| Extended Bibliography: |
Show bibliography
| Ref #: |
65940 |
| Author(s): |
Ruimy,R.;Riegel,P.;Carlotti,A.;Boiron,P.;Bernardin,G.;Monteil,H.;Wallace RJ,J.r.;Christen,R. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Nocardia pseudobrasiliensis sp. nov., a new species of Nocardia which groups bacterial strains previously identified as Nocardia brasiliensis and associated with invasive diseases |
| Volume: |
46 |
| Page(s): |
259-64 |
| Year: |
1996 |
| Keyword(s): |
GENBANK/X84850
GENBANK/X84851
GENBANK/X84852
GENBANK/X84853
GENBANK/X84854
GENBANK/X84855
GENBANK/X84856
GENBANK/X84857
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Molecular Sequence Data
Nocardia/chemistry/*classification/genetics/metabolism
Nocardia Infections/*microbiology
Nucleic Acid Hybridization
Phylogeny
|
| Remarks: |
We studied five strains of a new Nocardia taxon recently identified among Nocardia brasiliensis strains associated with invasive diseases (R. J. Wallace, Jr., B. A. Brown, Z. Blacklock, R. Ulrich, K. Jost, J. M. Brown, M. M. McNeil, G. Onyi, V. A. Steingrube, and J. Gibson, J. Clin. Microbiol. 33:1528-1533, 1995) to determine their taxonomic status. Several characteristics of these organisms, including the presence of chemotype IV cell walls, nocardomycolic acids, a predominant menaquinone similar to that of Nocardia asteroides ATCC 19247T (T = type strain), and G+C contents ranging from 67 to 68 mol%, are characteristics of the genus Nocardia. Phylogenies based on small-subunit ribosomal DNA sequences clearly confirmed that all five strains belong to the genus Nocardia and occur on a single branch that is clearly distinct from N. brasiliensis. This branch forms a clade with Nocardia vaccinii, Nocardia nova, Nocardia otitidiscaviarum, and Nocardia seriolae. The five new strains exhibited high levels of DNA relatedness with each other, as determined by DNA-DNA hybridization experiments (S1 nuclease procedure), but not with N. brasiliensis strains or with strains of the four phylogenetically related Nocardia species mentioned above. The five new strains differ from N. brasiliensis in the following characteristics: mycolic acid pattern, decomposition of adenine, nitrate reduction, and antimicrobial agent susceptibilities. Therefore, we propose that these strains belong to a new species, Nocardia pseudobrasiliensis. The type strain is strain ATCC 51512, which was isolated from a leg abscess on a patient suffering from ulcerative colitis. |
| URL: |
8573505 |
|
| Ref #: |
65647 |
| Author(s): |
Patel,J.B.;Wallace RJ,J.r.;Brown-Elliott,B.A.;Taylor,T.;Imperatrice,C.;Leonard,D.G.;Wilson,R.W.;Mann,L.;Jost,K.C.;Nachamkin,I. |
| Journal: |
J Clin Microbiol |
| Title: |
Sequence-based identification of aerobic actinomycetes |
| Volume: |
42 |
| Page(s): |
2530-40 |
| Year: |
2004 |
| Keyword(s): |
Actinobacteria/classification/genetics/*isolation & purification
Aerobiosis
DNA, Ribosomal/chemistry
Nocardia/genetics/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
|
| Remarks: |
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. |
| URL: |
15184431 |
|
| Ref #: |
95453 |
| Author(s): |
Rodriguez-Nava,V.;Couble,A.;Devulder,G.;Flandrois,J.P.;Boiron,P.;Laurent,F. |
| Journal: |
J Clin Microbiol |
| Title: |
Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species |
| Volume: |
44 |
| Page(s): |
536-46 |
| Year: |
2006 |
| Keyword(s): |
Animals
Bacterial Proteins/genetics
*Bacterial Typing Techniques
Databases, Genetic
Genes, rRNA
Heat-Shock Proteins/*genetics
Humans
Nocardia/*classification/genetics
Phylogeny
Polymerase Chain Reaction/*methods
RNA, Ribosomal, 16S/genetics
*Restriction Mapping
Sequence Analysis, DNA
Species Specificity
|
| Remarks: |
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. |
| URL: |
16455910 |
|
| Ref #: |
65999 |
| Author(s): |
Chun,J.;Goodfellow,M. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences |
| Volume: |
45 |
| Page(s): |
240-5 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/Z36925
GENBANK/Z36926
GENBANK/Z36927
GENBANK/Z36928
GENBANK/Z36929
GENBANK/Z36930
GENBANK/Z36933
GENBANK/Z36934
GENBANK/Z36935
GENBANK/Z36936
Base Sequence
DNA, Bacterial/+ACo-genetics
Genes, Bacterial
Molecular Sequence Data
Nocardia/chemistry/+ACo-classification/genetics
Phylogeny
RNA, Bacterial/+ACo-genetics
RNA, Ribosomal, 16S/+ACo-genetics
Rhodococcus/classification/genetics
Sequence Analysis
Vitamin K/analysis
|
| Remarks: |
Partial sequences of the 16S rRNA genes of the type strains of nine species of the genus Nocardia were determined following the isolation and cloning of the amplified genes. These sequences were aligned with the sequences of representatives of the genera Corynebacterium, Gordona, Mycobacterium, Rhodococcus, and Tsukamurella, and phylogenetic trees were inferred by using the Fitch-Margoliash and neighbor-joining methods. The genus Nocardia formed a distinct clade that was most closely associated with the genus Rhodococcus. The average level of sequence similarity found among the type strains of the Nocardia species was 97.2 0.7+ACU-. Two sublines were recognized within the Nocardia clade+ADs- one encompassed Nocardia asteroides and related species, and the other encompassed Nocardia otitidiscaviarum and allied taxa. Separation of the two sublines is based on differences in helix 37-1. The results of isoprenoid quinone analyses provided evidence that nocardiae can be distinguished from all other actinomycete taxa on the basis of their characteristic menaquinone profiles. Nocardiae typically contain hexahydrogenated menaquinones with eight isoprene units in which the two end units are cyclized. |
| URL: |
7537058 |
|
| Ref #: |
95438 |
| Author(s): |
Conville,P.S.;Zelazny,A.M.;Witebsky,F.G. |
| Journal: |
J Clin Microbiol |
| Title: |
Analysis of secA1 gene sequences for identification of Nocardia species |
| Volume: |
44 |
| Page(s): |
2760-6 |
| Year: |
2006 |
| Keyword(s): |
GENBANK/DQ360260
GENBANK/DQ360261
GENBANK/DQ360262
GENBANK/DQ360263
GENBANK/DQ360265
GENBANK/DQ360266
GENBANK/DQ360267
GENBANK/DQ360268
GENBANK/DQ360269
GENBANK/DQ360270
GENBANK/DQ360271
GENBANK/DQ360272
GENBANK/DQ360273
GENBANK/DQ360274
GENBANK/DQ360275
GENBANK/DQ360276
GENBANK/DQ360277
GENBANK/DQ360278
GENBANK/DQ360279
GENBANK/DQ360280
GENBANK/DQ360281
GENBANK/DQ360282
GENBANK/DQ360284
GENBANK/DQ360285
GENBANK/DQ360286
GENBANK/DQ360287
GENBANK/DQ360288
GENBANK/DQ360289
GENBANK/DQ360290
GENBANK/DQ366276
GENBANK/DQ659895
GENBANK/DQ659896
GENBANK/DQ659897
GENBANK/DQ659898
GENBANK/DQ659899
GENBANK/DQ659900
GENBANK/DQ659901
GENBANK/DQ659902
GENBANK/DQ659903
GENBANK/DQ659904
GENBANK/DQ659905
GENBANK/DQ659906
GENBANK/DQ659907
GENBANK/DQ659908
GENBANK/DQ659909
GENBANK/DQ659910
GENBANK/DQ659911
GENBANK/DQ659912
GENBANK/DQ659913
GENBANK/DQ659914
GENBANK/DQ659915
GENBANK/DQ659916
GENBANK/DQ659917
GENBANK/DQ659918
GENBANK/DQ659919
GENBANK/DQ659920
Adenosine Triphosphatases/*genetics
Bacterial Proteins/*genetics
Cluster Analysis
DNA, Bacterial/chemistry/*genetics
DNA, Ribosomal/genetics
Humans
Membrane Transport Proteins/*genetics
Molecular Sequence Data
Nocardia/*classification/*genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
*Sequence Analysis, DNA
Sequence Homology
|
| Remarks: |
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. |
| URL: |
16891489 |
|
| Ref #: |
13292 |
| Author(s): |
Chun,J.;Goodfellow,M. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences |
| Volume: |
45 |
| Page(s): |
240-5 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/Z36925
GENBANK/Z36926
GENBANK/Z36927
GENBANK/Z36928
GENBANK/Z36929
GENBANK/Z36930
GENBANK/Z36933
GENBANK/Z36934
GENBANK/Z36935
GENBANK/Z36936
Base Sequence
DNA, Bacterial/+ACo-genetics
Genes, Bacterial
Molecular Sequence Data
Nocardia/chemistry/+ACo-classification/genetics
Phylogeny
RNA, Bacterial/+ACo-genetics
RNA, Ribosomal, 16S/+ACo-genetics
Rhodococcus/classification/genetics
Sequence Analysis
Vitamin K/analysis
|
| Remarks: |
Partial sequences of the 16S rRNA genes of the type strains of nine species of the genus Nocardia were determined following the isolation and cloning of the amplified genes. These sequences were aligned with the sequences of representatives of the genera Corynebacterium, Gordona, Mycobacterium, Rhodococcus, and Tsukamurella, and phylogenetic trees were inferred by using the Fitch-Margoliash and neighbor-joining methods. The genus Nocardia formed a distinct clade that was most closely associated with the genus Rhodococcus. The average level of sequence similarity found among the type strains of the Nocardia species was 97.2 0.7+ACU-. Two sublines were recognized within the Nocardia clade+ADs- one encompassed Nocardia asteroides and related species, and the other encompassed Nocardia otitidiscaviarum and allied taxa. Separation of the two sublines is based on differences in helix 37-1. The results of isoprenoid quinone analyses provided evidence that nocardiae can be distinguished from all other actinomycete taxa on the basis of their characteristic menaquinone profiles. Nocardiae typically contain hexahydrogenated menaquinones with eight isoprene units in which the two end units are cyclized. |
| URL: |
95244306 |
|
| Ref #: |
13291 |
| Author(s): |
Ruimy,R.;Riegel,P.;Carlotti,A.;Boiron,P.;Bernardin,G.;Monteil,H.;Wallace RJ,J.r.;Christen,R. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Nocardia pseudobrasiliensis sp. nov., a new species of Nocardia which groups bacterial strains previously identified as Nocardia brasiliensis and associated with invasive diseases |
| Volume: |
46 |
| Page(s): |
259-64 |
| Year: |
1996 |
| Keyword(s): |
GENBANK/X84850
GENBANK/X84851
GENBANK/X84852
GENBANK/X84853
GENBANK/X84854
GENBANK/X84855
GENBANK/X84856
GENBANK/X84857
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Molecular Sequence Data
Nocardia/chemistry/*classification/genetics/metabolism
Nocardia Infections/*microbiology
Nucleic Acid Hybridization
Phylogeny
Support, Non-U.S. Gov't
|
| Remarks: |
We studied five strains of a new Nocardia taxon recently identified among Nocardia brasiliensis strains associated with invasive diseases (R. J. Wallace, Jr., B. A. Brown, Z. Blacklock, R. Ulrich, K. Jost, J. M. Brown, M. M. McNeil, G. Onyi, V. A. Steingrube, and J. Gibson, J. Clin. Microbiol. 33:1528-1533, 1995) to determine their taxonomic status. Several characteristics of these organisms, including the presence of chemotype IV cell walls, nocardomycolic acids, a predominant menaquinone similar to that of Nocardia asteroides ATCC 19247T (T = type strain), and G+C contents ranging from 67 to 68 mol%, are characteristics of the genus Nocardia. Phylogenies based on small-subunit ribosomal DNA sequences clearly confirmed that all five strains belong to the genus Nocardia and occur on a single branch that is clearly distinct from N. brasiliensis. This branch forms a clade with Nocardia vaccinii, Nocardia nova, Nocardia otitidiscaviarum, and Nocardia seriolae. The five new strains exhibited high levels of DNA relatedness with each other, as determined by DNA-DNA hybridization experiments (S1 nuclease procedure), but not with N. brasiliensis strains or with strains of the four phylogenetically related Nocardia species mentioned above. The five new strains differ from N. brasiliensis in the following characteristics: mycolic acid pattern, decomposition of adenine, nitrate reduction, and antimicrobial agent susceptibilities. Therefore, we propose that these strains belong to a new species, Nocardia pseudobrasiliensis. The type strain is strain ATCC 51512, which was isolated from a leg abscess on a patient suffering from ulcerative colitis. |
| URL: |
96138987 |
|
| Ref #: |
1300 |
| Author(s): |
Skerman,V.B.D.;McGowan,V.;Sneath,P.H.A.(ed) |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Approved Lists of Bacterial Names. |
| Volume: |
30 |
| Page(s): |
225-420 |
| Year: |
1980 |
|
| Ref #: |
6413 |
| Journal: |
J. Bacteriol. |
| Volume: |
127 |
| Page(s): |
584-594 |
| Year: |
1976 |
|
| Ref #: |
755 |
| Author(s): |
Gordon,R.E.;Mihm,J.M. |
| Journal: |
J. Gen. Microbiol. |
| Title: |
A comparison of Nocardia asteroides and Nocardia brasiliensis. |
| Volume: |
20 |
| Page(s): |
129-135 |
| Year: |
1959 |
|
|
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