Publications

Integrating genomic and Tn-Seq data to identify common in vivo fitness mechanisms across multiple bacterial species

Fouts DE, Clarke TH, Severin GB, Brown AN, Ottosen EN, Holmes CL, Moricz BS, Mason S, Sinha R, Anderson MT, DiRita V, Bachman MA, Mobley HLT

PMID: 40981419

Abstract

Sepsis, a life-threatening organ dysfunction, is due to an unregulated immune response to infection. Bacteremia is a leading cause of sepsis, and members of the Enterobacterales cause nearly half of bacteremia cases annually. Although previous Tn-Seq studies identified novel bacteremia-fitness genes, evidence for common pathways across species is lacking. To identify common fitness pathways in five bacteremia-causing Enterobacterales species, we utilized our pan-genome pipeline to integrate Tn-Seq fitness data with multiple available functional data types. Core genes from species pan-genomes were used to construct a multi-species core pan-genome, producing 2,850 core gene clusters found in four of five species. Integration of Tn-Seq fitness data identified 373 protein clusters conserved in all five species and a fitness gene in at least one of them. A scoring rubric was applied to these clusters, which incorporated Tn-Seq fitness defects, operon localization, and antibiotic susceptibility data, which reduced the number of bacteremia-fitness genes and identified seven common fitness mechanisms. Independent mutational validation of one prioritized fitness gene, showed reduced fitness across all species tested and increased susceptibility to β-lactams that was restored following complementation . By integrating known operon structures and antibiotic susceptibility with Tn-Seq fitness data, common genes within the core pan-genome emerged and revealed mechanisms essential for survival in the mammalian bloodstream. Our prediction and validation of as a common bacteremia fitness factor supports the utility of this bioinformatic approach. This study represents a major step forward in prioritizing novel targets for therapy against sepsis infections.