{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T23:25:00Z","timestamp":1792020300752,"version":"4.4.0"},"reference-count":79,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T00:00:00Z","timestamp":1680048000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["301084\/2019-0"],"award-info":[{"award-number":["301084\/2019-0"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["Finance Code 001."],"award-info":[{"award-number":["Finance Code 001."]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["301084\/2019-0"],"award-info":[{"award-number":["301084\/2019-0"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["Finance Code 001."],"award-info":[{"award-number":["Finance Code 001."]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Salmonella Gallinarum (SG) is the causative agent of fowl typhoid (FT), a disease that is harmful to the poultry industry. Despite sanitation and prophylactic measures, this pathogen is associated with frequent disease outbreaks in developing countries, causing high morbidity and mortality. We characterized the complete genome sequence of Colombian SG strains and then performed a comparative genome analysis with other SG strains found in different regions worldwide. Eight field strains of SG plus a 9R-derived vaccine were subjected to whole-genome sequencing (WGS) and bioinformatics analysis, and the results were used for subsequent molecular typing; virulome, resistome, and mobilome characterization; and a comparative genome study. We identified 26 chromosome-located resistance genes that mostly encode efflux pumps, and point mutations were found in gyrase genes (gyrA and gyrB), with the gyrB mutation S464T frequently found in the Colombian strains. Moreover, we detected 135 virulence genes, mainly in 15 different Salmonella pathogenicity islands (SPIs). We generated an SPI profile for SG, including C63PI, CS54, ssaD, SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-6, SPI-9, SPI-10, SPI-11, SPI-12, SPI-13, and SPI-14. Regarding mobile genetic elements, we found the plasmids Col(pHAD28) and IncFII(S) in most of the strains and 13 different prophage sequences, indicating a frequently obtained profile that included the complete phage Gifsy_2 and incomplete phage sequences resembling Escher_500465_2, Shigel_SfIV, Entero_mEp237, and Salmon_SJ46. This study presents, for the first time, the genomic content of Colombian SG strains and a profile of the genetic elements frequently found in SG, which can be further studied to clarify the pathogenicity and evolutionary characteristics of this serotype.<\/jats:p>","DOI":"10.3390\/genes14040823","type":"journal-article","created":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T03:17:35Z","timestamp":1680146255000},"page":"823","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Genomic Characterization and Genetic Profiles of Salmonella Gallinarum Strains Isolated from Layers with Fowl Typhoid in Colombia"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1044-7450","authenticated-orcid":false,"given":"Ruy D.","family":"Chac\u00f3n","sequence":"first","affiliation":[{"name":"Department of Pathology, School of Veterinary Medicine, University of S\u00e3o Paulo, S\u00e3o Paulo 05508-270, Brazil"},{"name":"Inter-Units Program in Biotechnology, University of S\u00e3o Paulo, S\u00e3o Paulo 05508-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Ram\u00edrez","sequence":"additional","affiliation":[{"name":"Unidad de Bioinform\u00e1tica, Centro de Investigaciones Tecnol\u00f3gicas, Biom\u00e9dicas y Medioambientales, Bellavista 07006, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0975-6122","authenticated-orcid":false,"given":"Carmen L.","family":"Rodr\u00edguez-Cueva","sequence":"additional","affiliation":[{"name":"Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0978-5740","authenticated-orcid":false,"given":"Christian","family":"S\u00e1nchez","sequence":"additional","affiliation":[{"name":"Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), 28040 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilma Ursula","family":"Quispe-Rojas","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudete S.","family":"Astolfi-Ferreira","sequence":"additional","affiliation":[{"name":"Department of Pathology, School of Veterinary Medicine, University of S\u00e3o Paulo, S\u00e3o Paulo 05508-270, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0086-5181","authenticated-orcid":false,"given":"Antonio J.","family":"Piantino Ferreira","sequence":"additional","affiliation":[{"name":"Department of Pathology, School of Veterinary Medicine, University of S\u00e3o Paulo, S\u00e3o Paulo 05508-270, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.resmic.2009.10.002","article-title":"Supplement 2003\u20132007 (No. 47) to the White-Kauffmann-Le Minor Scheme","volume":"161","author":"Guibourdenche","year":"2010","journal-title":"Res. 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