Antibiotic resistance genes can be present in the microbiome without an active pathogenic infection. This is because bacteria utilize horizontal gene transfer, meaning they share resistance genes with each other. According to this article (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390938/) "genetic material encoding resistance and virulence traits spreads between microbial cells and species in environments in which antibiotics are present."
How can Gut Zoomer results show antibiotic resistance genes detected, but no pathogens?
Adair