Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples

Countering the rise of antibiotic resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g. via resource competition), but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonization by focal E. coli, they also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibi...

对抗抗生素耐药病原体的兴起，需要深入理解耐药性在单个物种中如何产生和传播——这些物种往往嵌于复杂的微生物群落（如人类肠道微生物组）之中。此类群落中与其他微生物的相互作用，可能会抑制单个物种的生长和耐药性进化（例如通过资源竞争），但也可能通过耐药基因的水平转移加速耐药性进化。目前尚不清楚这些不同效应如何相互平衡，部分原因在于难以直接观察它们。在此，我们采用肠道微宇宙方法，量化了三种人类肠道微生物组群落对大肠杆菌（Escherichia coli）焦点菌株生长及耐药性进化的影响。我们发现，常驻微生物群落不仅抑制了焦点大肠杆菌菌株的生长和定殖，还阻止其在暴露于β-内酰胺类抗生素时进化出耐药性……