Mortality In Cystic Fibrosis Research Articles

A longitudinal analysis of chronic MRSA and Pseudomonas aeruginosa co-infection in cystic fibrosis: A single-center study

BackgroundFew studies have examined the association between chronic methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (PA) co-infection and health outcomes despite evidence that these pathogens alone contribute to higher morbidity and mortality in cystic fibrosis (CF). This study examines outcomes among CF patients with chronic MRSA and PA co-infection compared with patients with either or neither of these organisms. MethodsCF patients attending the care center in Atlanta, GA from 2007–2013 comprised the study cohort. Chronic co-infection was defined as >50% PA+ cultures and >50% MRSA+ cultures and modeled as time-varying. The rate of decline in lung function (FEV1) and the rate of IV treatments were the main outcomes. ResultsAmong all patients (N=354), chronic co-infection was associated with a significantly more rapid rate of FEV1 decline compared with patients with chronic PA alone [adjusted difference: −0.60% predicted/year (−1.13, −0.08)] and chronic MRSA alone [adjusted difference: −0.89% predicted/year (−1.56, −0.22)]. Rate of IV treatments was significantly higher among patients with chronic co-infection compared with patients with chronic PA alone [adjusted IRR: 1.24 (1.01, 1.52)] and chronic MRSA alone [adjusted IRR: 1.34 (1.03, 1.74)]. ConclusionsData from the Atlanta Care Center suggest that chronic MRSA and PA co-infection may be associated with increased rate of lung function decline and rate of intravenous antibiotics compared with patients with either pathogen alone.

Mortality from cystic fibrosis in Europe: 1994-2010.

To date, available mortality trends due to cystic fibrosis (CF) have been limited to the analysis of certain countries in different parts of the world showing that mortality trends have been constantly decreasing. However, no studies have examined Europe as a whole. The present study aims to analyze CF mortality trends by gender within the European Union (EU) and to quantify potential years of life lost (PYLL). Deaths from the 27 EU countries were obtained from the statistical office of the EU from the years 1994-2010. Crude and age-standardized mortality rates (ASR) were estimated for women and men using the standard European population, expressed in deaths per 1,000,000 persons. The PYLL from ages 0 up to 30 years were estimated. Trends were studied by a joinpoint regression analysis. During the study period, 5,130 deaths (2,443 in males and 2,687 in females) were identified. Females had a slightly higher mortality rate than males, with a downward trend observed for both genders. In males, the ASR changed from 1.34 in 1994 to 1.03 in 2010. In females, the ASR changed from 1.42 in 1994 to 0.92 in 2010. The mean age at death and PYLL increased for both genders. The joinpoint analysis did not identify any significant joinpoint for either gender for ASR or PYLL. Our data suggest a continued downward trend of CF mortality throughout the EU, with differences by country and gender.

Genome-wide Screen of Pseudomonas aeruginosa in Saccharomyces cerevisiae Identifies New Virulence Factors.

Pseudomonas aeruginosa is a human opportunistic pathogen that causes mortality in cystic fibrosis and immunocompromised patients. While many virulence factors of this pathogen have already been identified, several remain to be discovered. In this respect we set an unprecedented genome-wide screen of a P. aeruginosa expression library based on a yeast growth phenotype. Fifty-one candidates were selected in athree-round screening process. The robustness of the screen was validated by the selection of three well known secreted proteins including one demonstrated virulence factor, the protease LepA. Further in silico sorting of the 51 candidates highlighted three potential new Pseudomonas effector candidates (Pec). By testing the cytotoxicity of wild type P. aeruginosa vs. pec mutants toward macrophages and the virulence in the Caenorhabditis elegans model, we demonstrated that the three selected Pecs are novel virulence factors of P. aeruginosa. Additional cellular localization experiments in the host revealed specific localization for Pec1 and Pec2 that could inform about their respective functions.

Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung

ABSTRACTPulmonary infections caused by Pseudomonas aeruginosa are a recalcitrant problem in cystic fibrosis (CF) patients. While the clinical implications and long-term evolutionary patterns of these infections are well studied, we know little about the short-term population dynamics that enable this pathogen to persist despite aggressive antimicrobial therapy. Here, we describe a short-term population genomic analysis of 233 P. aeruginosa isolates collected from 12 sputum specimens obtained over a 1-year period from a single patient. Whole-genome sequencing and antimicrobial susceptibility profiling identified the expansion of two clonal lineages. The first lineage originated from the coalescence of the entire sample less than 3 years before the end of the study and gave rise to a high-diversity ancestral population. The second expansion occurred 2 years later and gave rise to a derived population with a strong signal of positive selection. These events show characteristics consistent with recurrent selective sweeps. While we cannot identify the specific mutations responsible for the origins of the clonal lineages, we find that the majority of mutations occur in loci previously associated with virulence and resistance. Additionally, approximately one-third of all mutations occur in loci that are mutated multiple times, highlighting the importance of parallel pathoadaptation. One such locus is the gene encoding penicillin-binding protein 3, which received three independent mutations. Our functional analysis of these alleles shows that they provide differential fitness benefits dependent on the antibiotic under selection. These data reveal that bacterial populations can undergo extensive and dramatic changes that are not revealed by lower-resolution analyses.

The Evolution of Cystic Fibrosis Care

Cystic fibrosis (CF) is the most common life-limiting inherited illness of whites. Most of the morbidity and mortality in CF stems from impaired mucociliary clearance leading to chronic, progressive airways obstruction and damage. Significant progress has been made in the care of patients with CF, with advances focused on improving mucociliary clearance, minimizing inflammatory damage, and managing infections; these advances include new antimicrobial therapies, mucolytic and osmotic agents, and antiinflammatory treatments. More recently, researchers have targeted disease-causing mutations using therapies to promote gene transcription and improve channel function, which has led to impressive physiologic changes in some patients. As we develop more advanced, allele-directed therapies for the management of CF, it will become increasingly important to understand the specific genetic and environmental interactions that cause the significant heterogeneity of lung disease seen in the CF population. This understanding of CF endotypes will allow for more targeted, personalized therapies for future patients. This article reviews the genetic and molecular basis of CF lung disease, the treatments currently available, and novel therapies that are in development.

Towards quantitative SERS detection of hydrogen cyanide at ppb level for human breath analysis

Lung infections with Pseudomonas aeruginosa (PA) is the most common cause of morbidity and mortality in cystic fibrosis (CF) patients. Due to its ready adaptation to the dehydrated mucosa of CF airways, PA infections tend to become chronic, eventually killing the patient. Hydrogen cyanide (HCN) at ppb level has been reported to be a PA biomarker. For early PA detection in CF children not yet chronically lung infected a non-invasive Surface-Enhanced Raman Spectroscopy (SERS)-based breath nanosensor is being developed. The triple bond between C and N in cyanide, with its characteristic band at ∼2133cm−1, is an excellent case for the SERS-based detection due to the infrequent occurrence of triple bonds in nature. For demonstration of direct HCN detection in the gas phase, a gold-coated silicon nanopillar substrate was exposed to 5ppm HCN in N2. Results showed that HCN adsorbed on the SERS substrate can be consistently detected under different experimental conditions and up to 9days after exposure. For detection of lower cyanide concentrations serial dilution experiments using potassium cyanide (KCN) demonstrated cyanide quantification down to 1μM in solution (corresponding to 18ppb). Lower KCN concentrations of 10 and 100nM (corresponding to 0.18 and 1.8ppb) produced SERS intensities that were relatively similar to the reference signal. Since HCN concentration in the breath of PA colonized CF children is reported to be ∼13.5ppb, the detection of cyanide is within the required range.

EPS06.8 Cigarette smoke-induced changes in phenotype and virulence in Pseudomonas aeruginosa

Objectives The health risks of either direct or passive smoking in Cystic Fibrosis (CF) have been well established (Kopp et al., 2015). Chronic infection with Pseudomonas aeruginosa (PA) is associated with considerable morbidity and mortality in CF, but the direct effect of cigarette smoke (CS) on PA has not been established. This study aimed to determine the impact of CS on PA phenotype and virulence. Methods Cigarette smoke extract (CSE) was prepared as described previously (Comer et al, 2012). Respiratory PA isolates (n = 4) and type strain (n = 1; ATCC 27853) were grown aerobically at 37°C +/– CSE and total viable count cfu/ml (TVC) determined at a range of CSE concentrations. Pyocyanin production was quantified following chloroform extraction. Biofilm formation was examined using a microtitre tray assay with quantification by crystal violet staining (Stepanovic et al., 2000). Virulence of PA was determined in the Galleria mellonella infection model. Results Growth of PA isolates was not completely inhibited by any concentration of CSE used. Both pyocyanin production and biofilm formation were significantly greater when isolates were exposed to CSE (biofilm: p G. mellonella model when PA isolates were exposed to CSE, indicating increased virulence. Conclusion Exposure of PA to CSE in vitro increases PA virulence. Further clinical studies are required to more fully correlate these changes in phenotype with clinical outcomes.

62 Molecular diagnosis of Pseudomonas aeruginosa infection in culture-negative samples from cystic fibrosis patients

Pseudomonas aeruginosa infection is the main cause of morbidity and mortality in cystic fibrosis (CF) patients. Cultural methods, the gold standard for bacterial detection, are hampered by alginate overproduction and the possible presence of dormant cells. This work aimed at developing a sensitive and specific diagnostic tool capable of detecting P. aeruginosa in culture-negative sputum from CF patients. DNA was extracted with the QIAamp DNA kit after cell spin-down to remove free DNA. Real-time PCR assays targeting 3 species-specific genes, ecfX, gyrB and oprL, were developed using previously designed and new primers. The LOD was determined by spiking different amounts of P. aeruginosa ATCC9027 in a negative sputum sample. The PCR protocol targeting oprL was found to be unreliable, whereas those targeting ecfX and gyrB proved to be effective (LOD 60 cells/ml and 102 cells/ml, respectively). Examination of 33 randomly selected culture-negative samples yielded 6 positive samples from 3 patients: all 6 were ecfX-positive and 2 were positive for ecfX and gyrB. After 1 and 5 months additional samples from patients 1 and 2 were culture-positive; patient 3 received a 4-month antibiotic cycle and 2 months later he resulted still culture-negative and PCR-positive. These findings highlight the value of the Real-time PCRs developed, especially the one targeting ecfX, in diagnosing P. aeruginosa infection in CF samples. Protocol effectiveness was confirmed by the eventual cultural recovery of P. aeruginosa in the two PCR-positive patients, who were found to have chronic CF. Findings also seem to provide further support for a role of dormant forms in recurrent CF infection.

317 When Pseudomonas aeruginosa and orthodontic appliances go together!

Context P. aeruginosa lung infection is an important cause of morbidity and mortality in cystic fibrosis (CF). Management of mouthbreathing associated with chronic nasal and sinus obstruction in CF patients requires orthodontic treatment. The oral cavity, containing hundreds of different commensal microorganisms, is a colonisation place for opportunistic bacteria such P. aeruginosa . We reported a case of an 11-years-old CF girl that became first colonized to P. aeruginosa after an orthodontic treatment. Objective The aim was to investigate clonality of oral and pulmonary P. aeruginosa isolates in this patient. Methods Twenty-eight strains were isolated from oral samples and lung expectorations between January to June 2014. The longitudinal study involved prospective cultures of different oral swabs and sputum. Strains were characterized by cultural methods, disc diffusion antibiograms, Pulsed Field Gel Electrophoresis (PFGE) and Multi Locus Sequence Typing (MLST). Results Strains showed different morphotypes and resistance phenotypes, probably involving mechanisms such as overproduction of the active MexXY efflux system and β-lactamase overproduction. Moreover, the study of the sequential isolates revealed a unique and novel sequence type, ST1852. In addition, all isolates revealed the same PFGE pattern, representing consequently a unique clonal cluster. Conclusion This study demonstrated for this patient that a single clone was found in oral cavity and lung expectoration. These results suggested that the oral cavity is a reservoir of P. aeruginosa for lung (re-)colonization. Orthodontic appliances containing methyl methacrylate favors the maintenance of these strains.

Lung diseases in children

Lung diseases belong to the most common acute and chronic childhood diseases. With specific diagnostics and therapy the outcome of many congenital and acquired pulmonary diseases in children and adults can be substantially improved. The aim of this review is the presentation and evaluation of important lung diseases in children taking recent developments into consideration. This article presents a review of the literature on selected acute and chronic lung diseases in children and adolescents. Acute pneumonia remains one of the most frequent causes of mortality in children worldwide. Antibiotic treatment has reduced the morbidity and mortality in Western industrialized countries; however, the treatment of complications, such as pleural empyema and lung abscesses remains challenging. With a prevalence of 10 %, asthma has evolved into the most common chronic disease in children and adolescents in Germany. Using anti-inflammatory inhalation therapy, effective control of asthma symptoms can be achieved in most patients. Cystic fibrosis (CF) remains the most common fatal inherited disease among Caucasians. More than 90 % of the mortality and morbidity of CF are caused by an early onset and progressive chronic obstructive lung disease. Approval of the first causal mutation-specific pharmacotherapy for a subgroup of patients with CF represents a milestone in individualized therapy of lung diseases. The pathogenesis of other rare chronic lung diseases including interstitial lung diseases (ILD) is still mostly unknown. Continuous improvement in the diagnostics and therapy is crucial to further improve the management and outcome of acute and chronic lung diseases in children. Pediatric pulmonology, as an interdisciplinary subspecialty at the interface of pediatrics, pulmonology and infectious diseases, plays a key role in the translation of scientific progress into clinical practice.

Oxygen uptake kinetics and exercise capacity in children with cystic fibrosis.

Exercise capacity, an objective measure of exercise intolerance, is known to predict quality of life and mortality in cystic fibrosis (CF). The mechanisms for exercise intolerance in patients with cystic fibrosis (CF), however, have yet to be fully elucidated. Accordingly, this study sought to investigate oxygen uptake kinetics and the impact of fat-free mass (FFM) on exercise capacity in young patients with CF. 16 young patients with CF (age 13 ± 4 years; 10 female) and 15 matched controls (age 14 ± 3 years; nine female) participated. Pulmonary function and a maximal exercise test on a cycle ergometer using the Godfrey protocol were performed. Exercise capacity (VO2 peak), VO2 response time (VO2 RT), and functional VO2 gain (ΔVO2 /ΔWR) were all determined. Lung function was the only demographic parameter significantly lower (P < 0.05) in CF compared to controls. Exercise capacity was lower in CF (P < 0.014) only when VO2 peak was normalized for FFM (43.5 ± 7.7 vs. 50.6 ± 7.4 ml/kg-FFM/min) or expressed as % predicted (70.1 ± 14.3 vs. 85.4 ± 16.0%). The VO2 RT was slower (36.1 ± 15.1 vs. 25.0 ± 12.4 sec; P = 0.03) and the ΔVO2 /ΔWR slope was lower (8.4 ± 3 ml/min/watt vs. 10.1 ± 1.4 ml/min/watt; P = 0.02) in patients compared to controls, respectively. In conclusion, a delayed VO2 response time coupled with the lower functional VO2 gain (ΔVO2 /ΔWR) suggest that young patients with CF have impairment in oxygen transport and oxygen utilization by the muscles. These data in addition to differences in VO2 peak normalized for FFM provide some insight that muscle mass and muscle metabolism contribute to exercise intolerance in CF.

Diabetes-related Mortality in Adults with Cystic Fibrosis. Role of Genotype and Sex

Diabetes is associated with increased mortality in cystic fibrosis. Aggressive screening and early institution of insulin treatment significantly reduced this risk over the period of 1992-2008. To determine if progressive improvement in cystic fibrosis-related diabetes (CFRD) mortality has continued since 2008, and examine associations with CFTR genotypes linked to pancreatic insufficiency and to sex. Chart review was performed on 664 patients followed from 2008 to 2012. Overall mortality for patients with CFRD was 1.8 per 100 person-years, compared with 0.5 in patients with CF without diabetes (P = 0.0002); neither rate changed significantly from mortality reported for 2003-2008. Genotype impacted both mortality and diabetes risk: adults with severe CFTR genotypes experienced greater mortality at every age older than 32 years than those with mild genotypes (P = 0.002), and the risk of developing CFRD was also greatly increased in those with severe genotypes (prevalence 60% in adult patients with severe vs. 14% in adults with mild mutations). CFRD had a direct influence on mortality because it was associated with increased risk of death within each genotype category (20 vs. 2%, P = 0.007 for mild; 12 vs. 4%, P = 0.012 for severe). There was also a sex difference in adults with severe CFTR genotypes; both mortality and CFRD prevalence were higher at every age in females than males. Despite substantial improvement over time, mortality for CFRD patients greater than 30 years remains higher than for patients with CF without diabetes.

CD4+ T cell epitopes of FliC conserved between strains of Burkholderia: implications for vaccines against melioidosis and cepacia complex in cystic fibrosis.

Burkholderia pseudomallei is the causative agent of melioidosis characterized by pneumonia and fatal septicemia and prevalent in Southeast Asia. Related Burkholderia species are strong risk factors of mortality in cystic fibrosis (CF). The B. pseudomallei flagellar protein FliC is strongly seroreactive and vaccination protects challenged mice. We assessed B. pseudomallei FliC peptide binding affinity to multiple HLA class II alleles and then assessed CD4 T cell immunity in HLA class II transgenic mice and in seropositive individuals in Thailand. T cell hybridomas were generated to investigate cross-reactivity between B. pseudomallei and the related Burkholderia species associated with Cepacia Complex CF. B. pseudomallei FliC contained several peptide sequences with ability to bind multiple HLA class II alleles. Several peptides were shown to encompass strong CD4 T cell epitopes in B. pseudomallei-exposed individuals and in HLA transgenic mice. In particular, the p38 epitope is robustly recognized by CD4 T cells of seropositive donors across diverse HLA haplotypes. T cell hybridomas against an immunogenic B. pseudomallei FliC epitope also cross-reacted with orthologous FliC sequences from Burkholderia multivorans and Burkholderia cenocepacia, important pathogens in CF. Epitopes within FliC were accessible for processing and presentation from live or heat-killed bacteria, demonstrating that flagellin enters the HLA class II Ag presentation pathway during infection of macrophages with B. cenocepacia. Collectively, the data support the possibility of incorporating FliC T cell epitopes into vaccination programs targeting both at-risk individuals in B. pseudomallei endemic regions as well as CF patients.

Esophageal Cancer in Patients With Cystic Fibrosis

Introduction: Incidence of gastrointestinal malignancies (GIM) is increased in patients with Cystic Fibrosis (CF), and development of GIM is further accelerated by immunosuppression. This is an issue of increasing concern for CF patients as their life expectancy has significantly increased over the recent decades and they often become recipients of solid organ transplants. We have previously published that initiation of screening colonoscopies at age 40 results in a high yield of advanced adenoma detection. However, CF patients are also at risk for other GIM, including esophageal cancer. We report two cases of esophageal cancer identified within the cohort of 95 CF patients age 40 and above and discuss the associated implications. Case 1: A 40-year-old male with history of CF s/p lung transplant presented for EGD to evaluate for odynophagia. He was found to have a large, partially obstructing esophageal tumor. Biopsies showed adenocarcinoma and staging revealed widely metastatic disease. He was started on palliative chemotherapy with initial response, but has unfortunately had disease progression resistant to additional chemotherapy. Case 2: A 52-year-old male with history of CF (not transplanted) presented for EGD to evaluate for dysphagia and weight loss. He was found to have a large, fungating mass in the middle third of the esophagus extending to the lesser curve of the stomach. Biopsy showed adenocarcinoma. Staging again revealed metastatic disease. The patient started on palliative chemotherapy but ultimately passed away from worsening disease. Although pulmonary complications are still the primary cause of death in CF patients, GIM are increasingly becoming important contributors to CF morbidity and mortality as this population ages. We have previously suggested earlier initiation of colorectal cancer screening in adult CF patients, especially since detection and removal of precursor polyp lesions has the potential of cancer prevention. Similarly, anecdotal data suggest that incidence of Barrett’s esophagus, the precursor lesion of esophageal adenocarcinoma, may be increased in CF. Identification of two advanced esophageal cancers within a relatively small patient cohort suggests that a more systematic evaluation of upper gastrointestinal tract screening standards may be warranted in CF. At the minimum these should be considered in the pre-transplant evaluation.

CFTR: a missing link between exocrine and endocrine pancreas?

CFTR: a missing link between exocrine and endocrine pancreas?

Neutrophil-mediated phagocytic host defense defect in myeloid Cftr-inactivated mice.

Cystic fibrosis (CF) is a common and deadly inherited disease, caused by mutations in the CFTR gene that encodes a cAMP-activated chloride channel. One outstanding manifestation of the disease is the persistent bacterial infection and inflammation in the lung, which claims over 90% of CF mortality. It has been debated whether neutrophil-mediated phagocytic innate immunity has any intrinsic defect that contributes to the host lung defense failure. Here we compared phagosomal CFTR targeting, hypochlorous acid (HOCl) production, and microbial killing of the neutrophils from myeloid Cftr-inactivated (Myeloid-Cftr−/−) mice and the non-inactivated control (Cftrfl10) mice. We found that the mutant CFTR that lacked Exon-10 failed to target to the neutrophil phagosomes. This dysfunction resulted in impaired intraphagosomal HOCl production and neutrophil microbial killing. In vivo lung infection with a lethal dose of Pseudomonas aeruginosa caused significantly higher mortality in the myeloid CF mice than in the controls. The myeloid-Cftr−/− lungs were deficient in bacterial clearance, and had sustained neutrophilic inflammation and stalled transition from early to late immunity. These manifestations recapitulated the symptoms of human CF lungs. The data altogether suggest that myeloid CFTR expression is critical to normal host lung defense. CFTR dysfunction in neutrophils compromises the phagocytic innate immunity, which may predispose CF lungs to infection.

Cystic fibrosis mortality trend in Italy from 1970 to 2011

BackgroundSurvival in cystic fibrosis (CF) has progressively improved and the female-gender disadvantage first described many years ago remains controversial. ObjectivesTo describe the mortality trend due to CF in Italy over the last decades; to verify the female-mortality disadvantage; to compare the comorbidities reported in death certificates of CF patients with those of the general population. MethodsMortality data were extracted from the database of underlying cause of death (1970–2011) and multiple causes of death (2003–2011) of the Italian National Institute of Statistics. Age-standardized mortality ratio (SMR) was calculated to compare the mortality between genders. The association between CF and other contributing causes of death was verified by calculating the age- and gender-adjusted proportional mortality ratio (PMR). ResultsDuring the study period, 1947 death certificates reported CF as the underlying cause of death. Mortality rate due to CF decreased in newborns and children and by the end of the 1990s also in adolescents and young adults. Adult mortality started to increase in the early 1990s. Over the whole period an excess in mortality was observed in young CF females (1–29years). The multiple causes of death database included 531 certificates with CF listed as cause of death. Pneumonia, chronic lower respiratory diseases, pulmonary heart disease and diseases of pulmonary circulation, aspergillosis, sepsis, renal failure, diabetes, malnutrition and amyloidosis were more frequently reported in CF death certificates compared to those of the general population (PMR>1). ConclusionsThis mortality trend provides evidence of a consistent improvement in survival, although the excess female-mortality persists despite aggressive treatment of CF lung disease. Several extra-pulmonary conditions associated with CF contributed to the morbidity leading to death.

291 Cystic fibrosis mortality trend in Italy between 1970 and 2011

291 Cystic fibrosis mortality trend in Italy between 1970 and 2011

Monitoring early lung disease in cystic fibrosis: where are we now?

<h3>Educational aims</h3> To understand which techniques are available to monitor early lung disease in cystic fibrosis, recognise difficulties inherent to each measure, and describe the use of tests in clinical practice or interventional trials. <h3>Summary</h3> It is a particular challenge to detect and monitor lung disease in children younger than 6 years old. Various methods exist that can reveal abnormality in young children, but each technique presents difficulties on performing the test or interpreting results. Most children with cystic fibrosis are now diagnosed shortly after birth, but it is still unclear how to evaluate new therapies, or at what age to initiate them. This review summarises current options for monitoring early disease, limitations of individual techniques and how evidence to date influences their use in research and clinical practice. <h3>Key points</h3> Lung disease remains the major cause of morbidity and mortality in cystic fibrosis Despite clear improvements in outcomes such as nutrition, the benefit of early diagnosis by newborn screening on pulmonary health in cystic fibrosis has yet to be proven. Early lung disease is challenging to detect and monitor in young children with cystic fibrosis, but there is an urgent requirement to define useful outcome measures in this population, particularly as new treatments emerge. Many techniques are available, but difficulties with measurement or interpretation must be recognised when appraising past studies, considering their use in practice or as endpoints in clinical trials. There is no superior monitoring test at present, but emerging evidence from longitudinal studies in children with cystic fibrosis will help define which are most useful.

Microbiota and Metabolite Profiling Reveal Specific Alterations in Bacterial Community Structure and Environment in the Cystic Fibrosis Airway during Exacerbation

Chronic polymicrobial infections of the lung are the foremost cause of morbidity and mortality in cystic fibrosis (CF) patients. The composition of the microbial flora of the airway alters considerably during infection, particularly during patient exacerbation. An understanding of which organisms are growing, their environment and their behaviour in the airway is of importance for designing antibiotic treatment regimes and for patient prognosis. To this end, we have analysed sputum samples taken from separate cohorts of CF and non-CF subjects for metabolites and in parallel, and we have examined both isolated DNA and RNA for the presence of 16S rRNA genes and transcripts by high-throughput sequencing of amplicon or cDNA libraries. This analysis revealed that although the population size of all dominant orders of bacteria as measured by DNA- and RNA- based methods are similar, greater discrepancies are seen with less prevalent organisms, some of which we associated with CF for the first time. Additionally, we identified a strong relationship between the abundance of specific anaerobes and fluctuations in several metabolites including lactate and putrescine during patient exacerbation. This study has hence identified organisms whose occurrence within the CF microbiome has been hitherto unreported and has revealed potential metabolic biomarkers for exacerbation.