publication . Article . Other literature type . 2012

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts.

Ronald Collman; Frederic D Bushman;
Open Access
  • Published: 06 Sep 2012 Journal: PLoS ONE, volume 7, page e42786 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
Abstract
Microbes of the human respiratory tract are important in health and disease, but accurate sampling of the lung presents challenges. Lung microbes are commonly sampled by bronchoscopy, but to acquire samples the bronchoscope must pass through the upper respiratory tract, which is rich in microbes. Here we present methods to identify authentic lung microbiota in bronchoalveolar lavage (BAL) fluid that contains substantial oropharyngeal admixture. We studied clinical BAL samples from six selected subjects with potential heavy lung colonization. A single sample of BAL fluid was obtained from each subject along with contemporaneous oral wash (OW) to sample the oropha...
Subjects
Medical Subject Headings: respiratory tract diseases
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Research Article, Biology, Anatomy and Physiology, Respiratory System, Computational Biology, Genomics, Genome Sequencing, Biological Data Management, Sequence Analysis, Medicine, Clinical Immunology, Immunologic Subspecialties, Transplantation, Pulmonology, Respiratory Infections, R, Science, Q
Funded by
NIH| Training in bacteriology
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T32AI060516-04
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Human Respiratory Tract Microbiome in Health, HIV Infection and HIV Lung Disease
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HL098957-05
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
44 references, page 1 of 3

1 Jordan GW, Wong GA, Hoeprich PD (1976) Bacteriology of the lower respiratory tract as determined by fiber-optic bronchoscopy and transtracheal aspiration. J Infect Dis 134: 428–435.993617 [OpenAIRE] [PubMed]

2 Kirkpatrick MB, Bass JB Jr (1989) Quantitative bacterial cultures of bronchoalveolar lavage fluids and protected brush catheter specimens from normal subjects. Am Rev Respir Dis 139: 546–548.2913899 [PubMed]

3 Pecora DV (1963) A Comparison of Transtracheal Aspiration with Other Methods of Determining the Bacterial Flora of the Lower Respiratory Tract. N Engl J Med 269: 664–666.14050970 [OpenAIRE] [PubMed]

4 Bartlett JG, Alexander J, Mayhew J, Sullivan-Sigler N, Gorbach SL (1976) Should fiberoptic bronchoscopy aspirates be cultured? Am Rev Respir Dis 114: 73–78.7173 [PubMed]

5 Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, et al (2011) Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 184: 957–963.21680950 [OpenAIRE] [PubMed]

6 Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, et al (2011) Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One 6: e16384.21364979 [OpenAIRE] [PubMed]

7 Beal M, Chesson A, Garcia T, Caldito G, Stucker F, et al (2004) A pilot study of quantitative aspiration in patients with symptoms of obstructive sleep apnea: comparison to a historic control group. Laryngoscope 114: 965–968.15179196 [OpenAIRE] [PubMed]

8 Gleeson K, Eggli DF, Maxwell SL (1997) Quantitative aspiration during sleep in normal subjects. Chest 111: 1266–1272.9149581 [OpenAIRE] [PubMed]

9 Huxley EJ, Viroslav J, Gray WR, Pierce AK (1978) Pharyngeal aspiration in normal adults and patients with depressed consciousness. Am J Med 64: 564–568.645722 [OpenAIRE] [PubMed]

10 Bousbia S, Papazian L, Auffray JP, Fenollar F, Martin C, et al (2010) Tropheryma whipplei in patients with pneumonia. Emerg Infect Dis 16: 258–263.20113556 [OpenAIRE] [PubMed]

11 Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, et al (2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A 104: 20529–20533.18077362 [OpenAIRE] [PubMed]

12 Nasidze I, Li J, Quinque D, Tang K, Stoneking M (2009) Global diversity in the human salivary microbiome. Genome Res 19: 636–643.19251737 [OpenAIRE] [PubMed]

13 Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721–5732.16272510 [OpenAIRE] [PubMed]

14 Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, et al (2011) Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8: 761–763.21765408 [OpenAIRE] [PubMed]

15 Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, et al (2012) Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 13: 47–58.

44 references, page 1 of 3
Abstract
Microbes of the human respiratory tract are important in health and disease, but accurate sampling of the lung presents challenges. Lung microbes are commonly sampled by bronchoscopy, but to acquire samples the bronchoscope must pass through the upper respiratory tract, which is rich in microbes. Here we present methods to identify authentic lung microbiota in bronchoalveolar lavage (BAL) fluid that contains substantial oropharyngeal admixture. We studied clinical BAL samples from six selected subjects with potential heavy lung colonization. A single sample of BAL fluid was obtained from each subject along with contemporaneous oral wash (OW) to sample the oropha...
Subjects
Medical Subject Headings: respiratory tract diseases
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Research Article, Biology, Anatomy and Physiology, Respiratory System, Computational Biology, Genomics, Genome Sequencing, Biological Data Management, Sequence Analysis, Medicine, Clinical Immunology, Immunologic Subspecialties, Transplantation, Pulmonology, Respiratory Infections, R, Science, Q
Funded by
NIH| Training in bacteriology
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T32AI060516-04
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Human Respiratory Tract Microbiome in Health, HIV Infection and HIV Lung Disease
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HL098957-05
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
44 references, page 1 of 3

1 Jordan GW, Wong GA, Hoeprich PD (1976) Bacteriology of the lower respiratory tract as determined by fiber-optic bronchoscopy and transtracheal aspiration. J Infect Dis 134: 428–435.993617 [OpenAIRE] [PubMed]

2 Kirkpatrick MB, Bass JB Jr (1989) Quantitative bacterial cultures of bronchoalveolar lavage fluids and protected brush catheter specimens from normal subjects. Am Rev Respir Dis 139: 546–548.2913899 [PubMed]

3 Pecora DV (1963) A Comparison of Transtracheal Aspiration with Other Methods of Determining the Bacterial Flora of the Lower Respiratory Tract. N Engl J Med 269: 664–666.14050970 [OpenAIRE] [PubMed]

4 Bartlett JG, Alexander J, Mayhew J, Sullivan-Sigler N, Gorbach SL (1976) Should fiberoptic bronchoscopy aspirates be cultured? Am Rev Respir Dis 114: 73–78.7173 [PubMed]

5 Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, et al (2011) Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 184: 957–963.21680950 [OpenAIRE] [PubMed]

6 Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, et al (2011) Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One 6: e16384.21364979 [OpenAIRE] [PubMed]

7 Beal M, Chesson A, Garcia T, Caldito G, Stucker F, et al (2004) A pilot study of quantitative aspiration in patients with symptoms of obstructive sleep apnea: comparison to a historic control group. Laryngoscope 114: 965–968.15179196 [OpenAIRE] [PubMed]

8 Gleeson K, Eggli DF, Maxwell SL (1997) Quantitative aspiration during sleep in normal subjects. Chest 111: 1266–1272.9149581 [OpenAIRE] [PubMed]

9 Huxley EJ, Viroslav J, Gray WR, Pierce AK (1978) Pharyngeal aspiration in normal adults and patients with depressed consciousness. Am J Med 64: 564–568.645722 [OpenAIRE] [PubMed]

10 Bousbia S, Papazian L, Auffray JP, Fenollar F, Martin C, et al (2010) Tropheryma whipplei in patients with pneumonia. Emerg Infect Dis 16: 258–263.20113556 [OpenAIRE] [PubMed]

11 Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, et al (2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A 104: 20529–20533.18077362 [OpenAIRE] [PubMed]

12 Nasidze I, Li J, Quinque D, Tang K, Stoneking M (2009) Global diversity in the human salivary microbiome. Genome Res 19: 636–643.19251737 [OpenAIRE] [PubMed]

13 Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721–5732.16272510 [OpenAIRE] [PubMed]

14 Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, et al (2011) Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8: 761–763.21765408 [OpenAIRE] [PubMed]

15 Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, et al (2012) Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 13: 47–58.

44 references, page 1 of 3
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