Microbial Contamination and Associated Risk Factors from Slaughter to Retail: Forward-tracing of meat in the Pork Value Chain in Uganda

Uganda has the highest per-capita pork consumption in East Africa, with most pigs raised in free-range smallholder systems. Pork is largely produced and sold in informal markets with limited infrastructure, regulation, and hygiene. By forward-tracing pork from slaughter to retail, this study assessed factors associated with contamination with non-typhoidal Salmonella (NTS) and total bacterial count (TBC), and identified critical control points along the pork value chain. Two pork value chains were evaluated: a Multiple Slaughter unit Value Chain (MSVC),15 slaughter points supplying 27 retail outlets, and a Single Slaughter unit Value Chain (SSVC), one slaughter point supplying 35 retail outlets. A repeat cross-sectional survey conducted across three regions between December 2021 and December 2022 collected 1,535 samples and hygiene observations. Overall NTS prevalence was 30.5% on carcasses (95% CI: 23.6-38.2), 33.1% in raw pork (95% CI: 26.1-40.6), and 4.0% in cooked pork (95% CI: 1.9-8.4). Mean TBC in the MSVC were 5.70 Log CFU/cm2 on carcasses, 6.00 Log CFU/g in raw pork, and 1.23 Log CFU/g in cooked pork, compared with 5.32, 5.34, and 0.03 Log CFU/g respectively, in the SSVC. Although raw pork TBC complied with regional limits (< 6.0 Log CFU/g), they exceeded international standards (< 5.6 Log CFU/g). TBC were significantly higher in the MSVC (p < 0.05) but NTS prevalence did not differ between value chains (p > 0.05). Contaminated meat handlers’ hands, rinsing water, floors, and chopping surfaces were identified as key contributors to microbial contamination. These findings highlight substantial contamination along the pork value chain and the need to strengthen hygiene prerequisites and critical control points to improve pork safety.