Prevalence of Antibiotic Resistance Bacteria in Manure, Soil, and Vegetables in Urban Blantyre, Malawi, from a Farm-to-Fork Perspective

The use of untreated livestock manure in urban agriculture sustains soil fertility but risks disseminating antimicrobial resistance (AMR) in resource-limited settings. This study characterized antibiotic-resistant bacteria (ARB) prevalence across manure–soil–vegetable pathways in Blantyre, Malawi. Using a cross-sectional design, we collected 35 samples (poultry/pig manure, farm/home soils, Brassica rapa subsp. chinensis, Brassica rapa, and Amaranthus spp.) from five livestock farms. Microbiological analysis with API 20E identification and disk diffusion testing revealed clear differences in contamination: Escherichia coli dominated pig manure (52%) and farm soil (35%), with detection in vegetables suggesting possible transfer (e.g., 20% in Brassica rapa subsp. chinensis), while Klebsiella pneumoniae contaminated all sample types (peak: 60% vegetables and 67% home soils). All manure isolates exhibited sulfamethoxazole–trimethoprim resistance, with 50% of pig manure E. coli showing cefotaxime resistance. Soil isolates mirrored these patterns (100% ampicillin resistance in K. pneumoniae and 77% cefotaxime resistance in farm soil E. coli). Vegetables displayed severe multidrug resistance (100% E. coli and 80% K. pneumoniae resistant to ≥3 classes), including critical gentamicin resistance (100% E. coli). Composting for ≤6 weeks, as practiced on the studied farms, did not eliminate ARBs, suggesting that longer durations may be needed. Notably, this study provides the first phenotypic evidence of presumptive Pasteurella-like organisms on edible leafy vegetables, specifically 45% in Amaranthus spp. and 6.1% in Brassica rapa, suggesting a potential zoonotic transmission route from livestock farms that requires molecular confirmation. These findings demonstrate manure-amended farms as AMR reservoirs, necessitating extended composting and antibiotic stewardship to mitigate One Health risks.