1. |
Conville PS,
Zelazny AM,
Witebsky FG,
( 2006 ) Analysis of secA1 gene sequences for identification of Nocardia species. PMID : 16891489 : DOI : 10.1128/JCM.00155-06 PMC : PMC1594632 Abstract >>
Molecular methodologies, especially 16S rRNA gene sequence analysis, have allowed the recognition of many new species of Nocardia and to date have been the most precise methods for identifying isolates reliably to the species level. We describe here a novel method for identifying Nocardia isolates by using sequence analysis of a portion of the secA1 gene. A region of the secA1 gene of 30 type or reference strains of Nocardia species was amplified using secA1-specific primers. Sequence analysis of 468 bp allowed clear differentiation of all species, with a range of interspecies similarity of 85.0% to 98.7%. Corresponding 16S rRNA gene sequences of a 1,285-bp region for the same isolates showed a range of interspecies similarity of 94.4 to 99.8%. In addition to the type and reference strains, a 468-bp fragment of the secA1 gene was sequenced from 40 clinical isolates of 12 Nocardia species previously identified by 16S rRNA gene sequence analysis. The secA1 gene sequences of most isolates showed >99.0% similarity to the secA1 sequences of the type or reference strain to which their identification corresponded, with a range of 95.3 to 100%. Comparison of the deduced 156 amino acid sequences of the SecA1 proteins of the clinical isolates showed between zero and two amino acid residue differences compared to that of the corresponding type or reference strain. Sequencing of the secA1 gene, and using deduced amino acid sequences of the SecA1 protein, may provide a more discriminative and precise method for the identification of Nocardia isolates than 16S rRNA gene sequencing.
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2. |
Rodríguez-Nava V,
Couble A,
Devulder G,
Flandrois JP,
Boiron P,
Laurent F,
( 2006 ) Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species. PMID : 16455910 : DOI : 10.1128/JCM.44.2.536-546.2006 PMC : PMC1392680 Abstract >>
Nocardia identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the hsp65 gene to differentiate Nocardia species, including 36 new species. Our results confirm that hsp65 PRA must no longer be used for Nocardia species identification, as many species have the same restriction pattern. We then compared sequencing-based strategies using an hsp65 database and a 16S rRNA database and found that the hsp65 region contained sufficient polymorphisms for comprehensive Nocardia species identification.
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3. |
Takeda K,
Kang Y,
Yazawa K,
Gonoi T,
Mikami Y,
( 2010 ) Phylogenetic studies of Nocardia species based on gyrB gene analyses. PMID : 19833784 : DOI : 10.1099/jmm.0.011346-0 Abstract >>
Phylogenetic analyses of 56 type species of Nocardia were conducted using the partial nucleotide sequences of the gyrase B-encoding gene (gyrB). The interspecies similarities of the gyrB gene for the 56 type species were 82.4-99.9 %, which corresponded to 270-2 nt differences in the partial gene sequences of approximately 1200 nt. In comparison with phylogenetic relationships, gyrB gene sequence information was generally consistent with that of 16S rRNA gene sequences with minor exceptions. However, the degree of divergence of the gyrB gene sequences was approximately 3.6 times greater than those of the 16S rRNA gene, suggesting a higher discriminative power of gyrB sequence information compared with 16S rRNA gene sequences for Nocardia species. The Nocardia type species were clustered based on gyrB sequence similarity values of 93.5 % and above. Among the 56 type species, 38 were distributed in 13 clusters, each comprising 2 to 7 species. The remaining 18 species were classified into an independent cluster, in which the similarity between each species and the other 55 Nocardia species was less than 93.5 %. Among the eight mycolic acid-containing actinomycete genera in the suborder Corynebacterineae, Nocardia was clearly differentiated from the other genera, such as Rhodococcus, by gyrB gene analyses (similarity values of gyrB sequences for Nocardia and Rhodococcus were 75-85 %), indicating that the gyrB gene is a useful alternative to the 16S rRNA gene for the determination of phylogenetic relationships between the genus Nocardia and the seven other actinomycete genera.
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