Abstract
Lower respiratory tract infections (LRTIs) are one of the most common forms of infection in children. Bronchoscopy has become an invaluable tool for the diagnosis and treatment of children with complicated or recalcitrant infections. It allows for both visualization of airway and mucosal surfaces and local sampling that can facilitate identification of pathogens and histopathological changes that are indicative of an infectious process. The results of bronchoscopy can help simplify an antimicrobial regimen, limiting unnecessary antibiotic use and all of the attendant risks such as organ toxicities, allergic reactions, and the fostering of antibiotic resistance. Bronchoscopic evaluation with sampling by either bronchoalveolar lavage (BAL) or biopsy may be considered in critically ill patients, high-risk patients (i.e., cystic fibrosis and immunocompromised), any child with high clinical suspicion for mycobacterial or fungal disease, and children who have failed to respond, worsened, or relapsed after empiric therapy. Although the diagnostic yield varies highly across patient populations, BAL with culture has become the gold standard for microbiological diagnosis of bacterial, mycobacterial, and fungal pneumonia, with specificity approaching 100% in some studies. Meanwhile, the use of molecular diagnostic techniques, such as polymerase chain reaction (PCR) and nucleic acid amplification tests, enables detection of rare and difficult-to-culture organisms, such as viruses, atypical bacteria, and fungi. Despite major advancements in these identification/detection techniques, limitations persist in the ability to differentiate between colonization and infection. This chapter summarizes the pros and cons of available diagnostic techniques for various infectious causes of LRTI in children.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Chellapandian D, Lehrnbecher T, Phillips B, Fisher BT, Zaoutis TE, Steinbach WJ, et al. Bronchoalveolar lavage and lung biopsy in patients with cancer and hematopoietic stem-cell transplantation recipients: a systematic review and meta-analysis. J Clin Oncol. 2015;33(5):501–9.
Efrati O, Sadeh-Gornik U, Modan-Moses D, Barak A, Szeinberg A, Vardi A, et al. Flexible bronchoscopy and bronchoalveolar lavage in pediatric patients with lung disease. Pediatr Crit Care Med. 2009;10(1):80–4.
Marchetti O, Lamoth F, Mikulska M, Viscoli C, Verweij P, Bretagne S, et al. ECIL recommendations for the use of biological markers for the diagnosis of invasive fungal diseases in leukemic patients and hematopoietic SCT recipients. Bone Marrow Transplant. 2012;47(6):846–54.
Lehrnbecher T, Robinson P, Fisher B, Alexander S, Ammann RA, Beauchemin M, et al. Guideline for the management of fever and neutropenia in children with cancer and hematopoietic stem-cell transplantation recipients: 2017 update. J Clin Oncol. 2017;35(18):2082–94.
Batra S, Li B, Underhill N, Maloney R, Katz BZ, Hijiya N. Clinical utility of bronchoalveolar lavage and respiratory tract biopsies in diagnosis and management of suspected invasive respiratory fungal infections in children. Pediatr Blood Cancer. 2015;62(9):1579–86.
Qualter E, Satwani P, Ricci A, Jin Z, Geyer MB, Alobeid B, et al. A comparison of bronchoalveolar lavage versus lung biopsy in pediatric recipients after stem cell transplantation. Biol Blood Marrow Transplant. 2014;20(8):1229–37.
Kottmann RM, Kelly J, Lyda E, Gurell M, Stalica J, Ormsby W, et al. Bronchoscopy with bronchoalveolar lavage: determinants of yield and impact on management in immunosuppressed patients. Thorax. 2011;66(9):823.
Nadimpalli S, Foca M, Satwani P, Sulis ML, Constantinescu A, Saiman L. Diagnostic yield of bronchoalveolar lavage in immunocompromised children with malignant and non-malignant disorders. Pediatr Pulmonol. 2017;52(6):820–6.
Peikert T, Rana S, Edell ES. Safety, diagnostic yield, and therapeutic implications of flexible bronchoscopy in patients with febrile neutropenia and pulmonary infiltrates. Mayo Clin Proc. 2005;80(11):1414–20.
Pagano L, Pagliari G, Basso A, Marra R, Sica S, Frigieri L, et al. The role of bronchoalveolar lavage in the microbiological diagnosis of pneumonia in patients with haematological malignancies. Ann Med. 1997;29(6):535–40.
Stokes DC, Shenep JL, Parham D, Bozeman PM, Marienchek W, Mackert PW. Role of flexible bronchoscopy in the diagnosis of pulmonary infiltrates in pediatric patients with cancer. J Pediatr. 1989;115(4):561–7.
Park JR, Fogarty S, Brogan TV. Clinical utility of bronchoalveolar lavage in pediatric cancer patients. Med Pediatr Oncol. 2002;39(3):175–80.
Rao U, Piccin A, Malone A, O’Hanlon K, Breatnach F, O’Meara A, et al. Utility of bronchoalveolar lavage in the diagnosis of pulmonary infection in children with haematological malignancies. Ir J Med Sci. 2013;182(2):177–83.
Carrillo-Marquez MA, Hulten KG, Hammerman W, Lamberth L, Mason EO, Kaplan SL. Staphylococcus aureus pneumonia in children in the era of community-acquired methicillin-resistance at Texas Children’s Hospital. Pediatr Infect Dis J. 2011;30(7):545–50.
Frush JM, Zhu Y, Edwards KM, Grijalva CG, Thomsen IP, Self WH, et al. Prevalence of Staphylococcus aureus and Use of Antistaphylococcal Therapy in Children Hospitalized with Pneumonia. J Hosp Med. 2018;13(12):848–52.
Jain S, Williams DJ, Arnold SR, Ampofo K, Bramley AM, Reed C, et al. Community-acquired pneumonia requiring hospitalization among U.S. children. N Engl J Med. 2015;372(9):835–45.
De Schutter I, De Wachter E, Crokaert F, Verhaegen J, Soetens O, Pierard D, et al. Microbiology of bronchoalveolar lavage fluid in children with acute nonresponding or recurrent community-acquired pneumonia: identification of nontypeable Haemophilus influenzae as a major pathogen. Clin Infect Dis. 2011;52(12):1437–44.
Shah SS, Dugan MH, Bell LM, Grundmeier RW, Florin TA, Hines EM, et al. Blood cultures in the emergency department evaluation of childhood pneumonia. Pediatr Infect Dis J. 2011;30(6):475–9.
Neuman MI, Hall M, Lipsett SC, Hersh AL, Williams DJ, Gerber JS, et al. Utility of Blood Culture Among Children Hospitalized With Community-Acquired Pneumonia. Pediatrics. 2017;140(3):e20171013.
Hickey RW, Bowman MJ, Smith GA. Utility of blood cultures in pediatric patients found to have pneumonia in the emergency department. Ann Emerg Med. 1996;27(6):721–5.
Bonadio WA. Bacteremia in febrile children with lobar pneumonia and leukocytosis. Pediatr Emerg Care. 1988;4(4):241–2.
Myers AL, Hall M, Williams DJ, Auger K, Tieder JS, Statile A, et al. Prevalence of bacteremia in hospitalized pediatric patients with community-acquired pneumonia. Pediatr Infect Dis J. 2013;32(7):736–40.
Byington CL, Spencer LY, Johnson TA, Pavia AT, Allen D, Mason EO, et al. An epidemiological investigation of a sustained high rate of pediatric parapneumonic empyema: risk factors and microbiological associations. Clin Infect Dis. 2002;34(4):434–40.
Waterer GW, Wunderink RG. The influence of the severity of community-acquired pneumonia on the usefulness of blood cultures. Respir Med. 2001;95(1):78–82.
Picard E, Joseph L, Goldberg S, Mimouni FB, Deeb M, Kleid D, et al. Predictive factors of morbidity in childhood parapneumonic effusion-associated pneumonia: a retrospective study. Pediatr Infect Dis J. 2010;29(9):840–3.
Freij BJ, Kusmiesz H, Nelson JD, McCracken GH Jr. Parapneumonic effusions and empyema in hospitalized children: a retrospective review of 227 cases. Pediatr Infect Dis. 1984;3(6):578–91.
Hoff SJ, Neblett WW, Edwards KM, Heller RM, Pietsch JB, Holcomb GW Jr, et al. Parapneumonic empyema in children: decortication hastens recovery in patients with severe pleural infections. Pediatr Infect Dis J. 1991;10(3):194–9.
Loens K, Van Heirstraeten L, Malhotra-Kumar S, Goossens H, Ieven M. Optimal sampling sites and methods for detection of pathogens possibly causing community-acquired lower respiratory tract infections. J Clin Microbiol. 2009;47(1):21–31.
Heiskanen-Kosma T, Korppi M, Jokinen C, Kurki S, Heiskanen L, Juvonen H, et al. Etiology of childhood pneumonia: serologic results of a prospective, population-based study. Pediatr Infect Dis J. 1998;17(11):986–91.
McCracken GH Jr. Etiology and treatment of pneumonia. Pediatr Infect Dis J. 2000;19(4):373–7.
Tsolia MN, Psarras S, Bossios A, Audi H, Paldanius M, Gourgiotis D, et al. Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections. Clin Infect Dis. 2004;39(5):681–6.
Xu D, Li S, Chen Z, Du L. Detection of Mycoplasma pneumoniae in different respiratory specimens. Eur J Pediatr. 2011;170(7):851–8.
Parides GC, Bloom JW, Ampel NM, Ray CG. Mycoplasma and ureaplasma in bronchoalveolar lavage fluids from immunocompromised hosts. Diagn Microbiol Infect Dis. 1988;9(1):55–7.
Phin N, Parry-Ford F, Harrison T, Stagg HR, Zhang N, Kumar K, et al. Epidemiology and clinical management of Legionnaires’ disease. Lancet Infect Dis. 2014;14(10):1011–21.
Pierre DM, Baron J, Yu VL, Stout JE. Diagnostic testing for Legionnaires’ disease. Ann Clin Microbiol Antimicrob. 2017;16(1):59.
Mercante JW, Winchell JM. Current and emerging Legionella diagnostics for laboratory and outbreak investigations. Clin Microbiol Rev. 2015;28(1):95–133.
Venkatachalam V, Hendley JO, Willson DF. The diagnostic dilemma of ventilator-associated pneumonia in critically ill children. Pediatr Crit Care Med. 2011;12(3):286–96.
Srinivasan R, Asselin J, Gildengorin G, Wiener-Kronish J, Flori HR. A prospective study of ventilator-associated pneumonia in children. Pediatrics. 2009;123(4):1108–15.
Charles MP, Kali A, Easow JM, Joseph NM, Ravishankar M, Srinivasan S, et al. Ventilator-associated pneumonia. Australas Med J. 2014;7(8):334–44.
Robert R, Grollier G, Frat JP, Godet C, Adoun M, Fauchere JL, et al. Colonization of lower respiratory tract with anaerobic bacteria in mechanically ventilated patients. Intensive Care Med. 2003;29(7):1062–8.
Klompas M. Does this patient have ventilator-associated pneumonia? JAMA. 2007;297(14):1583–93.
Gauvin F, Dassa C, Chaibou M, Proulx F, Farrell CA, Lacroix J. Ventilator-associated pneumonia in intubated children: comparison of different diagnostic methods. Pediatr Crit Care Med. 2003;4(4):437–43.
Chastre J, Fagon JY, Bornet-Lecso M, Calvat S, Dombret MC, al Khani R, et al. Evaluation of bronchoscopic techniques for the diagnosis of nosocomial pneumonia. Am J Respir Crit Care Med. 1995;152(1):231–40.
Fabregas N, Ewig S, Torres A, El-Ebiary M, Ramirez J, de La Bellacasa JP, et al. Clinical diagnosis of ventilator associated pneumonia revisited: comparative validation using immediate post-mortem lung biopsies. Thorax. 1999;54(10):867–73.
Torres A, Fabregas N, Ewig S, de la Bellacasa JP, Bauer TT, Ramirez J. Sampling methods for ventilator-associated pneumonia: validation using different histologic and microbiological references. Crit Care Med. 2000;28(8):2799–804.
Fagon JY, Chastre J, Wolff M, Gervais C, Parer-Aubas S, Stephan F, et al. Invasive and noninvasive strategies for management of suspected ventilator-associated pneumonia. A randomized trial. Ann Intern Med. 2000;132(8):621–30.
Shorr AF, Sherner JH, Jackson WL, Kollef MH. Invasive approaches to the diagnosis of ventilator-associated pneumonia: a meta-analysis. Crit Care Med. 2005;33(1):46–53.
Canadian Critical Care Trials G. A randomized trial of diagnostic techniques for ventilator-associated pneumonia. N Engl J Med. 2006;355(25):2619–30.
Wood AY, Davit AJ 2nd, Ciraulo DL, Arp NW, Richart CM, Maxwell RA, et al. A prospective assessment of diagnostic efficacy of blind protective bronchial brushings compared to bronchoscope-assisted lavage, bronchoscope-directed brushings, and blind endotracheal aspirates in ventilator-associated pneumonia. J Trauma. 2003;55(5):825–34.
Labenne M, Poyart C, Rambaud C, Goldfarb B, Pron B, Jouvet P, et al. Blind protected specimen brush and bronchoalveolar lavage in ventilated children. Crit Care Med. 1999;27(11):2537–43.
Gauvin F, Lacroix J, Guertin MC, Proulx F, Farrell CA, Moghrabi A, et al. Reproducibility of blind protected bronchoalveolar lavage in mechanically ventilated children. Am J Respir Crit Care Med. 2002;165(12):1618–23.
Zucker A, Pollack M, Katz R. Blind use of the double-lumen plugged catheter for diagnosis of respiratory tract infections in critically ill children. Crit Care Med. 1984;12(10):867–70.
Sachdev A, Chugh K, Raghunathan V, Gupta D, Wattal C, Menon GR. Diagnosis of bacterial ventilator-associated pneumonia in children: reproducibility of blind bronchial sampling. Pediatr Crit Care Med. 2013;14(1):e1–7.
Muscedere J, Dodek P, Keenan S, Fowler R, Cook D, Heyland D, et al. Comprehensive evidence-based clinical practice guidelines for ventilator-associated pneumonia: diagnosis and treatment. J Crit Care. 2008;23(1):138–47.
Sachdev A, Chugh K, Sethi M, Gupta D, Wattal C, Menon G. Diagnosis of ventilator-associated pneumonia in children in resource-limited setting: a comparative study of bronchoscopic and nonbronchoscopic methods. Pediatr Crit Care Med. 2010;11(2):258–66.
Morrow BM, Argent AC, Jeena PM, Green RJ. Guideline for the diagnosis, prevention and treatment of paediatric ventilator-associated pneumonia. S Afr Med J. 2009;99(4 Pt 2):255–67.
Rizik S, Hakim F, Bentur L, Arad-Cohen N, Kassis I. Bronchoscopy and bronchoalveolar lavage in the diagnosis and management of pulmonary infections in immunocompromised children. J Pediatr Hematol Oncol. 2018;40(7):532–5.
Zachariah P, Ryan C, Nadimpalli S, Coscia G, Kolb M, Smith H, et al. Culture-independent analysis of pediatric bronchoalveolar lavage specimens. Ann Am Thorac Soc. 2018;15(9):1047–56.
Muhlebach MS, Hatch JE, Einarsson GG, McGrath SJ, Gilipin DF, Lavelle G, et al. Anaerobic bacteria cultured from cystic fibrosis airways correlate to milder disease: a multisite study. Eur Respir J. 2018;52(1):1800242.
Sherrard LJ, Bell SC, Tunney MM. The role of anaerobic bacteria in the cystic fibrosis airway. Curr Opin Pulm Med. 2016;22(6):637–43.
Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G, Muhlebach MS, et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med. 2008;177(9):995–1001.
Foundation CF. Patient registry annual report. Bethesda, Maryland; 2017.
Chung JC, Becq J, Fraser L, Schulz-Trieglaff O, Bond NJ, Foweraker J, et al. Genomic variation among contemporary Pseudomonas aeruginosa isolates from chronically infected cystic fibrosis patients. J Bacteriol. 2012;194(18):4857–66.
Foweraker JE, Laughton CR, Brown DF, Bilton D. Phenotypic variability of Pseudomonas aeruginosa in sputa from patients with acute infective exacerbation of cystic fibrosis and its impact on the validity of antimicrobial susceptibility testing. J Antimicrob Chemother. 2005;55(6):921–7.
Winstanley C, O’Brien S, Brockhurst MA. Pseudomonas aeruginosa evolutionary adaptation and diversification in cystic fibrosis chronic lung infections. Trends Microbiol. 2016;24(5):327–37.
Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H, Garudathri J, et al. Regional isolation drives bacterial diversification within cystic fibrosis lungs. Cell Host Microbe. 2015;18(3):307–19.
Goddard AF, Staudinger BJ, Dowd SE, Joshi-Datar A, Wolcott RD, Aitken ML, et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci U S A. 2012;109(34):13769–74.
Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, et al. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol. 2012;46(2):127–31.
Willner D, Haynes MR, Furlan M, Schmieder R, Lim YW, Rainey PB, et al. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J. 2012;6(2):471–4.
Eyns H, Pierard D, De Wachter E, Eeckhout L, Vaes P, Malfroot A. Respiratory bacterial culture sampling in expectorating and non-expectorating patients with cystic fibrosis. Front Pediatr. 2018;6:403.
Ramsey BW, Wentz KR, Smith AL, Richardson M, Williams-Warren J, Hedges DL, et al. Predictive value of oropharyngeal cultures for identifying lower airway bacteria in cystic fibrosis patients. Am Rev Respir Dis. 1991;144(2):331–7.
Armstrong DS, Grimwood K, Carlin JB, Carzino R, Olinsky A, Phelan PD. Bronchoalveolar lavage or oropharyngeal cultures to identify lower respiratory pathogens in infants with cystic fibrosis. Pediatr Pulmonol. 1996;21(5):267–75.
Burns JL, Gibson RL, McNamara S, Yim D, Emerson J, Rosenfeld M, et al. Longitudinal assessment of Pseudomonas aeruginosa in young children with cystic fibrosis. J Infect Dis. 2001;183(3):444–52.
Equi AC, Pike SE, Davies J, Bush A. Use of cough swabs in a cystic fibrosis clinic. Arch Dis Child. 2001;85(5):438–9.
Rosenfeld M, Emerson J, Accurso F, Armstrong D, Castile R, Grimwood K, et al. Diagnostic accuracy of oropharyngeal cultures in infants and young children with cystic fibrosis. Pediatr Pulmonol. 1999;28(5):321–8.
Jung A, Kleinau I, Schonian G, Bauernfeind A, Chen C, Griese M, et al. Sequential genotyping of Pseudomonas aeruginosa from upper and lower airways of cystic fibrosis patients. Eur Respir J. 2002;20(6):1457–63.
Doumit M, Belessis Y, Stelzer-Braid S, Mallitt KA, Rawlinson W, Jaffe A. Diagnostic accuracy and distress associated with oropharyngeal suction in cystic fibrosis. J Cyst Fibros. 2016;15(4):473–8.
Aaron SD, Kottachchi D, Ferris WJ, Vandemheen KL, St Denis ML, Plouffe A, et al. Sputum versus bronchoscopy for diagnosis of Pseudomonas aeruginosa biofilms in cystic fibrosis. Eur Respir J. 2004;24(4):631–7.
Jain K, Wainwright C, Smyth AR. Bronchoscopy-guided antimicrobial therapy for cystic fibrosis. Cochrane Database Syst Rev. 2018;9:CD009530.
Laguna TA, Wagner BD, Williams CB, Stevens MJ, Robertson CE, Welchlin CW, et al. Airway microbiota in bronchoalveolar lavage fluid from clinically well infants with cystic fibrosis. PLoS One. 2016;11(12):e0167649.
Hogan DA, Willger SD, Dolben EL, Hampton TH, Stanton BA, Morrison HG, et al. Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis lung disease. PLoS One. 2016;11(3):e0149998.
Hoppe JE, Towler E, Wagner BD, Accurso FJ, Sagel SD, Zemanick ET. Sputum induction improves detection of pathogens in children with cystic fibrosis. Pediatr Pulmonol. 2015;50(7):638–46.
Suri R, Marshall LJ, Wallis C, Metcalfe C, Shute JK, Bush A. Safety and use of sputum induction in children with cystic fibrosis. Pediatr Pulmonol. 2003;35(4):309–13.
Al-Saleh S, Dell SD, Grasemann H, Yau YC, Waters V, Martin S, et al. Sputum induction in routine clinical care of children with cystic fibrosis. J Pediatr. 2010;157(6):1006–11 e1.
Ho SA, Ball R, Morrison LJ, Brownlee KG, Conway SP. Clinical value of obtaining sputum and cough swab samples following inhaled hypertonic saline in children with cystic fibrosis. Pediatr Pulmonol. 2004;38(1):82–7.
Mussaffi H, Fireman EM, Mei-Zahav M, Prais D, Blau H. Induced sputum in the very young: a new key to infection and inflammation. Chest. 2008;133(1):176–82.
Henig NR, Tonelli MR, Pier MV, Burns JL, Aitken ML. Sputum induction as a research tool for sampling the airways of subjects with cystic fibrosis. Thorax. 2001;56(4):306–11.
Angrill J, Agusti C, de Celis R, Rano A, Gonzalez J, Sole T, et al. Bacterial colonisation in patients with bronchiectasis: microbiological pattern and risk factors. Thorax. 2002;57(1):15–9.
Ronchetti K, Tame JD, Paisey C, Thia LP, Doull I, Howe R, et al. The CF-Sputum Induction Trial (CF-SpIT) to assess lower airway bacterial sampling in young children with cystic fibrosis: a prospective internally controlled interventional trial. Lancet Respir Med. 2018;6(6):461–71.
Blau H, Linnane B, Carzino R, Tannenbaum EL, Skoric B, Robinson PJ, et al. Induced sputum compared to bronchoalveolar lavage in young, non-expectorating cystic fibrosis children. J Cyst Fibros. 2014;13(1):106–10.
O’Horo JC, Thompson D, Safdar N. Is the gram stain useful in the microbiologic diagnosis of VAP? A meta-analysis. Clin Infect Dis. 2012;55(4):551–61.
Meduri GU, Baselski V. The role of bronchoalveolar lavage in diagnosing nonopportunistic bacterial pneumonia. Chest. 1991;100(1):179–90.
de Blic J, Midulla F, Barbato A, Clement A, Dab I, Eber E, et al. Bronchoalveolar lavage in children. ERS Task Force on bronchoalveolar lavage in children. European Respiratory Society. Eur Respir J. 2000;15(1):217–31.
Jourdain B, Joly-Guillou ML, Dombret MC, Calvat S, Trouillet JL, Gibert C, et al. Usefulness of quantitative cultures of BAL fluid for diagnosing nosocomial pneumonia in ventilated patients. Chest. 1997;111(2):411–8.
Kirkpatrick MB, Bass JB Jr. Quantitative bacterial cultures of bronchoalveolar lavage fluids and protected brush catheter specimens from normal subjects. Am Rev Respir Dis. 1989;139(2):546–8.
Cantral DE, Tape TG, Reed EC, Spurzem JR, Rennard SI, Thompson AB. Quantitative culture of bronchoalveolar lavage fluid for the diagnosis of bacterial pneumonia. Am J Med. 1993;95(6):601–7.
Rasmussen TR, Korsgaard J, Moller JK, Sommer T, Kilian M. Quantitative culture of bronchoalveolar lavage fluid in community-acquired lower respiratory tract infections. Respir Med. 2001;95(11):885–90.
Thorpe JE, Baughman RP, Frame PT, Wesseler TA, Staneck JL. Bronchoalveolar lavage for diagnosing acute bacterial pneumonia. J Infect Dis. 1987;155(5):855–61.
Prats E, Dorca J, Pujol M, Garcia L, Barreiro B, Verdaguer R, et al. Effects of antibiotics on protected specimen brush sampling in ventilator-associated pneumonia. Eur Respir J. 2002;19(5):944–51.
Torres A, el-Ebiary M, Padro L, Gonzalez J, de la Bellacasa JP, Ramirez J, et al. Validation of different techniques for the diagnosis of ventilator-associated pneumonia. Comparison with immediate postmortem pulmonary biopsy. Am J Respir Crit Care Med. 1994;149(2 Pt 1):324–31.
Kim ES, Kim EC, Lee SM, Yang SC, Yoo CG, Kim YW, et al. Bacterial yield from quantitative cultures of bronchoalveolar lavage fluid in patients with pneumonia on antimicrobial therapy. Korean J Intern Med. 2012;27(2):156–62.
Torres A, Lee N, Cilloniz C, Vila J, Van der Eerden M. Laboratory diagnosis of pneumonia in the molecular age. Eur Respir J. 2016;48(6):1764–78.
Falguera M, Lopez A, Nogues A, Porcel JM, Rubio-Caballero M. Evaluation of the polymerase chain reaction method for detection of Streptococcus pneumoniae DNA in pleural fluid samples. Chest. 2002;122(6):2212–6.
Lahti E, Mertsola J, Kontiokari T, Eerola E, Ruuskanen O, Jalava J. Pneumolysin polymerase chain reaction for diagnosis of pneumococcal pneumonia and empyema in children. Eur J Clin Microbiol Infect Dis. 2006;25(12):783–9.
Krenke K, Sadowy E, Podsiadly E, Hryniewicz W, Demkow U, Kulus M. Etiology of parapneumonic effusion and pleural empyema in children. The role of conventional and molecular microbiological tests. Respir Med. 2016;116:28–33.
Le Monnier A, Carbonnelle E, Zahar JR, Le Bourgeois M, Abachin E, Quesne G, et al. Microbiological diagnosis of empyema in children: comparative evaluations by culture, polymerase chain reaction, and pneumococcal antigen detection in pleural fluids. Clin Infect Dis. 2006;42(8):1135–40.
Abdeldaim GM, Stralin K, Olcen P, Blomberg J, Herrmann B. Toward a quantitative DNA-based definition of pneumococcal pneumonia: a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment. Diagn Microbiol Infect Dis. 2008;60(2):143–50.
Johansson N, Kalin M, Giske CG, Hedlund J. Quantitative detection of Streptococcus pneumoniae from sputum samples with real-time quantitative polymerase chain reaction for etiologic diagnosis of community-acquired pneumonia. Diagn Microbiol Infect Dis. 2008;60(3):255–61.
Menezes-Martins LF, Menezes-Martins JJ, Michaelsen VS, Aguiar BB, Ermel T, Machado DC. Diagnosis of parapneumonic pleural effusion by polymerase chain reaction in children. J Pediatr Surg. 2005;40(7):1106–10.
Abdeldaim GM, Stralin K, Olcen P, Blomberg J, Molling P, Herrmann B. Quantitative fucK gene polymerase chain reaction on sputum and nasopharyngeal secretions to detect Haemophilus influenzae pneumonia. Diagn Microbiol Infect Dis. 2013;76(2):141–6.
Abdeldaim GM, Herrmann B. PCR detection of Haemophilus influenzae from respiratory specimens. Methods Mol Biol. 2013;943:115–23.
Johansson N, Kalin M, Tiveljung-Lindell A, Giske CG, Hedlund J. Etiology of community-acquired pneumonia: increased microbiological yield with new diagnostic methods. Clin Infect Dis. 2010;50(2):202–9.
Stralin K, Korsgaard J, Olcen P. Evaluation of a multiplex PCR for bacterial pathogens applied to bronchoalveolar lavage. Eur Respir J. 2006;28(3):568–75.
Xirogianni A, Tsolia M, Voyiatzi A, Sioumala M, Makri A, Argyropoulou A, et al. Diagnosis of upper and lower respiratory tract bacterial infections with the use of multiplex PCR assays. Diagnostics (Basel). 2013;3(2):222–31.
Sansot M, Fradin E, Chenouard R, Kempf M, Kouatchet A, Lasocki S, et al. Performance of the extended use of the FilmArray((R)) BCID panel kit for bronchoalveolar lavage analysis. Mol Biol Rep. 2019;46(3):2685–92.
Murdoch DR, Anderson TP, Beynon KA, Chua A, Fleming AM, Laing RT, et al. Evaluation of a PCR assay for detection of Streptococcus pneumoniae in respiratory and nonrespiratory samples from adults with community-acquired pneumonia. J Clin Microbiol. 2003;41(1):63–6.
Stralin K, Tornqvist E, Kaltoft MS, Olcen P, Holmberg H. Etiologic diagnosis of adult bacterial pneumonia by culture and PCR applied to respiratory tract samples. J Clin Microbiol. 2006;44(2):643–5.
Stralin K, Herrmann B, Abdeldaim G, Olcen P, Holmberg H, Molling P. Comparison of sputum and nasopharyngeal aspirate samples and of the PCR gene targets lytA and Spn9802 for quantitative PCR for rapid detection of pneumococcal pneumonia. J Clin Microbiol. 2014;52(1):83–9.
Carvalho Mda G, Tondella ML, McCaustland K, Weidlich L, McGee L, Mayer LW, et al. Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol. 2007;45(8):2460–6.
Abdeldaim G, Herrmann B, Molling P, Holmberg H, Blomberg J, Olcen P, et al. Usefulness of real-time PCR for lytA, ply, and Spn9802 on plasma samples for the diagnosis of pneumococcal pneumonia. Clin Microbiol Infect. 2010;16(8):1135–41.
Albrich WC, Madhi SA, Adrian PV, Telles JN, Paranhos-Baccala G, Klugman KP. Genomic load from sputum samples and nasopharyngeal swabs for diagnosis of pneumococcal pneumonia in HIV-infected adults. J Clin Microbiol. 2014;52(12):4224–9.
Albrich WC, Madhi SA, Adrian PV, van Niekerk N, Mareletsi T, Cutland C, et al. Use of a rapid test of pneumococcal colonization density to diagnose pneumococcal pneumonia. Clin Infect Dis. 2012;54(5):601–9.
Lorente ML, Falguera M, Nogues A, Gonzalez AR, Merino MT, Caballero MR. Diagnosis of pneumococcal pneumonia by polymerase chain reaction (PCR) in whole blood: a prospective clinical study. Thorax. 2000;55(2):133–7.
Sheppard CL, Harrison TG, Kearns AM, Guiver M, Creek M, Evans R, et al. Diagnosis of invasive pneumococcal infection by PCR amplification of Streptococcus pneumoniae genomic fragments in blood: a multi-centre comparative study. Commun Dis Public Health. 2003;6(3):221–7.
Yang S, Lin S, Khalil A, Gaydos C, Nuemberger E, Juan G, et al. Quantitative PCR assay using sputum samples for rapid diagnosis of pneumococcal pneumonia in adult emergency department patients. J Clin Microbiol. 2005;43(7):3221–6.
Peters RP, de Boer RF, Schuurman T, Gierveld S, Kooistra-Smid M, van Agtmael MA, et al. Streptococcus pneumoniae DNA load in blood as a marker of infection in patients with community-acquired pneumonia. J Clin Microbiol. 2009;47(10):3308–12.
Smith MD, Sheppard CL, Hogan A, Harrison TG, Dance DA, Derrington P, et al. Diagnosis of Streptococcus pneumoniae infections in adults with bacteremia and community-acquired pneumonia: clinical comparison of pneumococcal PCR and urinary antigen detection. J Clin Microbiol. 2009;47(4):1046–9.
Gollomp K, Rankin SC, White C, Mattei P, Harris MC, Kilpatrick LE, et al. Broad-range bacterial polymerase chain reaction in the microbiologic diagnosis of complicated pneumonia. J Hosp Med. 2012;7(1):8–13.
Adjemian J, Olivier KN, Seitz AE, Falkinham JO, Holland SM, Prevots DR. Spatial clusters of nontuberculous mycobacterial lung disease in the United States. Am J Respir Crit Care Med. 2012;186(6):553–8.
Prevots DR, Shaw PA, Strickland D, Jackson LA, Raebel MA, Blosky MA, et al. Nontuberculous mycobacterial lung disease prevalence at four integrated health care delivery systems. Am J Respir Crit Care Med. 2010;182(7):970–6.
Brode SK, Daley CL, Marras TK. The epidemiologic relationship between tuberculosis and non-tuberculous mycobacterial disease: a systematic review. Int J Tuberc Lung Dis. 2014;18(11):1370–7.
Adjemian J, Olivier KN, Seitz AE, Holland SM, Prevots DR. Prevalence of nontuberculous mycobacterial lung disease in U.S. Medicare beneficiaries. Am J Respir Crit Care Med. 2012;185(8):881–6.
Henkle E, Hedberg K, Schafer S, Novosad S, Winthrop KL. Population-based incidence of pulmonary nontuberculous mycobacterial disease in Oregon 2007 to 2012. Ann Am Thorac Soc. 2015;12(5):642–7.
Runyon EH. Anonymous mycobacteria in pulmonary disease. Med Clin North Am. 1959;43(1):273–90.
WHO. Global tuberculosis report. Geneva: World Health Organization; 2017.
Keshavjee S, Farmer PE. Tuberculosis, drug resistance, and the history of modern medicine. N Engl J Med. 2012;367(10):931–6.
Ellner J. Tuberculosis. In: Goldman L, Schafer AI, editors. Goldman’s cecil medicine. 24th ed. New York: Elsevier; 2012. p. 1939–48.
American Academy of Pediatrics. Tuberculosis. In: Kimberlin D, Brady M, Jackson MA, Long S, editors. Red book. Elk Grove Village: American Academy of Pediatrics; 2018. p. 829–53.
Goussard P, Gie R. The role of bronchoscopy in the diagnosis and management of pediatric pulmonary tuberculosis. Expert Rev Respir Med. 2014;8(1):101–9.
Martiniano SL, Nick JA, Daley CL. Nontuberculous mycobacterial infections in cystic fibrosis. Clin Chest Med. 2016;37(1):83–96.
Faro A. Pulmonary disease in cystic fibrosis. In: Bush A, Wilmott R, Chernick V, Boat T, Ratjen F, Deterding R, editors. Kendig & Chernick’s disorders of the respiratory tract in children. Philadelphia, PA: Elsevier; 2012. p. 770–80.
Ashbolt NJ. Environmental (Saprozoic) pathogens of engineered water systems: understanding their ecology for risk assessment and management. Pathogens. 2015;4(2):390–405.
Parkins MD, Floto RA. Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis. J Cyst Fibros. 2015;14(3):293–304.
Ramsay KA, Stockwell RE, Bell SC, Kidd TJ. Infection in cystic fibrosis: impact of the environment and climate. Expert Rev Respir Med. 2016;10(5):505–19.
Whittaker LA, Teneback C. Atypical mycobacterial and fungal infections in cystic fibrosis. Semin Respir Crit Care Med. 2009;30(5):539–46.
Holland SM. The nontuberculous mycobacteria. In: Goldman L, Schafer AI, editors. Goldman’s cecil medicine. New York: Elsevier; 2012. p. 1948–50.
Adjemian J, Olivier KN, Prevots DR. Nontuberculous mycobacteria among patients with cystic fibrosis in the United States: screening practices and environmental risk. Am J Respir Crit Care Med. 2014;190(5):581–6.
Adjemian J, Daniel-Wayman S, Ricotta E, Prevots DR. Epidemiology of nontuberculous mycobacteriosis. Semin Respir Crit Care Med. 2018;39(3):325–35.
Donohue MJ, Wymer L. Increasing prevalence rate of nontuberculous mycobacteria infections in five states, 2008-2013. Ann Am Thorac Soc. 2016;13(12):2143–50.
Hoefsloot W, van Ingen J, Andrejak C, Angeby K, Bauriaud R, Bemer P, et al. The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study. Eur Respir J. 2013;42(6):1604–13.
Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, et al. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med. 2007;175(4):367–416.
Koh WJ. Nontuberculous mycobacteria-overview. Microbiol Spectr. 2017;5(1) https://doi.org/10.1128/microbiolspec.TNMI7-0024-2016.
Adjemian J, Alison MB, Kenneth NO, Prevots DR. Nontuberculous mycobacterial disease among cystic fibrosis patients in the United States: Environmental Risk and NTM Screening Practices. C17 CYSTIC FIBROSIS LUNG INFECTIONS. American Thoracic Society International Conference Abstracts: American Thoracic Society; 2014. p. A3955-A.
Bar-On O, Mussaffi H, Mei-Zahav M, Prais D, Steuer G, Stafler P, et al. Increasing nontuberculous mycobacteria infection in cystic fibrosis. J Cyst Fibros. 2015;14(1):53–62.
Martiniano SL, Davidson RM, Nick JA. Nontuberculous mycobacteria in cystic fibrosis: updates and the path forward. Pediatr Pulmonol. 2017;52(S48):S29–36.
Binder AM, Adjemian J, Olivier KN, Prevots DR. Epidemiology of nontuberculous mycobacterial infections and associated chronic macrolide use among persons with cystic fibrosis. Am J Respir Crit Care Med. 2013;188(7):807–12.
Olivier KN, Weber DJ, Wallace RJ, Faiz AR, Lee JH, Zhang Y, et al. Nontuberculous mycobacteria. I: multicenter prevalence study in cystic fibrosis. Am J Respir Crit Care Med. 2003;167(6):828–34.
Smith MJ, Efthimiou J, Hodson ME, Batten JC. Mycobacterial isolations in young adults with cystic fibrosis. Thorax. 1984;39(5):369–75.
Raidt L, Idelevich EA, Dübbers A, Küster P, Drevinek P, Peters G, et al. Increased prevalence and resistance of important pathogens recovered from respiratory specimens of cystic fibrosis patients during a decade. Pediatr Infect Dis J. 2015;34(7):700–5.
Saiman L, Siegel JD, LiPuma JJ, Brown RF, Bryson EA, Chambers MJ, et al. Infection prevention and control guideline for cystic fibrosis: 2013 update. Infect Control Hosp Epidemiol. 2014;35(Suppl 1):S1–S67.
Olivier KN, Weber DJ, Lee JH, Handler A, Tudor G, Molina PL, et al. Nontuberculous mycobacteria. II: nested-cohort study of impact on cystic fibrosis lung disease. Am J Respir Crit Care Med. 2003;167(6):835–40.
Catherinot E, Roux AL, Vibet MA, Bellis G, Lemonnier L, Le Roux E, et al. Inhaled therapies, azithromycin and Mycobacterium abscessus in cystic fibrosis patients. Eur Respir J. 2013;41(5):1101–6.
Catherinot E, Roux AL, Vibet MA, Bellis G, Ravilly S, Lemonnier L, et al. Mycobacterium avium and Mycobacterium abscessus complex target distinct cystic fibrosis patient subpopulations. J Cyst Fibros. 2013;12(1):74–80.
Coolen N, Morand P, Martin C, Hubert D, Kanaan R, Chapron J, et al. Reduced risk of nontuberculous mycobacteria in cystic fibrosis adults receiving long-term azithromycin. J Cyst Fibros. 2015;14(5):594–9.
Leung JM, Olivier KN. Nontuberculous mycobacteria in patients with cystic fibrosis. Semin Respir Crit Care Med. 2013;34(1):124–34.
Verregghen M, Heijerman HG, Reijers M, van Ingen J, van der Ent CK. Risk factors for Mycobacterium abscessus infection in cystic fibrosis patients; a case-control study. J Cyst Fibros. 2012;11(4):340–3.
Viviani L, Harrison MJ, Zolin A, Haworth CS, Floto RA. Epidemiology of nontuberculous mycobacteria (NTM) amongst individuals with cystic fibrosis (CF). J Cyst Fibros. 2016;15(5):619–23.
Girón RM, Máiz L, Barrio I, Martínez MT, Salcedo A, Prados C. Nontuberculous mycobacterial infection in patients with cystic fibrosis: a multicenter prevalence study. Arch Bronconeumol. 2008;44(12):679–84.
Levy I, Grisaru-Soen G, Lerner-Geva L, Kerem E, Blau H, Bentur L, et al. Multicenter cross-sectional study of nontuberculous mycobacterial infections among cystic fibrosis patients, Israel. Emerg Infect Dis. 2008;14(3):378–84.
Radhakrishnan DK, Yau Y, Corey M, Richardson S, Chedore P, Jamieson F, et al. Non-tuberculous mycobacteria in children with cystic fibrosis: isolation, prevalence, and predictors. Pediatr Pulmonol. 2009;44(11):1100–6.
Jennifer A, Alison MB, Kenneth NO, Prevots DR. Nontuberculous mycobacterial disease among cystic fibrosis patients in the United States: Environmental Risk and NTM Screening Practices. C17 Cystic Fibrosis Lung Infections. American Thoracic Society International Conference Abstracts: American Thoracic Society; 2014. p. A3955-A.
Jennifer A, Kenneth NO, Prevots DR. Predictors of prolonged nontuberculous mycobacterial infections in patients with cystic fibrosis. C105 Nontuberculous Mycobacteria Epidemiology. American Thoracic Society International Conference Abstracts: American Thoracic Society; 2015. p. A5255-A.
Mussaffi H, Rivlin J, Shalit I, Ephros M, Blau H. Nontuberculous mycobacteria in cystic fibrosis associated with allergic bronchopulmonary aspergillosis and steroid therapy. Eur Respir J. 2005;25(2):324–8.
Sermet-Gaudelus I, Le Bourgeois M, Pierre-Audigier C, Offredo C, Guillemot D, Halley S, et al. Mycobacterium abscessus and children with cystic fibrosis. Emerg Infect Dis. 2003;9(12):1587–91.
Bouso JM, Burns JJ, Amin R, Livingston FR, Elidemir O. Household proximity to water and nontuberculous mycobacteria in children with cystic fibrosis. Pediatr Pulmonol. 2017;52(3):324–30.
Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, et al. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet. 2013;381(9877):1551–60.
Harris KA, Underwood A, Kenna DT, Brooks A, Kavaliunaite E, Kapatai G, et al. Whole-genome sequencing and epidemiological analysis do not provide evidence for cross-transmission of mycobacterium abscessus in a cohort of pediatric cystic fibrosis patients. Clin Infect Dis. 2015;60(7):1007–16.
Prevots DR, Adjemian J, Fernandez AG, Knowles MR, Olivier KN. Environmental risks for nontuberculous mycobacteria. Individual exposures and climatic factors in the cystic fibrosis population. Ann Am Thorac Soc. 2014;11(7):1032–8.
Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, et al. Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium. Science (New York). 2016;354(6313):751–7.
Esther CR, Henry MM, Molina PL, Leigh MW. Nontuberculous mycobacterial infection in young children with cystic fibrosis. Pediatr Pulmonol. 2005;40(1):39–44.
Esther CR, Esserman DA, Gilligan P, Kerr A, Noone PG. Chronic Mycobacterium abscessus infection and lung function decline in cystic fibrosis. J Cyst Fibros. 2010;9(2):117–23.
Park IK, Olivier KN. Nontuberculous mycobacteria in cystic fibrosis and non-cystic fibrosis bronchiectasis. Semin Respir Crit Care Med. 2015;36(2):217–24.
Floto RA, Olivier KN, Saiman L, Daley CL, Herrmann JL, Nick JA, et al. US Cystic Fibrosis Foundation and European Cystic Fibrosis Society consensus recommendations for the management of non-tuberculous mycobacteria in individuals with cystic fibrosis: executive summary. Thorax. 2016;71(1):88–90.
Scott JP, Ji Y, Kannan M, Wylam ME. Inhaled granulocyte-macrophage colony-stimulating factor for Mycobacterium abscessus in cystic fibrosis. Eur Respir J. 2018;51(4):1702127.
Floto RA, Olivier KN, Saiman L, Daley CL, Herrmann JL, Nick JA, et al. US Cystic Fibrosis Foundation and European Cystic Fibrosis Society consensus recommendations for the management of non-tuberculous mycobacteria in individuals with cystic fibrosis. Thorax. 2016;71(Suppl 1):i1–22.
American Academy of Pediatrics. Nontuberculous mycobacteria. In: Kimberlin D, Brady M, Jackson MA, Long S, editors. Red book. Elk Grove Village: American Academy of Pediatrics; 2018. p. 854–61.
Brown-Elliott BA, Nash KA, Wallace RJ Jr. Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev. 2012;25(3):545–82.
Cowman SA, Loebinger MR. Diagnosis of nontuberculous mycobacteria lung disease. Semin Respir Crit Care Med. 2018;39(3):343–50.
Ichiyama S, Iinuma Y, Yamori S, Hasegawa Y, Shimokata K, Nakashima N. Mycobacterium growth indicator tube testing in conjunction with the AccuProbe or the AMPLICOR-PCR assay for detecting and identifying mycobacteria from sputum samples. J Clin Microbiol. 1997;35(8):2022–5.
Blakemore R, Story E, Helb D, Kop J, Banada P, Owens MR, et al. Evaluation of the analytical performance of the Xpert MTB/RIF assay. J Clin Microbiol. 2010;48(7):2495–501.
Lee H, Park HJ, Cho SN, Bai GH, Kim SJ. Species identification of mycobacteria by PCR-restriction fragment length polymorphism of the rpoB gene. J Clin Microbiol. 2000;38(8):2966–71.
Bannalikar AS, Verma R. Detection of Mycobacterium avium & M. tuberculosis from human sputum cultures by PCR-RFLP analysis of hsp65 gene & pncA PCR. Indian J Med Res. 2006;123(2):165–72.
Devallois A, Goh KS, Rastogi N. Rapid identification of mycobacteria to species level by PCR-restriction fragment length polymorphism analysis of the hsp65 gene and proposition of an algorithm to differentiate 34 mycobacterial species. J Clin Microbiol. 1997;35(11):2969–73.
Devallois A, Picardeau M, Paramasivan CN, Vincent V, Rastogi N. Molecular characterization of Mycobacterium avium complex isolates giving discordant results in AccuProbe tests by PCR-restriction enzyme analysis, 16S rRNA gene sequencing, and DT1-DT6 PCR. J Clin Microbiol. 1997;35(11):2767–72.
Dobner P, Feldmann K, Rifai M, Loscher T, Rinder H. Rapid identification of mycobacterial species by PCR amplification of hypervariable 16S rRNA gene promoter region. J Clin Microbiol. 1996;34(4):866–9.
Patel JB, Leonard DG, Pan X, Musser JM, Berman RE, Nachamkin I. Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system. J Clin Microbiol. 2000;38(1):246–51.
Roth A, Reischl U, Streubel A, Naumann L, Kroppenstedt RM, Habicht M, et al. Novel diagnostic algorithm for identification of mycobacteria using genus-specific amplification of the 16S-23S rRNA gene spacer and restriction endonucleases. J Clin Microbiol. 2000;38(3):1094–104.
Suffys PN, da Silva Rocha A, de Oliveira M, Campos CE, Barreto AM, Portaels F, et al. Rapid identification of Mycobacteria to the species level using INNO-LiPA Mycobacteria, a reverse hybridization assay. J Clin Microbiol. 2001;39(12):4477–82.
Aravindhan V, Sulochana S, Narayanan S, Paramasivam CN, Narayanan PR. Identification & differentiation of Mycobacterium avium & M. intracellulare by PCR- RFLP assay using the groES gene. Indian J Med Res. 2007;126(6):575–9.
Alcaide F, Amlerova J, Bou G, Ceyssens PJ, Coll P, Corcoran D, et al. How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry. Clin Microbiol Infect. 2018;24(6):599–603.
Ceyssens PJ, Soetaert K, Timke M, Van den Bossche A, Sparbier K, De Cremer K, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for combined species identification and drug sensitivity testing in mycobacteria. J Clin Microbiol. 2017;55(2):624–34.
Kodana M, Tarumoto N, Kawamura T, Saito T, Ohno H, Maesaki S, et al. Utility of the MALDI-TOF MS method to identify nontuberculous mycobacteria. J Infect Chemother. 2016;22(1):32–5.
Buckwalter SP, Olson SL, Connelly BJ, Lucas BC, Rodning AA, Walchak RC, et al. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of mycobacterium species, Nocardia species, and other aerobic Actinomycetes. J Clin Microbiol. 2016;54(2):376–84.
Tudo G, Monte MR, Vergara A, Lopez A, Hurtado JC, Ferrer-Navarro M, et al. Implementation of MALDI-TOF MS technology for the identification of clinical isolates of Mycobacterium spp. in mycobacterial diagnosis. Eur J Clin Microbiol Infect Dis. 2015;34(8):1527–32.
Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF assay for the diagnosis of pulmonary and extrapulmonary TB in adults and children: policy update. WHO Guidelines Approved by the Guidelines Review Committee. Geneva; 2013.
Yin QQ, Jiao WW, Han R, Jiao AX, Sun L, Tian JL, et al. Rapid diagnosis of childhood pulmonary tuberculosis by Xpert MTB/RIF assay using bronchoalveolar lavage fluid. Biomed Res Int. 2014;2014:310194.
Mathew P, Kuo YH, Vazirani B, Eng RH, Weinstein MP. Are three sputum acid-fast bacillus smears necessary for discontinuing tuberculosis isolation? J Clin Microbiol. 2002;40(9):3482–4.
Nolan VG, Arnold SR, Bramley AM, Ampofo K, Williams DJ, Grijalva CG, et al. Etiology and impact of coinfections in children hospitalized with community-acquired pneumonia. J Infect Dis. 2018;218(2):179–88.
Costa C, Elia M, Astegiano S, Sidoti F, Terlizzi ME, Solidoro P, et al. Quantitative detection of Epstein-Barr virus in bronchoalveolar lavage from transplant and nontransplant patients. Transplantation. 2008;86(10):1389–94.
Costa C, Delsedime L, Solidoro P, Curtoni A, Bergallo M, Libertucci D, et al. Herpesviruses detection by quantitative real-time polymerase chain reaction in bronchoalveolar lavage and transbronchial biopsy in lung transplant: viral infections and histopathological correlation. Transplant Proc. 2010;42(4):1270–4.
Dioverti MV, Razonable RR. Cytomegalovirus. Microbiol Spectr. 2016;4(4) https://doi.org/10.1128/microbiolspec.DMIH2-0022-2015.
Liu P, Xu M, He L, Su L, Wang A, Fu P, et al. Epidemiology of respiratory pathogens in children with lower respiratory tract infections in Shanghai, China, from 2013 to 2015. Jpn J Infect Dis. 2018;71(1):39–44.
Esther CR Jr, Lin FC, Kerr A, Miller MB, Gilligan PH. Respiratory viruses are associated with common respiratory pathogens in cystic fibrosis. Pediatr Pulmonol. 2014;49(9):926–31.
Michelow IC, Olsen K, Lozano J, Rollins NK, Duffy LB, Ziegler T, et al. Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children. Pediatrics. 2004;113(4):701–7.
Ruuskanen O, Lahti E, Jennings LC, Murdoch DR. Viral pneumonia. Lancet. 2011;377(9773):1264–75.
Reeves RM, Hardelid P, Gilbert R, Warburton F, Ellis J, Pebody RG. Estimating the burden of respiratory syncytial virus (RSV) on respiratory hospital admissions in children less than five years of age in England, 2007-2012. Influenza Other Respi Viruses. 2017;11(2):122–9.
Ogimi C, Waghmare AA, Kuypers JM, Xie H, Yeung CC, Leisenring WM, et al. Clinical significance of human coronavirus in bronchoalveolar lavage samples from hematopoietic cell transplant recipients and patients with hematologic malignancies. Clin Infect Dis. 2017;64(11):1532–9.
Chatzis O, Darbre S, Pasquier J, Meylan P, Manuel O, Aubert JD, et al. Burden of severe RSV disease among immunocompromised children and adults: a 10 year retrospective study. BMC Infect Dis. 2018;18(1):111.
Scheltema NM, Gentile A, Lucion F, Nokes DJ, Munywoki PK, Madhi SA, et al. Global respiratory syncytial virus-associated mortality in young children (RSV GOLD): a retrospective case series. Lancet Glob Health. 2017;5(10):e984–e91.
Azadeh N, Sakata KK, Saeed A, Mullon JJ, Grys TE, Limper AH, et al. Comparison of respiratory pathogen detection in upper versus lower respiratory tract samples using the BioFire FilmArray respiratory panel in the immunocompromised host. Can Respir J. 2018;2018:2685723.
Lachant DJ, Croft DP, McGrane Minton H, Prasad P, Kottmann RM. Nasopharyngeal viral PCR in immunosuppressed patients and its association with virus detection in bronchoalveolar lavage by PCR. Respirology. 2017;22(6):1205–11.
Wurzel DF, Marchant JM, Clark JE, Mackay IM, Wang CY, Sloots TP, et al. Respiratory virus detection in nasopharyngeal aspirate versus bronchoalveolar lavage is dependent on virus type in children with chronic respiratory symptoms. J Clin Virol. 2013;58(4):683–8.
Restrepo-Gualteros SM, Jaramillo-Barberi LE, Gonzalez-Santos M, Rodriguez-Martinez CE, Perez GF, Gutierrez MJ, et al. Characterization of cytomegalovirus lung infection in non-HIV infected children. Viruses. 2014;6(5):2038–51.
Goussard P, Kling S, Gie RP, Nel ED, Heyns L, Rossouw GJ, et al. CMV pneumonia in HIV-infected ventilated infants. Pediatr Pulmonol. 2010;45(7):650–5.
Zampoli M, Morrow B, Hsiao NY, Whitelaw A, Zar HJ. Prevalence and outcome of cytomegalovirus-associated pneumonia in relation to human immunodeficiency virus infection. Pediatr Infect Dis J. 2011;30(5):413–7.
Gooskens J, Templeton KE, Claas EC, van Bussel MJ, Smit VT, Kroes AC. Quantitative detection of herpes simplex virus DNA in the lower respiratory tract. J Med Virol. 2007;79(5):597–604.
Wu JL, Ma HY, Lu CY, Chen JM, Lee PI, Jou ST, et al. Risk factors and outcomes of cytomegalovirus viremia in pediatric hematopoietic stem cell transplantation patients. J Microbiol Immunol Infect. 2017;50(3):307–13.
Rowe RG, Guo D, Lee M, Margossian S, London WB, Lehmann L. Cytomegalovirus infection in pediatric hematopoietic stem cell transplantation: risk factors for primary infection and cases of recurrent and late infection at a single center. Biol Blood Marrow Transplant. 2016;22(7):1275–83.
Chemaly RF, Yen-Lieberman B, Castilla EA, Reilly A, Arrigain S, Farver C, et al. Correlation between viral loads of cytomegalovirus in blood and bronchoalveolar lavage specimens from lung transplant recipients determined by histology and immunohistochemistry. J Clin Microbiol. 2004;42(5):2168–72.
Tan SK, Burgener EB, Waggoner JJ, Gajurel K, Gonzalez S, Chen SF, et al. Molecular and culture-based bronchoalveolar lavage fluid testing for the diagnosis of cytomegalovirus pneumonitis. Open Forum Infect Dis. 2016;3(1):ofv212.
Boeckh M, Stevens-Ayers T, Travi G, Huang ML, Cheng GS, Xie H, et al. Cytomegalovirus (CMV) DNA quantitation in bronchoalveolar lavage fluid from hematopoietic stem cell transplant recipients with CMV pneumonia. J Infect Dis. 2017;215(10):1514–22.
Lodding IP, Schultz HH, Jensen JU, Kirkby N, Perch M, Andersen C, et al. Cytomegalovirus viral load in bronchoalveolar lavage to diagnose lung transplant associated CMV pneumonia. Transplantation. 2018;102(2):326–32.
Chemaly RF, Yen-Lieberman B, Chapman J, Reilly A, Bekele BN, Gordon SM, et al. Clinical utility of cytomegalovirus viral load in bronchoalveolar lavage in lung transplant recipients. Am J Transplant. 2005;5(3):544–8.
Govender K, Jeena P, Parboosing R. Clinical utility of bronchoalveolar lavage cytomegalovirus viral loads in the diagnosis of cytomegalovirus pneumonitis in infants. J Med Virol. 2017;89(6):1080–7.
Beam E, Germer JJ, Lahr B, Yao JDC, Limper AH, Binnicker MJ, et al. Cytomegalovirus (CMV) DNA quantification in bronchoalveolar lavage fluid of immunocompromised patients with CMV pneumonia. Clin Transplant. 2018;32(1) https://doi.org/10.1111/ctr.13149.
Cunha BA, Eisenstein LE, Dillard T, Krol V. Herpes simplex virus (HSV) pneumonia in a heart transplant: diagnosis and therapy. Heart Lung. 2007;36(1):72–8.
Frangoul H, Wills M, Crossno C, Engel M, Domm J. Acyclovir-resistant herpes simplex virus pneumonia post-unrelated stem cell transplantation: a word of caution. Pediatr Transplant. 2007;11(8):942–4.
Gasparetto EL, Escuissato DL, Inoue C, Marchiori E, Müller NL. Herpes simplex virus type 2 pneumonia after bone marrow transplantation: high-resolution CT findings in 3 patients. J Thorac Imaging. 2005;20(2):71–3.
Linssen CF, Jacobs JA, Stelma FF, van Mook WN, Terporten P, Vink C, et al. Herpes simplex virus load in bronchoalveolar lavage fluid is related to poor outcome in critically ill patients. Intensive Care Med. 2008;34(12):2202–9.
Saugel B, Jakobus J, Huber W, Hoffmann D, Holzapfel K, Protzer U, et al. Herpes simplex virus in bronchoalveolar lavage fluid of medical intensive care unit patients: association with lung injury and outcome. J Crit Care. 2016;32:138–44.
Assink-de Jong E, Groeneveld AB, Pettersson AM, Koek A, Vandenbroucke-Grauls CM, Beishuizen A, et al. Clinical correlates of herpes simplex virus type 1 loads in the lower respiratory tract of critically ill patients. J Clin Virol. 2013;58(1):79–83.
Kotzbauer D, Frank G, Dong W, Shore S. Clinical and laboratory characteristics of disseminated herpes simplex virus infection in neonates. Hosp Pediatr. 2014;4(3):167–71.
Capretti MG, Marsico C, Lazzarotto T, Gabrielli L, Bagni A, De Angelis M, et al. Herpes Simplex Virus 1 infection: misleading findings in an infant with disseminated disease. New Microbiol. 2013;36(3):307–13.
Inokuchi R, Nakamura K, Sato H, Shinohara K, Aoki Y, Doi K, et al. Bronchial ulceration as a prognostic indicator for varicella pneumonia: case report and systematic literature review. J Clin Virol. 2013;56(4):360–4.
Chiner E, Ballester I, Betlloch I, Blanquer J, Aguar MC, Blanquer R, et al. Varicella-zoster virus pneumonia in an adult population: has mortality decreased? Scand J Infect Dis. 2010;42(3):215–21.
Richaud C, Ngo MT, Agbessi CA, Boru B, Elkharrat D, Chinet T. Bronchial involvement in an immunocompetent adult with varicella pneumonia. Rev Mal Respir. 2008;25(1):59–62.
Libert N, Bigaillon C, Chargari C, Bensalah M, Muller V, Merat S, et al. Epstein-Barr virus reactivation in critically ill immunocompetent patients. Biomed J. 2015;38(1):70–6.
Banks CA, Meier JD, Stallworth CR, White DR. Recurrent posttransplant lymphoproliferative disorder involving the larynx and trachea: case report and review of the literature. Ann Otol Rhinol Laryngol. 2012;121(5):291–5.
O’Neill AF, Adil EA, Irace AL, Neff L, Davis IJ, Perez-Atayde AR, et al. Post-transplant lymphoproliferative disorder of the pediatric airway: Presentation and management. Int J Pediatr Otorhinolaryngol. 2016;86:218–23.
Feuillet S, Meignin V, Briere J, Brice P, Rocha V, Socie G, et al. Endobronchial Epstein-Barr Virus associated post-transplant lymphoproliferative disorder in hematopoietic stem cell transplantation. Clin Med Case Rep. 2009;2:11–5.
Fortes HR, von Ranke FM, Escuissato DL, Araujo Neto CA, Zanetti G, Hochhegger B, et al. Recurrent respiratory papillomatosis: a state-of-the-art review. Respir Med. 2017;126:116–21.
Pritt BS, Aubry MC. Histopathology of viral infections of the lung. Semin Diagn Pathol. 2017;34(6):510–7.
Smyth RL, Higenbottam TW, Scott JP, Wreghitt TG, Stewart S, Clelland CA, et al. Herpes simplex virus infection in heart-lung transplant recipients. Transplantation. 1990;49(4):735–9.
Costa C, Libertucci D, Solidoro P, Sinesi F, Bergallo M, Margio S, et al. Rapid shell vial culture for the detection of respiratory viruses from bronchoalveolar lavage in immunocompromised patients. Panminerva Med. 2007;49(1):1–6.
Marcos MA, Esperatti M, Torres A. Viral pneumonia. Curr Opin Infect Dis. 2009;22(2):143–7.
Prendergast C, Papenburg J. Rapid antigen-based testing for respiratory syncytial virus: moving diagnostics from bench to bedside? Future Microbiol. 2013;8(4):435–44.
Chartrand C, Tremblay N, Renaud C, Papenburg J. Diagnostic accuracy of rapid antigen detection tests for respiratory syncytial virus infection: systematic review and meta-analysis. J Clin Microbiol. 2015;53(12):3738–49.
Chartrand C, Leeflang MM, Minion J, Brewer T, Pai M. Accuracy of rapid influenza diagnostic tests: a meta-analysis. Ann Intern Med. 2012;156(7):500–11.
Bennett JE. Introduction to Mycoses. In: Bennett J, Dolin R, Blaser M, editors. Mandell, Douglas, and Bennett’s principles and practice of infectious diseases. 8th ed. Philadelphia, PA: Elsevier; 2016.
De Pauw B, Walsh TJ, Donnelly JP, Stevens DA, Edwards JE, Calandra T, et al. Revised definitions of invasive fungal disease from the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) Consensus Group. Clin Infect Dis. 2008;46(12):1813–21.
Anantasit N, Nuntacharruksa N, Incharoen P, Preutthipan A. Clinical and pathological correlation in pediatric invasive pulmonary Aspergillosis. Front Pediatr. 2018;6:31.
Maturu VN, Agarwal R. Prevalence of Aspergillus sensitization and allergic bronchopulmonary aspergillosis in cystic fibrosis: systematic review and meta-analysis. Clin Exp Allergy. 2015;45(12):1765–78.
Agarwal R, Aggarwal AN, Gupta D, Jindal SK. Aspergillus hypersensitivity and allergic bronchopulmonary aspergillosis in patients with bronchial asthma: systematic review and meta-analysis. Int J Tuberc Lung Dis. 2009;13(8):936–44.
Agarwal R, Chakrabarti A, Shah A, Gupta D, Meis JF, Guleria R, et al. Allergic bronchopulmonary aspergillosis: review of literature and proposal of new diagnostic and classification criteria. Clin Exp Allergy. 2013;43(8):850–73.
Neofytos D, Fishman JA, Horn D, Anaissie E, Chang CH, Olyaei A, et al. Epidemiology and outcome of invasive fungal infections in solid organ transplant recipients. Transpl Infect Dis. 2010;12(3):220–9.
Neofytos D, Horn D, Anaissie E, Steinbach W, Olyaei A, Fishman J, et al. Epidemiology and outcome of invasive fungal infection in adult hematopoietic stem cell transplant recipients: analysis of Multicenter Prospective Antifungal Therapy (PATH) Alliance registry. Clin Infect Dis. 2009;48(3):265–73.
Krenke R, Grabczak EM. Tracheobronchial manifestations of Aspergillus infections. Scientific World Journal. 2011;11:2310–29.
Moura S, Cerqueira L, Almeida A. Invasive pulmonary aspergillosis: current diagnostic methodologies and a new molecular approach. Eur J Clin Microbiol Infect Dis. 2018;37(8):1393–403.
Walzer P, Smulian A, Miller R. Pneumocystis species. In: Bennett J, Dolin R, Blaser M, editors. Mandell, Douglas, and Bennett’s principles and practice of infectious diseases. 8th ed. Philadelphia, PA: Elsevier; 2016.
Inagaki K, Blackshear C, Hobbs CV. Pneumocystis infection in children: national trends and characteristics in the United States, 1997-2012. Pediatr Infect Dis J. 2019;38(3):241–7.
Vera C, Aguilar YA, Velez LA, Rueda ZV. High transient colonization by Pneumocystis jirovecii between mothers and newborn. Eur J Pediatr. 2017;176(12):1619–27.
Oladele RO, Otu AA, Richardson MD, Denning DW. Diagnosis and management of Pneumocystis pneumonia in resource-poor settings. J Health Care Poor Underserved. 2018;29(1):107–58.
Toma P, Bertaina A, Castagnola E, Colafati GS, D’Andrea ML, Finocchi A, et al. Fungal infections of the lung in children. Pediatr Radiol. 2016;46(13):1856–65.
Fillaux J, Malvy S, Alvarez M, Fabre R, Cassaing S, Marchou B, et al. Accuracy of a routine real-time PCR assay for the diagnosis of Pneumocystis jirovecii pneumonia. J Microbiol Methods. 2008;75(2):258–61.
Lease ED, Alexander BD. Fungal diagnostics in pneumonia. Semin Respir Crit Care Med. 2011;32(6):663–72.
Summah H, Zhu YG, Falagas ME, Vouloumanou EK, Qu JM. Use of real-time polymerase chain reaction for the diagnosis of Pneumocystis pneumonia in immunocompromised patients: a meta-analysis. Chin Med J (Engl). 2013;126(10):1965–73.
Fan LC, Lu HW, Cheng KB, Li HP, Xu JF. Evaluation of PCR in bronchoalveolar lavage fluid for diagnosis of Pneumocystis jirovecii pneumonia: a bivariate meta-analysis and systematic review. PLoS One. 2013;8(9):e73099.
Karageorgopoulos DE, Qu JM, Korbila IP, Zhu YG, Vasileiou VA, Falagas ME. Accuracy of beta-D-glucan for the diagnosis of Pneumocystis jirovecii pneumonia: a meta-analysis. Clin Microbiol Infect. 2013;19(1):39–49.
Katragkou A, Fisher BT, Groll AH, Roilides E, Walsh TJ. Diagnostic imaging and invasive fungal diseases in children. J Pediatric Infect Dis Soc. 2017;6(suppl_1):S22–31.
Durairaj L, Mohamad Z, Launspach JL, Ashare A, Choi JY, Rajagopal S, et al. Patterns and density of early tracheal colonization in intensive care unit patients. J Crit Care. 2009;24(1):114–21.
Meersseman W, Lagrou K, Spriet I, Maertens J, Verbeken E, Peetermans WE, et al. Significance of the isolation of Candida species from airway samples in critically ill patients: a prospective, autopsy study. Intensive Care Med. 2009;35(9):1526–31.
Terraneo S, Ferrer M, Martin-Loeches I, Esperatti M, Di Pasquale M, Giunta V, et al. Impact of Candida spp. isolation in the respiratory tract in patients with intensive care unit-acquired pneumonia. Clin Microbiol Infect. 2016;22(1):94.e1–8.
AbdulWahab A, Salah H, Chandra P, Taj-Aldeen SJ. Persistence of Candida dubliniensis and lung function in patients with cystic fibrosis. BMC Res Notes. 2017;10(1):326.
Shirley RM, Baddley JW. Cryptococcal lung disease. Curr Opin Pulm Med. 2009;15(3):254–60.
Fyfe M, MacDougall L, Romney M, Starr M, Pearce M, Mak S, et al. Cryptococcus gattii infections on Vancouver Island, British Columbia, Canada: emergence of a tropical fungus in a temperate environment. Can Commun Dis Rep. 2008;34(6):1–12.
Shaheen AA, Somayaji R, Myers R, Mody CH. Epidemiology and trends of cryptococcosis in the United States from 2000 to 2007: A population-based study. Int J STD AIDS. 2018;29(5):453–60.
Liu L, Guo L, Liu Y, Chen T, Li S, Yang Y, et al. Clinical characteristics and prognosis of pediatric cryptococcosis in Beijing Children’s Hospital, 2002-2014. Eur J Pediatr. 2017;176(9):1235–44.
Lamoth F, Alexander BD. Nonmolecular methods for the diagnosis of respiratory fungal infections. Clin Lab Med. 2014;34(2):315–36.
Lass-Florl C. Current challenges in the diagnosis of fungal infections. Methods Mol Biol (Clifton, NJ). 2017;1508:3–15.
Pappas PG, Perfect JR, Cloud GA, Larsen RA, Pankey GA, Lancaster DJ, et al. Cryptococcosis in human immunodeficiency virus-negative patients in the era of effective azole therapy. Clin Infect Dis. 2001;33(5):690–9.
Xie X, Xu B, Yu C, Chen M, Yao D, Xu X, et al. Clinical analysis of pulmonary cryptococcosis in non-HIV patients in south China. Int J Clin Exp Med. 2015;8(3):3114–9.
Kralovic SM, Rhodes JC. Utility of routine testing of bronchoalveolar lavage fluid for cryptococcal antigen. J Clin Microbiol. 1998;36(10):3088–9.
Baughman RP, Rhodes JC, Dohn MN, Henderson H, Frame PT. Detection of cryptococcal antigen in bronchoalveolar lavage fluid: a prospective study of diagnostic utility. Am Rev Respir Dis. 1992;145(5):1226–9.
Senghor Y, Guitard J, Angoulvant A, Hennequin C. Cryptococcal antigen detection in broncho-alveolar lavage fluid. Med Mycol. 2018;56(6):774–7.
Kontoyiannis DP, Lewis RE. Agents of mucormycosis and entomophthoramycosis. In: Bennett J, Dolin R, Blaser M, editors. Mandell, Douglas, and Bennett’s principles and practice of infectious diseases. 8th ed. Philadelphia, PA: Elsevier; 2015.
Walsh TJ, Gamaletsou MN, McGinnis MR, Hayden RT, Kontoyiannis DP. Early clinical and laboratory diagnosis of invasive pulmonary, extrapulmonary, and disseminated mucormycosis (zygomycosis). Clin Infect Dis. 2012;54(Suppl 1):S55–60.
McBride JA, Gauthier GM, Klein BS. Clinical manifestations and treatment of blastomycosis. Clin Chest Med. 2017;38(3):435–49.
Goughenour KD, Rappleye CA. Antifungal therapeutics for dimorphic fungal pathogens. Virulence. 2017;8(2):211–21.
Baddley JW, Winthrop KL, Patkar NM, Delzell E, Beukelman T, Xie F, et al. Geographic distribution of endemic fungal infections among older persons, United States. Emerg Infect Dis. 2011;17(9):1664–9.
Martinez R. New trends in paracoccidioidomycosis epidemiology. J Fungi (Basel). 2017;3(1):1.
Hage CA, Knox KS, Wheat LJ. Endemic mycoses: overlooked causes of community acquired pneumonia. Respir Med. 2012;106(6):769–76.
McKinsey DS, McKinsey JP. Pulmonary histoplasmosis. Semin Respir Crit Care Med. 2011;32(6):735–44.
Denning DW, Chakrabarti A. Pulmonary and sinus fungal diseases in non-immunocompromised patients. Lancet Infect Dis. 2017;17(11):e357–e66.
Wheat LJ. Approach to the diagnosis of the endemic mycoses. Clin Chest Med. 2009;30(2):379–89. viii.
Hage CA, Azar MM, Bahr N, Loyd J, Wheat LJ. Histoplasmosis: up-to-date evidence-based approach to diagnosis and management. Semin Respir Crit Care Med. 2015;36(5):729–45.
Hage CA, Wheat LJ. Diagnosis of pulmonary histoplasmosis using antigen detection in the bronchoalveolar lavage. Expert Rev Respir Med. 2010;4(4):427–9.
Hage CA, Ribes JA, Wengenack NL, Baddour LM, Assi M, McKinsey DS, et al. A multicenter evaluation of tests for diagnosis of histoplasmosis. Clin Infect Dis. 2011;53(5):448–54.
Tarrand JJ, Lichterfeld M, Warraich I, Luna M, Han XY, May GS, et al. Diagnosis of invasive septate mold infections. A correlation of microbiological culture and histologic or cytologic examination. Am J Clin Pathol. 2003;119(6):854–8.
Lehrnbecher T, Robinson PD, Fisher BT, Castagnola E, Groll AH, Steinbach WJ, et al. Galactomannan, beta-D-glucan, and polymerase chain reaction-based assays for the diagnosis of invasive fungal disease in pediatric cancer and hematopoietic stem cell transplantation: a systematic review and meta-analysis. Clin Infect Dis. 2016;63(10):1340–8.
Loeffler J, Hafner J, Mengoli C, Wirth C, Heussel CP, Loffler C, et al. Prospective biomarker screening for diagnosis of invasive aspergillosis in high-risk pediatric patients. J Clin Microbiol. 2017;55(1):101–9.
Avni T, Levy I, Sprecher H, Yahav D, Leibovici L, Paul M. Diagnostic accuracy of PCR alone compared to galactomannan in bronchoalveolar lavage fluid for diagnosis of invasive pulmonary aspergillosis: a systematic review. J Clin Microbiol. 2012;50(11):3652–8.
Trubiano JA, Dennison AM, Morrissey CO, Chua KY, Halliday CL, Chen SC, et al. Clinical utility of panfungal polymerase chain reaction for the diagnosis of invasive fungal disease: a single center experience. Med Mycol. 2016;54(2):138–46.
Hage CA, Davis TE, Fuller D, Egan L, Witt JR 3rd, Wheat LJ, et al. Diagnosis of histoplasmosis by antigen detection in BAL fluid. Chest. 2010;137(3):623–8.
Huang YT, Hung CC, Liao CH, Sun HY, Chang SC, Chen YC. Detection of circulating galactomannan in serum samples for diagnosis of Penicillium marneffei infection and cryptococcosis among patients infected with human immunodeficiency virus. J Clin Microbiol. 2007;45(9):2858–62.
Park SY, Lee SO, Choi SH, Sung H, Kim MN, Choi CM, et al. Aspergillus galactomannan antigen assay in bronchoalveolar lavage fluid for diagnosis of invasive pulmonary aspergillosis. J Infect. 2010;61(6):492–8.
de Mol M, de Jongste JC, van Westreenen M, Merkus PJ, de Vries AH, Hop WC, et al. Diagnosis of invasive pulmonary aspergillosis in children with bronchoalveolar lavage galactomannan. Pediatr Pulmonol. 2013;48(8):789–96.
Desai R, Ross LA, Hoffman JA. The role of bronchoalveolar lavage galactomannan in the diagnosis of pediatric invasive aspergillosis. Pediatr Infect Dis J. 2009;28(4):283–6.
Zhang S, Wang S, Wan Z, Li R, Yu J. The diagnosis of invasive and noninvasive pulmonary aspergillosis by serum and bronchoalveolar lavage fluid galactomannan assay. Biomed Res Int. 2015;2015:943691.
Zhou W, Li H, Zhang Y, Huang M, He Q, Li P, et al. Diagnostic value of galactomannan antigen test in serum and bronchoalveolar lavage fluid samples from patients with nonneutropenic invasive pulmonary aspergillosis. J Clin Microbiol. 2017;55(7):2153–61.
Nguyen MH, Leather H, Clancy CJ, Cline C, Jantz MA, Kulkarni V, et al. Galactomannan testing in bronchoalveolar lavage fluid facilitates the diagnosis of invasive pulmonary aspergillosis in patients with hematologic malignancies and stem cell transplant recipients. Biol Blood Marrow Transplant. 2011;17(7):1043–50.
Zhang XB, Chen GP, Lin QC, Lin X, Zhang HY, Wang JH. Bronchoalveolar lavage fluid galactomannan detection for diagnosis of invasive pulmonary aspergillosis in chronic obstructive pulmonary disease. Med Mycol. 2013;51(7):688–95.
Pasqualotto AC, Xavier MO, Sanchez LB, de Oliveira Costa CD, Schio SM, Camargo SM, et al. Diagnosis of invasive aspergillosis in lung transplant recipients by detection of galactomannan in the bronchoalveolar lavage fluid. Transplantation. 2010;90(3):306–11.
Mohammadi S, Khalilzadeh S, Goudarzipour K, Hassanzad M, Mahdaviani A, Aarabi N, et al. Bronchoalveolar galactomannan in invasive pulmonary aspergillosis: a prospective study in pediatric patients. Med Mycol. 2015;53(7):709–16.
He S, Hang JP, Zhang L, Wang F, Zhang DC, Gong FH. A systematic review and meta-analysis of diagnostic accuracy of serum 1,3-beta-D-glucan for invasive fungal infection: focus on cutoff levels. J Microbiol Immunol Infect. 2015;48(4):351–61.
Egger M, Pruller F, Raggam R, Divjak MK, Kurath-Koller S, Lackner H, et al. False positive serum levels of (1-3)-ss-D-Glucan after infusion of intravenous immunoglobulins and time to normalisation. J Infect. 2018;76(2):206–10.
Liss B, Cornely OA, Hoffmann D, Dimitriou V, Wisplinghoff H. 1,3-ss-D-glucan concentrations in blood products predict false positive post-transfusion results. Mycoses. 2016;59(1):39–42.
Goudjil S, Chazal C, Moreau F, Leke A, Kongolo G, Chouaki T. Blood product transfusions are associated with an increase in serum (1-3)-beta-d-glucan in infants during the initial hospitalization in neonatal intensive care unit (NICU). J Matern Fetal Neonatal Med. 2017;30(8):933–7.
Calitri C, Caviglia I, Cangemi G, Furfaro E, Bandettini R, Fioredda F, et al. Performance of 1,3-beta-D-glucan for diagnosing invasive fungal diseases in children. Mycoses. 2017;60(12):789–95.
Shabaan AE, Elbaz LM, El-Emshaty WM, Shouman B. Role of serum 1,3beta-d-glucan assay in early diagnosis of invasive fungal infections in a neonatal intensive care unit. J Pediatr (Rio J). 2018;94(5):559–65.
Shi XY, Liu Y, Gu XM, Hao SY, Wang YH, Yan D, et al. Diagnostic value of (1 --> 3)-beta-D-glucan in bronchoalveolar lavage fluid for invasive fungal disease: a meta-analysis. Respir Med. 2016;117:48–53.
Salerno D, Mushatt D, Myers L, Zhuang Y, de la Rua N, Calderon EJ, et al. Serum and bal beta-D-glucan for the diagnosis of Pneumocystis pneumonia in HIV positive patients. Respir Med. 2014;108(11):1688–95.
Maguire JH. Introduction to helminth infections. In: Bennett J, Dolin R, Blaser M, editors. Mandell, Douglas, and Bennett’s principles and practice of infectious diseases. 8th ed. Philadelphia, PA: Elsevier; 2015.
Korpe PS, Ravdin JI, Petri WA. Introduction to protozoal diseases. In: Bennett J, Dolin R, Blaser M, editors. Mandell, Douglas, and Bennett’s principles and practice of infectious diseases. 8th ed. Philadelphia, PA: Elsevier; 2015.
Taylor WRJ, Hanson J, Turner GDH, White NJ, Dondorp AM. Respiratory manifestations of malaria. Chest. 2012;142(2):492–505.
de Souza GK, Costa AN, Apanavicius A, Teixeira FB, Fernandes CJ, Helito AS, et al. Tomographic findings of acute pulmonary toxoplasmosis in immunocompetent patients. BMC Pulm Med. 2014;14:185.
Rey MF, Mary C, Sanguinetti D, Ranque S, Bartoli C, L’Ollivier C. Successful treatment of pulmonary and cerebral toxoplasmosis associated with pneumocystis pneumonia in an HIV patient. Diseases (Basel). 2017;5(4):35.
Sumi M, Norose K, Hikosaka K, Kaiume H, Takeda W, Kirihara T, et al. Clinical characteristics and computed tomography findings of pulmonary toxoplasmosis after hematopoietic stem cell transplantation. Int J Hematol. 2016;104(6):729–40.
Roth A, Roth B, Hoffken G, Steuber S, Khalifa KI, Janitschke K. Application of the polymerase chain reaction in the diagnosis of pulmonary toxoplasmosis in immunocompromised patients. Eur J Clin Microbiol Infect Dis. 1992;11(12):1177–81.
Diehl AR, Dos Santos RP, Zimmerman R, Luz PL, Weiss T, Jacobson P, et al. Microscopy and polymerase chain reaction detection of Leishmania chagasi in the pleural and ascitic fluid of a patient with AIDS: case report and review of diagnosis and therapy of visceral leishmaniasis. Can J Infect Dis Med Microbiol. 2004;15(4):231–4.
Zakaria A, Al-Share B, Al Asad K. Primary pulmonary amebiasis complicated with multicystic empyema. Case Rep Pulmonol. 2016;2016:8709347.
Shamsuzzaman SM, Hashiguchi Y. Thoracic amebiasis. Clin Chest Med. 2002;23(2):479–92.
Cunha BA, Nausheen S, Szalda D. Pulmonary complications of babesiosis: case report and literature review. Euro J Clin Microbiol Infect Dis. 2007;26(7):505–8.
Cheepsattayakorn A, Cheepsattayakorn R. Parasitic pneumonia and lung involvement. Biomed Res Int. 2014;2014:874021.
Vasilakopoulou A, Dimarongona K, Samakovli A, Papadimitris K, Avlami A. Balantidium coli pneumonia in an immunocompromised patient. Scand J Infect Dis. 2003;35(2):144–6.
Anargyrou K, Petrikkos GL, Suller MT, Skiada A, Siakantaris MP, Osuntoyinbo RT, et al. Pulmonary Balantidium coli infection in a leukemic patient. Am J Hematol. 2003;73(3):180–3.
Reina FT, Ribeiro CA, Araujo RS, Matte MH, Castanho RE, Tanaka II, et al. Intestinal and pulmonary infection by Cryptosporidium parvum in two patients with HIV/AIDS. Rev Inst Med Trop Sao Paulo. 2016;58:21.
Poirot JL, Deluol AM, Antoine M, Heyer F, Cadranel J, Meynard JL, et al. Broncho-pulmonary cryptosporidiosis in four HIV-infected patients. J Eukaryot Microbiol. 1996;43(5):78s–9s.
Lanzafame M, Bonora S, Di Perri G, Allegranzi B, Guasparri I, Cazzadori A, et al. Microsporidium species in pulmonary cavitary lesions of AIDS patients infected with Rhodococcus equi. Clin Infect Dis. 1997;25(4):926–7.
Yao G, Zhou B, Zeng L. Imaging characteristics of bronchopulmonary Lophomonas blattarum infection: case report and literature review. J Thorac Imaging. 2009;24(1):49–51.
Saldana NG, Mendoza FJO, Larrauri FR, Trujillo DMG, Montoya EV, De La Garza EA, et al. Bronchopulmonary infection by Lophomonas blattarum in a pediatric patient after hematopoietic progenitor cell transplantation: first report in Mexico. J Thorac Dis. 2017;9(10):E899–e902.
Zhang X, Xu L, Wang LL, Liu S, Li J, Wang X. Bronchopulmonary infection with Lophomonas blattarum: a case report and literature review. J Int Med Res. 2011;39(3):944–9.
Barratt JL, Harkness J, Marriott D, Ellis JT, Stark D. Importance of nonenteric protozoan infections in immunocompromised people. Clin Microbiol Rev. 2010;23(4):795–836.
Schwartz C, Hams E, Fallon PG. Helminth modulation of lung inflammation. Trends Parasitol. 2018;34(5):388–403.
Craig JM, Scott AL. Helminths in the lungs. Parasite Immunol. 2014;36(9):463–74.
Loukas A, Hotez PJ, Diemert D, Yazdanbakhsh M, McCarthy JS, Correa-Oliveira R, et al. Hookworm infection. Nat Rev Dis Primers. 2016;2:16088.
Allen J, Wert M. Eosinophilic Pneumonias. J Allergy Clin Immunol Pract. 2018;6(5):1455–61.
Pavlin BI, Kozarsky P, Cetron MS. Acute pulmonary schistosomiasis in travelers: case report and review of the literature. Travel Med Infect Dis. 2012;10(5–6):209–19.
Schwartz E. Pulmonary schistosomiasis. Clin Chest Med. 2002;23(2):433–43.
Dantas-Torres F, Otranto D. Dirofilariosis in the Americas: a more virulent Dirofilaria immitis? Parasit Vectors. 2013;6(1):288.
Li CY, Chang YL, Lee YC. Human pulmonary dirofilariasis coexisting with intercostal neurilemmoma: a case report and literature review. J Formos Med Assoc. 2013;112(10):644–7.
Park KH, Kim YS, Kim SK, Choi NC, Kwon OY, Lim B, et al. Toxocara canis-associated myelitis with eosinophilic pneumonia. Exp Neurobiol. 2016;25(3):139–42.
Mazur-Melewska K, Jonczyk-Potoczna K, Kemnitz P, Mania A, Figlerowicz M, Sluzewski W. Pulmonary presentation of Toxocara sp. infection in children. Pneumonol Alergol Pol. 2015;83(4):250–5.
Blair D. Paragonimiasis. Adv Exp Med Biol. 2014;766:115–52.
Lamberton PH, Jourdan PM. Human ascariasis: diagnostics update. Curr Trop Med Rep. 2015;2(4):189–200.
Gupta N, Ray A, Ghosh S, Malla S, Vyas S. First things first: Importance of eosinophil count in diagnosing occult parasites. Drug Discov Ther. 2018;12(1):55–7.
Kilic D, Tercan F, Sahin E, Bilen A, Hatipoglu A. Unusual radiologic manifestations of the echinococcus infection in the thorax. J Thorac Imaging. 2006;21(1):32–6.
Vaideeswar P, Agnihotri MA, Hira P. Unusual manifestations of pleuro-pulmonary hydatidosis. Indian J Pathol Microbiol. 2012;55(1):111–2.
Sarkar M, Pathania R, Jhobta A, Thakur BR, Chopra R. Cystic pulmonary hydatidosis. Lung India. 2016;33(2):179–91.
Ali SR, Mehta AC. Alive in the airways: live endobronchial foreign bodies. Chest. 2017;151(2):481–91.
Gan RW, Gohil R, Belfield K, Davies P, Daniel M. Acute airway obstruction by Ascaris lumbricoides in a 14-month-old boy. Int J Pediatr Otorhinolaryngol. 2014;78(10):1795–8.
Bailey JK, Warner P. Respiratory arrest from Ascaris lumbricoides. Pediatrics. 2010;126(3):e712–5.
Nabeya D, Haranaga S, Parrott GL, Kinjo T, Nahar S, Tanaka T, et al. Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases. BMC Infect Dis. 2017;17(1):320.
Alsharif A, Sodhi A, Murillo LC, Headley AS, Kadaria D. Wait!!! no steroids for this asthma. Am J Case Rep. 2015;16:398–400.
Rajapurkar M, Hegde U, Rokhade M, Gang S, Gohel K. Respiratory hyperinfection with Strongyloides stercoralis in a patient with renal failure. Nat Clin Pract Nephrol. 2007;3(10):573–7.
Pozio E, Gomez Morales MA, Dupouy-Camet J. Clinical aspects, diagnosis and treatment of trichinellosis. Expert Rev Anti Infect Ther. 2003;1(3):471–82.
Genetu Bayih A, Debnath A, Mitre E, Huston CD, Laleu B, Leroy D, et al. Susceptibility testing of medically important parasites. Clin Microbiol Rev. 2017;30(3):647–69.
Buonfrate D, Requena-Mendez A, Angheben A, Cinquini M, Cruciani M, Fittipaldo A, et al. Accuracy of molecular biology techniques for the diagnosis of Strongyloides stercoralis infection-a systematic review and meta-analysis. PLoS Negl Trop Dis. 2018;12(2):e0006229.
Schijman AG. Molecular diagnosis of Trypanosoma cruzi. Acta Trop. 2018;184:59–66.
Amir A, Cheong FW, De Silva JR, Lau YL. Diagnostic tools in childhood malaria. Parasit Vectors. 2018;11(1):53.
Singh R, Singh DP, Gupta R, Savargaonkar D, Singh OP, Nanda N, et al. Comparison of three PCR-based assays for the non-invasive diagnosis of malaria: detection of Plasmodium parasites in blood and saliva. Euro J Clin Microbiol Infect Dis. 2014;33(9):1631–9.
Murat JB, Hidalgo HF, Brenier-Pinchart MP, Pelloux H. Human toxoplasmosis: which biological diagnostic tests are best suited to which clinical situations? Expert Rev Anti Infect Ther. 2013;11(9):943–56.
Adeyemo FE, Singh G, Reddy P, Stenstrom TA. Methods for the detection of Cryptosporidium and Giardia: from microscopy to nucleic acid based tools in clinical and environmental regimes. Acta Trop. 2018;184:15–28.
Garcia LS, Arrowood M, Kokoskin E, Paltridge GP, Pillai DR, Procop GW, et al. Laboratory diagnosis of parasites from the gastrointestinal tract. Clin Microbiol Rev. 2018;31(1):e00025–17.
Boland JM, Pritt BS. Histopathology of parasitic infections of the lung. Semin Diagn Pathol. 2017;34(6):550–9.
Zhu H, Min X, Li S, Feng M, Zhang G, Yi X. Amebic lung abscess with coexisting lung adenocarcinoma: a unusual case of amebiasis. Int J Clin Exp Pathol. 2014;7(11):8251–4.
Hizem A, M’rad S, Oudni-M’rad M, Mestiri S, Hammedi F, Mezhoud H, et al. Molecular genotyping of Echinococcus granulosus using formalin-fixed paraffin-embedded preparations from human isolates in unusual tissue sites. J Helminthol. 2016;90(4):417–21.
Rivasi F, Boldorini R, Criante P, Leutner M, Pampiglione S. Detection of Dirofilaria (Nochtiella) repens DNA by polymerase chain reaction in embedded paraffin tissues from two human pulmonary locations. APMIS. 2006;114(7–8):567–74.
Gobbi F, Formenti F, Perandin F, Buonfrate D, Angheben A, Paiano S, et al. Real-time polymerase chain reaction assay on bronchoalveolar lavage: an alternative method for diagnosing chronic pulmonary schistosomiasis? Am J Trop Med Hyg. 2017;97(6):1808–9.
Izadi M, Jonaidi Jafari N, Mahmoodzadeh Poornaki A, Sadraei J, Rezavand B, Mirzaei HR, et al. Detection of Toxoplasma gondii from clinical specimens of patients receiving renal transplant using ELISA and PCR. Nephrourol Mon. 2013;5(5):983–7.
Özkoç S, Bayram Delibaş S, Akısü Ç. Evaluation of pulmonary microsporidiosis in iatrogenically immunosuppressed patients. Tuberk Toraks. 2016;64(1):9–16.
Desoubeaux G, Cabanne E, Franck-Martel C, Gombert M, Gyan E, Lissandre S, et al. Pulmonary toxoplasmosis in immunocompromised patients with interstitial pneumonia: a single-centre prospective study assessing PCR-based diagnosis. J Clin Pathol. 2016;69(8):726–30.
Montresor A, Crompton DWT, Hall A, Bundy DAP, Savioli L. Guidelines for the evaluation of soil-transmitted helminthiasis and schistosomiasis at community level: a guide for managers of control programmes. Geneva: World Health Organization; 1998.
Itoh N, Tsukahara M, Yamasaki H, Morishima Y, Sugiyama H, Kurai H. Paragonimus westermani infection mimicking recurrent lung cancer: a case report. J Infect Chemother. 2016;22(12):815–8.
Guerrero-Wooley R, Aranda-Aguirre E, Li W, Wilkin A, Palavecino E. Case report: Strongyloides stercoralis hyperinfection in a patient with chronic lymphocytic leukemia. Am J Trop Med Hyg. 2017;97(5):1629–31.
Wang LF, Xu L, Luo SQ, Xie H, Chen W, Wu ZD, et al. Diagnosis of Strongyloides stercoralis by morphological characteristics combine with molecular biological methods. Parasitol Res. 2017;116(4):1159–63.
Kinjo T, Tsuhako K, Nakazato I, Ito E, Sato Y, Koyanagi Y, et al. Extensive intra-alveolar haemorrhage caused by disseminated strongyloidiasis. Int J Parasitol. 1998;28(2):323–30.
Tanyuksel M, Petri WA Jr. Laboratory diagnosis of amebiasis. Clin Microbiol Rev. 2003;16(4):713–29.
Chaudhry IU, Manah W, Alghamdi M, Mutairi H. A rare cause of asymptomatic solitary pulmonary nodule: adult Schistosoma worm. BMJ Case Rep. 2014;2014:bcr2013202840.
Yasar Z, Acat M, Turgut E, Onaran H, Dincer HE, Arda N, et al. Diagnosis of pulmonary hydatid cyst by bronchoscopy. J Bronchology Interv Pulmonol. 2015;22(4):343–6.
Komurcuoglu B, Ozkaya S, Cirak AK, Yalniz E, Polat G. Pulmonary hydatid cyst: the characteristics of patients and diagnostic efficacy of bronchoscopy. Exp Lung Res. 2012;38(6):277–80.
Prasad R, Goel MK, Mukerji PK, Agarwal PK. Microfilaria in bronchial aspirate. Indian J Chest Dis Allied Sci. 1994;36(4):223–5.
Anupindi L, Sahoo R, Rao RV, Verghese G, Rao PV. Microfilariae in bronchial brushing cytology of symptomatic pulmonary lesions. A report of two cases. Acta Cytol. 1993;37(3):397–9.
Cui L, Morris A, Huang L, Beck JM, Twigg HL 3rd, von Mutius E, et al. The microbiome and the lung. Ann Am Thorac Soc. 2014;11(Suppl 4):S227–32.
Pendleton KM, Erb-Downward JR, Bao Y, Branton WR, Falkowski NR, Newton DW, et al. Rapid pathogen identification in bacterial pneumonia using real-time metagenomics. Am J Respir Crit Care Med. 2017;196(12):1610–2.
Dickson RP, Erb-Downward JR, Prescott HC, Martinez FJ, Curtis JL, Lama VN, et al. Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid. J Clin Microbiol. 2014;52(10):3605–13.
Marsh RL, Kaestli M, Chang AB, Binks MJ, Pope CE, Hoffman LR, et al. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. Microbiome. 2016;4(1):37.
Marsh RL, Smith-Vaughan HC, Chen ACH, Marchant JM, Yerkovich ST, Gibson PG, et al. Multiple respiratory microbiota profiles are associated with lower airway inflammation in children with protracted bacterial bronchitis. Chest. 2019;155(4):778–86.
Zemanick ET, Wagner BD, Robertson CE, Ahrens RC, Chmiel JF, Clancy JP, et al. Airway microbiota across age and disease spectrum in cystic fibrosis. Eur Respir J. 2017;50(5):1700832.
Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, et al. Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A. 2007;104(51):20529–33.
Prevaes SM, de Winter-de Groot KM, Janssens HM, de Steenhuijsen Piters WA, Tramper-Stranders GA, Wyllie AL, et al. Development of the nasopharyngeal microbiota in infants with cystic fibrosis. Am J Respir Crit Care Med. 2016;193(5):504–15.
Renwick J, McNally P, John B, DeSantis T, Linnane B, Murphy P, et al. The microbial community of the cystic fibrosis airway is disrupted in early life. PLoS One. 2014;9(12):e109798.
Blainey PC, Milla CE, Cornfield DN, Quake SR. Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Sci Transl Med. 2012;4(153):153ra30.
Zemanick ET, Wagner BD, Robertson CE, Stevens MJ, Szefler SJ, Accurso FJ, et al. Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc. 2015;12(2):221–9.
Boutin S, Graeber SY, Weitnauer M, Panitz J, Stahl M, Clausznitzer D, et al. Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis. PLoS One. 2015;10(1):e0116029.
Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, Kehagia V, et al. Use of 16S rRNA gene profiling by terminal restriction fragment length polymorphism analysis to compare bacterial communities in sputum and mouthwash samples from patients with cystic fibrosis. J Clin Microbiol. 2006;44(7):2601–4.
Brown PS, Pope CE, Marsh RL, Qin X, McNamara S, Gibson R, et al. Directly sampling the lung of a young child with cystic fibrosis reveals diverse microbiota. Ann Am Thorac Soc. 2014;11(7):1049–55.
Dickson RP, Erb-Downward JR, Freeman CM, McCloskey L, Falkowski NR, Huffnagle GB, et al. Bacterial topography of the healthy human lower respiratory tract. MBio. 2017;8(1):e02287–16.
Bassis CM, Erb-Downward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio. 2015;6(2):e00037.
Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011;184(8):957–63.
Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, et al. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One. 2012;7(9):e42786.
Nguyen LD, Viscogliosi E, Delhaes L. The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol. 2015;6:89.
Bousbia S, Papazian L, Saux P, Forel JM, Auffray JP, Martin C, et al. Repertoire of intensive care unit pneumonia microbiota. PLoS One. 2012;7(2):e32486.
McTaggart LR, Copeland JK, Surendra A, Wang PW, Husain S, Coburn B, et al. Mycobiome sequencing and analysis applied to fungal community profiling of the lower respiratory tract during fungal pathogenesis. Front Microbiol. 2019;10:512.
Bittinger K, Charlson ES, Loy E, Shirley DJ, Haas AR, Laughlin A, et al. Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biol. 2014;15(10):487.
Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, et al. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Respir Crit Care Med. 2012;186(6):536–45.
Cui L, Lucht L, Tipton L, Rogers MB, Fitch A, Kessinger C, et al. Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease. Am J Respir Crit Care Med. 2015;191(8):932–42.
Halwachs B, Madhusudhan N, Krause R, Nilsson RH, Moissl-Eichinger C, Hogenauer C, et al. Critical issues in mycobiota analysis. Front Microbiol. 2017;8:180.
Krause R, Halwachs B, Thallinger GG, Klymiuk I, Gorkiewicz G, Hoenigl M, et al. Characterisation of candida within the mycobiome/microbiome of the lower respiratory tract of ICU patients. PLoS One. 2016;11(5):e0155033.
Krause R, Moissl-Eichinger C, Halwachs B, Gorkiewicz G, Berg G, Valentin T, et al. Mycobiome in the lower respiratory tract - a clinical perspective. Front Microbiol. 2016;7:2169.
Fraczek MG, Chishimba L, Niven RM, Bromley M, Simpson A, Smyth L, et al. Corticosteroid treatment is associated with increased filamentous fungal burden in allergic fungal disease. J Allergy Clin Immunol. 2018;142(2):407–14.
Young JC, Chehoud C, Bittinger K, Bailey A, Diamond JM, Cantu E, et al. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am J Transplant. 2015;15(1):200–9.
Lewandowska DW, Schreiber PW, Schuurmans MM, Ruehe B, Zagordi O, Bayard C, et al. Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection. PLoS One. 2017;12(5):e0177340.
Langelier C, Zinter MS, Kalantar K, Yanik GA, Christenson S, O’Donovan B, et al. Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Am J Respir Crit Care Med. 2018;197(4):524–8.
Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, et al. Pulmonary metagenomic sequencing suggests missed infections in immunocompromised children. Clin Infect Dis. 2019;68(11):1847–55.
Mitchell AB, Oliver BG, Glanville AR. Translational aspects of the human respiratory virome. Am J Respir Crit Care Med. 2016;194(12):1458–64.
Yang J, Yang F, Ren L, Xiong Z, Wu Z, Dong J, et al. Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach. J Clin Microbiol. 2011;49(10):3463–9.
Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. Sequence analysis of the human virome in febrile and afebrile children. PLoS One. 2012;7(6):e27735.
Zoll J, Rahamat-Langendoen J, Ahout I, de Jonge MI, Jans J, Huijnen MA, et al. Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information. J Clin Virol. 2015;66:6–11.
Wang Y, Zhu N, Li Y, Lu R, Wang H, Liu G, et al. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin Microbiol Infect. 2016;22(5):458 e1–9.
Zhou Y, Fernandez S, Yoon IK, Simasathien S, Watanaveeradej V, Yang Y, et al. Metagenomics study of viral pathogens in undiagnosed respiratory specimens and identification of human enteroviruses at a Thailand Hospital. Am J Trop Med Hyg. 2016;95(3):663–9.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Downes, K.J., Bouso, J.M., Planet, P.J. (2021). Bronchoalveolar Lavage: Microbial Evaluation. In: Goldfarb, S., Piccione, J. (eds) Diagnostic and Interventional Bronchoscopy in Children. Respiratory Medicine. Humana, Cham. https://doi.org/10.1007/978-3-030-54924-4_9
Download citation
DOI: https://doi.org/10.1007/978-3-030-54924-4_9
Published:
Publisher Name: Humana, Cham
Print ISBN: 978-3-030-54923-7
Online ISBN: 978-3-030-54924-4
eBook Packages: MedicineMedicine (R0)