scholarly journals The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates

Cells ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 1129 ◽  
Author(s):  
Jelena Erdmann ◽  
Janne G. Thöming ◽  
Sarah Pohl ◽  
Andreas Pich ◽  
Christof Lenz ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Species ◽  
Protein Profile ◽  
Opportunistic Pathogen ◽  
Growth Conditions ◽  
Protein Quantification ◽  
Clinical Isolates ◽  
Biofilm Growth ◽  
Regulatory Pathways ◽  
Data Independent Acquisition

Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.

scholarly journals Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Janne G. Thöming ◽  
Jürgen Tomasch ◽  
Matthias Preusse ◽  
Michal Koska ◽  
Nora Grahl ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Parallel Evolution ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
Transcriptional Responses ◽  
Regulatory Pathways ◽  
Extracellular Matrix Components ◽  
The Individual ◽  
Biofilm Development ◽  
General Response

AbstractStudying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.

scholarly journals Acquisition of multidrug resistance transposon Tn6061 and IS6100-mediated large chromosomal inversions in Pseudomonas aeruginosa clinical isolates

Microbiology ◽  
2010 ◽  
Vol 156 (5) ◽  
pp. 1448-1458 ◽  
Author(s):  
Sébastien Coyne ◽  
Patrice Courvalin ◽  
Marc Galimand
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistance ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
Chromosomal Inversions ◽  
Gene Acquisition ◽  
Drug Classes ◽  
Horizontal Acquisition

Pseudomonas aeruginosa is a major human opportunistic pathogen, especially for patients in intensive care units or with cystic fibrosis. Multidrug resistance is a common feature of this species. In a previous study we detected the ant(4′)-IIb gene in six multiresistant clinical isolates of P. aeruginosa, and determination of the environment of the gene led to characterization of Tn6061. This 26 586 bp element, a member of the Tn3 family of transposons, carried 10 genes conferring resistance to six drug classes. The ant(4′)-IIb sequence was flanked by directly repeated copies of ISCR6 in all but one of the strains studied, consistent with ISCR6-mediated gene acquisition. Tn6061 was chromosomally located in six strains and plasmid-borne in the remaining isolate, suggesting horizontal acquisition. Duplication-insertion of IS6100, that ended Tn6061, was responsible for large chromosomal inversions. Acquisition of Tn6061 and chromosomal inversions are further examples of intricate mechanisms that contribute to the genome plasticity of P. aeruginosa.

scholarly journals Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments

2020 ◽  
Vol 19 (6) ◽  
pp. 944-959 ◽  
Author(s):  
Tsung-Heng Tsai ◽  
Meena Choi ◽  
Balazs Banfai ◽  
Yansheng Liu ◽  
Brendan X. MacLean ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Profile ◽  
Protein Quantification ◽  
Selected Reaction Monitoring ◽  
Estimation Accuracy ◽  
Spectral Features ◽  
Data Set ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Manual Curation

In bottom-up mass spectrometry-based proteomics, relative protein quantification is often achieved with data-dependent acquisition (DDA), data-independent acquisition (DIA), or selected reaction monitoring (SRM). These workflows quantify proteins by summarizing the abundances of all the spectral features of the protein (e.g. precursor ions, transitions or fragments) in a single value per protein per run. When abundances of some features are inconsistent with the overall protein profile (for technological reasons such as interferences, or for biological reasons such as post-translational modifications), the protein-level summaries and the downstream conclusions are undermined. We propose a statistical approach that automatically detects spectral features with such inconsistent patterns. The detected features can be separately investigated, and if necessary, removed from the data set. We evaluated the proposed approach on a series of benchmark-controlled mixtures and biological investigations with DDA, DIA and SRM data acquisitions. The results demonstrated that it could facilitate and complement manual curation of the data. Moreover, it can improve the estimation accuracy, sensitivity and specificity of detecting differentially abundant proteins, and reproducibility of conclusions across different data processing tools. The approach is implemented as an option in the open-source R-based software MSstats.

scholarly journals Spatiotemporal Distribution of Pseudomonas aeruginosa Alkyl Quinolones under Metabolic and Competitive Stress

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Tianyuan Cao ◽  
Jonathan V. Sweedler ◽  
Paul W. Bohn ◽  
Joshua D. Shrout
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Species ◽  
Metabolic Stress ◽  
Opportunistic Pathogen ◽  
Cell Interaction ◽  
Chemical Imaging ◽  
Carbon Limitation ◽  
Bacterial Strains ◽  
Content Type ◽  
High Level

ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen important to diseases such as cystic fibrosis. P. aeruginosa has multiple quorum-sensing (QS) systems, one of which utilizes the signaling molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal [PQS]). Here, we use hyperspectral Raman imaging to elucidate the spatiotemporal PQS distributions that determine how P. aeruginosa regulates surface colonization and its response to both metabolic stress and competition from other bacterial strains. These chemical imaging experiments illustrate the strong link between environmental challenges, such as metabolic stress caused by nutritional limitations or the presence of another bacterial species, and PQS signaling. Metabolic stress elicits a complex response in which limited nutrients induce the bacteria to produce PQS earlier, but the bacteria may also pause PQS production entirely if the nutrient concentration is too low. Separately, coculturing P. aeruginosa in the proximity of another bacterial species, or its culture supernatant, results in earlier production of PQS. However, these differences in PQS appearance are not observed for all alkyl quinolones (AQs) measured; the spatiotemporal response of 2-heptyl-4-hydroxyquinoline N-oxide (HQNO) is highly uniform for most conditions. These insights on the spatiotemporal distributions of quinolones provide additional perspective on the behavior of P. aeruginosa in response to different environmental cues. IMPORTANCE Alkyl quinolones (AQs), including Pseudomonas quinolone signal (PQS), made by the opportunistic pathogen Pseudomonas aeruginosa have been associated with both population density and stress. The regulation of AQ production is known to be complex, and the stimuli that modulate AQ responses are not fully clear. Here, we have used hyperspectral Raman chemical imaging to examine the temporal and spatial profiles of AQs exhibited by P. aeruginosa under several potentially stressful conditions. We found that metabolic stress, effected by carbon limitation, or competition stress, effected by proximity to other species, resulted in accelerated PQS production. This competition effect did not require cell-to-cell interaction, as evidenced by the fact that the addition of supernatants from either Escherichia coli or Staphylococcus aureus led to early appearance of PQS. Lastly, the fact that these modulations were observed for PQS but not for all AQs suggests a high level of complexity in AQ regulation that remains to be discerned.

scholarly journals An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jeanyoung Jo ◽  
Krista L Cortez ◽  
William Cole Cornell ◽  
Alexa Price-Whelan ◽  
Lars EP Dietrich
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Cytochrome C ◽  
Opportunistic Pathogen ◽  
Bacterial Pathogenesis ◽  
Cytochrome Oxidase Subunit ◽  
Biofilm Growth ◽  
Unique Role ◽  
High Affinity ◽  
Biofilm Model ◽  
Biofilm Development

Hypoxia is a common challenge faced by bacteria during associations with hosts due in part to the formation of densely packed communities (biofilms). cbb3-type cytochrome c oxidases, which catalyze the terminal step in respiration and have a high affinity for oxygen, have been linked to bacterial pathogenesis. The pseudomonads are unusual in that they often contain multiple full and partial (i.e. ‘orphan’) operons for cbb3-type oxidases and oxidase subunits. Here, we describe a unique role for the orphan catalytic subunit CcoN4 in colony biofilm development and respiration in the opportunistic pathogen Pseudomonas aeruginosa PA14. We also show that CcoN4 contributes to the reduction of phenazines, antibiotics that support redox balancing for cells in biofilms, and to virulence in a Caenorhabditis elegans model of infection. These results highlight the relevance of the colony biofilm model to pathogenicity and underscore the potential of cbb3-type oxidases as therapeutic targets.

scholarly journals Heterogeneity in surface sensing produces a division of labor in Pseudomonas aeruginosa populations

2019 ◽  
Author(s):  
Catherine R. Armbruster ◽  
Calvin K. Lee ◽  
Jessica Parker-Gilham ◽  
Jaime de Anda ◽  
Aiguo Xia ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Division Of Labor ◽  
Bacterial Species ◽  
Biofilm Growth ◽  
Surface Attachment ◽  
Sensing Systems ◽  
Current Thinking ◽  
Surface Exploration ◽  
Surface Sensing ◽  
Second Messenger Signaling

AbstractThe second messenger signaling molecule cyclic diguanylate monophosphate (c-di-GMP) drives the transition from planktonic to biofilm growth in many bacterial species. Pseudomonas aeruginosa has two surface sensing systems that produce c-di-GMP in response to surface adherence. The current thinking in the field is that once cells attach to a surface, they uniformly respond with elevated c-di-GMP. Here, we describe how the Wsp system generates heterogeneity in surface sensing, resulting in two physiologically distinct subpopulations of cells. One subpopulation has elevated c-di-GMP and produces biofilm matrix, serving as the founders of initial microcolonies. The other subpopulation has low c-di-GMP and engages in surface motility, allowing for exploration of the surface. We also show that this heterogeneity strongly correlates to surface behavior for descendent cells. Together, our results suggest that after surface attachment, P. aeruginosa engages in a division of labor that persists across generations, accelerating early biofilm formation and surface exploration.

scholarly journals Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates

2021 ◽  
Author(s):  
Sakthivel Ambreetha ◽  
Ponnusammy Marimuthu ◽  
Kalai Mathee ◽  
Dananjeyan Balachandar
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
Clinical Strains ◽  
Hospital Acquired Infections ◽  
Metabolic Traits ◽  
Potential Source ◽  
Salad Vegetables ◽  
Hospital Acquired ◽  
Indole 3 Acetic Acid

Pseudomonas aeruginosa, a leading opportunistic pathogen causing hospital-acquired infections is predominantly present in agricultural settings. There are minimal attempts to examine the molecular and functional attributes shared by agricultural and clinical strains of P. aeruginosa. This study aims to investigate the presence of P. aeruginosa in edible vegetable plants (including salad vegetables) and analyze the evolutionary and metabolic relatedness of the agricultural and clinical strains. Eighteen rhizospheric and endophytic P. aeruginosa strains were isolated from cucumber, tomato, eggplant, and chili directly from the farms. The identity of these strains was confirmed using biochemical, and molecular markers and their genetic and metabolic traits were compared with clinical isolates. DNA fingerprinting analyses and 16S rDNA-based phylogenetic tree revealed that the plant- and human-associated strains are evolutionarily related. Both agricultural and clinical isolates possessed plant-beneficial properties, including mineral solubilization (phosphorous, potassium, and zinc), ammonification, and the ability to release extracellular siderophore and indole-3 acetic acid. These findings suggest that rhizospheric and endophytic P. aeruginosa strains are genetically and functionally analogous to the clinical isolates. This study highlights the edible plants as a potential source for human and animal transmission of P. aeruginosa.

scholarly journals Poly (acetyl arginyl) glucosamine attenuates Pseudomonas aeruginosa in a rat lung infection model

2021 ◽  
Author(s):  
Bryan Garcia ◽  
Melissa S. McDaniel ◽  
Allister J. Loughran ◽  
J. Dixon Johns ◽  
Vidya Narayanaswamy ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Respiratory Infections ◽  
Bacterial Species ◽  
Membrane Integrity ◽  
Opportunistic Pathogen ◽  
Infection Model ◽  
Total Biomass ◽  
Chronic Infections

Pseudomonas aeruginosa is a common opportunistic pathogen that can cause chronic infections in multiple disease states, including respiratory infections in patients with cystic fibrosis (CF) and non-CF bronchiectasis. Like many opportunists, P. aeruginosa forms multicellular biofilm communities that are widely thought to be an important determinant of bacterial persistence and resistance to antimicrobials and host immune effectors during chronic/recurrent infections. Poly (acetyl, arginyl) glucosamine (PAAG) is a glycopolymer which has antimicrobial activity against a broad range of bacterial species, and also has mucolytic activity which can normalize rheologic properties of cystic fibrosis mucus. In this study, we sought to evaluate the effect of PAAG on P. aeruginosa bacteria within biofilms in vitro, and in the context of experimental pulmonary infection in a rodent infection model. PAAG treatment caused significant bactericidal activity against P. aeruginosa biofilms, and a reduction in the total biomass of preformed P. aeruginosa biofilms on abiotic surfaces, as well as on the surface of immortalized cystic fibrosis human bronchial epithelial cells. Studies of membrane integrity indicated that PAAG causes changes to P. aeruginosa cell morphology and dysregulates membrane polarity. PAAG treatment reduced infection and consequent tissue inflammation in experimental P. aeruginosa rat infections. Based on these findings we conclude that PAAG represents a novel means to combat P. aeruginosa infection, which may warrant further evaluation as a therapeutic.

scholarly journals Heterogeneity in surface sensing suggests a division of labor in Pseudomonas aeruginosa populations

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Catherine R Armbruster ◽  
Calvin K Lee ◽  
Jessica Parker-Gilham ◽  
Jaime de Anda ◽  
Aiguo Xia ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Division Of Labor ◽  
Bacterial Species ◽  
Biofilm Growth ◽  
Surface Attachment ◽  
Sensing Systems ◽  
Current Thinking ◽  
Surface Exploration ◽  
Surface Sensing ◽  
Second Messenger Signaling

The second messenger signaling molecule cyclic diguanylate monophosphate (c-di-GMP) drives the transition between planktonic and biofilm growth in many bacterial species. Pseudomonas aeruginosa has two surface sensing systems that produce c-di-GMP in response to surface adherence. Current thinking in the field is that once cells attach to a surface, they uniformly respond by producing c-di-GMP. Here, we describe how the Wsp system generates heterogeneity in surface sensing, resulting in two physiologically distinct subpopulations of cells. One subpopulation has elevated c-di-GMP and produces biofilm matrix, serving as the founders of initial microcolonies. The other subpopulation has low c-di-GMP and engages in surface motility, allowing for exploration of the surface. We also show that this heterogeneity strongly correlates to surface behavior for descendent cells. Together, our results suggest that after surface attachment, P. aeruginosa engages in a division of labor that persists across generations, accelerating early biofilm formation and surface exploration.

RpoS Mutation Leads to Prolonged Biofilm Mode of Growth and a Higher Fitness in Pseudomonas Aeruginosa Biofilms

2021 ◽  
Author(s):  
Xiangke Duan ◽  
Yanrong Pan ◽  
Zhao Cai ◽  
Yumei Liu ◽  
Yingdan Zhang ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Treatment ◽  
Biofilm Formation ◽  
Point Mutations ◽  
Opportunistic Pathogen ◽  
Antimicrobial Treatment ◽  
Clinical Isolates ◽  
High Dose ◽  
Sequencing Analysis ◽  
Cyclic Treatment

Abstract BackgroundPseudomonas aeruginosa is a notorious opportunistic pathogen causing various biofilm-related infections. Biofilm formation is a unique microbial strategy that allows P. aeruginosa to survive adverse conditions such as antibiotic treatment and human immune responses. ResultsIn this study, we experimentally evolved P. aeruginosa PAO1 biofilms for cyclic treatment in the presence of high dose of imipenem, and enriched hyperbiofilm mutants within six cycles in two independent lineages. The competition assay showed the evolved hyperbiofilm mutants can outcompete the ancestral strain within biofilm by prolonging the biofilm mode of growth but not in planktonic cultures. Whole-genome sequencing analysis revealed the hyperbiofilm phenotype is caused by point mutations in rpoS gene in all independently evolved mutants and the same mutation was found in P. aeruginosa clinical isolates. We further showed that mutation in rpoS enhanced biofilm formation by prolonging the biofilm mode of growth and elevating the intracellular c-di-GMP level. Mutation in rpoS increased pyocyanin production and virulence in both P. aeruginosa laboratory strains and clinical isolates. ConclusionHere, our study revealed that antibiotic treatment of biofilm-related P. aeruginosa infections might induce a hyperbiofilm phenotype via rpoS mutation, which might partially explain antimicrobial treatment failure of many P. aeruginosa biofilm-related infections.

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