Simulating the host niche: balancing complexity and control in the experimental evolution of antibiotic resistance and pathoadaptation

The 'ESKAPE' pathogens cause the majority of antibiotic-resistant infections in humans, with associated mortality expected to surpass that of cancer by 2050. Outbreak strains of these pathogens often demonstrate a remarkable ability to establish infection and easily acquire novel antimicrobial resistance mechanisms. Because the expression of virulence factors and antimicrobial resistance genes often imposes a fitness cost, successful host-adapted strains must evolve without compromising their ability to colonize the niches found in the human body. The ongoing spread of these multidrug-resistant strains suggests that these bacterial pathogens are actively adapting to antibiotic-treated hosts. With whole-genome sequencing, we can now identify the multiple genetic changes associated with host adaptation and increased antibiotic resistance. Yet, pinpointing the specific mutations responsible for phenotypic shifts through sequencing of clinical isolates remains challenging due to the high mutational load accumulated during infection. For this reason, our understanding of how pathogens evolve within specific host niches, both in the presence and absence of antibiotics, remains limited. Experimental evolution within host tissues now allows us to more accurately simulate the conditions under which antibiotic resistance and pathoadaptations emerge. In this Perspective article, we evaluate some of the systems currently employed, discuss their respective advantages and limitations and introduce engineered human microtissue models as a promising platform for bacterial experimental evolution.