Detection of Extended-spectrum β-lactamase-producing Escherichia coli isolates by isothermal amplification and association of their virulence genes and phylogroups with extraintestinal infection

Extraintestinal pathogenic Escherichia coli (ExPEC) producing extended-spectrum β-lactamases (ESBL) cause serious human infections due to their virulence and multidrug resistance (MDR) profiles. We characterized 144 ExPEC strains (collected from a tertiary cancer institute) in terms of antimicrobial susceptibility spectrum, ESBL variants, virulence factors (VF) patterns, and Clermont’s phylogroup classification. The developed multiplex recombinase polymerase amplification and thermophilic helicase-dependent amplification (tHDA) assays for bla(CTX-M), bla(OXA), bla(SHV,) and bla(TEM) detection, respectively, were validated using PCR-sequencing results. All ESBL-ExPEC isolates carried bla(CTX-M) genes with following prevalence frequency of variants: bla(CTX-M-15) (50.5%) > bla(CTX-M-55) (17.9%) > bla(CTX-M-27) (16.8%) > bla(CTX-M-14) (14.7%). The multiplex recombinase polymerase amplification assay had 100% sensitivity, and specificity for bla(CTX-M), bla(OXA), bla(SHV), while tHDA had 86.89% sensitivity, and 100% specificity for bla(TEM). The VF genes showed the following prevalence frequency: traT (67.4%) > ompT (52.6%) > iutA (50.5%) > fimH (47.4%) > iha (33.7%) > hlyA (26.3%) > papC (12.6%) > cvaC (3.2%), in ESBL-ExPEC isolates which belonged to phylogroups A (28.4%), B2 (28.4%), and F (22.1%). The distribution of traT, ompT, and hlyA and phylogroup B2 were significantly different (P < 0.05) between ESBL-ExPEC and non-ESBL-ExPEC isolates. Thus, these equipment-free isothermal resistance gene amplification assays contribute to effective treatment and control of virulent ExPEC, especially antimicrobial resistance strains.