Donald Sin

Decades of research have shown that the microbiome plays a fundamental role in how the immune system develops and how inflammatory responses are shaped and regulated. The gut and airways are two microbiome sites that have been extensively studied in chronic obstructive lung diseases like asthma and chronic obstructive pulmonary disease (COPD). Dysbiosis of the gut microbiome is implicated in the development and progression of asthma and to some extent COPD. The field of COPD microbiome research is rapidly growing and with advances in sequencing techniques, people have been able to characterize various omes that when collectively analyzed may provide insights into the mechanisms that underlie COPD pathogenesis. Emerging studies highlight a novel biological cross-talk between the microbiome and host cells in the small airways of patients with COPD. While host-microbiome interactions have been previously investigated in COPD, the effects of specific steroid formulations on this complex cross-talk remain obscure. In this thesis, we examine host transcriptome and small airway microbiome changes in a randomized controlled cohort of COPD patients treated with salmeterol/fluticasone, formoterol/budesonide or formoterol-only. Our findings reveal that in COPD patients treated with salmeterol/fluticasone, the expression levels of host genes (mainly inflammatory genes) are significantly related to changes in both the alpha diversity and the relative abundance of Haemophilus in the small airways. Collectively, our data argue that ICS therapy, particularly salmeterol/fluticasone, is tightly linked to alterations in host transcriptome and shifts in the microbiome composition of the small airway microenvironment. These data may provide insights into why some COPD patients treated with inhaled corticosteroids are at an increased risk for airway infection, including pneumonia.

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Chronic Obstructive Pulmonary Disease (COPD) is a common chronic airway disease characterized by progressive airway limitation and significant social and economic burden. Hospitalizations due to COPD account for the greatest portion of the economic costs for this disease. Unplanned COPD readmissions greatly impact the patient and healthcare costs and, to some extent, are related to gaps in the healthcare system such as discharge planning and post-discharge care and follow-up. Identifying and targeting factors contributing to unplanned rehospitalizations could reduce healthcare costs and improve COPD patients' health outcomes. We retrospectively examined the outcome and efficacy of a comprehensive case management program in reducing the length of stay and hospital readmissions in patients with COPD across five large hospitals in Vancouver, BC, Canada. A total of 1,564 patients with a clinical diagnosis of COPD were identified from 2,719 hospital admissions during the 3 years of study. The disease management program reduced COPD-related hospitalizations by 30% and hospitalizations for all causes by 13.6%. Similarly, the rate of readmission for all causes showed a significant decline, with hazard ratios (HRs) of 0.55 (year 1) and 0.51 (year 2) of intervention (P
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Long-acting β2-agonists (LABAs) are a staple of Chronic Obstructive Pulmonary Disease (COPD) maintenance treatment frequently prescribed to patients for prolonged bronchodilation. Recent studies have suggested that they may also be anti-inflammatory, as demonstrated by lowered neutrophil infiltration and lower mucus secretion. The mechanism of action behind these effects are unknown and further study is needed to elucidate the pathways involved. The purpose of this project was to study the effect of the LABA olodaterol on an in vitro model of the airway epithelium in response to an inflammatory stimulus. Primary airway epithelial cells derived from COPD and control non-COPD patient bronchial brushings were grown into air-liquid interface (ALI) cultures. Cells underwent priming with olodaterol in addition to respiratory syncytial virus (RSV) infection. Culture media was quantified for interleukin-8 (IL-8) secretion via ELISA. Whole cultures underwent immunohistochemistry for quantification of Muc5AC staining, an airway mucin protein. The 1HAEo- and the NCI-H292 cell lines were used to model the bronchial epithelium. Olodaterol was used to pre-treat both cell lines, after which either RSV or lipopolysaccharide (LPS) was added as an inflammatory stimulus and the IL-8 content was measured. Protein lysates were characterized using western blotting for the β2-adrenergic receptor (β2AR), the binding receptor for LABAs. siRNA was used to silence the β2AR. RT-qPCR was used to quantify the knockdown efficiency.ALI cultures showed that COPD subjects secreted higher baseline IL-8 levels than non-COPD controls, indicating that COPD subjects have an altered inflammatory phenotype. When both COPD and non-COPD ALIs were treated with olodaterol and RSV, olodaterol attenuated RSV-induced secretion of IL-8 and Muc5AC in both subject groups. In both 1HAEo- and NCI-H292 cells, RSV and LPS were able to stimulate high IL-8 secretion that was inhibited by treatment with olodaterol. siRNA gene silencing of β2AR in NCI-H292 cells negated olodaterol-mediated attenuation of LPS and RSV-induced IL-8 secretion, suggesting that the anti-inflammatory effect of olodaterol proceeds through the canonical binding receptor. LABAs such as olodaterol have clear anti-inflammatory effects in vitro and may hold clinical relevance. Further studies are needed to determine if these effects have a significant impact on patient therapy.

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Chronic obstructive pulmonary disease(COPD) is an age-related disease and demonstrates many biological hallmarks of aging including telomere shortening and epigenetic alterations. This study examined the relationship between telomere length, reflecting replicative senescence, and Alu and LINE-1(L1) methylation, reflecting one of the major epigenetic changes of peripheral blood leukocytes, and clinical outcomes, including lung function, health status, rate of exacerbations, and risk of mortality with different COPD stages.Using quantitative polymerase chain reaction, we measured the absolute telomere length(aTL) of DNA extracted from blood samples of 576 participants with moderate-to-severe COPD treated with either azithromycin or placebo in the Macrolide Azithromycin for Prevention of Exacerbations of COPD(MACRO) study. Using bisulfite pyrosequencing, we measured the percentage(%) Alu and L1 methylation of DNA extracted from blood samples of 495 participants with acute-exacerbating-COPD(AECOPD) in the COPD Rapid Transition Program(RTP), and 373 participants with non-COPD in the Canadian Cohort of Obstructive Lung Disease(CanCOLD).Participants with shorter aTL (defined as below the median cutoff value for aTL) had worse health status as defined by higher St. George’s Respiratory Questionnaire(SGRQ) scores (P=0.034). In the placebo arm, the rate of exacerbations (P=0.002) and the risk of mortality (P=0.015) were significantly higher in the shorter telomere group than in the longer telomere group. % Alu methylation was significantly related to FEV₁% predicted, FEV₁ in liters(L) and FEV₁/FVC ratio (P
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The 2009 H1N1 pandemic observed a large percentage of morbidity and mortality attributed to individuals with asthma. However, a consistent lack of preventative and therapeutic interventions failed to protect this vulnerable population. Vaccines are the most effective method of prevention, yet they take at least 6 months to be developed following outbreak of a pandemic strain. Meanwhile, antiviral drugs are the sole method of treatment, yet their clinical use can be restricted due to drug resistance. Hence, pre-planning is required to develop interventions that could protect the vulnerable asthmatic population prior to the occurrence of the next influenza pandemic. A Th2-skewed inflammatory response has been implicated in the development of some of the characteristics of asthma, whereby IL-4, IL-5, and IL-13 signaling promotes airway eosinophilia and lung remodeling. IL-4 and IL-13 signal through the common alpha subunit of the IL-4 receptor (IL-4Rα) to induce their effector function. Clinical trials have found the blockade of IL-4Rα to be highly effective at reducing the rate of asthmatic exacerbations. However, it has yet to be determined whether IL-4Rα blockade could protect against pandemic H1N1 (pH1N1)-mediated morbidity. We hypothesized that IL-4Rα blockade could be used as a treatment method in an established pH1N1 infection, and as a prevention method prior to and after pH1N1 infection, in a murine model of allergic asthma. Our findings indicate that both the treatment and prevention strategies of IL-4Rα blockade induce a significant reduction in pH1N1-mediated weight-loss in house dust-mite (HDM) sensitized mice. Furthermore, reduced weight-loss was associated with a significant reduction in the number of viral copies, indicating improved viral control. Lastly, IL-4Rα preventative intervention induced a significant reduction in the level of airway goblet cell metaplasia and the percentage of eosinophils in Bronchoalveolar Lavage (BAL), pointing to lessened allergic manifestations. While influenza pandemics are rare, they have a devastating effect on the most vulnerable individuals suffering from asthma. Hence, developing pharmaceutical interventions that could benefit this population are of outmost value. Findings from our study could be considered as a strategy to reduce the risk of complications in asthmatic individuals during an H1N1 influenza pandemic.

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Previous studies have demonstrated the existence of a gut-lung axis and its proposed role in altering immune response and respiratory disease pathogenesis. The lung and gut microbiomes have been individually studied in the context of Human Immunodeficiency Virus (HIV) infection; however the gut-lung axis in HIV remains relatively unexplored and requires further investigation. This study examined the microbiomes of the gut-lung axis and telomere attrition in HIV subjects using paired human lung and small intestine tissue.Paired lung and small intestine tissue autopsy specimens were obtained from ART-treated HIV-positive and HIV-negative donors through the National NeuroAIDS Tissue Consortium. Frozen samples were sectioned on dry ice and weighed for DNA extraction using the QIAGEN DNeasy® Blood and Tissue kit. Droplet digital PCR was used to measure bacterial load and quantitative PCR was performed to determine absolute telomere length (aTL). The 16S rRNA V4 region was sequenced using the MiSeq sequencing platform. Extraction negatives were run through the entire workflow alongside samples for quality control. Raw sequence reads were processed using QIIME2 (Quantitative Insights Into Microbial Ecology 2, v2018.2) followed by statistical analysis using R studio. Several t-tests, linear regression, PERMANOVA and ANCOVA were used for statistical analysis.Microbial composition was not found to differ significantly between ART-treated HIV-positive and HIV-negative donors in both lung and small intestine. However, bacterial load and abundance of individual amplicon sequence variants (ASVs) were found to be correlated in the lung and small intestine. Bacteroides was decreased in ART-treated HIV-positive donors and identified as one of the bacteria most likely to help explain differences between HIV-negative and ART-treated HIV-positive microbiomes. Telomere length was demonstrated to be shortened in lungs of ART-treated HIV-positive donors in comparison to HIV-negative but no differences were found between the two groups in the small intestine.ART-treated HIV donors present microbiomes similar to HIV-negative donors, suggesting that ART can provide the microenvironment necessary to maintain a “healthy” microbiome. Furthermore, microbiomes of the gut-lung axis have demonstrated a correlation in bacterial load and abundance of individuals ASVs, suggesting a strong relationship between the two sites in both ART-treated HIV donors and HIV-negative donors.

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Background: With the advent of antiretroviral therapy, patients infected with human immunodeficiency virus (HIV) can achieve near normal life expectancies. However, the risk for chronic illnesses such as chronic obstructive pulmonary disease (COPD) remains higher in HIV-infected patients despite improved survival. In disease states such as COPD, the microenvironment of the lungs can change dramatically, which creates permissive niches that allow for selective growth and reproduction of microbes. These changes may influence or be influenced by epigenetic alterations, specifically the methylation and demethylation of sites along the genetic code. We hypothesize that the microbiome and methylation profiles in the lower airway of HIV-infected patients are different compared to those of uninfected patients. These changes may prove relevant to the progression of chronic lung complications.Experimental Approach: This thesis examined small airway epithelial cells collected from patients infected with HIV and from uninfected subjects. Data on bacterial microbiome were obtained by using touchdown polymerase chain reaction (PCR) on epithelial cell DNA followed by MiSeq sequencing of specific variable regions on the bacterial 16S rRNA gene. For methylation profiling, DNA samples from the same airway epithelial cells were bisulfite converted and sequenced with the Illumina Infinium 450K HumanMethylation platform. Microbial diversity calculations, and linear regression models of methylation data were analyzed on Vegan and Limma packages in R, respectively.Results: The bacterial microbiome from small airway epithelial cells within the lungs of HIV-infected patients was distinct from that in uninfected patients. These changes included decreased diversity and decreased richness. Moreover, certain operational taxonomic units (OTUs) were able to distinguish HIV from non-HIV samples. Furthermore, a significant difference in global methylation patterns was identified.Conclusion: The microbiome and methylation profiles from small airway epithelial cells in HIV-infected individuals are significantly different from those in uninfected individuals, which may in part explain the heightened susceptibility of HIV-infected patients to COPD.

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Rationale: There are currently no generally accepted and validated blood tests available for diagnosing acute exacerbations of chronic obstructive pulmonary disease (AECOPD). There is an urgent need of biomarkers that can guide therapeutic management in AECOPD. Based on literature review, systemic inflammation and mild cardiac dysfunction are often associated with AECOPD. We hypothesized that certain protein markers can indeed be useful in tracking and diagnosing AECOPD progression.Methods: The study cohort consisted of 368 patients recruited in the chronic obstructive pulmonary disease (COPD) Rapid Transition Program who were hospitalized with a primary diagnosis of AECOPD, and 76 stable COPD patients who served as controls. We first determined the relationship of AECOPD of C-reactive protein (CRP) and the N-terminal of the prohormone brain natriuretic peptide (NT-proBNP). We then performed a discriminatory analysis using receiver-operating characteristics (ROC) curve in a logistic regression model. We compared the area under the curve (AUC) of 4 different combinations of CRP and NT-proBNP models. Lastly, we examined several potential biomarkers that were implicated in AECOPD.Results: The demographic data of the cohort and the controls were well matched, with an average age of 68 versus 65 years old, 64% versus 77% male, and a forced expiratory volume in 1 second (FEV1) % predicted of 52% versus 58%. The CRP and NT-proBNP levels at exacerbation onset were found to be the highest and progressively decreased over time. Of the 4 models of ROC curves, the leave-one-out cross-validated model including both CRP and NT-proBNP had an AUC of 0.80. This model replicated well in an external LEUKO dataset. On the iiother hand, D-Dimer, pulmonary and activation-regulated chemokine (PARC) and troponin I, showed minimal or no temporal changes during hospitalization and were no different than those with stable COPD.Conclusions: In summary, this thesis demonstrated that biomarkers such as CRP and NT-proBNP are significantly elevated during AECOPD and decreased with recovery. Secondly, a combination of CRP and NT-proBNP could discriminate patients who were hospitalized for their AECOPD from stable patients. Together, these two biomarkers show promise in diagnosing and tracking AECOPD.

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A disproportionately large number of asthmatics experienced morbidity and mortality during the 2009 H1N1 pandemic. To date, there is little information on the mechanisms behind this epidemiological and clinical observation. Using a murine asthma model, we sought to determine the effects of airway inflammation on host responses to pandemic H1N1 (pH1N1) infection. We hypothesized that mice with an allergic airway phenotype would have a greater viral susceptibility to pH1N1 infection and a dysregulated host response that prevents effective viral clearance and leads to increased burden of pulmonary inflammation, resulting in poor clinical outcomes. We established a murine allergic airway model using house dust mite (HDM) extract. We intranasally instilled male BALB/c mice with HDM or sham PBS daily for two weeks; after which we introduced a single intranasal dose of pH1N1 virus or control vehicle fluid (CAF). HDM or PBS instillation continued daily post-viral infection (pi) forming four groups: 1) sham-sensitized + CAF, 2) HDM-sensitized + CAF, 3) sham-sensitized + pH1N1, and 4) HDM-sensitized + pH1N1. Mice were weighed daily. Virus-infected animals were euthanized at 1-hr pi and on Day 1, 2, 4, 5, 6, and 8 pi and non-infected animals were euthanized on Day 0 and 8 pi. Viral titre, interferon-β (IFN β), and interferon-stimulated gene (ISG) expression patterns were determined by qPCR on RNA extracted from homogenized lung tissue. IFN β protein levels were evaluated by ELISA in bronchoalveolar lavage. Pulmonary inflammation was quantified using H&E stain on formalin-fixed paraffin-embedded lung tissue. HDM-sensitized animals exhibited significantly greater weight loss than sham-sensitized animals following infection. Also, HDM-sensitized mice had significantly higher viral titres on Day 8 pi as compared to sham-sensitized mice. Downstream ISG inductions were dampened in HDM-sensitized, virus-infected animals despite comparable initial IFN β response in HDM- and sham-sensitized mice. We also observed mixed-type pulmonary inflammation in HDM-sensitized mice following pH1N1 infection. Our data suggest dysregulated host ISG responses, combined with the overwhelming burden of pulmonary inflammation, contribute to impaired viral clearance and weight loss indicative of detrimental health outcomes in animals sensitized with HDM following pH1N1 infection.

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With recent advances in highly active antiretroviral therapy (HAART) and HIV-patient care, the longevity of individuals living with human immunodeficiency virus (HIV) infection has drastically increased. However, long term complications like chronic obstructive pulmonary disease (COPD) are synchronously more prevalent among this population. The fact that clinical manifestations of COPD develop in young HIV-infected individuals (20 to 50 years of age) compared older uninfected smokers (>50 years of age) suggests HIV-associated COPD may reflect a state of accelerated aging. In this thesis, we presented the clinical and HIV-related variables associated with telomere length, a measure of cellular age, in an HIV-infected cohort and explored the variables that determine poorer respiratory related health quality in this cohort. By using a novel technique to determine telomere length in peripheral leukocytes of HIV-infected and uninfected male subjects, we found that: firstly, telomere lengths were significantly shorter with HIV-infection even after adjusting for age, BMI, and smoking; secondly, telomere lengths were significantly and independently associated with age, FEV1(% of predicted), and soluble cluster of differentiation (sCD14); and thirdly, shorter telomere lengths were seen with worse emphysema scores as enumerated by computed tomography (CT) scans. Furthermore, the advantage of this new telomere length assay allowed us to determine that participants in our study demonstrated a “telomere age” roughly 40 years older than their biologic age, yet their respective slopes of decline with age remained parallel, when compared to an uninfected cohort. The St. George’s Respiratory Questionnaire was used to assess the influence of respiratory symptoms on a patient’s self-perceived health, social, and psychological status. Strikingly, we found HIV-infected patients are plagued with considerable respiratory limitations when compared to uninfected and even COPD counterparts. Also, we found that FEV1%pred, CD4 cell count, interleukin-6 (IL-6), but not telomere length were associated with worse respiratory health.

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Elevated concentrations of surfactant protein D (SP-D) in the serum have been associated with cardiovascular disease (CVD) mortality. It is not known, however, whether this relationship is causal or an epiphenomenon of lung disease or inflammation. The primary purpose of this thesis was to investigate the effects of SP-D on atherosclerosis. The overarching hypothesis driving this study is that SP-D is pro-atherogenic by modulating plasma lipids and systemic inflammation. These studies will enable development of SP-D as a biomarker of atherosclerosis, ischemic heart disease, and stroke and determine whether SP-D can be a therapeutic target to reduce CVD. To address the hypothesis, SP-D-knockout (KO) mice were crossed with apolipoprotein E (ApoE)-KO mice to produce mice deficient in both SP-D and ApoE. These mice were fed a high fat diet (HFD) for twelve weeks. We then measured the size of atherosclerotic lesions in aorta, determined the lipid profile in the serum, and measured circulating inflammatory cytokines and white blood cell counts in mice. We also challenged SP-D-deficient mice with lipopolysaccharide (LPS), which was microsprayed directly into the trachea. We then determined endothelial function of the descending aorta, 24 hours after the LPS challenge.We found that in the atherosclerotic plaque was significantly smaller in ApoE-KO mice lacking SP-D compared with apoE mice with intact SP-D. Absence of SP-D in the apo-E KO mice resulted in reduced levels of low density lipoprotein (LDL) cholesterol and total cholesterols, and a marked attenuation of certain parameters of systemic inflammation including neutrophil to lymphocyte ratios (NLR) and interleukin (IL)-6 in serum. Deficiency of SP-D was also associated with improved endothelial function following intratracheal LPS challenge. Together, these findings indicate that SP-D plays an active role in modulating lipid profile and systemic inflammation and most importantly may enhance atherosclerosis and thus contribute directly to excess cardiovascular morbidity and mortality.

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The evidence for the role of accelerated aging in COPD progression is growing and the senescence hypothesis is one possible molecular pathway by which COPD develops. Telomeres are used as a biomarker of cellular aging, and cellular aging is accelerated by the presence of oxidative stress and inflammation. Previous studies have shown that telomeres of peripheral blood cells are significantly shorter in COPD patients, but no studies to date explored the relationship of telomere length to important health outcomes such as mortality. Using samples from Lung Health Study (LHS), we examined the role of telomere length and polymorphisms in genes involved in aging process in health outcomes in COPD patients. There were no significant differences in age, sex, BMI, race of cumulative smoking exposure (pack-years) among 4 groups, divided on basis of telomere length. However, the risk of all cause mortality was similar across the first 3 quartiles (short telomere) but dropped significantly in the 4th quartile (longest telomere, hazard ratio (HR), 1.30). Compared to individuals in the 4th quartile of relative telomere length, the remaining participants had significantly higher risk of cancer mortality (HR, 1.48). Smoking status did not make a significant difference in leukocyte telomere length but when compared to non-COPD, age matched control group, all smoker groups in LHS had shorter telomeres. We also investigated the role of SNPs that were previously associated with leukocyte telomere length in disease outcome. Although no SNPs were associated with leukocyte telomere length, several SNPs of telomere biology genes were associated with cardiovascular and lung cancer mortality. The rate of telomere attrition is influenced by both extrinsic factors, such as inflammation and oxidative stress and intrinsic factors such as genetic predisposition. Here, we have shown that accelerated aging of peripheral blood cells, indicated by short telomeres, seems to play a role in disease outcome of COPD. Although we failed to show significant associations between leukocyte telomere length and genetic polymorphisms of telomere regulatory genes, the SNPs may contribute to risk of mortality. Further research is needed to elucidate the pathways underlying these observations.

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Granzymes, and particularly granzyme B (GzmB), are classically known to be involved in cell-mediated immunity and the induction of apoptosis through cell-specific targeting activity of cytotoxic T-lymphocytes in conjunction with perforin. However, recent literature has emerged that describes a largely overlooked role for GzmB in potentially mediating disease progression. This pathogenic role has been based on findings that GzmB can cleave extracellular matrix proteins while functioning independently of perforin. In chronic inflammatory lung states such as chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF), there are important implications including the degradation of extracellular matrix leading to airway remodelling, reduced lung integrity, and emphysema. The generation of autoantigens may also result from cleavage of extracellular matrix proteins, contributing to inflammation. We measured GzmB levels in plasma and lung tissue homogenates of COPD subjects by enzyme-linked immunosorbent assays (ELISAs) to determine the relationship with lung function, measured by FEV₁% predicted and FEV₁/FVC ratio, and clinical COPD severity. We found that GzmB levels in the lung were positively associated with lung function. The data raise the possibility that the GzmB we measured may be part of a protective inflammatory response in the microenvironment, or it may be pathogenic in the early but not the later phases of COPD. In CF subjects, we measured levels of GzmB and other inflammatory biomarkers in plasma samples to determine their relationship with lung function parameters and hospitalization status. While plasma levels of GzmB were not related to lung function or hospitalization status, we found that IL-6, IL-1β, and LPS levels were significantly higher in hospitalized patients, and CRP, IL-6, IL-1β, and LBP were significantly correlated with lung function impairment. The results provide evidence that systemic inflammation is an independent factor associated with disease progression in CF and suggests an important role for chronic bacterial colonization in the lungs. Further research is needed to validate the pathogenic contributions of GzmB in diseases with chronic inflammatory lung states and to delineate the mechanisms of such potential contributions.

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Until recently the normal human lung was thought to be sterile below the larynx, but recent reports from other laboratories indicate that a diverse microbiome exists and becomes less diverse in smokers. These reports led naturally to the hypothesis that pathogens emerging from the abnormal microbiome in smokers could drive the innate and adaptive immune response that has been associated with the pathology of peripheral lung abnormalities observed in Chronic Obstructive Pulmonary Disease (COPD). The purpose of the present study was to examine this hypothesis in human lung tissue. This began with a preliminary experiment in which DNA isolated from 2 samples from a control lung were compared to DNA isolated from 5 different samples of a severe COPD lung, using 75 based pair-end tag sequencing (metagenomic sequencing). For bacteria, a weighted average genome size representing bacterial species identified was applied and the results validated using PCR and qPCR assays. This preliminary experiment was followed by a qPCR, T-RFLP, and targeted sequencing analysis of the bacterial 16S rRNA gene in DNA isolated from single samples of frozen lung tissue obtained from 8 non-smoking and 8 smoking controls, 8 COPD (GOLD 4), and 8 cystic fibrosis patients. The metagenomic sequencing conducted in the preliminary study showed that the 5 samples from a single COPD patient had an average of 2.4 ± 0.7 bacteria/1000 human genomes while the smoking control had 1.6 ± 0.8 bacteria/1000 human genomes. The qPCR results obtained from a single sample from 32 different subjects showed that on average the 8 samples/group of non-smokers, smokers, and COPD (GOLD 4) patients had 34.5 ± 21.8, 44.3 ± 47.0, and 24.1 ± 36.9 bacteria/1000 human cells, respectively, while cystic fibrosis patients had (20 ± 54) x 10 4 bacteria /1000 human cells. T-RFLP analysis showed three distinct community compositions: smokers and non-smokers, cystic fibrosis, and COPD (GOLD 4) patients. These results confirm the presence of a small number of bacteria within the human lung of non-smoker and smoker controls and in COPD patients with a shift in bacterial composition in lungs of those with COPD (GOLD 4).

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