51
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Raju SV, Kim H, Byzek SA, Tang LP, Trombley JE, Jackson P, Rasmussen L, Wells JM, Libby EF, Dohm E, Winter L, Samuel SL, Zinn KR, Blalock JE, Schoeb TR, Dransfield MT, Rowe SM. A ferret model of COPD-related chronic bronchitis. JCI Insight 2016; 1:e87536. [PMID: 27699245 DOI: 10.1172/jci.insight.87536] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death in the US. The majority of COPD patients have symptoms of chronic bronchitis, which lacks specific therapies. A major impediment to therapeutic development has been the absence of animal models that recapitulate key clinical and pathologic features of human disease. Ferrets are well suited for the investigation of the significance of respiratory diseases, given prior data indicating similarities to human airway physiology and submucosal gland distribution. Here, we exposed ferrets to chronic cigarette smoke and found them to approximate complex clinical features of human COPD. Unlike mice, which develop solely emphysema, smoke-exposed ferrets exhibited markedly higher numbers of early-morning spontaneous coughs and sporadic infectious exacerbations as well as a higher level of airway obstruction accompanied by goblet cell metaplasia/hyperplasia and increased mucus expression in small airways, indicative of chronic bronchitis and bronchiolitis. Overall, we demonstrate the first COPD animal model exhibiting clinical and pathologic features of chronic bronchitis to our knowledge, providing a key advance that will greatly facilitate the preclinical development of novel treatments for this disease.
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Affiliation(s)
| | | | | | | | | | | | | | - J Michael Wells
- Department of Medicine.,UAB Lung Health Center, and.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Emily Falk Libby
- Department of Medicine.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Erik Dohm
- Animal Resources Program, Birmingham, Alabama, USA
| | | | | | | | - J Edwin Blalock
- Department of Medicine.,UAB Lung Health Center, and.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Trenton R Schoeb
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Genetics, and
| | - Mark T Dransfield
- Department of Medicine.,UAB Lung Health Center, and.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Steven M Rowe
- Department of Medicine.,UAB Lung Health Center, and.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics.,Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Beck JM, Schloss PD, Venkataraman A, Twigg H, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med 2016; 192:1335-44. [PMID: 26247840 DOI: 10.1164/rccm.201501-0128oc] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RATIONALE Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear. OBJECTIVES We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects. METHODS Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38). MEASUREMENTS AND MAIN RESULTS Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects. CONCLUSIONS The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.
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Affiliation(s)
- James M Beck
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.,2 Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado
| | - Patrick D Schloss
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Arvind Venkataraman
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Homer Twigg
- 4 Department of Medicine, Indiana University, Indianapolis, Indiana
| | - Kathleen A Jablonski
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | | | - Thomas B Campbell
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Emily S Charlson
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristina Crothers
- 8 Department of Medicine, University of Washington, Seattle, Washington
| | - Jeffrey L Curtis
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,9 Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Kimberly L Drews
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Sonia C Flores
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Andrew P Fontenot
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Mary A Foulkes
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Ian Frank
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elodie Ghedin
- 10 Department of Computational and Systems Biology and
| | - Laurence Huang
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Susan V Lynch
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Alison Morris
- 12 Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brent E Palmer
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Thomas M Schmidt
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Erica Sodergren
- 13 The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Vincent B Young
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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53
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Understanding persistent bacterial lung infections: clinical implications informed by the biology of the microbiota and biofilms. ACTA ACUST UNITED AC 2016; 23:57-66. [PMID: 27004018 DOI: 10.1097/cpm.0000000000000108] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The infections found in chronic obstructive pulmonary disease, cystic fibrosis, and bronchiectasis share a number of clinical similarities, the most striking of which is bacterial persistence despite the use of antibiotics. These infections have been clinically described using culture-based methods usually performed on sputum samples, and treatment has been directed towards the bacteria found in this manner. Unfortunately the clinical response to antibiotics is frequently not predictable based on these cultures, and the role of these cultured organisms in disease progression has been debated. The past 20 years have seen a revolution in the techniques used to describe bacterial populations and their growth patterns. These techniques have revealed these persistent lung infections are vastly more complicated than described by traditional, and still widely relied upon, sputum cultures. A better understanding of the initiation and evolution of these infections, and better clinical tools to describe them, will dramatically alter the way patients are cared for. While clinical tests to more accurately describe these infections are not yet available, the better appreciation of these infections afforded by current science should enlighten practitioners as to the care of their patients with these diseases.
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54
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Margelidon-Cozzolino V, Chbini K, Freymond N, Devouassoux G, Belaaouaj A, Pacheco Y. [COPD: An early disease]. REVUE DE PNEUMOLOGIE CLINIQUE 2016; 72:49-60. [PMID: 26657351 PMCID: PMC7126852 DOI: 10.1016/j.pneumo.2015.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/16/2015] [Indexed: 05/04/2023]
Abstract
This general review deals with the mechanisms which underlie the genetic factors in COPD. Many cellular and biochemical mechanisms occur in bronchial inflammation. We present the experimental models of COPD, insisting on the importance of oxydative stress, and on recent knowledge about the lung microbiome. Starting from this pathophysiology basis, we show how various genetic targets are able to interfere with the disease model. Thanks to these genetic targets, new markers in exhaled breath condensates and new drug targets are rising.
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Affiliation(s)
- V Margelidon-Cozzolino
- Service de pneumologie A, centre hospitalier de Lyon Sud, hospices civils de Lyon, faculté de médecine, université Claude-Bernard Lyon 1, 69310 Pierre-Bénite, France.
| | - K Chbini
- Service de cardiologie, CHU Mohammed VI, faculté de médecine et de pharmacie, université Cadi Ayyad, Marrakech, Maroc
| | - N Freymond
- Service de pneumologie A, centre hospitalier de Lyon Sud, hospices civils de Lyon, 69310 Pierre-Bénite, France
| | - G Devouassoux
- Service de pneumologie, hôpital de la Croix Rousse, hospices civils de Lyon, faculté de médecine Lyon Sud, université Claude-Bernard Lyon 1, 69005 Lyon, France
| | - A Belaaouaj
- Inserm 1111, faculté de médecine Lyon Sud, chemin du Grand-Revoyet, 69310 Pierre-Bénite, France
| | - Y Pacheco
- Service de pneumologie A, centre hospitalier de Lyon Sud, hospices civils de Lyon, faculté de médecine Lyon Sud, université Claude-Bernard Lyon 1, 69310 Pierre-Bénite, France
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55
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Wang DD, Zheng MQ, Zhang N, An CL. Investigation of Pneumocystis jirovecii colonization in patients with chronic pulmonary diseases in the People's Republic of China. Int J Chron Obstruct Pulmon Dis 2015; 10:2079-85. [PMID: 26491278 PMCID: PMC4598221 DOI: 10.2147/copd.s89666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The detection of Pneumocystis jirovecii DNA in respiratory specimen from individuals who do not have signs or symptoms of pneumonia has been defined as colonization. The role of P. jirovecii colonization in the development or progression of various lung diseases has been reported, but little information about P. jirovecii colonization in patients is available in the People's Republic of China. OBJECTIVE To determine the prevalence of P. jirovecii colonization in patients with various pulmonary diseases, including the acute and stable stage of COPD, interstitial lung diseases, cystic fibrosis, and chronic bronchiectasis. MATERIALS AND METHODS A loop-mediated isothermal amplification (LAMP) and a conventional polymerase chain reaction (PCR) method for detecting P. jirovecii were developed. Ninety-eight HIV-negative patients who were followed-up and who had undergone bronchoscopy for diagnosis of various underlying respiratory diseases were included in the study. Sputa of these patients were analyzed with LAMP amplification of P. jirovecii gene. In addition, conventional PCR, Giemsa and Gomori's methenamine silver nitrate staining assays were applied to all specimens. RESULTS The sensitivity and specificity test showed that there was no cross-reaction with other fungi or bacteria in detecting the specific gene of P. jirovecii by LAMP, and the minimum detection limits by LAMP was 50 copies/mL. P. jirovecii DNA was detected in 62 of 98 (63.3%) sputa specimens by LAMP assay and 22.45% (22/98) by conventional PCR. However, no P. jirovecii cysts were found by Giemsa and Gomori's methenamine silver nitrate in all of gene-positive specimens. CONCLUSION The results of our study showed that prevalence of P. jirovecii colonization is particularly high in patients with chronic pulmonary diseases in the People's Republic of China, and the LAMP method is better for evaluation of the colonization of P. jirovecii in sputum specimen than conventional PCR.
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Affiliation(s)
- Dong-Dong Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Ming-Quan Zheng
- Department of Microbiology and Parasitology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China ; Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Nan Zhang
- Department of Microbiology and Parasitology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Chun-Li An
- Department of Microbiology and Parasitology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
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56
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Su J, Liu HY, Tan XL, Ji Y, Jiang YX, Prabhakar M, Rong ZH, Zhou HW, Zhang GX. Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD. PLoS One 2015; 10:e0130736. [PMID: 26147303 PMCID: PMC4493005 DOI: 10.1371/journal.pone.0130736] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/24/2015] [Indexed: 12/25/2022] Open
Abstract
The changes in the microbial community structure during acute exacerbations of severe chronic obstructive pulmonary disease (COPD) in hospitalized patients remain largely uncharacterized. Therefore, further studies focused on the temporal dynamics and structure of sputum microbial communities during acute exacerbation of COPD (AECOPD) would still be necessary. In our study, the use of molecular microbiological techniques provided insight into both fungal and bacterial diversities in AECOPD patients during hospitalization. In particular, we examined the structure and varieties of lung microbial community in 6 patients with severe AECOPD by amplifying 16S rRNA V4 hyper-variable and internal transcribed spacer (ITS) DNA regions using barcoded primers and the Illumina sequencing platform. Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity. Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences. The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella. Our findings highlight that COPD patients have personalized structures and varieties in sputum microbial community during hospitalization periods.
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Affiliation(s)
- Jin Su
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China; Department of Respiratory Physicians, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Hai-yue Liu
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - Xi-lan Tan
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China; Department of Hospital Infection Management, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yong Ji
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - Yun-xia Jiang
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - M Prabhakar
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - Zu-hua Rong
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - Hong-wei Zhou
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
| | - Guo-xia Zhang
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China
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Aho VTE, Pereira PAB, Haahtela T, Pawankar R, Auvinen P, Koskinen K. The microbiome of the human lower airways: a next generation sequencing perspective. World Allergy Organ J 2015; 8:23. [PMID: 26140078 PMCID: PMC4468963 DOI: 10.1186/s40413-015-0074-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 06/01/2015] [Indexed: 12/22/2022] Open
Abstract
For a long time, the human lower airways were considered a sterile environment where the presence of microorganisms, typically revealed by culturing, was interpreted as an abnormal health state. More recently, high-throughput sequencing-based studies have led to a shift in this perception towards the notion that even in healthy conditions the lower airways show either transient presence or even permanent colonization by microorganisms. However, challenges related to low biomass and contamination in samples still remain, and the composition, structure and dynamics of such putative microbial communities are unclear. Here, we review the evidence for the presence of microbial communities in the human lower airways, in healthy subjects and within the context of medical conditions of interest. We also provide an overview of the methodology pertinent to high-throughput sequencing studies, specifically those based on amplicon sequencing, including a discussion of good practices and common pitfalls.
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Affiliation(s)
- Velma T. E. Aho
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
| | - Pedro A. B. Pereira
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Ruby Pawankar
- Division of Allergy, Department of Pediatrics, Nippon Medical School, Tokyo, Japan
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
| | - Kaisa Koskinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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58
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Excess costs of comorbidities in chronic obstructive pulmonary disease: a systematic review. PLoS One 2015; 10:e0123292. [PMID: 25875204 PMCID: PMC4405814 DOI: 10.1371/journal.pone.0123292] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/26/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. Comorbidities are often reported in patients with COPD and may influence the cost of care. Yet, the extent by which comorbidities affect costs remains to be determined. OBJECTIVES To review, quantify and evaluate excess costs of comorbidities in COPD. METHODS Using a systematic review approach, Pubmed and Embase were searched for studies analyzing excess costs of comorbidities in COPD. Resulting studies were evaluated according to study characteristics, comorbidity measurement and cost indicators. Mark-up factors were calculated for respective excess costs. Furthermore, a checklist of quality criteria was applied. RESULTS Twelve studies were included. Nine evaluated comorbidity specific costs; three examined index-based results. Pneumonia, cardiovascular disease and diabetes were associated with the highest excess costs. The mark-up factors for respective excess costs ranged between 1.5 and 2.5 in the majority of cases. On average the factors constituted a doubling of respective costs in the comorbid case. The main cost driver, among all studies, was inpatient cost. Indirect costs were not accounted for by the majority of studies. Study heterogeneity was high. CONCLUSIONS The reviewed studies clearly show that comorbidities are associated with significant excess costs in COPD. The inclusion of comorbid costs and effects in future health economic evaluations of preventive or therapeutic COPD interventions seems highly advisable.
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Abstract
Until recently, the airways were thought to be sterile unless infected; however, a shift towards molecular methods for the quantification and sequencing of bacterial DNA has revealed that the airways harbour a unique steady-state microbiota. This paradigm shift is changing the way that respiratory research is approached, with a clear need now to consider the effects of host-microorganism interactions in both healthy and diseased lungs. We propose that akin to recent discoveries in intestinal research, dysbiosis of the airway microbiota could underlie susceptibility to, and progression and chronicity of lung disease. In this Opinion article, we summarize current knowledge of the airway microbiota and outline how host-microorganism interactions in the lungs and other tissues might influence respiratory health and disease.
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60
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Redinbo MR. The microbiota, chemical symbiosis, and human disease. J Mol Biol 2014; 426:3877-91. [PMID: 25305474 PMCID: PMC4252811 DOI: 10.1016/j.jmb.2014.09.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/07/2014] [Accepted: 09/19/2014] [Indexed: 02/07/2023]
Abstract
Our understanding of mammalian-microbial mutualism has expanded by combing microbial sequencing with evolving molecular and cellular methods, as well as unique model systems. Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments-nasal, lung, and gastrointestinal tract-is reviewed with a focus on new knowledge about the taxa, species, proteins, and chemistry that promote health and impact progression toward disease. The information presented is further organized by specific diseases now associated with the microbiota: Staphylococcus aureus infection and rhinosinusitis in the nasal-sinus mucosa, as well as cystic fibrosis, chronic obstructive pulmonary disorder, and asthma in the pulmonary tissues. For the vast and microbially dynamic gastrointestinal compartment, several disorders are considered, including obesity, atherosclerosis, Crohn's disease, ulcerative colitis, drug toxicity, and even autism. Our appreciation of the chemical symbiosis ongoing between human systems and the microbiota continues to grow and suggests new opportunities for modulating this symbiosis using designed interventions.
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Affiliation(s)
- Matthew R Redinbo
- Department of Chemistry, Department of Biochemistry and Biophysics, Department of Microbiology and Immunology, College of Arts and Sciences, Integrative Program for Biological and Genome Sciences, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA.
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61
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Sze MA, Abbasi M, Hogg JC, Sin DD. A comparison between droplet digital and quantitative PCR in the analysis of bacterial 16S load in lung tissue samples from control and COPD GOLD 2. PLoS One 2014; 9:e110351. [PMID: 25329701 PMCID: PMC4199711 DOI: 10.1371/journal.pone.0110351] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/18/2014] [Indexed: 12/21/2022] Open
Abstract
Background Low biomass in the bacterial lung tissue microbiome utilizes quantitative PCR (qPCR) 16S bacterial assays at their limit of detection. New technology like droplet digital PCR (ddPCR) could allow for higher sensitivity and accuracy of quantification. These attributes are needed if specific bacteria within the bacterial lung tissue microbiome are to be evaluated as potential contributors to diseases such as chronic obstructive pulmonary disease (COPD). We hypothesize that ddPCR is better at quantifying the total bacterial load in lung tissue versus qPCR. Methods Control (n = 16) and COPD GOLD 2 (n = 16) tissue samples were obtained from patients who underwent lung resection surgery, were cut on a cryotome, and sections were assigned for use in quantitative histology or for DNA extraction. qPCR and ddPCR were performed on these samples using primers spanning the V2 region on the 16S rRNA gene along with negative controls. Total 16S counts were compared between the two methods. Both methods were assessed for correlations with quantitative histology measurements of the tissue. Results There was no difference in the average total 16S counts (P>0.05) between the two methods. However, the negative controls contained significantly lower counts in the ddPCR (0.55 ± 0.28 16S/uL) than in the qPCR assay (1.00 ± 0.70 16S copies) (P <0.05). The coefficient of variation was significantly lower for the ddPCR assay (0.18 ± 0.14) versus the qPCR assay (0.62 ± 0.29) (P<0.05). Conclusion Overall the ddPCR 16S assay performed better by reducing the background noise in 16S of the negative controls compared with 16S qPCR assay.
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Affiliation(s)
- Marc A. Sze
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - James C. Hogg
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- * E-mail:
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Whiteson KL, Bailey B, Bergkessel M, Conrad D, Delhaes L, Felts B, Harris JK, Hunter R, Lim YW, Maughan H, Quinn R, Salamon P, Sullivan J, Wagner BD, Rainey PB. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography. Am J Respir Crit Care Med 2014; 189:1309-15. [PMID: 24702670 DOI: 10.1164/rccm.201312-2129pp] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A continuously mixed series of microbial communities inhabits various points of the respiratory tract, with community composition determined by distance from colonization sources, colonization rates, and extinction rates. Ecology and evolution theory developed in the context of biogeography is relevant to clinical microbiology and could reframe the interpretation of recent studies comparing communities from lung explant samples, sputum samples, and oropharyngeal swabs. We propose an island biogeography model of the microbial communities inhabiting different niches in human airways. Island biogeography as applied to communities separated by time and space is a useful parallel for exploring microbial colonization of healthy and diseased lungs, with the potential to inform our understanding of microbial community dynamics and the relevance of microbes detected in different sample types. In this perspective, we focus on the intermixed microbial communities inhabiting different regions of the airways of patients with cystic fibrosis.
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63
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Ryu E, Hasegawa A, Saegusa S, Ichiki H. An investigation of canine leptospiral antibodies in Tokyo and Yokohama. Comparison of Canine Positive rates between rapid microscopic agglutination test and Schüffner-Mochtar test. INTERNATIONAL JOURNAL OF ZOONOSES 1974; 1:82-90. [PMID: 4468963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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