Salmonella Persistence in Infection: Molecular Regulation, Host Microenvironments, and Multiscale Heterogeneity

Salmonella persistence contributes to infection relapse, chronic carriage, and reduced antibiotic efficacy. Traditionally viewed as dormant subpopulations that passively survive antibiotic exposure, persister cells are now increasingly recognized as dynamic, heterogeneous, and context-dependent physiological states shaped by bacterial regulatory programs and host microenvironmental pressures. This review examines Salmonella persistence from a multiscale perspective. We first clarify key antibiotic survival phenotypes, including resistance, heteroresistance, tolerance, persistence, and viable but non-culturable states. We then discuss how host-derived stressors, such as phagosomal acidification, nutritional restriction, metal perturbation, and reactive oxygen and nitrogen species, promote growth-restricted, persistence-associated bacterial states. At the bacterial level, we summarize stress-response networks involving the stringent response, SOS response, toxin–antitoxin systems, and auxiliary regulators that coordinate metabolic remodeling, growth restriction, and antibiotic survival. At the host level, we highlight how organ reservoirs, immune cell subsets, metabolic cues, and Salmonella-mediated immune niche remodeling shape persistence-associated phenotypes in vivo. Finally, we discuss clinical and translational implications, including endogenous relapse, resistance evolution, and emerging anti-persistence strategies. Together, this review provides a framework for understanding Salmonella persistence as a multiscale, niche-dependent process relevant to recurrent and chronic infection.