Comparative Genomics of Clinical Isolates of Pseudomonas fluorescens, Including the Discovery of a Novel Disease-Associated Subclade.

Taxonomically, there are over 52 Pseudomonas species that group within the Pseudomonas fluorescens species-complex. Prior to beginning this project, we identified that the lung microbiome of COPD patients contained abundant levels of P. fluorescens. This finding was highly unexpected; P. fluorescens colonization was not previously reported in chronic respiratory disease and there was no taxonomic information on clinical P. fluorescens strains. This raised the question of whether there were differences between P. fluorescens strains isolated from clinical vs. environmental sources. To begin to address this question, I sequenced a collection of Pseudomonas spp. isolates from individuals with chronic lung disease, including 22 clinical P. fluorescens strains. Twelve grouped within previously defined subclades (I - III) of the P. fluorescens species-complex, however, 10 strains were distinct and clustered as a unique fourth subclade. I performed additional comparative genomic analyses on all four subclades and identified genomic attributes that were associated with growth in humans. Subclade III clinical isolates were almost indistinguishable from environmental isolates except that clinical isolates contained additional homologues of genes involved in metal toxicity resistance. In sharp contrast, subclade IV strains displayed marked reductions in genome size, gene diversity and GC content, as well as containing all genetic elements for a type III secretion system that was extremely similar to that found in P. aeruginosa. Furthermore, our subclade IV strains, collected from geographic locations across the U.S., had high levels of shared nucleotide identity and a small accessory genome, suggesting that they may have evolved from living in multi-trophic environments to a life in a much narrower niche, perhaps human airways. We also identified that some colonies of inbred mice contained indigenous P. fluorescens in their lung microbiome and chronic inflammation was associated with an outgrowth of P. fluorescens. Expanding my analysis to human respiratory disease, P. fluorescens was found to increase in lung samples from diseased but not healthy subjects. Altogether, these studies reveal that P. fluorescens is an under-appreciated colonizer of humans, particularly in the context of pulmonary inflammation, and lay the groundwork for future studies delineating the contribution and molecular mechanisms of this host-microbe interaction.PHDMicrobiology and ImmunologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/116756/1/britstar_2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/116756/2/britstar_3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/116756/3/britstar_1.pd