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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.

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2018-12-13
2020-01-26
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References

  1. Swedish Board of Agriculture Flerårig nationell strategisk plan för vattenbruket i Sverige 2014–2020. Appendix of protocol IV 5, March 19 2015, N2015/2183/FJR 2015
    [Google Scholar]
  2. Ekman E.. Natural and experimental infections with Flavobacterium psychrophilum in Salmonid Fish. Diss.. Acta Universitatis Agriculturae Sueciae. Veterinaria, 1401-6257; 160 2003
    [Google Scholar]
  3. Castillo D, Christiansen RH, Dalsgaard I, Madsen L, Espejo R et al. Comparative genome analysis provides insights into the Pathogenicity of Flavobacterium psychrophilum. PLoS One 2016;11:e0152515 [CrossRef][PubMed]
    [Google Scholar]
  4. Duchaud E, Boussaha M, Loux V, Bernardet JF, Michel C et al. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nat Biotechnol 2007;25:763–769 [CrossRef][PubMed]
    [Google Scholar]
  5. Duchaud E, Rochat T, Habib C, Barbier P, Loux V et al. Genomic diversity and evolution of the fish pathogen Flavobacterium psychrophilum. Front Microbiol 2018;9:138 [CrossRef][PubMed]
    [Google Scholar]
  6. Clinical and Laboratory Standards Institute CLSI Performance Standards for Antimicrobial Suceptibility Testing of Bacteria Isolated from Aquatic Animals, Second Informational Supplement VET03/VET04-S2. 2014
    [Google Scholar]
  7. Smith P, Endris R, Kronvall G, Thomas V, Verner-Jeffreys D et al. Epidemiological cut-off values for Flavobacterium psychrophilum MIC data generated by a standard test protocol. J Fish Dis 2016;39:143–154 [CrossRef][PubMed]
    [Google Scholar]
  8. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357–359 [CrossRef][PubMed]
    [Google Scholar]
  9. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2011;27:2987–2993 [CrossRef][PubMed]
    [Google Scholar]
  10. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006;23:254–267 [CrossRef][PubMed]
    [Google Scholar]
  11. Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S et al. Benchmarking of methods for genomic taxonomy. J Clin Microbiol 2014;52:1529–1539 [CrossRef][PubMed]
    [Google Scholar]
  12. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  13. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  14. Fujiwara-Nagata E, Chantry-Darmon C, Bernardet JF, Eguchi M, Duchaud E et al. Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan. Vet Res 2013;44:34 [CrossRef][PubMed]
    [Google Scholar]
  15. Nicolas P, Mondot S, Achaz G, Bouchenot C, Bernardet JF et al. Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl Environ Microbiol 2008;74:3702–3709 [CrossRef][PubMed]
    [Google Scholar]
  16. Izumi S, Aranishi F. Relationship between gyrA mutations and quinolone resistance in Flavobacterium psychrophilum isolates. Appl Environ Microbiol 2004;70:3968–3972 [CrossRef][PubMed]
    [Google Scholar]
  17. Akinbowale OL, Peng H, Barton MD. Diversity of tetracycline resistance genes in bacteria from aquaculture sources in Australia. J Appl Microbiol 2007;103:2016–2025 [CrossRef][PubMed]
    [Google Scholar]
  18. Wu AK, Kropinski AM, Lumsden JS, Dixon B, Macinnes JI. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T). Stand Genomic Sci 2015;10:3 [CrossRef][PubMed]
    [Google Scholar]
  19. Nilsen H, Sundell K, Duchaud E, Nicolas P, Dalsgaard I et al. Multilocus sequence typing identifies epidemic clones of Flavobacterium psychrophilum in Nordic countries. Appl Environ Microbiol 2014;80:2728–2736 [CrossRef][PubMed]
    [Google Scholar]
  20. Madetoja J, Nystedt S, Wiklund T. Survival and virulence of Flavobacterium psychrophilum in water microcosms. FEMS Microbiol Ecol 2003;43:217–223 [CrossRef][PubMed]
    [Google Scholar]
  21. Brown LL, Cox WT, Levine RP. Evidence that the causal agent of bacterial cold-water disease Flavobacterium psychrophilum is transmitted within salmonid eggs.. Dis Aquat Organ 1997;29:6
    [Google Scholar]
  22. Bustos PA, Calbuyahue J, Montana J, Opazo B, Entrala P et al. First isolation of Flexibacter psychrophilus as causative agent of rainbow trout fry syndrome (RTFS), producing rainbow trout mortality in Chile. Bulletin of The European Association of Fish Pathologists 1995;15:3
    [Google Scholar]
  23. Izumi S, Wakabayashi H. Use of PCR to Detect Cytophaga psychrophila from Apparently Healthy Juvenile Ayu and Coho Salmon Eggs. Fish Pathol 1997;32:169–173 [CrossRef]
    [Google Scholar]
  24. Chen S, Blom J, Loch TP, Faisal M, Walker ED. The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation. Front Microbiol 2017;8:2339 [CrossRef][PubMed]
    [Google Scholar]
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