Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance

This review explores the ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence in patients and how they vary across bacterial infections. It highlights four major mechanisms: spontaneous resistance mutations, in situ horizontal gene transfer, selection of pre-existing resistance, and immigration of resistant lineages. The importance of each mechanism varies between bacterial species and infection sites. The review suggests that integrating ecological and evolutionary analysis into clinical trials of antimicrobials could help understand why these mechanisms vary between pathogens, infections, and individuals.