Microbial Safety of Tomatoes in Burkina Faso: Estimating Prevalence and Concentration of Escherichia coli and Non-Typhoidal Salmonella enterica via Pooled Sampling

• Pooled sampling enables low-cost detection of tomato contamination. • Market tomatoes often carried E. coli ; NTS was less common. • Damaged tomatoes had a higher E. coli contamination risk. • Findings support better handling, training, and consumer safety practices. Contamination of fresh produce with enteric pathogens is a public health concern in low- and middle-income countries (LMICs), especially in informal markets. We assessed the microbiological safety of tomatoes sold at urban markets in Burkina Faso by evaluating the prevalence and concentration of generic Escherichia coli and non-typhoidal Salmonella enterica . Tomatoes were visually categorized into three levels by the amount of damage on tomato surfaces (intact, slightly damaged, severely damaged), and samples were analyzed using a pooled sampling design through Monte Carlo simulations. Mean E. coli prevalence estimates ranged from 4.0 – 18.3 %, with both prevalence and mean concentration (3.4 – 4.1 log 10 CFU/tomato) increasing significantly with surface damage. Salmonella enterica prevalence ranged from 0.6 – 2.5 %, although prevalence did not vary across damage levels, mean concentrations did increase with tomato damage (1.0 – 1.5 log 10 MPN/tomato). Other market-level factors, including vendor hygiene, ripeness stage, and stall conditions, were not associated with microbial contamination. We did not find a significant correlation between the presence of generic E. coli and Salmonella among market tomatoes. Overall, our findings highlight the utility of visual damage assessment as a proxy for contamination risk. Public health interventions should prioritize damage prevention, improved sorting, vendor training, and consumer education on the safe handling and preparation of tomatoes to reduce foodborne disease burden. Damaged tomatoes were associated with higher levels of microbial contamination and should be cooked and not eaten raw.