{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T21:49:14Z","timestamp":1759960154200,"version":"3.37.3"},"reference-count":162,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2015,12,5]],"date-time":"2015-12-05T00:00:00Z","timestamp":1449273600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia (PT)","doi-asserted-by":"publisher","award":["SFRH\/BPD\/95616\/2013"],"award-info":[{"award-number":["SFRH\/BPD\/95616\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Appl Microbiol Biotechnol"],"published-print":{"date-parts":[[2016,2]]},"DOI":"10.1007\/s00253-015-7177-x","type":"journal-article","created":{"date-parts":[[2015,12,5]],"date-time":"2015-12-05T02:14:02Z","timestamp":1449281642000},"page":"1163-1181","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy"],"prefix":"10.1007","volume":"100","author":[{"given":"Andreia P.","family":"Magalh\u00e3es","sequence":"first","affiliation":[]},{"given":"Nuno F.","family":"Azevedo","sequence":"additional","affiliation":[]},{"given":"Maria O.","family":"Pereira","sequence":"additional","affiliation":[]},{"given":"Susana P.","family":"Lopes","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,12,5]]},"reference":[{"key":"7177_CR1","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1007\/s002530100703","volume":"56","author":"EH Alexander","year":"2001","unstructured":"Alexander EH, Hudson MC (2001) Factors influencing the internalization of Staphylococcus aureus and impacts on the course of infections in humans. Appl Microbiol Biotechnol 56:361\u2013366","journal-title":"Appl Microbiol Biotechnol"},{"key":"7177_CR2","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1038\/nrmicro3232","volume":"12","author":"RC Allen","year":"2014","unstructured":"Allen RC, Popat R, Diggle SP, Brown SP (2014) Targeting virulence: can we make evolution-proof drugs? Nat Rev Microbiol 12:300\u2013308. doi: 10.1038\/nrmicro3232","journal-title":"Nat Rev Microbiol"},{"key":"7177_CR3","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1378\/chest.09-1103","volume":"137","author":"R Amin","year":"2010","unstructured":"Amin R, Dupuis A, Aaron SD, Ratjen F (2010) The effect of chronic infection with Aspergillus fumigatus on lung function and hospitalization in patients with cystic fibrosis. Chest 137:171\u2013176. doi: 10.1378\/chest.09-1103","journal-title":"Chest"},{"key":"7177_CR4","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1001\/archpedi.1938.01980140114013","volume":"56","author":"DH Andersen","year":"1938","unstructured":"Andersen DH (1938) Cystic fibrosis of the pancreas and its relation to celiac disease. Am J Dis Child 56:344. doi: 10.1001\/archpedi.1938.01980140114013","journal-title":"Am J Dis Child"},{"key":"7177_CR5","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1111\/2049-632X.12015","volume":"67","author":"GG Anderson","year":"2013","unstructured":"Anderson GG, Kenney TF, Macleod DL, Henig NR, O\u2019Toole GA (2013) Eradication of Pseudomonas aeruginosa biofilms on cultured airway cells by a fosfomycin\/tobramycin antibiotic combination. Pathog Dis 67:39\u201345. doi: 10.1111\/2049-632X.12015","journal-title":"Pathog Dis"},{"key":"7177_CR6","first-page":"85","volume":"322","author":"GG Anderson","year":"2008","unstructured":"Anderson GG, O\u2019Toole GA (2008) Innate and induced resistance mechanisms of bacterial biofilms. Curr Top Microbiol Immunol 322:85\u2013105","journal-title":"Curr Top Microbiol Immunol"},{"key":"7177_CR7","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1128\/AAC.34.11.2043","volume":"34","author":"H Anwar","year":"1990","unstructured":"Anwar H, Dasgupta MK, Costerton JW (1990) Testing the susceptibility of bacteria in biofilms to antibacterial agents. Antimicrob Agents Chemother 34:2043\u20132046","journal-title":"Antimicrob Agents Chemother"},{"key":"7177_CR8","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1128\/AAC.48.4.1175-1187.2004","volume":"48","author":"N Bagge","year":"2004","unstructured":"Bagge N, Schuster M, Hentzer M, Ciofu O, Givskov M, Greenberg EP, H\u00f8iby N (2004) Pseudomonas aeruginosa biofilms exposed to imipenem exhibit changes in global gene expression and beta-lactamase and alginate production. Antimicrob Agents Chemother 48:1175\u20131187","journal-title":"Antimicrob Agents Chemother"},{"key":"7177_CR9","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1046\/j.1439-0507.2003.00830.x","volume":"46","author":"N Bakare","year":"2003","unstructured":"Bakare N, Rickerts V, Bargon J, Just-N\u00fcbling G (2003) Prevalence of Aspergillus fumigatus and other fungal species in the sputum of adult patients with cystic fibrosis. Mycoses 46:19\u201323","journal-title":"Mycoses"},{"key":"7177_CR10","author":"R Baldan","year":"2014","unstructured":"Baldan R, Cigana C, Testa F, Bianconi I, De Simone M, Pellin D, Di Serio C, Bragonzi A, Cirillo DM (2014) Adaptation of Pseudomonas aeruginosa in cystic fibrosis airways influences virulence of Staphylococcus aureus in vitro and murine models of co-infection. PLoS One. doi: 10.1371\/journal.pone.0089614","journal-title":"PLoS One"},{"key":"7177_CR11","doi-asserted-by":"crossref","unstructured":"Barton RC, Borman AM, Johnson EM, Houbraken J, Hobson RP, Denton M, Conway SP, Brownlee KG, Peckham D, Lee TWR (2010) Isolation of the fungus Geosmithia argillacea in sputum of people with cystic fibrosis. J Clin Microbiol 48:2615\u20132617. doi: 10.1128\/JCM.00184-10","DOI":"10.1128\/JCM.00184-10"},{"key":"7177_CR12","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1128\/JCM.35.4.1024-1026.1997","volume":"35","author":"SM Ben Dekhil","year":"1997","unstructured":"Ben Dekhil SM, Peel MM, Lennox VA, Stackebrandt E, Sly LI (1997) Isolation of Lautropia mirabilis from sputa of a cystic fibrosis patient. J Clin Microbiol 35:1024\u20131026","journal-title":"J Clin Microbiol"},{"key":"7177_CR13","doi-asserted-by":"crossref","first-page":"e0118319","DOI":"10.1371\/journal.pone.0118319","volume":"10","author":"M Benedyk","year":"2015","unstructured":"Benedyk M, Byrne DP, Glowczyk I, Potempa J, Olczak M, Olczak T, Smalley JW (2015) Pyocycanin, a contributory factor in haem acquisition and virulence enhancement of Porphyromonas gingivalis in the lung. PLoS One 10:e0118319. doi: 10.1371\/journal.pone.0118319","journal-title":"PLoS One"},{"key":"7177_CR14","doi-asserted-by":"crossref","first-page":"e2908","DOI":"10.1371\/journal.pone.0002908","volume":"3","author":"F Bittar","year":"2008","unstructured":"Bittar F, Richet H, Dubus J-C, Reynaud-Gaubert M, Stremler N, Sarles J, Raoult D, Rolain J-M (2008) Molecular detection of multiple emerging pathogens in sputa from cystic fibrosis patients. PLoS One 3:e2908. doi: 10.1371\/journal.pone.0002908","journal-title":"PLoS One"},{"key":"7177_CR15","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1111\/j.1469-0691.2010.03236.x","volume":"16","author":"F Bittar","year":"2010","unstructured":"Bittar F, Rolain J-M (2010) Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients. Clin Microbiol Infect 16:809\u2013820. doi: 10.1111\/j.1469-0691.2010.03236.x","journal-title":"Clin Microbiol Infect"},{"key":"7177_CR16","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1002\/ppul.21011","volume":"44","author":"T Bjarnsholt","year":"2009","unstructured":"Bjarnsholt T, Jensen P\u00d8, Fiandaca MJ, Pedersen J, Hansen CR, Andersen CB, Pressler T, Givskov M, H\u00f8iby N (2009) Pseudomonas aeruginosa biofilms in the respiratory tract of cystic fibrosis patients. Pediatr Pulmonol 44:547\u2013558. doi: 10.1002\/ppul.21011","journal-title":"Pediatr Pulmonol"},{"key":"7177_CR17","first-page":"346","volume":"9","author":"M Bodas","year":"2010","unstructured":"Bodas M, Vij N (2010) The NF-kappaB signaling in cystic fibrosis lung disease: pathophysiology and therapeutic potential. Discov Med 9:346\u2013356","journal-title":"Discov Med"},{"key":"7177_CR18","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1038\/ismej.2007.76","volume":"2","author":"C Boon","year":"2008","unstructured":"Boon C, Deng Y, Wang L-H, He Y, Xu J-L, Fan Y, Pan SQ, Zhang L-H (2008) A novel DSF-like signal from Burkholderia cenocepacia interferes with Candida albicans morphological transition. Isme j 2:27\u201336. doi: 10.1038\/ismej.2007.76","journal-title":"Isme j"},{"key":"7177_CR19","doi-asserted-by":"crossref","first-page":"2659","DOI":"10.1128\/AAC.48.7.2659-2664.2004","volume":"48","author":"G Borriello","year":"2004","unstructured":"Borriello G, Werner E, Roe F, Kim AM, Ehrlich GD, Stewart PS (2004) Oxygen limitation contributes to antibiotic tolerance of Pseudomonas aeruginosa in biofilms. Antimicrob Agents Chemother 48:2659\u20132664. doi: 10.1128\/AAC.48.7.2659-2664.2004","journal-title":"Antimicrob Agents Chemother"},{"key":"7177_CR20","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1111\/j.1365-2796.2006.01744.x","volume":"261","author":"RC Boucher","year":"2007","unstructured":"Boucher RC (2007) Evidence for airway surface dehydration as the initiating event in CF airway disease. J Intern Med 261:5\u201316. doi: 10.1111\/j.1365-2796.2006.01744.x","journal-title":"J Intern Med"},{"key":"7177_CR21","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1183\/09031936.03.00057003","volume":"23","author":"RC Boucher","year":"2004","unstructured":"Boucher RC (2004) New concepts of the pathogenesis of cystic fibrosis lung disease. Eur Respir J 23:146\u2013158","journal-title":"Eur Respir J"},{"key":"7177_CR22","author":"A Bragonzi","year":"2012","unstructured":"Bragonzi A, Farulla I, Paroni M, Twomey KB, Pirone L, Lor\u00e8 NI, Bianconi I, Dalmastri C, Ryan RP, Bevivino A (2012) Modelling co-infection of the cystic fibrosis lung by Pseudomonas aeruginosa and Burkholderia cenocepacia reveals influences on biofilm formation and host response. PLoS One. doi: 10.1371\/journal.pone.0052330","journal-title":"PLoS One"},{"key":"7177_CR23","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.tim.2013.12.004","volume":"22","author":"M Burm\u00f8lle","year":"2014","unstructured":"Burm\u00f8lle M, Ren D, Bjarnsholt T, S\u00f8rensen SJ (2014) Interactions in multispecies biofilms: do they actually matter? Trends Microbiol 22:84\u201391. doi: 10.1016\/j.tim.2013.12.004","journal-title":"Trends Microbiol"},{"key":"7177_CR24","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1111\/j.1574-695X.2010.00714.x","volume":"59","author":"M Burm\u00f8lle","year":"2010","unstructured":"Burm\u00f8lle M, Thomsen TR, Fazli M, Dige I, Christensen L, Hom\u00f8e P, Tvede M, Nyvad B, Tolker-Nielsen T, Givskov M, Moser C, Kirketerp-M\u00f8ller K, Johansen HK, H\u00f8iby N, Jensen P\u00d8, S\u00f8rensen SJ, Bjarnsholt T (2010) Biofilms in chronic infections\u2014a matter of opportunity\u2014monospecies biofilms in multispecies infections. FEMS Immunol Med Microbiol 59:324\u2013336. doi: 10.1111\/j.1574-695X.2010.00714.x","journal-title":"FEMS Immunol Med Microbiol"},{"key":"7177_CR25","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1086\/514631","volume":"27","author":"JL Burns","year":"1998","unstructured":"Burns JL, Emerson J, Stapp JR, Yim DL, Krzewinski J, Louden L, Ramsey BW, Clausen CR (1998) Microbiology of sputum from patients at cystic fibrosis centers in the United States. Clin Infect Dis 27:158\u2013163","journal-title":"Clin Infect Dis"},{"key":"7177_CR26","doi-asserted-by":"crossref","first-page":"3449","DOI":"10.1128\/JCM.00765-07","volume":"45","author":"WR Butler","year":"2007","unstructured":"Butler WR, Sheils CA, Brown-Elliott BA, Charles N, Colin AA, Gant MJ, Goodill J, Hindman D, Toney SR, Wallace RJ, Yakrus MA (2007) First isolations of Segniliparus rugosus from patients with cystic fibrosis. J Clin Microbiol 45:3449\u20133452. doi: 10.1128\/JCM.00765-07","journal-title":"J Clin Microbiol"},{"key":"7177_CR27","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.mib.2011.11.001","volume":"15","author":"M Callaghan","year":"2012","unstructured":"Callaghan M, McClean S (2012) Bacterial host interactions in cystic fibrosis. Curr Opin Microbiol 15:71\u201377. doi: 10.1016\/j.mib.2011.11.001","journal-title":"Curr Opin Microbiol"},{"key":"7177_CR28","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1099\/jmm.0.47544-0","volume":"57","author":"E Caraher","year":"2008","unstructured":"Caraher E, Collins J, Herbert G, Murphy PG, Gallagher CG, Crowe MJ, Callaghan M, McClean S (2008) Evaluation of in vitro virulence characteristics of the genus Pandoraea in lung epithelial cells. J Med Microbiol 57:15\u201320. doi: 10.1099\/jmm.0.47544-0","journal-title":"J Med Microbiol"},{"key":"7177_CR29","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.jcf.2008.03.009","volume":"7","author":"C Castellani","year":"2008","unstructured":"Castellani C, Cuppens H, Macek M, Cassiman JJ, Kerem E, Durie P, Tullis E, Assael BM, Bombieri C, Brown A, Casals T, Claustres M, Cutting GR, Dequeker E, Dodge J, Doull I, Farrell P, Ferec C, Girodon E, Johannesson M, Kerem B, Knowles M, Munck A, Pignatti PF, Radojkovic D, Rizzotti P, Schwarz M, Stuhrmann M, Tzetis M, Zielenski J, Elborn JS (2008) Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros 7:179\u2013196. doi: 10.1016\/j.jcf.2008.03.009","journal-title":"J Cyst Fibros"},{"key":"7177_CR30","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1111\/j.1399-3011.2005.00217.x","volume":"65","author":"C Chan","year":"2005","unstructured":"Chan C, Burrows LL, Deber CM (2005) Alginate as an auxiliary bacterial membrane: binding of membrane-active peptides by polysaccharides. J Pept Res 65:343\u2013351. doi: 10.1111\/j.1399-3011.2005.00217.x","journal-title":"J Pept Res"},{"key":"7177_CR31","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1128\/IAI.01192-09","volume":"78","author":"SS Chattoraj","year":"2010","unstructured":"Chattoraj SS, Murthy R, Ganesan S, Goldberg JB, Zhao Y, Hershenson MB, Sajjan US (2010) Pseudomonas aeruginosa alginate promotes Burkholderia cenocepacia persistence in cystic fibrosis transmembrane conductance regulator knockout mice. Infect Immun 78:984\u2013993. doi: 10.1128\/IAI.01192-09","journal-title":"Infect Immun"},{"key":"7177_CR32","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1080\/j.1365-280X.1999.00232.x","volume":"37","author":"B Cimon","year":"1999","unstructured":"Cimon B, Carrere J, Chazalette JP, Vinatier JF, Chabasse D, Bouchara JP (1999) Chronic airway colonization by Penicillium emersonii in a patient with cystic fibrosis. Med Mycol 37:291\u2013293","journal-title":"Med Mycol"},{"key":"7177_CR33","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1128\/JCM.43.3.1484-1487.2005","volume":"43","author":"B Cimon","year":"2005","unstructured":"Cimon B, Challier S, B\u00e9guin H, Carr\u00e8re J, Chabasse D, Bouchara J-P (2005) Airway colonization by Acrophialophora fusispora in patients with cystic fibrosis. J Clin Microbiol 43:1484\u20131487. doi: 10.1128\/JCM.43.3.1484-1487.2005","journal-title":"J Clin Microbiol"},{"key":"7177_CR34","doi-asserted-by":"crossref","first-page":"2062","DOI":"10.1128\/JCM.40.6.2062-2069.2002","volume":"40","author":"T Coenye","year":"2002","unstructured":"Coenye T, Goris J, Spilker T, Vandamme P, LiPuma JJ (2002) Characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of Inquilinus limosus gen. nov., sp. nov. J Clin Microbiol 40:2062\u20132069","journal-title":"J Clin Microbiol"},{"key":"7177_CR35","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1164\/rccm.201009-1478CI","volume":"183","author":"M Cohen-Cymberknoh","year":"2011","unstructured":"Cohen-Cymberknoh M, Shoseyov D, Kerem E (2011) Managing cystic fibrosis: strategies that increase life expectancy and improve quality of life. Am J Respir Crit Care Med 183:1463\u20131471. doi: 10.1164\/rccm.201009-1478CI","journal-title":"Am J Respir Crit Care Med"},{"key":"7177_CR36","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1099\/jmm.0.022657-0","volume":"60","author":"A Costello","year":"2011","unstructured":"Costello A, Herbert G, Fabunmi L, Schaffer K, Kavanagh KA, Caraher EM, Callaghan M, McClean S (2011) Virulence of an emerging respiratory pathogen, genus Pandoraea, in vivo and its interactions with lung epithelial cells. J Med Microbiol 60:289\u2013299. doi: 10.1099\/jmm.0.022657-0","journal-title":"J Med Microbiol"},{"key":"7177_CR37","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/S0966-842X(00)01918-1","volume":"9","author":"JW Costerton","year":"2001","unstructured":"Costerton JW (2001) Cystic fibrosis pathogenesis and the role of biofilms in persistent infection. Trends Microbiol 9:50\u201352","journal-title":"Trends Microbiol"},{"key":"7177_CR38","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1111\/j.1365-2958.2007.05840.x","volume":"65","author":"C Cugini","year":"2007","unstructured":"Cugini C, Calfee MW, Farrow JM, Morales DK, Pesci EC, Hogan DA (2007) Farnesol, a common sesquiterpene, inhibits PQS production in Pseudomonas aeruginosa. Mol Microbiol 65:896\u2013906. doi: 10.1111\/j.1365-2958.2007.05840.x","journal-title":"Mol Microbiol"},{"key":"7177_CR39","doi-asserted-by":"crossref","first-page":"e27317","DOI":"10.1371\/journal.pone.0027317","volume":"6","author":"T Dalton","year":"2011","unstructured":"Dalton T, Dowd SE, Wolcott RD, Sun Y, Watters C, Griswold JA, Rumbaugh KP (2011) An in vivo polymicrobial biofilm wound infection model to study interspecies interactions. PLoS One 6:e27317. doi: 10.1371\/journal.pone.0027317","journal-title":"PLoS One"},{"key":"7177_CR40","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1164\/rccm.200505-840OE","volume":"173","author":"PB Davis","year":"2006","unstructured":"Davis PB (2006) Cystic fibrosis since 1938. Am J Respir Crit Care Med 173:475\u2013482. doi: 10.1164\/rccm.200505-840OE","journal-title":"Am J Respir Crit Care Med"},{"key":"7177_CR41","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1136\/thx.2005.043539","volume":"61","author":"K Boeck De","year":"2006","unstructured":"De Boeck K, Wilschanski M, Castellani C, Taylor C, Cuppens H, Dodge J, Sinaasappel M (2006) Cystic fibrosis: terminology and diagnostic algorithms. Thorax 61:627\u2013635. doi: 10.1136\/thx.2005.043539","journal-title":"Thorax"},{"key":"7177_CR42","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1128\/JCM.40.6.2108-2114.2002","volume":"40","author":"A Defontaine","year":"2002","unstructured":"Defontaine A, Zouhair R, Cimon B, Carr\u00e8re J, Bailly E, Symoens F, Diouri M, Hallet J-N, Bouchara J-P (2002) Genotyping study of Scedosporium apiospermum isolates from patients with cystic fibrosis. J Clin Microbiol 40:2108\u20132114","journal-title":"J Clin Microbiol"},{"key":"7177_CR43","doi-asserted-by":"crossref","first-page":"e36313","DOI":"10.1371\/journal.pone.0036313","volume":"7","author":"L Delhaes","year":"2012","unstructured":"Delhaes L, Monchy S, Fr\u00e9alle E, Hubans C, Salleron J, Leroy S, Prevotat A, Wallet F, Wallaert B, Dei-Cas E, Sime-Ngando T, Chab\u00e9 M, Viscogliosi E (2012) The airway microbiota in cystic fibrosis: a complex fungal and bacterial community\u2013implications for therapeutic management. PLoS One 7:e36313. doi: 10.1371\/journal.pone.0036313","journal-title":"PLoS One"},{"key":"7177_CR44","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/j.jcf.2012.10.004","volume":"11","author":"G D\u00f6ring","year":"2012","unstructured":"D\u00f6ring G, Flume P, Heijerman H, Elborn JS (2012) Treatment of lung infection in patients with cystic fibrosis: current and future strategies. J Cyst Fibros 11:461\u2013479. doi: 10.1016\/j.jcf.2012.10.004","journal-title":"J Cyst Fibros"},{"key":"7177_CR45","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1111\/j.1469-0691.2010.03237.x","volume":"16","author":"P Drevinek","year":"2010","unstructured":"Drevinek P, Mahenthiralingam E (2010) Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence. Clin Microbiol Infect 16:821\u2013830. doi: 10.1111\/j.1469-0691.2010.03237.x","journal-title":"Clin Microbiol Infect"},{"key":"7177_CR46","doi-asserted-by":"crossref","first-page":"1477","DOI":"10.1046\/j.1365-2958.2003.03803.x","volume":"50","author":"K Duan","year":"2003","unstructured":"Duan K, Dammel C, Stein J, Rabin H, Surette MG (2003) Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication. Mol Microbiol 50:1477\u20131491. doi: 10.1046\/j.1365-2958.2003.03803.x","journal-title":"Mol Microbiol"},{"key":"7177_CR47","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1136\/thoraxjnl-2011-200160","volume":"67","author":"A-T Essilfie","year":"2012","unstructured":"Essilfie A-T, Simpson JL, Dunkley ML, Morgan LC, Oliver BG, Gibson PG, Foster PS, Hansbro PM (2012) Combined Haemophilus influenzae respiratory infection and allergic airways disease drives chronic infection and features of neutrophilic asthma. Thorax 67:588\u2013599. doi: 10.1136\/thoraxjnl-2011-200160","journal-title":"Thorax"},{"key":"7177_CR48","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1016\/j.jpeds.2008.05.005","volume":"153","author":"PM Farrell","year":"2008","unstructured":"Farrell PM, Rosenstein BJ, White TB, Accurso FJ, Castellani C, Cutting GR, Durie PR, Legrys VA, Massie J, Parad RB, Rock MJ, Campbell PW (2008) Guidelines for diagnosis of cystic fibrosis in newborns through older adults: cystic fibrosis foundation consensus report. J Pediatr 153:S4\u2013S14. doi: 10.1016\/j.jpeds.2008.05.005","journal-title":"J Pediatr"},{"key":"7177_CR49","doi-asserted-by":"crossref","first-page":"e1002606","DOI":"10.1371\/journal.pcbi.1002606","volume":"8","author":"K Faust","year":"2012","unstructured":"Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8:e1002606. doi: 10.1371\/journal.pcbi.1002606","journal-title":"PLoS Comput Biol"},{"key":"7177_CR50","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1586\/17476348.2014.896205","volume":"8","author":"SB Fiel","year":"2014","unstructured":"Fiel SB (2014) Aerosolized antibiotics in cystic fibrosis: an update. Expert Rev Respir Med 8:305\u2013314. doi: 10.1586\/17476348.2014.896205","journal-title":"Expert Rev Respir Med"},{"key":"7177_CR51","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/nrmicro2907","volume":"10","author":"A Folkesson","year":"2012","unstructured":"Folkesson A, Jelsbak L, Yang L, Johansen HK, Ciofu O, H\u00f8iby N, Molin S (2012) Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat Rev Microbiol 10:841\u2013851. doi: 10.1038\/nrmicro2907","journal-title":"Nat Rev Microbiol"},{"issue":"Suppl 3","key":"7177_CR52","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1016\/S0924-8579(10)70003-0","volume":"36","author":"GL French","year":"2010","unstructured":"French GL (2010) The continuing crisis in antibiotic resistance. Int J Antimicrob Agents 36(Suppl 3):S3\u2013S7. doi: 10.1016\/S0924-8579(10)70003-0","journal-title":"Int J Antimicrob Agents"},{"key":"7177_CR53","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0075380","volume":"8","author":"VP Friman","year":"2013","unstructured":"Friman VP, Ghoul M, Molin S, Johansen HK, Buckling A (2013) Pseudomonas aeruginosa adaptation to lungs of cystic fibrosis patients leads to lowered resistance to phage and protist enemies. PLoS One 8:1\u20139. doi: 10.1371\/journal.pone.0075380","journal-title":"PLoS One"},{"key":"7177_CR54","author":"A Fug\u00e8re","year":"2014","unstructured":"Fug\u00e8re A, S\u00e9guin DL, Mitchell G, D\u00e9ziel E, Dekimpe V, Cantin AM, Frost E, Malouin F (2014) Interspecific small molecule interactions between clinical isolates of Pseudomonas aeruginosa and Staphylococcus aureus from adult cystic fibrosis patients. PLoS One. doi: 10.1371\/journal.pone.0086705","journal-title":"PLoS One"},{"key":"7177_CR55","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1128\/jb.176.2.269-275.1994","volume":"176","author":"WC Fuqua","year":"1994","unstructured":"Fuqua WC, Winans SC, Greenberg EP (1994) Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol 176:269\u2013275","journal-title":"J Bacteriol"},{"key":"7177_CR56","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1164\/rccm.200304-505SO","volume":"168","author":"RL Gibson","year":"2003","unstructured":"Gibson RL, Burns JL, Ramsey BW (2003) Pathophysiology and management of pulmonary infections in cystic fibrosis. Am J Respir Crit Care Med 168:918\u2013951. doi: 10.1164\/rccm.200304-505SO","journal-title":"Am J Respir Crit Care Med"},{"key":"7177_CR57","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1136\/thx.2006.060889","volume":"62","author":"CH Goss","year":"2007","unstructured":"Goss CH, Burns JL (2007) Exacerbations in cystic fibrosis. 1: epidemiology and pathogenesis. Thorax 62:360\u2013367. doi: 10.1136\/thx.2006.060889","journal-title":"Thorax"},{"key":"7177_CR58","unstructured":"Government US a (2013) Annual Data Report."},{"key":"7177_CR59","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/ismej.2010.88","volume":"5","author":"AM Guss","year":"2011","unstructured":"Guss AM, Roeselers G, Newton ILG, Young CR, Klepac-Ceraj V, Lory S, Cavanaugh CM (2011) Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. Isme j 5:20\u201329. doi: 10.1038\/ismej.2010.88","journal-title":"Isme j"},{"key":"7177_CR60","doi-asserted-by":"crossref","first-page":"20529","DOI":"10.1073\/pnas.0709804104","volume":"104","author":"JK Harris","year":"2007","unstructured":"Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, Kaess H, Deterding RR, Accurso FJ, Pace NR (2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A 104:20529\u201320533. doi: 10.1073\/pnas.0709804104","journal-title":"Proc Natl Acad Sci U S A"},{"key":"7177_CR61","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1099\/mic.0.2006\/004077-0","volume":"153","author":"F Harrison","year":"2007","unstructured":"Harrison F (2007) Microbial ecology of the cystic fibrosis lung. Microbiology 153:917\u2013923. doi: 10.1099\/mic.0.2006\/004077-0","journal-title":"Microbiology"},{"key":"7177_CR62","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1016\/S0169-409X(02)00152-7","volume":"54","author":"DJ Hassett","year":"2002","unstructured":"Hassett DJ, Cuppoletti J, Trapnell B, Lymar SV, Rowe JJ, Yoon SS, Hilliard GM, Parvatiyar K, Kamani MC, Wozniak DJ, Hwang SH, McDermott TR, Ochsner UA (2002) Anaerobic metabolism and quorum sensing by Pseudomonas aeruginosa biofilms in chronically infected cystic fibrosis airways: rethinking antibiotic treatment strategies and drug targets. Adv Drug Deliv Rev 54:1425\u20131443","journal-title":"Adv Drug Deliv Rev"},{"key":"7177_CR63","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1517\/14728220903454988","volume":"14","author":"DJ Hassett","year":"2010","unstructured":"Hassett DJ, Korfhagen TR, Irvin RT, Schurr MJ, Sauer K, Lau GW, Sutton MD, Yu H, Hoiby N (2010) Pseudomonas aeruginosa biofilm infections in cystic fibrosis: insights into pathogenic processes and treatment strategies. Expert Opin Ther Targets 14:117\u2013130. doi: 10.1517\/14728220903454988","journal-title":"Expert Opin Ther Targets"},{"key":"7177_CR64","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.tim.2008.12.003","volume":"17","author":"DJ Hassett","year":"2009","unstructured":"Hassett DJ, Sutton MD, Schurr MJ, Herr AB, Caldwell CC, Matu JO (2009) Pseudomonas aeruginosa hypoxic or anaerobic biofilm infections within cystic fibrosis airways. Trends Microbiol 17:130\u2013138. doi: 10.1016\/j.tim.2008.12.003","journal-title":"Trends Microbiol"},{"key":"7177_CR65","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1128\/CMR.00036-10","volume":"24","author":"AR Hauser","year":"2011","unstructured":"Hauser AR, Jain M, Bar-Meir M, McColley SA (2011) Clinical significance of microbial infection and adaptation in cystic fibrosis. Clin Microbiol Rev 24:29\u201370. doi: 10.1128\/CMR.00036-10","journal-title":"Clin Microbiol Rev"},{"key":"7177_CR66","doi-asserted-by":"crossref","first-page":"e90934","DOI":"10.1371\/journal.pone.0090934","volume":"9","author":"PM Hauser","year":"2014","unstructured":"Hauser PM, Bernard T, Greub G, Jaton K, Pagni M, Hafen GM (2014) Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. PLoS One 9:e90934. doi: 10.1371\/journal.pone.0090934","journal-title":"PLoS One"},{"key":"7177_CR67","doi-asserted-by":"crossref","first-page":"3091","DOI":"10.1128\/JCM.00460-09","volume":"47","author":"PW Hickey","year":"2009","unstructured":"Hickey PW, Sutton DA, Fothergill AW, Rinaldi MG, Wickes BL, Schmidt HJ, Walsh TJ (2009) Trichosporon mycotoxinivorans, a novel respiratory pathogen in patients with cystic fibrosis. J Clin Microbiol 47:3091\u20133097. doi: 10.1128\/JCM.00460-09","journal-title":"J Clin Microbiol"},{"key":"7177_CR68","doi-asserted-by":"crossref","first-page":"19890","DOI":"10.1073\/pnas.0606756104","volume":"103","author":"LR Hoffman","year":"2006","unstructured":"Hoffman LR, D\u00e9ziel E, D\u2019Argenio DA, L\u00e9pine F, Emerson J, McNamara S, Gibson RL, Ramsey BW, Miller SI (2006) Selection for Staphylococcus aureus small-colony variants due to growth in the presence of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 103:19890\u201319895. doi: 10.1073\/pnas.0606756104","journal-title":"Proc Natl Acad Sci U S A"},{"key":"7177_CR69","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1111\/j.1365-2958.2004.04349.x","volume":"54","author":"D A Hogan","year":"2004","unstructured":"Hogan DA, Vik \u00c5, Kolter R (2004) A Pseudomonas aeruginosa quorum-sensing molecule influences Candida albicans morphology. Mol Microbiol 54:1212\u20131223. doi: 10.1111\/j.1365-2958.2004.04349.x","journal-title":"Mol Microbiol"},{"key":"7177_CR70","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1016\/j.ijantimicag.2009.12.011","volume":"35","author":"N H\u00f8iby","year":"2010","unstructured":"H\u00f8iby N, Bjarnsholt T, Givskov M, Molin S, Ciofu O (2010a) Antibiotic resistance of bacterial biofilms. Int J Antimicrob Agents 35:322\u2013332. doi: 10.1016\/j.ijantimicag.2009.12.011","journal-title":"Int J Antimicrob Agents"},{"key":"7177_CR71","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.2217\/fmb.10.125","volume":"5","author":"N H\u00f8iby","year":"2010","unstructured":"H\u00f8iby N, Ciofu O, Bjarnsholt T (2010b) Pseudomonas aeruginosa biofilms in cystic fibrosis. Future Microbiol 5:1663\u20131674. doi: 10.2217\/fmb.10.125","journal-title":"Future Microbiol"},{"key":"7177_CR72","doi-asserted-by":"crossref","first-page":"55","DOI":"10.4248\/IJOS11026","volume":"3","author":"N H\u00f8iby","year":"2011","unstructured":"H\u00f8iby N, Ciofu O, Johansen HK, Song Z, Moser C, Jensen P\u00d8, Molin S, Givskov M, Tolker-Nielsen T, Bjarnsholt T (2011) The clinical impact of bacterial biofilms. Int J Oral Sci 3:55\u201365. doi: 10.4248\/IJOS11026","journal-title":"Int J Oral Sci"},{"key":"7177_CR73","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1099\/mic.0.037549-0","volume":"156","author":"LJ Holcombe","year":"2010","unstructured":"Holcombe LJ, McAlester G, Munro CA, Enjalbert B, AJP B, N. A. R G, Ding C, Butler G, O\u2019Gara F, Morrissey JP (2010) Pseudomonas aeruginosa secreted factors impair biofilm development in Candida albicans. Microbiology 156:1476\u20131485. doi: 10.1099\/mic.0.037549-0","journal-title":"Microbiology"},{"key":"7177_CR74","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.ejpb.2013.10.019","volume":"86","author":"M Hoppentocht","year":"2014","unstructured":"Hoppentocht M, Hagedoorn P, Frijlink HW, de Boer AH (2014) Developments and strategies for inhaled antibiotic drugs in tuberculosis therapy: a critical evaluation. Eur J Pharm Biopharm 86:23\u201330. doi: 10.1016\/j.ejpb.2013.10.019","journal-title":"Eur J Pharm Biopharm"},{"key":"7177_CR75","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1586\/ers.11.76","volume":"5","author":"YJ Huang","year":"2011","unstructured":"Huang YJ, Lynch SV (2011) The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med 5:809\u2013821. doi: 10.1586\/ers.11.76","journal-title":"Expert Rev Respir Med"},{"key":"7177_CR76","doi-asserted-by":"crossref","first-page":"603.e9","DOI":"10.1016\/j.cmi.2015.01.025","volume":"21","author":"M Iaria","year":"2015","unstructured":"Iaria M, Caccuri F, Apostoli P, Giagulli C, Pelucchi F, Padoan RF, Caruso A, Fiorentini S (2015) Detection of KI WU and Merkel cell polyomavirus in respiratory tract of cystic fibrosis patients. Clin Microbiol Infect 21:603.e9\u2013603.e15. doi: 10.1016\/j.cmi.2015.01.025","journal-title":"Clin Microbiol Infect"},{"key":"7177_CR77","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/s004310050844","volume":"157","author":"I Jacques","year":"1998","unstructured":"Jacques I, Derelle J, Weber M, Vidailhet M (1998) Pulmonary evolution of cystic fibrosis patients colonized by Pseudomonas aeruginosa and\/or Burkholderia cepacia. Eur J Pediatr 157:427\u2013431","journal-title":"Eur J Pediatr"},{"key":"7177_CR78","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1016\/j.ijmm.2010.08.002","volume":"300","author":"BC Kahl","year":"2010","unstructured":"Kahl BC (2010) Impact of Staphylococcus aureus on the pathogenesis of chronic cystic fibrosis lung disease. Int J Med Microbiol 300:514\u2013519. doi: 10.1016\/j.ijmm.2010.08.002","journal-title":"Int J Med Microbiol"},{"key":"7177_CR79","unstructured":"Kenney DMC, Brown KE, Allison DG (1995) Influence of Pseudomonas aeruginosa exoproducts on virulence factor production in Burkholderia cepacia\u202f: evidence of interspecies communication. Influ Pseudomonas aeruginosa Exoproducts Virulence Factor Prod Burkholderia Cepacia\u202f: Evid 177:6989\u20136992"},{"key":"7177_CR80","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1128\/JCM.00014-09","volume":"47","author":"TJ Kidd","year":"2009","unstructured":"Kidd TJ, Ramsay KA, Hu H, Bye PTP, Elkins MR, Grimwood K, Harbour C, Marks GB, Nissen MD, Robinson PJ, Rose BR, Sloots TP, Wainwright CE, Bell SC (2009) Low rates of Pseudomonas aeruginosa misidentification in isolates from cystic fibrosis patients. J Clin Microbiol 47:1503\u20131509. doi: 10.1128\/JCM.00014-09","journal-title":"J Clin Microbiol"},{"key":"7177_CR81","doi-asserted-by":"crossref","unstructured":"Kim YJ, Paek SH, Jin S, Park BS, Ha UH (2014) A novel Pseudomonas aeruginosa-derived effector cooperates with flagella to mediate the upregulation of interleukin 8 in human epithelial cells. Microb Pathog 66:24\u201328. doi: 10.1016\/j.micpath.2013.12.001","DOI":"10.1016\/j.micpath.2013.12.001"},{"key":"7177_CR82","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.prrv.2010.10.011","volume":"12","author":"P King","year":"2011","unstructured":"King P (2011) Pathogenesis of bronchiectasis. Paediatr Respir Rev 12:104\u2013110. doi: 10.1016\/j.prrv.2010.10.011","journal-title":"Paediatr Respir Rev"},{"key":"7177_CR83","doi-asserted-by":"crossref","first-page":"59","DOI":"10.2147\/CE.S11181","volume":"6","author":"S Kirkby","year":"2011","unstructured":"Kirkby S, Novak K, McCoy K (2011) Aztreonam (for inhalation solution) for the treatment of chronic lung infections in patients with cystic fibrosis: an evidence-based review. Core Evid 6:59\u201366. doi: 10.2147\/CE.S11181","journal-title":"Core Evid"},{"key":"7177_CR84","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1078\/1438-4221-00265","volume":"293","author":"M Kolak","year":"2003","unstructured":"Kolak M, Karpati F, Monstein H-J, Jonasson J (2003) Molecular typing of the bacterial flora in sputum of cystic fibrosis patients. Int J Med Microbiol 293:309\u2013317. doi: 10.1078\/1438-4221-00265","journal-title":"Int J Med Microbiol"},{"key":"7177_CR85","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1073\/pnas.1214550110","volume":"110","author":"A Korgaonkar","year":"2013","unstructured":"Korgaonkar A, Trivedi U, Rumbaugh KP, Whiteley M (2013) Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection. Proc Natl Acad Sci U S A 110:1059\u20131064. doi: 10.1073\/pnas.1214550110","journal-title":"Proc Natl Acad Sci U S A"},{"key":"7177_CR86","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1189\/jlb.0910513","volume":"89","author":"S Kotrange","year":"2011","unstructured":"Kotrange S, Kopp B, Akhter A, Abdelaziz D, Abu Khweek A, Caution K, Abdulrahman B, Wewers MD, McCoy K, Marsh C, Loutet SA, Ortega X, Valvano MA, Amer AO (2011) Burkholderia cenocepacia O polysaccharide chain contributes to caspase-1-dependent IL-1beta production in macrophages. J Leukoc Biol 89:481\u2013488. doi: 10.1189\/jlb.0910513","journal-title":"J Leukoc Biol"},{"key":"7177_CR87","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1007\/BF02113255","volume":"151","author":"G Kusenbach","year":"1992","unstructured":"Kusenbach G, Skopnik H, Haase G, Friedrichs F, D\u00f6hmen H (1992) Exophiala dermatitidis pneumonia in cystic fibrosis. Eur J Pediatr 151:344\u2013346","journal-title":"Eur J Pediatr"},{"key":"7177_CR88","first-page":"61","volume":"7","author":"J Lam","year":"2013","unstructured":"Lam J, Vaughan S, Parkins MD (2013) Tobramycin inhalation powder (TIP): an efficient treatment strategy for the management of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Clin Med Insights Circ Respir Pulm Med 7:61\u201377. doi: 10.4137\/CCRPM.S10592","journal-title":"Clin Med Insights Circ Respir Pulm Med"},{"issue":"Suppl 4","key":"7177_CR89","first-page":"22","volume":"95","author":"PA Lambert","year":"2002","unstructured":"Lambert PA (2002) Mechanisms of antibiotic resistance in Pseudomonas aeruginosa. J R Soc Med 95(Suppl 4):22\u201326","journal-title":"J R Soc Med"},{"key":"7177_CR90","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.diagmicrobio.2009.06.011","volume":"66","author":"RS Le\u00e3o","year":"2010","unstructured":"Le\u00e3o RS, Pereira RHV, Ferreira AG, Lima AN, Albano RM, Marques EA (2010) First report of Paenibacillus cineris from a patient with cystic fibrosis. Diagn Microbiol Infect Dis 66:101\u2013103. doi: 10.1016\/j.diagmicrobio.2009.06.011","journal-title":"Diagn Microbiol Infect Dis"},{"key":"7177_CR91","doi-asserted-by":"crossref","first-page":"156","DOI":"10.4065\/mcp.2010.0639","volume":"86","author":"S Leekha","year":"2011","unstructured":"Leekha S, Terrell CL, Edson RS (2011) General principles of antimicrobial therapy. Mayo Clin Proc 86:156\u2013167. doi: 10.4065\/mcp.2010.0639","journal-title":"Mayo Clin Proc"},{"key":"7177_CR92","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1128\/JCM.02204-13","volume":"52","author":"YW Lim","year":"2014","unstructured":"Lim YW, Evangelista JS, Schmieder R, Bailey B, Haynes M, Furlan M, Maughan H, Edwards R, Rohwer F, Conrad D, Forbes BA (2014) Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. J Clin Microbiol 52:425\u2013437. doi: 10.1128\/JCM.02204-13","journal-title":"J Clin Microbiol"},{"key":"7177_CR93","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.jcf.2012.07.009","volume":"12","author":"YW Lim","year":"2013","unstructured":"Lim YW, Schmieder R, Haynes M, Willner D, Furlan M, Youle M, Abbott K, Edwards R, Evangelista J, Conrad D, Rohwer F (2013) Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J Cyst Fibros 12:154\u2013164. doi: 10.1016\/j.jcf.2012.07.009","journal-title":"J Cyst Fibros"},{"key":"7177_CR94","author":"SP Lopes","year":"2014","unstructured":"Lopes SP, Azevedo NF, Pereira MO (2014a) Microbiome in cystic fibrosis: shaping polymicrobial interactions for advances in antibiotic therapy. Crit Rev Microbiol. doi: 10.3109\/1040841X.2013.847898","journal-title":"Crit Rev Microbiol"},{"key":"7177_CR95","first-page":"678301","volume":"2014","author":"SP Lopes","year":"2014","unstructured":"Lopes SP, Azevedo NF, Pereira MO (2014b) Emergent bacteria in cystic fibrosis: in vitro biofilm formation and resilience under variable oxygen conditions. Biomed Res Int 2014:678301. doi: 10.1155\/2014\/678301","journal-title":"Biomed Res Int"},{"key":"7177_CR96","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.ijantimicag.2012.04.020","volume":"40","author":"SP Lopes","year":"2012","unstructured":"Lopes SP, Ceri H, Azevedo NF, Pereira MO (2012) Antibiotic resistance of mixed biofilms in cystic fibrosis: impact of emerging microorganisms on treatment of infection. Int J Antimicrob Agents 40:260\u2013263. doi: 10.1016\/j.ijantimicag.2012.04.020","journal-title":"Int J Antimicrob Agents"},{"key":"7177_CR97","doi-asserted-by":"crossref","first-page":"e35648","DOI":"10.1371\/journal.pone.0035648","volume":"7","author":"NI Lor\u00e8","year":"2012","unstructured":"Lor\u00e8 NI, Cigana C, De Fino I, Riva C, Juhas M, Schwager S, Eberl L, Bragonzi A (2012) Cystic fibrosis-niche adaptation of Pseudomonas aeruginosa reduces virulence in multiple infection hosts. PLoS One 7:e35648. doi: 10.1371\/journal.pone.0035648","journal-title":"PLoS One"},{"key":"7177_CR98","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1007\/s10096-001-0687-8","volume":"21","author":"R Lumb","year":"2002","unstructured":"Lumb R, Greville H, Martin J, Sangster N, Holmes M (2002) Nocardia asteroides isolated from three patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 21:230\u2013233. doi: 10.1007\/s10096-001-0687-8","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"7177_CR99","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1128\/CMR.15.2.194-222.2002","volume":"15","author":"JB Lyczak","year":"2002","unstructured":"Lyczak JB, Cannon CL, Pier GB (2002) Lung infections associated with cystic fibrosis. Clin Microbiol Rev 15:194\u2013222","journal-title":"Clin Microbiol Rev"},{"key":"7177_CR100","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1055\/s-0029-1238918","volume":"30","author":"JP Lynch","year":"2009","unstructured":"Lynch JP (2009) Burkholderia cepacia complex: impact on the cystic fibrosis lung lesion. Semin Respir Crit Care Med 30:596\u2013610. doi: 10.1055\/s-0029-1238918","journal-title":"Semin Respir Crit Care Med"},{"key":"7177_CR101","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1093\/jac\/dkp282","volume":"64","author":"DL MacLeod","year":"2009","unstructured":"MacLeod DL, Barker LM, Sutherland JL, Moss SC, Gurgel JL, Kenney TF, Burns JL, Baker WR (2009) Antibacterial activities of a fosfomycin\/tobramycin combination: a novel inhaled antibiotic for bronchiectasis. J Antimicrob Chemother 64:829\u2013836. doi: 10.1093\/jac\/dkp282","journal-title":"J Antimicrob Chemother"},{"key":"7177_CR102","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1517\/14656566.2013.790366","volume":"14","author":"L M\u00e1iz","year":"2013","unstructured":"M\u00e1iz L, Gir\u00f3n RM, Olveira C, Quintana E, Lamas A, Pastor D, Cant\u00f3n R, Mensa J (2013) Inhaled antibiotics for the treatment of chronic bronchopulmonary Pseudomonas aeruginosa infection in cystic fibrosis: systematic review of randomised controlled trials. Expert Opin Pharmacother 14:1135\u20131149. doi: 10.1517\/14656566.2013.790366","journal-title":"Expert Opin Pharmacother"},{"key":"7177_CR103","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1111\/myc.12340","volume":"58","author":"T Matos","year":"2015","unstructured":"Matos T, Cerar T, Praprotnik M, Krivec U, Pir\u0161 M (2015) First recovery of Rasamsonia argillacea species complex isolated in adolescent patient with cystic fibrosis in Slovenia\u2014case report and review of literature. Mycoses 58:506\u2013510. doi: 10.1111\/myc.12340","journal-title":"Mycoses"},{"key":"7177_CR104","doi-asserted-by":"crossref","first-page":"e69763","DOI":"10.1371\/journal.pone.0069763","volume":"8","author":"G McCaughey","year":"2013","unstructured":"McCaughey G, Diamond P, Elborn JS, McKevitt M, Tunney MM (2013) Resistance development of cystic fibrosis respiratory pathogens when exposed to fosfomycin and tobramycin alone and in combination under aerobic and anaerobic conditions. PLoS One 8:e69763. doi: 10.1371\/journal.pone.0069763","journal-title":"PLoS One"},{"key":"7177_CR105","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.jcf.2011.11.003","volume":"11","author":"G McCaughey","year":"2012","unstructured":"McCaughey G, McKevitt M, Elborn JS, Tunney MM (2012) Antimicrobial activity of fosfomycin and tobramycin in combination against cystic fibrosis pathogens under aerobic and anaerobic conditions. J Cyst Fibros 11:163\u2013172. doi: 10.1016\/j.jcf.2011.11.003","journal-title":"J Cyst Fibros"},{"key":"7177_CR106","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/1752-1947-2-373","volume":"2","author":"M Menuet","year":"2008","unstructured":"Menuet M, Bittar F, Stremler N, Dubus J-C, Sarles J, Raoult D, Rolain J-M (2008) First isolation of two colistin-resistant emerging pathogens, Brevundimonas diminuta and Ochrobactrum anthropi, in a woman with cystic fibrosis: a case report. J Med Case Rep 2:373. doi: 10.1186\/1752-1947-2-373","journal-title":"J Med Case Rep"},{"key":"7177_CR107","doi-asserted-by":"crossref","first-page":"13811","DOI":"10.1073\/pnas.1206855109","volume":"109","author":"WJ Moree","year":"2012","unstructured":"Moree WJ, Phelan VV, Wu C-H, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC (2012) Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proc Natl Acad Sci 109:13811\u201313816. doi: 10.1073\/pnas.1206855109","journal-title":"Proc Natl Acad Sci"},{"key":"7177_CR108","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1128\/JCM.42.5.1915-1922.2004","volume":"42","author":"SM Moskowitz","year":"2004","unstructured":"Moskowitz SM, Foster JM, Emerson J, Burns JL (2004) Clinically feasible biofilm susceptibility assay for isolates of Pseudomonas aeruginosa from patients with cystic fibrosis. J Clin Microbiol 42:1915\u20131922","journal-title":"J Clin Microbiol"},{"key":"7177_CR109","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1111\/j.1574-6968.2010.02130.x","volume":"313","author":"E Mowat","year":"2010","unstructured":"Mowat E, Rajendran R, Williams C, McCulloch E, Jones B, Lang S, Ramage G (2010) Pseudomonas aeruginosa and their small diffusible extracellular molecules inhibit Aspergillus fumigatus biofilm formation. FEMS Microbiol Lett 313:96\u2013102. doi: 10.1111\/j.1574-6968.2010.02130.x","journal-title":"FEMS Microbiol Lett"},{"key":"7177_CR110","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1007\/s12275-014-4067-3","volume":"52","author":"JL Murray","year":"2014","unstructured":"Murray JL, Connell JL, Stacy A, Turner KH, Whiteley M (2014) Mechanisms of synergy in polymicrobial infections. J Microbiol 52:188\u2013199. doi: 10.1007\/s12275-014-4067-3","journal-title":"J Microbiol"},{"key":"7177_CR111","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1136\/adc.2007.119503","volume":"92","author":"Y Nagano","year":"2007","unstructured":"Nagano Y, Millar BC, Goldsmith CE, Elborn JS, Rendall J, Moore JE (2007) Emergence of Scedosporium apiospermum in patients with cystic fibrosis. Arch Dis Child 92:607\u2013607. doi: 10.1136\/adc.2007.119503","journal-title":"Arch Dis Child"},{"key":"7177_CR112","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1067\/mpd.2001.112897","volume":"138","author":"GM Nixon","year":"2001","unstructured":"Nixon GM, Armstrong DS, Carzino R, Carlin JB, Olinsky A, Robertson CF, Grimwood K (2001) Clinical outcome after early Pseudomonas aeruginosa infection in cystic fibrosis. J Pediatr 138:699\u2013704. doi: 10.1067\/mpd.2001.112897","journal-title":"J Pediatr"},{"key":"7177_CR113","doi-asserted-by":"crossref","first-page":"e0126980","DOI":"10.1371\/journal.pone.0126980","volume":"10","author":"K O\u2019Neill","year":"2015","unstructured":"O\u2019Neill K, Bradley JM, Johnston E, McGrath S, McIlreavey L, Rowan S, Reid A, Bradbury I, Einarsson G, Elborn JS, Tunney MM (2015) Reduced bacterial colony count of anaerobic bacteria is associated with a worsening in lung clearance index and inflammation in cystic fibrosis. PLoS One 10:e0126980. doi: 10.1371\/journal.pone.0126980","journal-title":"PLoS One"},{"key":"7177_CR114","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1002\/ppul.20517","volume":"41","author":"HV Olesen","year":"2006","unstructured":"Olesen HV, Nielsen LP, Schiotz PO (2006) Viral and atypical bacterial infections in the outpatient pediatric cystic fibrosis clinic. Pediatr Pulmonol 41:1197\u20131204. doi: 10.1002\/ppul.20517","journal-title":"Pediatr Pulmonol"},{"key":"7177_CR115","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/j.ijmm.2010.08.009","volume":"300","author":"A Oliver","year":"2010","unstructured":"Oliver A (2010) Mutators in cystic fibrosis chronic lung infection: prevalence, mechanisms, and consequences for antimicrobial therapy. Int J Med Microbiol 300:563\u2013572. doi: 10.1016\/j.ijmm.2010.08.009","journal-title":"Int J Med Microbiol"},{"key":"7177_CR116","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1128\/IAI.00054-13","volume":"81","author":"YR Patankar","year":"2013","unstructured":"Patankar YR, Lovewell RR, Poynter ME, Jyot J, Kazmierczak BI, Berwin B (2013) Flagellar motility is a key determinant of the magnitude of the inflammasome response to Pseudomonas aeruginosa. Infect Immun 81:2043\u20132052. doi: 10.1128\/IAI.00054-13","journal-title":"Infect Immun"},{"key":"7177_CR117","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1128\/CMR.00013-11","volume":"25","author":"BM Peters","year":"2012","unstructured":"Peters BM, Jabra-Rizk MA, O\u2019May GA, Costerton JW, Shirtliff ME, William Costerton J, Shirtliff ME (2012) Polymicrobial interactions: impact on pathogenesis and human disease. Clin Microbiol Rev 25:193\u2013213. doi: 10.1128\/CMR.00013-11","journal-title":"Clin Microbiol Rev"},{"key":"7177_CR118","doi-asserted-by":"crossref","first-page":"L575","DOI":"10.1152\/ajplung.00226.2010","volume":"301","author":"R Pilkington","year":"2011","unstructured":"Pilkington R, Callaghan M, McClean S (2011) Activation of MMP-9 by human lung epithelial cells in response to the cystic fibrosis-associated pathogen Burkholderia cenocepacia reduced wound healing in. Am J Physiol - Lung Cell Mol Physiol 301:L575\u2013L586. doi: 10.1152\/ajplung.00226.2010","journal-title":"Am J Physiol - Lung Cell Mol Physiol"},{"key":"7177_CR119","doi-asserted-by":"crossref","first-page":"951","DOI":"10.3389\/fmicb.2015.00951","volume":"6","author":"A Pompilio","year":"2015","unstructured":"Pompilio A, Crocetta V, De Nicola S, Verginelli F, Fiscarelli E, Di Bonaventura G (2015) Cooperative pathogenicity in cystic fibrosis: Stenotrophomonas maltophilia modulates Pseudomonas aeruginosa virulence in mixed biofilm. Front Microbiol 6:951. doi: 10.3389\/fmicb.2015.00951","journal-title":"Front Microbiol"},{"key":"7177_CR120","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/2049-2618-1-27","volume":"1","author":"KE Price","year":"2013","unstructured":"Price KE, Hampton TH, Gifford AH, Dolben EL, Hogan DA, Morrison HG, Sogin ML, O\u2019Toole GA (2013) Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Microbiome 1:27. doi: 10.1186\/2049-2618-1-27","journal-title":"Microbiome"},{"key":"7177_CR121","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1128\/IAI.02234-14","volume":"83","author":"C Pustelny","year":"2015","unstructured":"Pustelny C, Komor U, Pawar V, Lorenz A, Bielecka A, Moter A, Gocht B, Eckweiler D, M\u00fcsken M, Grothe C, L\u00fcnsdorf H, Weiss S, H\u00e4ussler S (2015) Contribution of veillonella parvula to Pseudomonas aeruginosa-mediated pathogenicity in a murine tumor model system. Infect Immun 83:417\u2013429. doi: 10.1128\/IAI.02234-14","journal-title":"Infect Immun"},{"key":"7177_CR122","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1513\/AnnalsATS.201310-346OC","volume":"11","author":"IA Ramirez","year":"2014","unstructured":"Ramirez IA, Caverly LL, Kalikin LM, Goldsmith AM, Lewis TC, Burke DT, JJ LP, Sajjan US, Hershenson MB (2014) Differential responses to rhinovirus- and influenza-associated pulmonary exacerbations in patients with cystic fibrosis. Ann Am Thorac Soc 11:554\u2013561. doi: 10.1513\/AnnalsATS.201310-346OC","journal-title":"Ann Am Thorac Soc"},{"key":"7177_CR123","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1056\/NEJMoa1105185","volume":"365","author":"BW Ramsey","year":"2011","unstructured":"Ramsey BW, Davies J, McElvaney NG, Tullis E, Bell SC, D\u0159ev\u00ednek P, Griese M, McKone EF, Wainwright CE, Konstan MW, Moss R, Ratjen F, Sermet-Gaudelus I, Rowe SM, Dong Q, Rodriguez S, Yen K, Ordo\u00f1ez C, Elborn JS (2011) A CFTR potentiator in patients with cystic fibrosis and the G551D mutation. N Engl J Med 365:1663\u20131672. doi: 10.1056\/NEJMoa1105185","journal-title":"N Engl J Med"},{"key":"7177_CR124","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nrd3013","volume":"9","author":"DA Rasko","year":"2010","unstructured":"Rasko DA, Sperandio V (2010) Anti-virulence strategies to combat bacteria-mediated disease. Nat Rev Drug Discov 9:117\u2013128. doi: 10.1038\/nrd3013","journal-title":"Nat Rev Drug Discov"},{"key":"7177_CR125","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1378\/chest.09-0132","volume":"136","author":"S Razvi","year":"2009","unstructured":"Razvi S, Quittell L, Sewall A, Quinton H, Marshall B, Saiman L (2009) Respiratory microbiology of patients with cystic fibrosis in the United States, 1995 to 2005. Chest 136:1554\u20131560. doi: 10.1378\/chest.09-0132","journal-title":"Chest"},{"key":"7177_CR126","doi-asserted-by":"crossref","first-page":"5176","DOI":"10.1128\/JCM.42.11.5176-5183.2004","volume":"42","author":"GB Rogers","year":"2004","unstructured":"Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, Bruce KD (2004) 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 42:5176\u20135183. doi: 10.1128\/JCM.42.11.5176-5183.2004","journal-title":"J Clin Microbiol"},{"key":"7177_CR127","doi-asserted-by":"crossref","first-page":"3548","DOI":"10.1128\/JCM.41.8.3548-3558.2003","volume":"41","author":"GB Rogers","year":"2003","unstructured":"Rogers GB, Hart CA, Mason JR, Hughes M, Walshaw MJ, Bruce KD (2003) Bacterial diversity in cases of lung infection in cystic fibrosis patients: 16S ribosomal DNA (rDNA) length heterogeneity PCR and 16S rDNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol 41:3548\u20133558","journal-title":"J Clin Microbiol"},{"key":"7177_CR128","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.tim.2013.03.004","volume":"21","author":"GB Rogers","year":"2013","unstructured":"Rogers GB, Hoffman LR, Carroll MP, Bruce KD (2013) Interpreting infective microbiota: the importance of an ecological perspective. Trends Microbiol 21:271\u2013276. doi: 10.1016\/j.tim.2013.03.004","journal-title":"Trends Microbiol"},{"key":"7177_CR129","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1056\/NEJMra043184","volume":"352","author":"SM Rowe","year":"2005","unstructured":"Rowe SM, Miller S, Sorscher EJ (2005) Cystic fibrosis. N Engl J Med 352:1992\u20132001. doi: 10.1056\/NEJMra043184","journal-title":"N Engl J Med"},{"key":"7177_CR130","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/1471-2180-14-56","volume":"14","author":"M R\u00fcger","year":"2014","unstructured":"R\u00fcger M, Ackermann M, Reichl U (2014) Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry. BMC Microbiol 14:56. doi: 10.1186\/1471-2180-14-56","journal-title":"BMC Microbiol"},{"key":"7177_CR131","author":"ST Rutherford","year":"2012","unstructured":"Rutherford ST, Bassler BL (2012) Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb Perspect Med. doi: 10.1101\/cshperspect.a012427","journal-title":"Cold Spring Harb Perspect Med"},{"key":"7177_CR132","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/j.ijmm.2010.08.007","volume":"300","author":"M Schobert","year":"2010","unstructured":"Schobert M, Jahn D (2010) Anaerobic physiology of Pseudomonas aeruginosa in the cystic fibrosis lung. Int J Med Microbiol 300:549\u2013556. doi: 10.1016\/j.ijmm.2010.08.007","journal-title":"Int J Med Microbiol"},{"key":"7177_CR133","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1093\/jac\/dku192","volume":"69","author":"LJ Sherrard","year":"2014","unstructured":"Sherrard LJ, Schaible B, Graham KA, McGrath SJ, McIlreavey L, Hatch J, Wolfgang MC, Muhlebach MS, Gilpin DF, Schneiders T, Elborn JS, Tunney MM (2014) Mechanisms of reduced susceptibility and genotypic prediction of antibiotic resistance in Prevotella isolated from cystic fibrosis (CF) and non-CF patients. J Antimicrob Chemother 69:2690\u20132698. doi: 10.1093\/jac\/dku192","journal-title":"J Antimicrob Chemother"},{"key":"7177_CR134","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1016\/j.tim.2014.05.007","volume":"22","author":"FL Short","year":"2014","unstructured":"Short FL, Murdoch SL, Ryan RP (2014) Polybacterial human disease: the ills of social networking. Trends Microbiol 22:508\u2013516. doi: 10.1016\/j.tim.2014.05.007","journal-title":"Trends Microbiol"},{"key":"7177_CR135","doi-asserted-by":"crossref","first-page":"e1000184","DOI":"10.1371\/journal.ppat.1000184","volume":"4","author":"CD Sibley","year":"2008","unstructured":"Sibley CD, Duan K, Fischer C, Parkins MD, Storey DG, Rabin HR, Surette MG (2008) Discerning the complexity of community interactions using a Drosophila model of polymicrobial infections. PLoS Pathog 4:e1000184. doi: 10.1371\/journal.ppat.1000184","journal-title":"PLoS Pathog"},{"key":"7177_CR136","doi-asserted-by":"crossref","first-page":"53","DOI":"10.2217\/17460913.1.1.53","volume":"1","author":"CD Sibley","year":"2006","unstructured":"Sibley CD, Rabin H, Surette MG (2006) Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol 1:53\u201361. doi: 10.2217\/17460913.1.1.53","journal-title":"Future Microbiol"},{"key":"7177_CR137","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1136\/adc.73.2.117","volume":"73","author":"AR Smyth","year":"1995","unstructured":"Smyth AR, Smyth RL, Tong CY, Hart CA, Heaf DP (1995) Effect of respiratory virus infections including rhinovirus on clinical status in cystic fibrosis. Arch Dis Child 73:117\u2013120","journal-title":"Arch Dis Child"},{"key":"7177_CR138","doi-asserted-by":"crossref","unstructured":"Sousa AM, Pereira MO (2014) Pseudomonas aeruginosa diversification during infection development in cystic fibrosis lungs\u2014a review. Pathog (Basel, Switzerland) 3:680\u2013703. doi: 10.3390\/pathogens3030680","DOI":"10.3390\/pathogens3030680"},{"key":"7177_CR139","doi-asserted-by":"crossref","first-page":"29","DOI":"10.4137\/MBI.S10792","volume":"6","author":"D Sriramulu","year":"2013","unstructured":"Sriramulu D (2013) Evolution and impact of bacterial drug resistance in the context of cystic fibrosis disease and nosocomial settings. Microbiol Insights 6:29\u201336. doi: 10.4137\/MBI.S10792","journal-title":"Microbiol Insights"},{"key":"7177_CR140","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1099\/jmm.0.45969-0","volume":"54","author":"DD Sriramulu","year":"2005","unstructured":"Sriramulu DD, L\u00fcnsdorf H, Lam JS, R\u00f6mling U (2005) Microcolony formation: a novel biofilm model of Pseudomonas aeruginosa for the cystic fibrosis lung. J Med Microbiol 54:667\u2013676. doi: 10.1099\/jmm.0.45969-0","journal-title":"J Med Microbiol"},{"key":"7177_CR141","first-page":"1945","volume":"86","author":"TJ Standiford","year":"1990","unstructured":"Standiford TJ, Kunkel SL, Basha MA, Chensue SW, Lynch JP, Toews GB, Westwick J, Strieter RM (1990) Interleukin-8 gene expression by a pulmonary epithelial cell line. A Model for Cytokine Networks in the Lung J Clin Invest 86:1945\u20131953. doi: 10.1172\/JCI114928","journal-title":"A Model for Cytokine Networks in the Lung J Clin Invest"},{"key":"7177_CR142","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1164\/rccm.200509-1459OC","volume":"174","author":"TD Starner","year":"2006","unstructured":"Starner TD, Zhang N, Kim G, Apicella MA, McCray PB (2006) Haemophilus influenzae forms biofilms on airway epithelia: implications in cystic fibrosis. Am J Respir Crit Care Med 174:213\u2013220. doi: 10.1164\/rccm.200509-1459OC","journal-title":"Am J Respir Crit Care Med"},{"key":"7177_CR143","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1136\/thoraxjnl-2011-200932","volume":"67","author":"FA Stressmann","year":"2012","unstructured":"Stressmann FA, Rogers GB, van der Gast CJ, Marsh P, Vermeer LS, Carroll MP, Hoffman L, Daniels TWV, Patel N, Forbes B, Bruce KD (2012) Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience. Thorax 67:867\u2013873. doi: 10.1136\/thoraxjnl-2011-200932","journal-title":"Thorax"},{"key":"7177_CR144","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1517\/17425240903110710","volume":"6","author":"D Traini","year":"2009","unstructured":"Traini D, Young PM (2009) Delivery of antibiotics to the respiratory tract: an update. Expert Opin Drug Deliv 6:897\u2013905. doi: 10.1517\/17425240903110710","journal-title":"Expert Opin Drug Deliv"},{"key":"7177_CR145","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1002\/ppul.20665","volume":"42","author":"MM Treggiari","year":"2007","unstructured":"Treggiari MM, Rosenfeld M, Retsch-Bogart G, Gibson R, Ramsey B (2007) Approach to eradication of initial Pseudomonas aeruginosa infection in children with cystic fibrosis. Pediatr Pulmonol 42:751\u2013756. doi: 10.1002\/ppul.20665","journal-title":"Pediatr Pulmonol"},{"key":"7177_CR146","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1164\/rccm.200708-1151OC","volume":"177","author":"MM Tunney","year":"2008","unstructured":"Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G, Muhlebach MS, Wolfgang MC, Boucher R, Gilpin DF, McDowell A, Elborn JS (2008) Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med 177:995\u20131001. doi: 10.1164\/rccm.200708-1151OC","journal-title":"Am J Respir Crit Care Med"},{"key":"7177_CR147","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1136\/thx.2010.137281","volume":"66","author":"MM Tunney","year":"2011","unstructured":"Tunney MM, Klem ER, Fodor AA, Gilpin DF, Moriarty TF, Mcgrath SJ, Muhlebach MS, Boucher RC, Cardwell C, Doering G, Elborn JS, Wolfgang MC (2011) 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 66:579\u2013584. doi: 10.1136\/thx.2010.137281","journal-title":"Thorax"},{"key":"7177_CR148","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1038\/ismej.2011.167","volume":"6","author":"KB Twomey","year":"2012","unstructured":"Twomey KB, O\u2019Connell OJ, McCarthy Y, Dow JM, O\u2019Toole GA, Plant BJ, Ryan RP (2012) Bacterial cis-2-unsaturated fatty acids found in the cystic fibrosis airway modulate virulence and persistence of Pseudomonas aeruginosa. Isme j 6:939\u2013950. doi: 10.1038\/ismej.2011.167","journal-title":"Isme j"},{"key":"7177_CR149","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1136\/thx.2010.137745","volume":"65","author":"M Ulrich","year":"2010","unstructured":"Ulrich M, Beer I, Braitmaier P, Dierkes M, Kummer F, Krismer B, Schumacher U, Gr\u00e4pler-Mainka U, Riethm\u00fcller J, Jensen P\u00d8, Bjarnsholt T, H\u00f8iby N, Bellon G, D\u00f6ring G (2010) Relative contribution of Prevotella intermedia and Pseudomonas aeruginosa to lung pathology in airways of patients with cystic fibrosis. Thorax 65:978\u2013984. doi: 10.1136\/thx.2010.137745","journal-title":"Thorax"},{"key":"7177_CR150","doi-asserted-by":"crossref","first-page":"343","DOI":"10.2165\/11316240-000000000-00000","volume":"12","author":"M Westreenen van","year":"2010","unstructured":"van Westreenen M, Tiddens HAWM (2010) New antimicrobial strategies in cystic fibrosis. Paediatr Drugs 12:343\u2013352. doi: 10.2165\/11316240-000000000-00000","journal-title":"Paediatr Drugs"},{"key":"7177_CR151","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1128\/AAC.01024-08","volume":"53","author":"L Vettoretti","year":"2009","unstructured":"Vettoretti L, Pl\u00e9siat P, Muller C, El Garch F, Phan G, Attr\u00e9e I, Ducruix A, Llanes C (2009) Efflux unbalance in Pseudomonas aeruginosa isolates from cystic fibrosis patients. Antimicrob Agents Chemother 53:1987\u20131997. doi: 10.1128\/AAC.01024-08","journal-title":"Antimicrob Agents Chemother"},{"key":"7177_CR152","doi-asserted-by":"crossref","first-page":"20983","DOI":"10.3390\/ijms141020983","volume":"14","author":"Q Wei","year":"2013","unstructured":"Wei Q, Ma LZ (2013) Biofilm matrix and its regulation in Pseudomonas aeruginosa. Int J Mol Sci 14:20983\u201321005. doi: 10.3390\/ijms141020983","journal-title":"Int J Mol Sci"},{"key":"7177_CR153","doi-asserted-by":"crossref","unstructured":"Wellinghausen N, Wirths B, Poppert S (2006) Fluorescence in situ hybridization for rapid identification of Achromobacter xylosoxidans and Alcaligenes faecalis recovered from cystic fibrosis patients. J Clin Microbiol 44:3415\u20133417. doi: 10.1128\/JCM.00508-06","DOI":"10.1128\/JCM.00508-06"},{"key":"7177_CR154","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1038\/ismej.2013.229","volume":"8","author":"KL Whiteson","year":"2014","unstructured":"Whiteson KL, Meinardi S, Lim YW, Schmieder R, Maughan H, Quinn R, Blake DR, Conrad D, Rohwer F (2014) Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation. Isme j 8:1247\u20131258. doi: 10.1038\/ismej.2013.229","journal-title":"Isme j"},{"key":"7177_CR155","first-page":"127","volume":"15","author":"M Wilschanski","year":"2013","unstructured":"Wilschanski M (2013) Novel therapeutic approaches for cystic fibrosis. Discov Med 15:127\u2013133","journal-title":"Discov Med"},{"key":"7177_CR156","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6968.2008.01394.x","volume":"290","author":"C Winstanley","year":"2009","unstructured":"Winstanley C, Fothergill JL (2009) The role of quorum sensing in chronic cystic fibrosis Pseudomonas aeruginosa infections. FEMS Microbiol Lett 290:1\u20139. doi: 10.1111\/j.1574-6968.2008.01394.x","journal-title":"FEMS Microbiol Lett"},{"key":"7177_CR157","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1111\/j.1469-0691.2008.02659.x","volume":"15","author":"D Worlitzsch","year":"2009","unstructured":"Worlitzsch D, Rintelen C, B\u00f6hm K, Wollschl\u00e4ger B, Merkel N, Borneff-Lipp M, D\u00f6ring G (2009) Antibiotic-resistant obligate anaerobes during exacerbations of cystic fibrosis patients. Clin Microbiol Infect 15:454\u2013460. doi: 10.1111\/j.1469-0691.2008.02659.x","journal-title":"Clin Microbiol Infect"},{"key":"7177_CR158","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1172\/JCI0213870","volume":"109","author":"D Worlitzsch","year":"2002","unstructured":"Worlitzsch D, Tarran R, Ulrich M, Schwab U, Cekici A, Meyer KC, Birrer P, Bellon G, Berger J, Weiss T, Botzenhart K, Yankaskas JR, Randell S, Boucher RC, D\u00f6ring G (2002) Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J Clin Invest 109:317\u2013325. doi: 10.1172\/JCI13870","journal-title":"J Clin Invest"},{"key":"7177_CR159","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.diagmicrobio.2005.08.020","volume":"54","author":"JH Yang","year":"2006","unstructured":"Yang JH, Spilker T, LiPuma JJ (2006) Simultaneous coinfection by multiple strains during Burkholderia cepacia complex infection in cystic fibrosis. Diagn Microbiol Infect Dis 54:95\u201398. doi: 10.1016\/j.diagmicrobio.2005.08.020","journal-title":"Diagn Microbiol Infect Dis"},{"key":"7177_CR160","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1111\/j.1462-2920.2011.02459.x","volume":"13","author":"L Yang","year":"2011","unstructured":"Yang L, Jelsbak L, Molin S (2011a) Microbial ecology and adaptation in cystic fibrosis airways. Environ Microbiol 13:1682\u20131689. doi: 10.1111\/j.1462-2920.2011.02459.x","journal-title":"Environ Microbiol"},{"key":"7177_CR161","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1111\/j.1574-695X.2011.00820.x","volume":"62","author":"L Yang","year":"2011","unstructured":"Yang L, Liu Y, Markussen T, H\u00f8iby N, Tolker-Nielsen T, Molin S (2011b) Pattern differentiation in co-culture biofilms formed by Staphylococcus aureus and Pseudomonas aeruginosa. FEMS Immunol Med Microbiol 62:339\u2013347. doi: 10.1111\/j.1574-695X.2011.00820.x","journal-title":"FEMS Immunol Med Microbiol"},{"key":"7177_CR162","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/S1534-5807(02)00295-2","volume":"3","author":"SS Yoon","year":"2002","unstructured":"Yoon SS, Hennigan RF, Hilliard GM, Ochsner UA, Parvatiyar K, Kamani MC, Allen HL, DeKievit TR, Gardner PR, Schwab U, Rowe JJ, Iglewski BH, McDermott TR, Mason RP, Wozniak DJ, Hancock REW, Parsek MR, Noah TL, Boucher RC, Hassett DJ (2002) Pseudomonas aeruginosa anaerobic respiration in biofilms: relationships to cystic fibrosis pathogenesis. Dev Cell 3:593\u2013603","journal-title":"Dev Cell"}],"container-title":["Applied Microbiology and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00253-015-7177-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00253-015-7177-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00253-015-7177-x","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,12]],"date-time":"2020-09-12T08:00:49Z","timestamp":1599897649000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00253-015-7177-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12,5]]},"references-count":162,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2016,2]]}},"alternative-id":["7177"],"URL":"https:\/\/doi.org\/10.1007\/s00253-015-7177-x","relation":{},"ISSN":["0175-7598","1432-0614"],"issn-type":[{"type":"print","value":"0175-7598"},{"type":"electronic","value":"1432-0614"}],"subject":[],"published":{"date-parts":[[2015,12,5]]}}}