhynchus mykiss), but smaller volumes of Arctic charr (Salvelinus alpinus), brown trout (Salmo trutta) and Atlantic salmon (Salmo salar) are produced [1]. Fish for food production are predominantly raised in cage systems in natural freshwater lakes. These systems are a cost-effective way to provide hygienic conditions for the farmed fish, they allow wild and farmed fish to exchange pathogens and serve as reservoirs of infectious disease agents for each other. The health status of Swedish farmed fish is generally good, but outbreaks of infectious diseases occur regularly and cause major economic losses. One of the main pathogens that cause economic losses for salmonid fish farms in Sweden, as well as worldwide, is the bacterium Flavobacterium psychrophilum, the causative agent of diseases referred to as bacterial cold-water disease (BCWD) and rainbow trout fry syndrome (RTFS) [1, 2].
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