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 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal Of Microbiological Methods Elsevier

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

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Publisher
Elsevier
Copyright
Copyright © 2007 Elsevier B.V.
ISSN
0167-7012
eISSN
1872-8359
D.O.I.
10.1016/j.mimet.2007.02.005
Publisher site
See Article on Publisher Site

Abstract

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.

Journal

Journal Of Microbiological MethodsElsevier

Published: May 1, 2007

References

  • Review and re-analysis of domain-specific 16S primers
    Baker, G.C.; Smith, J.J.; Cowan, D.A.
  • Bacterial species identification after DNA amplification with a universal primer pair
    McCabe, K.M.; Zhang, Y.H.; Huang, B.L.; Wagar, E.A.; McCabe, E.R.
  • Molecular beacons for multiplex detection of four bacterial bioterrorism agents
    Varma-Basil, M.; El-Hajj, H.; Marras, S.A.; Hazbon, M.H.; Mann, J.M.; Connell, N.D.; Kramer, F.R.; Alland, D.

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