Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance

Bacterial communication plays an important role in many population-based phenotypes and interspecies interactions, including those in host environments. These interspecies interactions may prove critical to some infectious diseases, and it follows that communication between pathogenic bacteria and commensal bacteria is a subject of growing interest. Recent studies have shown that Escherichia coli uses the signaling molecule indole to increase antibiotic tolerance throughout its population. Here, we show that the intestinal pathogen Salmonella typhimurium increases its antibiotic tolerance in response to indole, even though S. typhimurium does not natively produce indole. Increased antibiotic tolerance can be induced in S. typhimurium by both exogenous indole added to clonal S. typhimurium populations and indole produced by E. coli in mixed-microbial communities. Our data show that indole-induced tolerance in S. typhimurium is mediated primarily by the oxidative stress response and, to a lesser extent, by the phage shock response, which were previously shown to mediate indole-induced tolerance in E. coli. Further, we find that indole signaling by E. coli induces S. typhimurium antibiotic tolerance in a Caenorhabditis elegans model for gastrointestinal infection. These results suggest that the intestinal pathogen S. typhimurium can intercept indole signaling from the commensal bacterium E. coli to enhance its antibiotic tolerance in the host intestine.Rather than acting autonomously, bacterial cells communicate with one another to coordinate their efforts and relay vital information. Interspecies and intraspecies bacterial communication has been implicated in many community-dependent behaviors including virulence (1), biofilm formation (2), and antibiotic tolerance (3). Communication may therefore allow control of heterogeneity, which is important in determining fitness of microbial populations (4). Recently, we reported that bacterial communication through indole signaling induces persister formation in Escherichia coli (3). Persistence is an antibiotic-tolerant phenotype in which a dormant subpopulation of cells (persisters) survives antibiotic treatment without having genetically encoded resistance factors (5, 6). In E. coli, we found that indole signaling induced oxidative stress response and phage shock response pathways, thereby increasing the persister frequency within the population. This work suggested that bacteria can use intraspecies signaling to modify the antibiotic tolerance of their population in response to environmental conditions.Indole signaling is used by bacteria in the distal intestine of humans and other mammals (7). In this environment, alkaline and low nutrient conditions induce expression of the indole-producing tryptophanase (tnaA) enzyme in commensal E. coli and related bacteria (8). Indole concentrations in the mammalian intestine (∼300 µM to 1 mM) (9, 10) can induce antibiotic tolerance in E. coli without adversely affecting growth (11). As the mammalian intestine contains a richly mixed microbial population (12), signaling molecules such as indole might be detected and used by both commensal and pathogenic bacteria. Although there is increasing interest in the roles that commensal bacteria play in mammalian health (13), the mechanisms by which commensal bacteria interact with invading pathogens are not yet well understood.We hypothesized that pathogenic bacteria could use communication signals produced by commensal bacteria to sense and adjust their physiological state to the host environment. As indole induces antibiotic tolerance in E. coli, we hypothesized that it might also increase tolerance in related pathogens. Salmonella typhimurium is one such pathogen which, although it does not produce indole (14), has been shown to respond to signaling molecules produced by other bacteria (15). S. typhimurium is a common gastrointestinal pathogen and a major epidemiological threat, as it is a causative agent of gastroenteritis and sepsis. This pathogen can survive macrophage engulfment and persist within phagocytes, resulting in an asymptomatic but infectious carrier state (16) where antibiotic tolerance is a significant problem (17). We therefore sought to determine if indole signaling by E. coli might be exploited by S. typhimurium, leading to increased tolerance of the pathogen in a host intestinal environment.Here we show that indole signaling can indeed increase the antibiotic tolerance of S. typhimurium. This tolerance can be induced by exogenous indole in Salmonella-only cultures or by indole produced by E. coli in a mixed-microbial population. Our data suggest that this tolerance is mediated, in part, by oxidative stress and phage shock response systems. Further, we find, using a Caernohabditis elegans infection model (18), that indole induces antibiotic tolerance of S. typhimurium in a mixed-microbial, intestinal environment.