Genomic characterization of multidrug-resistant Escherichia coli strains identified from patients with urinary tract infection in Egypt

Abstract

Extended-spectrum β-lactamases-producing Escherichia coli (ESBL-EC) pose a serious threat. Moreover, widespread antimicrobial use in Egypt increased the prevalence of antimicrobial resistance (AMR). In this study, whole-genome sequencing (WGS) using the Illumina NovaSeq 6000 was performed on two isolates (UPE7 and UPE139) recovered from participants with urinary tract infections to characterize their resistomes and virulomes. Antibiotic resistance and virulence genes of the two clinical E. coli strains were predicted using computational analysis tools. Several virulence traits and antibiotic resistance genes (ARGs) were identified. Strain UPE7 harbored bla_TEM-1B, bla_CTM-X-15, bla_CMY-2, and strain UPE139 revealed the presence of bla_OXA-244, bla_TEM-12, bla_TEM-82, and bla_CTM-X-15 rending the resistance phenotype. The presence of mobile genetic elements adjacent to ARGs thereby suggests their potential for dissemination through horizontal gene transfer. Furthermore, the serotyping in silico investigation revealed that E. coli UPE7 and UPE139 serotypes were O8:H9 and O9:H30, respectively. Notably, key mutations in the gyrA, parC, and parE genes were predicted, consistent with their confirmed resistance to levofloxacin. These findings emphasize the importance of genomic surveillance to guide antimicrobial therapy and monitor emerging high-risk clones, and they support the need for larger-scale genomic studies to improve epidemiological understanding and clinical relevance.