Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum

Significance The opportunistic pathogen Pseudomonas aeruginosa thrives in cystic fibrosis (CF) lung sputum. Here, we define the essential genome of two P. aeruginosa strains in laboratory media and in CF sputum. We also use genomic methods to profile P. aeruginosa genetic requirements for fitness in both natural and synthetic CF sputum. Finally, we show that the essential genomes of different strains of P. aeruginosa are distinct, suggesting that the architecture of genetic networks is a primary determinant of a gene’s role in fitness. This has implications for the development of strain-independent therapeutics and underscores the importance of functional studies in pathogenic strains of interest. Defining the essential genome of bacterial pathogens is central to developing an understanding of the biological processes controlling disease. This has proven elusive for Pseudomonas aeruginosa during chronic infection of the cystic fibrosis (CF) lung. In this paper, using a Monte Carlo simulation-based method to analyze high-throughput transposon sequencing data, we establish the P. aeruginosa essential genome with statistical precision in laboratory media and CF sputum. Reconstruction of the global requirements for growth in CF sputum compared with defined growth conditions shows that the latter requires several cofactors including biotin, riboflavin, and pantothenate. Comparison of P. aeruginosa strains PAO1 and PA14 demonstrates that essential genes are primarily restricted to the core genome; however, some orthologous genes in these strains exhibit differential essentiality. These results indicate that genes with similar molecular functions may have distinct genetic roles in different P. aeruginosa strains during growth in CF sputum. We also show that growth in a defined growth medium developed to mimic CF sputum yielded virtually identical fitness requirements to CF sputum, providing support for this medium as a relevant in vitro model for CF microbiology studies.

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