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, <i>Brassica rapa</i> subsp. <i>chinensis</i>, <i>Brassica rapa</i>, and <i>Amaranthus</i> spp.) from five livestock farms. Microbiological analysis with API 20E identification and disk diffusion testing revealed clear differences in contamination: <i>Escherichia coli</i> dominated pig manure (52%) and farm soil (35%), with detection in vegetables suggesting possible transfer (e.g., 20% in <i>Brassica rapa</i> subsp. <i>chinensis</i>), while <i>Klebsiella pneumoniae</i> contaminated all sample types (peak: 60% vegetables and 67% home soils). All manure isolates exhibited sulfamethoxazole-trimethoprim resistance, with 50% of pig manure <i>E. coli</i> showing cefotaxime resistance. Soil isolates mirrored these patterns (100% ampicillin resistance in <i>K. pneumoniae</i> and 77% cefotaxime resistance in farm soil <i>E. coli</i>). Vegetables displayed severe multidrug resistance (100% <i>E. coli</i> and 80% <i>K. pneumoniae</i> resistant to ≥3 classes), including critical gentamicin resistance (100% <i>E. coli</i>). 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 <i>Pasteurella</i>-like organisms on edible leafy vegetables, specifically 45% in <i>Amaranthus</i> spp. and 6.1% in <i>Brassica rapa</i>, 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.