Airway microbiota across age and disease spectrum in cystic fibrosis

European Respiratory Journal

Volumn 50, Issue 5, 2017, Pages

  Zemanick, Edith T ^a   Wagner, Brandie D ^a,b   Robertson, Charles E ^a   Ahrens, Richard C ^c   Chmiel, James F ^d   Clancy, John P ^e   Gibson, Ronald L ^f   Harris, William T ^g   Kurland, Geoffrey ^h   Laguna, Theresa A ⁱ   McColley, Susanna A ^j   McCoy, Karen ^k   Retsch Bogart, George ^l   Sobush, Kurtis T ^m   Zeitlin, Pamela L ⁿ   Stevens, Mark J ^a   Accurso, Frank J ^a   Sagel, Scott D ^a   Harris, J Kirk ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b Food Science and Human Nutrition   (United States)

^c UNIVERSITY OF IOWA   (United States)

^d CASE WESTERN RESERVE UNIVERSITY   (United States)

^e CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^f UNIVERSITY OF WASHINGTON   (United States)

^g UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^h CHILDREN S HOSPITAL OF PITTSBURGH   (United States)

ⁱ UNIVERSITY OF MINNESOTA   (United States)

^j NORTHWESTERN UNIVERSITY   (United States)

^k NATIONWIDE CHILDREN S HOSPITAL   (United States)

^l UNIVERSITY OF NORTH CAROLINA   (United States)

^m SAINT LOUIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁿ JOHNS HOPKINS UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; BACTERIAL DNA;

ACHROMOBACTER; ADULT; AGE; AIRWAY MICROBIOTA; ARTICLE; BACTERIAL LOAD; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BORDETELLA; BRONCHOALVEOLAR LAVAGE FLUID; BURKHOLDERIA; CONTROLLED STUDY; CORYNEBACTERIUM; CYSTIC FIBROSIS; DISEASE ASSOCIATION; DISEASE COURSE; DISEASE EXACERBATION; DISEASE SPECTRUM; DNA SEQUENCE; FEMALE; HAEMOPHILUS; HUMAN; INFLAMMATION; MAJOR CLINICAL STUDY; MALE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROFLORA; MORAXELLA; MYCOPLASMA; NEISSERIA; NONHUMAN; POPULATION ABUNDANCE; PREVOTELLA; PRIORITY JOURNAL; PSEUDOMONAS; RESPIRATORY TRACT INFLAMMATION; SEQUENCE ANALYSIS; STAPHYLOCOCCUS; STENOTROPHOMONAS; STREPTOCOCCUS; TAXONOMIC IDENTIFICATION; VEILLONELLA; ADOLESCENT; CASE CONTROL STUDY; CHILD; CLINICAL TRIAL; COMPLICATION; INFANT; LUNG; MICROBIOLOGY; MIDDLE AGED; MULTICENTER STUDY; MULTIVARIATE ANALYSIS; PRESCHOOL CHILD; REGRESSION ANALYSIS; SPUTUM; YOUNG ADULT;

ADOLESCENT; ADULT; AGE FACTORS; BRONCHOALVEOLAR LAVAGE FLUID; CASE-CONTROL STUDIES; CHILD; CHILD, PRESCHOOL; CYSTIC FIBROSIS; DISEASE PROGRESSION; DNA, BACTERIAL; FEMALE; HUMANS; INFANT; INFLAMMATION; LUNG; MALE; MICROBIOTA; MIDDLE AGED; MULTIVARIATE ANALYSIS; REGRESSION ANALYSIS; SPUTUM; YOUNG ADULT;

EID: 85034983492     PISSN: 09031936     EISSN: 13993003     Source Type: Journal    
DOI: 10.1183/13993003.00832-2017     Document Type: Article

References (51)

1. Gibson RL, Burns JL, Ramsey BW. Pathophysiology and management of pulmonary infections in cystic fibrosis. Am J Respir Crit Care Med 2003; 168: 918-951.
2. Razvi S, Quittell L, Sewall A, et al. Respiratory microbiology of patients with cystic fibrosis in the United States, 1995-2005. Chest 2009; 136: 1554-1560.
3. Sibley CD, Rabin H, Surette MG. Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol 2006; 1: 53-61.
4. Bittar F, Richet H, Dubus JC, et al. Molecular detection of multiple emerging pathogens in sputa from cystic fibrosis patients. PLoS One 2008; 3: e2908.
5. Rogers GB, Carroll MP, Serisier DJ, et al. Characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16S ribosomal DNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol 2004; 42: 5176-5183.
6. Zhao J, Schloss PD, Kalikin LM, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA 2012; 109: 5809-5814.
7. Cox MJ, Allgaier M, Taylor B, et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One 2010; 5: e11044.
8. Stressmann FA, Rogers GB, Klem ER, et al. Analysis of the bacterial communities present in lungs of patients with cystic fibrosis from American and British centers. J Clin Microbiol 2011; 49: 281-291.
9. Stressmann FA, Rogers GB, van der Gast CJ, et al. Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience. Thorax 2012; 67: 867-873.
10. Tunney MM, Field TR, Moriarty TF, et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med 2008; 177: 995-1001.
11. Worlitzsch D, Rintelen C, Bohm K, et al. Antibiotic-resistant obligate anaerobes during exacerbations of cystic fibrosis patients. Clin Microbiol Infect 2009; 15: 454-460.
12. Sibley CD, Grinwis ME, Field TR, et al. Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PLoS One 2011; 6: e22702.
13. Goddard AF, Staudinger BJ, Dowd SE, et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci USA 2012; 109: 13769-13774.
14. Whiteson KL, Bailey BF, Bergkessel MF, et al. 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: 1309-1315.
15. Mogayzel PJ Jr, Naureckas ET, Robinson KA, et al. Cystic Fibrosis Foundation pulmonary guideline. pharmacologic approaches to prevention and eradication of initial Pseudomonas aeruginosa infection. Ann Am Thorac Soc 2014; 11: 1640-1650.
16. Jain K, Wainwright C, Smyth AR. Bronchoscopy-guided antimicrobial therapy for cystic fibrosis. Cochrane Database Syst Rev 2013; 12: CD009530.
17. Wainwright CE, Vidmar S, Armstrong DS, et al. Effect of bronchoalveolar lavage-directed therapy on Pseudomonas aeruginosa infection and structural lung injury in children with cystic fibrosis: a randomized trial. JAMA 2011; 306: 163-171.
18. Moodie M, Lal A, Vidmar S, et al. Costs of bronchoalveolar lavage-directed therapy in the first 5 years of life for children with cystic fibrosis. J Pediatr 2014; 165: 564-569.
19. Hilty M, Burke C, Pedro H, et al. Disordered microbial communities in asthmatic airways. PLoS One 2010; 5: e8578.
20. Erb-Downward JR, Thompson DL, Han MK, et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS One 2011; 6: e16384.
21. Molyneaux PL, Cox MJ, Willis-Owen SA, et al. The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2014; 190: 906-913.
22. Morris A, Beck JM, Schloss PD, et al. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013; 187: 1067-1075.
23. Harris JK, De Groote MA, Sagel SD, et al. Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci USA 2007; 104: 20529-20533.
24. Renwick J, McNally P, John B, et al. The microbial community of the cystic fibrosis airway is disrupted in early life. PLoS One 2014; 9: e109798.
25. Zemanick ET, Wagner BD, Anthony M, et al. Airway microbiota detected from clinically obtained bronchoalveolar lavage fluid samples from CF patients and disease controls. Pediatr Pulmonol 2014; 49: 322-323.
26. Rosenfeld M, Emerson J, Williams-Warren J, et al. Defining a pulmonary exacerbation in cystic fibrosis. J Pediatr 2001; 139: 359-365.
27. Harris PA, Taylor R, Thielke R, et al. Research electronic data capture (REDCap)-A metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform 2009; 42: 377-381.
28. Burns JL, Emerson J, Stapp JR, et al. Microbiology of sputum from patients at cystic fibrosis centers in the United States. Clin Infect Dis 1998; 27: 158-163.
29. Nadkarni MA, Martin FE, Jacques NA, et al. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 2002; 148: 257-266.
30. Markle JG, Frank DN, Mortin-Toth S, et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science 2013; 339: 1084-1088.
31. Hara N, Alkanani AK, Ir D, et al. Prevention of virus-induced type 1 diabetes with antibiotic therapy. J Immunol 2012; 189: 3805-3814.
32. Ramakrishnan VR, Gitomer S, Kofonow JM, et al. Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis. Int Forum Allergy Rhinol 2017; 7: 16-23.
33. Handorean A, Robertson CE, Harris JK, et al. Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting. Microbiome 2015; 3: 72.
34. Beck JM, Schloss PD, Venkataraman A, et al. Multicenter comparison of lung and oral microbiomes of HIV-infected and HIV-uninfected individuals. Am J Respir Crit Care Med 2015; 192: 1335-1344.
35. Lozupone C, Cota-Gomez A, Palmer BE, et al. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med 2013; 187: 1110-1117.
36. Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28: 1823-1829.
37. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41: D590-D596.
38. Robertson CE, Harris JK, Wagner BD, et al. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Bioinformatics 2013; 29: 3100-3101.
39. Salsgiver EL, Fink AK, Knapp EA, et al. Changing epidemiology of the respiratory bacteriology of patients with cystic fibrosis. Chest 2016; 149: 390-400.
40. Zemanick ET, Wagner BD, Robertson CE, et al. Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc 2015; 12: 221-229.
41. Carmody LA, Zhao J, Schloss PD, et al. Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc 2013; 10: 179-187.
42. Paganin P, Fiscarelli EV, Tuccio V, et al. Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function. PLoS One 2015; 10: e0124348.
43. Zemanick ET, Harris JK, Wagner BD, et al. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013; 8: e62917.
44. Ulrich M, Beer I, Braitmaier P, et al. Relative contribution of Prevotella intermedia and Pseudomonas aeruginosa to lung pathology in airways of patients with cystic fibrosis. Thorax 2010; 65: 978-984.
45. Field TR, Sibley CD, Parkins MD, et al. The genus Prevotella in cystic fibrosis airways. Anaerobe 2010; 16: 337-344.
46. Segal LN, Alekseyenko AV, Clemente JC, et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome 2013; 1: 19.
47. Gangell C, Gard S, Douglas T, et al. Inflammatory responses to individual microorganisms in the lungs of children with cystic fibrosis. Clin Infect Dis 2011; 53: 425-432.
48. Sagel SD, Gibson RL, Emerson J, et al. Impact of Pseudomonas and Staphylococcus infection on inflammation and clinical status in young children with cystic fibrosis. J Pediatr 2009; 154: 183-188.
49. Caverly LJ, Carmody LA, Haig SJ, et al. Culture-independent identification of nontuberculous mycobacteria in cystic fibrosis respiratory samples. PLoS One 2016; 11: e0153876.
50. Coburn B, Wang PW, Diaz Caballero J, et al. Lung microbiota across age and disease stage in cystic fibrosis. Sci Rep 2015; 5: 10241.
51. Laguna TA, Wagner BD, Williams CB, et al. Airway microbiota in bronchoalveolar lavage fluid from clinically well infants with cystic fibrosis. PLoS One 2016; 11: e0167649.