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Sequence-based identification of aerobic actinomycetes.
Jean Baldus Patel1, Richard J Wallace, Barbara A Brown-Elliott
1Epidemiology and Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd., Mailstop G08, Atlanta, GA 30333, USA. vzp4@cdc.gov
Journal of Clinical Microbiology
|June 9, 2004
Summary
Partial 16S rRNA gene sequencing aids in identifying aerobic actinomycetes. However, significant sequence divergence within species and unnamed Nocardia taxa highlight the need for further taxonomic definition.
Area of Science:
- Microbiology
- Molecular Biology
- Taxonomy
Background:
- Aerobic actinomycetes are clinically significant microorganisms.
- Accurate identification of these bacteria is crucial for effective treatment.
- Current taxonomic classifications may not fully reflect genetic diversity.
Purpose of the Study:
- To evaluate the effectiveness of 500-bp 16S rRNA gene sequencing for identifying clinically relevant aerobic actinomycetes.
- To assess the genetic diversity within Nocardia species and other aerobic actinomycetes.
- To identify potential new taxa and resolve taxonomic ambiguities.
Main Methods:
- Sequencing of the 16S rRNA gene (500 bp) from reference strains and clinical isolates.
- Comparative analysis with non-sequencing methods: growth, biochemical tests, PCR-restriction enzyme analysis, susceptibility testing, and HPLC.
- Phylogenetic analysis of Nocardia and other aerobic actinomycete genera.
Main Results:
- 16S rRNA gene sequencing demonstrated utility in identifying aerobic actinomycetes.
- High sequence variability was observed within Nocardia transvalensis, N. otitidiscaviarum, and N. nova, suggesting they represent species complexes.
- Several taxa did not match recognized species, indicating the presence of unnamed taxa, particularly within Nocardia.
- The type strain of Nocardia asteroides (ATCC 19247) does not represent common clinical isolates.
Conclusions:
- Partial 16S rRNA gene sequencing is a valuable tool for aerobic actinomycete identification.
- Significant intra-species sequence divergence necessitates re-evaluation of current taxonomic boundaries.
- The Nocardia genus requires further taxonomic refinement, with proposed designation of N. transvalensis, N. otitidiscaviarum, and N. nova as complexes.
- The current N. asteroides type strain is inadequate for representing clinical isolates.