References
- Bassis CM, Erb-Downward JR, Dickson RP, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio. 2015;6:e00037.
- Charlson ES, Bittinger K, Haas AR, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011;184:957–963.
- Bennett WD, Foster WM, Chapman WF. Cough-enhanced mucus clearance in the normal lung. J Appl Physiol. 1990;69:1670–1675.
- Bennett WD, Laube BL, Corcoran T, et al. Multisite comparison of mucociliary and cough clearance measures using standardized methods. J Aerosol Med Pulm Drug Deliv. 2013;26:157–164.
- Lloyd CM, Marsland BJ. Lung homeostasis: influence of age, microbes, and the immune system. Immunity. 2017;46:549–561.
- Dickson RP, Erb-Downward JR, Huffnagle GB. Homeostasis and its disruption in the lung microbiome. Am J Physiol Lung Cell Mol Physiol. 2015;309:L1047–L1055.
- Musher DM, Roig IL, Cazares G, et al. Can an etiologic agent be identified in adults who are hospitalized for community-acquired pneumonia: results of a one-year study. J Infect. 2013;67:11–18.
- Jain S, Self WH, Wunderink RG, et al. community-acquired pneumonia requiring hospitalization among U.S. adults. N Engl J Med. 2015;373:415–427.
- Anand N, Kollef MH. The alphabet soup of pneumonia: CAP, HAP, HCAP, NHAP, and VAP. Semin Respir Crit Care Med. 2009;30:3–9.
- Lanks CW, Musani AI, Hsia DW. Community-acquired pneumonia and hospital-acquired pneumonia. Med Clin North Am. 2019;103:487–501.
- Roquilly A, Torres A, Villadangos JA, et al. Pathophysiological role of respiratory dysbiosis in hospital-acquired pneumonia. Lancet Respir Med. 2019;7:710–720.
- Kalil AC, Metersky ML, Klompas M, et al. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the infectious diseases society of America and the American Thoracic Society. Clin Infect Dis. 2016;63:e61–e111.
- Kalanuria AA, Ziai W, Mirski M. Ventilator-associated pneumonia in the ICU. Crit Care. 2014;18:208.
- Zakharkina T, Martin-Loeches I, Matamoros S, et al. The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia. Thorax. 2017;72:803–810.
- Magill SS, Li Q, Gross C, et al. Incidence and characteristics of ventilator-associated events reported to the national healthcare safety network in 2014. Crit Care Med. 2016;44:2154–2162.
- Rello J, Ollendorf DA, Oster G, et al., Group VAPOSA. Epidemiology and outcomes of ventilator-associated pneumonia in a large US database. Chest. 2002;122:2115–2121.
- Esperatti M, Ferrer M, Theessen A, et al. Nosocomial pneumonia in the intensive care unit acquired by mechanically ventilated versus nonventilated patients. Am J Respir Crit Care Med. 2010;182:1533–1539.
- Klompas M, Kleinman K, Murphy MV. Descriptive epidemiology and attributable morbidity of ventilator-associated events. Infect Control Hosp Epidemiol. 2014;35:502–510.
- Chastre J, Fagon JY. Ventilator-associated pneumonia. Am J Respir Crit Care Med. 2002;165:867–903.
- Lillehoj ER, Kim KC. Airway mucus: its components and function. Arch Pharm Res. 2002;25:770–780.
- Roussel P, Degand P, Lamblin G, et al. Biochemical definition of human tracheobronchial mucus. Lung. 1978;154:241–260.
- Radtke T, Boni L, Bohnacker P, et al. The many ways sputum flows - Dealing with high within-subject variability in cystic fibrosis sputum rheology. Respir Physiol Neurobiol. 2018;254:36–39.
- Kirkham S, Sheehan JK, Knight D, et al. Heterogeneity of airways mucus: variations in the amounts and glycoforms of the major oligomeric mucins MUC5AC and MUC5B. Biochem J. 2002;361:537–546.
- Bansil R, Turner BS. The biology of mucus: composition, synthesis and organization. Adv Drug Deliv Rev. 2018;124:3–15.
- Wilms EB, Touw DJ, Heijerman HG. Pharmacokinetics and sputum penetration of azithromycin during once weekly dosing in cystic fibrosis patients. J Cyst Fibros. 2008;7:79–84.
- Wilms EB, Touw DJ, Heijerman HG. Pharmacokinetics of azithromycin in plasma, blood, polymorphonuclear neutrophils and sputum during long-term therapy in patients with cystic fibrosis. Ther Drug Monit. 2006;28:219–225.
- Voynow JA, Rubin BK. Mucins, mucus, and sputum. Chest. 2009;135:505–512.
- Tettelin H, Nelson KE, Paulsen IT, et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science. 2001;293:498–506.
- Herbert S, Ziebandt AK, Ohlsen K, et al. Repair of global regulators in Staphylococcus aureus 8325 and comparative analysis with other clinical isolates. Infect Immun. 2010;78:2877–2889.
- Schneider CA, Rasband WS, Eliceiri KW. NIH image to imageJ: 25 years of image analysis. Nat Methods. 2012;9:671–675.
- de Smet AM, Kluytmans JA, Cooper BS, et al. Decontamination of the digestive tract and oropharynx in ICU patients. N Engl J Med. 2009;360:20–31.
- Veloo AC, Elgersma PE, Friedrich AW, et al. The influence of incubation time, sample preparation and exposure to oxygen on the quality of the MALDI-TOF MS spectrum of anaerobic bacteria. Clin Microbiol Infect. 2014;20:O1091–O1097.
- Heida FH, van Zoonen A, Hulscher JBF, et al. A necrotizing enterocolitis-associated gut microbiota is present in the meconium: results of a prospective study. Clin Infect Dis. 2016;62:863–870.
- Bartram AK, Lynch MD, Stearns JC, et al. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol. 2011;77:3846–3852.
- Masella AP, Bartram AK, Truszkowski JM, et al. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics. 2012;13:31.
- Ludwig W, Strunk O, Westram R, et al. ARB: a software environment for sequence data. Nucleic Acids Res. 2004;32:1363–1371.
- van Heel AJ, de Jong A, Song C, et al. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 2018;46:W278–W281.
- Wise R, Wills PJ, Andrews JM, et al. Activity of the cefotaxime (HR756) desacetyl metabolite compared with those of cefotaxime and other cephalosporins. Antimicrob Agents Chemother. 1980;17:84–86.
- Huang JX, Blaskovich MA, Pelingon R, et al. Mucin binding reduces colistin antimicrobial activity. Antimicrob Agents Chemother. 2015;59:5925–5931.