Correlation among antibiotic resistance and virulence traits in human gut microbiomes

Human beings have used large amounts of antibiotic, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still co-occurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes issuing from different individuals from different human populations across the world. We found a great diversity of antibiotic resistance determinants (ARd) and virulence factors (VFd) in metagenomes. Importantly, even after correcting for metagenome sizes, there is a correlation between ARd and VFd. In the human gut there are less ARd and VFd than in more diversified environments, and yet the ARd/VFd correlations are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to non-existent in the uncontacted Amerindians. We conclude that there is co-occurrence of resistance and virulence determinants, suggesting a possible coselective phenomenon. Therefore, by selecting for resistant bacteria, we may be selecting for more virulent strains, as a side effect of antimicrobial therapy.