Combining Quantitative Genetic Footprinting and Trait Enrichment Analysis to Identify Fitness Determinants of a Bacterial Pathogen

• DOI: 10.1371/journal.pgen.1003716
• Publication Date: 2013-08-22T21:06:37Z
• Authors: Travis J. Wiles; J. Paul Norton; Colin W. Russell; Brian K. Dalley; Kael F. Fischer; Matthew A. Mulvey
• Keywords: Footprinting; Trait; Quantitative Genetics; Microbial genetics; Human evolutionary genetics

Strains of Extraintestinal Pathogenic Escherichia coli (ExPEC) exhibit an array virulence strategies and are a major cause urinary tract infections, sepsis meningitis. Efforts to understand ExPEC pathogenesis challenged by the high degree genetic phenotypic variation that exists among isolates. Determining which traits widespread strain-specific will greatly benefit design more effective therapies. Towards this goal, we utilized quantitative footprinting technique known as transposon insertion sequencing (Tn-seq) in conjunction with comparative pathogenomics functionally dissect repertoire reference isolate. Using Tn-seq high-throughput zebrafish infection models, tracked changes abundance variants within saturated mutant libraries following selection distinct host niches. Nine hundred seventy bacterial genes (18% genome) were found promote pathogen fitness either niche-dependent or independent manner. To identify highest therapeutic diagnostic potential, novel Trait Enrichment Analysis (TEA) algorithm was developed ascertain phylogenetic distribution candidate genes. TEA revealed significant portion 970 identified have homologues often contained genomes other pathogens, which, suggested first axiom molecular Koch's postulates, is considered be key feature true determinants. Three these Tn-seq-derived pathogen-associated genes—a transcriptional repressor, putative metalloendopeptidase toxin hypothetical DNA binding protein—were deleted shown independently affect mouse models infection. Together, approaches observations reported herein provide resource for future pathogenomics-based research highlight diversity factors required single isolate survive varying environments.