The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis

American Journal of Respiratory and Critical Care Medicine

Volumn 190, Issue 8, 2014, Pages 906-913

  Molyneaux, Phillip L ^a,b   Cox, Michael J ^a   Willis Owen, Saffron A G ^a   Mallia, Patrick ^a,c   Russell, Kirsty E ^a   Russell, Anne Marie ^a,b   Murphy, Elissa ^d   Johnston, Sebastian L ^a,c   Schwartz, David A ^d   Wells, Athol U ^b   Cookson, William O C ^a,b   Maher, Toby M ^a,b   Moffatt, Miriam F ^a  

^a NATIONAL HEART AND LUNG INSTITUTE   (United Kingdom)

^b ROYAL BROMPTON HOSPITAL   (United Kingdom)

^c IMPERIAL COLLEGE HEALTHCARE NHS TRUST   (United Kingdom)

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

Author keywords

Bacteria; Idiopathic pulmonary fibrosis; Microbiome; Muc5b

Indexed keywords

ANTIBIOTIC AGENT; CORTICOSTEROID; GENOMIC DNA; MUCIN 5B; RNA 16S; BACTERIAL DNA; GENETIC MARKER; MUC5B PROTEIN, HUMAN;

ADULT; AGED; ANTIBIOTIC THERAPY; ARTICLE; BACTERIAL LOAD; BACTERIUM; CELL COUNT; CHRONIC OBSTRUCTIVE LUNG DISEASE; COMPARATIVE STUDY; COMPUTER ASSISTED TOMOGRAPHY; CONTROLLED STUDY; CORTICOSTEROID THERAPY; DISEASE COURSE; DISEASE SEVERITY; FEMALE; FIBEROPTIC BRONCHOSCOPY; FIBROSING ALVEOLITIS; GENE DOSAGE; GENE SEQUENCE; GENETIC POLYMORPHISM; GENOTYPE; HAEMOPHILUS; HOST SUSCEPTIBILITY; HUMAN; LOWER RESPIRATORY TRACT INFECTION; LUNG LAVAGE; LUNG VOLUME; MAJOR CLINICAL STUDY; MALE; MICROBIAL COMMUNITY; NEISSERIA; PATHOGENESIS; POLYMERASE CHAIN REACTION; PREVOTELLA; PRIORITY JOURNAL; PROSPECTIVE STUDY; PYROSEQUENCING; SMOKING; SPUTUM ANALYSIS; STREPTOCOCCUS; VEILLONELLA; BACTERIA; BRONCHOSCOPY; CASE CONTROL STUDY; DNA SEQUENCE; GENETIC MARKER; GENETICS; GENOTYPING TECHNIQUE; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; MORTALITY; PATHOPHYSIOLOGY; STATISTICAL MODEL;

AGED; BACTERIA; BACTERIAL LOAD; BRONCHOALVEOLAR LAVAGE; BRONCHOALVEOLAR LAVAGE FLUID; BRONCHOSCOPY; CASE-CONTROL STUDIES; DISEASE PROGRESSION; DNA, BACTERIAL; FEMALE; GENETIC MARKERS; GENOTYPING TECHNIQUES; HUMANS; IDIOPATHIC PULMONARY FIBROSIS; LOGISTIC MODELS; MALE; MICROBIOTA; MIDDLE AGED; MUCIN-5B; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; PROSPECTIVE STUDIES; SEQUENCE ANALYSIS, DNA;

EID: 84918777951     PISSN: 1073449X     EISSN: 15354970     Source Type: Journal    
DOI: 10.1164/rccm.201403-0541OC     Document Type: Article

References (41)

1. Maher TM, Wells AU, Laurent GJ. Idiopathic pulmonary fibrosis: multiple causes and multiple mechanisms? Eur Respir J 2007;30:835-839.
2. Navaratnam V, Fleming KM, West J, Smith CJP, Jenkins RG, Fogarty A, Hubbard RB. The rising incidence of idiopathic pulmonary fibrosis in the UK. Thorax 2011;66:462-467.
3. Ley B, Collard HR, King TE, King TE Jr. Clinical course and prediction of survival in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2010;183:431-440.
4. Seibold MA, Wise AL, Speer MC, Steele MP, Brown KK, Loyd JE, Fingerlin TE, Zhang W, Gudmundsson G, Groshong SD, et al. A common MUC5B promoter polymorphism and pulmonary fibrosis. N Engl J Med 2011;364:1503-1512.
5. Noth I, Zhang Y, Ma S-F, Flores C, Barber M, Huang Y, Broderick SM, Wade MS, Hysi P, Scuirba J, et al. Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genome-wide association study. Lancet Respir Med 2013;1:309-317.
6. Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, et al. Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nat Genet 2013;45:613-620.
7. Peljto AL, Zhang Y, Fingerlin TE, Ma S-F, Garcia JG, Richards TJ, Silveira LJ, Lindell KO, Steele MP, Loyd JE, et al. Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis. JAMA 2013;309:2232-2239.
8. Lawson WE, Loyd JE, Degryse AL. Genetics in pulmonary fibrosis-familial cases provide clues to the pathogenesis of idiopathic pulmonary fibrosis. Am J Med Sci 2011;341:439-443.
9. Taskar VS, Coultas DB. Is idiopathic pulmonary fibrosis an environmental disease? Proc Am Thorac Soc 2006;3:293-298.
10. Stock CJ, Sato H, Fonseca C, Banya WA, Molyneaux PL, Adamali H, Russell A-M, Denton CP, Abraham DJ, Hansell DM, et al. Mucin 5B promoter polymorphism is associated with idiopathic pulmonary fibrosis but not with development of lung fibrosis in systemic sclerosis or sarcoidosis. Thorax 2013;68:436-441.
11. Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, et al. Muc5b is required for airway defence. Nature 2014;505:412-416.
12. Yang IV, Luna LG, Cotter J, Talbert J, Leach SM, Kidd R, Turner J, Kummer N, Kervitsky D, Brown KK, et al. The peripheral blood transcriptome identifies the presence and extent of disease in idiopathic pulmonary fibrosis. PLoS ONE 2012;7:e37708.
13. Wootton SC, Kim DS, Kondoh Y, Chen E, Lee JS, Song JW, Huh JW, Taniguchi H, Chiu C, Boushey H, et al. Viral infection in acute exacerbation of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2011;183:1-30.
14. Molyneaux PL, Maher TM. The role of infection in the pathogenesis of idiopathic pulmonary fibrosis. Eur Respir Rev 2013;22:376-381.
15. Song JW, Hong S-B, Lim C-M, Koh Y, Kim DS. Acute exacerbation of idiopathic pulmonary fibrosis: incidence, risk factors and outcome. Eur Respir J 2011;37:356-363.
16. Raghu G, Anstrom KJ, King TE, Lasky JA, Martinez FJ. Prednisone, azathioprine, and N-acetylcysteine for pulmonary fibrosis. N Engl J Med 2012;366:1968-1977.
17. Shulgina L, Cahn AP, Chilvers ER, Parfrey H, Clark AB, Wilson ECF, Twentyman OP, Davison AG, Curtin JJ, Crawford MB, et al. Treating idiopathic pulmonary fibrosis with the addition of co-trimoxazole: a randomised controlled trial. Thorax 2013;68:155-162.
18. Molyneaux PL, Russell AM, Cox MJ, Moffatt MF, Cookson WOC, Maher TM. The respiratory microbiome in idiopathic pulmonary fibrosis [abstract]. Am J Respir Crit Care Med 2012;185:A5174.
19. Raghu G, Collard HR, Egan JJ, Martinez FJ, Behr J, Brown KK, Colby TV, Cordier JF, Flaherty KR, Lasky JA, et al. An official ATS/ERS/JRS/ALAT statement: idiopathic pulmonary fibrosis: evidence-based guidelines for diagnosis and management. Am J Respir Crit Care Med 2011;183:788-824.
20. Meyer KC, Raghu G, Baughman RP, Brown KK, Costabel U, du Bois RM, Drent M, Haslam PL, Kim DS, Nagai S, et al. An official American Thoracic Society clinical practice guideline: the clinical utility of bronchoalveolar lavage cellular analysis in interstitial lung disease. Am J Respir Crit Care Med 2012;185:1004-1014.
21. Molyneaux PL, Mallia P, Cox MJ, Footitt J, Willis-Owen SAG, Homola D, Trujillo-Torralbo M-B, Elkin S, Kon OM, Cookson WOC, et al. Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2013;188:1224-1231.
22. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335-336.
23. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 2009;6:639-641.
24. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011;21:494-504.
25. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010;26:2460-2461.
26. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010;26:266-267.
27. White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLOS Comput Biol 2009;5:e1000352.
28. Shannon CE. A mathematical theory of communication. ACM SIGMOBILE Mob Comput Commun Rev 2001;5:3.
29. Lozupone C, Hamady M, Knight R. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 2006;7:371.
30. Collard HR, King TE, Bartelson BB, Vourlekis JS, Schwarz MI, Brown KK. Changes in clinical and physiologic variables predict survival in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2003;168:538-542.
31. Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, et al. Disordered microbial communities in asthmatic airways. PLoS ONE 2010;5:e8578.
32. Cardenas PA, Cooper PJ, Cox MJ, Chico M, Arias C, Moffatt MF, Cookson WO. Upper airways microbiota in antibiotic-naïve wheezing and healthy infants from the tropics of rural Ecuador. PLoS ONE 2012;7:e46803.
33. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS 2010;14:9-59.
34. Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG. Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One 2010;5:e15216.
35. King TE, Pardo A, Selman M. Idiopathic pulmonary fibrosis. Lancet 2011;378:1949-1961.
36. Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL, Sundaram B, et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS ONE 2011;6:e16384.
37. Han MK, Zhou Y, Murray S, Tayob N, Noth I, Lama VN, Moore BB, White ES, Flaherty KR, Huffnagle GB, et al . Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respir Med 2014;2:548-556.
38. Molyneaux PL, Maher TM. Respiratory microbiome in IPF: cause, effect, or biomarker? Lancet Respir Med 2014;2600:10-11.
39. Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS ONE 2012;7:e42786.
40. Sze MA, Dimitriu PA, Hayashi S, Elliott WM, McDonough JE, Gosselink JV, Cooper J, Sin DD, Mohn WW, Hogg JC. The lung tissue microbiome in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2012;185:1073-1080.
41. Sim K, Cox MJ, Wopereis H, Martin R, Knol J, Li M-S, Cookson WOCM, Moffatt MF, Kroll JS. Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS ONE 2012;7:e32543.