Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection

Manuscript Description

In this study, we aim to identify genes associated with infection in patients colonized by Klebsiella. Surprisingly, we identified several novel genes associated with infection, in lieu of canonical virulence factors or a conserved antimicrobial resistance cassette, such as what may be observed during an outbreak. One potential explanation for this finding is that patients in this study were colonized by diverse Klebsiella, rather than a conserved population of genetically similar Klebsiella. Our hope is that this study lays the groundwork for the development of molecular diagnostics to identify patients at risk for infection prior to infection occurring. An accompanying blogpost can be found here: https://microbiologycommunity.nature.com/posts/the-whole-nine-yards-an-integrated-approach-to-understanding-klebsiella-infection.

Link

https://www.nature.com/articles/s41467-022-31990-1

Abstract

Members of the Klebsiella pneumoniae species complex frequently colonize the gut and colonization is associated with subsequent infection. To identify genes associated with progression from colonization to infection, we undertook a case-control comparative genomics study. Concordant cases (N = 85), where colonizing and invasive isolates were identical strain types, were matched to asymptomatically colonizing controls (N = 160). Thirty-seven genes are associated with infection, 27 of which remain significant following adjustment for patient variables and bacterial phylogeny. Infection-associated genes are not previously characterized virulence factors, but instead a diverse group of stress resistance, regulatory and antibiotic resistance genes, despite careful adjustment for antibiotic exposure. Many genes are plasmid borne, and for some, the relationship with infection is mediated by gut dominance. Five genes were validated in a geographically-independent cohort of colonized patients. This study identifies several genes reproducibly associated with progression to infection in patients colonized by diverse Klebsiella.

Citation

Vornhagen, J., Roberts, E.K., Unverdorben, L. et al. Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection. Nat Commun 13, 4459 (2022). https://doi.org/10.1038/s41467-022-31990-1