Escherichia coli O157:H7, a Common Contaminant of Raw Milk from Ecuador: Isolation and Molecular Identification

<i>Escherichia coli</i> (<i>E. coli</i>), especially the Shiga toxin-producing O157:H7 strain, poses severe health risks. In rural Ecuador, raw milk consumption heightens contamination risks. This study analyzed 633 raw milk samples from Pichincha and Manabí to assess <i>E. coli</i> O157:H7 prevalence. The samples were enriched using BHI broth, and then specific culture media were used to isolate <i>E. coli</i> O157:H7. The pathogen in the enriched raw milk was identified, and the isolates were specifically confirmed through the application of a newly designed qPCR assay. The novel qPCR assay demonstrated remarkable sensitivity, capable of detecting up to one copy of genetic material, and specificity (no amplification of other bacteria). An extremely high <i>E. coli</i> O157:H7 prevalence of 0.63 (n = 401) was detected, where the province with the highest number of positive samples was Manabí with 72.8% (n = 225/309) and 54.3% (n = 179/324) for Pichincha. In both provinces, the presence of <i>E. coli</i> O157:H7 contamination exhibited a favorable correlation with small-scale farms and elevated temperatures. This research provides valuable data on the microbiological contamination of <i>E. coli</i> O157:H7 present in raw milk, in addition to an improved method that has been demonstrated to be faster, more sensitive, and more specific than conventional and previously published methods, highlighting the associated risk of food-borne infections and pointing out potential shortcomings in the regulation of agricultural practices and the need for periodic monitoring of bacterial contamination levels with updated methods.