The main pathogenic bacteria associated with mortality due to antimicrobial inefficacy include Escherichia coli strains that produce extended-spectrum β-lactamases (ESBL-EC) and are usually also resistant to fluoroquinolones. In the first part of our research, we focused on the molecular characteristics of selected isolates related to bacterial resistance to antimicrobials and virulence-associated genes. We also investigated the ability to form biofilms and compared the phenotypic and genotypic characteristics of the isolates before and during the COVID-19 pandemic. The main objective of our research was to characterize ESBL-EC isolates from lower respiratory tract samples in selected Slovenian hospitals from 2002 to 2022. Most isolates were assigned to phylogenetic group B2 and sequence type ST131, which is dominant among pathogenic ESBL strains. Isolates isolated from different patients, from different years and even from different hospital departments and institutions, including remote locations, had the same ERIC-PCR profile, indicating persistent hospital isolates. Among the 563 isolates, we detected a high proportion of blaCTX-M-1 and a lower proportion of plasmid-mediated quinolone resistance genes. The presence of genes related to biocide resistance and biofilm formation was confirmed. We also monitored biofilm formation by growing the isolates in microtiter plates and confirmed a significant positive correlation between strong biofilm formation, ST131 and certain virulence-associated genes. A comparison of phenotypes and genotypes of isolates obtained before and during the COVID-19 period showed higher clonal diversity and higher susceptibility to fluoroquinolones and trimethoprim-sulfamethoxazole. With all these results, we were able to better define ESBL-EC isolates from the lower respiratory tract and highlight several possible reasons for the successful global spread of ST131, especially in clinical settings.
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