Naylor RL, Hardy RW, Buschmann AH, Bush SR, Cao L, Klinger DH, Little DC, Lubchenco J, Shumway SE, Troell M. A 20-year retrospective review of global aquaculture. Nature. 2021;591:551–63. https://doi.org/10.1038/s41586-021-03308-6.
Article CAS PubMed Google Scholar
Horký P. Freshwater resources and fisheries in the Czech Republic. In: Craig FJ, editor. Freshwater Fisheries Ecology. Oxford: Wiley-Blackwell; 2015. p. 201–7.
Mořický J, Tomášek O, Chalupa P, Ptáček R. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2023. https://eagri.cz/public/portal/-a37152---VeKC--P-/publikace-situacni-a-vyhledova-zprava-ryby-2022?_linka=a552322. Accessed 24.4.2024.
Ženíšková H, Gall V. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2011. https://eagri.cz/public/portal/-q321509---yeBf07T3/situacni-a-vyhledova-zprava-ryby. Accessed 24.4.2024.
The Ministry of Agriculture of the Czech Republic. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2013. https://eagri.cz/public/portal/-q319301---ScbF0MF8/ryby-situacni-a-vyhledova-zprava-2013?_linka=a235061. Accessed 24.4.2024.
The Ministry of Agriculture of the Czech Republic. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2014. https://eagri.cz/public/portal/-q319275---lNmtybr1/ryby-11-2014?_linka=a235025. Accessed 24.4.2024.
Ženíšková H, Chalupa P. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2015 https://eagri.cz/public/portal/-q319297---ZlGTEf10/ryby-11-2015. Accessed 24.4.2024.
Ženíšková H, Chalupa P. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2016. https://eagri.cz/public/portal/-q319299---X_iyUYs0/ryby-11-2016?_linka=a235059. Accessed 24.4.2024.
Ženíšková H, Chalupa P, Heimlich R. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2017. https://eagri.cz/public/portal/-q321545---uQOO3T8m/svz-ryby-2017?_linka=a235051. Accessed 24.4.2024.
The Ministry of Agriculture of the Czech Republic. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2018. https://eagri.cz/public/portal/-q321531---Ftyyj7-T/ryby-2018?_linka=a235043. Accessed 24.4.2024.
Mareš L, Ženíšková H, Chalupa P, Mořiský J. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2019. https://eagri.cz/public/portal/-q321563---xkJ6msTA/situacni-a-vyhledova-zprava-ryby-2019. Accessed 24.4.2024.
Mořický J, Mareš L, Ženíšková H, Chalupa P. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2020. https://eagri.cz/public/portal/-q321551---C41-pHlP/situacni-a-vyhledova-zprava-ryby-2020?_linka=a544866. Accessed 24.4.2024.
Mořický J, Mareš L, Ženíšková H, Chalupa P. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2021. https://eagri.cz/public/portal/-q321499---ZqMeMQEt/situacni-a-vyhledova-zprava-ryby-2021?_linka=a235021. Accessed 24.4.2024.
Mořický J, Ženíšková H, Chalupa P, Ptáček R. Situation and Outlook Report: Fish (In Czech). In: Situation and Outlook Reports of The Ministry of Agriculture of the Czech Republic. 2022. https://eagri.cz/public/portal/-q321521---GXo22cjp/situacni-a-vyhledova-zprava-ryby-2022?_linka=a552324. Accessed 24.4.2024.
Palíková M, Navrátil S, Mareš J. Preventive, prophylactic and curative interventions to reduce the risk of occurrence and outbreak of disease in recirculating systems of the Danish type: Certified methodology (In Czech). Brno: Mendel University; 2015.
Saticioglu IB, Duman M, Smith P, Wiklund T, Altun S. Antimicrobial resistance and resistance genes in Flavobacterium psychrophilum isolates from Turkey. Aquaculture. 2019;512:734293. https://doi.org/10.1016/j.aquaculture.2019.734293.
Li S, Chai J, Knupp C, Nicolas P, Wang D, Cao Y, Deng F, Chen F, Lu T, Loch TP. Phenotypic and genetic characterization of Flavobacterium psychrophilum recovered from diseased salmonids in China. Microbiol Spectr. 2021:e00330–21. https://doi.org/10.1128/Spectrum.00330-21.
Sundell K, Landor L, Nicolas P, Jørgensen J, Castillo D, Middelboe M, Dalsgaard I, Donati V, Madsen L, Wiklund T. Phenotypic and Genetic Predictors of Pathogenicity and Virulence in Flavobacterium psychrophilum. Front Microbiol. 2019;10:1711. https://doi.org/10.3389/fmicb.2019.01711.
Article PubMed PubMed Central Google Scholar
Nilsen H, Sundell K, Duchaud E, Nicolas P, Dalsgaard I, Madsen L, Aspán A, Jansson E, Culquhoun DJ, Wiklund T. Multilocus sequence typing identifies epidemic clones of Flavobacterium psychrophilum in nordic countries. Appl Environ Microb. 2014;80:2728–36. https://doi.org/10.1128/AEM.04233-13.
Strepparava N, Nicolas P, Wahli T, Segner H, Petrini O. Molecular epidemiology of Flavobacterium psychrophilum from Swiss fish farms. Dis Aquat Organ. 2013;105:203–10. https://doi.org/10.3354/dao02609.
Article CAS PubMed Google Scholar
Siekoula-Nguedia C, Blanc G, Duchaud E, Calvez S. Genetic diversity of Flavobacterium psychrophilum isolated from rainbow trout in France: Predominance of a clonal complex. Vet Microbiol. 2012;161:169–78. https://doi.org/10.1016/j.vetmic.2012.07.022.
Article CAS PubMed Google Scholar
Nicolas P, Mondot S, Achaz G, Bouchenot C, Bernardet JF, Duchaud E. Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl Environ Microbi. 2008;74:3702–9. https://doi.org/10.1128/AEM.00244-08.
Cepeda C, Santos Y. Rapid and low-level toxic PCR-based method for routine identification of Flavobacterium psychrophilum. Int Microbiol. 2000;3:235–8.
Dashti AA, Jadaon MM, Abdulsamad AM, Dashti HM. Heat treatment of bacteria: a simple method of DNA extraction for molecular techniques. Kuwait Med J. 2009;41:117–22.
Rochat T, Fujiwara-Nagata E, Calvez S, Dalsgaard I, Madsen L, Calteau A, Lunazzi A, Nicolas P, Wiklund T, Bernardet JF, Duchaud E. Genomic characterization of Flavobacterium psychrophilum serotypes and development of a multiplex PCR-based serotyping scheme. Front Microbiol. 2017;8:1752. https://doi.org/10.3389/fmicb.2017.01752.
Article PubMed PubMed Central Google Scholar
Avendaño-Herrera RE, Tapia-Cammas D, Duchaud É. Serological diversity in Flavobacterium psychrophilum: A critical update using isolates retrieved from Chilean salmon farms. J Fish Dis. 2020;43:877–88. https://doi.org/10.1111/jfd.13199.
Article CAS PubMed Google Scholar
CLSI. Methods for broth dilution susceptibility testing of bacteria isolated from aquatic animals approved guideline M49-A. 2nd edition. 960 West Valley Road, Suite 1400, Wyane, PA: Clinical and Laboratory Standards Institute; 2014.
CLSI. Performance Standards for Antimicrobial Susceptibility Testing of Bacteria Isolated From Aquatic Animals VET04. 3rd edition. 960 West Valley Road, Suite 1400, Wyane, PA:Clinical and Laboratory Standards Institute; 2020.
Van Vliet D, Loch TP, Smith P, Faisal M. Antimicrobial Susceptibilities of Flavobacterium psychrophilum Isolates from the Great Lakes Basin. Michigan Microb Drug Resist. 2017;23:791–8. https://doi.org/10.1089/mdr.2016.0103.
Article CAS PubMed Google Scholar
Pérez-Pascual D, Rochat T, Kerouault B, Gómez E, Neulat-Ripoll F, Henry C, Quillet E, Guijarro JA, Bernardet JF, Duchaud E. More than gliding: Involvement of GldD and GldG in the virulence of Flavobacterium psychrophilum. Front Microbiol. 2017;8:2168. https://doi.org/10.3389/fmicb.2017.02168.
Article PubMed PubMed Central Google Scholar
Australian Institute for Microbiology: University Technology Sydney Sequencing Facility. https://www.sequencingatuts.org/. Accessed 5.2.2022.
Babraham Institute: Babraham Bioinformatics, FastQC. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 3.2.2022.
Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2014;31:587–9. https://doi.org/10.1093/bioinformatics/btu661.
Article CAS PubMed Google Scholar
Jolley K, Bray J, Maiden MCJJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. https://doi.org/10.12688/wellcomeopenres.14826.1.
Article CAS PubMed PubMed Central Google Scholar
Fujiwara-Nagata E, Chantry-Darmon C, Bernardet JF, Eguchi M, Duchaud E, Nicolas P. Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan. Vet Res. 2013;44:1–9. https://doi.org/10.1186/1297-9716-44-34.
Francisco AP, Bugalho M, Ramirez M, Carriço JA. Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics. 2009;10:1–15. https://doi.org/10.1186/1471-2105-10-152.
Prokka ST. Rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. https://doi.org/10.1093/bioinformatics/btu153.
Cantalapiedra CP, Hern̗andez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38:5825–9. https://doi.org/10.1093/molbev/msab293.
Article CAS PubMed PubMed Central Google Scholar
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3. https://doi.org/10.1093/bioinformatics/btv421.
Article CAS PubMed PubMed Central Google Scholar
Wishart DS, Han S, Saha S, Oler E, Peters H, Grant JR, Stothard P, Gautam V. PHASTEST: Faster than PHASTER, better than PHAST. Nucleic Acids Res. 2023;51:W443-450. https://doi.org/10.1093/nar/gkad382.
Article CAS PubMed PubMed Central Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. https://doi.org/10.1093/molbev/mst010.
留言 (0)