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Title: Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates

Abstract

A diagnostic, genome-independent microbial fingerprinting method using DNA oligonucleotide microarrays was used for high-resolution differentiation between closely related Bacillus strains, including two strains of Bacillus anthracis that are monomorphic (indistinguishable) via amplified fragment length polymorphism fingerprinting techniques. Replicated hybridizations on 391-probe nonamer arrays were used to construct a prototype fingerprint library for quantitative comparisons. Descriptive analysis of the fingerprints, including phylogenetic reconstruction, is consistent with previous taxonomic organization of the genus. Newly developed statistical analysis methods were used to quantitatively compare and objectively confirm apparent differences in microarray fingerprints with the statistical rigor required for microbial forensics and clinical diagnostics. These data suggest that a relatively simple fingerprinting microarray and statistical analysis method can differentiate between species in the Bacillus cereus complex, and between strains of B. anthracis. A synthetic DNA standard was used to understand underlying microarray and process-level variability, leading to specific recommendations for the development of a standard operating procedure and/or continued technology enhancements for microbial forensics and diagnostics.

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
878134
Report Number(s):
PNNL-SA-45391
Journal ID: ISSN 0095-1137; JCMIDW; 830403000; TRN: US200609%%189
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Clinical Microbiology; Journal Volume: 44; Journal Issue: 1
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; BACILLUS; BACILLUS CEREUS; DNA; OLIGONUCLEOTIDES; RECOMMENDATIONS; STRAINS; microarrays; fingerprinting; microbes

Citation Formats

Chandler, Darrell P., Alferov, Oleg, Chernov, Boris, Daly, Don S., Golova, Julia, Perov, Alexander N., Protic, Miroslava, Robison, Richard, Shipma, Matthew, White, Amanda M., and Willse, Alan R. Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates. United States: N. p., 2006. Web. doi:10.1128/JCM.44.1.244-250.2006.
Chandler, Darrell P., Alferov, Oleg, Chernov, Boris, Daly, Don S., Golova, Julia, Perov, Alexander N., Protic, Miroslava, Robison, Richard, Shipma, Matthew, White, Amanda M., & Willse, Alan R. Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates. United States. doi:10.1128/JCM.44.1.244-250.2006.
Chandler, Darrell P., Alferov, Oleg, Chernov, Boris, Daly, Don S., Golova, Julia, Perov, Alexander N., Protic, Miroslava, Robison, Richard, Shipma, Matthew, White, Amanda M., and Willse, Alan R. Sun . "Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates". United States. doi:10.1128/JCM.44.1.244-250.2006.
@article{osti_878134,
title = {Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates},
author = {Chandler, Darrell P. and Alferov, Oleg and Chernov, Boris and Daly, Don S. and Golova, Julia and Perov, Alexander N. and Protic, Miroslava and Robison, Richard and Shipma, Matthew and White, Amanda M. and Willse, Alan R.},
abstractNote = {A diagnostic, genome-independent microbial fingerprinting method using DNA oligonucleotide microarrays was used for high-resolution differentiation between closely related Bacillus strains, including two strains of Bacillus anthracis that are monomorphic (indistinguishable) via amplified fragment length polymorphism fingerprinting techniques. Replicated hybridizations on 391-probe nonamer arrays were used to construct a prototype fingerprint library for quantitative comparisons. Descriptive analysis of the fingerprints, including phylogenetic reconstruction, is consistent with previous taxonomic organization of the genus. Newly developed statistical analysis methods were used to quantitatively compare and objectively confirm apparent differences in microarray fingerprints with the statistical rigor required for microbial forensics and clinical diagnostics. These data suggest that a relatively simple fingerprinting microarray and statistical analysis method can differentiate between species in the Bacillus cereus complex, and between strains of B. anthracis. A synthetic DNA standard was used to understand underlying microarray and process-level variability, leading to specific recommendations for the development of a standard operating procedure and/or continued technology enhancements for microbial forensics and diagnostics.},
doi = {10.1128/JCM.44.1.244-250.2006},
journal = {Journal of Clinical Microbiology},
number = 1,
volume = 44,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
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