C. H. Goss and J. L. Burns, Exacerbations in cystic fibrosis. 1: Epidemiology and pathogenesis, Thorax, vol.62, issue.4, pp.360-367, 2007.

H. G. Ahlgren, A. Benedetti, J. S. Landry, J. Bernier, E. Matouk et al., Clinical outcomes associated with Staphylococcus aureus and Pseudomonas aeruginosa airway infections in adult cystic fibrosis patients, BMC Pulm Med, vol.15, p.67, 2015.

P. M. Barnabie and M. Whiteley, Iron-Mediated Control of Pseudomonas aeruginosa-Staphylococcus aureus Interactions in the Cystic Fibrosis Lung, J Bacteriol, vol.197, issue.14, pp.2250-2251, 2015.

Y. J. Huang, E. S. Charlson, R. G. Collman, S. Colombini-hatch, F. D. Martinez et al., The role of the lung microbiome in health and disease. A National Heart, Lung, and Blood Institute workshop report, Am J Respir Crit Care Med, vol.187, issue.12, pp.1382-1389, 2013.

J. P. Kiley, Advancing respiratory research, Chest, vol.140, issue.2, pp.497-501, 2011.

G. B. Rogers, C. J. Van-der-gast, L. Cuthbertson, S. K. Thomson, K. D. Bruce et al., Clinical measures of disease in adult non-CF bronchiectasis correlate with airway microbiota composition, Thorax, vol.68, issue.8, pp.731-738, 2013.

D. Willner, M. Furlan, M. Haynes, R. Schmieder, F. E. Angly et al., Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals, PLoS One, vol.4, issue.10, p.7370, 2009.

J. Zhao, P. D. Schloss, L. M. Kalikin, L. A. Carmody, B. K. Foster et al., Decade-long bacterial community dynamics in cystic fibrosis airways, Proc Natl Acad Sci, vol.109, issue.15, pp.5809-5823, 2012.

C. D. Sibley and M. G. Surette, The polymicrobial nature of airway infections in cystic fibrosis: Cangene Gold Medal Lecture, Can J Microbiol, vol.57, issue.2, pp.69-77, 2011.

L. Yang, L. Jelsbak, and S. Molin, Microbial ecology and adaptation in cystic fibrosis airways, Environ Microbiol, vol.13, issue.7, pp.1682-1691, 2011.

M. Beaume, T. Kohler, T. Fontana, M. Tognon, A. Renzoni et al., Metabolic pathways of Pseudomonas aeruginosa involved in competition with respiratory bacterial pathogens, Front Microbiol, vol.6, p.321, 2015.

M. Keravec, J. Mounier, E. Prestat, S. Vallet, J. K. Jansson et al., Insights into the respiratory tract microbiota of patients with cystic fibrosis during early Pseudomonas aeruginosa colonization, Springerplus, vol.4, p.405, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01272828

M. D. Parkins and R. A. Floto, Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis, J Cyst Fibros, vol.14, issue.3, pp.293-304, 2015.

V. Klepac-ceraj, K. P. Lemon, T. R. Martin, M. Allgaier, S. W. Kembel et al., Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa, Environ Microbiol, vol.12, issue.5, pp.1293-303, 2010.

L. A. Carmody, J. Zhao, L. M. Kalikin, W. Lebar, R. H. Simon et al., The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation, Microbiome, vol.3, p.25834733, 2015.

K. B. Twomey, A. M. An, S. Q. O'connell, O. J. Mccarthy, Y. Swarbreck et al., Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation, PLoS One, vol.8, issue.12, p.82432, 2013.

L. J. Sherrard, M. M. Tunney, and J. S. Elborn, Antimicrobial resistance in the respiratory microbiota of people with cystic fibrosis, Lancet, vol.384, issue.9944, pp.703-716, 2014.

J. Zhao, S. Murray, and J. J. Lipuma, Modeling the impact of antibiotic exposure on human microbiota, Sci Rep, vol.4, p.4345, 2014.

K. J. Psoter, D. Aj, J. Wakefield, J. D. Mayer, M. Bryan et al., Association of meteorological and geographical factors and risk of initial Pseudomonas aeruginosa acquisition in young children with cystic fibrosis, Epidemiol Infect, vol.2015, pp.1-9

P. C. Goeminne, T. S. Nawrot, D. Boeck, K. Nemery, B. Dupont et al., Proximity to blue spaces and risk of infection with Pseudomonas aeruginosa in cystic fibrosis: A case-control analysis, J Cyst Fibros, 2015.

C. Brady, P. Ackerman, M. Johnson, and J. Mcnamara, Bordetella bronchiseptica in a pediatric Cystic Fibrosis center, J Cyst Fibros, vol.13, issue.1, pp.43-51, 2014.

L. Cuthbertson, G. B. Rogers, A. W. Walker, A. Oliver, L. E. Green et al., Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention, ISME J, 2015.

Z. A. Machan, G. W. Taylor, T. L. Pitt, P. J. Cole, and R. Wilson, 2-Heptyl-4-hydroxyquinoline N-oxide, an antistaphylococcal agent produced by Pseudomonas aeruginosa, J Antimicrob Chemother, vol.30, issue.5, pp.615-638, 1992.

D. S. Toder, S. J. Ferrell, J. L. Nezezon, L. Rust, and B. H. Iglewski, lasA and lasB genes of Pseudomonas aeruginosa: analysis of transcription and gene product activity, Infect Immun, vol.62, issue.4, pp.1320-1327, 1994.

W. J. Moree, V. V. Phelan, C. H. Wu, N. Bandeira, D. S. Cornett et al., Interkingdom metabolic transformations captured by microbial imaging mass spectrometry, Proc Natl Acad Sci, vol.109, issue.34, pp.13811-13817, 2012.

K. Duan, C. Dammel, J. Stein, H. Rabin, and M. G. Surette, Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication, Mol Microbiol, vol.50, issue.5, pp.1477-91, 2003.

F. Harrison, Microbial ecology of the cystic fibrosis lung, Microbiology, vol.153, pp.917-940, 2007.

C. D. Sibley, K. Duan, C. Fischer, M. D. Parkins, D. G. Storey et al., Discerning the complexity of community interactions using a Drosophila model of polymicrobial infections, PLoS Pathog, vol.4, issue.10, p.1000184, 2008.

G. Mitchell, D. L. Seguin, A. E. Asselin, E. Deziel, A. M. Cantin et al., Staphylococcus aureus sigma B-dependent emergence of small-colony variants and biofilm production following exposure to Pseudomonas aeruginosa 4-hydroxy-2-heptylquinoline-N-oxide, BMC Microbiol, vol.10, p.33, 2010.

R. A. Whiley, E. V. Fleming, R. Makhija, and R. D. Waite, Environment and colonisation sequence are key parameters driving cooperation and competition between Pseudomonas aeruginosa cystic fibrosis strains and oral commensal streptococci, PLoS One, vol.10, issue.2, p.115513, 2015.

T. M. Gihring, S. J. Green, and C. W. Schadt, Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes, Environ Microbiol, vol.14, issue.2, pp.285-90, 2012.

A. J. Pinto and L. Raskin, PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets, PLoS One, vol.7, issue.8, p.43093, 2012.

C. Quince, A. Lanzen, R. J. Davenport, and P. J. Turnbaugh, Removing noise from pyrosequenced amplicons, BMC Bioinformatics, vol.12, p.38, 2011.

V. Kunin, A. Engelbrektson, H. Ochman, and P. Hugenholtz, Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates, Environ Microbiol, vol.12, issue.1, pp.118-141, 2010.

J. Birtel, J. C. Walser, S. Pichon, H. Burgmann, and B. Matthews, Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions, PLoS One, vol.10, issue.4, p.125356, 2015.

C. F. Davenport and B. Tummler, Advances in computational analysis of metagenome sequences, Environ Microbiol, vol.15, issue.1, pp.1-5, 2013.

S. Nazaret, F. Assade, E. Brothier, A. M. Freydiere, G. Bellon et al., RISA-HPLC analysis of lung bacterial colonizers of cystic fibrosis children, J Microbiol Methods, vol.76, issue.1, pp.58-69, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02555051

W. G. Flight, A. Smith, C. Paisey, J. R. Marchesi, M. J. Bull et al., Rapid Detection of Emerging Pathogens and Loss of Microbial Diversity Associated with Severe Lung Disease in Cystic Fibrosis, J Clin Microbiol, vol.53, issue.7, pp.2022-2031, 2015.

J. Van-dorst, A. Bissett, A. S. Palmer, M. Brown, I. Snape et al., Community fingerprinting in a sequencing world, FEMS Microbiol Ecol, vol.89, issue.2, pp.316-346, 2014.

I. Hewson and J. A. Fuhrman, Improved strategy for comparing microbial assemblage fingerprints, Microb Ecol, vol.51, issue.2, p.16437287, 2006.

R. Danovaro, G. M. Luna, A. Dell'anno, and B. Pietrangeli, Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments, Appl Environ Microbiol, vol.72, issue.9, pp.5982-5991, 2006.

R. Baldan, C. Cigana, F. Testa, I. Bianconi, D. Simone et al., Adaptation of Pseudomonas aeruginosa in Cystic Fibrosis airways influences virulence of Staphylococcus aureus in vitro and murine models of co-infection, PLoS One, vol.9, issue.3, p.89614, 2014.

J. Tyrrell and M. Callaghan, Iron acquisition in the Cystic Fibrosis lung and potential for novel therapeutic strategies, 2015.

A. Pompilio, V. Crocetta, D. Nicola, S. Verginelli, F. Fiscarelli et al., Cooperative pathogenicity in cystic fibrosis: Stenotrophomonas maltophilia modulates Pseudomonas aeruginosa virulence in mixed biofilm, Front Microbiol, vol.6, p.951, 2015.

H. J. Fuchs, D. S. Borowitz, D. H. Christiansen, E. M. Morris, M. L. Nash et al., Effect of aerosolized recombinant human DNase on exacerbations of respiratory symptoms and on pulmonary function in patients with cystic fibrosis. The Pulmozyme Study Group, N Engl J Med, vol.331, issue.10, pp.637-679, 1994.

R. Lavenir, D. Jocktane, F. Laurent, S. Nazaret, and B. Cournoyer, Improved reliability of Pseudomonas aeruginosa PCR detection by the use of the species-specific ecfX gene target, J Microbiol Methods, vol.70, issue.1, pp.20-29, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02590054

P. D. Schloss, S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann et al., Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities, Appl Environ Microbiol, vol.75, issue.23, pp.7537-7578, 2009.

M. M. Fisher and E. W. Triplett, Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities, Appl Environ Microbiol, vol.65, issue.10, pp.4630-4636, 1999.

C. Colinon, D. Jocktane, E. Brothier, G. M. Rossolini, B. Cournoyer et al., Genetic analyses of Pseudomonas aeruginosa isolated from healthy captive snakes: evidence of high inter-and intrasite dissemination and occurrence of antibiotic resistance genes, Environ Microbiol, vol.12, issue.3, pp.716-745, 2010.

U. Romling, B. Fiedler, J. Bosshammer, D. Grothues, J. Greipel et al., Epidemiology of chronic Pseudomonas aeruginosa infections in cystic fibrosis, J Infect Dis, vol.170, issue.6, pp.1616-1637, 1994.

F. C. Tenover, R. D. Arbeit, R. V. Goering, P. A. Mickelsen, B. E. Murray et al., Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing, J Clin Microbiol, vol.33, issue.9, pp.2233-2242, 1995.

R. Bonnet, J. Bru, F. Carron, V. Cattoir, V. Jarlier et al., Comité de l'Antibiogramme-Société Francaise de Microbiologie, p.p, 2014.

S. Ishii, K. Kadota, and K. Senoo, Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data, Journal of Microbiologic Methods, vol.78, pp.344-50, 2009.

R. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2015.

E. H. Simpson, Measurement of diversity, Nature, vol.163, p.688, 1949.

S. Lê, J. Josse, and F. Husson, FactoMineR: An R Package for Multivariate Analysis, Journal of Statistical Software, vol.25, issue.1, pp.1-18, 2008.

L. A. Carmody, J. Zhao, P. D. Schloss, J. F. Petrosino, S. Murray et al., Changes in cystic fibrosis airway microbiota at pulmonary exacerbation, Ann Am Thorac Soc, vol.10, issue.3, pp.179-87, 2013.

G. B. Rogers, L. R. Hoffman, M. P. Carroll, and K. D. Bruce, Interpreting infective microbiota: the importance of an ecological perspective, Trends Microbiol, vol.21, issue.6, pp.271-277, 2013.

L. Raidt, E. A. Idelevich, A. Dubbers, P. Kuster, P. Drevinek et al., Increased Prevalence and Resistance of Important Pathogens Recovered from Respiratory Specimens of Cystic Fibrosis Patients During a Decade, Pediatr Infect Dis J, vol.34, issue.7, pp.700-705, 2015.

C. H. Goss, N. Mayer-hamblett, M. L. Aitken, G. D. Rubenfeld, and B. W. Ramsey, Association between Stenotrophomonas maltophilia and lung function in cystic fibrosis, Thorax, vol.59, issue.11, pp.955-964, 2004.

J. Renwick, P. Mcnally, B. John, T. Desantis, B. Linnane et al., The microbial community of the cystic fibrosis airway is disrupted in early life, PLoS One, vol.9, issue.12, p.109798, 2014.

M. J. Cox, M. Allgaier, B. Taylor, M. S. Baek, Y. J. Huang et al., Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients, PLoS One, vol.5, issue.6, p.11044, 2010.

K. E. Price, T. H. Hampton, A. H. Gifford, E. L. Dolben, D. A. Hogan et al., Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation, Microbiome, vol.1, issue.1, p.27, 2013.

T. M. Jarry and A. L. Cheung, Staphylococcus aureus escapes more efficiently from the phagosome of a cystic fibrosis bronchial epithelial cell line than from its normal counterpart, Infect Immun, vol.74, issue.5, pp.2568-77, 2006.

R. E. Wood and M. W. Leigh, What is a "pulmonary exacerbation" in cystic fibrosis?, J Pediatr, vol.111, issue.6, pp.841-843, 1987.

J. Emerson, M. Rosenfeld, S. Mcnamara, B. Ramsey, and R. L. Gibson, Pseudomonas aeruginosa and other predictors of mortality and morbidity in young children with cystic fibrosis, Pediatr Pulmonol, vol.34, issue.2, pp.91-100, 2002.

S. L. Vandenbranden, A. Mcmullen, M. S. Schechter, D. J. Pasta, R. L. Michaelis et al., Lung function decline from adolescence to young adulthood in cystic fibrosis, Pediatr Pulmonol, vol.47, issue.2, pp.135-178, 2012.

V. Klepac-ceraj, C. A. Hayes, W. P. Gilhooly, T. W. Lyons, R. Kolter et al., Microbial diversity under extreme euxinia: Mahoney Lake, Canada. Geobiology, vol.10, issue.3, pp.223-258, 2012.

M. Adabi, M. Talebi-taher, L. Arbabi, M. Afshar, S. Fathizadeh et al., Spread of Efflux Pump Overexpressing-Mediated Fluoroquinolone Resistance and Multidrug Resistance in Pseudomonas aeruginosa by using an Efflux Pump Inhibitor, Infect Chemother, vol.47, issue.2, pp.98-104, 2015.

R. L. Gibson, J. Emerson, S. Mcnamara, J. L. Burns, M. Rosenfeld et al., Significant microbiological effect of inhaled tobramycin in young children with cystic fibrosis, Am J Respir Crit Care Med, vol.167, issue.6, pp.841-850, 2003.

M. Ballmann, P. Rabsch, V. Der-hardt, and H. , Long-term follow up of changes in FEV1 and treatment intensity during Pseudomonas aeruginosa colonisation in patients with cystic fibrosis, Thorax, vol.53, issue.9, pp.732-739, 1998.

K. A. Ramsey, S. Ranganathan, J. Park, B. Skoric, A. M. Adams et al., Early respiratory infection is associated with reduced spirometry in children with cystic fibrosis, Am J Respir Crit Care Med, vol.190, issue.10, pp.1111-1117, 2014.