Whole-Genome Analysis of Multidrug-Resistant Escherichia coli from Bloodstream Infections in Iraqi Cancer Patients

In Iraq, oncology patients with bloodstream infections face escalating treatment challenges due to rising antimicrobial resistance in Escherichia coli, compounded by limited diagnostic capacity and restricted therapeutic options. However, data from oncology settings in Iraq are limited. This study aimed to characterize and compare the antimicrobial resistance gene profiles of multidrug-resistant and antibiotic-sensitive E. coli isolates from cancer patients, to inform infection control and stewardship strategies.

A prospective, multicenter investigation was conducted in three oncology hospitals in Baghdad. Fifty-five Escherichia coli bloodstream isolates, 36 multidrug-resistant (MDR) (65.5%) and 19 antibiotic-sensitive (34.5%), underwent phenotypic susceptibility testing using VITEK® 2 and disk diffusion. Whole-genome sequencing (Illumina MiSeq) was performed, and antimicrobial resistance genes (ARGs) were identified using AMRFinderPlus and classified by functional category.

MDR isolates showed a broad resistome dominated by efflux systems. Across all isolates, a total of 36 unique antimicrobial resistance genes were identified, underscoring substantial resistome diversity., efflux pump genes were detected in 100%, β-lactamase genes in 88.9%, macrolide resistance genes in 66.7%, tetracycline resistance genes in 55.6%, and aminoglycoside resistance genes in 41.7%. Representative determinants included AcrAB-TolC/EmrAB-TolC/MdtABC-TolC (efflux) and BlaEC family/CMY-42/TEM types (β-lactams). Among sensitive isolates, only 11 antibiotic-associated genes, mainly efflux or regulators (e.g., acrF, emrD, emrR, emrY, tolC; regulators marR, evgA; target parC; others baeS, cpxA, cysB), overlapped with MDR, suggesting a shared core that is insufficient alone for phenotypic resistance without additional high-level mechanisms.

Multidrug-resistant E. coli from oncology patients harbor dense, efflux-driven resistomes supplemented by diverse β-lactamases and other resistance determinants, while sensitive isolates retain a limited core set of genes. Genomic surveillance in cancer centers is critical for anticipating resistance emergence and informing targeted antimicrobial strategies.