Apple resistome Metagenome. Apple resistome

A detailed understanding of antimicrobial resistance trends among human-related environments is key to combat global health threats. Until now, the resistome is little considered in food science. Here we studied the apple microbiome and resistome from different cultivars and origin by metagenomics approaches, genome reconstruction and isolate sequencing. All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs). They are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low. Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs. Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and highlight the need for surveillance of resistance emergence along complex food chains to ensure food quality and safety.