The epidemiology of ceftriaxone and cotrimoxazole-resistant Escherichia coli from humans, poultry, and their environment in central Malawi: A cross-sectional study

The poultry industry represents an important reservoir for clinical antibiotic resistance, especially in low- and middle-income-countries where food security pressures drive intensified farming and antibiotic use. However, evidence linking poultry production to public health risks remains limited in settings such as Malawi. This study examined Escherichia coli resistance to ceftriaxone and cotrimoxazole, two antibiotics with distinct stewardship priorities. We conducted a cross-sectional study between July and September 2022 in Malawi’s Central region, targeting poultry farms. Our mixed-methods design combined microbiological sampling from farm workers, poultry, and effluent water with a structured questionnaire on antibiotic use. E. coli isolates underwent antimicrobial susceptibility testing by disk diffusion for ceftriaxone and cotrimoxazole. 376 poultry farms were enrolled and among these, 17.6% reported using Trimovet, a veterinary formulation containing the same active ingredients as cotrimoxazole. Antibiotic use was more common among farms using commercial feed (aOR = 6.97; 95% CI: 3.43–14.17), and among farm workers with prior antibiotic knowledge (aOR = 5.56; 95% CI: 3.01–10.25). From 1,432 E. coli isolates recovered across all sources, resistance to cotrimoxazole was high: 80% in humans, 75% in environmental specimens, and 64% in poultry. In contrast, ceftriaxone resistance remained comparatively low (7.9%, 12%, and 7.3%, respectively). Predictors of cotrimoxazole resistance included farms in Nkhotakota district (aOR = 3.26; 95% CI: 1.84–6.01), fully housed chickens (aOR = 2.60; 95% CI: 1.67–4.08), commercial feed use (aOR = 1.54; 95% CI: 1.09–2.18), and prior antibiotic use (aOR = 1.67; 95% CI: 1.19–2.35). These findings highlight the risk that commercial poultry farming systems pose to public health, particularly for cotrimoxazole, which remains a cornerstone of Human Immunodeficiency Virus (HIV) prophylaxis and community care in Malawi. Strengthening antimicrobial stewardship across both human and animal sectors is urgently needed to mitigate transmission at the human–animal–environment interface.