Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region
<i>Salmonella</i> Dublin (<i>S.</i> Dublin) and <i>Salmonella</i> Typhimurium (<i>S.</i> Typhimurium) are commonly linked to bovine salmonellosis. <i>S.</i> Dublin is, however, considered a bovine-adapted serovar for primarily infecting and...
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2025-04-01
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| author | Kingsley E. Bentum Emmanuel Kuufire Rejoice Nyarku Viona Osei Benjamin Adu-Addai Jonathan G. Frye Charlene R. Jackson Temesgen Samuel Woubit Abebe |
| author_facet | Kingsley E. Bentum Emmanuel Kuufire Rejoice Nyarku Viona Osei Benjamin Adu-Addai Jonathan G. Frye Charlene R. Jackson Temesgen Samuel Woubit Abebe |
| author_sort | Kingsley E. Bentum |
| collection | DOAJ |
| description | <i>Salmonella</i> Dublin (<i>S.</i> Dublin) and <i>Salmonella</i> Typhimurium (<i>S.</i> Typhimurium) are commonly linked to bovine salmonellosis. <i>S.</i> Dublin is, however, considered a bovine-adapted serovar for primarily infecting and thriving in cattle. Using <i>S.</i> Typhimurium (a generalist serovar) as a benchmark, this study investigates genomic factors contributing to <i>S.</i> Dublin’s adaptation to cattle hosts in the U.S. A total of 1337 <i>S.</i> Dublin and 787 <i>S.</i> Typhimurium whole-genome sequences from bovine sources were analyzed with CARD (version 4.0.0), ARG-NOTT (version 6), and AMRfinderPlus (version 4.0.3) for antimicrobial resistance (AMR) genes; VFDB and AMRfinderPlus for virulence genes; AMRFinderPlus for stress genes; and Plasmidfinder for plasmids. Existing clonal groups among isolates of the two serovars were also investigated using the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) model. The results revealed minimal genomic variation among <i>S.</i> Dublin isolates. Comparatively, the IncX1 plasmid was somewhat exclusively identified in <i>S.</i> Dublin isolates and each carried an average of four plasmids (<i>p</i>-value < 0.05). Furthermore, <i>S</i>. Dublin isolates exhibited a higher prevalence of AMR genes against key antimicrobials, including aminoglycosides, beta-lactams, tetracyclines, and sulfonamides, commonly used in U.S. cattle production. Additionally, Type VI secretion system genes <i>tssJKLM</i> and <i>hcp2</i>/<i>tssD2</i>, essential for colonization, were found exclusively in <i>S.</i> Dublin isolates with over 50% of these isolates possessing genes that confer resistance to heavy metal stressors, like mercury. These findings suggest that <i>S.</i> Dublin’s adaptation to bovine hosts in the U.S. is supported by a conserved genetic makeup enriched with AMR genes, virulence factors, and stress-related genes, enabling it to colonize and persist in the bovine gut. |
| format | Article |
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| issn | 2076-2607 |
| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-83110efb3d4b42218944e6c73687bd722025-08-20T02:18:04ZengMDPI AGMicroorganisms2076-26072025-04-0113488610.3390/microorganisms13040886Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the RegionKingsley E. Bentum0Emmanuel Kuufire1Rejoice Nyarku2Viona Osei3Benjamin Adu-Addai4Jonathan G. Frye5Charlene R. Jackson6Temesgen Samuel7Woubit Abebe8Center for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USACenter for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USACenter for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USACenter for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USADepartment of Biomedical Science, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USAPoultry Microbiological Safety and Processing Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USAPoultry Microbiological Safety and Processing Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USACenter for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USACenter for Food Animal Health, Food Safety and Defense, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA<i>Salmonella</i> Dublin (<i>S.</i> Dublin) and <i>Salmonella</i> Typhimurium (<i>S.</i> Typhimurium) are commonly linked to bovine salmonellosis. <i>S.</i> Dublin is, however, considered a bovine-adapted serovar for primarily infecting and thriving in cattle. Using <i>S.</i> Typhimurium (a generalist serovar) as a benchmark, this study investigates genomic factors contributing to <i>S.</i> Dublin’s adaptation to cattle hosts in the U.S. A total of 1337 <i>S.</i> Dublin and 787 <i>S.</i> Typhimurium whole-genome sequences from bovine sources were analyzed with CARD (version 4.0.0), ARG-NOTT (version 6), and AMRfinderPlus (version 4.0.3) for antimicrobial resistance (AMR) genes; VFDB and AMRfinderPlus for virulence genes; AMRFinderPlus for stress genes; and Plasmidfinder for plasmids. Existing clonal groups among isolates of the two serovars were also investigated using the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) model. The results revealed minimal genomic variation among <i>S.</i> Dublin isolates. Comparatively, the IncX1 plasmid was somewhat exclusively identified in <i>S.</i> Dublin isolates and each carried an average of four plasmids (<i>p</i>-value < 0.05). Furthermore, <i>S</i>. Dublin isolates exhibited a higher prevalence of AMR genes against key antimicrobials, including aminoglycosides, beta-lactams, tetracyclines, and sulfonamides, commonly used in U.S. cattle production. Additionally, Type VI secretion system genes <i>tssJKLM</i> and <i>hcp2</i>/<i>tssD2</i>, essential for colonization, were found exclusively in <i>S.</i> Dublin isolates with over 50% of these isolates possessing genes that confer resistance to heavy metal stressors, like mercury. These findings suggest that <i>S.</i> Dublin’s adaptation to bovine hosts in the U.S. is supported by a conserved genetic makeup enriched with AMR genes, virulence factors, and stress-related genes, enabling it to colonize and persist in the bovine gut.https://www.mdpi.com/2076-2607/13/4/886<i>Salmonella</i> Dublin<i>Salmonella</i> Typhimuriumserovarantimicrobial resistancecattlehost |
| spellingShingle | Kingsley E. Bentum Emmanuel Kuufire Rejoice Nyarku Viona Osei Benjamin Adu-Addai Jonathan G. Frye Charlene R. Jackson Temesgen Samuel Woubit Abebe Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region Microorganisms <i>Salmonella</i> Dublin <i>Salmonella</i> Typhimurium serovar antimicrobial resistance cattle host |
| title | Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region |
| title_full | Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region |
| title_fullStr | Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region |
| title_full_unstemmed | Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region |
| title_short | Comparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region |
| title_sort | comparative genomic profiles of i salmonella i typhimurium and i salmonella i dublin bovine isolates from the u s indicate possible factors associated with the host adaptation of i salmonella i dublin in the region |
| topic | <i>Salmonella</i> Dublin <i>Salmonella</i> Typhimurium serovar antimicrobial resistance cattle host |
| url | https://www.mdpi.com/2076-2607/13/4/886 |
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