Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain
S. enterica isolates (n = 78) obtained from the vegetable supply chain (farms, distribution centers, markets) in two Cambodian provinces (Siem Reap, Battambang) were sequenced and analyzed. In silico identification of serotypes and detection of antimicrobial resistance genes was performed using SIST...
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| Language: | English |
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Elsevier
2025-02-01
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| Series: | Journal of Food Protection |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0362028X2400231X |
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| author | Abimel Salazar Navin Sreng Chanthol Peng Yehzi Fu Erin M. Nawrocki Taejung Chung Jessie Vipham Edward G. Dudley Jasna Kovac |
| author_facet | Abimel Salazar Navin Sreng Chanthol Peng Yehzi Fu Erin M. Nawrocki Taejung Chung Jessie Vipham Edward G. Dudley Jasna Kovac |
| author_sort | Abimel Salazar |
| collection | DOAJ |
| description | S. enterica isolates (n = 78) obtained from the vegetable supply chain (farms, distribution centers, markets) in two Cambodian provinces (Siem Reap, Battambang) were sequenced and analyzed. In silico identification of serotypes and detection of antimicrobial resistance genes was performed using SISTR and ABRicate, respectively. Isolates’ relatedness was assessed based on high-quality single nucleotide polymorphisms (hqSNPs) identified within each serotype using the CFSAN SNP pipeline. Among 29 detected serotypes, Paratyphi B var. Java was most abundant (n = 14), followed by Hvittingfoss (n = 11) and Thompson (n = 7). Paratyphi B var. Java was mostly found in farms (n = 5) and markets (n = 6), Hvittingfoss within distribution centers (n = 8), and Thompson at markets (n = 4) and farms (n = 3). Among Paratyphi B var. Java isolates, one phylogenetic clade contained four closely related isolates (0–1 SNP difference), collected at markets in different provinces on different days. Another clade contained two isolates that differed by one SNP, one obtained from a Battambang farm and one from a Siem Reap distribution center, suggesting a broad spread of Paratyphi B var. Java in the Cambodian vegetable supply chain. Hvittingfoss isolates clustered in two clades; one contained five identical isolates, four of which were obtained in different months from the distribution center and a farm in Battambang, suggesting possible transmission among supply chain stages. The second clade contained three isolates from the Battambang distribution center that differed by 0–1 SNP and were isolated in October and November, indicating possible persistence. Lastly, among 78 analyzed isolates, 14 carried antimicrobial resistance genes and seven out of these 14 carried genes with predicted resistance to more than three classes of antibiotics. Overall, highly similar isolates of Salmonella were identified over time and at different supply chain stages, suggesting possible persistence and transmission of Salmonella within and between supply chain stages. |
| format | Article |
| id | doaj-art-41d3445aebe14bf99fe67216d90d0039 |
| institution | Kabale University |
| issn | 0362-028X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Food Protection |
| spelling | doaj-art-41d3445aebe14bf99fe67216d90d00392025-02-02T05:26:43ZengElsevierJournal of Food Protection0362-028X2025-02-01882100447Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply ChainAbimel Salazar0Navin Sreng1Chanthol Peng2Yehzi Fu3Erin M. Nawrocki4Taejung Chung5Jessie Vipham6Edward G. Dudley7Jasna Kovac8Department of Food Science, The Pennsylvania State University, University Park, PA 16802, United StatesLaboratory of Environment and Food Safety, Institut Pasteur du Cambodge, Phnom Penh 120210, CambodiaResearch and Innovation Center, Institute of Technology of Cambodia, Phnom Penh 120404, CambodiaDepartment of Food Science, The Pennsylvania State University, University Park, PA 16802, United StatesDepartment of Food Science, The Pennsylvania State University, University Park, PA 16802, United StatesDepartment of Food Science, The Pennsylvania State University, University Park, PA 16802, United StatesDepartment of Animal Sciences and Industry, Kansas State University, KS 66506, United StatesDepartment of Food Science, The Pennsylvania State University, University Park, PA 16802, United StatesDepartment of Food Science, The Pennsylvania State University, University Park, PA 16802, United States; Corresponding author.S. enterica isolates (n = 78) obtained from the vegetable supply chain (farms, distribution centers, markets) in two Cambodian provinces (Siem Reap, Battambang) were sequenced and analyzed. In silico identification of serotypes and detection of antimicrobial resistance genes was performed using SISTR and ABRicate, respectively. Isolates’ relatedness was assessed based on high-quality single nucleotide polymorphisms (hqSNPs) identified within each serotype using the CFSAN SNP pipeline. Among 29 detected serotypes, Paratyphi B var. Java was most abundant (n = 14), followed by Hvittingfoss (n = 11) and Thompson (n = 7). Paratyphi B var. Java was mostly found in farms (n = 5) and markets (n = 6), Hvittingfoss within distribution centers (n = 8), and Thompson at markets (n = 4) and farms (n = 3). Among Paratyphi B var. Java isolates, one phylogenetic clade contained four closely related isolates (0–1 SNP difference), collected at markets in different provinces on different days. Another clade contained two isolates that differed by one SNP, one obtained from a Battambang farm and one from a Siem Reap distribution center, suggesting a broad spread of Paratyphi B var. Java in the Cambodian vegetable supply chain. Hvittingfoss isolates clustered in two clades; one contained five identical isolates, four of which were obtained in different months from the distribution center and a farm in Battambang, suggesting possible transmission among supply chain stages. The second clade contained three isolates from the Battambang distribution center that differed by 0–1 SNP and were isolated in October and November, indicating possible persistence. Lastly, among 78 analyzed isolates, 14 carried antimicrobial resistance genes and seven out of these 14 carried genes with predicted resistance to more than three classes of antibiotics. Overall, highly similar isolates of Salmonella were identified over time and at different supply chain stages, suggesting possible persistence and transmission of Salmonella within and between supply chain stages.http://www.sciencedirect.com/science/article/pii/S0362028X2400231XCambodiaFood safetyPersistenceSalmonella entericaTransmissionVegetable supply chain |
| spellingShingle | Abimel Salazar Navin Sreng Chanthol Peng Yehzi Fu Erin M. Nawrocki Taejung Chung Jessie Vipham Edward G. Dudley Jasna Kovac Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain Journal of Food Protection Cambodia Food safety Persistence Salmonella enterica Transmission Vegetable supply chain |
| title | Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain |
| title_full | Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain |
| title_fullStr | Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain |
| title_full_unstemmed | Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain |
| title_short | Genomic Diversity and Potential Transmission and Persistence of Salmonella in the Cambodian Vegetable Supply Chain |
| title_sort | genomic diversity and potential transmission and persistence of salmonella in the cambodian vegetable supply chain |
| topic | Cambodia Food safety Persistence Salmonella enterica Transmission Vegetable supply chain |
| url | http://www.sciencedirect.com/science/article/pii/S0362028X2400231X |
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