Type IV pili is a critical virulence factor in clinical isolates of Paenibacillus thiaminolyticus

Hehnly, C.; Shi, A.; Ssentongo, P.; Zhang, L.; Isaacs, A.; Morton, S. U.; Streck, N.; Erdmann-Gilmore, P.; Tolstoy, I.; Townsend, R. R.; Limbrick, D. D.; Paulson, J. N.; Ericson, J. E.; Galperin, M. Y.; Schiff, S. J.; Broach, J. R.

doi:10.1101/2022.01.24.477451

bioRxiv · 10.1101/2022.01.24.477451

Type IV pili is a critical virulence factor in clinical isolates of Paenibacillus thiaminolyticus

Hehnly, C.·Shi, A.·Ssentongo, P.·Zhang, L.·Isaacs, A.·Morton, S. U.·Streck, N.·Erdmann-Gilmore, P.·Tolstoy, I.·Townsend, R. R.·Limbrick, D. D.·Paulson, J. N.·Ericson, J. E.·Galperin, M. Y.·Schiff, S. J.·Broach, J. R.

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Abstract

Hydrocephalus, the leading indication for childhood neurosurgery worldwide, is particularly prevalent in low-and-middle-income countries (LMICs). Hydrocephalus preceded by an infection, or postinfectious hydrocephalus (PIH), accounts for up to 60% of hydrocephalus in LMICs. Since many children with hydrocephalus suffer poor long-term outcomes despite surgical intervention, prevention of hydrocephalus remains paramount. Our previous studies implicated a novel bacterial pathogen, Paenibacillus thiaminolyticus, as a contributor to PIH in Uganda. Here we report the isolation of three P. thiaminolyticus strains, Mbale, Mbale2, and Mbale3, from patients with PIH and the demonstration that the three clinical isolates exhibit virulence in mice while P. thiaminolyticus type strain, B-4156, does not. We constructed complete genome assemblies of the clinical isolates as well as the reference strain and performed comparative genomics and proteomics analyses to identify potential virulence factors. One candidate virulence factor is a cluster of genes carried on a mobile genetic element that encodes a type IV pilus and is present in all three PIH patient strains but absent in the type strain. Proteomic and transcriptomic data confirmed the expression of this cluster of genes in the Mbale strain, while CRISPR-mediated deletion of the gene cluster substantially reduced the virulence of this strain. Our comparative proteogenomic analysis also identified various antibiotic resistance loci in the virulent strains. These results provide insight into the mechanism of virulence of Paenibacillus thiaminolyticus and suggest avenues for the diagnosis and treatment of this novel bacterial pathogen. Author SummaryPostinfectious hydrocephalus (PIH), a devastating sequela of neonatal infection, is associated with increased childhood mortality and morbidity. Paenibacillus thiaminolyticus was recently identified as the dominant organism highly associated with PIH in an African cohort. Our whole-genome sequencing, RNA sequencing and proteomics of three clinical isolates and a type strain in combination with CRISPR editing has revealed the type IV pili (T4P), encoded in a mobile genetic element, as a critical virulence factor for P. thiaminolyticus infection. Given the widespread presence of T4P in pathogens, the presence of T4P operon could serve as an important diagnostic and therapeutic target in P. thiaminolyticus and related bacteria.

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Hehnly, C., Shi, A., Ssentongo, P., Zhang, L., Isaacs, A., Morton, S. U., Streck, N., Erdmann-Gilmore, P., Tolstoy, I., Townsend, R. R., Limbrick, D. D., Paulson, J. N., Ericson, J. E., Galperin, M. Y., Schiff, S. J., Broach, J. R.. 2022-01-24. Type IV pili is a critical virulence factor in clinical isolates of Paenibacillus thiaminolyticus. https://doi.org/10.1101/2022.01.24.477451

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