Journal article
Fingerprinting Closely Related Xanthomonas Pathovars with Random Nonamer Oligonucleotide Microarrays
Applied and environmental microbiology, Vol.68(12), pp.6361-6370
12/2002
Handle:
https://hdl.handle.net/2376/108894
PMCID: PMC134374
PMID: 12450861
Abstract
Current bacterial DNA-typing methods are typically based on gel-based fingerprinting methods. As such, they access a limited complement of genetic information and many independent restriction enzymes or probes are required to achieve statistical rigor and confidence in the resulting pattern of DNA fragments. Furthermore, statistical comparison of gel-based fingerprints is complex and nonstandardized. To overcome these limitations of gel-based microbial DNA fingerprinting, we developed a prototype, 47-probe microarray consisting of randomly selected nonamer oligonucleotides. Custom image analysis algorithms and statistical tools were developed to automatically extract fingerprint profiles from microarray images. The prototype array and new image analysis algorithms were used to analyze 14 closely related
Xanthomonas
pathovars. Of the 47 probes on the prototype array, 10 had diagnostic value (based on a chi-squared test) and were used to construct statistically robust microarray fingerprints. Analysis of the microarray fingerprints showed clear differences between the 14 test organisms, including the separation of
X. oryzae
strains 43836 and 49072, which could not be resolved by traditional gel electrophoresis of REP-PCR amplification products. The proof-of-application study described here represents an important first step to high-resolution bacterial DNA fingerprinting with microarrays. The universal nature of the nonamer fingerprinting microarray and data analysis methods developed here also forms a basis for method standardization and application to the forensic identification of other closely related bacteria.
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Details
- Title
- Fingerprinting Closely Related Xanthomonas Pathovars with Random Nonamer Oligonucleotide Microarrays
- Creators
- Mark T Kingsley - Environmental Characterization and Risk AssessmentTimothy M Straub - Environmental Characterization and Risk AssessmentDouglas R Call - Environmental Characterization and Risk AssessmentDon S Daly - Environmental Characterization and Risk AssessmentSharon C Wunschel - Environmental Characterization and Risk AssessmentDarrell P Chandler - Environmental Characterization and Risk Assessment
- Publication Details
- Applied and environmental microbiology, Vol.68(12), pp.6361-6370
- Academic Unit
- Paul G. Allen School for Global Animal Health
- Publisher
- American Society for Microbiology
- Identifiers
- 99900547198101842
- Language
- English
- Resource Type
- Journal article