Assignment of reference 5'-end 16S rDNA sequences and species-specific sequence polymorphisms improves species identification of Nocardia.

ABSTRACT: 16S rDNA sequence analysis is the most accurate method for definitive species identification of nocardiae. However, conflicting results can be found due to sequence errors in gene databases. This study tested the feasibility of species identification of Nocardia by partial (5'-end 606-bp) 16S rDNA sequencing, based on sequence comparison with "reference" sequences of well-annotated strains. This new approach was evaluated using 96 American Type Culture Collection (n=6), and clinical (n=90) Nocardia isolates. Nucleotide sequence-based polymorphisms within species were indicative of "sequence types" for that species. Sequences were compared with those in the GenBank, Bioinformatics Bacteria Identification and Ribosomal Database Project databases. Compared with the reference sequence set, all

SUBMITTER: Kong F 

PROVIDER: S-EPMC2714554 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature