Repertoire of intensive care unit pneumonia microbiota
Open accessAbstract
Despite the considerable number of studies reported to date, the causative agents of pneumonia are not completely identified. We comprehensively applied modern and traditional laboratory diagnostic techniques to identify microbiota in patients who were admitted to or developed pneumonia in intensive care units (ICUs). During a three-year period, we tested the bronchoalveolar lavage (BAL) of patients with ventilator-associated pneumonia, community-acquired pneumonia, non-ventilator ICU pneumonia and aspiration pneumonia, and compared the results with those from patients without pneumonia (controls). Samples were tested by amplification of 16S rDNA, 18S rDNA genes followed by cloning and sequencing and by PCR to target specific pathogens. We also included culture, amoeba co-culture, detection of antibodies to selected agents and urinary antigen tests. Based on molecular testing, we identified a wide repertoire of 160 bacterial species of which 73 have not been previously reported in pneumonia. Moreover, we found 37 putative new bacterial phylotypes with a 16S rDNA gene divergence ≥ 98% from known phylotypes. We also identified 24 fungal species of which 6 have not been previously reported in pneumonia and 7 viruses. Patients can present up to 16 different microorganisms in a single BAL (mean ± SD; 3.77 ± 2.93). Some pathogens considered to be typical for ICU pneumonia such as Pseudomonas aeruginosa and Streptococcus species can be detected as commonly in controls as in pneumonia patients which strikingly highlights the existence of a core pulmonary microbiota. Differences in the microbiota of different forms of pneumonia were documented.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The predicted effect of ecological forces in the lungs of critically ill patients is a state of increased immigration, decreased elimination, and favourable growth conditions for potential pathogens.
“The predicted effect of these ecological forces in the lungs, therefore, is a state of increased immigration, decreased elimination, and favourable growth conditions for potential pathogens.”
From The microbiome and critical illness (2016) · cites this paper as [82]
Many daily therapies and interventions in intensive care increase intestinal permeability, bacterial translocation, and bacterial virulence.
“Many daily therapies and interventions in intensive care increase intestinal permeability (eg, nonsteroidal anti-inflammatory drugs109 and parenteral feeding55,82), bacterial translocation (eg, antibiotics,65 corticosteroids,110 and opiates111), and bacterial virulence (eg, opiates19 and catecholamines22,51).”
From The microbiome and critical illness (2016) · cites this paper as [82]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
Tamura, K., Dudley, J. T., Nei, M., & Kumar, S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm092 · Cited by 28,734 · see citing works
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,770 · see citing works
Manual of Clinical Microbiology.
(1980) · Annals of Internal Medicine · doi:10.7326/0003-4819-93-6-939_2 · Cited by 14,435 · see citing works
Mandell, L. A., Wunderink, R. G., Anzueto, A., Bartlett, J. G., Campbell, G. D., Dean, N. C., Dowell, S. F., File, T. M., Musher, D. M., Niederman, M. S., et al. (2007) · Clinical Infectious Diseases · doi:10.1086/511159 · Cited by 6,182 · see citing works
(2005) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.200405-644st · Cited by 5,870 · see citing works
Disordered Microbial Communities in Asthmatic Airways
Hilty, M., Burke, C. M., Pedro, H., Cárdenas, P., Bush, A., Bossley, C. J., Davies, J. C., Ervine, A., Poulter, L. W., Pachter, L. S., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008578 · Cited by 1,818 · see citing works
Aspiration Pneumonitis and Aspiration Pneumonia
Marik, P. E. (2001) · New England Journal of Medicine · doi:10.1056/nejm200103013440908 · Cited by 1,617 · see citing works
Analysis of the lung microbiome in the “healthy” smoker and in COPD.
Erb-Downward, J. R., Thompson, D. L., Han, M. K., Freeman, C. M., McCloskey, L., Schmidt, L. A., Young, V. B., Toews, G. B., Curtis, J. L., Sundaram, B., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016384 · Cited by 973 · see citing works
Déziel, É., Lepine, F. L., Milot, S. M., He, J., Mindrinos, M. N., Tompkins, R. G., & Rahme, L. G. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307694100 · Cited by 638 · see citing works
Hoffman, L. R., Déziel, É., D’Argenio, D. A., Lepine, F. L., Emerson, J., McNamara, S., Gibson, R. L., Ramsey, B. W., & Miller, S. I. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606756104 · Cited by 470 · see citing works
Quantification of Leishmania infantum DNA by a Real-Time PCR Assay with High Sensitivity
Mary, C., Faraut, F., Lascombe, L., & Dumon, H. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.11.5249-5255.2004 · Cited by 425 · see citing works
Scola, B. L., & Raoult, D. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008041 · Cited by 383 · see citing works
Self-citationHarris, J. K., Groote, M. A. D., Sagel, S. D., Zemanick, E. T., Kapsner, R. K., Penvari, C., Kaess, H., Deterding, R. R., Accurso, F. J., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709804104 · Cited by 373 · see citing works
Human polymicrobial infections
BROGDEN, K., Guthmiller, J. M., & TAYLOR, C. (2005) · The Lancet · doi:10.1016/s0140-6736(05)70155-0 · Cited by 369 · see citing works
Q fever serology: cutoff determination for microimmunofluorescence
Dupont, H. T., Thirion, X., & Raoult, D. (1994) · Clinical and Diagnostic Laboratory Immunology · doi:10.1128/cdli.1.2.189-196.1994 · Cited by 339 · see citing works
Self-citationColonization of dental plaque: A source of nosocomial infections in intensive care unit patients
Fourrier, F., Duvivier, B., Boutigny, H., Roussel‐Delvallez, M., & Chopin, C. (1998) · Critical Care Medicine · doi:10.1097/00003246-199802000-00032 · Cited by 292 · see citing works
Molecular and Cultural Analysis of the Microflora Associated with Endodontic Infections
Munson, M. A., Ford, T. P., Bs, C., Weightman, A. J., & Wade, W. G. (2002) · Journal of Dental Research · doi:10.1177/154405910208101108 · Cited by 266 · see citing works
Molecular and Cultural Analysis of the Microflora Associated with Endodontic Infections
Munson, M. A., Ford, T. P., Chong, B., Weightman, A. J., & Wade, W. G. (2002) · Journal of Dental Research · doi:10.1177/0810761 · Cited by 264 · see citing works
Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections
Sakamoto, M., Rôças, I. N., Siqueira, J. F., Jr., et al. (2006) · Oral Microbiology and Immunology · doi:10.1111/j.1399-302x.2006.00270.x · Cited by 237 · see citing works
Molecular Detection of Multiple Emerging Pathogens in Sputa from Cystic Fibrosis Patients
Bittar, F., Richet, H., Dubus, J. ‐., Reynaud‐Gaubert, M., Stremler, N., Sarles, J., Raoult, D., & Rolain, J. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002908 · Cited by 223 · see citing works
Self-citationEsperatti, M., Ferrer, M., Theessen, A., Liapikou, A., Valencia, M., Saucedo, L. M., Zavala, E., Welte, T., & Torres, A. (2010) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201001-0094oc · Cited by 194 · see citing works
Heo, S., Haase, E. M., Lesse, A. J., Gill, S. R., & Scannapieco, F. A. (2008) · Clinical Infectious Diseases · doi:10.1086/593193 · Cited by 189 · see citing works
Prokaryote–eukaryote interactions identified by using Caenorhabditis elegans
Peleg, A. Y., Tampakakis, E., Fuchs, B. B., Eliopoulos, G. M., Moellering, R. C., & Mylonakis, E. E. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805048105 · Cited by 188 · see citing works
Chiche, L., Forel, J.-M., Roch, A., et al. (2009) · Critical Care Medicine · doi:10.1097/ccm.0b013e31819ffea6 · Cited by 178 · see citing works
Self-citationBahrani-Mougeot, F. K., Paster, B. J., Coleman, S., Barbuto, S., Brennan, M. T., Noll, J., Kennedy, T., Fox, P. C., & Lockhart, P. B. (2007) · Journal of Clinical Microbiology · doi:10.1128/jcm.01963-06 · Cited by 176 · see citing works
Bronchoscopic BAL in the Diagnosis of Ventilator-Associated Pneumonia
Torres, A., & El-Ebiary, M. (2000) · CHEST Journal · doi:10.1378/chest.117.4_suppl_2.198s · Cited by 175 · see citing works
Gontcharova, V., Youn, E., Wolcott, R. D., Hollister, E. B., Gentry, T. J., & Dowd, S. E. (2010) · The Open Microbiology Journal · doi:10.2174/1874285801004010047 · Cited by 174 · see citing works
Ameba-associated Microorganisms and Diagnosis of Nosocomial Pneumonia
Berger, P., Papazian, L., Drancourt, M., Scola, B. L., Auffray, J., & Raoult, D. (2006) · Emerging infectious diseases · doi:10.3201/eid1202.050434 · Cited by 157 · see citing works
Self-citationPapazian, L., Fraisse, A., Garbe, L., et al. (1996) · Anesthesiology · doi:10.1097/00000542-199602000-00005 · Cited by 154 · see citing works
Self-citationVial, L., Lepine, F. L., Milot, S. M., et al. (2008) · Journal of Bacteriology · doi:10.1128/jb.00400-08 · Cited by 145 · see citing works
Qin, Z., Yang, L., Qu, D., Molin, S., & Tolker‐Nielsen, T. (2009) · Microbiology · doi:10.1099/mic.0.028001-0 · Cited by 140 · see citing works
Roux, D., Gaudry, S., Dreyfuss, D., El-Benna, J., de Prost, N., Denamur, E., Saumon, G., & Ricard, J.-D. (2009) · Critical Care Medicine · doi:10.1097/ccm.0b013e31819629d2 · Cited by 129 · see citing works
Tropheryma whippleiin Patients with Pneumonia
Bousbia, S., Papazian, L., Auffray, J., Fenollar, F., Martin, C., Li, W., Chiche, L., Scola, B. L., & Raoult, D. (2010) · Emerging infectious diseases · doi:10.3201/eid1602.090610 · Cited by 113 · see citing works
Self-citationWaites, K. B., Xiao, L., Paralanov, V., Viscardi, R. M., & Glass, J. I. (2012) · Humana Press eBooks · doi:10.1007/978-1-62703-185-1_16 · Cited by 112 · see citing works
Molecular Epidemiology of O139Vibrio cholerae: Mutation, Lateral Gene Transfer, and Founder Flush
Garg, P., Aydanian, A., Smith, D. L., Morris, J. G., Nair, G. B., & Stine, O. C. (2003) · Emerging infectious diseases · doi:10.3201/eid0907.020760 · Cited by 112 · see citing works
Etiology and Diagnosis of Pneumonia Requiring ICU Admission
Potgieter, P. D., & Hammond, J. (1992) · CHEST Journal · doi:10.1378/chest.101.1.199 · Cited by 109 · see citing works
Value of Microimmunofluorescence for Diagnosis and Follow-up of Bartonella Endocarditis
Fournier, P., Mainardi, J., & Raoult, D. (2002) · Clinical and Vaccine Immunology · doi:10.1128/cdli.9.4.795-801.2002 · Cited by 97 · see citing works
Self-citationMicrobial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing
Armougom, F., Bittar, F., Stremler, N., Rolain, J., Robert, C., Dubus, J. ‐., Sarles, J., Raoult, D., & Scola, B. L. (2009) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-009-0749-x · Cited by 93 · see citing works
Self-citationDetection of Legionella pneumonophila antigen in urine by enzyme-linked immunospecific assay
Berdal, B. P., FARSHY, C. E., & Feeley, J. C. (1979) · Journal of Clinical Microbiology · doi:10.1128/jcm.9.5.575-578.1979 · Cited by 90 · see citing works
Chlamydia-like bacteria in respiratory samples of community-acquired pneumonia patients
Haider, S., Collingro, A., Walochnik, J., et al. (2008) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2008.01099.x · Cited by 89 · see citing works
Zuravleff, J. J. (1983) · JAMA · doi:10.1001/jama.250.15.1981 · Cited by 75 · see citing works
Cost-Effectiveness of Blood Agar for Isolation of Mycobacteria
Drancourt, M., & Raoult, D. (2007) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0000083 · Cited by 72 · see citing works
Self-citationScola, B. L. (2000) · FEMS Microbiology Ecology · doi:10.1016/s0168-6496(00)00084-2 · Cited by 60 · see citing works
Mailman, T., & Schmidt, M. H. (2005) · Canadian Journal of Infectious Diseases and Medical Microbiology · doi:10.1155/2005/486417 · Cited by 57 · see citing works
Vincent, A., Scola, B. L., Forel, J.-M., et al. (2008) · Critical Care Medicine · doi:10.1097/ccm.0b013e318192fa8b · Cited by 57 · see citing works
Self-citationHerpes simplex virus: A marker of severity in bacterial ventilator-associated pneumonia
Bouza, E., Giannella, M., Torres, M. V., Catalán, P., Sánchez‐Carrillo, C., Insa, R., & Muñóz, P. (2010) · Journal of Critical Care · doi:10.1016/j.jcrc.2010.10.008 · Cited by 54 · see citing works
Evaluation of nested and real-time PCR assays in the diagnosis of candidaemia
Khlif, M., Mary, C., Sellami, H., et al. (2009) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2009.02762.x · Cited by 53 · see citing works
Diagnosis of Legionnaires' Disease
Zuravleff, J. J. (1983) · JAMA · doi:10.1001/jama.1983.03340150023020 · Cited by 51 · see citing works
Amoeba-Resisting Bacteria and Ventilator-Associated Pneumonia
Scola, B. L., Boyadjiev, I., Greub, G., et al. (2003) · Emerging infectious diseases · doi:10.3201/eid0907.030065 · Cited by 51 · see citing works
Luyt, C., Combes, A., Nieszkowska, A., et al. (2008) · Current Opinion in Critical Care · doi:10.1097/mcc.0b013e32830f1e12 · Cited by 49 · see citing works
Kawanami, T., Fukuda, K., Yatera, K., Kido, T., Yoshii, C., Taniguchi, H., & Kido, M. (2008) · Journal of Clinical Microbiology · doi:10.1128/jcm.01429-08 · Cited by 30 · see citing works
Bousbia, S., Papazian, L., Scola, B. L., & Raoult, D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011298 · Cited by 23 · see citing works
Self-citationAcetobacter indonesiensisPneumonia after Lung Transplant
Bittar, F., Reynaud‐Gaubert, M., Thomas, P., et al. (2008) · Emerging infectious diseases · doi:10.3201/eid1406.071236 · Cited by 21 · see citing works
Diagnosis of Legionnaires' Disease
Wagner, K. F. (1984) · JAMA · doi:10.1001/jama.1984.03340470015006 · Cited by 16 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The microbiome and critical illness
Dickson, R. P. (2016) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(15)00427-0 · Cited by 460 · see citing works
Barbier, F., Andremont, A., Wolff, M., & Bouadma, L. (2013) · Current Opinion in Pulmonary Medicine · doi:10.1097/mcp.0b013e32835f27be · Cited by 281 · see citing works
Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients
de Steenhuijsen Piters, W. A. A., Huijskens, E. G. W., Wyllie, A. L., Biesbroek, G., van den Bergh, M. R., Veenhoven, R. H., Wang, X., Trzciński, K., Bonten, M. J., Rossen, J. W. A., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2015.99 · Cited by 235 · see citing works
Salk, H. M., Simon, W. L., Lambert, N. D., Kennedy, R. B., Grill, D. E., Kabat, B. F., & Poland, G. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0162803 · Cited by 75 · see citing works
Mycobiome in the Lower Respiratory Tract – A Clinical Perspective
Krause, R., Moissl-Eichinger, C., Halwachs, B., Gorkiewicz, G., Berg, G., Valentin, T., Prattes, J., Högenauer, C., & Zollner-Schwetz, I. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.02169 · Cited by 43 · see citing works
- Authors
- Bousbia, S., Papazian, L., Saux, P., Forel, J. M., Auffray, J.-P., Martin, C., Raoult, D., & La Scola, B.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Hôpital Nord (FR)
- Hôpital de la Timone (FR)
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-02-28
- Volume
- 7
- Issue
- 2
- Pages
- e32486
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3289664
- OpenAlex
- W2062970569
- Cited by
- 118
- References
- 54
- Citations by year
- 2026: 6 · 2025: 3 · 2024: 4 · 2023: 5 · 2022: 9 · 2021: 7 · 2020: 12 · 2019: 13 · 2018: 7 · 2017: 4 · 2016: 11 · 2015: 10 · 2014: 11 · 2013: 14 · 2012: 2
- FWCI
- 9.89
- Type
- journal article
- Language
- en
- Update notices
- expression_of_concern (2022-12-13)
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Topics
- Health Sciences › Medicine › Critical Care and Intensive Care Medicine › Nosocomial Infections in ICU
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Health Sciences › Medicine › Epidemiology › Pneumonia and Respiratory Infections
- Keywords
- ventilator-associated pneumonia, community-acquired pneumonia, aspiration pneumonia, fungal pathogens, viral pathogens, Pseudomonas aeruginosa, Streptococcus, 16S rRNA gene, 18S rDNA, urinary antigen test
- MeSH terms
- Bacteria, Bronchoalveolar Lavage Fluid, DNA, Ribosomal, Humans, Intensive Care Units, Molecular Sequence Data, Phylogeny, Pneumonia
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
