Genome profiling of vancomycin-resistant entercoccal clinical isolates from Lebanon. (c2019)

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dc.contributor.author Panossian, Balig V.
dc.date.accessioned 2019-11-25T08:29:06Z
dc.date.available 2019-11-25T08:29:06Z
dc.date.copyright 2019 en_US
dc.date.issued 2019-11-25
dc.date.submitted 2019-05-09
dc.identifier.uri http://hdl.handle.net/10725/11575
dc.description.abstract Vancomycin resistant enterococci (VRE) are a considerable burden on treatment, and infection and transmission control. Studying the intricacies on the wholegenome single nucleotide level is more informative than routine phenotypic analysis. In this study, 21 clinical isolates of enterococci were first identified by MALDI-TOF, and disk diffusion and E-test were used to determine antimicrobial susceptibility profiles. Whole-genome sequencing (WGS) was conducted using Illumina MiSeq platform. Resistance genes, ST-types, wgSNPs, cgSNPs, pangenomes of coding and non-coding regions, as well as recombination hotspots were evaluated for all the isolates using different bioinformatic approaches. The VRE isolates clustered under two main ST types (ST80, ST203) with some isolates having very similar whole-genome average nucleotide identities (wgANI). Pan genome analysis revealed that the isolates were much more unique in their protein coding sequences and showed pronounced heterogeneity as a population. A closer look at the resistance determinants, in particular, the vancomycin resistance genes flanked by transposon fragments and recombination loci, revealed uniquely evolved features that emphasized the polyclonal spread of these pathogens. The vancomycinsusceptible isolates also showed unique genomic features some of which had closely related genomic profiles as that of the vancomycin-resistant clones of similar ST types. A notable case was EF6 (vancomycin-susceptible), which was almost identical (99.91% average nucleotide identity) to EF15 (vancomycin resistant) except for the vancomycin resistance cassette. A few isolates were too diverse for batched intergenomic comparative analyses, and one isolate harbored additional antibiotic resistance determinants uncommon in the other enterococci. This study provided the first insights on the genomic diversity of vancomycinresistant enterococci circulating in Lebanon. Our results demonstrated how an endto- end whole-genome sequence-based outbreak surveillance, and resistance profiling scheme could help in differentiating between closely related VRE isolates, whereas phenotypic or even classical molecular approaches fail to highlight these complexities. en_US
dc.language.iso en en_US
dc.subject Lebanese American University -- Dissertations en_US
dc.subject Dissertations, Academic en_US
dc.subject Enterococcal infections en_US
dc.subject Enterococcus -- Genetic aspects en_US
dc.subject Vancomycin resistance en_US
dc.subject Enterococcal infections -- Lebanon en_US
dc.title Genome profiling of vancomycin-resistant entercoccal clinical isolates from Lebanon. (c2019) 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 201304460 en_US
dc.author.commembers Rizk, Sandra
dc.author.commembers Khalil, Christian
dc.author.department Natural Sciences en_US
dc.description.embargo 18M en_US
dc.description.physdesc 1 hard copy: xiii, 63 leaves: ill., charts; 30 cm. available at RNL. en_US
dc.author.advisor Tokajian, Sima
dc.author.advisor Khazen, Georges
dc.keywords Enterococcus faecalis en_US
dc.keywords Enterococcus faecium en_US
dc.keywords Whole Genome Sequencing en_US
dc.keywords Antibiotic Resistance en_US
dc.keywords Vancomycin en_US
dc.keywords Single Nucleotide Polymorphisms (SNP) en_US
dc.description.bibliographiccitations Bibliography: (leaves 53-63). en_US
dc.identifier.doi https://doi.org/10.26756/th.2019.141 en_US
dc.author.email balig.panossian@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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