{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T22:26:40Z","timestamp":1788906400491,"version":"build-2803163510"},"reference-count":48,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T00:00:00Z","timestamp":1780704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Atypical Salmonella enterica strains that evade conventional detection pose significant challenges to food safety surveillance. A hydrogen sulfide (H2S)-negative and serologically untypable S. enterica strain (SF1060) was detected by qPCR from cooked farmed mussels in Galicia, Spain, and characterized using phenotypic and genomic approaches. Despite typical biochemical profiles, SF1060 failed to produce black colonies on Xylose Lysine Deoxycholate (XLD) agar and lacked detectable somatic antigens by conventional serotyping. Hybrid genome assembly using nanopore and illumina sequencing yielded a closed chromosome and five plasmids. In silico analyses identified the strain as S. Senftenberg ST14. Comparative genomics revealed a chromosomal inversion at the rfb operon (encoding enzymes needed to synthesize deoxysugars and O antigens) mediated by IS5-family transposase ISEc68, which truncated the rfbD gene and separated the remaining rfb genes at rfbD, disrupting O-antigen biosynthesis, explaining the inconclusive phenotypic serotyping results. The phs operon responsible for H2S production lacked premature stop codons, suggesting the H2S-negative phenotype may result from an alternative mechanism. This study demonstrates how whole-genome sequencing resolves identification of atypical strains that fail culture-based detection and emphasizes the critical need for molecular surveillance methods in seafood safety programs, particularly in regions where atypical S. enterica variants may be endemic.<\/jats:p>","DOI":"10.3390\/microorganisms14061284","type":"journal-article","created":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T02:32:46Z","timestamp":1780885966000},"page":"1284","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genomic Characterization of an O-Antigen-Deficient, Hydrogen Sulfide-Negative Salmonella enterica Serovar Senftenberg Isolated from Cooked Mussels"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7283-9372","authenticated-orcid":false,"given":"Alexandre","family":"Lamas","sequence":"first","affiliation":[{"name":"Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition, and Bromatology, Veterinary School, Campus Terra, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Lozano-Le\u00f3n","sequence":"additional","affiliation":[{"name":"Health & Nutrition Laboratory Manager, SGS Seafood Laboratory, 36939 Bueu, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4587-8418","authenticated-orcid":false,"given":"Alejandro","family":"Garrido-Maestu","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and Technology of Marine Products (MicroTEC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4568-0022","authenticated-orcid":false,"given":"Narjol","family":"Gonzalez-Escalona","sequence":"additional","affiliation":[{"name":"Genomics Development and Applications Branch, Division of Food Safety Genomics, Office of Applied Microbiology and Technology (OAMT), Office of Laboratory Operations and Applied Science (OLOAS), Human Foods Program, Food and Drug Administration, College Park, MD 20740, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,6]]},"reference":[{"key":"ref_1","first-page":"771","article-title":"Microbiological safety of smoked fish: A review of Escherichia coli and Salmonella spp. contamination in traditional markets of Kendari City, Indonesia","volume":"14","author":"Tina","year":"2025","journal-title":"Int. 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