TNF signaling maintains local restriction of bacterial founder populations in intestinal and systemic sites during oral Yersinia infection

Enteroinvasive bacterial pathogens are responsible for an enormous worldwide disease burden that critically affects the young and immunocompromised. Yersinia pseudotuberculosisis a Gram-negative enteric pathogen, closely related to the plague agent Y. pestis, that colonizes intestinal tissues, induces the formation of pyogranulomas along the intestinal tract, and disseminates to systemic organs following oral infection of experimental rodents. Prior studies proposed that systemic tissues were colonized by a pool of intestinal replicating bacteria distinct from populations within Peyer’s patches and mesenteric lymph nodes. Whether bacteria within intestinal pyogranulomas serve as the source for systemic dissemination, and the relationship between bacterial populations within different tissue sites, is poorly defined. Moreover, the factors regulating Yersinia colonization and dissemination are poorly understood. Here, we demonstrate, using Sequence Tag-based Analysis of Microbial Populations in R (STAMPR), that remarkably small founder populations independently colonize intestinal and systemic tissues. Notably, intestinal pyogranulomas contain clonal populations of bacteria that are restricted and do not spread to other tissues. However, populations of Yersinia are shared among systemic organs and the blood, suggesting that systemic dissemination occurs via hematogenous spread. Finally, we demonstrate that TNF signaling is a key contributor to the bottlenecks limiting both tissue colonization and lymphatic dissemination of intestinal bacterial populations. Altogether, this study reveals previously undescribed aspects of the infection dynamics of enteric bacterial pathogens.

Methods
Sample harvesting

Samples were harvested as described in Extended Methods (Supplemental Information).

All samples had 100uL serially diluted tenfold in PBS, plated on LB agar supplemented with 2 μg/ml triclosan and 100 mg/mL kanamycin, and incubated for two days at room temperature. Dilutions of each sample were plated in triplicate and expressed as the mean CFU per gram or per biopsy. Remaining 900uL of homogenized samples were plated on 15 cm dishes with LB agar supplemented with 2 μg/ml triclosan (irgasan) and 100 mg/mL kanamycin and incubated for two days at room temperature.

STAMP sample processing

Y. ptb colonies were washed off plates, collected in PBS with 25% glycerol, diluted in water, and boiled for 15 minutes at 95°C. The barcode-containing region was amplified from the genome using custom forward and reverse primers(Campbell et al., 2023; Holmes et al., 2025; Hotinger et al., 2025). Sequence tag-based analysis of microbial populations (STAMP) was performed as previously described(Holmes et al., 2025). Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Statistics

Graphing and statistical analyses of data were performed using Prism 9 software (GraphPad). Statistical significance was determined using the statistical tests indicated in each figure legend. Differences were considered statistically significant if the P value was less than or equal to 0.05.