A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria.

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Research Abstract Details 

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A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Abstract Text:

Soumitesh Chakravorty,Danica Helb,Michele Burday,Nancy Connell,David Alland,

Bacterial 16S ribosomal RNA (rRNA) genes contain nine "hypervariable regions" (V1-V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations. No single region can differentiate among all bacteria; therefore, systematic studies that compare the relative advantage of each region for specific diagnostic goals are needed. We characterized V1-V8 in 110 different bacterial species including common blood borne pathogens, CDC-defined select agents and environmental microflora. Sequence similarity dendrograms were created for hypervariable regions V1-V8, and for selected combinations of regions or short segments within individual hypervariable regions that might be appropriate for DNA probing and real-time PCR. We determined that V1 best differentiated among Staphylococcus aureus and coagulase negative Staphylococcus sp. V2 and V3 were most suitable for distinguishing all bacterial species to the genus level except for closely related enterobacteriaceae. V2 best distinguished among Mycobacterium species and V3 among Haemophilus species. The 58 nucleotides-long V6 could distinguish among most bacterial species except enterobacteriaceae. V6 was also noteworthy for being able to differentiate among all CDC-defined select agents including Bacillus anthracis, which differed from B. cereus by a single polymorphism. V4, V5, V7 and V8 were less useful targets for genus or species-specific probes. The hypervariable sequence-specific dendrograms and the "MEGALIGN" files provided online will be highly useful tools for designing specific probes and primers for molecular assays to detect pathogenic bacteria, including select agents.

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Publishing Authors By Initials

S Chakravorty,D Helb,M Burday,N Connell,D Alland,

For similar genetic phenomena: variation (genetics) research abstracts see: genetic phenomena: variation (genetics) research

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A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Journal of microbiological methods

VOLUME: 69

Page Numbers: 330-9

Journal Abbreviation:

ISSN: 0167-7012

DAY: 22

MONTH: 02

YEAR: 2007

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Information

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LANGUAGE: eng

NlmUniqueID: 8306883

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Keywords Mesh Terms:

KEYWORDS: Variation (Genetics)

MESH TERMS: genetics

Chemical & Substance for Abstract: A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Information

Substance Name: RNA, Ribosomal, 16S

Registry Number: 0

Grant and Affiliation Information for A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria.

AFFILIATION: Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, NJ 07103, USA.

Country: Netherlands

AGENCY: United States NIAID

GRANT: U01 AI056689-01

ACRONYM: AI

MEDLINETA: J Microbiol Methods

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