A functional polymorphism at the miR­491­5p binding site in the 3'­untranslated region of the MMP­9 gene increases the risk of developing ventilator­associated pneumonia.

Matrix metalloproteinase (MMP)­9 is associated with the severity of ventilator­associated pneumonia (VAP), while an rs1056629 SNP located in the 3'­untranslated region (UTR) of MMP­9 affects the microRNA (miRNA/miR)­491­mediated regulation of MMP­9 expression. In the present study, the effect of rs1056629 on the development of VAP in patients with chronic obstructive pulmonary disease (COPD) was investigated. Patients with COPD were enrolled in the study and their genotypes of rs1056629 (CC, CA or AA) were determined. ELISA was used to analyze the levels of TNF­α and IL­6 in the monocytes of patients with COPD carrying differential genotypes of rs1056629. Reverse transcription­quantitative PCR was carried out to evaluate the expression of miR­491 and MMP­9 mRNA in the different groups of patients with COPD. Luciferase assay was used to confirm the inhibitory role of miR­491 in MMP­9 expression. Western blot analysis was carried out to assess the expression of MMP­9 protein in A549 and H1299 cells transfected with miR­491 mimics. The risk and severity of VAP were significantly elevated in patients with COPD carrying the CC and AC genotypes of rs1056629. Although there was no difference in the expression of miR­491 in patients carrying different genotypes of rs1056629, the expression levels of TNF­α, IL­6 and MMP­9 were increased in patients with COPD carrying the CC and AC genotypes of rs1056629. The results of luciferase assay revealed that miR­491 inhibited the expression of MMP­9 through direct binding to the 3'UTR of MMP­9. Transfection of miR­491 mimics into A549 and H1299 cells markedly suppressed the expression of MMP­9 in a concentration­dependent manner. On the whole, the findings of the present study confirm that the CC and AC genotypes of rs1056629 increase the risk of developing VAP in patients with COPD by increasing the expression of MMP­9.

Effect of rs4719839 polymorphism on risk of ventilator-associated pneumonia, expression of microRNA-148 and autophagy-related 16-like 1 (ATG16L1).

MiR-148 is a negative regulator of autophagy 16-like 1 (ATG16L1), a gene implicated in the pathogenesis of ventilator-associated pneumonia (VAP). Therefore, the role of miR-148 polymorphism in the pathogenesis of VAP was studied here. The expression of miR-148, ATG16L1, Beclin-I, LC3-II, TNF-α and IL-6 in serum and peripheral blood mononuclear cells (PBMCs) of VAP patients was detected to study their relationship in the pathogenesis of VAP. Chronic obstructive pulmonary disease patients carrying the AA/AG genotypes of miR-148 rs4719839 single nucleotide polymorphism (SNP) were more prone to VAP due to the higher expression of miR-148, TNF-α and IL-6 along with suppressed expression of ATG16L1, Beclin-I and LC3-II in their serum and PBMCs. Transfection of miR-148 mimics to primary PBMCs genotyped as GG and AA decreased the expression of ATG16L1, Beclin-I and LC3-II. Finally, cells carrying the AA genotype of rs4719839 SNP were more sensitive to the role of LPS stimulation in suppressing ATG16L1, Beclin-I and LC3-II expression while activating TNF-α and IL-6 expression. Our work presented detailed evidence, suggesting that the rs4719839 polymorphism can affect the risk of VAP.

Molecular Profiling of Innate Immune Response Mechanisms in Ventilator-associated Pneumonia.

Ventilator-associated pneumonia (VAP) is a common hospital-acquired infection, leading to high morbidity and mortality. Currently, bronchoalveolar lavage (BAL) is used in hospitals for VAP diagnosis and guiding treatment options. Although BAL collection procedures are invasive, alternatives such as endotracheal aspirates (ETA) may be of diagnostic value, however, their use has not been thoroughly explored. Longitudinal ETA and BAL were collected from 16 intubated patients up to 15 days, of which 11 developed VAP. We conducted a comprehensive LC-MS/MS based proteome and metabolome characterization of longitudinal ETA and BAL to detect host and pathogen responses to VAP infection. We discovered a diverse ETA proteome of the upper airways reflective of a rich and dynamic host-microbe interface. Prior to VAP diagnosis by microbial cultures from BAL, patient ETA presented characteristic signatures of reactive oxygen species and neutrophil degranulation, indicative of neutrophil mediated pathogen processing as a key host response to the VAP infection. Along with an increase in amino acids, this is suggestive of extracellular membrane degradation resulting from proteolytic activity of neutrophil proteases. The metaproteome approach successfully allowed simultaneous detection of pathogen peptides in patients' ETA, which may have potential use in diagnosis. Our findings suggest that ETA may facilitate early mechanistic insights into host-pathogen interactions associated with VAP infection and therefore provide its diagnosis and treatment.

Combined Use of Three Machine Learning Modeling Methods to Develop a Ten-Gene Signature for the Diagnosis of Ventilator-Associated Pneumonia.

BACKGROUND This study aimed to use three modeling methods, logistic regression analysis, random forest analysis, and fully-connected neural network analysis, to develop a diagnostic gene signature for the diagnosis of ventilator-associated pneumonia (VAP). MATERIAL AND METHODS GSE30385 from the Gene Expression Omnibus (GEO) database identified differentially expressed genes (DEGs) associated with patients with VAP. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment identified the molecular functions of the DEGs. The least absolute shrinkage and selection operator (LASSO) regression analysis algorithm was used to select key genes. Three modeling methods, including logistic regression analysis, random forest analysis, and fully-connected neural network analysis, also known as also known as the feed-forward multi-layer perceptron (MLP), were used to identify the diagnostic gene signature for patients with VAP. RESULTS Sixty-six DEGs were identified for patients who had VAP (VAP+) and who did not have VAP (VAP-). Ten essential or feature genes were identified. Upregulated genes included matrix metallopeptidase 8 (MMP8), arginase 1 (ARG1), haptoglobin (HP), interleukin 18 receptor 1 (IL18R1), and NLR family apoptosis inhibitory protein (NAIP). Down-regulated genes included complement factor D (CFD), pleckstrin homology-like domain family A member 2 (PHLDA2), plasminogen activator, urokinase (PLAU), laminin subunit beta 3 (LAMB3), and dual-specificity phosphatase 2 (DUSP2). Logistic regression, random forest, and MLP analysis showed receiver operating characteristic (ROC) curve area under the curve (AUC) values of 0.85, 0.86, and 0.87, respectively. CONCLUSIONS Logistic regression analysis, random forest analysis, and MLP analysis identified a ten-gene signature for the diagnosis of VAP.

One functional variant in the 3'-untranslated region of TLR4 is associated with the elevated risk of ventilator-associated pneumonia in the patients with chronic obstructive pulmonary disease.

The aim of this study was to identify the association polymorphism (rs11536889) in the 3'-untranslated region (3'-UTR) of Toll-like receptors 4 (TLR4) and the risk for ventilator-associated pneumonia (VAP). miRNA database online and luciferase assays were used to validate TLR4 as the target gene of miR-1236. Enzyme-linked immunosorbent assay analysis and western blot were used to analyze the level of TLR4 in different genotype groups. In the present study, miR-1236 was predicted to bind to the rs11536889 G allele rather than the rs11536889 C allele, which was further confirmed by the luciferase activity suppressed by a fragment of 3'-UTR containing the rs11536889 G allele induced by lipopolysaccharide (LPS) and interleukin-6 (IL-6). Bronchial epithelial cells isolated from participants genotyped as GG, GC, and CC, with no remarkable difference in TLR4 messenger RNA (mRNA) levels were observed among these genotype groups. After stimulating by LPS, a TLR4 ligand, the CC-genotyped cells expressed higher levels of IL-8, IL-6, and tumor necrosis factor alpha (TNF-α) on their surfaces than cells with the other genotypes. Finally, the western blot analysis results showed that the expression level of IL-8, IL-6, and TNF-α protein was much higher in the CC group than the GC and GG groups subsequent to stimulation by LPS, and the IL-8, IL-6, and TNF-α protein levels in the GC were grouped much lower compared with the GG group. These findings indicated the regulatory association of miR-1236 with TLR4 and the abnormal expression of TLR4 caused by the presence of rs11536889 in the 3'-UTR of mRNA, which interfere with its interaction with the miR-1236, contributing to the risk of VAP.

16S pan-bacterial PCR can accurately identify patients with ventilator-associated pneumonia.

Ventilator-associated pneumonia (VAP) remains a challenge to intensive care units, with secure diagnosis relying on microbiological cultures that take up to 72 hours to provide a result. We sought to derive and validate a novel, real-time 16S rRNA gene PCR for rapid exclusion of VAP. Bronchoalveolar lavage (BAL) was obtained from two independent cohorts of patients with suspected VAP. Patients were recruited in a 2-centre derivation cohort and a 12-centre confirmation cohort. Confirmed VAP was defined as growth of >104 colony forming units/ml on semiquantitative culture and compared with a 16S PCR assay. Samples were tested from 67 patients in the derivation cohort, 10 (15%) of whom had confirmed VAP. Using cycles to cross threshold (Ct) values as the result of the 16S PCR test, the area under the receiver operating characteristic (ROC) curve (AUROC) was 0.94 (95% CI 0.86 to 1.0, p<0.0001). Samples from 92 patients were available from the confirmation cohort, 26 (28%) of whom had confirmed VAP. The AUROC for Ct in this cohort was 0.89 (95% CI 0.83 to 0.95, p<0.0001). This study has derived and assessed the diagnostic accuracy of a novel application for 16S PCR. This suggests that 16S PCR in BAL could be used as a rapid test in suspected VAP and may allow better stewardship of antibiotics. TRIAL REGISTRATION NUMBER: VAPRAPID trial ref NCT01972425.

Add-on effect of Qinbei Qingfei Yiqi granules for ventilator-associated pneumonia in intensive care units: a randomized controlled trial.

OBJECTIVE: To evaluate the add-on effect of Qinbei Qingfei Yiqi (QBQFYQ) granules for ventilator-associated pneumonia (VAP) in non-infectious critically ill patients. METHODS: In this randomized controlled trial, 80 non-infectious critically ill patients undergoing mechanical ventilation in the intensive care unit (ICU) were randomly divided into two groups: those receiving QBQFYQ granules plus usual treatment (experimental group, n = 50) and those receiving only the usual treatment (control group, n = 30). The main outcome measures were VAP rate, time of VAP occurrence, duration of mechanical ventilation, and length of ICU stay. Interleukin-6 (IL-6), C-reactive protein (CRP), and T-lymphocyte (CD4+, CD8+, and CD4+/CD8+ ratio) serum levels were also evaluated before and after treatment. RESULTS: Compared with the control group treatment QBQFYQ administration significantly reduced the duration of mechanical ventilation [(9.58 ± 3.14) vs (12.52 ± 4.33) days] and length of ICU stay [(14.57 ± 3.72) vs (17.82 ± 5.24) days] and delayed VAP occurrence [(4.31 ± 0.86) vs (2.43 ± 0.27) days]. Additionally, CRP and IL-6 serum levels and CD4+/CD8+ ratio were significantly lower in the experimental group (P < 0.05) than in the control group. However, there were no significant differences in hospital mortality rate (30.0% vs 33.3% ) and adverse events (4.0% vs 6.7%). adverse events (4.0% vs 6.7%). CONCLUSION: QBQFYQ delays the time of VAP occurrence and shortens the duration of mechanical ventilation in non-infectious critically ill patients, possibly through anti-inflammatory and immunomodulatory mechanisms.

Pseudomonas aeruginosa colonization enhances ventilator-associated pneumonia-induced lung injury.

BACKGROUND: Pseudomonas aeruginosa (PA) is the single-most common pathogen of ventilator-associated pneumonia (VAP). Large quantities of PA in the trachea of ventilated patients are associated with an increased risk of death. However, the role of PA colonization in PA VAP-induced lung injury remains elusive. This study examined the effect and mechanism of PA colonization in VAP-induced lung injury. METHODS: C57BL/6 wild-type (WT) and c-Jun N-terminal kinase knockout (JNK1(-/-)) mice received mechanical ventilation for 3 h at 2 days after receiving nasal instillation of PA (1 × 10(6) colony forming unit) or normal saline. RESULTS: Intranasal instillation of PA or mechanical ventilation induced the expression of interleukin-6 (IL-6) in the lungs. Phospho-JNK protein expression in the lungs was significantly increased in mice receiving mechanical ventilation after PA instillation as compared with those receiving ventilation alone. Mechanical ventilation after PA instillation significantly increased the expression of tumor necrosis factor-α (TNF-α), IL-1ß, and macrophage inflammatory protein-2 (MIP-2) proteins; neutrophil sequestration; and TNF-α, IL-1ß, and IL-6 levels in the lungs of WT mice, but not in JNK1(-/-) mice. CONCLUSION: PA colonization plays an important role in PA VAP-induced lung injury through the induction of JNK1-mediated inflammation. PA-induced VAP causes lung injury through JNK signaling pathway in the lungs. JNK inhibition in ICU patients with higher percentages of PA colonization may reduce VAP-induced lung injury and mortality.

Gene expression profile analysis of ventilator-associated pneumonia.

Based on the gene expression profile of patients with ventilator-associated pneumonia (VAP) and patients not affected by the disease, the present study aimed to enhance the current understanding of VAP development using bioinformatics methods. The expression profile GSE30385 was downloaded from the Gene Expression Omnibus database. The Linear Models for Microarray Data package in R language was used to screen and identify differentially expressed genes (DEGs), which were grouped as up­ and down­regulated genes. The up­ and downregulated genes were functionally enriched using the Database for Annotation, Visualization and Integrated Discovery system and then annotated according to TRANSFAC, Tumor Suppressor Gene and Tumor Associated Gene databases. Subsequently, the protein­protein interaction (PPI) network was constructed, followed by module analysis using CFinder software. A total of 69 DEGs, including 33 up­ and 36 downregulated genes were screened out in patients with VAP. Upregulated genes were mainly enriched in functions and pathways associated with the immune response (including the genes ELANE and LTF) and the mitogen-activated protein kinase (MAPK) signaling pathway (including MAPK14). The PPI network comprised 64 PPI pairs and 44 nodes. The top two modules were enriched in different pathways, including the MAPK signaling pathway. Genes including ELANE, LTF and MAPK14 may have important roles in the development of VAP via altering the immune response and the MAPK signaling pathway.

Identification of crucial genes in ventilator associated pneumonia through protein-protein interaction network.

PURPOSE: Ventilator-associated pneumonia (VAP) is still an important cause of morbidity and mortality in patients receiving mechanical ventilation. This research aimed to investigate the genes related to VAP and potential diagnosis targets. MATERIALS AND METHODS: Gene expression profiles data of GSE30385 were downloaded from Gene Expression Omnibus, which included 10 samples of patients with VAP and 10 samples of patients without VAP. The differentially expressed genes (DEGs) between two types of patients were identified by limma package and the functions and pathways of DEGs were predicted by Gene Ontology and KEGG pathway enrichment analyses. Next, the protein-protein interaction (PPI) pairs of all genes in the samples were obtained from STRING database. Then we searched genes related to VAP in NCBI, and constructed a PPI network of these genes. Subsequently, the overlapped genes between genes in the PPI network and DEGs were searched, followed by expression patterns analysis. Furthermore, genes in PPI network were subjected to function and pathway enrichment analysis, and transcription factors were screened on the basis of TRANSFAC database. RESULT: A total of 69 DEGs were screened between two types of patient samples, and 7 genes related to VAP were obtained. The overlapped genes (e.g. LTF, MAPK14) were enriched in MAPK cascade and immune system-related processes. In addition, MAPK14 was enriched in MAPK signaling pathway. CONCLUSION: The VAP-related genes (MAPK14 and LTF) might be the crucial genes in the pathogenesis of VAP, and be served as potential diagnostic targets.

Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks.

BACKGROUND: Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus, using PPI data to functionally annotate proteins has been extensively studied. However, most existing network-based approaches do not work well when annotation and interaction information is inadequate in the networks. RESULTS: In this paper, we proposed a new method that combines PPI information and protein sequence information to boost the prediction performance based on collective classification. Our method divides function prediction into two phases: First, the original PPI network is enriched by adding a number of edges that are inferred from protein sequence information. We call the added edges implicit edges, and the existing ones explicit edges correspondingly. Second, a collective classification algorithm is employed on the new network to predict protein function. CONCLUSIONS: We conducted extensive experiments on two real, publicly available PPI datasets. Compared to four existing protein function prediction approaches, our method performs better in many situations, which shows that adding implicit edges can indeed improve the prediction performance. Furthermore, the experimental results also indicate that our method is significantly better than the compared approaches in sparsely-labeled networks, and it is robust to the change of the proportion of annotated proteins.

Proteomic profiling of bronchoalveolar lavage fluid in critically ill patients with ventilator-associated pneumonia.

RATIONALE: Ventilator-associated pneumonia (VAP) is a common complication in patients with acute lung injury (ALI) and can lead to increased morbidity and mortality. Identifying protein profiles specific to VAP in bronchoalveolar lavage fluid (BALF) may aid in earlier diagnosis, elucidate mechanisms of disease, and identify putative targets for therapeutic intervention. METHODS: BALF was obtained from 5 normal subjects and 30 ALI patients: 14 with VAP (VAP(+)) and 16 without VAP (VAP(-)). Each sample underwent shotgun proteomic analysis based on tandem mass spectrometry. Differentially expressed proteins between the groups were identified using statistical methods based on spectral counting. Mechanisms of disease were explored using functional annotation and protein interaction network analysis. Supervised classification algorithms were implemented to discover a proteomic classifier for identifying critically ill patients with VAP. RESULTS: ALI patients had distinct BALF proteomic profiles compared to normal controls. Within the ALI group, we identified 76 differentially expressed proteins between VAP(+) and VAP(-). Functional analysis of these proteins suggested activation of pro-inflammatory pathways during VAP. We identified and validated a limited proteomic signature that discriminated VAP(+) from VAP(-) patients comprised of three proteins: S100A8, lactotransferrin (LTF), and actinin 1 (ACTN1). CONCLUSIONS: Combining proteomic with computational analyses is a powerful approach to study the BALF proteome during lung injury and development of VAP. This integrative methodology is a promising strategy to differentiate clinically relevant subsets of ALI patients, including those suffering from VAP.

[Etiology of ventilator-associated pneumonia at the Cardiovascular Surgery Clinic of Iasi]. / Etiologia pneumoniei asociata ventilatiei mecanice la clinica de chirurgie cardiovasculara din Iasi.

AIM: We want to assess the etiology of ventilator-associated pneumonia (VAP) and emergence of resistant phenotypes for greater efficiency of the first-line antimicrobial treatment post-cardiac surgery. The study focuses on patients with VAP post-cardiac surgery at the Institute of Cardiovascular Surgery between April 2nd 2002 and August 27th 2008, divided in two groups, before and after June 14th, 2005. MATERIAL AND METHODS: The tracheal aspirates were examined quantitatively (microscopy, culture). The isolates with clinical significance (> or = 106 CFU/mL) were identified by standard methods and tested by disk difussion or with the breakpoints method for susceptibility to antibiotics. RESULTS: Among the 1527 operated patients, 28 of them were diagnosed with VAP through the clinical pulmonary infection score > or = 6. The 9 most common pathogens in VAP etiology were Pseudomonas aeruginosa 23.81%, Acinetobacter baumannii 19.05%, Stenotrophomonas maltophilia 11.91%, Candida albicans 9.53%, while Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Corynebacterium striatum/amycolatum, Pneumocystis jirovecii amounted 4.76% each. Acinetobacter baumannii and S.maltophilia appear starting with June 15th, 2005. From that moment on we isolated with a higher frequency the gram-negative bacilli which produce extended-spectrum beta-lactamases 15.62%, with multidrug resistance (MDR) 46.86%. The MDR phenotype was more frequent at A.baumannii (15.62%), S. maltophilia (15.62%) and P. aeruginosa (12.50%) compared to K .pneumoniae (3.12%) or E. coli (0%). Methicillin-resistant S. aureus was isolated with a 6.25% frequency. CONCLUSIONS: The most common etiologic agents of ventilator-associated pneumonia post-cardiac surgery are Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia and Candida albicans. The large use of antibiotics selects infectious agents with intrinsic resistance and multiresistant

Developing a gene expression model for predicting ventilator-associated pneumonia in trauma patients: a pilot study.

BACKGROUND: Ventilator-associated pneumonia (VAP) carries significant mortality and morbidity. Predicting which patients will become infected could lead to measures to reduce the incidence of VAP. METHODOLOGY/PRINCIPAL FINDINGS: The goal was to begin constructing a model for VAP prediction in critically-injured trauma patients, and to identify differentially expressed genes in patients who go on to develop VAP compared to similar patients who do not. Gene expression profiles of lipopolysaccharide stimulated blood cells in critically injured trauma patients that went on to develop ventilator-associated pneumonia (n=10) was compared to those that never developed the infection (n=10). Eight hundred and ten genes were differentially expressed between the two groups (ANOVA, P<0.05) and further analyzed by hierarchical clustering and principal component analysis. Functional analysis using Gene Ontology and KEGG classifications revealed enrichment in multiple categories including regulation of protein translation, regulation of protease activity, and response to bacterial infection. A logistic regression model was developed that accurately predicted critically-injured trauma patients that went on to develop VAP (VAP+) and those that did not (VAP-). Five genes (PIK3R3, ATP2A1, PI3, ADAM8, and HCN4) were common to all top 20 significant genes that were identified from all independent training sets in the cross validation. Hierarchical clustering using these five genes accurately categorized 95% of patients and PCA visualization demonstrated two discernable groups (VAP+ and VAP-). CONCLUSIONS/SIGNIFICANCE: A logistic regression model using cross-validation accurately predicted patients that developed ventilator-associated pneumonia and should now be tested on a larger cohort of trauma patients.

Genetic polymorphisms within tumor necrosis factor gene promoter region: a role for susceptibility to ventilator-associated pneumonia.

Debatable findings exist among various studies regarding the impact of single nucleotide polymorphisms (SNPs) within the promoter region of the tumor necrosis factor (TNF) gene for susceptibility to infections. Their impact was investigated in a cohort of mechanically ventilated patients who developed ventilator-associated pneumonia (VAP). Two-hundred and thirteen mechanically ventilated patients who developed VAP were enrolled. Genomic DNA was extracted and SNPs at the -376, -308 and -238 position of the promoter region of the TNF gene were assessed by restriction fragment length polymorphisms. Monocytes were isolated from 47 patients when they developed sepsis and stimulated by bacterial endotoxin for the production of TNFα and of interleukin-6 (IL-6). Patients were divided into two groups; 166 patients bearing only wild-type alleles of all three studied polymorphisms; and 47 patients carrying at least one A allele of the three studied SNPs. Time between start of mechanical ventilation and advent of VAP was significantly shorter in the second group than in the first group (log-rank: 4.416, p: 0.041). When VAP supervened, disease severity did not differ between groups. Stimulation of TNFα and of IL-6 was much greater by monocytes for patients carrying A alleles. Carriage of at least one A allele of the three studied SNPs at the promoter region of the TNF-gene is associated with shorter time to development of VAP but it is not associated with disease severity. Findings may be related with a role of the studied SNPs in the production of pro-inflammatory cytokines.

Intubated patients developing tracheobronchitis or pneumonia have distinctive complement system gene expression signatures in the pre-infection period: a pilot study.

INTRODUCTION: It remains unknown why some intubated patients remain infection-free while others develop tracheobronchitis (VAT) or pneumonia (VAP). OBJECTIVE: To identify and compare VAP/VAT gene expression "signatures" using genome-wide oligonucleotide microarrays. MATERIAL AND METHODS: A prospective translational study of gene expression profiles of VAP and VAT groups was carried out, establishing comparisons in both pre-infection and infection phases. Pathway and functional analyses were performed with Ingenuity Pathway Analysis (IPA). Data analysis and hierarchical clustering of the genes involved in the signalling pathways expressed differentially in the two groups were performed with GeneSpring GX 11.0. RESULTS: Eight patients developing respiratory infections (3 VAP and 5 VAT) after 4 days of mechanical ventilation were assessed. Comparison of gene expression profiles in the pre-infection period revealed 5595 genes expressed differentially between VAP and VAT (p<0.01, fold change >2). Comparative IPA analysis identified a significant depression of the complement system signalling pathway in the VAP group, affecting the classical pathway along with the final common pathway (p<0.05). In addition, the cAMP and calcium signalling pathways were also significantly depressed in the VAP group during the pre-infection phase also. CONCLUSION: Intubated patients complicated with pneumonia developed immune impairment in the pre-infection period, manifesting as a relatively lower expression of genes involved in the complement system that differed from patients developing tracheobronchitis. These findings suggest that a significant proportion of VAP episodes cannot be prevented, but might be treatable through pre-emptive therapy.

Estimating sparse gene regulatory networks using a bayesian linear regression.

In this paper, we propose a gene regulatory network (GRN) estimation method, which assumes that such networks are typically sparse, using time-series microarray datasets. We represent the regulatory relationships between the genes using weights, with the "net" regulation influence on a gene's expression being the summation of the independent regulatory inputs. We estimate the weights using a Bayesian linear regression method for sparse parameter vectors. We apply our proposed method to the extraction of differential gene expression software selected genes of a human buffy-coat microarray expression profile dataset of ventilator-associated pneumonia (VAP), and compare the estimation result with the GRNs estimated using both a correlation coefficient method and a database-based method ingenuity pathway analysis. A biological analysis of the resulting consensus network that is derived using the GRNs, estimated with both our and the correlation-coefficient methods results in four biologically meaningful subnetworks. Also, our method performs either better than or competitively with the existing well-established GRN estimation methods. Moreover, it performs comparatively with respect to: 1) the ground-truth GRNs for the in silico 50- and 100-gene datasets reported recently in the DREAM3 challenge and 2) the GRN estimated using a mutual information-based method for the top-ranked Bayesian analysis of time series (a Bayesian user-friendly software for analyzing time-series microarray experiments) selected genes of the VAP dataset.

Detection of plant DNA in the bronchoalveolar lavage of patients with ventilator-associated pneumonia.

BACKGROUND: Hospital-acquired infections such as nosocomial pneumonia are a serious cause of mortality for hospitalized patients, especially for those admitted to intensive care units (ICUs). Despite the number of the studies reported to date, the causative agents of pneumonia are not completely known. Herein, we found by molecular technique that vegetable and tobacco DNA may be detected in the bronchoalveolar lavage from patients with ventilator-associated pneumonia (VAP). METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we studied bronchoalveolar lavage (BAL) from patients admitted to ICUs with ventilator-associated pneumonia. BAL fluids were assessed with molecular tests, culture and blood culture. We successfully identified plant DNA in six patients out of 106 (6%) with ventilator-associated pneumonia. Inhalation was confirmed in four cases and suspected in the other two cases. Inhalation was significantly frequent in patients with plant DNA (four out of six patients) than those without plant DNA (three out of 100 patients) (P<0.001). Nicotiana tabacum chloroplast DNA was identified in three patients who were smokers (cases 2, 3 and 6). Cucurbita pepo, Morus bombycis and Triticum aestivum DNA were identified in cases 1, 4 and 5 respectively. Twenty-three different bacterial species, two viruses and five fungal species were identified from among these six patients by using molecular and culture techniques. Several of the pathogenic microorganisms identified are reported to be food-borne or tobacco plant-associated pathogens. CONCLUSIONS/SIGNIFICANCE: Our study shows that plants DNA may be identified in the BAL fluid of pneumonia patients, especially when exploring aspiration pneumonia, but the significance of the presence of plant DNA and its role in the pathogenesis of pneumonia is unknown and remains to be investigated. However, the identification of these plants may be a potential marker of aspiration in patients with pneumonia.

Influence of genetic variations in TLR4 and TIRAP/Mal on the course of sepsis and pneumonia and cytokine release: an observational study in three cohorts.

INTRODUCTION: It has been proposed that individual genetic variation contributes to the course of severe infections and sepsis. Recent studies of single nucleotide polymorphisms (SNPs) within the endotoxin receptor and its signaling system showed an association with the risk of disease development. This study aims to examine the response associated with genetic variations of TLR4, the receptor for bacterial LPS, and a central intracellular signal transducer (TIRAP/Mal) on cytokine release and for susceptibility and course of severe hospital acquired infections in distinct patient populations. METHODS: Three intensive care units in tertiary care university hospitals in Greece and Germany participated. 375 and 415 postoperative patients and 159 patients with ventilator associated pneumonia (VAP) were included. TLR4 and TIRAP/Mal polymorphisms in 375 general surgical patients were associated with risk of infection, clinical course and outcome. In two prospective studies, 415 patients following cardiac surgery and 159 patients with newly diagnosed VAP predominantly caused by Gram-negative bacteria were studied for cytokine levels in-vivo and after ex-vivo monocyte stimulation and clinical course. RESULTS: Patients simultaneously carrying polymorphisms in TIRAP/Mal and TLR4 and patients homozygous for the TIRAP/Mal SNP had a significantly higher risk of severe infections after surgery (odds ratio (OR) 5.5; confidence interval (CI): 1.34 - 22.64; P = 0.02 and OR: 7.3; CI: 1.89 - 28.50; P < 0.01 respectively). Additionally we found significantly lower circulating cytokine levels in double-mutant individuals with ventilator associated pneumonia and reduced cytokine production in an ex-vivo monocyte stimulation assay, but this difference was not apparent in TIRAP/Mal-homozygous patients. In cardiac surgery patients without infection, the cytokine release profiles were not changed when comparing different genotypes. CONCLUSIONS: Carriers of mutations in sequential components of the TLR signaling system may have an increased risk for severe infections. Patients with this genotype showed a decrease in cytokine release when infected which was not apparent in patients with sterile inflammation following cardiac surgery.

Genetic variation in complement component 2 of the classical complement pathway is associated with increased mortality and infection: a study of 627 patients with trauma.

BACKGROUND: Trauma is a disease of inflammation. Complement Component 2 (C2) is a protease involved in activation of complement through the classical pathway and has been implicated in a variety of chronic inflammatory diseases. We hypothesized that genetic variation in C2 (E318D) identifies a high-risk subgroup of patients with trauma reflecting increased mortality and infection (ventilator-associated pneumonia [VAP]). Consequently, genetic variation in C2 may stratify patient risk and illuminate underlying mechanisms for therapeutic intervention. METHODS: DNA samples from 702 patients with trauma were genotyped for C2 E318D and linked with covariates (age: mean 42.8 years, gender: 74% male, ethnicity: 80% white, mechanism: 84% blunt, injury severity score: mean 25.0, admission lactate: mean 3.13 mEq/L) and outcomes: mortality 9.9% and VAP: 18.5%. VAP was defined by quantitative bronchoalveolar lavage (> 10). Multivariate regression analysis determined the relationship of genotype and covariates to risk of death and VAP. However, patients with injury severity score > or = 45 were excluded from the multivariate analysis, as magnitude of injury overwhelms genetics and covariates in determining outcome. RESULTS: Fifty-two patients (8.3%) had the high-risk heterozygous genotype, associated with a significant increase in mortality and VAP. CONCLUSION: In 702 patients with trauma, 8.3% had a high-risk genetic variation in C2 associated with increased mortality (odds ratio = 2.65) and infection (odds ratio = 2.00). This variation: (1) identifies a previously unknown high-risk group for infection and mortality; (2) can be determined at admission; (3) may provide opportunity for early therapeutic intervention; and (4) requires validation in a distinct cohort of patients.