Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis

被引:122
作者
Boutin, Sebastien [1 ,5 ]
Graeber, Simon Y. [2 ,3 ,4 ,5 ]
Weitnauer, Michael [1 ]
Panitz, Jessica [1 ,5 ]
Stahl, Mirjam [2 ,3 ,4 ,5 ]
Clausznitzer, Diana [6 ]
Kaderali, Lars [6 ]
Einarsson, Gisli [7 ]
Tunney, Michael M. [7 ,8 ]
Elborn, J. Stuart [7 ,9 ]
Mall, Marcus A. [2 ,3 ,4 ,5 ]
Dalpke, Alexander H. [1 ,5 ]
机构
[1] Univ Heidelberg Hosp, Dept Infect Dis Med Microbiol & Hyg, Heidelberg, Germany
[2] Univ Heidelberg Hosp, Dept Translat Pulmonol, Heidelberg, Germany
[3] Univ Heidelberg Hosp, Div Pediat Pulmonol & Allergol, Heidelberg, Germany
[4] Univ Heidelberg Hosp, Cyst Fibrosis Ctr, Dept Pediat, Heidelberg, Germany
[5] Translat Lung Res Ctr Heidelberg TLRC, Heidelberg, Germany
[6] Tech Univ Dresden, Inst Med Informat & Biometry, D-01062 Dresden, Germany
[7] Queens Univ Belfast, CF & Airways Microbiol Grp, Belfast, Antrim, North Ireland
[8] Queens Univ Belfast, Sch Pharm, Belfast, Antrim, North Ireland
[9] Queens Univ Belfast, Sch Med Dent & Biomed Sci, Ctr Infect & Immun, Belfast, Antrim, North Ireland
关键词
PSEUDOMONAS-AERUGINOSA; INFECTION; IDENTIFICATION; EPIDEMIOLOGY; BACTERIA; DISEASE;
D O I
10.1371/journal.pone.0116029
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];
摘要
Changes in the airway microbiome may be important in the pathophysiology of chronic lung disease in patients with cystic fibrosis. However, little is known about the microbiome in early cystic fibrosis lung disease and the relationship between the microbiomes from different niches in the upper and lower airways. Therefore, in this cross-sectional study, we examined the relationship between the microbiome in the upper (nose and throat) and lower (sputum) airways from children with cystic fibrosis using next generation sequencing. Our results demonstrate a significant difference in both a and beta-diversity between the nose and the two other sampling sites. The nasal microbiome was characterized by a polymicrobial community while the throat and sputum communities were less diverse and dominated by a few operational taxonomic units. Moreover, sputum and throat microbiomes were closely related especially in patients with clinically stable lung disease. There was a high inter-individual variability in sputum samples primarily due to a decrease in evenness linked to increased abundance of potential respiratory pathogens such as Pseudomonas aeruginosa. Patients with chronic Pseudomonas aeruginosa infection exhibited a less diverse sputum microbiome. A high concordance was found between pediatric and adult sputum microbiomes except that Burkholderia was only observed in the adult cohort. These results indicate that an adult-like lower airways microbiome is established early in life and that throat swabs may be a good surrogate in clinically stable children with cystic fibrosis without chronic Pseudomonas aeruginosa infection in whom sputum sampling is often not feasible.
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页数:19
相关论文
共 49 条
[1]
The microbiome of the lung [J].
Beck, James M. ;
Young, Vincent B. ;
Huffnagle, Gary B. .
TRANSLATIONAL RESEARCH, 2012, 160 (04) :258-266
[2]
Upper and lower airway cultures in children with cystic fibrosis: Do not neglect the upper airways [J].
Bonestroo, Hilde J. C. ;
de Winter-de Groot, Karin M. ;
van der Ent, Cornelis K. ;
Arets, Hubertus G. M. .
JOURNAL OF CYSTIC FIBROSIS, 2010, 9 (02) :130-134
[3]
GROWTH VELOCITY FOR SUPINE LENGTH HEIGHT OF NORMAL-CHILDREN FROM BIRTH TO 16 YEARS - LONGITUDINAL-STUDY BONN DORTMUND [J].
BRANDT, I ;
REINKEN, L .
KLINISCHE PADIATRIE, 1988, 200 (06) :451-456
[4]
Longitudinal assessment of Pseudomonas aeruginosa in young children with cystic fibrosis [J].
Burns, JL ;
Gibson, RL ;
McNamara, S ;
Yim, D ;
Emerson, J ;
Rosenfeld, M ;
Hiatt, P ;
McCcoy, K ;
Castile, R ;
Smith, AL ;
Ramsey, BW .
JOURNAL OF INFECTIOUS DISEASES, 2001, 183 (03) :444-452
[5]
Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract [J].
Charlson, Emily S. ;
Bittinger, Kyle ;
Haas, Andrew R. ;
Fitzgerald, Ayannah S. ;
Frank, Ian ;
Yadav, Anjana ;
Bushman, Frederic D. ;
Collman, Ronald G. .
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 2011, 184 (08) :957-963
[6]
Infection by Ralstonia species in cystic fibrosis patients:: Identification of R-pickettii and R-mannitolilytica by polymerase chain reaction [J].
Coenye, T ;
Vandamme, P ;
LiPuma, JJ .
EMERGING INFECTIOUS DISEASES, 2002, 8 (07) :692-696
[7]
Bacterial Community Variation in Human Body Habitats Across Space and Time [J].
Costello, Elizabeth K. ;
Lauber, Christian L. ;
Hamady, Micah ;
Fierer, Noah ;
Gordon, Jeffrey I. ;
Knight, Rob .
SCIENCE, 2009, 326 (5960) :1694-1697
[8]
Bacterial biofilms: A common cause of persistent infections [J].
Costerton, JW ;
Stewart, PS ;
Greenberg, EP .
SCIENCE, 1999, 284 (5418) :1318-1322
[9]
Cox MJ, 2010, PLOS ONE, V5, DOI [10.1371/journal.pone.0012132, 10.1371/journal.pone.0011044]
[10]
New clinical diagnostic procedures for cystic fibrosis in Europe [J].
De Boeck, K. ;
Derichs, N. ;
Fajac, I. ;
de Jonge, H. R. ;
Bronsveld, I. ;
Sermet, I. ;
Vermeulen, F. ;
Sheppard, D. N. ;
Cuppens, H. ;
Hug, M. ;
Melotti, P. ;
Middleton, P. G. ;
Wilschanski, M. .
JOURNAL OF CYSTIC FIBROSIS, 2011, 10 :S53-S66