{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T05:42:50Z","timestamp":1784180570576,"version":"3.55.0"},"reference-count":104,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2021,6,4]],"date-time":"2021-06-04T00:00:00Z","timestamp":1622764800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005036","name":"Universitetet i Bergen","doi-asserted-by":"publisher","award":["n\/n"],"award-info":[{"award-number":["n\/n"]}],"id":[{"id":"10.13039\/501100005036","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Pasteurellosis in farmed lumpsuckers, Cyclopterus lumpus, has emerged as a serious disease in Norwegian aquaculture in recent years. Genomic characterization of the causative agent is essential in understanding the biology of the bacteria involved and in devising an efficient preventive strategy. The genomes of two clinical Pasteurella atlantica isolates were sequenced (\u22482.3 Mbp), and phylogenetic analysis confirmed their position as a novel species within the Pasteurellaceae. In silico analyses revealed 11 genomic islands and 5 prophages, highlighting the potential of mobile elements as driving forces in the evolution of this species. The previously documented pathogenicity of P. atlantica is strongly supported by the current study, and 17 target genes were recognized as putative primary drivers of pathogenicity. The expression level of a predicted vaccine target, an uncharacterized adhesin protein, was significantly increased in both broth culture and following the exposure of P. atlantica to lumpsucker head kidney leucocytes. Based on in silico and functional analyses, the strongest gene target candidates will be prioritized in future vaccine development efforts to prevent future pasteurellosis outbreaks.<\/jats:p>","DOI":"10.3390\/microorganisms9061215","type":"journal-article","created":{"date-parts":[[2021,6,4]],"date-time":"2021-06-04T11:12:13Z","timestamp":1622805133000},"page":"1215","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genomic Analysis of Pasteurella atlantica Provides Insight on Its Virulence Factors and Phylogeny and Highlights the Potential of Reverse Vaccinology in Aquaculture"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1520-4017","authenticated-orcid":false,"given":"Rebecca Marie","family":"Ellul","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3029-783X","authenticated-orcid":false,"given":"Panos G.","family":"Kalatzis","sequence":"additional","affiliation":[{"name":"Department of Biology, Marine Biological Section, University of Copenhagen, DK-3000 Helsing\u00f8r, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cyril","family":"Frantzen","sequence":"additional","affiliation":[{"name":"STIM\/ACD Pharma AS, Karl Johans Gate 16, 0154 Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gyri Teien","family":"Haugland","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7135-9227","authenticated-orcid":false,"given":"Snorre","family":"Gulla","sequence":"additional","affiliation":[{"name":"Norwegian Veterinary Institute, Ullev\u00e5lsveien 68, P.O. Box 8146 Dep, N-0033 Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duncan John","family":"Colquhoun","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway"},{"name":"Norwegian Veterinary Institute, Ullev\u00e5lsveien 68, P.O. 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(2013). Fiskehelserapporten 2012, Veterin\u00e6rinstituttet."},{"key":"ref_2","unstructured":"Sommerset, I., Walde, C., Bang Jensen, B., Born\u00f8, G., Haukaas, A., and Brun, E. (2020). Helsesituasjonen hos rensefisk. Fiskehelserapporten 2019, Veterin\u00e6rinstituttet."},{"key":"ref_3","unstructured":"Sommerset, I., Bang Jensen, B., Born\u00f8, G., Haukaas, A., and Brun, E. (2021). Pasteurella infeksjon hos laks. Fiskehelserapporten 2020, Veterin\u00e6rinstituttet."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1111\/jfd.12366","article-title":"Pasteurellosis in lumpsucker Cyclopterus lumpus, farmed in Norway","volume":"39","author":"Gulla","year":"2016","journal-title":"J. Fish Dis."},{"key":"ref_5","unstructured":"Kui, S. (2017). Stamfisk screening. Proceedings of the Rensefiskkonferansen, PatoGen Analyse."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.fsi.2019.11.016","article-title":"Protection and antibody reactivity in lumpsucker (Cyclopterus lumpus L.) following vaccination against Pasteurella sp.","volume":"95","author":"Ellul","year":"2019","journal-title":"Fish Shellfish Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.3389\/fimmu.2018.02315","article-title":"Bacterial vaccine antigen discovery in the reverse vaccinology 2.0 Era: Progress and challenges","volume":"9","author":"Bidmos","year":"2018","journal-title":"Front. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Ong, E., Cooke, M.F., Huffman, A., Xiang, Z., Wong, M.U., Wang, H., Seetharaman, M., Valdez, N., and He, Y. (2021). Vaxign2: The second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acids Res., gkab279.","DOI":"10.1093\/nar\/gkab279"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"297505","DOI":"10.1155\/2010\/297505","article-title":"Vaxign: The first web-based vaccine design program for reverse vaccinology and applications for vaccine development","volume":"2010","author":"He","year":"2010","journal-title":"J. Biomed. Biotechnol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s11274-021-03021-6","article-title":"Advanced strategies for development of vaccines against human bacterial pathogens","volume":"37","author":"Sharma","year":"2021","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1126\/science.287.5459.1816","article-title":"Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing","volume":"287","author":"Pizza","year":"2000","journal-title":"Science."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"751","DOI":"10.3389\/fimmu.2019.00751","article-title":"The development of a vaccine against Meningococcus B using reverse vaccinology","volume":"10","author":"Masignani","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1080\/15216540212651","article-title":"Transcriptomics and Proteomics: Tools for the Identification of Novel Drug Targets and Vaccine Candidates for Tuberculosis","volume":"53","author":"Betts","year":"2002","journal-title":"IUBMB Life"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1128\/IAI.70.1.368-379.2002","article-title":"Genomic approach for analysis of surface proteins in Chlamydia pneumoniae","volume":"70","author":"Montigiani","year":"2002","journal-title":"Infect. Immun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1128\/IAI.69.3.1593-1598.2001","article-title":"Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection","volume":"69","author":"Wizemann","year":"2001","journal-title":"Infect. Immun."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/S0264-410X(00)00256-5","article-title":"Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates","volume":"19","author":"Chakravarti","year":"2000","journal-title":"Vaccine"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4135","DOI":"10.1016\/S0264-410X(01)00173-6","article-title":"Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis","volume":"19","author":"Ross","year":"2001","journal-title":"Vaccine"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"6817","DOI":"10.1128\/IAI.70.12.6817-6827.2002","article-title":"Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: In silico and in vitro screening","volume":"70","author":"Ariel","year":"2002","journal-title":"Infect. Immun."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"747","DOI":"10.3389\/fmicb.2015.00747","article-title":"Whole genome protein microarrays for serum profiling of immunodominant antigens of Bacillus anthracis","volume":"6","author":"Kempsell","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3185","DOI":"10.1093\/bioinformatics\/btaa119","article-title":"Vaxign-ML: Supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens","volume":"36","author":"Ong","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_21","unstructured":"Sails, A., Poxton, I., Liu, D., and Schwartzman, J. (2014). Adhesion and colonisation. Molecular Medical Microbiology, Elsevier Science."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/0264-410X(93)90020-X","article-title":"Vaccines for preventing enterotoxigenic Escherichia coli infections in farm animals","volume":"11","author":"Moon","year":"1993","journal-title":"Vaccine"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1086\/315258","article-title":"Vaccination with FimH Adhesin Protects Cynomolgus Monkeys from Colonization and Infection by Uropathogenic Escherichia coli","volume":"181","author":"Langermann","year":"2000","journal-title":"J. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1016\/j.fsi.2003.10.003","article-title":"Cloning, characterisation and expression of Aeromonas hydrophila major adhesin","volume":"16","author":"Fang","year":"2004","journal-title":"Fish Shellfish Immunol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.vetimm.2012.07.013","article-title":"Evaluation of two outer membrane proteins, Aha1 and OmpW of Aeromonas hydrophila as vaccine candidate for common carp","volume":"149","author":"Maiti","year":"2012","journal-title":"Vet. Immunol. Immunopathol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.fsi.2018.11.037","article-title":"Identification of outer membrane protein TolC as the major adhesin and potential vaccine candidate for Vibrio harveyi in hybrid grouper, Epinephelus fuscoguttatus (\u2640) \u00d7 E. lanceolatus (\u2642)","volume":"86","author":"Zhu","year":"2019","journal-title":"Fish Shellfish Immunol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"736596","DOI":"10.1016\/j.aquaculture.2021.736596","article-title":"Edwardsiella tarda outer membrane protein 1 is a virulence factor and a protective immunogen","volume":"539","author":"Jin","year":"2021","journal-title":"Aquaculture"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1111\/jfd.12905","article-title":"Pathogenicity of Pasteurella sp. in lumpsuckers (Cyclopterus lumpus L.)","volume":"42","author":"Ellul","year":"2018","journal-title":"J. Fish Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1089\/cmb.2013.0084","article-title":"Assembling single-cell genomes and mini-metagenomes from chimeric MDA products","volume":"20","author":"Nurk","year":"2013","journal-title":"J. Comput. Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","article-title":"Identifying bacterial genes and endosymbiong DNA with Glimmer","volume":"23","author":"Delcher","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1099\/00207713-35-3-309","article-title":"Reclassification of the genus Pasteurella Trevisan 1887 on the basis of deoxyribonucleic acid homology, with proposals for the new species Pasteurella dagmatis, Pasteurella canis, Pasteurella stomatis, Pasteurella anatis, and Pasteurella langaa","volume":"35","author":"Mutters","year":"1985","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1099\/00207713-32-2-201","article-title":"Pasteurella testudinis sp. nov.: A Parasite of Desert Tortoises (Gopherus agassizi)","volume":"32","author":"Snipes","year":"1982","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1099\/ijs.0.035246-0","article-title":"Classification of Pasteurella species B as Pasteurella oralis sp. nov.","volume":"62","author":"Christensen","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1099\/00207713-52-3-699","article-title":"Pasteurella skyensis sp. nov., isolated from Atlantic salmon (Salmo salar L.)","volume":"52","author":"Birkbeck","year":"2002","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1099\/00207713-50-1-135","article-title":"Phocoenobacter uteri gen. nov., sp. nov., a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from a harbour porpoise (Phocoena phocoena)","volume":"50","author":"Foster","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12879-018-3324-1","article-title":"BMScan: Using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species","volume":"18","author":"Topaz","year":"2018","journal-title":"BMC Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Roach, D.J., Burton, J.N., Lee, C., Stackhouse, B., Butler-Wu, S.M., Cookson, B.T., Shendure, J., and Salipante, S.J. (2015). A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. PLoS Genet., 11.","DOI":"10.1371\/journal.pgen.1005413"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Nichols, M., Topaz, N., Wang, X., Wang, X., and Boxrud, D. (2018). Draft genome sequences for a diverse set of isolates from 10 Neisseria species. Genome Announc., 6.","DOI":"10.1128\/genomeA.00409-18"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1099\/ijsem.0.003730","article-title":"Phylogenomic analysis of Haemophilus parasuis and proposed reclassification to Glaesserella parasuis, gen. Nov., comb. nov.","volume":"70","author":"Dickerman","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1111\/j.1439-0450.2001.00433.x","article-title":"Pathogenicity of Actinobacillus minor, Actinobacillus indolicus and Actinobacillus porcinus Strains for Gnotobiotic Piglets","volume":"131","author":"Chiers","year":"2001","journal-title":"J. Vet. Med. Sci."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1128\/genomeA.00318-13","article-title":"Complete genome sequence of Mannheimia haemolytica strain 42548 from a case of bovine respiratory disease","volume":"1","author":"Eidam","year":"2013","journal-title":"Genome Announc."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","article-title":"OrthoANI: An improved algorithm and software for calculating average nucleotide identity","volume":"66","author":"Lee","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: Fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"D581","DOI":"10.1093\/nar\/gkt1099","article-title":"PATRIC, the bacterial bioinformatics database and analysis resource","volume":"42","author":"Wattam","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center","volume":"45","author":"Wattam","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2016.00118","article-title":"PATtyFams: Protein families for the microbial genomes in the PATRIC database","volume":"7","author":"Davis","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: Freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1080\/10635150802429642","article-title":"A rapid bootstrap algorithm for the RAxML web-servers","volume":"57","author":"Stamatakis","year":"2008","journal-title":"Syst. Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree of Life (iTOL) v4: Recent updates and new developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: A comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"D693","DOI":"10.1093\/nar\/gky999","article-title":"Victors: A web-based knowledge base of virulence factors in human and animal pathogens","volume":"47","author":"Sayers","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1093\/bioinformatics\/btu631","article-title":"Curation, integration and visualization of bacterial virulence factors in PATRIC","volume":"31","author":"Mao","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/s41587-019-0036-z","article-title":"SignalP 5. 0 improves signal peptide predictions using deep neural networks","volume":"37","author":"Armenteros","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1093\/bioinformatics\/bti028","article-title":"SPAAN: A software program for prediction of adhesins and adhesin-like proteins using neural networks","volume":"21","author":"Sachdeva","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modelling, prediction, and analysis","volume":"10","author":"Kelly","year":"2015","journal-title":"Nat. Protoc."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Lopes, A., Tavares, P., Petit, M.-A., Gu\u00e9rois, R., and Zinn-Justin, S. (2014). Automated classification of tailed bacteriophages according to their neck organization. BMC Genomics, 15.","DOI":"10.1186\/1471-2164-15-1027"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.fsi.2009.03.019","article-title":"Atlantic salmon bath challenged with Moritella viscosa\u2014Pathogen invasion and host response","volume":"26","author":"Colquhoun","year":"2009","journal-title":"Fish Shellfish Immunol."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Doytchinova, I.A., and Flower, D.R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-4"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2-\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Haugland, G.T., Jakobsen, R.A., Vestvik, N., Ulven, K., Stokka, L., and Wergeland, H.I. (2012). Phagocytosis and Respiratory Burst Activity in Lumpsucker (Cyclopterus lumpus L.) Leucocytes Analysed by Flow Cytometry. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0047909"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"e00001-17","DOI":"10.1128\/mSystems.00001-17","article-title":"Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits","volume":"2","author":"Castillo","year":"2017","journal-title":"mSystems"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.gene.2018.05.084","article-title":"Pan-genomic approach shows insight of genetic divergence and pathogenic-adaptation of Pasteurella multocida","volume":"670","author":"Hurtado","year":"2018","journal-title":"Gene"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Zhu, D., He, J., Yang, Z., Wang, M., Jia, R., Chen, S., Liu, M., Zhao, X., Yang, Q., and Wu, Y. (2019). Comparative analysis reveals the Genomic Islands in Pasteurella multocida population genetics: On Symbiosis and adaptability. BMC Genom., 20.","DOI":"10.1186\/s12864-018-5366-6"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Niu, Y.D., Cook, S.R., Wang, J., Klima, C.L., Hsu, Y., Kropinski, A.M., Turner, D., and Mcallister, T.A. (2015). Comparative analysis of multiple inducible phages from Mannheimia haemolytica. BMC Microbiol., 15.","DOI":"10.1186\/s12866-015-0494-5"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1177\/1040638711404143","article-title":"Detection of a bacteriophage gene encoding a Mu-like portal protein in Haemophilus parasuis reference strains and field isolates by nested polymerase chain reaction","volume":"23","author":"Zehr","year":"2011","journal-title":"J. Vet. Diagnostic Investig."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/S1438-4221(00)80102-2","article-title":"Bacterial adhesins: Function and structure","volume":"290","author":"Klemm","year":"2000","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/sj.emboj.7600100","article-title":"The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel \u03b2-roll","volume":"23","author":"Nummelin","year":"2004","journal-title":"EMBO J."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"6005","DOI":"10.1128\/JB.182.21.6005-6013.2000","article-title":"The Haemophilus influenzae Hia adhesin is an autotransporter protein that remains uncleaved at the C terminus and fully cell associated","volume":"182","author":"Cutter","year":"2000","journal-title":"J. Bacteriol."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., and Thompson, F. (2013). The Prokaryotes: Gammaproteobacteria, Springer.","DOI":"10.1007\/978-3-642-30144-5"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1128\/AEM.00058-15","article-title":"The fur gene as a new phylogenetic marker for Vibrionaceae species identification","volume":"81","author":"Machado","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"19856","DOI":"10.1155\/2015\/198560","article-title":"Phylogenomic and molecular demarcation of the core members of the polyphyletic Pasteurellaceae genera Actinobacillus, Haemophilus, and Pasteurella","volume":"2015","author":"Naushad","year":"2015","journal-title":"Int. J. Genomics"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Aktories, K., Orth, J.H.C., and Adler, B. (2012). Pasteurella multocida: Diseases and Pathogenesis. Pasteurella multocida: Molecular Biology, Toxins and Infection, Springer.","DOI":"10.1007\/978-3-642-31017-1"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/j.vetmic.2017.04.015","article-title":"Characterization of Pasteurella multocida associated with ovine pneumonia using multi-locus sequence typing ( MLST ) and virulence-associated gene pro file analysis and comparison with porcine isolates","volume":"204","author":"Vela","year":"2017","journal-title":"Vet. Microbiol."},{"key":"ref_80","first-page":"148","article-title":"Pasteurellosis in Atlantic salmon (Salmo salar) in Western Norway","volume":"40","year":"2020","journal-title":"Bull. Eur. Assoc. Fish Pathol."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Castillo, D., Kauffman, K., Hussain, F., Kalatzis, P., R\u00f8rbo, N., Polz, M.F., and Middelboe, M. (2018). Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-28326-9"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"5458","DOI":"10.1128\/AEM.71.9.5458-5464.2005","article-title":"Interaction of Pasteurella multocida with free-living amoebae","volume":"71","author":"Hundt","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/nrmicro1233","article-title":"Mobile DNA in obligate intracellular bacteria","volume":"3","author":"Bordenstein","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0151409","article-title":"Mobilization of genomic islands of Staphylococcus aureus by temperate bacteriophage","volume":"11","author":"Moon","year":"2016","journal-title":"PLoS ONE"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"15010","DOI":"10.1038\/nmicrobiol.2015.10","article-title":"Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants","volume":"1","author":"Ingle","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"113","DOI":"10.2174\/1389202915999140328163125","article-title":"Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method","volume":"15","author":"Zhang","year":"2014","journal-title":"Curr. Genom."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/S1286-4579(00)00273-2","article-title":"Salmonella pathogenicity islands: Big virulence in small packages","volume":"2","author":"Marcus","year":"2000","journal-title":"Microbes Infect."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Vivona, S., Bernante, F., and Filippini, F. (2006). NERVE: New Enhanced Reverse Vaccinology Environment. BMC Biotechnol., 6.","DOI":"10.1186\/1472-6750-6-35"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fimmu.2019.00113","article-title":"Comparison of open-source reverse vaccinology programs for bacterial vaccine antigen discovery","volume":"10","author":"Dalsass","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"He, Y. (2015). Bacterial Whole-Genome Determination and Applications. Molecular Medical Microbiology, Academic Press.","DOI":"10.1016\/B978-0-12-397169-2.00020-2"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3389\/fcimb.2011.00005","article-title":"Structure and function of the Haemophilus influenzae autotransporters","volume":"1","author":"Spahich","year":"2011","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/s00430-019-00649-y","article-title":"Immunogenicity of trimeric autotransporter adhesins and their potential as vaccine targets","volume":"209","author":"Thibau","year":"2020","journal-title":"Med. Microbiol. Immunol."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1078\/1438-4221-00119","article-title":"YadA, the multifaceted Yersinia adhesin","volume":"291","author":"Skurnik","year":"2001","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1292\/jvms.16-0528","article-title":"A study on the efficacy of the recombinant Yersinia adhesin A vaccine against yersiniosis in the early phase","volume":"79","author":"Tsugo","year":"2017","journal-title":"J. Vet. Med. Sci."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.tim.2006.04.005","article-title":"Trimeric autotransporter adhesins: Variable structure, common function","volume":"14","author":"Linke","year":"2006","journal-title":"Trends Microbiol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1128\/CVI.00090-09","article-title":"Antibodies specific for the Hia adhesion proteins of nontypeable Haemophilus influenzae mediate opsonophagocytic activity","volume":"16","author":"Winter","year":"2009","journal-title":"Clin. Vaccine Immunol."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Winter, L.E., and Barenkamp, S.J. (2017). Immunogenicity of Nontypeable Haemophilus influenzae Outer Membrane Vesicles and Protective Ability in the Chinchilla Model of Otitis Media. Clin. Vaccine Immunol., 24.","DOI":"10.1128\/CVI.00138-17"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1093\/femspd\/fty016","article-title":"Protein adhesins as vaccine antigens for Group A Streptococcus","volume":"76","author":"Raynes","year":"2018","journal-title":"Pathog. Dis."},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Ma, J., Bruce, T.J., Jones, E.M., and Cain, K.D. (2019). A Review of Fish Vaccine Development Strategies: Conventional Methods and Modern Biotechnological Approaches. Microorganisms, 7.","DOI":"10.3390\/microorganisms7110569"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0171944","article-title":"Subunit vaccine candidates against Aeromonas salmonicida in rainbow trout Oncorhynchus mykiss","volume":"12","author":"Marana","year":"2017","journal-title":"PLoS ONE"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.fsi.2020.07.045","article-title":"Development of IglC and GroEL recombinant vaccines for francisellosis in Nile tilapia, Oreochromis niloticus","volume":"105","author":"Shahin","year":"2020","journal-title":"Fish Shellfish Immunol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1016\/j.vaccine.2006.10.032","article-title":"Protective efficacy of recombinant OmpTS protein of Aeromonas hydrophila in Indian major carp","volume":"25","author":"Khushiramani","year":"2007","journal-title":"Vaccine"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.aquaculture.2012.03.033","article-title":"Outer membrane protein K as a subunit vaccine against V. anguillarum","volume":"354\u2013355","author":"Hamod","year":"2012","journal-title":"Aquaculture"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.resmic.2012.03.001","article-title":"Recombinant Aeromonas hydrophila outer membrane protein 48 (Omp48) induces a protective immune response against Aeromonas hydrophila and Edwardsiella tarda","volume":"163","author":"Khushiramani","year":"2012","journal-title":"Res. Microbiol."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/6\/1215\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:10:48Z","timestamp":1760163048000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/6\/1215"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,4]]},"references-count":104,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2021,6]]}},"alternative-id":["microorganisms9061215"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms9061215","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,4]]}}}