Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities

Daily consumption of fresh vegetables is highly recommended by international health organizations, because of their high content of nutrients. However, fresh vegetables might harbour several pathogenic microorganisms or contribute to spread antibiotic resistance, thus representing a hazard for consumers. In addition, little is known about the transmission routes of the residential microbiome from the food handling environment to vegetables. Therefore, we collected environmental and food samples from three manufactures producing fresh vegetables to estimate the relevance of the built environment microbiome on that of the finished products. Our results show that food contact surfaces sampled after routine cleaning and disinfection procedures host a highly diverse microbiome, including pathogens such as the enterotoxigenic Bacillus cereus sensu stricto. In addition, we provide evidence of the presence of a wide range of antibiotic resistance and virulence genes on food contact surfaces associated with multiple taxa, thus supporting the hypothesis that selection of resistant and pathogenic taxa might occur on sanitized surfaces. This study also highlights the potential of microbiome mapping routinely applied in food industries monitoring programs to ensure food safety.