Non-typhoidal Salmonella strains are responsible for invasive infections associated with
high mortality and recurrence in sub-Saharan Africa and there is strong evidence for clonal
relapse following antibiotic treatment. Persisters are non-growing bacteria that are thought to
be responsible for the recalcitrance of many infections to antibiotics. Toxin-antitoxin systems
are stress-responsive elements that are important for Salmonella persister formation,
specifically during infection. Here we report analysis of persister formation of clinical invasive strains of S. Typhimurium and Enteritidis in human primary macrophages. We show that all
the invasive clinical isolates of both serovars that we tested produce high levels of persisters following internalization by human macrophages. Our genome comparison reveals that S.Enteritidis and S. Typhimurium strains contain three acetyltransferase toxins that we characterize structurally and functionally. We show that all induce the persister state by
inhibiting translation through acetylation of aminoacyl-tRNAs. However, they differ in their
potency and target partially different subsets of aminoacyl-tRNAs, potentially accounting for
their non-redundant effect.