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International audience; Human metagenomes with a high diversity of virulence genes tend to have a high diversity of antibiotic-resistance genes and vice-versa. To understand this positive correlation, we simulated the transfer of these genes and bacterial pathogens in a community of interacting people that take antibiotics when infected by pathogens. Simulations show that people with higher diversity of virulence and resistance genes took antibiotics long ago, not recently. On the other extreme, we find people with low diversity of both gene types because they took antibiotics recently—while antibiotics select specific resistance genes, they also decrease gene diversity by eliminating bacteria. In general, the diversity of virulence and resistance genes becomes positively correlated whenever the transmission probability between people is higher than the probability of losing resistance genes. The positive correlation holds even under changes of several variables, such as the relative or total diversity of virulence and resistance genes, the contamination probability between individuals, the loss rate of resistance genes, or the social network type. Because the loss rate of resistance genes may be shallow, we conclude that the transmission between people and antibiotic usage are the leading causes for the positive correlation between virulence and antibiotic-resistance genes.

Antibiotics have been used on a large scale in veterinary and medical contexts. The massive and continuous exposure to antimicrobial drugs has led to the emergence and spread of antibiotic resistance, which is nowadays one of the greatest threats to public health. Although antibiotics are used to treat bacterial infections, it is not only pathogenic bacteria that are affected. Upon exposure to antimicrobial drugs, bacteria that are resistant to the antibiotic administered are selected. Therefore, resistance and pathogenicity may be associated. It was recently shown that there is a positive correlation between the diversity of antibiotic resistance genes and the diversity of pathogenicity genes in human metagenomes from different geographical origins. Our study aimed to understand the factors that lead to the establishment of this positive correlation in human populations using computer simulations. Our results suggest that this positive correlation emerges if the contagion probability between individuals is higher or, at least, not much lower than the loss rate of resistance genes. We argue that the loss rate may be very low, or even null, leaving contagion probability between people as the main factor. Moreover, antibiotic usage throughout tens of years selected resistance genes, which was key to establishing resistance genes diversity across human metagenomes, hence contributing to explain the positive correlation between antibiotic resistance gene diversity and virulence gene diversity.