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The main research goal was to reveal new insights into possible virulence genes by comparing the genomes of bacterial isolates that could induce tissue damage and mortality versus the genome of a non-virulent isolate. The results indicated that only the genomes of the virulent isolates possessed unique genes encoding amongst others a methyl-accepting chemotaxis protein possibly involved in the initial colonization of tissue, and several VgrG proteins engaged in interbacterial competition. Furthermore, comparisons of genes unique for the genomes of the highly virulent (HV) carp and trout isolates versus the, respectively, low and non-virulent carp and trout isolates were performed. An important part of the identified unique virulence genes of the HV-trout isolate was located in one particular gene region identified as a genomic island. This region contained <jats:italic>ara<\/jats:italic>C and <jats:italic>nod<\/jats:italic>T genes, both linked to pathogenic and multidrug-resistance, and a <jats:italic>lux<\/jats:italic>R-gene, functional in bacterial cell-to-cell communication. Furthermore, the genome of the HV-trout isolate possessed unique sugar-transferases possibly important in bacterial adhesion. The second research goal was to obtain insights into the genetic basis of acquired antimicrobial resistance. Several point-mutations were discovered in gyrase-genes of an isolate showing phenotypic resistance towards first and second-generation quinolones, which were absent in isolates susceptible to quinolones. Tetracycline-resistance gene <jats:italic>tet<\/jats:italic>A was found in an isolate displaying acquired phenotypic resistance towards oxytetracycline. Although not localized on a prophage, several flanking genes were indicative of the gene\u2019s mobile character.<\/jats:p>","DOI":"10.1186\/s13567-021-00899-w","type":"journal-article","created":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T20:35:32Z","timestamp":1613162132000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Comparative genomics of Flavobacterium columnare unveils novel insights in virulence and antimicrobial resistance mechanisms"],"prefix":"10.1186","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6041-9597","authenticated-orcid":false,"given":"Annelies Maria","family":"Declercq","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurentijn","family":"Tilleman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yannick","family":"Gansemans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chlo\u00eb","family":"De Witte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Freddy","family":"Haesebrouck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filip","family":"Van Nieuwerburgh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annemieke","family":"Smet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annemie","family":"Decostere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,2,12]]},"reference":[{"key":"899_CR1","volume-title":"The prokaryotes: a handbook on the biology of bacteria: vol 7: proteobacteria: delta and epsilon subclasses. 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