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How long does it take to cue a Pseudomonas aeruginosa chronic infection phenotype in the lab? Insights from transcriptome analysis in a cystic fibrosis lung model

https://doi.org/10.1101/2022.06.30.498312

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Toward understanding the origin and evolution of cellular organisms

inferredcites →https://doi.org/10.1007/82_2011_199openalex-snapshot

Microevolution of Pseudomonas aeruginosa to a Chronic Pathogen of the Cystic Fibrosis Lung

inferredcites →https://doi.org/10.1016/j.bioflm.2020.100024openalex-snapshot

Building a better biofilm - Formation of in vivo-like biofilm structures by Pseudomonas aeruginosa in a porcine model of cystic fibrosis lung infection

inferredcites →https://doi.org/10.1016/j.ijantimicag.2009.12.011openalex-snapshot

Antibiotic resistance of bacterial biofilms

inferredcites →https://doi.org/10.1016/j.ijmm.2010.08.007openalex-snapshot

Anaerobic physiology of Pseudomonas aeruginosa in the cystic fibrosis lung

inferredcites →https://doi.org/10.1016/j.resmic.2010.01.003openalex-snapshot

Phenazines affect biofilm formation by Pseudomonas aeruginosa in similar ways at various scales

inferredcites →https://doi.org/10.1023/a:1020867221861openalex-snapshot

Human airway mucin glycosylation: A combinatory of carbohydrate determinants which vary in cystic fibrosis

inferredcites →https://doi.org/10.1038/s41396-021-01008-7openalex-snapshot

Phosphorus stress induces the synthesis of novel glycolipids in Pseudomonas aeruginosa that confer protection against a last-resort antibiotic

inferredcites →https://doi.org/10.1038/s41467-018-05944-5openalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41467-019-10201-4openalex-snapshot

The Pseudomonas aeruginosa lectin LecB binds to the exopolysaccharide Psl and stabilizes the biofilm matrix

inferredcites →https://doi.org/10.1038/s41579-020-00477-5openalex-snapshot

Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis

inferredcites →https://doi.org/10.1038/s41587-019-0201-4openalex-snapshot

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

inferredcites →https://doi.org/10.1038/s41598-019-42653-5openalex-snapshot

Connected partner-switches control the life style of Pseudomonas aeruginosa through RpoS regulation

inferredcites →https://doi.org/10.1073/pnas.0511100103openalex-snapshot

An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants

inferredcites →https://doi.org/10.1073/pnas.0602138103openalex-snapshot

Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients

inferredcites →https://doi.org/10.1073/pnas.1717525115openalex-snapshot

Pseudomonas aeruginosa transcriptome during human infection

inferredcites →https://doi.org/10.1074/jbc.m117.812842openalex-snapshot

PelA and PelB proteins form a modification and secretion complex essential for Pel polysaccharide-dependent biofilm formation in Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1089/omi.2011.0118openalex-snapshot

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

inferredcites →https://doi.org/10.1093/bioinformatics/bts611openalex-snapshot

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/glycob/cwi061openalex-snapshot

Altered O-glycosylation and sulfation of airway mucins associated with cystic fibrosis

inferredcites →https://doi.org/10.1093/jac/dkv152openalex-snapshot

Full characterization of the integrative and conjugative element carrying the metallo-β-lactamase bla SPM-1 and bicyclomycin bcr1 resistance genes found in the pandemic Pseudomonas aeruginosa clone SP/ST277 : Figure 1.

inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/gkaa970openalex-snapshot

KEGG: integrating viruses and cellular organisms

inferredcites →https://doi.org/10.1093/nar/gkv1227openalex-snapshot

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database

inferredcites →https://doi.org/10.1093/nar/gkz114openalex-snapshot

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

inferredcites →https://doi.org/10.1093/nar/gkz935openalex-snapshot

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

inferredcites →https://doi.org/10.1099/jmm.0.047167-0openalex-snapshot

Desulfurization of mucin by Pseudomonas aeruginosa: influence of sulfate in the lungs of cystic fibrosis patients

inferredcites →https://doi.org/10.1099/mgen.0.000681openalex-snapshot

Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection

inferredcites →https://doi.org/10.1099/mic.0.000352openalex-snapshot

An ex vivo lung model to study bronchioles infected with Pseudomonas aeruginosa biofilms

inferredcites →https://doi.org/10.1111/j.1365-2958.2006.05306.xopenalex-snapshot

The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1111/j.1365-2958.2007.05772.xopenalex-snapshot

Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration

inferredcites →https://doi.org/10.1111/j.1462-2920.2006.001001.xopenalex-snapshot

The galactophilic lectin, LecA, contributes to biofilm development in Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1128/aac.00904-15openalex-snapshot

Pseudomonas aeruginosa High-Level Resistance to Polymyxins and Other Antimicrobial Peptides Requires cprA , a Gene That Is Disrupted in the PAO1 Strain

inferredcites →https://doi.org/10.1128/aem.01789-21openalex-snapshot

Transcriptome Analysis of Pseudomonas aeruginosa Biofilm Infection in an Ex Vivo Pig Model of the Cystic Fibrosis Lung

inferredcites →https://doi.org/10.1128/jb.00754-18openalex-snapshot

Proteomic Analysis of the Pseudomonas aeruginosa Iron Starvation Response Reveals PrrF Small Regulatory RNA-Dependent Iron Regulation of Twitching Motility, Amino Acid Metabolism, and Zinc Homeostasis Proteins

inferredcites →https://doi.org/10.1128/jb.00889-07openalex-snapshot

Transcriptomic Analysis of the Sulfate Starvation Response of Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1128/jb.01138-07openalex-snapshot

Nutritional Cues Control Pseudomonas aeruginosa Multicellular Behavior in Cystic Fibrosis Sputum

inferredcites →https://doi.org/10.1128/jb.144.1.159-163.1980openalex-snapshot

Regulation of enzyme synthesis in the arginine deiminase pathway of Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1128/jb.186.14.4596-4604.2004openalex-snapshot

Long-Term Anaerobic Survival of the Opportunistic Pathogen Pseudomonas aeruginosa via Pyruvate Fermentation

inferredcites →https://doi.org/10.1128/jb.187.3.1074-1090.2005openalex-snapshot

Sulfur and Nitrogen Limitation inEscherichia coliK-12: Specific Homeostatic Responses

inferredcites →https://doi.org/10.1128/jb.188.2.659-668.2006openalex-snapshot

Anaerobic Survival of Pseudomonas aeruginosa by Pyruvate Fermentation Requires an Usp-Type Stress Protein

inferredcites →https://doi.org/10.1128/mbio.00767-15openalex-snapshot

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation

inferredcites →https://doi.org/10.1136/thx.2009.114512openalex-snapshot

Polymorphonuclear leucocytes consume oxygen in sputum from chronic Pseudomonas aeruginosa pneumonia in cystic fibrosis

inferredcites →https://doi.org/10.1172/jci114171openalex-snapshot

Increased sulfation of glycoconjugates by cultured nasal epithelial cells from patients with cystic fibrosis.

inferredcites →https://doi.org/10.1172/jci200213870openalex-snapshot

Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients

inferredcites →https://doi.org/10.1186/gb-2005-6-5-r47openalex-snapshot

The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1371/journal.pone.0083124openalex-snapshot

Loss of Social Behaviours in Populations of Pseudomonas aeruginosa Infecting Lungs of Patients with Cystic Fibrosis

inferredcites →https://doi.org/10.1371/journal.pone.0147811openalex-snapshot

RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium

inferredcites →https://doi.org/10.1371/journal.ppat.1001264openalex-snapshot

The Pel Polysaccharide Can Serve a Structural and Protective Role in the Biofilm Matrix of Pseudomonas aeruginosa

inferredcites →https://doi.org/10.1371/journal.ppat.1005258openalex-snapshot

Cystic Fibrosis Lung Infections: Polymicrobial, Complex, and Hard to Treat

inferredcites →https://doi.org/10.32614/cran.package.venndiagramopenalex-snapshot

VennDiagram: Generate High-Resolution Venn and Euler Plots

inferredcites →https://doi.org/10.3389/fcimb.2018.00252openalex-snapshot

Differential Regulation of the Phenazine Biosynthetic Operons by Quorum Sensing in Pseudomonas aeruginosa PAO1-N

inferredcites →https://doi.org/10.3791/62187openalex-snapshot

Antibiotic Efficacy Testing in an Ex vivo Model of Pseudomonas aeruginosa and Staphylococcus aureus Biofilms in the Cystic Fibrosis Lung

inferredcites →https://doi.org/10.5799/jmid.434595openalex-snapshot

Transcriptional expression of PmrB and arnA within polymyxin-resistant nosocomial isolates of Pseudomonas aeruginosa from India

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