Vogt, S. L. | Search bioRxiv

bioRxiv2026

Vancomycin promotes key microbiota-pathogen interactions and removes protective bottlenecks to enteric infection

Antibiotic exposure disrupts enteric pathogen colonization resistance, yet how antibiotics reshape pathogen population dynamics, infection bottlenecks, and strain-level heterogeneity in the gut remains poorly understood. Here, we combine high-resolution pathogen barcoding, transcriptomic, and metabolomic analyses to quantify how short-term vancomycin perturbation alters infection ecology in vivo. We use Citrobacter rodentium as a model for human infection by pathogenic Escherichia coli-an antimicrobial resistance priority group-to demonstrate that just two days of vancomycin pre-treatment profoundly reshapes infection trajectories, driving rapid, global gut colonization, a dramatic increase in pathogen founding population size, and preservation of strain diversity across intestinal sites. Notably, vancomycin eliminated the hallmark heterogeneity of C. rodentium infection, resulting in fully reproducible colonization across hosts. Population-level analysis revealed that antibiotic treatment relaxes competitive constraints both with the resident microbiota and among clonal pathogen lineages, allowing early-established founders to persist and expand. Despite accelerated pathogen engraftment and tissue pathology, transcriptomic analysis revealed reduced virulence gene expression. Instead, antibiotic-induced metabolic restructuring of the gut created permissive conditions for pathogen expansion. Interactions with a vancomycin-altered microbiota, dominated by Akkermansia and Bacteroides, further promoted nutrient cross-feeding and influenced epithelial attachment. Together, we illustrate how short-term antibiotic exposure reshapes enteric infection by removing ecological bottlenecks that normally constrain strain diversity and infection outcomes. These findings have implications for antibiotic use, antimicrobial resistance transmission, and therapeutic strategies that rely on competition-driven dynamics, such as strain replacement.

microbiology↗

bioRxiv2021

Dual perspective proteomics infectome profiling discovers Salmonella type III secretion system effector functions in macrophages

Intracellular bacterial pathogens have evolved sophisticated infection strategies, including the release and secretion of virulence factors to interfere with host cell functions and to perturb immune responses. For Salmonella enterica serovar Typhimurium (S. Typhimurium), the type III secretion systems encoded on Salmonella pathogenicity islands (SPI) 1 and 2 mediates invasion of the bacterium into innate immune cells and regulates bacterial replication and survival within the hostile environment of the host, respectively. Here, we explore the temporal and strain-specific dual perspective response of both the host and pathogen during cellular infection via quantitative proteomics. We report time- and pathogenicity island-specific expression and secretion of infection-associated proteins (i.e., SL1344_1263, SL1344_3112, SL1344_1563, and YnhG) and regulated immune response proteins in macrophage, including Cd86, Cd40, Casp4, C3, IL-1, and Cd69). Through intracellular macrophage and in vivo murine models of infection, we reveal a role in virulence for three of the bacterial proteins (SL1344_1263, SL1344_1563, and YnhG), defining their importance as novel T3SS effectors. We characterize the temporal intra- and extracellular production of the effectors and identify their interaction networks in host cells, representing inhibitory and stimulatory pathways mounted by invading bacterial pathogens. Author SummaryThe relationship between a host and pathogen is intricate, and regulation of the host immune response correlates with the progressive timing of infection and tailored responses to the pathogen. Relying on detection and quantification of protein-level changes using mass spectrometry-based proteomics, we explore the production of known and novel effectors by Salmonella during intracellular survival within macrophage. Our results portray a role for these effectors in bacterial virulence using an in vivo murine model of infection, and we define a dynamic network of interaction between the effectors and host proteins. These interactions reveal opportunity for drug design to disrupt modulation of the host by the invading bacterium as a new strategy for combatting infection. Our approach is dynamic and universal, with the power to alter therapeutic discovery against infectious diseases.

microbiology↗