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However, <jats:italic>Salmonella<\/jats:italic> virulence gene distributions and mechanisms remain unestablished. In the Philippines, studies mainly report <jats:italic>Salmonella<\/jats:italic> incidences and antimicrobial resistance, but little to none on virulence profiles, their associations to animal sources, collection sites and <jats:italic>Salmonella<\/jats:italic> serogroups. Hence, a total of 799 <jats:italic>Salmonella<\/jats:italic> isolates, previously obtained from pig, cow, and chicken meat samples in wet markets and abattoirs (wet markets: 124 chicken, 151 cow, and 352 pig meat isolates; abattoirs: 172 pig tonsil and jejunum isolates) in Metro Manila, Philippines, were revived and confirmed as <jats:italic>Salmonella<\/jats:italic> through <jats:italic>invA<\/jats:italic> gene polymerase chain reaction (PCR). Isolates were then screened for eight virulence genes, namely <jats:italic>avrA<\/jats:italic>, <jats:italic>hilA<\/jats:italic>, <jats:italic>sseC<\/jats:italic>, <jats:italic>mgtC<\/jats:italic>, <jats:italic>spi4R<\/jats:italic>, <jats:italic>pipB<\/jats:italic>, <jats:italic>spvC<\/jats:italic> and <jats:italic>spvR<\/jats:italic>, by optimized multiplex PCR and significant pair associations between virulence genes were determined through Fisher\u2019s exact test. Gene frequency patterns were also determined. <jats:italic>Salmonella<\/jats:italic> serogroups in addition to animal sources and location types were also used to predict virulence genes prevalence using binary logistic regression.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>High frequencies (64 to 98%) of SPI virulence genes were detected among 799 <jats:italic>Salmonella<\/jats:italic> isolates namely <jats:italic>mgtC<\/jats:italic>, <jats:italic>pipB<\/jats:italic>, <jats:italic>avrA<\/jats:italic>, <jats:italic>hilA<\/jats:italic>, <jats:italic>spi4R<\/jats:italic> and <jats:italic>sseC,<\/jats:italic> from most to least. However, only one isolate was positive for plasmid-borne virulence genes, <jats:italic>spvC<\/jats:italic> and <jats:italic>spvR<\/jats:italic>. Diversity in virulence genes across <jats:italic>Salmonella<\/jats:italic> serogroups for 587 <jats:italic>Salmonella<\/jats:italic> isolates (O:3\u2009=\u2009250, O:4\u2009=\u2009133, O:6,7\u00a0=\u200999, O:8\u2009=\u200993, O:9\u2009=\u200912) was also demonstrated through statistical predictions, particularly for <jats:italic>avrA<\/jats:italic>, <jats:italic>hilA<\/jats:italic>, <jats:italic>sseC<\/jats:italic>, and <jats:italic>mgtC<\/jats:italic>. <jats:italic>mgtC<\/jats:italic>, the most frequent virulence gene, was predicted by serogroup O:9, while <jats:italic>sseC<\/jats:italic>, the least frequent, was predicted by serogroup O:4 and chicken animal source. The highest virulence gene pattern involved SPIs 1-5 genes which suggests the wide distribution and high pathogenic potential of <jats:italic>Salmonella<\/jats:italic>. Statistical analyses showed five virulence gene pair associations, namely <jats:italic>avrA<\/jats:italic> and <jats:italic>hilA<\/jats:italic>, <jats:italic>avrA<\/jats:italic> and <jats:italic>spi4R<\/jats:italic>, <jats:italic>hilA<\/jats:italic> and <jats:italic>spi4R<\/jats:italic>, <jats:italic>sseC<\/jats:italic> and <jats:italic>spi4R<\/jats:italic>, and <jats:italic>mgtC<\/jats:italic> and <jats:italic>pipB<\/jats:italic>. The animal sources predicted the presence of virulence genes, <jats:italic>sseC<\/jats:italic> and <jats:italic>pipB<\/jats:italic>, whereas location type for <jats:italic>hilA<\/jats:italic> and <jats:italic>spi4R<\/jats:italic>, suggesting that these factors may contribute to the type and pathogenicity of <jats:italic>Salmonella<\/jats:italic> present.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The high prevalence of virulence genes among <jats:italic>Salmonella<\/jats:italic> in the study suggests the high pathogenic potential of <jats:italic>Salmonella<\/jats:italic> from abattoirs and wet markets of Metro Manila, Philippines which poses food safety and public health concerns and threatens the Philippine food animal industry. Statistical associations between virulence genes and prediction analyses across <jats:italic>Salmonella<\/jats:italic> serogroups and external factors such as animal source and location type and presence of virulence genes suggest the diversity of <jats:italic>Salmonella<\/jats:italic> virulence and illustrate determining factors to <jats:italic>Salmonella<\/jats:italic> pathogenicity. This study recommends relevant agencies in the Philippines to improve standards in food animal industries and increase efforts in monitoring of foodborne pathogens.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-022-02697-6","type":"journal-article","created":{"date-parts":[[2022,12,6]],"date-time":"2022-12-06T08:04:04Z","timestamp":1670313844000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Genotypic virulence profiles and associations in Salmonella isolated from meat samples in wet markets and abattoirs of Metro Manila, Philippines"],"prefix":"10.1186","volume":"22","author":[{"given":"Rance Derrick N.","family":"Pavon","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo D. 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Front Vet Sci. 2020;6:502. https:\/\/doi.org\/10.3389\/fvets.2019.00502.","journal-title":"Front Vet Sci"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-022-02697-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-022-02697-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-022-02697-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,10]],"date-time":"2022-12-10T10:03:38Z","timestamp":1670666618000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmicrobiol.biomedcentral.com\/articles\/10.1186\/s12866-022-02697-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,6]]},"references-count":85,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["2697"],"URL":"https:\/\/doi.org\/10.1186\/s12866-022-02697-6","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,6]]},"assertion":[{"value":"9 August 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 December 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Ethical review and approval were waived for this study due to informed consent obtained from the Philippine National Meat Inspection Service. Animal slaughter and evisceration were performed according to national regulations. Informed consent was also obtained from veterinarians in charge of the abattoirs, and farm owners for sample collection.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that the research was conducted without any commercial or financial relationships that could be construed as potential competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"292"}}