Molecular diversity and structural profiling of the EmrD efflux pump in multidrug-resistant uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) presents a significant therapeutic challenge due to increasing multidrug resistance (MDR). While acquired resistance mechanisms are well-documented, the genetic variability of intrinsic efflux pumps like EmrD remains less characterized. This study investigated the genomic diversity and structural conservation of the EmrD transporter in ten clinical MDR isolates from the Kurdistan Region, Iraq. Isolates were screened for the emrD and β-lactamase genes, followed by emrD sequencing, phylogenetic analysis, and in silico protein modeling. Results confirmed the universal presence of emrD alongside multiple resistance genes. Phylogenetic analysis identified notable local genetic diversity, including a highly divergent lineage (DUH 11). Protein modeling mapped non-synonymous substitutions to transmembrane helices 6 and 12, regions critical for the “rocker-switch” conformational changes required for substrate translocation. These findings suggest that while EmrD is a stable component of the MDR machinery, localized genomic divergence may potentially influence efflux efficiency among clinical lineages, warranting future functional validation.