title: Sequence-based identification of aerobic actinomycetes.
abstract: We investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the genera Streptomyces, Gordonia, and Tsukamurella and 10 taxa of Nocardia were studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65 hsp gene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing of Nocardia species revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences of Nocardia transvalensis, N. otitidiscaviarum, and N. nova isolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within the Nocardia spp. are unnamed at present. A major unresolved issue is the type strain of N. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis.
authors.affiliation: Epidemiology and Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd., Mailstop G08, Atlanta, GA 30333, USA. vzp4@cdc.gov
authors.forename: Jean Baldus
authors.initials: JB
authors.lastname: Patel
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Wallace
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Brown-Elliott
authors.forename: Tony
authors.initials: T
authors.lastname: Taylor
authors.forename: Carol
authors.initials: C
authors.lastname: Imperatrice
authors.forename: Deborah G B
authors.initials: DG
authors.lastname: Leonard
authors.forename: Rebecca W
authors.initials: RW
authors.lastname: Wilson
authors.forename: Linda
authors.initials: L
authors.lastname: Mann
authors.forename: Kenneth C
authors.initials: KC
authors.lastname: Jost
authors.forename: Irving
authors.initials: I
authors.lastname: Nachamkin
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D000332:Aerobiosis; D004275:DNA, Ribosomal / Q000737:chemistry; D009615:Nocardia / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S