Emergence of multidrug-resistant and virulent Escherichia coli with APEC‑associated traits in broiler chickens from Ismailia, Egypt

Abstract

Abstract Colibacillosis in poultry is a significant disease that leads to substantial economic losses and poses a potential zoonotic threat through the emergence of antimicrobial‑resistant strains. This study aimed to investigate the prevalence, antimicrobial resistance patterns, phylogenetic distribution, and virulence and resistance gene profiles of Escherichia coli isolates from broiler chickens on two private farms in Ismailia Governorate, Egypt. During April–July 2024, cloacal swabs were collected from diseased broiler chickens showing diarrhea and respiratory symptoms. Post-mortem examination revealed lesions consistent with colibacillosis, including Perihepatitis, Pericarditis, Enteritis, Splenomegaly, and Airsacculitis. E. coli was isolated and identified using selective culture media, biochemical assays, and PCR verification methods targeting the pho A gene. Antimicrobial susceptibility was assessed by the disc diffusion method against nine different antibiotic classes. Phylogenetic typing and PCR-based detection of virulence ( omp A, iss , iut A, iro N, eae A, kps MTII) and resistance genes ( bla TEM , bla CTX−M , tet A, aad A1, sul 1, qnr A, bla VIM−1 , bla IMP−1 ) were performed on the strains, and the data were statistically analyzed. Fifty-seven (28.5%) isolates were identified as E. coli , and both the hemolysis test and the Congo red binding test were positive for all isolates. Phylogenetic analysis showed that most isolates belonged to groups B2 (59.6%), B1 (21.1%), and D (19.3%). Notably, all isolates were resistant to ampicillin and tetracycline, while 93% of the isolates were resistant to cefuroxime and ceftriaxone. Overall, 100% were multidrug-resistant (MDR) strains, with a high MAR index (≥ 0.56). The most predominant resistance genes were bla TEM and tet A (100%), followed by bla CTX−M (91.2%) and aad A1 (85.9%). The main virulence determinants were omp A (100%), iss (78.9%), and iut A (64.9%). We observed correlations between phenotypic resistance, genotypic resistance, and the presence of virulence genes. The high burden of multidrug‑resistant isolates E.coli harbouring multiple virulence and extended‑spectrum β‑lactamase genes in Egyptian broilers underscores a serious threat to poultry production and public health. These findings highlight the urgent need for rational antimicrobial use, strengthened farm biosecurity, and continuous molecular surveillance within a One Health framework.