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Gastric acid and escape to systemic circulation represent major bottlenecks to host infection by Citrobacter rodentium


The gastrointestinal (GI) environment plays a critical role in shaping enteric infections. Host environmental factors create bottlenecks, restrictive events that reduce the genetic diversity of invading bacterial populations. However, the identity and impact of bottleneck events on bacterial infection are largely unknown. We used Citrobacter rodentium infection of mice, a model of human pathogenic Escherichia coli infections, to examine bacterial population dynamics and quantify bottlenecks to host colonization. Using Sequence Tag-based Analysis of Microbial Populations (STAMP) we characterized the founding population size (Nb′) and relatedness of C. rodentium populations at relevant tissue sites during early- and peak-infection. We demonstrate that the GI environment severely restricts the colonizing population, with an average Nb′ of only 12–43 lineages (of 2,000+ inoculated) identified regardless of time or biogeographic location. Passage through gastric acid and escape to the systemic circulation were identified as major bottlenecks during C. rodentium colonization. Manipulating such events by increasing gastric pH dramatically increased intestinal Nb′. Importantly, removal of the stomach acid barrier had downstream consequences on host systemic colonization, morbidity, and mortality. These findings highlight the capability of the host GI environment to limit early pathogen colonization, controlling the population of initial founders with consequences for downstream infection outcomes.

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Fig. 1: Evidence for bottlenecks during C. rodentium infection.
Fig. 2: A small population size exists across gut regions despite a high overall CFU burden.
Fig. 3: Diversity within the infecting population is lost within the first two days of infection.
Fig. 4: Escape to the systemic circulation is a major bottleneck during C. rodentium infection.
Fig. 5: Pre-treatment to neutralize the stomach acid bottleneck with either sodium bicarbonate or proton pump inhibitor Lansoprazole dramatically increases intestinal founding population size independent of CFUs.
Fig. 6: Antacid pre-treatment has unintended consequences to systemic colonization and susceptibility to enteric infection.

Data availability

The datasets generated during the current study are available in the NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA810564.


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We thank our colleagues in the Finlay laboratory for their support and assistance; particularly W Deng and L Thorson. We would also like to thank R Vander Werff, T Stach, and E Limber for technical support, as well as M Whitlock for early consultation on conceptual design. This work was supported by grants from the Canadian Institutes of Health Research (CIHR) to BB Finlay (FDN-159935). SE Woodward is a CIHR CGS-D Graduate Scholar, supported by a UBC Four Year Fellowship and Dmitry Apel Memorial Scholarship. RA Melnyk was a supported by Simons Foundation Fellowship through the Life Sciences Research Foundation. CH Haney was supported by a Canada Research Chairs salary award. Supporting images were created using

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SEW and SLV conceived the project with guidance from CHH and BBF, SEW and SLV designed experiments. SEW, SLV, JP-D, ASP, LMN, KEH, and MAW performed experiments. SEW, JP-D, RAM, and MC wrote bioinformatics pipelines and analyzed data. SEW wrote the original draft of the manuscript with input from all authors. BBF acquired funding for the project.

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Correspondence to B. Brett Finlay.

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Woodward, S.E., Vogt, S.L., Peña-Díaz, J. et al. Gastric acid and escape to systemic circulation represent major bottlenecks to host infection by Citrobacter rodentium. ISME J 17, 36–46 (2023).

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