The cystic fibrosis lung microbiome

Annals of the American Thoracic Society

Volumn 11, Issue SUPPL. 1, 2014, Pages

  Surette, Michael G ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Cystic fibrosis; Microbiome; Polymicrobial infections; Pseudomonas aeruginosa; Respiratory infections

Indexed keywords

ACHROMOBACTER; BACTEROIDACEAE INFECTIONS; COINFECTION; CYSTIC FIBROSIS; GRAM-NEGATIVE BACTERIAL INFECTIONS; HUMANS; LUNG; MICROBIOTA; MYCOBACTERIUM; MYCOBACTERIUM INFECTIONS; PREVOTELLA; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTIONS; RESPIRATORY TRACT INFECTIONS; STAPHYLOCOCCAL INFECTIONS; STAPHYLOCOCCUS AUREUS; STENOTROPHOMONAS MALTOPHILIA;

EID: 84893954530     PISSN: 23256621     EISSN: None     Source Type: Journal    
DOI: 10.1513/AnnalsATS.201306-159MG     Document Type: Conference Paper

References (43)

1. Riordan JR, Rommens JM, Kerem B, Alon N, Rozmahel R, Grzelczak Z, Zielenski J, Lok S, Plavsic N, Chou JL, et al. Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 1989;245:1066-1073.
2. O'Sullivan BP, Freedman SD. Cystic fibrosis. Lancet 2009;373:1891-1904.
3. The Canadian Cystic Fibrosis Registry 2012 annual report. 2012 [accessed June 3, 2013]. Available from: http://www.cysticfibrosis.ca/assets/files/pdf/ CFC-AnnualReport2012-EN-FINAL-singles.pdf
4. Lipuma JJ. The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 2010;23:299-323.
5. Lyczak JB, Cannon CL, Pier GB. Lung infections associated with cystic fibrosis. Clin Microbiol Rev 2002;15:194-222.
6. Quon BS, Aitken ML. Cystic fibrosis: what to expect now in the early adult years. Paediatr Respir Rev 2012;13:206-214.
7. Collins SM, Surette M, Bercik P. The interplay between the intestinal microbiota and the brain. Nat Rev Microbiol 2012;10:735-742.
8. Pflughoeft KJ, Versalovic J. Human microbiome in health and disease. Annu Rev Pathol 2012;7:99-122.
9. Shanahan F. The colonic microbiota in health and disease. Curr Opin Gastroenterol 2013;29:49-54.
10. Stearns JC, Lynch MD, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, Croitoru K, Moreno-Hagelsieb G, Neufeld JD. Bacterial biogeography of the human digestive tract. Sci Rep 2011;1:170.
11. Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Transl Res 2012;160:258-266.
12. Boucher RC. Airway surface dehydration in cystic fibrosis: pathogenesis and therapy. Annu Rev Med 2007;58:157-170.
13. Sibley CD, Parkins MD, Rabin HR, Duan K, Norgaard JC, Surette MG. A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci USA 2008;105:15070-15075.
14. Dasenbrook EC. Update on methicillin-resistant staphylococcus aureus in cystic fibrosis. Curr Opin Pulm Med 2011;17:437-441.
15. Hill UG, Floto RA, Haworth CS. Non-tuberculous mycobacteria in cystic fibrosis. J R Soc Med 2012;105:S14-S18.
16. Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, Reacher M, Haworth CS, Curran MD, Harris SR, et al. Whole-genome sequencing to identify transmission of mycobacterium abscessus between patients with cystic fibrosis: A retrospective cohort study. Lancet 2013;381:1551-1560.
17. LiPuma J. The new microbiology of cystic fibrosis: it takes a community. Thorax 2012;67:851-852.
18. Lynch SV, Bruce KD. The cystic fibrosis airway microbiome. Cold Spring Harb Perspect Med 2013;3:a009738.
19. Sibley CD, Rabin H, Surette MG. Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol 2006;1:53-61.
20. Rogers GB, Stressmann FA, Walker AW, Carroll MP, Bruce KD. Lung infections in cystic fibrosis: deriving clinical insight from microbial complexity. Expert Rev Mol Diagn 2010;10:187-196.
21. Rogers GB, Skelton S, Serisier DJ, van der Gast CJ, Bruce KD. Determining cystic fibrosis-affected lung microbiology: comparison of spontaneous and serially induced sputum samples by use of terminal restriction fragment length polymorphism profiling. J Clin Microbiol 2010;48:78-86.
22. Willner D, Haynes MR, Furlan M, Schmieder R, Lim YW, Rainey PB, Rohwer F, Conrad D. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J 2012;6:471-474.
23. Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, Rainey PB, Schmieder R, Youle M, Conrad D, et al. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol 2012;46:127-131.
24. Rogers GB, Marsh P, Stressmann AF, Allen CE, Daniels TV, Carroll MP, Bruce KD. The exclusion of dead bacterial cells is essential for accurate molecular analysis of clinical samples. Clin Microbiol Infect 2010;16:1656-1658.
25. Zhao J, Carmody LA, Kalikin LM, Li J, Petrosino JF, Schloss PD, Young VB, LiPuma JJ. Impact of enhanced staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoS ONE 2012;7:e33127.
26. Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS ONE 2010;5:e11044.
27. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA 2012;109:5809-5814.
28. Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, Morrison HG, Paster BJ, O'Toole GA. Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. J Bacteriol 2012;194:4709-4717.
29. Daniels TW, Rogers GB, Stressmann FA, van der Gast CJ, Bruce KD, Jones GR, Connett GJ, Legg JP, Carroll MP. Impact of antibiotic treatment for pulmonary exacerbations on bacterial diversity in cystic fibrosis. J Cyst Fibros 2013;12:22-28.
30. Fodor AA, Klem ER, Gilpin DF, Elborn JS, Boucher RC, Tunney MM, Wolfgang MC. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS ONE 2012;7:e45001.
31. Stressmann FA, Rogers GB, van der Gast CJ, Marsh P, Vermeer LS, Carroll MP, Hoffman L, Daniels TW, Patel N, Forbes B, 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.
32. Zemanick ET, Wagner BD, Sagel SD, Stevens MJ, Accurso FJ, Harris JK. Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens. PLoS ONE 2010;5:e15101.
33. Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, Accurso FJ, Laguna TA. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS ONE 2013;8:e62917.
34. Sibley CD, Grinwis ME, Field TR, Parkins MD, Norgaard JC, Gregson DB, Rabin HR, Surette MG. McKay agar enables routine quantification of the 'Streptococcus milleri' group in cystic fibrosis patients. J Med Microbiol 2010;59:534-540.
35. Sibley CD, Sibley KA, Leong TA, Grinwis ME, Parkins MD, Rabin HR, Surette MG. The Streptococcus milleri population of a cystic fibrosis clinic reveals patient specificity and intraspecies diversity. J Clin Microbiol 2010;48:2592-2594.
36. Sibley CD, Parkins MD, Rabin HR, Surette MG. The relevance of the polymicrobial nature of airway infection in the acute and chronic management of patients with cystic fibrosis. Curr Opin Investig Drugs 2009;10:787-794.
37. Field TR, Sibley CD, Parkins MD, Rabin HR, Surette MG. The genus Prevotella in cystic fibrosis airways. Anaerobe 2010;16:337-344.
38. Sibley CD, Grinwis ME, Field TR, Eshaghurshan CS, Faria MM, Dowd SE, Parkins MD, Rabin HR, Surette MG. Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PLoS ONE 2011;6:e22702.
39. Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G, Muhlebach MS, Wolfgang MC, Boucher R, Gilpin DF, McDowell A, 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.
40. Tunney MM, Klem ER, Fodor AA, Gilpin DF, Moriarty TF, McGrath SJ, Muhlebach MS, Boucher RC, Cardwell C, Doering G, et al. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 2011;66:579-584.
41. Flume PA, Liou TG, Borowitz DS, Li H, Yen K, Ordonez CL, Geller DE. Ivacaftor in subjects with cystic fibrosis who are homozygous for the f508del-cftr mutation. Chest 2012;142:718-724.
42. Rabin HR, Surette MG. The cystic fibrosis airway microbiome. Curr Opin Pulm Med 2012;18:622-627.
43. Sibley CD, Surette MG. The polymicrobial nature of airway infections in cystic fibrosis: Cangene gold medal lecture. Can J Microbiol 2011;57:69-77.