Uncovering Resistance Pathways in Escherichia coli: WGS-Based Insights into Human and Animal Isolates from Baghdad
The escalating threat of antimicrobial resistance (AMR) among Escherichia coli populations presents a significant global and regional health challenge, particularly in regions with limited surveillance frameworks such as Iraq. This study employs whole-genome sequencing (WGS) to investigate the resistome and mutational landscapes of four E. coli isolates—two derived from human clinical sources (H13, H41) and two from animals (A13, A45)—collected from Baghdad. The aim was to delineate the genetic determinants underlying resistance and to explore the potential cross-transmission of resistance traits between human and animal reservoirs. All isolates were confirmed as E. coli via PCR targeting the uidA gene and 4 were subjected to Illumina-based WGS. Bioinformatics analysis revealed diverse AMR gene profiles, including those encoding antibiotic-inactivating enzymes, target protection proteins, and efflux pumps. Human-derived isolates displayed a broader array of resistance determinants, particularly aminoglycoside-modifying enzymes and extended-spectrum β-lactamases, compared to their animal-derived counterparts. Notably, efflux systems such as AcrAB-TolC and regulatory operons like MarA/MarB/MarR were ubiquitously present, indicating conserved multidrug resistance pathways. Comparative SNP analysis in quinolone resistance-determining regions (QRDRs) highlighted significant mutations (e.g., gyrA p.S83L and p.D87N; parC p.S80I; parE p.S458A) in isolates A13 and H13, correlating with resistance to nalidixic acid and ciprofloxacin. Conversely, isolates A45 and H41 lacked such mutations, suggesting variable exposure to fluoroquinolones across environments. Additionally, the consistent detection of resistance-associated genes such as KatG, gidB, and GdpD across isolates underscores the evolutionary stability of certain AMR mechanisms within local E. coli populations. This research underscores the power of WGS in elucidating the genomic architecture of AMR and suggests that environmental and clinical antibiotic pressures shape distinct resistance profiles. The findings advocate for a One Health approach to AMR surveillance and control, integrating human, animal, and environmental health strategies to mitigate the spread of multidrug-resistant pathogens in Iraq.