{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,26]],"date-time":"2026-07-26T06:29:29Z","timestamp":1785047369047,"version":"3.55.0"},"reference-count":55,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T00:00:00Z","timestamp":1729123200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Bavarian State Ministry of Food, Agriculture, Forestry and Tourism (StMELF)","award":["A\/20\/12"],"award-info":[{"award-number":["A\/20\/12"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Outbreaks of furunculosis cause significant losses in salmonid aquaculture worldwide. With a recent rise in antimicrobial resistance, regulatory measures to minimize the use of antibiotics in animal husbandry, including aquaculture, have increased scrutiny and availability of veterinary medical products to control this disease in production facilities. In such a regulatory environment, the utility of autogenous vaccines to assist with disease prevention and control as a veterinary-guided prophylactic measure is of high interest to the producers and veterinary services alike. However, evolving concepts of epidemiological units and epidemiological links need to be considered during approval and acceptance procedures for the application of autogenous vaccines in multiple aquaculture facilities. Here, we present the results of solid-state nanopore sequencing (Oxford Nanopore Technologies, ONT) performed on 54 isolates of Aeromonas salmonicida ssp. salmonicida sampled during clinical outbreaks of furunculosis in different aquaculture facilities from Bavaria, Germany, from 2017 to 2020. All of the performed analyses (phylogeny, single nucleotide polymorphism and 3D protein modeling for major immunogenic proteins) support a high probability that all studied isolates belong to the same epidemiological unit. Simultaneously, we describe a cost\/effective method of whole genome analysis with the usage of ONT as a viable strategy to study outbreaks of other pathogens in the field of aquatic veterinary medicine for the purpose of developing the best autogenous vaccine candidates applicable to multiple aquaculture establishments.<\/jats:p>","DOI":"10.3390\/pathogens13100908","type":"journal-article","created":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T09:14:03Z","timestamp":1729156443000},"page":"908","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Genomic Analysis of Aeromonas salmonicida ssp. salmonicida Isolates Collected During Multiple Clinical Outbreaks Supports Association with a Single Epidemiological Unit"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1145-8263","authenticated-orcid":false,"given":"Konrad","family":"Wojnarowski","sequence":"first","affiliation":[{"name":"Chair for Fish Diseases and Fisheries Biology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, 80539 M\u00fcnchen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5880-6400","authenticated-orcid":false,"given":"Paulina","family":"Cholewi\u0144ska","sequence":"additional","affiliation":[{"name":"Chair for Fish Diseases and Fisheries Biology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, 80539 M\u00fcnchen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Steinbauer","sequence":"additional","affiliation":[{"name":"Tiergesundheitsdienst Bayern e.V., 85586 Poing, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Lautwein","sequence":"additional","affiliation":[{"name":"Genomics & Transcriptomics Laboratory, Biological and Medical Research Centre (BMFZ), Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanvisa","family":"Hussein","sequence":"additional","affiliation":[{"name":"Chair for Fish Diseases and Fisheries Biology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, 80539 M\u00fcnchen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6884-3533","authenticated-orcid":false,"given":"Lisa-Marie","family":"Streb","sequence":"additional","affiliation":[{"name":"Helmholtz Munich, Research Unit Comparative Microbiome Analysis, 85764 Neuherberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2980-821X","authenticated-orcid":false,"given":"Du\u0161an","family":"Pali\u0107","sequence":"additional","affiliation":[{"name":"Chair for Fish Diseases and Fisheries Biology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, 80539 M\u00fcnchen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,17]]},"reference":[{"key":"ref_1","unstructured":"FAO (2023). Top 10 Species Groups in Global Aquaculture 2021, FAO."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Liu, D. (2015). Aeromonas. Molecular Medical Microbiology, Academic Press.","DOI":"10.1016\/B978-0-12-397169-2.00061-5"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"127","DOI":"10.3389\/fmicb.2017.00127","article-title":"Evolutionary roots and diversification of the genus Aeromonas","volume":"8","author":"Sanglas","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Fern\u00e1ndez-Bravo, A., and Figueras, M.J. (2020). An update on the genus Aeromonas: Taxonomy, epidemiology, and pathogenicity. Microorganisms, 8.","DOI":"10.3390\/microorganisms8010129"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Bertran, X., Rubio, M., G\u00f3me, L., Llovet, T., Mu\u00f1oz, C., Navarro, F., and Miro, E. (2021). Taxonomic identification of different species of the genus Aeromonas by whole-genome sequencing and use of their species-specific \u03b2-lactamases as phylogenetic markers. Antibiotics, 10.","DOI":"10.3390\/antibiotics10040354"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1111\/raq.12633","article-title":"Autogenous vaccination in aquaculture: A locally enabled solution towards reduction of the global antimicrobial resistance problem","volume":"14","author":"Barnes","year":"2022","journal-title":"Rev. Aquac."},{"key":"ref_7","unstructured":"Bernoth, E.M., Ellis, A.E., Midtlyng, P.J., Olivier, G., and Smith, P. (1997). Furunculosis: Multidisciplinary Fish Disease Research, Elsevier."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Chong, R.S.M. (2022). Furunculosis. Aquaculture Pathophysiology, Academic Press.","DOI":"10.1016\/B978-0-12-812211-2.00030-5"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1126\/science.adk7368","article-title":"Antibacterial activity of nonantibiotics is orthogonal to standard antibiotics","volume":"384","author":"Guillen","year":"2024","journal-title":"Science"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Elbaz, M., Stein, E., Raykhshtat, E., Weiss-Meilik, A., Cohen, R., and Ben-Ami, R. (2023). Exposure to Non-Antimicrobial Drugs and Risk of Infection with Antibiotic-Resistant Enterobacteriaceae. Antibiotics, 12.","DOI":"10.3390\/antibiotics12040789"},{"key":"ref_11","first-page":"487","article-title":"Study III: Studies on the Sensitization of Patients with Bronchial Asthma to Bacterial Proteins as Demonstrated by the Skin Reaction and the Methods Employed in the Preparation of These Proteins","volume":"35","author":"Walker","year":"1917","journal-title":"J. Med. Res."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Giedrys-Kalemba, S., Czernomysy-Furowicz, D., Fija\u0142kowski, K., and Jursa-Kulesza, J. (2018). Autovaccines in individual therapy of staphylococcal infections. Pet-To-Man Travelling Staphylococci, Academic Press.","DOI":"10.1016\/B978-0-12-813547-1.00019-4"},{"key":"ref_13","unstructured":"Behr, K.P., Zeller, G., and Selbitz, H.-J. (2023). Manual of Autogenous Vaccines (AV), The Association of European Manufacturers of Autogenous Vaccines and Sera."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"lqab019","DOI":"10.1093\/nargab\/lqab019","article-title":"Sequencing error profiles of Illumina sequencing instruments","volume":"3","author":"Stoler","year":"2021","journal-title":"NAR Genom. Bioinform."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"bbaa403","DOI":"10.1093\/bib\/bbaa403","article-title":"Oxford nanopore sequencing in clinical microbiology and infection diagnostics","volume":"22","author":"Sheka","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e00246-24","DOI":"10.1128\/jcm.00246-24","article-title":"An evolution of Nanopore next-generation sequencing technology: Implications for medical microbiology and public health","volume":"62","author":"Mostafa","year":"2024","journal-title":"J. Clin. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/1477-5956-11-42","article-title":"The Aeromonas salmonicida subsp. salmonicida exoproteome: Determination of the complete repertoire of Type-Three Secretion System effectors and identification of other virulence factors","volume":"11","author":"Heller","year":"2013","journal-title":"Proteome Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1477-5956-11-44","article-title":"The Aeromonas salmonicida subsp. salmonicida exoproteome: Global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis","volume":"11","author":"Heller","year":"2013","journal-title":"Proteome Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.fsi.2020.06.005","article-title":"Aeromonas salmonicida infection kinetics and protective immune response to vaccination in sablefish (Anoplopoma fimbria)","volume":"104","author":"Vasquez","year":"2020","journal-title":"Fish Shellfish Immunol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1006\/fsim.1994.1004","article-title":"Iron-regulated outer membrane proteins of Aeromonas salmonicida are important protective antigens in Atlantic salmon against furunculosis","volume":"4","author":"Hirst","year":"1994","journal-title":"Fish Shellfish Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1007\/s12026-016-8807-9","article-title":"Recombinant outer membrane protein C of Aeromonas hydrophila elicits mixed immune response and generates agglutinating antibodies","volume":"64","author":"Yadav","year":"2016","journal-title":"Immunol. Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1007\/s11033-014-3033-9","article-title":"Characterization of immune response elicited by the recombinant outer membrane protein OmpF of Aeromonas hydrophila, a potential vaccine candidate in murine model","volume":"41","author":"Yadav","year":"2014","journal-title":"Mol. Biol. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1111\/j.1365-2761.1992.tb00658.x","article-title":"Serine protease and glycerophospholipid: Cholesterol acyltransferase of Aeromonas salmonicida work in concert in thrombus formation; in vitro the process is counteracted by plasma antithrombin and \u03b12-macroglobulin","volume":"15","author":"Salte","year":"1992","journal-title":"J. Fish Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"15258","DOI":"10.1016\/S0021-9258(18)98611-4","article-title":"Structure of the tetragonal surface virulence array protein and gene of Aeromonas salmonicida","volume":"266","author":"Chu","year":"1991","journal-title":"J. Biol. Chem."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3137","DOI":"10.1128\/iai.63.8.3137-3142.1995","article-title":"A conserved Aeromonas salmonicida porin provides protective immunity to rainbow trout","volume":"63","author":"Lutwyche","year":"1995","journal-title":"Infect. Immun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3354\/dao068029","article-title":"Identification of the major outer membrane proteins of Aeromonas salmonicida","volume":"68","author":"Ebanks","year":"2005","journal-title":"Dis. Aquat. Org."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1186\/1471-2164-9-427","article-title":"The genome of Aeromonas salmonicida subsp. salmonicida A449: Insights into the evolution of a fish pathogen","volume":"9","author":"Reith","year":"2008","journal-title":"BMC Genom."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"104211","DOI":"10.1016\/j.micpath.2020.104211","article-title":"Recombinant outer membrane protein C of Aeromonas salmonicida subsp. masoucida, a potential vaccine candidate for rainbow trout (Oncorhynchus mykiss)","volume":"145","author":"Diao","year":"2020","journal-title":"Microb. Pathog."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3854","DOI":"10.1128\/JCM.41.8.3854-3856.2003","article-title":"Type III secretion genes in Aeromonas salmonicida subsp. salmonicida are located on a large thermolabile virulence plasmid","volume":"41","author":"Stuber","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","volume":"44","author":"Afgan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_31","unstructured":"Batut, B., Nasr, E., and Zierep, P. (2024, May 03). Pathogen Detection from (Direct Nanopore) Sequencing Data Using Galaxy\u2014Foodborne Edition (Galaxy Training Materials). Available online: https:\/\/training.galaxyproject.org\/training-material\/topics\/microbiome\/tutorials\/pathogen-detection-from-nanopore-foodborne-data\/tutorial.html."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: Hierarchical and refined dataset for big data analysis\u201410 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_34","first-page":"e000093","article-title":"Microreact: Visualizing and sharing data for genomic epidemiology and phylogeography","volume":"2","author":"Abudahab","year":"2016","journal-title":"Microb. Genom."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"ref_36","first-page":"10","article-title":"Novel plasmid-mediated colistin resistance gene mcr-3 in Escherichia coli","volume":"8","author":"Yin","year":"2017","journal-title":"MBio"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Gonzalez-Avila, L.U., Loyola-Cruz, M.A., Hern\u00e1ndez-Cortez, C., Bello-L\u00f3pez, J.M., and Castro-Escarpulli, G. (2021). Colistin resistance in Aeromonas spp.. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22115974"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"863","DOI":"10.3389\/fmicb.2017.00863","article-title":"Occurrence and variety of \u03b2-lactamase genes among Aeromonas spp. isolated from urban wastewater treatment plant","volume":"8","author":"Piotrowska","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"4990","DOI":"10.1128\/AAC.00628-15","article-title":"Identification of new natural CphA metallo-\u03b2-Lactamases CphA4 and CphA5 in Aeromonas veronii and Aeromonas hydrophila isolates from municipal sewage in central Italy","volume":"59","author":"Bottoni","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1093\/jac\/dkx184","article-title":"OXA-427, a new plasmid-borne carbapenem-hydrolysing class D \u03b2-lactamase in Enterobacteriaceae","volume":"72","author":"Bogaerts","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1128\/CMR.00039-09","article-title":"The genus Aeromonas: Taxonomy, pathogenicity, and infection","volume":"23","author":"Janda","year":"2010","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1111\/jfd.13767","article-title":"Comparative genomic analysis provides insights into taxonomy and temperature adaption of Aeromonas salmonicida","volume":"46","author":"Long","year":"2023","journal-title":"J. Fish Dis."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Charette, S.J. (2023). Aeromonas salmonicida: Genomics, Taxonomy, Diversity, Pathogenesis, Treatments and Beyond. Microorganisms, 11.","DOI":"10.3390\/microorganisms11051189"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.vetmic.2013.06.025","article-title":"Virulence, genomic features, and plasticity of Aeromonas salmonicida subsp. salmonicida, the causative agent of fish furunculosis","volume":"169","author":"Tanaka","year":"2014","journal-title":"Vet. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/nyas.14503","article-title":"The Aeromonas salmonicida plasmidome: A model of modular evolution and genetic diversity","volume":"1488","author":"Vincent","year":"2021","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1471-2180-13-36","article-title":"Clustering subspecies of Aeromonas salmonicida using IS630typing","volume":"13","author":"Studer","year":"2013","journal-title":"BMC Microbiol."},{"key":"ref_47","first-page":"259","article-title":"Phenotypic, genotypic, and phylogenetic discrepancies to differentiate Aeromonas salmonicida from Aeromonas bestiarum","volume":"8","author":"Soler","year":"2005","journal-title":"Int. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"106100","DOI":"10.1016\/j.micpath.2023.106100","article-title":"Isolation of Aeromonas salmonicida subspecies salmonicida from aquaculture environment in India: Polyphasic identification, virulence characterization, and antibiotic susceptibility","volume":"179","author":"Pradhan","year":"2023","journal-title":"Microb. Pathog."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2411","DOI":"10.3389\/fmicb.2017.02411","article-title":"Epidemiology of Danish Aeromonas salmonicida subsp. salmonicida in fish farms using whole genome sequencing","volume":"8","author":"Bartkova","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"5754","DOI":"10.1016\/j.vaccine.2013.08.053","article-title":"Protective efficacy of PLGA microspheres loaded with divalent DNA vaccine encoding the ompA gene of Aeromonas veronii and the hly gene of Aeromonas hydrophila in mice","volume":"31","author":"Gao","year":"2013","journal-title":"Vaccine"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1847","DOI":"10.1099\/mic.0.28768-0","article-title":"Contribution of the type III secretion system (TTSS) to virulence of Aeromonas salmonicida subsp. salmonicida","volume":"152","author":"Dacanay","year":"2006","journal-title":"Microbiology"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1099\/mic.0.28485-0","article-title":"Expression of and secretion through the Aeromonas salmonicida type III secretion system","volume":"152","author":"Ebanks","year":"2006","journal-title":"Microbiology"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Marcoux, P.\u00c9., Vincent, A.T., Massicotte, M.A., Paquet, V.E., Doucet, \u00c9.J., Hosseini, N., and Charette, S.J. (2020). Systematic analysis of the stress-induced genomic instability of Type Three Secretion System in Aeromonas salmonicida subsp. salmonicida. Microorganisms, 9.","DOI":"10.3390\/microorganisms9010085"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2111","DOI":"10.1099\/mic.0.27926-0","article-title":"Attenuated virulence of an Aeromonas salmonicida subsp. salmonicida type III secretion mutant in a rainbow trout model","volume":"151","author":"Burr","year":"2005","journal-title":"Microbiology"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.vetmic.2011.04.034","article-title":"Alteration of virulence factors and rearrangement of pAsa5 plasmid caused by the growth of Aeromonas salmonicida in stressful conditions","volume":"152","author":"Daher","year":"2011","journal-title":"Vet. Microbiol."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/13\/10\/908\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:15:18Z","timestamp":1760112918000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/13\/10\/908"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,17]]},"references-count":55,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2024,10]]}},"alternative-id":["pathogens13100908"],"URL":"https:\/\/doi.org\/10.3390\/pathogens13100908","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,17]]}}}