Agaisse, H. F. | Search bioRxiv

bioRxiv2026

Shigella flexneri undergoes niche-specific adaptation during infection

Shigella flexneri is a leading cause of diarrheal disease worldwide, yet bacterial factors required within distinct host niches remain poorly understood. Here, we used genome-wide transposon sequencing in an infant rabbit model of shigellosis to identify genes promoting bacterial fitness in vivo. The screen identified virulence factors on the large virulence plasmid and novel chromosomal fitness factors. Characterization of zitB, encoding a cation diffusion facilitator family Zn transporter, revealed a niche-specific fitness contribution. The {Delta}zitB mutant showed no growth defect in vitro in rich media or in vivo during the early infection phase (8 hpi) in epithelial cells. However, bacterial burden was reduced during the late infection phase (24 hpi) in vivo, when bacteria interact with immune cells, in both competitive and mono-infection assays. Reduced bacterial burden was associated with increased MARCO-specific macrophages, suggesting impaired colonization and killing by the {Delta}zitB mutant. Consistently, {Delta}zitB fitness was impaired in THP-1-derived macrophages. Metal chelation increased bacterial burden, indicating a role for macrophage-mediated metal toxicity. The {Delta}zitB mutant also showed increased sensitivity to zinc and copper. Finally, macrophage depletion in vivo restored bacterial burden to wild-type levels. Together, these findings identify ZitB as a niche-specific bacterial factor promoting S. flexneri fitness during macrophage-associated metal stress.

microbiology↗

bioRxiv2026

Sequential invasion of epithelial and immune cells in Shigellosis

Shigella flexneri, the agent of shigellosis, invades the colonic mucosa, which leads to mucosal erosion, blood and immune cell infiltration, culminating in the hallmark of the disease, bloody diarrhea. Here, we conducted a microscopy-based analysis of time-resolved infection experiments in the infant rabbit model of shigellosis. We observed two stages of infection in the colonic tissue. During the early stage of infection, bacteria invaded and spread in epithelial cells, which correlated with mucosal erosion and blood infiltration. During the late stage of infection, the bacteria transitioned from their primary niche, the epithelial compartment, to their secondary niche, the lamina propria. Transcriptomic analysis of the late stage of infection assigned identities to various epithelial, immune, and stromal cells. The vast majority of the bacteria were associated with neutrophils or macrophages during the late stage of infection. We provide a discussion of how this model compares and contrasts with previous models of shigellosis.

microbiology↗

bioRxiv2024

Host PIK3C3 promotes Shigella flexneri spread from cell to cell through vacuole formation

Shigella flexneri is a human intracellular pathogen responsible for bacillary dysentery (bloody diarrhea). S. flexneri invades colonic epithelial cells and spreads from cell to cell, leading to massive epithelial cell fenestration, a critical determinant of pathogenesis. Cell- to-cell spread relies on actin-based motility, which leads to formation of membrane protrusions, as bacteria project into adjacent cells. Membrane protrusions resolve into intermediate structures termed vacuole-like protrusions (VLPs), which remain attached to the primary infected cell by a membranous tether. The resolution of the membranous tether leads to formation of double-membrane vacuoles (DMVs), from which S. flexneri escapes to gain access to the cytosol of adjacent cells. Here, we identify the class III PI3K family member PIK3C3 as a critical determinant of S. flexneri cell-to-cell spread. Inhibition of PIK3C3 decreased the size of infection foci formed by S. flexneri in HT-29 cells. Tracking experiments using live-fluorescence confocal microscopy showed that PIK3C3 is required for efficient resolution of VLPs into DMVs. PIK3C3-dependent accumulation of PtdIns(3)P at the VLP membrane in adjacent cells correlated with the transient recruitment of the membrane scission machinery component Dynamin 2 at the neck of VLPs at the time of DMV formation. By contrast, Listeria monocytogenes did not form VLPs and protrusions resolved directly into DMVs. However, PIK3C3 was also required for L. monocytogenes dissemination, but at the stage of vacuole escape. Finally, we showed that PIK3C3 inhibition decreased S. flexneri dissemination in the infant rabbit model of shigellosis. We propose a model of Shigella dissemination in which vacuole formation relies on the PIK3C3-dependent accumulation of PtdIns(3)P at the VLP stage of cell-to-cell spread, thereby supporting the resolution of VLPs into DMVs through recruitment of the membrane scission machinery component, DNM2. Author summaryShigella flexneri is an intracellular pathogen causing bacillary dysentery, a disease responsible for more than 200,000 deaths each year in the world. With the lack of efficient vaccines and the dramatic increase in multi-drug-resistant clinical isolates, it is critical to better understand Shigella pathogenesis to suggest new therapeutic treatments. Previous studies demonstrated that invasion of epithelial cells in the human colon and subsequent spread from cell to cell are critical determinants of pathogenesis. Cell-to-cell spread relies on manipulation of the host cell actin cytoskeleton supporting bacterial movement in the cytosol of infected cells. At cell-cell contacts, bacteria project into adjacent cells through formation of membrane protrusions that resolve into vacuoles from which the bacteria escape to gain access to the cytosol of adjacent cells. Here, we show that the host cell kinase PIK3C3 is critical for efficient cell-to-cell spread through resolution of protrusions into vacuoles. Our work suggests that inhibitors of PIK3C3 may represent novel avenues of therapeutic intervention in shigellosis.

microbiology↗