Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa
Open accessAbstract
Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence.
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Bacterial pneumonia is characterised by increased bacterial burden and low community diversity, generally one dominant pathogen.
“Bacterial pneumonia, a true lung infection, exemplifies these features: it is characterised by increased bacterial burden and low community diversity (generally one dominant pathogen).”
From The microbiome and critical illness (2016) · cites this paper as [62]
At the current pace of development, point-of-care community sequencing and identification of pathogens will be available and affordable within years rather than decades.
“At the current pace of development, point-of-care community sequencing and identification of pathogens will be available and affordable within years rather than decades.”
From The microbiome and critical illness (2016) · cites this paper as [62]
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Cites
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,962 · see citing works
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891 · see citing works
Self-citationLane, D. (1991) · Medical Entomology and Zoology · Cited by 7,944 · see citing works
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · see citing works
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993 · see citing works
Base-Calling of Automated Sequencer Traces Using <i>Phred.</i> II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439 · see citing works
QUORUM SENSING: Cell-to-Cell Communication in Bacteria
Waters, C. M., & Bassler, B. L. (2005) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.21.012704.131001 · Cited by 3,989 · see citing works
Schloss, P. D., & Handelsman, J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.3.1501-1506.2005 · Cited by 2,503 · see citing works
Bacterial Diversity in Human Subgingival Plaque
Paster, B. J., Boches, S. K., Galvin, J. L., Ericson, R. E., Lau, C. N., Levanos, V. A., Sahasrabudhe, A., & Dewhirst, F. E. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.12.3770-3783.2001 · Cited by 2,008 · see citing works
Genetic diversity in Sargasso Sea bacterioplankton
Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., & Field, K. G. (1990) · Nature · doi:10.1038/345060a0 · Cited by 1,654 · see citing works
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
Huber, T., Faulkner, G. J., & Hugenholtz, P. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth226 · Cited by 1,532 · see citing works
Self-citationSuau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G. R., Collins, M. D., & Doré, J. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.11.4799-4807.1999 · Cited by 1,490 · see citing works
16S rRNA sequences reveal numerous uncultured microorganisms in a natural community
Ward, D. M., Weller, R., & Bateson, M. M. (1990) · Nature · doi:10.1038/345063a0 · Cited by 1,382 · see citing works
Chastre, J., Wolff, M., Fagon, J.-Y., Chevret, S., Thomas, F., Wermert, D., Clementi, E., Gonzalez, J., Jusserand, D., Asfar, P., et al. (2003) · JAMA · doi:10.1001/jama.290.19.2588 · Cited by 1,376 · see citing works
Frank, S. A. (1996) · The Quarterly Review of Biology · doi:10.1086/419267 · Cited by 1,370 · see citing works
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
DeSantis, T. Z., Hugenholtz, P., Keller, K., Brodie, E., Larsen, N., Piceno, Y. M., Phan, R., & Andersen, G. L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl244 · Cited by 1,028 · see citing works
Self-citationAnalysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing
Schmidt, T. M., DeLong, E. F., & Pace, N. R. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.14.4371-4378.1991 · Cited by 845 · see citing works
The Ecology of Genetically Diverse Infections
Read, A. F., & Taylor, L. H. (2001) · Science · doi:10.1126/science.1059410 · Cited by 648 · see citing works
Status of the Microbial Census
Schloss, P. D., & Handelsman, J. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.4.686-691.2004 · Cited by 574 · see citing works
DeSantis, T. Z., Brodie, E., Parker, J. M., Zubieta, I. X., Piceno, Y. M., & Andersen, G. L. (2007) · Microbial Ecology · doi:10.1007/s00248-006-9134-9 · Cited by 509 · see citing works
Self-citationBrodie, E., DeSantis, T. Z., Joyner, D. C., Baek, S. M., Larsen, J. T., Andersen, G. L., Hazen, T. C., Richardson, P. M., Herman, D. J., Tokunaga, T. K., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.00246-06 · Cited by 437 · see citing works
Self-citationZoetendal, E. G., Vaughan, E. E., & de Vos, W. M. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05056.x · Cited by 388 · see citing works
Bond, P. L., Smriga, S., & Banfield, J. F. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.9.3842-3849.2000 · Cited by 349 · see citing works
High-Density Microarray of Small-Subunit Ribosomal DNA Probes
Wilson, K. H., Wilson, W. J., Radosevich, J. L., DeSantis, T. Z., Viswanathan, V. S., Kuczmarski, T. A., & Andersen, G. L. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.5.2535-2541.2002 · Cited by 281 · see citing works
Self-citationMolecular 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
Does multiple infection select for raised virulence?
Brown, S. P., Hochberg, M., & Grenfell, B. T. (2002) · Trends in Microbiology · doi:10.1016/s0966-842x(02)02413-7 · Cited by 256 · see citing works
Molecular Analysis of Microbial Diversity in Advanced Caries
Chhour, K.-L., Nadkarni, M. A., Byun, R., Martin, F. E., Jacques, N. A., & Hunter, N. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.2.843-849.2005 · Cited by 252 · see citing works
Molecular identification of potential pathogens in water and air of a hospital therapy pool
Angenent, L. T., Kelley, S. T., Amand, A. L. S., Pace, N. R., & Hernandez, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501235102 · Cited by 249 · see citing works
Feldman, C. H., Kassel, M., Cantrell, J., Kaka, S., Morar, R., Mahomed, A. G., & Philips, J. (1999) · European Respiratory Journal · doi:10.1183/09031936.99.13354699 · Cited by 243 · see citing works
Antibiotic Resistance: An Ecological Imbalance
Levy, S. B. (2007) · Novartis Foundation symposium · doi:10.1002/9780470515358.ch1 · Cited by 229 · see citing works
Nosocomial pulmonary infection
Sottile, F. D., Marrie, T. J., Prough, D. S., Hobgood, C., Gower, D. J., Webb, L. X., Costerton, J. W., & Gristina, A. G. (1986) · Critical Care Medicine · doi:10.1097/00003246-198604000-00001 · Cited by 214 · see citing works
NOSOCOMIAL PULMONARY INFECTION
Sottile, F. D., Prough, D. S., Gristina, A. G., Gower, D. J., Hobgood, C., Webb, L. X., Marrie, T. J., & Costerton, J. W. (1985) · Critical Care Medicine · doi:10.1097/00003246-198504000-00063 · Cited by 209 · see citing works
Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences
Stahl, D. A., Lane, D. J., Olsen, G. J., & Pace, N. R. (1985) · Applied and Environmental Microbiology · doi:10.1128/aem.49.6.1379-1384.1985 · Cited by 194 · see citing works
Hugenholtz, P., Tyson, G. W., & Blackall, L. L. (2003) · Humana Press eBooks · doi:10.1385/1-59259-238-4:029 · Cited by 186 · see citing works
Self-citationThe Microbiota of Young Children from Tooth and Tongue Samples
Tanner, A. C. R., Milgrom, P., Kent, R., Mokeem, S. A., Page, R. C., Riedy, C. A., Weinstein, P., & BRUSS, J. B. (2002) · Journal of Dental Research · doi:10.1177/002203450208100112 · Cited by 185 · see citing works
Molecular Analysis of the Subgingival Microbiota in Health and Disease
Ledder, R. G., Gilbert, P., Huws, S., Aarons, L. J., Ashley, M. P., Hull, P. S., & McBain, A. J. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01419-06 · Cited by 171 · see citing works
Statistical Analyses of Complex Denaturing Gradient Gel Electrophoresis Profiles
Gafan, G. P., Lucas, V. S., ROBERTS, G. J., Petrie, A., Wilson, M., & Spratt, D. A. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.8.3971-3978.2005 · Cited by 156 · see citing works
Grap, M. J., Munro, C. L., Elswick, R. K., Sessler, C. N., & Ward, K. R. (2004) · Heart & Lung · doi:10.1016/j.hrtlng.2003.12.004 · Cited by 142 · see citing works
Interference competition and parasite virulence
Massey, R. C., Buckling, A., & ffrench‐Constant, R. H. (2004) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2004.2676 · Cited by 134 · see citing works
Flamm, R. K., Weaver, M. K., Thornsberry, C., Jones, M. E., Karlowsky, J. A., & Sahm, D. F. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.7.2431-2436.2004 · Cited by 122 · see citing works
Lau, S. K. P., Woo, P. C. Y., Teng, J. L. L., Leung, K. W., & Yuen, K. Y. (2002) · Molecular Pathology · doi:10.1136/mp.55.3.182 · Cited by 120 · see citing works
Torres, A., El-Ebiary, M., Soler, N., Montón, C., Fàbregas, N., & Hernández, C. (1996) · European Respiratory Journal · doi:10.1183/09031936.96.09081729 · Cited by 108 · see citing works
Bacterial Diversity in Necrotizing Ulcerative Periodontitis in HIV‐Positive Subjects
Paster, B. J., Russell, M. K., Alpagot, T., Lee, A. M., Boches, S. K., Galvin, J. L., & Dewhirst, F. E. (2002) · Annals of Periodontology · doi:10.1902/annals.2002.7.1.8 · Cited by 107 · see citing works
DeSantis, T. Z., Stone, C. E., Murray, S. R., Parker, J. M., & Andersen, G. L. (2005) · FEMS Microbiology Letters · doi:10.1016/j.femsle.2005.03.016 · Cited by 95 · see citing works
Self-citationInterspecies communication betweenBurkholderia cepaciaandPseudomonas aeruginosa
Lewenza, S., Visser, M. B., & Sokol, P. A. (2002) · Canadian Journal of Microbiology · doi:10.1139/w02-068 · Cited by 87 · see citing works
Molecular characterization of the bacteria adherent to human colorectal mucosa
Green, G. L., Brostoff, J., Hudspith, B. N., Michael, M., Mylonaki, M., Rayment, N. B., Staines, N. A., Sanderson, J. D., Rampton, D. S., & Bruce, K. D. (2006) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2005.02783.x · Cited by 75 · see citing works
The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off
Kreft, J., & Bonhoeffer, S. (2005) · Microbiology · doi:10.1099/mic.0.27415-0 · Cited by 74 · see citing works
Analysis of the c- kit gene in patients with slow transit constipation
Tong, W.-D., Liu, B.-H., Zhang, L.-Y., & Zhang, S.-B. (2006) · Gut · doi:10.1136/gut.2006.094953 · Cited by 65 · see citing works
Molecular analysis of bacterial flora associated with chronically inflamed maxillary sinuses
Paju, S., Bernstein, J. M., Haase, E. M., & Scannapieco, F. A. (2003) · Journal of Medical Microbiology · doi:10.1099/jmm.0.05062-0 · Cited by 65 · see citing works
Ray, G. T., Baxter, R. P., & DeLorenze, G. N. (2005) · Clinical Infectious Diseases · doi:10.1086/431980 · Cited by 45 · see citing works
EDWARDS, M. L., Lilley, A. K., Timms-Wilson, T. H., Thompson, I. P., & Cooper, I. (2001) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2001.tb00815.x · Cited by 36 · see citing works
Vakevainen, S. M., Tillonen, J., Blom, M., Jousimies-Somer, H. R., & Salaspuro, M. P. (2001) · Alcoholism Clinical and Experimental Research · doi:10.1111/j.1530-0277.2001.tb02230.x · Cited by 30 · see citing works
Actinomyces odontolyticus pulmonary infection.
Iancu, D., Chua, A., Schoch, P. E., & Cunha, B. A. (1999) · PubMed · Cited by 21 · see citing works
The role of the gastric reservoir in ventilator-associated pneumonia
Torres, A., El-Ebiary, M., Soler, N., Montón, C., González, J., & de la Bellacasa, J. P. (1995) · Clinical Intensive Care · doi:10.1080/714028893 · Cited by 10 · see citing works
The role of the gastric reservoir in ventilator-associated pneumonia
Torres, A., El-Ebiary, M., Soler, N., et al. (1995) · Clinical Intensive Care · doi:10.3109/tcic.6.4.174.180 · Cited by 8 · see citing works
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Impacts of biodiversity on the emergence and transmission of infectious diseases
Keesing, F., Belden, L. K., Daszak, P., Dobson, A., Harvell, C. D., Holt, R. D., Hudson, P., Jolles, A., Jones, K. E., Mitchell, C. E., et al. (2010) · Nature · doi:10.1038/nature09575 · Cited by 2,043 · see citing works
Next‐generation sequencing technologies for environmental DNA research
Shokralla, S., Spall, J. L., Gibson, J. F., & Hajibabaei, M. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05538.x · Cited by 939 · see citing works
Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma
Huang, Y. J., Nelson, C. E., Brodie, E., DeSantis, T. Z., Baek, M. S., Liu, J., Woyke, T., Allgaier, M., Bristow, J., Wiener-Kronish, J. P., et al. (2010) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2010.10.048 · Cited by 693 · see citing works
Self-citationEscapa, I. F., Chen, T., Huang, Y., Gajare, P., Dewhirst, F. E., & Lemon, K. P. (2018) · mSystems · doi:10.1128/msystems.00187-18 · Cited by 593 · see citing works
Metagenomic Pyrosequencing and Microbial Identification
Petrosino, J. F., Highlander, S. K., Luna, R. A., Gibbs, R. A., & Versalovic, J. A. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2008.107565 · Cited by 536 · see citing works
Human Microbiome in Health and Disease
Pflughoeft, K. J., & Versalovic, J. A. (2011) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-011811-132421 · Cited by 528 · see citing works
A renaissance for the pioneering 16S rRNA gene
Tringe, S. G., & Hugenholtz, P. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.011 · Cited by 509 · see citing works
Self-citationThe 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
Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients
Cox, M. J., Allgaier, M., Taylor, B., Baek, M. S., Huang, Y. J., Daly, R. A., Karaöz, U., Andersen, G. L., Brown, R., Fujimura, K. E., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011044 · Cited by 448 · see citing works
Self-citationThe role of the bacterial microbiome in lung disease
Dickson, R. P., Erb‐Downward, J. R., & Huffnagle, G. B. (2013) · Expert Review of Respiratory Medicine · doi:10.1586/ers.13.24 · Cited by 412 · see citing works
Langelier, C., Kalantar, K. L., Moazed, F., Wilson, M. R., Crawford, E. D., Deiss, T., Belzer, A., Bolourchi, S., Caldera, S., Fung, M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809700115 · Cited by 411 · see citing works
Diversity of Bacteria at Healthy Human Conjunctiva
Dong, Q., Brulc, J. M., Iovieno, A., Bates, B., Garoutte, A., Miller, D., Revanna, K. V., Gao, X., Antonopoulos, D. A., Slepak, V. Z., et al. (2011) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.10-6939 · Cited by 386 · see citing works
Cystic fibrosis lung environment and Pseudomonas aeruginosa infection
Bhagirath, A. Y., Li, Y., Somayajula, D., Dadashi, M., Badr, S., & Duan, K. (2016) · BMC Pulmonary Medicine · doi:10.1186/s12890-016-0339-5 · Cited by 370 · see citing works
Global Survey of Antibiotic Resistance Genes in Air
Li, J., Cao, J., Zhu, Y., Chen, Q., Shen, F., Wu, Y. H., Xu, S., Fan, H., Da, G., Huang, R., et al. (2018) · Environmental Science & Technology · doi:10.1021/acs.est.8b02204 · Cited by 371 · see citing works
Beck, J. M., Young, V. B., & Huffnagle, G. B. (2012) · Translational research · doi:10.1016/j.trsl.2012.02.005 · Cited by 362 · see citing works
A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells
Wrighton, K. C., Agbo, P., Warnecke, F., Weber, K. A., Brodie, E., DeSantis, T. Z., Hugenholtz, P., Andersen, G. L., & Coates, J. D. (2008) · The ISME Journal · doi:10.1038/ismej.2008.48 · Cited by 353 · see citing works
Self-citationCharlson, E. S., Diamond, J. M., Bittinger, K., Fitzgerald, A. S., Yadav, A., Haas, A. R., Bushman, F. D., & Collman, R. G. (2012) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201204-0693oc · Cited by 348 · see citing works
Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease
Huang, Y. J., Sethi, S., Murphy, T., Nariya, S., Boushey, H. A., & Lynch, S. V. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.00035-14 · Cited by 323 · see citing works
Self-citationComparative analyses of the bacterial microbiota of the human nostril and oropharynx
Lemon, K. P., Klepac-Ceraj, V., Schiffer, H. K., Brodie, E. L., Lynch, S. V., & Kolter, R. (2010) · mBio · doi:10.1128/mbio.00129-10 · Cited by 322 · see citing works
Self-citationThe Human Microbiome and Its Potential Importance to Pediatrics
Johnson, C. L., & Versalovic, J. A. (2012) · PEDIATRICS · doi:10.1542/peds.2011-2736 · Cited by 310 · see citing works
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Fujitani, S., Sun, H., Yu, V. L., & Weingarten, J. A. (2011) · CHEST Journal · doi:10.1378/chest.10-0166 · Cited by 275 · see citing works
Huang, Y. J., Kim, E., Cox, M. J., Brodie, E., Brown, R., Wiener-Kronish, J. P., & Lynch, S. V. (2010) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2009.0100 · Cited by 241 · see citing works
Self-citationPrice, L. B., Liu, C. M., Melendez, J. H., Frankel, Y. M., Engelthaler, D., Aziz, M., Bowers, J., Rattray, R., Ravel, J., Kingsley, C., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006462 · Cited by 237 · see citing works
Defining the normal core microbiome of conjunctival microbial communities
Huang, Y., Yang, B., & Li, W. (2016) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2016.04.008 · Cited by 233 · see citing works
Klepac‐Ceraj, V., Lemon, K. P., Martin, T. R., Allgaier, M., Kembel, S. W., Knapp, A. A., Lory, S. J., Brodie, E., Lynch, S. V., Bohannan, B. J. M., et al. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02173.x · Cited by 219 · see citing works
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Self-citationKerckhoffs, A. P. M., Amor, K. B., Samsom, M., van der Rest, M. E., de Vogel, J., Knol, J., & Akkermans, L. M. A. (2010) · Journal of Medical Microbiology · doi:10.1099/jmm.0.022848-0 · Cited by 124 · see citing works
Freeland, J. R. (2016) · Genome · doi:10.1139/gen-2016-0100 · Cited by 119 · see citing works
Escapa, I. F., Huang, Y., Chen, T., Lin, M., Kokaras, A. S., Dewhirst, F. E., & Lemon, K. P. (2020) · Microbiome · doi:10.1186/s40168-020-00841-w · Cited by 111 · see citing works
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Duc, M. T. L., Osman, S., Vaishampayan, P., Piceno, Y. M., Andersen, G. L., Spry, J. A., & Venkateswaran, K. J. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01073-09 · Cited by 95 · see citing works
Self-citationLiu, C. M., Soldanova, K., Nordstrom, L., Dwan, M. G., Moss, O. L., Contente‐Cuomo, T., Keim, P., Price, L. B., & Lane, A. P. (2013) · International Forum of Allergy & Rhinology · doi:10.1002/alr.21195 · Cited by 90 · see citing works
From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome
Fierer, N., Ferrenberg, S. M., Flores, G. E., González, A., Kueneman, J. G., Legg, T. M., Lynch, R. C., McDonald, D. T., Mihaljevic, J. R., O’Neill, S., et al. (2012) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110411-160307 · Cited by 83 · see citing works
Möller, D. R., Koth, L. L., Maier, L. A., Morris, A., Drake, W. P., Rossman, M. D., Leader, J. K., Collman, R. G., Hamzeh, N. Y., Sweiss, N., et al. (2015) · Annals of the American Thoracic Society · doi:10.1513/annalsats.201503-172ot · Cited by 81 · see citing works
Oral and Airway Microbiota in HIV-Infected Pneumonia Patients
Iwai, S., Fei, M., Huang, D., Fong, S., Subramanian, A., Grieco, K., Lynch, S. V., & Huang, L. (2012) · Journal of Clinical Microbiology · doi:10.1128/jcm.00278-12 · Cited by 82 · see citing works
Self-citationPreventing Ventilator-Associated Pneumonia
O’Grady, N. P., Murray, P. R., & Ames, N. J. (2012) · JAMA · doi:10.1001/jama.2012.6445 · Cited by 79 · see citing works
Perkins, S. D., Woeltje, K. F., & Angenent, L. T. (2010) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2010.02.005 · Cited by 81 · see citing works
Toma, I., Siegel, M., Keiser, J. F., Yakovleva, A., Kim, A., Davenport, L., Devaney, J., Hoffman, E. P., Alsubail, R., Crandall, K. A., et al. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.01678-14 · Cited by 79 · see citing works
Assessing the diagnostic importance of nonviable bacterial cells in respiratory infections
Rogers, G. B., Stressmann, F. A., Koller, G., Daniels, T. W. V., Carroll, M. P., & Bruce, K. D. (2008) · Diagnostic Microbiology and Infectious Disease · doi:10.1016/j.diagmicrobio.2008.06.011 · Cited by 79 · see citing works
Shenoy, M. K., Iwai, S., Lin, D. L., Worodria, W. O., Ayakaka, I., Byanyima, P., Kaswabuli, S., Fong, S., Stone, S., Chang, E. G., et al. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201603-0523oc · Cited by 77 · see citing works
Self-citationJohani, K., Malone, M., Jensen, S. O., Dickson, H. G., Gosbell, I. B., Hu, H., Yang, Q., Schultz, G. S., & Vickery, K. (2017) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkx391 · Cited by 77 · see citing works
Profiling bacterial community in upper respiratory tracts
Yi, H., Yong, D., Lee, K., Cho, Y.-J., & Chun, J. (2014) · BMC Infectious Diseases · doi:10.1186/s12879-014-0583-3 · Cited by 75 · see citing works
Wu, C. H., Sercu, B., Werfhorst, L. C. V. D., Wong, J., DeSantis, T. Z., Brodie, E. L., Hazen, T. C., Holden, P. A., & Andersen, G. L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011285 · Cited by 75 · see citing works
Self-citationRespiratory microbiome in mechanically ventilated patients: a narrative review
Fromentin, M., Ricard, J.-D., & Roux, D. (2021) · Intensive Care Medicine · doi:10.1007/s00134-020-06338-2 · Cited by 72 · see citing works
Zhuo, H., Yang, K. Y., Lynch, S. V., Dotson, R. H., Glidden, D. V., Singh, G., Webb, W. R., Elicker, B. M., García, Ó., Brown, R., et al. (2008) · Critical Care Medicine · doi:10.1097/ccm.0b013e318183f3f8 · Cited by 70 · see citing works
Self-citationZhou, X., Li, C., Liu, L., Zhao, J., Zhang, J., Cai, Z., & Huang, X. (2018) · Microbiological Research · doi:10.1016/j.micres.2018.12.001 · Cited by 65 · see citing works
Pollock, F. J., Lamb, J. B., van de Water, J. A. J. M., Smith, H. A., Schaffelke, B., Willis, B. L., & Bourne, D. G. (2019) · Royal Society Open Science · doi:10.1098/rsos.190355 · Cited by 62 · see citing works
Krause, R., Halwachs, B., Thallinger, G., Klymiuk, I., Gorkiewicz, G., Hoenigl, M., Prattes, J., Valentin, T., Heidrich, K., Buzina, W., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155033 · Cited by 62 · see citing works
Vandecandelaere, I., & Coenye, T. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-11038-7_9 · Cited by 59 · see citing works
Langelier, C., Kalantar, K., Moazed, F., Wilson, M. R., Crawford, E. D., Deiss, T. J., Belzer, A., Bolourchi, S., Caldera, S., Fung, M., et al. (2019) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00476.2018 · Cited by 59 · see citing works
Iwai, S., Huang, D., Fong, S., Jarlsberg, L. G., Worodria, W., Yoo, S., Cattamanchi, A., Davis, J. L., Kaswabuli, S., Segal, M., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0095726 · Cited by 58 · see citing works
Self-citationZeineldin, M. M., Lowe, J. F., Grimmer, E. D., de Godoy, M. R. C., Ghanem, M. M., El-Raof, Y. M. A., & Aldridge, B. M. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1042-2 · Cited by 58 · see citing works
Thermal acclimation increases heat tolerance of the scleractinian coral Acropora pruinosa
Yu, X., Yu, K., Huang, W. L., Liang, J., Qin, Z., Chen, B., Yao, Q., & Liao, Z. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.139319 · Cited by 58 · see citing works
Novel Microarray Design Strategy To Study Complex Bacterial Communities
Huyghe, A., François, P., Charbonnier, Y., Bento, M., Bonetti, E.-J., Paster, B. J., Bolívar, I., Baratti-Mayer, D., Pittet, D., & Schrenzel, J. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01722-07 · Cited by 57 · see citing works
Yu, V. L. (2011) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(11)70005-6 · Cited by 55 · see citing works
The bacterial microbiota in inflammatory lung diseases
Huffnagle, G. B., & Dickson, R. P. (2015) · Clinical Immunology · doi:10.1016/j.clim.2015.05.022 · Cited by 53 · see citing works
Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease
Walters, S. S. (2014) · SOJ Microbiology & Infectious Diseases · doi:10.15226/sojmid/2/3/00122 · Cited by 53 · see citing works
Microbial diversity under extreme euxinia: Mahoney Lake, Canada
Klepac‐Ceraj, V., HAYES, C. A., Gilhooly, W., Lyons, T. W., Kolter, R., & Pearson, A. (2012) · Geobiology · doi:10.1111/j.1472-4669.2012.00317.x · Cited by 52 · see citing works
Taylor, D. L., Booth, M. G., McFarland, J. W., Herriott, I. C., Lennon, N. J., Nusbaum, C., & Marr, T. G. (2008) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2008.02094.x · Cited by 52 · see citing works
Diversity of Anaerobic Microbes in Spacecraft Assembly Clean Rooms
Probst, A. J., Vaishampayan, P., Osman, S., Moissl‐Eichinger, C., Andersen, G. L., & Venkateswaran, K. J. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.02167-09 · Cited by 52 · see citing works
Self-citationDetecting unknown sequences with DNA microarrays: explorative probe design strategies
Dugat‐Bony, É., Peyretaillade, É., Parisot, N., Biderre‐Petit, C., Jaziri, F., Hill, D. R. C., Rimour, S., & Peyret, P. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02559.x · Cited by 49 · see citing works
Wang, K., Chen, Y., Salido, M. M. S., Kohli, G. S., Kong, J., Liang, H., Yao, Z.-T., Xie, Y., Wu, H., Cai, S., et al. (2017) · Open Biology · doi:10.1098/rsob.170029 · Cited by 49 · see citing works
Lung microbiome and origins of the respiratory diseases
Belizário, J. E., Garay-Malpartida, M., & Faintuch, J. (2023) · Current Research in Immunology · doi:10.1016/j.crimmu.2023.100065 · Cited by 47 · see citing works
Complete genome sequence of Veillonella parvula type strain (Te3T)
Gronow, S., Welnitz, S., Lapidus, A. L., Nolan, M., Ivanova, N., del Rio, T. G., Copeland, A., Chen, F., Tice, H. N., Pitluck, S., et al. (2010) · Standards in Genomic Sciences · doi:10.4056/sigs.521107 · Cited by 47 · see citing works
Self-citationPediatric Ventilator-Associated Infections: The Ventilator-Associated INfection Study
Willson, D. F., Hoot, M. R., Khemani, R. G., Carroll, C. L., Kirby, A. L., Schwarz, A. J., Gedeit, R. G., Nett, S. T., Erickson, S. J., Flori, H. R., et al. (2016) · Pediatric Critical Care Medicine · doi:10.1097/pcc.0000000000001001 · Cited by 47 · see citing works
Respiratory microbiota and lower respiratory tract disease
Lanaspa, M., Bassat, Q., Medeiros, M. M., & Muñoz‐Almagro, C. (2017) · Expert Review of Anti-infective Therapy · doi:10.1080/14787210.2017.1349609 · Cited by 47 · see citing works
Novel strategies to combat bacterial virulence
Lynch, S. V., & Wiener-Kronish, J. P. (2008) · Current Opinion in Critical Care · doi:10.1097/mcc.0b013e32830f1dd5 · Cited by 47 · see citing works
Self-citationThe Impact of Omic Technologies on the Study of Food Microbes
O’Flaherty, S., & Klaenhammer, T. R. (2011) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030810-110338 · Cited by 45 · see citing works
Kalra, A., Palcu, C. T., Sobel, J. D., & Akins, R. A. (2007) · Current Infectious Disease Reports · doi:10.1007/s11908-007-0074-4 · Cited by 42 · see citing works
Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications
de Bruin, E. C., Taylor, T., & Swanton, C. (2013) · Genome Medicine · doi:10.1186/gm505 · Cited by 42 · see citing works
Cheng, Y., Yam, J. K. H., Cai, Z., Ding, Y., Zhang, L., Deng, Y., & Yang, L. (2019) · npj Biofilms and Microbiomes · doi:10.1038/s41522-018-0076-z · Cited by 42 · see citing works
The Effects of Corticosteroids on the Respiratory Microbiome: A Systematic Review
Hartmann, J. E., Albrich, W. C., Dmitrijeva, M., & Kahlert, C. R. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.588584 · Cited by 40 · see citing works
Vaishampayan, P., Osman, S., Andersen, G. L., & Venkateswaran, K. J. (2010) · Astrobiology · doi:10.1089/ast.2009.0443 · Cited by 39 · see citing works
Self-citationPeng, Y., Bi, J., Shi, J. C., Li, Y., Ye, X., Chen, X., & Yao, Z. (2014) · American Journal of Infection Control · doi:10.1016/j.ajic.2014.08.006 · Cited by 38 · see citing works
Aetiology of hospital-acquired pneumonia and trends in antimicrobial resistance
Enne, V. I., Personne, Y., Grgic, L., Gant, V. A., & Zumla, A. I. (2014) · Current Opinion in Pulmonary Medicine · doi:10.1097/mcp.0000000000000042 · Cited by 36 · see citing works
Field, E. K., D’Imperio, S., Miller, A. R., VanEngelen, M. R., Gerlach, R., Lee, B. D., Apel, W. A., & Peyton, B. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.01688-09 · Cited by 36 · see citing works
Tsitsiklis, A., Zha, B. S., Byrne, A., DeVoe, C., Rackaityte, E., Levan, S., Sunshine, S., Mick, E., Ghale, R., Love, C., et al. (2021) · medRxiv · doi:10.1101/2021.03.23.21253487 · Cited by 35 · see citing works
Self-citationThe respiratory microbiota during health and disease: a paediatric perspective
Koppena, I. J. N., Boscha, A. A. T. M., Sandersa, E. A. M., van Houtenb, M. A., & Bogaert, D. (2015) · Pneumonia · doi:10.15172/pneu.2015.6/656 · Cited by 35 · see citing works
Bacterial diversity in Cr(VI) and Cr(III)-contaminated industrial wastewaters
Katsaveli, K., Vayenas, D. V., Tsiamis, G., & Bourtzis, K. (2012) · Extremophiles · doi:10.1007/s00792-012-0429-0 · Cited by 35 · see citing works
Corsaro, D., Müller, K., & Michel, R. (2013) · Experimental Parasitology · doi:10.1016/j.exppara.2012.12.016 · Cited by 34 · see citing works
The Families Erysipelotrichaceae emend., Coprobacillaceae fam. nov., and Turicibacteraceae fam. nov.
Verbarg, S., Göker, M., Scheuner, C., Schümann, P., & Stackebrandt, E. S. (2014) · Springer eBooks · doi:10.1007/978-3-642-30120-9_205 · Cited by 32 · see citing works
Cooper, M., Duc, M. T. L., Probst, A. J., Vaishampayan, P., Stam, C., Benardini, J. N., Piceno, Y. M., Andersen, G. L., & Venkateswaran, K. J. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.00192-11 · Cited by 30 · see citing works
Self-citationAlsayed, A. R., Abed, A. I., Khader, H. A., Al-Shdifat, L., Hasoun, L., Al‐Rshaidat, M. M. D., Alkhatib, M., & Zihlif, M. A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24044086 · Cited by 29 · see citing works
New horizons for the infectious diseases specialist: How gut microflora promote health and disease
Rabizadeh, S., & Sears, C. L. (2008) · Current Infectious Disease Reports · doi:10.1007/s11908-008-0017-8 · Cited by 30 · see citing works
Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray
Schatz, M. C., Phillippy, A. M., Gajer, P., DeSantis, T. Z., Andersen, G. L., & Ravel, J. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00303-10 · Cited by 29 · see citing works
Self-citationProbiotic manipulation of the gastrointestinal microbiota
Rauch, M., & Lynch, S. V. (2010) · Gut Microbes · doi:10.4161/gmic.1.5.13169 · Cited by 28 · see citing works
Self-citationYu, X., Yu, K., Liao, Z., Liang, J., Deng, C., Huang, W. L., & Huang, Y. (2020) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2020.111199 · Cited by 25 · see citing works
Promiscuity in mice is associated with increased vaginal bacterial diversity
MacManes, M. D. (2011) · Die Naturwissenschaften · doi:10.1007/s00114-011-0848-2 · Cited by 26 · see citing works
Fan, C., Lee, P. K. H., Ng, W. J., Alvarez‐Cohen, L., Brodie, E., Andersen, G. L., & He, J. (2009) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-009-2201-7 · Cited by 26 · see citing works
Self-citationVentilator-associated pneumonia: Problems with diagnosis and therapy
Wiener-Kronish, J. P., & Dorr, H. I. (2008) · Best practice & research. Clinical anaesthesiology · doi:10.1016/j.bpa.2008.05.002 · Cited by 22 · see citing works
Self-citationZinter, M. S., Dvorak, C. C., Mayday, M. Y., Reyes, G. A., Simon, M. R., Pearce, E. M., Kim, H., Shaw, P. J., Rowan, C. M., Auletta, J. J., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-02999-4 · Cited by 21 · see citing works
Parenteral nutrition increases susceptibility of ileum to invasion by E coli
Pierre, J. F., Heneghan, A. F., Meudt, J. J., Shea, M. P., Krueger, C. G., Reed, J. D., Kudsk, K. A., & Shanmuganayagam, D. (2013) · Journal of Surgical Research · doi:10.1016/j.jss.2013.01.054 · Cited by 19 · see citing works
Risk factors for Pseudomonas aeruginosa pneumonia in the early twenty-first century
Rello, J., Borgatta, B., & Lisboa, T. C. (2013) · Intensive Care Medicine · doi:10.1007/s00134-013-3046-1 · Cited by 19 · see citing works
Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia
Spottiswoode, N., Tsitsiklis, A., Chu, V. T., Phan, H. V., DeVoe, C., Love, C., Ghale, R., Bloomstein, J. D., Zha, B. S., Maguire, C. P., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53566-x · Cited by 18 · see citing works
Zhou, Z., Shi, P., He, S., Liu, Y., Huang, G., Yao, B., & Ringø, E. (2009) · Aquaculture Research · doi:10.1111/j.1365-2109.2009.02209.x · Cited by 17 · see citing works
Zeng, Y., Liu, H., Zhu, T., Han, S., & Li, S. (2021) · The Plant Pathology Journal · doi:10.5423/ppj.oa.02.2021.0020 · Cited by 16 · see citing works
Exploring the complex relationship between the lung microbiome and ventilator-associated pneumonia
Bustos, I. G., Martín‐Loeches, I., Acosta‐González, A., Chotirmall, S. H., Dickson, R. P., & Reyes, L. F. (2023) · Expert Review of Respiratory Medicine · doi:10.1080/17476348.2023.2273424 · Cited by 16 · see citing works
Riggio, M. P., Dempsey, K. E., Lennon, A., Allan, D., Ramage, G., & Bagg, J. (2010) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-010-0934-y · Cited by 16 · see citing works
- Authors
- Flanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P., & Bristow, J.
- Affiliations
- University of California, San Francisco (US)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, California 94143
- ORCID
- Venue
- Journal of Clinical Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2007-06
- Volume
- 45
- Issue
- 6
- Pages
- 1954-1962
- ISSN
- 0095-1137 (ISSN-L)
- 1098-660X
- PMC
- PMC1933106
- OpenAlex
- W2164628641
- Cited by
- 180
- References
- 55
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 6 · 2023: 10 · 2022: 2 · 2021: 9 · 2020: 6 · 2019: 5 · 2018: 6 · 2017: 6 · 2016: 6 · 2015: 8 · 2014: 12 · 2013: 14 · 2012: 15
- FWCI
- 13.80
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Clinical Microbiology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (HL-024075, P01HL024075, R01HL069809, HL69809, P50HL074005, PH 50HL74005)
- Topics
- Health Sciences › Medicine › Critical Care and Intensive Care Medicine › Nosocomial Infections in ICU
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- Pseudomonas aeruginosa, bacterial diversity, antibiotic therapy, intubated patients, ventilator-associated pneumonia, tracheal aspirate, airway colonization, PhyloChip, bacterial community composition, antibiotic selection, bacilli, pathogen persistence, microbial ecology
- MeSH terms
- Aged, Aged, 80 and over, Anti-Bacterial Agents, Bacteria, Cloning, Molecular, DNA, Bacterial, Female, Humans, Infant, Intubation, Intratracheal, Lung, Male, Middle Aged, Molecular Sequence Data, Pseudomonas aeruginosa, Pseudomonas Infections, RNA, Ribosomal, 16S, Genetic Variation, Gene Library, Sequence Analysis, DNA, Ecosystem, Oligonucleotide Array Sequence Analysis
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