High-resolution in situ transcriptomics of Pseudomonas aeruginosa unveils genotype independent patho-phenotypes in cystic fibrosis lungs

Nature Communications
Elio RossiHelle Krogh Johansen

Abstract

Life-long bacterial infections in cystic fibrosis (CF) airways constitute an excellent model both for persistent infections and for microbial adaptive evolution in complex dynamic environments. Using high-resolution transcriptomics applied on CF sputum, we profile transcriptional phenotypes of Pseudomonas aeruginosa populations in patho-physiological conditions. Here we show that the soft-core genome of genetically distinct populations, while maintaining transcriptional flexibility, shares a common expression program tied to the lungs environment. We identify genetically independent traits defining P. aeruginosa physiology in vivo, documenting the connection between several previously identified mutations in CF isolates and some of the convergent phenotypes known to develop in later stages of the infection. In addition, our data highlight to what extent this organism can exploit its extensive repertoire of physiological pathways to acclimate to a new niche and suggest how alternative nutrients produced in the lungs may be utilized in unexpected metabolic contexts.

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Citations

Oct 12, 2019·The European Respiratory Journal·Sarah G ChuIvan O Rosas
Jul 15, 2020·Annual Review of Microbiology·Sheyda AzimiStephen P Diggle
Jan 15, 2020·NPJ Biofilms and Microbiomes·Janne G ThömingSusanne Häussler
Feb 9, 2019·Nature Communications·Jennifer A BartellHelle Krogh Johansen
Sep 8, 2019·Drug Resistance Updates : Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy·João BotelhoLuísa Peixe
Jan 15, 2021·Microbiology and Molecular Biology Reviews : MMBR·Miguel A MatillaTino Krell
Feb 19, 2021·Nature Reviews. Genetics·Alexander J Westermann, Jörg Vogel
Jan 10, 2021·NPJ Biofilms and Microbiomes·Janne G ThömingSusanne Häussler
Jun 4, 2021·Nature Communications·Kemal AvicanMaria Fällman
May 8, 2019·Journal of Proteome Research·Xia WuJames E Bruce
Jan 16, 2022·The Journal of Immunology : Official Journal of the American Association of Immunologists·Zhichao FanKlaus Ley

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Methods Mentioned

BETA
genetic modifications
RNA-seq
PCA
with environmental
Assay
chips

Software Mentioned

GATK
Trimmomatic
count
R package DESeq2
Roary tool
NBClust
htseq
term
Picard
BWA aligner

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