Quantitative dose-response analysis untangles host bottlenecks to enteric infection

Abstract

Host bottlenecks prevent many infections before the onset of disease by eliminating invading pathogens. By monitoring the diversity of a barcoded population of the diarrhea causing bacterium Citrobacter rodentium during colonization of its natural host, mice, we determine the number of cells that found the infection by establishing a replicative niche. In female mice the size of the pathogen’s founding population scales with dose and is controlled by a severe yet slow-acting bottleneck. Reducing stomach acid or changing host genotype modestly relaxes the bottleneck without breaking the fractional relationship between dose and founders. In contrast, disrupting the microbiota causes the founding population to no longer scale with the size of the inoculum and allows the pathogen to infect at almost any dose, indicating that the microbiota creates the dominant bottleneck. Further, in the absence of competition with the microbiota, the diversity of the pathogen population slowly contracts as the population is overtaken by bacteria having lost the critical virulence island, the locus of enterocyte effacement (LEE). Collectively, our findings reveal that the mechanisms of protection by colonization bottlenecks are reflected in and can be generally defined by the impact of dose on the pathogen’s founding population.

A discovery platform to identify inducible synthetic circuitry from varied microbial sources

“…By comparison, population bottlenecking caused barcode and strain diversity to drop quickly following administration to the gut, limiting experiment length (Supplementary Figure 3). This is similar to the observed dynamics of barcoded libraries of the pathogen C. rodentium (Campbell et al, 2023; Woodward et al, 2023). Nevertheless, higher numbers of barcodes per sensor should increase the robustness of results from short-term animal experiments.…”

Quantifying the intra- and inter-species community interaction in a microbiome by dynamic covariance mapping

“…For instance, Vasquez et al utilized ~200 barcodes in plasmids to explore colonization lineage dynamics in germ-free mice 52 . In a similar vein, STAMP (sequence tag-based analysis of microbial populations) was used to demonstrate the complex spatio-temporal dynamics of Vibrio cholerae infection along the rabbit gut, as well as to quantify the bottlenecks in Citrobacter rodentium in mice 81,82 . Additionally, Barroso-Batista et al used an isogenic E. coli population, differentiated only by chromosomally encoded YFP/CFP fluorescence markers, to track adaptive mutations and their fitness effects in mice 56 .…”

A bile metabolite atlas reveals infection-triggered interorgan mediators of intestinal homeostasis and defense

“…Female SPF mice (9 to 10-week-old age) were orally inoculated with Listeria monocytogenes or Citrobacter rodentium following the methods described previously 18, 61 . Briefly, mice were deprived of food for 6 hours, lightly sedated with isoflurane inhalation, and oro-gastrically inoculated with 3 ×10 9 CFU of Listeria monocytogenes 10403S InlA m strain in a 300 µl mixture of 200 mM CaCO3 in PBS, or with 1 ×10 9 CFU Citrobacter rodentium ICC168 strain in 200 µl PBS using 18G flexible feeding needles (DT 9928, Braintree Scientific).…”

“…Female SPF mice (9 to 10-week-old age) were orally inoculated with Listeria monocytogenes or Citrobacter rodentium following the methods described previously 18,61 . Briefly, mice were deprived of food for 6 hours, lightly sedated with isoflurane inhalation, and oro-gastrically inoculated with 3 ×10 9 infected mice, and 2-3 GF mice.…”