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Journal of Clinical Microbiology, April 2007, p. 1146-1151, Vol. 45, No. 4
0095-1137/07/$08.00+0     doi:10.1128/JCM.02482-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Analysis of Multiple Differing Copies of the 16S rRNA Gene in Five Clinical Isolates and Three Type Strains of Nocardia Species and Implications for Species Assignment

Microbiology Service, Department of Laboratory Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, U.S. Department of Health and Human Services, 10 Center Drive, MSC 1508, Bethesda, Maryland 20882-1508

Received 12 December 2006/ Returned for modification 31 January 2007/ Accepted 6 February 2007

Five clinical isolates of Nocardia that showed ambiguous bases within the variable region of the 16S rRNA gene sequence were evaluated for the presence of multiple copies of this gene. The type strains of three Nocardia species, Nocardia concava, Nocardia ignorata, and Nocardia yamanashiensis, which also showed ambiguous bases in the variable region, were also examined. Cloning experiments using an amplified region of the 16S rRNA that contains the variable region showed that each isolate possessed 16S rRNA genes with at least two different sequences. In addition, hybridization studies using a 16S rRNA gene-specific probe and extracted genomic DNA of the patient isolates and of the type strain of N. ignorata showed that each isolate possessed at least three copies of the gene. These multiple differing copies of the 16S rRNA gene and the results of DNA-DNA hybridization studies indicate problems of species definition and identification for such isolates. A broader species concept than that currently in vogue may be required to accommodate such organisms.

Published ahead of print on 14 February 2007.

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