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A total of 400 fish specimens were collected from affected tilapia farms within five Egyptian governorates. A total of 344 bacterial isolates were identified from the examined fish specimens. Bacterial isolates were grouped into seven genera based on API 20E results. The most prevalent pathogens were <jats:italic>Aeromonas<\/jats:italic> spp. (42%), <jats:italic>Vibrio<\/jats:italic> spp. (21%), and <jats:italic>Streptococcus agalactiae<\/jats:italic> (14.5%). Other emerging infections like, <jats:italic>Plesiomonas shigelloides<\/jats:italic> (10%), <jats:italic>Staphyloccocus<\/jats:italic> spp<jats:italic>.<\/jats:italic> (8%), <jats:italic>Pseudomonas oryzihabitans<\/jats:italic>, and <jats:italic>Acinetobacter lwoffii<\/jats:italic> (2.3%) were also detected. Sequence analysis of the 16S ribosomal RNA bacterial gene of some isolates, confirmed the phenotypic identification results. The analysis of antibiotic resistance genes revealed the presence of <jats:italic>aac<\/jats:italic>(6\u2032)\u2010<jats:italic>Ib\u2010cr<\/jats:italic> (35.7%), <jats:italic>bla<\/jats:italic>CTX gene (23.8%), <jats:italic>qnr<\/jats:italic>S (19%), <jats:italic>ampC<\/jats:italic> (16.7%), <jats:italic>floR<\/jats:italic> (14.3%), <jats:italic>sul<\/jats:italic>1, <jats:italic>tet<\/jats:italic>A, and <jats:italic>van<\/jats:italic>.C1 (2.4%) genes in some isolates. The antimicrobia resistance gene, <jats:italic>qac<\/jats:italic> was reported in 46% of screened isolates. Bacterial strains showed variable virulence genes profiles. <jats:italic>Aeromonas<\/jats:italic> spp. harboured (<jats:italic>act<\/jats:italic>, <jats:italic>gcat<\/jats:italic>, <jats:italic>aerA<\/jats:italic>, <jats:italic>lip<\/jats:italic>, <jats:italic>fla<\/jats:italic>, and <jats:italic>ser<\/jats:italic>) genes. All <jats:italic>Vibrio<\/jats:italic> spp. possessed the <jats:italic>hlyA<\/jats:italic> gene, while <jats:italic>cylE<\/jats:italic>, <jats:italic>hylB<\/jats:italic>, and <jats:italic>lmb<\/jats:italic> genes, were detected in <jats:italic>S. agalactiae<\/jats:italic> strains. Our findings point to the possible role of the identified bacterial pathogens in tilapia summer mortality syndrome and highlight the risk of the irresponsible use of antibiotics on antimicrobial resistance in aquaculture.<\/jats:p>","DOI":"10.1111\/jfd.13710","type":"journal-article","created":{"date-parts":[[2022,9,4]],"date-time":"2022-09-04T19:18:56Z","timestamp":1662319136000},"page":"1857-1871","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Genetic characterization and antimicrobial profiling of bacterial isolates collected from Nile tilapia (<i>Oreochromis niloticus<\/i>) affected by summer mortality syndrome"],"prefix":"10.1111","volume":"45","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0227-8124","authenticated-orcid":false,"given":"Shimaa E.","family":"Ali","sequence":"first","affiliation":[{"name":"WorldFish, Abbassa  Sharqia Egypt"},{"name":"Department of Hydrobiology Veterinary Research Institute, National Research Centre  Giza Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Osama","family":"Mahana","sequence":"additional","affiliation":[{"name":"Animal Health Research Institute, Agricultural Research Center  Giza Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chadag Vishnumurthy","family":"Mohan","sequence":"additional","affiliation":[{"name":"WorldFish, Jalan Batu Maung  Penang Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4169-2456","authenticated-orcid":false,"given":"Jerome","family":"Delamare\u2010Deboutteville","sequence":"additional","affiliation":[{"name":"WorldFish, Jalan Batu Maung  Penang Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mamdouh Y.","family":"Elgendy","sequence":"additional","affiliation":[{"name":"Department of Hydrobiology Veterinary Research Institute, National Research Centre  Giza Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2022,9,4]]},"reference":[{"key":"e_1_2_9_2_1","first-page":"328","article-title":"Occurrence, seasonal variations and virulence of Aeromonas hydrophila and Aeromonas caviae in fish farms at East Delta, Egypt","volume":"13","author":"Abd\u2010Elall A.","year":"2014","journal-title":"Global Veterinaria"},{"key":"e_1_2_9_3_1","first-page":"6","article-title":"Multifactorial causes of mass mortality in Oreochromis niloticus in Kafr El\u2010Sheikh, Egypt","volume":"41","author":"Abdel\u2010moneam D. 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