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Journal of Clinical Microbiology, February 2000, p. 513-520, Vol. 38, No. 2
0095-1137/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Rapid Identification of Bacteria from Positive Blood Cultures by Fluorescence-Based PCR-Single-Strand Conformation Polymorphism Analysis of the 16S rRNA Gene

Christine Y. Turenne,1,* Evelyn Witwicki,2 Daryl J. Hoban,1,2 James A. Karlowsky,1,2,3 and Amin M. Kabani1,2,4

Department of Medical Microbiology, Faculty of Medicine,1 and Faculty of Pharmacy,3 University of Manitoba, and Departments of Clinical Microbiology2 and Child Health,4 Health Sciences Centre, Winnipeg, Manitoba R3A 1R9, Canada

Received 12 July 1999/Returned for modification 3 September 1999/Accepted 5 November 1999

Bacteremia continues to result in significant morbidity and mortality, particularly in patients who are immunocompromised. Currently, patients with suspected bacteremia are empirically administered broad-spectrum antibiotics, as definitive diagnosis relies upon the use of blood cultures, which impose significant delays in and limitations to pathogen identification. To address the limitations of growth-based identification, the sequence variability of the 16S rRNA gene of bacteria was targeted for rapid identification of bacterial pathogens isolated directly from blood cultures using a fluorescence-based PCR-single-strand conformation polymorphism (SSCP) protocol. Species-specific SSCP patterns were determined for 25 of the most common bacterial species isolated from blood cultures; these isolates subsequently served as a reference collection for bacterial identification for new cases of bacteremia. A total of 272 blood-culture-positive patient specimens containing bacteria were tested. A previously determined SSCP pattern was observed for 251 (92%) specimens, with 21 (8%) specimens demonstrating SSCP patterns distinct from those in the reference collection. Time to identification from blood culture positivity ranged from 1 to 8 days with biochemical testing, whereas identification by fluorescence-based capillary electrophoresis was obtained as early as 7 h at a calculated cost of $10 (U.S. currency) per specimen when tested in batches of 10. Limitations encountered included the inability to consistently detect mixed cultures as well as some species demonstrating identical SSCP patterns. This method can be applied directly to blood cultures or whole-blood specimens, where early pathogen identification would result in a timely diagnosis with possible implications for patient management costs and the mortality and morbidity of infections.

* Corresponding author. Present address: Department of Clinical Microbiology, Health Sciences Centre, MS6-820 Sherbrook St., Winnipeg, Manitoba R3A 1R9, Canada. Phone: (204) 787-6038. Fax: (204) 789-2036. E-mail: cturenne{at}hc-sc.gc.ca.

Journal of Clinical Microbiology, February 2000, p. 513-520, Vol. 38, No. 2
0095-1137/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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