Comparative Genome Analysis and Characterization of Salmonella enterica using Whole-Genome Sequencing Approach

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dc.contributor.author Hdayed, Dana
dc.date.accessioned 2022-04-13T09:18:45Z
dc.date.available 2022-04-13T09:18:45Z
dc.date.copyright 2020 en_US
dc.date.issued 2020-05-18
dc.identifier.uri http://hdl.handle.net/10725/13492
dc.description.abstract Salmonella spp. are facultative rod-shaped Gram-negative bacteria and are a leading cause of worldwide foodborne gastroenteritis. We used in this study whole-genome sequencing and conventional approaches to characterize Salmonella enterica spp. clinical isolates recovered from Lebanon. Pulse-field gel electrophoresis (PFGE) and PCR-based replicon typing (PBRT) were used to type the isolates and determine plasmid types and distribution. blaTEM1B and aac(6’)-Iaa genes mediating resistance to ampicillin and aminoglycosides were among the detected resistance determinants. IncFIB and IncFII were the two most common incompatibility groups, with the IncX1 plasmid harboring the blaTEM1B. We also found six multi-locus sequence types (MLST) with ST11 being the most prevalent. Salmonella pathogenicity islands (SPI) encode for virulence determinants linked to survival, invasion, and ability of the organism to spread outside the intestines. SPI-1 to 5 were commonly detected across the different serovars in this study. The SPI-13 is conserved in the main serovars and is replaced in the same genomic locus by SPI-8, and this was evident in Salmonella enterica serovar Typhimurium. The question of whether the isolates were part of an outbreak or not was raised. We used Outbreaker workflow to follow and determine if they were close enough to be classified as originating from a common source. The constructed Gengraph, showed that the number of observed mutations was in the range of 1 to 50, thus ruling out the possibility of the isolates being linked to an epidemiologically defined outbreak. Our study provided a detailed whole genome molecular characterization of S. enterica isolates collected from Lebanon. The approach we used helped in having a more accurate overview, and SNP-based analysis proved to give a better insight into the genetic diversity than the traditionally used approaches. Our findings, accordingly, supported the notion of shifting towards the implementation of WGS as the best approach for outbreak detection being it in the food industry or hospital settings. en_US
dc.language.iso en en_US
dc.subject Salmonella enteritidis -- Pathogensis en_US
dc.subject Salmonella infections -- Pathogenesis en_US
dc.subject Lebanese American University -- Dissertations en_US
dc.subject Dissertations, Academic en_US
dc.title Comparative Genome Analysis and Characterization of Salmonella enterica using Whole-Genome Sequencing Approach en_US
dc.type Thesis en_US
dc.term.submitted Spring en_US
dc.author.degree MS in Molecular Biology en_US
dc.author.school SAS en_US
dc.author.idnumber 201400980 en_US
dc.author.commembers Khalaf, Roy
dc.author.department Natural Sciences en_US
dc.description.physdesc 1 online resource (xii, 57 leaves) : col. ill. en_US
dc.author.advisor Tokajian, Sima
dc.keywords Salmonella spp. en_US
dc.keywords PFGE en_US
dc.keywords MLST en_US
dc.keywords SNP en_US
dc.keywords WGS en_US
dc.keywords Outbreak en_US
dc.description.bibliographiccitations Includes bibliographical references (leaf 46-57) en_US
dc.identifier.doi https://doi.org/10.26756/th.2022.300
dc.author.email dana.hdayed@lau.edu.lb en_US
dc.identifier.tou http://libraries.lau.edu.lb/research/laur/terms-of-use/thesis.php en_US
dc.publisher.institution Lebanese American University en_US
dc.author.affiliation Lebanese American University en_US

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