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

Multidrug-resistant (MDR) Escherichia coli ( E. coli ) poses a serious threat to animal and human health, especially in low- and middle-income countries (LMICs), where antibiotic use in livestock is poorly regulated. Pigs act as reservoirs for resistant bacteria that can spread to humans 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. These samples included pig faecal (n = 152), human stool (n = 30), and effluent (n = 28) samples. E. coli was isolated via standard microbiological methods and confirmed via biochemical tests. Antibiotic susceptibility testing followed the Kirby–Bauer disk diffusion method, with MDR defined as resistance to three or more antibiotics. 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, 40.0% in humans, and 35.7% in effluents. All the isolates were resistant (100%) to cephalosporins, polymyxins, and penicillins, whereas the rates of fluoroquinolone resistance were 79.8%, 75.0%, and 90.0% in the pig, human, and effluent isolates, respectively. The multiple antibiotic resistance index (MARI) exceeded 0.2 across all the isolates. Awareness of AMR was poor, with 93% of respondents showing poor understanding of withdrawal periods. These findings indicate pigs and pig farm environments as a high-risk platform for MDR E. coli spread, underscoring the need for intensified antibiotic stewardship, farmer education, and AMR surveillance in livestock production systems in Nigeria and other LMICs.