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The evolution of multidrug antibiotic resistance in commensal bacteria is an important public health concern. Commensal bacteria such as  Escherichia coli ,  Streptococcus pneumoniae  or  Staphylococcus aureus , are also opportunistic pathogens causing a large fraction of the community-acquired and hospital-acquired bacterial infections. Multidrug resistance (MDR) makes these infections harder to treat with antibiotics and may thus cause substantial additional morbidity and mortality. Here, we develop an evolutionary epidemiology model to identify the factors favouring the evolution of MDR in commensal bacteria. The model describes the evolution of antibiotic resistance in a commensal bacterial species evolving in a host population subjected to multiple antibiotic treatments. We combine statistical analysis of a large number of simulations and mathematical analysis to understand the model behaviour. We find that MDR evolves more readily when it is less costly than expected from the combinations of single resistances (positive epistasis). MDR frequently evolves when bacteria are in contact with multiple drugs prescribed in the host population, even if individual hosts are only treated with a single drug at a time. MDR is favoured when the host population is structured in different classes that vary in their rates of antibiotic treatment. However, under most circumstances, recombination between loci involved in resistance does not meaningfully affect the equilibrium frequency of MDR. Together, these results suggest that MDR is a frequent evolutionary outcome in commensal bacteria that encounter the variety of antibiotics prescribed in the host population. A better characterization of the variability in antibiotic use across the host population (e.g. across age classes or geographical location) would help predict which MDR genotypes will most readily evolve.

Factors favouring the evolution of multidrug resistance in bacteria