Population-level impacts of antibiotic usage on the human gut microbiome

We conducted an extensive survey of antibiotic resistance genes (ARGs) in the human microbiome utilising 8,972 metagenomes. We found large highly significant correlations in the gut microbiome between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We used a large-scale collection of human gut metagenome assembled genomes (MAGs) to link these ARGs to taxa. This revealed that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype, has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network