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Introduction: The diagnosis of an acute exacerbation of IPF (AE-IPF) requires the exclusion of infective triggers, suggesting infection plays no role in the pathogenesis of these events. Following the recent characterisation of the respiratory microbiome in IPF this study aimed to assess for changes in the respiratory microbiome during an AE-IPF. Methods: Eighteen patients with AE-IPF and 14 stable IPF patients undergoing bronchoscopy were enrolled at the University of Ulsan, Korea. Patients had a negative lavage bacterial culture and respiratory virus screen. Bacterial DNA was extracted and a hyper-variable region of the 16S ribosomal RNA gene (16S rRNA) amplified, quantified and pyrosequenced. Results: Subjects had a mean age of 66 years and on average mild disease (DLco 68±13% predicted; FVC 78±16% predicted). AE-IPF subjects had on average 1.4x10 9 copies of the 16S rRNA gene per ml of BAL, more than four times higher than stable IPF subjects (3.1x10 8 ) ( P =0.012). The microbiota of the stable Korean IPF subjects is dominated by Firmicutes (34%), Proteobacteria (32%) and Bacteroidetes (16%). The same phyla predominate in the AE-IPF subjects, but proteobacteria account for over 40% of the total reads, with a higher relative abundance of two potentially pathogenic OTUs. Within paired samples there were clear changes in an individual9s microbiota during an exacerbation. Conclusions: AE-IPF is associated with an increased BAL bacterial burden compared to stable disease. There are detectable changes in the composition of the respiratory microbiome during an AE-IPF, an event that current guidelines would lead us to believe is non-infective.

Summary Background Idiopathic pulmonary fibrosis, a progressive and inevitably fatal disorder, has a highly variable clinical course. Biomarkers that reflect disease activity are urgently needed to inform patient management and for use as biomarkers of therapeutic response (theragnostic biomarkers) in clinical trials. We aimed to determine whether dynamic change in markers of extracellular matrix (ECM) turnover predicts progression of idiopathic pulmonary fibrosis as determined by change in forced vital capacity and death. Methods In this ongoing prospective, multicentre, observational cohort study (PROFILE), participants with idiopathic pulmonary fibrosis or idiopathic non-specific interstitial pneumonia diagnosed within the preceding 6 months were recruited from two coordinating centres (Nottingham, UK, and, Royal Brompton Hospital, London, UK). Serum samples were prospectively collected at baseline, 1 month, 3 months, and 6 months and were analysed for a panel of novel matrix metalloprotease (MMP)-degraded ECM proteins, by ELISA-based, neoepitope assay. 11 neoepitopes were tested in a discovery cohort of 55 patients to identify biomarkers of sufficient rigour for more detailed analyses. Eight were then further assessed in a validation cohort of 134 patients with 50 age-matched and sex-matched controls. Changes in biomarker concentrations were related to subsequent progression of idiopathic pulmonary fibrosis (defined as death or decline in forced vital capacity >10% at 12 months after study enrolment) using a repeated measures model. The PROFILE study is registered on ClinicalTrials.gov, numbers NCT01134822 and NCT01110694. Findings Of 214 eligible participants recruited between Sept 1, 2010, and March 31, 2012, 189 had a confirmed diagnosis of idiopathic pulmonary fibrosis and were included in subsequent analyses. In the discovery cohort, mean concentrations of seven neoepitopes (BGM, p=0·009; C1M, p=0·009; C3M, p=0·046; C6M, p=0·032; CRPM, p=0·008; ELM2, p=0·02; and VICM, p=0·0007) differed significantly between healthy controls and participants with idiopathic pulmonary fibrosis. Baseline concentrations of six neoepitopes (C1M, p=0·012; C3A, p=0·012; C3M, p=0·0005; C6M, p=0·0003; CRPM, p=0·021; and VICM, p=0·046) were significantly higher in patients with progressive idiopathic pulmonary fibrosis (n=32) than in those with stable disease (n=23). In the validation cohort, mean concentrations of C1M (p=0·001), C3M (p=0·044), C6M (p=0·003), and CRPM (p=0·024) at baseline were higher in patients with idiopathic pulmonary fibrosis than in healthy controls. When assessed longitudinally, concentrations of six neoepitopes (BGM, C1M, C3A, C3M, C6M, and CRPM) were significantly higher in patients with progressive idiopathic pulmonary fibrosis (n=71) than in patients with stable idiopathic pulmonary fibrosis (n=60) by 6 months. Baseline concentrations of two neoepitopes were associated with increased mortality (C1M: HR 1·62 [95% CI 1·14–2·31], p=0·0069; C3A: 1·91 [1·06–3·46], p=0·032). The rate of change between baseline and 3 months of six neoepitopes (BGM: HR 1·084 [95% CI 1·03–1·14], p=0·0019; C1M: 1·01 [1·003–1·017], p=0·0039; C3M: 1·106 [1·045–1·170], p=0·0005; C5M: 1·003 [1·001–1·005], p=0·0011; C6M: 1·042 [1·007–1·078], p=0·017; and CRPM: 1·38 [1·16–1·63], p=0·0002) was strongly predictive of overall survival, and the increased risk was proportional to the magnitude of change in neoepitope concentrations. The strongest association with 3-month rate of biomarker change was recorded for CRPM; greater than 0 ng/mL per month conferred a HR of 2·16 (95% CI 1·15–4·07), whereas a rate greater than 1 ng/mL per month resulted in an HR 4·08 (2·14–7·8), and a rate greater than 1·7 ng/mL per month was associated with an HR 6·61 (2·74–15·94). Interpretation Concentrations of protein fragments generated by MMP activity are increased in the serum of individuals with idiopathic pulmonary fibrosis compared with healthy controls. Increased neoepitope concentrations were associated with disease progression, and the rate of this increase predicted survival. Serial measurements of neoepitopes have potential to be used as theragnostic biomarkers in clinical trials and to guide management of idiopathic pulmonary fibrosis. Funding GlaxoSmithKline R&D and the Medical Research Council.

The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease. In all of these diseases, a loss of diversity, paralleled by an over-representation of Proteobacteria (dysbiosis), has been related to disease severity and exacerbations. However, it is unknown whether dysbiosis is a cause or a consequence of the damage to bronchoalveolar surfaces.Finally, little is known about bacterial functionality and the interactions between viruses, fungi and bacteria. It is expected that future research in bacterial gene expressions, metagenomics longitudinal analysis and host–microbiome animal models will help to move towards targeted microbiome interventions in respiratory diseases.

Rhinovirus infection is followed by significantly increased frequencies of positive, potentially pathogenic sputum cultures in chronic obstructive pulmonary disease (COPD). However, it remains unclear whether these represent de novo infections or an increased load of organisms from the complex microbial communities (microbiome) in the lower airways.To investigate the effect of rhinovirus infection on the airway bacterial microbiome.Subjects with COPD (n = 14) and healthy control subjects with normal lung function (n = 17) were infected with rhinovirus. Induced sputum was collected at baseline before rhinovirus inoculation and again on Days 5, 15, and 42 after rhinovirus infection and DNA was extracted. The V3-V5 region of the bacterial 16S ribosomal RNA gene was amplified and pyrosequenced, resulting in 370,849 high-quality reads from 112 of the possible 124 time points.At 15 days after rhinovirus infection, there was a sixfold increase in 16S copy number (P = 0.007) and a 16% rise in numbers of proteobacterial sequences, most notably in potentially pathogenic Haemophilus influenzae (P = 2.7 × 10(-20)), from a preexisting community. These changes occurred only in the sputum microbiome of subjects with COPD and were still evident 42 days after infection. This was in contrast to the temporal stability demonstrated in the microbiome of healthy smokers and nonsmokers.After rhinovirus infection, there is a rise in bacterial burden and a significant outgrowth of Haemophilus influenzae from the existing microbiota of subjects with COPD. This is not observed in healthy individuals. Our findings suggest that rhinovirus infection in COPD alters the respiratory microbiome and may precipitate secondary bacterial infections.

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, fibrotic lung disease with no clear etiology and a paucity of therapeutic options. Nintedanib (previously known as BIBF 1120) is a tyrosine kinase receptor antagonist which inhibits a number of key receptors, including those for platelet derived growth factor (PDGF), vascular endothelial growth factor (VEGF), and fibroblast growth factor (FGF). These growth factors are profibrotic and each has been investigated as a potential standalone therapeutic target in IPF. Simultaneous inhibition of these receptors, with an analog of nintedanib, has proved to be effective in experimental animal models of pulmonary fibrosis. This observation, together with extensive safety and pharmacokinetic data from studies of nintedanib in malignancy, paved the way for the clinical development of this drug in IPF. The Phase IIb TOMORROW trial demonstrated that treatment with nintedanib may potentially slow decline in lung function, decrease the frequency of acute exacerbations, and improve quality of life in patients with IPF. While these observations are drawn from a single clinical trial, taken together with the preclinical data they suggest that nintedanib may yet become an important therapeutic option for individuals with IPF. The results of ongoing parallel, international, multicenter Phase III clinical trials are therefore eagerly awaited.

We performed a genome-wide association study in non-Hispanic white subjects with fibrotic idiopathic interstitial pneumonias (N=1616) and controls (N=4683); replication was assessed in 876 cases and 1890 controls. We confirmed association with TERT and MUC5B on chromosomes 5p15 and 11p15, respectively, the chromosome 3q26 region near TERC, and identified 7 novel loci (PMeta = 2.4×10−8 to PMeta = 1.1×10−19). The novel loci include FAM13A (4q22), DSP (6p24), OBFC1 (10q24), ATP11A (13q34), DPP9 (19p13), and chromosomal regions 7q22 and 15q14-15. Our results demonstrate that genes involved in host defense, cell-cell adhesion, and DNA repair contribute to the risk of fibrotic IIP.

Introduction: Idiopathic pulmonary fibrosis (IPF) is an invariably fatal condition characterised by a variable course; prolonged periods of apparent disease stability are often interspersed by dramatic and often cryptogenic acute deteriorations. These acute exacerbation are a significant cause of morbidity and mortality in IPF. For lung transplant recipients, daily hand held spirometery has been shown to be an effective means of detecting acute rejection episodes. This exploratory study aims to determine the utility of daily hand held spirometry in IPF. Methods: Patients with IPF were recruited from amongst new referrals to our unit. Baseline severity was assessed by FVC, DLco and 6 minute walk. Patients were given a hand held spirometer (Carefusion, UK) and provided with instruction on how to self-administer spirometry. Patients were asked to record daily FEV1 and FVC values. Results: To date, 19 subjects have been recruited; 17 male, age 66.5±7.6 years (mean ± SD). Overall the subjects have moderate to severe disease with FVC 74.2±21.8% predicted, DLco 40.6±13.5% predicted and 6 minute walk distance 325±120m. For subjects thus far completing over 4 weeks of diary monitoring (n=9), mean hand held FVC correlates well with formal clinic spirometry (r 2 0.902). Reproducibility of daily FVC has been good with mean variance 6.9% (range 3.0-12.1%). Discussion: This pilot study suggests that daily spirometery can be reliably and reproducibly performed by patients with IPF. By recording daily FVC it is to be hoped that it will be possible to gain a clearer insight in to the true natural history of IPF and detect, and thus treat, acute exacerbations at an early stage in their evolution.

We welcome the recent guidelines from the British Thoracic Society on the management of Mycobacterium tuberculosis infection and disease in patients with chronic kidney disease (CKD).1 We note the paucity of evidence (particularly from the UK) in this population regarding the use of interferon gamma release assays (IGRA) in screening patients for latent tuberculosis infection (LTBI). We present data to show the first UK-based cohort comparing the tuberculin skin test (TST) and the two commercially available IGRA—T-SPOT.TB (Oxford Immunotec, Abingdon, UK) and Quantiferon-Gold-in-Tube (Cellestis, Carnegie, Australia)—in a population of inpatients with CKD. It involves the follow-up of 61 patients from a renal inpatient ward who were …

Chronic obstructive pulmonary disease (COPD) is the most common chronic respiratory condition in adults and is characterized by progressive airflow limitation that is not fully reversible. The main etiological agents linked with COPD are cigarette smoking and biomass exposure but respiratory infection is believed to play a major role in the pathogenesis of both stable COPD and in acute exacerbations. Acute exacerbations are associated with more rapid decline in lung function and impaired quality of life and are the major causes of morbidity and mortality in COPD. Preventing exacerbations is a major therapeutic goal but currently available treatments for exacerbations are not very effective. Historically, bacteria were considered the main infective cause of exacerbations but with the development of new diagnostic techniques, respiratory viruses are also frequently detected in COPD exacerbations. This article aims to provide a state-of-the art review of current knowledge regarding the role of infection in COPD, highlight the areas of ongoing debate and controversy, and outline emerging technologies and therapies that will influence future diagnostic and therapeutic pathways in COPD.

Summary Introduction Patients with suspected active Pulmonary Tuberculosis (PTB) who are Acid-Fast Bacilli (AFB) smear negative or non-productive of sputum may undergo bronchoalveolar lavage. However, post-bronchoscopy sputum (PBS) sampling is not routine. The aim of this study was to establish the potential diagnostic value of PBS sampling. Methods A retrospective study of patients attending a London University hospital with microbiologically confirmed PTB between January 2004 and December 2010. Patients who were AFB smear negative or non-productive of sputum were eligible if sputum sampling was performed within 7 days of bronchoscopy. Results Over the study period, 236 patients had microbiologically confirmed smear negative PTB of which 57 patients were eligible for the study. 15 patients (26.3%) were infected with HIV. 19 patients (33.3%) converted to AFB sputum smear positivity post-bronchoscopy and 5 patients (8.8%) were exclusively AFB sputum smear positive on PBS microscopy. Mycobacterium tuberculosis was cultured from the PBS of 43 patients (75.4%) and of these, 4 (7.0%) were exclusively PBS culture positive. Conclusion PBS analysis can provide a simple method of rapidly diagnosing pulmonary tuberculosis. In this cohort, M. tuberculosis culture yield was increased by 7% through PBS sampling. This study has important infection control implications with nearly one third of patients becoming more infectious after bronchoscopy.

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal disorder with a variable disease trajectory. The aim of this study was to assess potential biomarkers to predict outcomes for people with IPF. METHOD: PROFILE is a large prospective longitudinal cohort of treatment-naive patients with IPF. We adopted a two-stage discovery and validation design using patients from the PROFILE cohort. For the discovery analysis, we examined 106 patients and 50 age and sex matched healthy controls from Nottingham University Hospitals NHS Trust and the Royal Brompton Hospital. We did an unbiased, multiplex immunoassay assessment of 123 biomarkers. We further investigated promising novel markers by immunohistochemical assessment of IPF lung tissue. In the validation analysis, we examined samples from 206 people with IPF from among the remaining 212 patients recruited to PROFILE Central England. We used the samples to attempt to replicate the biomarkers identified from the discovery analysis by use of independent immunoassays for each biomarker. We investigated the predictive power of the selected biomarkers to identify individuals with IPF who were at risk of progression or death. The PROFILE studies are registered on ClinicalTrials.gov, numbers NCT01134822 (PROFILE Central England) and NCT01110694 (PROFILE Royal Brompton Hospital). FINDINGS: In the discovery analysis, we identified four serum biomarkers (surfactant protein D, matrix metalloproteinase 7, CA19-9, and CA-125) that were suitable for replication. Histological assessment of CA19-9 and CA-125 suggested that these proteins were markers of epithelial damage. Replication analysis showed that baseline values of surfactant protein D (46·6 ng/mL vs 34·6 ng/mL, p=0·0018) and CA19-9 (53·7 U/mL vs 22·2 U/mL; p

Idiopathic pulmonary fibrosis (IPF) is characterised by excessive extracellular matrix (ECM) deposition and remodelling. Measuring this activity provides an opportunity to develop tools capable of identifying individuals at-risk of progression. Longitudinal change in markers of ECM synthesis was assessed in 145 newly-diagnosed individuals with IPF. Serum levels of collagen synthesis neoepitopes, PRO-C3 and PRO-C6 (collagen type 3 and 6), were elevated in IPF compared with controls at baseline, and progressive disease versus stable disease during follow up, (PRO-C3 p 0 vs. LOW slope, slope