Analysis of antimicrobial resistance and virulence of pathogens in dairy products from Egypt by whole genome sequencing.

Abstract

Raw milk and dairy products can cause a variety of diseases due to environmental pollution. The objectives of this study were to identify the genetic variables, evaluate antibiotic resistance, and isolate microorganisms from raw milk and dairy products. Three hundred samples of raw milk were collected from farmers and marketplaces in Gamasa, Mansoura, and Damietta cities in Egypt. Various bacterial species were isolated using selective culture media, of which 101 (33.6%) were Staphylococcus species, 11 (3.6%) were Escherichia coli, and 1 (0.3%) was Salmonella. The isolates were confirmed by biochemical tests. The disk diffusion method was used to test antibiotic susceptibility. Additionally, resistance genes and virulence factors in 4 randomly selected Staphylococcus species samples were identified through MinION nanopore sequencing (Oxford Nanopore Technologies, Oxford, UK). Staphylococcus species showed resistance to antibiotics, including ampicillin (89%) and colistin (94%). Whole genome sequencing was used to identify the molecular traits of antibiotic-resistant Staphylococcus species. The genes associated with resistance to antibiotics in Staphylococcus species were examined. Four Staphylococcus samples were randomly selected for extracting DNA and nanopore sequencing. Staphylococcus species exhibited remarkable resistance to colistin because of the presence of putative serine protease proteins (colistinase) or resistance-nodulation-division (RND) efflux pumps (ACRB gene). The identification of resistant bacterial strains in unpasteurized milk and dairy products highlights the critical need for strict regulations to limit the overuse of antibacterial treatments in dairy herd management.