Early immune response to the components of the type III system of Pseudomonas aeruginosa in children with cystic fibrosis

Revisiting Host-Pathogen Interactions in Cystic Fibrosis Lungs in the Era of CFTR Modulators

Cystic fibrosis transmembrane conductance regulator (CFTR) modulators, a new series of therapeutics that correct and potentiate some classes of mutations of the CFTR, have provided a great therapeutic advantage to people with cystic fibrosis (pwCF). The main hindrances of the present CFTR modulators are related to their limitations in reducing chronic lung bacterial infection and inflammation, the main causes of pulmonary tissue damage and progressive respiratory insufficiency, particularly in adults with CF. Here, the most debated issues of the pulmonary bacterial infection and inflammatory processes in pwCF are revisited. Special attention is given to the mechanisms favoring the bacterial infection of pwCF, the progressive adaptation of Pseudomonas aeruginosa and its interplay with Staphylococcus aureus, the cross-talk among bacteria, the bronchial epithelial cells and the phagocytes of the host immune defenses. The most recent findings of the effect of CFTR modulators on bacterial infection and the inflammatory process are also presented to provide critical hints towards the identification of relevant therapeutic targets to overcome the respiratory pathology of pwCF.

Bioinformatics analyses for the designation of a hybrid protein against urinary tract infections caused by Pseudomonas aeruginosa and investigation of the presence of pre-existing antibodies in infected humans

Pseudomonas aeruginosa is an important pathogen causing urinary tract infections (UTIs) and resistance to antibiotics has increased the need for a vaccine against this bacterium. P. aeruginosa V-antigen (PcrV), which is a component of the type III secretion system, delivers exoenzymes such as exoenzyme S (ExoS) into the host cells. In the present study, we aimed to design and express a hybrid protein composed of PcrV and ExoS from P. aeruginosa using bioinformatics. Finally, pre-existing antibodies were evaluated in sera collected from patients with UTI. The prediction results showed that the hybrid protein ExoS.PcrV had a C-score of -0.85 and Z-score of -5.55 versus C-score of -2.93 and Z-score of -2.65 for PcrV.ExoS. Based on BepiPred and ABCpred, 15 and 14 linear B-cell epitopes, as well as five conformational epitopes were identified in ExoS.PcrV. The interaction between the protein and immune receptor was validated in silico. Molecular docking indicated that the hybrid protein interacted strongly with Toll-like receptor 2. ExoS.PcrV was expressed in pET28a-BL21 and purified with a size of 57 kD by Nickel resins. The protein reacted with all sera collected from humans infected with P. aeruginosa following Western blot. The infected patients produced significantly higher IgG levels against the protein compared to the control as indicated by ELISA. The protein ExoS.PcrV was determined as a promising candidate against UTI caused by P. aeruginosa and the presence of pre-existing antibodies indicated the advantage of the hybrid protein. Evaluation of the efficacy of hybrid protein is ongoing in mice model. Communicated by Ramaswamy H. Sarma.

Antibodies Inhibiting the Type III Secretion System of Gram-Negative Pathogenic Bacteria

Pathogenic bacteria are a global health threat, with over 2 million infections caused by Gram-negative bacteria every year in the United States. This problem is exacerbated by the increase in resistance to common antibiotics that are routinely used to treat these infections, creating an urgent need for innovative ways to treat and prevent virulence caused by these pathogens. Many Gram-negative pathogenic bacteria use a type III secretion system (T3SS) to inject toxins and other effector proteins directly into host cells. The T3SS has become a popular anti-virulence target because it is required for pathogenesis and knockouts have attenuated virulence. It is also not required for survival, which should result in less selective pressure for resistance formation against T3SS inhibitors. In this review, we will highlight selected examples of direct antibody immunizations and the use of antibodies in immunotherapy treatments that target the bacterial T3SS. These examples include antibodies targeting the T3SS of Pseudomonas aeruginosa, Yersinia pestis, Escherichia coli, Salmonella enterica, Shigella spp., and Chlamydia trachomatis.

Virulence attenuating combination therapy: a potential multi-target synergy approach to treat Pseudomonas aeruginosa infections in cystic fibrosis patients

The World Health Organization considers the discovery of new treatments for P. aeruginosa a top priority. Virulence attenuating combination therapy (VACT) is a pragmatic strategy to improve bacterial clearance, repurpose outmoded antibiotics, improve drug efficacy at lower doses, and reduce the evolution of resistance. In vitro and in vivo studies have shown that adding a quorum sensing inhibitor or an extracellular polymeric substance repressor to classical antibiotics synergistically improves antipseudomonal activity. This review highlights why VACT could specifically benefit cystic fibrosis patients harboring chronic P. aeruginosa infections, outlines the current landscape of synergistic combinations between virulence-targeting small-molecules and anti-pseudomonal drugs, and suggests future directions for VACT research.

Pseudomonas aeruginosa Bacteremic Patients Exhibit Nonprotective Antibody Titers Against Therapeutic Antibody Targets PcrV and Psl Exopolysaccharide

BACKGROUND

The type 3 secretion protein PcrV and Psl exopolysaccharide are promising therapeutic antibody targets against Pseudomonas aeruginosa. We examined P. aeruginosa bloodstream infection (BSI) isolates for the ability to express PcrV and Psl and evaluated corresponding patient serum for active titers to these targets.

METHODS

We identified 114 patients with acute P. aeruginosa BSI; 56 cases were accompanied by acute sera. Serum was evaluated for PcrV- and Psl-specific immunoglobulin G (IgG) and for cytotoxicity and opsonophagocytosis. Isolates were evaluated for susceptibility to antibiotics, expression of PcrV and Psl, and susceptibility to the anti-PcrV/Psl bispecific antibody and clinical candidate MEDI3902.

RESULTS

In-hospital mortality for patients with P. aeruginosa BSI was 39%. A total of 26% of isolates were resistant to ≥3 antibiotic classes. Although PcrV and/or Psl were detected in 99% of isolates, a majority of patients lacked active titers to PcrV (100%) and Psl (98%). In addition, MEDI3902 was active against all tested isolates.

CONCLUSIONS

A vast majority of P. aeruginosa BSI isolates express PcrV and Psl; however, patient sera most often lacked IgG and functionally active responses to these targets. These results suggest that therapies directed at PcrV and Psl could be a promising approach for combating P. aeruginosa bloodstream infections.

The deletion of TonB-dependent receptor genes is part of the genome reduction process that occurs during adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung

Chronic Pseudomonas aeruginosa infections are the main cause of morbidity among patients with cystic fibrosis (CF) due to persistent lung inflammation caused by interaction between this bacterium and the immune system. Longitudinal studies of clonally related isolates of a dominant CF clone have indicated that genome reduction frequently occurs during adaptation of P. aeruginosa in the CF lung. In this study, we have evaluated the P. aeruginosa population structure of patients attending the Universitair Ziekenhuis Brussel (UZ Brussel) CF reference center using a combination of genotyping methods. Although the UZ Brussel P. aeruginosa CF population is characterized by the absence of a dominant CF clone, some potential interpatient transmissions could be detected. Interestingly, one of these clones showed deletion of the alternative type I ferripyoverdine receptor gene fpvB. Furthermore, we found that several other TonB-dependent receptors are deleted as well. The genome of one potentially transmissible CF clone was sequenced, revealing large deleted regions including all type III secretion system genes and several virulence genes. Remarkably, a large number of deleted genes are shared between the P. aeruginosa CF clone described in this study and isolates belonging to the dominant Copenhagen CF DK2 clone, suggesting parallel evolution.

Structure and function of the Type III secretion system of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a dangerous pathogen particularly because it harbors multiple virulence factors. It causes several types of infection, including dermatitis, endocarditis, and infections of the urinary tract, eye, ear, bone, joints and, of particular interest, the respiratory tract. Patients with cystic fibrosis, who are extremely susceptible to Pseudomonas infections, have a bad prognosis and high mortality. An important virulence factor of P. aeruginosa, shared with many other gram-negative bacteria, is the type III secretion system, a hollow molecular needle that transfers effector toxins directly from the bacterium into the host cell cytosol. This complex macromolecular machine works in a highly regulated manner and can manipulate the host cell in many different ways. Here we review the current knowledge of the structure of the P. aeruginosa T3SS, as well as its function and recognition by the immune system. Furthermore, we describe recent progress in the development and use of therapeutic agents targeting the T3SS.

Pseudomonas aeruginosa serology and risk for re-isolation in the EPIC trial

BACKGROUND

The prognostic value of Pseudomonas aeruginosa serology for antibiotic therapy in cystic fibrosis patients is not well understood.

METHODS

Using five antigens from two ELISAs, we assessed whether positive serology in CF patients participating in the multi-center Early Pseudomonas Infection in Children (EPIC) trial would predict treatment failure, time to pulmonary exacerbation and risk for recurrent P. aeruginosa isolation post eradication.

RESULTS

Baseline positive P. aeruginosa serology was not significantly associated with failure of initial P. aeruginosa eradication measured at week 10 (adjusted for baseline culture) but seropositivity to the antigens alkaline protease and exotoxin A was significantly associated with increased risk for recurrent P. aeruginosa isolation during the 60 week post eradication follow-up period (p=0.003 and p=0.001 respectively). There was no association between baseline seropositivity and time to pulmonary exacerbation.

CONCLUSION

P. aeruginosa serology may complement culture results in clinicians' efforts to successfully monitor recurrence of early P. aeruginosa in CF patients.

Chest computed tomography scores of severity are associated with future lung disease progression in children with cystic fibrosis

RATIONALE

Most children with cystic fibrosis (CF) experience a slow decline in spirometry, although some children continue to be at risk for more significant lung disease progression. Chest computed tomography (CT) scans have been shown to be more sensitive to changes in lung disease than spirometry and may provide a means for predicting future lung disease progression.

OBJECTIVES

We hypothesized that Brody chest CT scan scores obtained in 2000 in a prospectively monitored cohort of children with CF would be associated with the most recent measures of lung disease severity.

METHODS

Brody chest CT scan scores were calculated for 81 children enrolled in the Wisconsin CF Neonatal Screening Project. Multivariable linear regression was used to determine associations between Brody scores and the most recent (age 21 yr or June 30, 2010, whichever was later) measures of CF lung disease.

MEASUREMENTS AND MAIN RESULTS

The mean observation time after the chest CT scan was 7.5 years. Brody chest CT scan scores were significantly associated with the most recent measures of spirometry (P < 0.001) and Wisconsin and Brasfield chest radiograph scores (P < 0.001). The strength of this association was much stronger than spirometry obtained near the time of the chest CT scan (P < 0.01) but not chest radiograph scores.

CONCLUSIONS

Chest CT scan scores are associated with future lung disease severity, and quantitative chest imaging(chest CT scan and chest radiograph scores) is more strongly associated with future lung disease severity than measures of spirometry. These findings may help clinicians identify patients at risk of future lung disease progression.

Chest computed tomography scores of severity are associated with future lung disease progression in children with cystic fibrosis

RATIONALE

Most children with cystic fibrosis (CF) experience a slow decline in spirometry, although some children continue to be at risk for more significant lung disease progression. Chest computed tomography (CT) scans have been shown to be more sensitive to changes in lung disease than spirometry and may provide a means for predicting future lung disease progression.

OBJECTIVES

We hypothesized that Brody chest CT scan scores obtained in 2000 in a prospectively monitored cohort of children with CF would be associated with the most recent measures of lung disease severity.

METHODS

Brody chest CT scan scores were calculated for 81 children enrolled in the Wisconsin CF Neonatal Screening Project. Multivariable linear regression was used to determine associations between Brody scores and the most recent (age 21 yr or June 30, 2010, whichever was later) measures of CF lung disease.

MEASUREMENTS AND MAIN RESULTS

The mean observation time after the chest CT scan was 7.5 years. Brody chest CT scan scores were significantly associated with the most recent measures of spirometry (P < 0.001) and Wisconsin and Brasfield chest radiograph scores (P < 0.001). The strength of this association was much stronger than spirometry obtained near the time of the chest CT scan (P < 0.01) but not chest radiograph scores.

CONCLUSIONS

Chest CT scan scores are associated with future lung disease severity, and quantitative chest imaging(chest CT scan and chest radiograph scores) is more strongly associated with future lung disease severity than measures of spirometry. These findings may help clinicians identify patients at risk of future lung disease progression.

Monomeric and dimeric IgG fractions show differential reactivity against pathogen-derived antigens

Polyvalent Ig preparations, derived from the pooled plasma of thousands of healthy donors, contain a complex mix of both 'acquired' and natural antibodies directed against pathogens as well as foreign and self/auto antigens (Ag). Depending on their formulation, donor pool size, etc., liquid Ig preparations contain monomeric and dimeric IgG. The dimeric IgG fraction is thought to represent mainly idiotype-antiidiotype Ab pairs. Treatment of all IgG fractions at pH 4 effectively monomerizes the IgG dimers resulting in separated idiotype-antiidiotype Ab pairs and thus in a comparable F(ab')(2) binding site availability of the different IgG fractions. Previously, we identified an increased anti-self-reactivity within the monomerized dimer fraction. This study addressed if, among the different IgG fractions, an analogous preferential reactivity was evident in the response against different pathogen-derived protein and carbohydrate antigens. Therefore, we assessed the activity of total unseparated IgG, the monomeric and dimeric IgG fractions against antigenic structures of bacterial and viral antigens/virulence factors. All fractions showed similar reactivity to protein antigens except for exotoxin A of Pseudomonas aeruginosa, where the dimeric fraction, especially when monomerized, showed a marked increase in reactivity. This suggests that the production of antiidiotypic IgG antibodies contributes to controlling the immune response to certain categories of pathogens. In contrast, the monomeric IgG fractions showed increased reactivity towards pathogen-associated polysaccharides, classically regarded as T-independent antigens. Taken together, the differential reactivity of the IgG fractions seems to indicate a preferential segregation of antibody reactivities according to the nature of the antigen.

Clinical significance of microbial infection and adaptation in cystic fibrosis

A select group of microorganisms inhabit the airways of individuals with cystic fibrosis. Once established within the pulmonary environment in these patients, many of these microbes adapt by altering aspects of their structure and physiology. Some of these microbes and adaptations are associated with more rapid deterioration in lung function and overall clinical status, whereas others appear to have little effect. Here we review current evidence supporting or refuting a role for the different microbes and their adaptations in contributing to poor clinical outcomes in cystic fibrosis.

Characterization of hydrogen peroxide production by Duox in bronchial epithelial cells exposed to Pseudomonas aeruginosa

Hydrogen peroxide production by the NADPH oxidase Duox1 occurs during activation of respiratory epithelial cells stimulated by purified bacterial ligands, such as lipopolysaccharide. Here, we characterize Duox activation using intact bacterial cells of several airway pathogens. We found that only Pseudomonas aeruginosa, not Burkholderia cepacia or Staphylococcus aureus, triggers H2O2 production in bronchial epithelial cells in a calcium-dependent but predominantly ATP-independent manner. Moreover, by comparing mutant Pseudomonas strains, we identify several virulence factors that participate in Duox activation, including the type-three secretion system. These data provide insight on Duox activation by mechanisms unique to P. aeruginosa.

Toxins from bacteria

Bacterial toxins damage the host at the site of bacterial infection or distant from the site. Bacterial toxins can be single proteins or oligomeric protein complexes that are organized with distinct AB structure-function properties. The A domain encodes a catalytic activity. ADP ribosylation of host proteins is the earliest post-translational modification determined to be performed by bacterial toxins; other modifications include glucosylation and proteolysis. Bacterial toxins also catalyze the non-covalent modification of host protein function or can modify host cell properties through direct protein-protein interactions. The B domain includes two functional domains: a receptor-binding domain, which defines the tropism of a toxin for a cell and a translocation domain that delivers the A domain across a lipid bilayer, either on the plasma membrane or the endosome. Bacterial toxins are often characterized based upon the secretion mechanism that delivers the toxin out of the bacterium, termed types I-VII. This review summarizes the major families of bacterial toxins and also describes the specific structure-function properties of the botulinum neurotoxins.

Association between mucoid Pseudomonas infection and bronchiectasis in children with cystic fibrosis

PURPOSE

To correlate the severity of bronchiectasis in children with cystic fibrosis with clinical and microbiologic variables in order to clarify risk factors for the development of irreversible lung disease.

MATERIALS AND METHODS

After institutional review board approval and parental informed consents were obtained, a HIPAA-compliant longitudinal epidemiologic evaluation was performed in patients with cystic fibrosis who were enrolled in the Wisconsin trial of newborn screening from 1985 to 2009. Thin-section chest computed tomography (CT) was used in a prospective cross-sectional design to study patients ranging in age from 6.6 to 17.6 years (mean, 11.5 years). Thin-section CT scores were determined objectively on coded images by multiple raters in a standardized fashion. Microbiologic data were obtained by means of culture of respiratory secretions by using methods for differentiation of Pseudomonas aeruginosa (PA) as either nonmucoid or mucoid.

RESULTS

Eighty-three percent of patients (68 of 82) showed bronchiectasis of varying severity. Of 12 potential risk factors, only respiratory infection with mucoid PA correlated significantly with bronchiectasis (P = .041).

CONCLUSION

The severity of bronchiectasis in children with cystic fibrosis is significantly related to respiratory infection with mucoid PA; attempts to prevent bronchiectasis should include reducing exposure to and early eradication of PA.

Proteomic identification of OprL as a seromarker for initial diagnosis of Pseudomonas aeruginosa infection of patients with cystic fibrosis

Identification of new immunogenic antigens that diagnose initial Pseudomonas aeruginosa infections in patients with cystic fibrosis (CF) alone or as an adjunct to microbiology is needed. In the present study, a proteomic analysis was performed to obtain a global assessment of the host immune response during the initial P. aeruginosa infection of patients with CF. Matrix-assisted laser desorption ionization-time of flight mass spectrometry was used to identify outer membrane protein L (OprL), a non-type III secretion system (TTSS) protein, as an early immunogenic protein during the initial P. aeruginosa infection of patients with CF. Longitudinal Western blot analysis of sera from 12 of 14 patients with CF detected antibodies to OprL during the initial P. aeruginosa infection. In addition, also detected were antibodies to ExoS, ExoU, or ExoS and ExoU, the latter indicating sequential P. aeruginosa infections during initial infections. Detection of serum reactivity to OprL, along with proteins of the TTSS, and in conjunction with microbiology may diagnose initial P. aeruginosa infections in patients with CF.

Antibody response to Pseudomonas aeruginosa in children with cystic fibrosis

Cystic fibrosis (CF) is the most frequent life threatening autosomal recessive disease in white subjects. The primary cause of morbidity and mortality in children with CF is chronic pulmonary infection, mainly caused by Pseudomonas aeruginosa. The purpose of this study was to assess the value of the measurement of antibodies to P. aeruginosa in diagnosing lung infection by the bacteria in CF patients. We assessed P. aeruginosa antibody titers in CF patients from Rio de Janeiro, Brazil, using cell lysate antigens as well as recombinant PcrV, a Type III Secretion System protein. Sputum (more than 70% of the specimens) or oropharyngeal swabs were obtained whenever patients were regularly followed for their pulmonary disease. Blood samples were obtained with an average interval of 6 months for a period of 2 years. The ELISA cut-offs were assigned as the positive 95% confidence interval of the mean antibody levels from non-fibrocystic controls. Our data showed that most CF patients (81%) of whom were not chronically infected by P. aeruginosa (Groups I and II), had their first serology positive for rPcrV. Cell-lysate ELISA was able to detect P. aeruginosa antibodies before positive culture in the first serum sample of 44% of the patients from Groups I and II. When serum reactivity to rPcrV and cell lysate were combined, 94% of CF patients from Groups I and II (n = 16) had the first serology positive for P. aeruginosa over a mean time of 20 months before the first isolation of P. aeruginosa. In conclusion, longitudinal P. aeruginosa serology should become part of respiratory care follow-up, in conjunction with other lung parameter functions.

Role of Pseudomonas aeruginosa type III effectors in disease

Pseudomonas aeruginosa uses a type III secretion system (T3SS) to directly inject four known effectors into host cells. ExoU is a potent cytotoxin with phospholipase A2 activity that causes rapid necrotic death in many cell types. The biological function of ExoY, an adenylate cyclase, remains incompletely defined. ExoS and ExoT are closely related bifunctional proteins with N-terminal GTPase activating protein (GAP) activity toward Rho family proteins and C-terminal ADP ribosylase (ADPRT) activity toward distinct and non-overlapping set of targets. While almost no strain encodes or secretes all four effectors, the commonly found combinations of ExoU/ExoT or ExoS/ExoT provides redundant and failsafe mechanisms to cause mucosal barrier injury, inhibit many arms of the innate immune response, and prevent wound repair.

Pseudomonas aeruginosa and Burkholderia cenocepacia infections in patients affected by cystic fibrosis: serum resistance and antibody response

Pseudomonas aeruginosa and Burkholderia cenocepacia are opportunistic pathogens causing important chronic pulmonary infections in patients affected by cystic fibrosis (CF). The interplay of bacterial and host factors involved in the establishment and evolution of these infections needs further clarification. We investigated the susceptibility of P. aeruginosa and B. cenocepacia derived from CF patients or from the environment to hyperimmune sera obtained from the same CF patients and evaluated the amount of specific antibodies present in these sera. Our data indicate that the bactericidal activity of human serum against these two bacteria is mostly complement-mediated, and that the mucous layer probably confers serum-resistance to B. cenocepacia. The mean amount of antibodies against P. aeruginosa was higher than that against B. cenocepacia. The contribution of these data to the assessment of the importance of the humoral immune response in CF pulmonary infections by Pseudomonas and Burkholderia is briefly discussed.

Early intervention in CF: how to monitor the effect

Early and aggressive therapy already at the stage when no apparent signs of significant lung disease are detectable, may delay the development and progression of cystic fibrosis (CF). Identification of markers for early pulmonary disease in CF is crucial to monitor adherence to preventive therapy and determine its success. Currently several surrogate markers are available that are used in both the decision making and evaluation of the timing and success of early intervention namely, pulmonary function tests (PFT), microbial cultures, imaging techniques, inflammatory markers, serological markers, and several general signs such as exacerbation rate and nutritional status. This review will present the current status and discuss the significance of their application as well as their limitations for patients with CF and no apparent pulmonary disease.

Pathogen proteins eliciting antibodies do not share epitopes with host proteins: a bioinformatics approach

The best way to prevent diseases caused by pathogens is by the use of vaccines. The advent of genomics enables genome-wide searches of new vaccine candidates, called reverse vaccinology. The most common strategy to apply reverse vaccinology is by designing subunit recombinant vaccines, which usually generate an humoral immune response due to B-cell epitopes in proteins. A major problem for this strategy is the identification of protective immunogenic proteins from the surfome of the pathogen. Epitope mimicry may lead to auto-immune phenomena related to several human diseases. A sequence-based computational analysis has been carried out applying the BLASTP algorithm. Therefore, two huge databases have been created, one with the most complete and current linear B-cell epitopes, and the other one with the surface-protein sequences of the main human respiratory bacterial pathogens. We found that none of the 7353 linear B-cell epitopes analysed shares any sequence identity region with human proteins capable of generating antibodies, and that only 1% of the 2175 exposed proteins analysed contain a stretch of shared sequence with the human proteome. These findings suggest the existence of a mechanism to avoid autoimmunity. We also propose a strategy for corroborating or warning about the viability of a protein linear B-cell epitope as a putative vaccine candidate in a reverse vaccinology study; so, epitopes without any sequence identity with human proteins should be very good vaccine candidates, and the other way around.

Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa

Background

Pseudomonas aeruginosa, an opportunistic pathogen, is often encountered in chronic lung diseases such as cystic fibrosis or chronic obstructive pneumonia, as well as acute settings like mechanical ventilation acquired pneumonia or neutropenic patients. It is a major cause of mortality and morbidity in these diseases. In lungs, P. aeruginosa settles in a biofilm mode of growth with the secretion of exopolysaccharides in which it is encapsulated, enhancing its antibiotic resistance and contributing to the respiratory deficiency of patients. However, bacteria must first multiply to a high density and display a cytotoxic phenotype to avoid the host's defences. A virulence determinant implicated in this step of infection is the type III secretion system (TTSS), allowing toxin injection directly into host cells. At the beginning of the infection, most strains isolated from patients' lungs possess an inducible TTSS allowing toxins injection or secretion upon in vivo or in vitro activation signals. As the infection persists most of the bacteria permanently loose this capacity, although no mutations have been evidenced. We name "non inducible" this phenotype. As suggested by the presence of a positive feedback circuit in the regulatory network controlling TTSS expression, it may be due to an epigenetic switch allowing heritable phenotypic modifications without genotype's mutations.

Results

Using the generalised logical method, we designed a minimal model of the TTSS regulatory network that could support the epigenetic hypothesis, and studied its dynamics which helped to define a discriminating experimental scenario sufficient to validate the epigenetic hypothesis. A mathematical framework based on formal methods from computer science allowed a rigorous validation and certification of parameters of this model leading to epigenetic behaviour. Then, we demonstrated that a non inducible strain of P. aeruginosa can stably acquire the capacity to be induced by calcium depletion for the TTSS after a short pulse of a regulatory protein. Finally, the increased cytotoxicity of a strain after this epigenetic switch was demonstrated in vivo in an acute pulmonary infection model.

Conclusion

These results may offer new perspectives for therapeutic strategies to prevent lethal infections by P. aeruginosa by reverting the epigenetic inducibility of type III cytotoxicity.

Microarray analysis of the osmotic stress response in Pseudomonas aeruginosa

Transcriptional profiling of Pseudomonas aeruginosa grown under steady-state hyperosmotic stress conditions showed an up-regulation of genes associated with osmoprotectant synthesis, putative hydrophilins, and the type III secretion system with associated cytotoxins. A large number of regulatory genes, including several two-component systems not previously known to be influenced by osmolarity, were differentially expressed by P. aeruginosa in immediate response to hyperosmotic shock.

Improved cell typing by charge-state deconvolution of matrix-assisted laser desorption/ionization mass spectra

Robust, specific, and rapid identification of toxic strains of bacteria and viruses, to guide the mitigation of their adverse health effects and optimum implementation of other response actions, remains a major analytical challenge. This need has driven the development of methods for classification of microorganisms using mass spectrometry, particularly matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), that allows high-throughput analyses with minimum sample preparation. We describe a novel approach to cell typing based on pattern recognition of MALDI mass spectra, which involves charge-state deconvolution in conjunction with a new correlation analysis procedure. The method is applicable to both prokaryotic and eukaryotic cells. Charge-state deconvolution improves the quantitative reproducibility of spectra because multiply charged ions resulting from the same biomarker attaching a different number of protons are recognized and their abundances are combined. This allows a clearer distinction of bacterial strains or of cancerous and normal liver cells. Improved class distinction provided by charge-state deconvolution was demonstrated by cluster spacing on canonical variate score charts and by correlation analyses. Deconvolution may enhance detection of early disease state or therapy progress markers in various tissues analyzed by MALDI-MS.