Antimicrobial resistance, Shiga toxin gene detection, and in silico analysis of Escherichia coli isolated from chronic kidney disease patients in Pakistan

Chronic kidney disease (CKD) is a progressive global health concern. Enterohemorrhagic Escherichia coli (EHEC) is clinically important due to its ability to cause renal damage through Shiga toxin–associated haemolytic uremic syndrome. But data on antimicrobial resistance and molecular characteristics of EHEC among CKD patients in Pakistan is still limited. A cross-sectional study was conducted from December 2024 to February 2025 in four tertiary care hospitals in Multan, Pakistan. Urine and blood ( n = 139) samples were collected from CKD patients. Bacterial identification was performed using Gram staining and biochemical tests. Antimicrobial susceptibility was determined by the Kirby–Bauer disc diffusion method. The presence of stx1 and stx2 genes was detected by polymerase chain reaction (PCR). In silico network analysis, protein–protein docking, and molecular dynamics simulations were used to investigate toxin–host interactions. Out of 139 samples, 115 (82.7%) were positive for E. coli . All isolates were drug-resistant, with resistance rates ranging from 34.2% (fosfomycin) to 50% (gentamicin). PCR detected stx1 and stx2 genes in 1.8% of isolates. Network pharmacology identified FOS as a key hub gene associated with MAPK signaling. Protein–protein docking identified stable hydrogen bond interactions between FOS and Shiga toxin proteins STX1 and STX2, and 50 ns molecular dynamics simulations confirmed complex stability. Drug-resistant E. coli is prevalent among CKD patients in Pakistan, although Shiga toxin genes are infrequent. Integrated in vitro and in silico analyses provide insight into potential toxin–host molecular interactions that may contribute to renal pathology. These findings combined offer significant epidemiological and molecular evidence about EHEC-related renal problems and may facilitate the advancement of enhanced diagnostic, preventative, and therapeutic strategies.