Emergent Antibiotic Persistence in Cross-Feeding Bacteria in Structured Habitats

Antibiotic persistence allows a sub-population of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-cell heterogeneity in the metabolic state both during growth and antibiotic killing. We tracked the ampicillin-induced death on agar surfaces in a model obligate mutualism ofEscherichia coliandSalmonella enterica. We found thatE. coliformed ∼100-fold more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence ofS. enterica, the presence of cross-feeding, or the growth rate differences between the mono- and co-cultures. Time-series fluorescent microscopy revealed increased cell-cell variation inE. colilag time in the mutualistic co-culture. Furthermore, we discovered that anE. colicell can survive antibiotic killing if the nearbyS. entericacells on which it relies die first—a mechanism we termed “dynamical loss of access to nutrient.” In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially-structured interactions during antibiotic treatment and to understand microbial community resilience more broadly.