Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken
Abstract Salmonella Enteritidis is a major foodborne pathogen, and the emergence of multidrug-resistant (MDR) S. Enteritidis poses a serious public health challenge. In this study, we report the genomic characterization of five S. Enteritidis isolates from clinical. These isolates exhibited resistan...
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BMC
2024-11-01
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| Online Access: | https://doi.org/10.1186/s12866-024-03651-4 |
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| author | Xiangfeng Bu Yufan Wu Yi Hong Juping Shi Jingdong Shao Kai Jia Qingli Dong Xiang Wang |
| author_facet | Xiangfeng Bu Yufan Wu Yi Hong Juping Shi Jingdong Shao Kai Jia Qingli Dong Xiang Wang |
| author_sort | Xiangfeng Bu |
| collection | DOAJ |
| description | Abstract Salmonella Enteritidis is a major foodborne pathogen, and the emergence of multidrug-resistant (MDR) S. Enteritidis poses a serious public health challenge. In this study, we report the genomic characterization of five S. Enteritidis isolates from clinical. These isolates exhibited resistance to seven classes of antimicrobials with four of the five characterized as MDR. Isolate 33 A exhibited resistance to colistin and polymyxin B, while no associated antimicrobial resistance genes (ARGs) were identified in its genome. Isolate 21 A and 44 A were extended-spectrum beta-lactamases-producing (ESBLs). Whole genome sequencing analysis revealed the presence of multiple mobile genetic elements (MGEs), including plasmids, prophages, and genomic islands, which may have facilitated the acquisition and dissemination of ARGs. Notably, several ARGs, including bla CTX−M−55 , bla TEM−141 , bla TEM−1B , aph(3’)-IIa, aph(3’’)-Ib, aph(6)-Id, tet(A), floR, fosA3, and sul2, were identified on plasmids. In addition, chromosomal point mutations in gyrA (D87G and D87Y) and acrB (F28L and L40P) were also observed in each isolate. Multiple virulence genes associated with the type III secretion system were identified on Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2. Phylogenetic analysis revealed that the five isolates, along with a clinical and chicken origin isolates in the database, clustered together, suggesting a probable common source of infection. Our findings highlight the intricate genetic mechanisms behind MDR in S. Enteritidis, emphasizing the ongoing necessity for surveillance and appropriate antimicrobial usage. This contributes to our understanding of S. Enteritidis transmission within the food chain. |
| format | Article |
| id | doaj-art-d2c6b5b7f3454b2fb6fc22413fc9a2d7 |
| institution | DOAJ |
| issn | 1471-2180 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
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| series | BMC Microbiology |
| spelling | doaj-art-d2c6b5b7f3454b2fb6fc22413fc9a2d72025-08-20T02:51:42ZengBMCBMC Microbiology1471-21802024-11-0124111710.1186/s12866-024-03651-4Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chickenXiangfeng Bu0Yufan Wu1Yi Hong2Juping Shi3Jingdong Shao4Kai Jia5Qingli Dong6Xiang Wang7School of Health Science and Engineering, University of Shanghai for Science and TechnologyCentre of Analysis and Test, School of Chemistry & Molecular Engineering, East China University of Science and TechnologySchool of Health Science and Engineering, University of Shanghai for Science and TechnologyZhangjiagang Centre for Disease Control and PreventionTechnology Center of Zhangjiagang CustomsSchool of Health Science and Engineering, University of Shanghai for Science and TechnologySchool of Health Science and Engineering, University of Shanghai for Science and TechnologySchool of Health Science and Engineering, University of Shanghai for Science and TechnologyAbstract Salmonella Enteritidis is a major foodborne pathogen, and the emergence of multidrug-resistant (MDR) S. Enteritidis poses a serious public health challenge. In this study, we report the genomic characterization of five S. Enteritidis isolates from clinical. These isolates exhibited resistance to seven classes of antimicrobials with four of the five characterized as MDR. Isolate 33 A exhibited resistance to colistin and polymyxin B, while no associated antimicrobial resistance genes (ARGs) were identified in its genome. Isolate 21 A and 44 A were extended-spectrum beta-lactamases-producing (ESBLs). Whole genome sequencing analysis revealed the presence of multiple mobile genetic elements (MGEs), including plasmids, prophages, and genomic islands, which may have facilitated the acquisition and dissemination of ARGs. Notably, several ARGs, including bla CTX−M−55 , bla TEM−141 , bla TEM−1B , aph(3’)-IIa, aph(3’’)-Ib, aph(6)-Id, tet(A), floR, fosA3, and sul2, were identified on plasmids. In addition, chromosomal point mutations in gyrA (D87G and D87Y) and acrB (F28L and L40P) were also observed in each isolate. Multiple virulence genes associated with the type III secretion system were identified on Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2. Phylogenetic analysis revealed that the five isolates, along with a clinical and chicken origin isolates in the database, clustered together, suggesting a probable common source of infection. Our findings highlight the intricate genetic mechanisms behind MDR in S. Enteritidis, emphasizing the ongoing necessity for surveillance and appropriate antimicrobial usage. This contributes to our understanding of S. Enteritidis transmission within the food chain.https://doi.org/10.1186/s12866-024-03651-4Antibiotic resistanceMobile genetic elementsMultidrug-resistantPhylogenetic analysisVirulence factorsWhole-genome sequencing |
| spellingShingle | Xiangfeng Bu Yufan Wu Yi Hong Juping Shi Jingdong Shao Kai Jia Qingli Dong Xiang Wang Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken BMC Microbiology Antibiotic resistance Mobile genetic elements Multidrug-resistant Phylogenetic analysis Virulence factors Whole-genome sequencing |
| title | Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken |
| title_full | Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken |
| title_fullStr | Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken |
| title_full_unstemmed | Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken |
| title_short | Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken |
| title_sort | comparative genomics analysis of salmonella enteritidis isolated from clinical cases associated with chicken |
| topic | Antibiotic resistance Mobile genetic elements Multidrug-resistant Phylogenetic analysis Virulence factors Whole-genome sequencing |
| url | https://doi.org/10.1186/s12866-024-03651-4 |
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