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Journal of Clinical Microbiology, June 2007, p. 1954-1962, Vol. 45, No. 6
0095-1137/07/$08.00+0     doi:10.1128/JCM.02187-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa{triangledown}

J. L. Flanagan,1,{dagger} E. L. Brodie,2,{dagger} L. Weng,3 S. V. Lynch,1 O. Garcia,1 R. Brown,1 P. Hugenholtz,3 T. Z. DeSantis,2 G. L. Andersen,2 J. P. Wiener-Kronish,1 and J. Bristow3*

Department of Anesthesia and Perioperative Care, University of California, San Francisco, California 94143,1 Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720,2 DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400-404, Walnut Creek, California 945983

Received 25 October 2006/ Returned for modification 8 January 2007/ Accepted 26 March 2007

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.

* Corresponding author. Mailing address: DOE Joint Genome Institute, 2800 Mitchell Dr., Bldg. 400-404, Walnut Creek, CA 94598. Phone: (925) 296-5609. Fax: (925) 296-5272. E-mail: jbristow{at}lbl.gov

{triangledown} Published ahead of print on 4 April 2007.

{dagger} E. L. Brodie and J. L. Flanagan contributed equally to this work.

Journal of Clinical Microbiology, June 2007, p. 1954-1962, Vol. 45, No. 6
0095-1137/07/$08.00+0     doi:10.1128/JCM.02187-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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