Bacterial community in fresh fruits and vegetables sold in streets and open-air markets of Dakar, Senegal

In the context of food transition, the agrifood sector has experienced increasingly strong demand for horticultural products. Fresh fruits and vegetables are mainly vehicles of microorganisms, including pathogens that cause human infections. Food safety and compliance with health standards in the fruits and vegetable value chain are significant concerns and multiple challenges, given the prevalence of foodborne pathologies in Southern countries, particularly in Senegal. This study aimed to describe the bacterial community and assess the microbiological quality of a range of fruits and vegetables sold on street stalls and open-air markets in Dakar, the capital city of Senegal. Samples purchased in seven sites were analyzed to isolate Escherichia coli (E. coli), Salmonella spp. and Vibrio spp. Some primary samples with a positive microbiological culture were subjected to DNA extraction and subsequent metagenomic analysis. A total of 240 fresh fruit and vegetable samples were collected, including lettuce (n = 40), tomatoes (n = 40), mango slices (n = 40), onion slices (n = 40), mint leaves (n = 40), strawberries and grapes (each n = 20). Of these samples, 50.83% (122/240) and 60.41% (145/240) were contaminated with E. coli and Vibrio spp., respectively, while Salmonella was not isolated in any product. E. coli and Vibrio spp. contamination levels, 1.3 10³ to 6 10⁶ Colonies Forming Units per gram of sample (CFU/g) and 4.55 10² to 8.73 10⁶ CFU/g, respectively, were significantly above the thresholds acceptable for human consumption. The most contaminated samples were lettuce, with a prevalence of 98% (39/40) for E. coli and Vibrio spp. followed by mint leaves with 100% (40/40) and 93% (37/40) of the samples containing E. coli and Vibrio spp. respectively. Out of 46 samples sequenced, the metagenomic analysis revealed high contamination rates for E. coli, Vibrio spp. and Salmonella spp., with 100%, 67.39% and 93.47% of prevalence, respectively. On the other hand, the alpha diversity analysis shows high bacterial diversity in lettuce and mint leaf samples, while the beta diversity analysis highlighted the presence of two major clusters. Our results stress the need for a surveillance system that extends this investigation to a national scale while increasing the number of sampling sites and products analyzed.