Milk Safety in Rwanda: Examining Practices, Microbial Contamination, and Antibiotic Residues Along the Milk Value Chain

Milk is widely recognized as a vital source of animal protein; however, it can also act as a conduit for foodborne infections. This study evaluated the microbiological quality and prevalence of antibiotic residues in raw cow milk along Rwanda's dairy value chain, including farms, milk transporters, milk collection centers (MCCs), and retail outlets. The research was conducted across four major milk sheds (regions) in Rwanda: Gicumbi, Gishwati, Nyagatare, and Nyanza. A total of 144 dairy farmers, 70 milk transporters, 12 MCCs, and 46 retail points were randomly selected. Data on milk production and handling practices were gathered using a structured questionnaire, and 390 milk samples were analyzed for hygiene indicator bacteria, Salmonella, and antibiotic residues. Milk was found to be transported from farms to MCCs without refrigeration. At the farm level, microbial counts for Total Mesophilic Bacteria (6.10 ± 0.08 log CFU/mL), Total Coliforms (4.85 ± 0.09 log CFU/mL), and Escherichia coli (3.79 ± 0.09 log CFU/mL) exceeded national safety thresholds. Contamination levels increased during transportation and peaked at MCCs, where the Total Mesophilic Count (TMC) reached 6.97 ± 0.14 log CFU/mL, and Salmonella was detected in 18% of samples. However, microbial quality improved at the retail level, likely due to boiling practices. Antibiotic residues were present in 48.5% of milk samples. Tetracyclines were the most frequently detected (40.0%), followed by Streptomycin (6.2%) and β-lactams (2.3%). Additionally, 95.8% of Salmonella isolates showed resistance to at least one antibiotic, and 54.2% exhibited multidrug resistance. These findings highlight the urgent need for targeted interventions to enhance on-farm hygiene, establish cold chain systems for milk transportation, and implement routine screening for antibiotic residues throughout the dairy value chain.