Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system

Klein, J. A.; Predeus, A. V.; Greissl, A.; Clark-Herrera, M.; Cruz, E.; Cundiff, J. A.; Haeberle, A. L.; Howell, M.; Lele, A.; Robinson, D. J.; Westerman, T. L.; Wrande, M.; Wright, S. J.; Green, N. M.; Vallance, B. A.; McClelland, M.; Mejia, A.; Goodman, A. G.; Elfenbein, J. R.; Knodler, L. A.

doi:10.1101/2024.06.07.595826

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bioRxiv · 10.1101/2024.06.07.595826

Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system

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Abstract

Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens-host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1b is widespread in Providencia spp. and encoded on the chromosome. T3SS1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS1a or T3SS1b was seen in the calf infection model. However, T3SS1b was required for the rapid killing of Drosophila melanogaster. We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.

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Klein, J. A., Predeus, A. V., Greissl, A., Clark-Herrera, M., Cruz, E., Cundiff, J. A., Haeberle, A. L., Howell, M., Lele, A., Robinson, D. J., Westerman, T. L., Wrande, M., Wright, S. J., Green, N. M., Vallance, B. A., McClelland, M., Mejia, A., Goodman, A. G., Elfenbein, J. R., Knodler, L. A.. 2024-06-07. Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system. https://doi.org/10.1101/2024.06.07.595826

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