Antibiotic-recalcitrant Salmonella exploits post-antibiotic microbiota disruption to achieve virulence-dependent...

Antibiotic-recalcitrant reservoirs contribute to clearance failure and relapse of bacterial infections in vivo. Salmonella Typhimurium survives antibiotic exposure in host tissue, later resuming replication and reseeding the gut lumen. It is not well understood how relapsing infection is shaped by Salmonella virulence factors nor how antibiotic therapy affects transmission from infected animals to new hosts. Here, we study how antibiotic therapy affects Salmonella during long-term systemic infection of 129/SvEv mice. Plateable pathogen loads decline during ceftriaxone treatment but gradually increase after the end of antibiotic therapy, and this regrowth is promoted by intracellular virulence factors. We observe massive pathogen blooms in the gut, which lead to clonal transmission and invasive infection of cagemates. Transmission is blocked when treated animals are co-housed with naive cagemates that harbor intact microbiota reservoirs, which confer community colonization resistance. Our work provides new insights into how antibiotic-recalcitrant tissue reservoirs are shaped by pathogen-host-microbiota dynamics.