Microbiological quality of high-demand foods from three major cities in Ecuador

Bacterial foodborne diseases are one of the most important public health issues worldwide but in Ecuador reports on the microbiological quality of foods are scarce. In this study, a total of 450 traditional food samples including bolon, encebollado, sauces, ceviche, fruit juices, fruit salads, cheese, raw chicken and ground beef were collected from popular markets in the cities of Guayaquil, Quito and Cuenca. Samples were assessed for microbiological quality using both culture dependent and culture independent techniques. Populations of total aerobic bacteria, total coliforms, fecal coliforms and E. coli were examined by plate count. Representative colonies from each culture were further identified using biochemical tests and sequencing of the 16S rRNA gene. For the culture independent analysis, bacterial DNA was extracted from food samples and submitted to next generation sequencing (NGS) of the v3-v4 region of 16S rDNA. By using culture dependent techniques, high prevalence of opportunistic and true pathogens including E. coli, Klebsiella pneumoneae, Salmonella spp., Listeria monocytogenes, Staphylococcus aureus, and Shigella flexneri was observed.Other potential pathogens were identified by NGS, including Clostridium spp.., Vibrio spp.., Helicobacter spp.., Campylobacter spp.., among others but no E. coli, Salmonella spp.. or Listeria spp. were detected. This is the first report on the microbiological quality of food from Ecuador.