UBC Theses and Dissertations
Genomic characterization and global contextualization of ESBL-producing E. coli from pediatric patients in Qatar Nguyen, Matthew Hoang Tu
Extended spectrum beta-lactamase (ESBL) producing Enterobacteriaceae such as E. coli and K. pneumoniae are found globally in hospital and community settings and represent a major healthcare challenge due to their limited effective treatment options. Several lineages are considered high-risk clones with an enhanced ability to spread and persist and increased pathogenicity and antimicrobial resistance (AMR). The prevalence of ESBL-producing Enterobacteriaceae in Qatar has steadily increased in the last two decades. Whole-genome sequencing can be used to characterize for the genomic characterization of these Qatari organisms; however, previous studies has focused only on core genes. Moreover, the genetic relationship of Qatari E. coli lineages to globally circulating high-risk clones has not been studied. This work presents an in-depth genomic characterization of ESBL-producing E. coli from a pediatric hospital in Qatar, with a focus on characterizing mobile genetic elements and plasmids. This work is also the first study to globally contextualize Qatari isolates against globally circulating lineages of ESBL-producing E. coli. This study reveals the presence of a putative emerging high-risk clone that may be endemic to Qatar, ST8881, that had not been previously studied. Through phylogenetic reconstruction from different genomic features, ST8881 is genetically distinguishable from other Qatari and global lineages by its mobile genetic element, virulence factor, and AMR marker profiles. This lineage is also characterized by factors affecting the stability of AMR genes: chromosomal integration of beta-lactamase genes, as well as the presence of a multiple-replicon plasmid encoding for five AMR genes. With Qatar being a major international travel hub, a high-risk clone could be easily exported; therefore, it is crucial to understand the genetic landscape of ESBL-producing E. coli in Qatar. The discovery and characterization of ST8881 provides a strong basis for future studies of AMR in Qatar.
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