Isolation and characterization of multidrug-resistant Escherichia coli in pigs, farm workers, and effluents in Calabar, southern Nigeria

Multidrug-resistant (MDR) Escherichia coli poses a serious threat to One Health, particularly in low- and middle-income countries (LMICs) where antibiotic use in livestock is often poorly regulated. Pigs are important sources of antimicrobial-resistant bacteria that may be transmitted through direct contact, contaminated pork, or the farm environment. This study aimed to determine the prevalence and resistance patterns of MDR E. coli in pigs, pig handlers, and farm effluents, and to assess farmers’ awareness of antimicrobial resistance (AMR) in Calabar, southern Nigeria. A cross-sectional study design was used to collect 210 samples across 17 farms, comprising pig fecal ( n = 152), human stool ( n = 30), and effluent ( n = 28) samples. E. coli was isolated using standard microbiological culture methods and confirmed by biochemical tests. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method and broth microdilution, with MDR defined as resistance to at least one agent in three or more antimicrobial classes. A semi-structured questionnaire was used to assess farmers’ knowledge and practices regarding antimicrobial use and AMR. The prevalence of E. coli was 63.8% in pigs (pooled pen-level), 40.0% in humans, and 35.7% in effluents. High levels of resistance were observed across multiple antibiotic classes, including cephalosporins, penicillins, and fluoroquinolones, with fluoroquinolone resistance rates of 79.8%, 75.0%, and 90.0% in pig, human, and effluent isolates, respectively. All isolates showed resistance to polymyxins based on phenotypic testing. The multiple antibiotic resistance index exceeded 0.2 across all isolates. Awareness of AMR was low, with 93% of respondents demonstrating poor understanding of antibiotic withdrawal periods. These findings indicate a high burden of multidrug-resistant E. coli within pig production systems and associated human-environmental interfaces. The results highlight the need for strengthened antibiotic stewardship, improved farmer education and AMR surveillance in livestock production systems in Nigeria and other LMICs.