Utility of Pyrosequencing in Identifying Bacteria Directly from Positive Blood Culture Bottles
Growth in liquid media is the gold standard for detecting microorganisms associated with bloodstream infections. The Gram stain provides the first clue as to the etiology of infection, with phenotypic identification completed 1 or 2 days later. Providing more detailed information than the Gram stain...
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Published in | Journal of Clinical Microbiology Vol. 47; no. 2; pp. 368 - 372 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
Washington, DC
American Society for Microbiology
01.02.2009
American Society for Microbiology (ASM) |
Subjects | |
Online Access | Get full text |
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Summary: | Growth in liquid media is the gold standard for detecting microorganisms associated with bloodstream infections. The Gram stain provides the first clue as to the etiology of infection, with phenotypic identification completed 1 or 2 days later. Providing more detailed information than the Gram stain can impart, and in less time than subculturing, would allow the use of more directed empirical therapy and, thus, reduce the patient's exposure to unnecessary or ineffective antibiotics sooner. The study had two objectives, as follows: (i) to identify new targets to improve our ability to differentiate among certain enteric gram-negative rods or among certain Streptococcus species and (ii) to determine whether real-time PCR and pyrosequencing could as accurately identify organisms directly from positive blood culture bottles as culture-based methods. Two hundred and fifty-five consecutive positive blood culture bottles were included. The results showed a high level of agreement between the two approaches; of the 270 bacteria isolated from the 255 blood culture bottles, results for pyrosequencing and culture-based identifications were concordant for 264/270 (97.8%) bacteria with three failed sequences, and three sequences without match. Additionally, compared to the universal 16S rRNA gene target, the new 23S rRNA gene targets greatly improved our ability to differentiate among certain enteric gram-negative rods or among certain Streptococcus species. In conclusion, combining real-time PCR and pyrosequencing provided valuable information beyond that derived from the initial Gram stain and in less time than phenotypic culture-based identification. This strategy, if implemented, could result in a more directed empirical therapy in patients and would promote responsible antibiotic stewardship. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Corresponding author. Present address: Department of Epidemiology and Biostatistics, School of Public Health and Health Services, George Washington University, 231 Ross Hall, 2300 I Street, NW, Washington, DC 20037. Phone: (202) 994-7062. Fax: (202) 994-0082. E-mail: sphjaj@gwumc.edu |
ISSN: | 0095-1137 1098-660X |
DOI: | 10.1128/JCM.01991-08 |