Escherichia marmotae is a recently described bacterial species, phylogenetically related to E. coli, originally isolated from Himalayan marmot faeces and lately discovered in various environments and animal species. In this master’s thesis, we phenotypically and genetically characterized a collection of E. marmotae isolates obtained from various ecosystems across Slovenia (karst waters, Opekarna ponds, Lake Bled, bat guano, and clinical samples) and assessed their pathogenic potential and antimicrobial susceptibility. To distinguish E. marmotae from E. coli, we used quadruplex PCR adapted from Clermont et al. (2012), which proved to be a fast and reliable method, as confirmed by whole genome analysis. Phylogenetic analysis revealed that the isolates only partially clustered according to sample type and sampling location, indicating strain circulation between environments and confirming the opportunistic pathogenicity of the species. All isolates contained a core set of virulence factor genes (e. g., adhesins, invasins, toxins, complement resistance factors, and iron acquisition systems), while genes or mutations associated with antimicrobial resistance (e. g., blaCTX-M-1) were present only in clinical isolates. We have demonstrated that the conjugative plasmid carrying the blaCTX-M-1 gene can be transferred between E. marmotae isolates as well as between E. marmotae and E. coli strains. Our results indicate that E. marmotae represents an environmental reservoir of potentially pathogenic strains with a rich repertoire of virulence factors and the ability to spread antimicrobial resistance genes among related bacteria.
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