Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics

Food products carry bacteria unless specifically sterilised. These bacteria can be pathogenic, commensal or associated with food spoilage, and may additionally be resistant to antimicrobials. Current methods for detecting bacteria on food rely on culturing for specific bacteria, a time-consuming process, or 16S metabarcoding that can identify different taxa but not their genetic content. Directly sequencing the metagenome of food is inefficient as foods of plant and animal origin have their own host DNA that vastly outnumbers the bacterial DNA present. In this study we optimised a host DNA depletion method for food that allows efficient sequencing of the prokaryotic metagenomes of food samples. We demonstrated its applicability for identifying the different bacterial taxa and antimicrobial resistance (AMR) genes present and calculating the AMR dosage of food samples. The approach described in this study is an efficient and effective method of identifying and quantifying the predominant bacteria and AMR genes on food.