Ribosomal internal transcribed spacer sequences are identical among Mycobacterium avium-intracellulare complex isolates from AIDS patients, but vary among isolates from elderly pulmonary disease patients

Smet, K. A. L. De; Brown, I. N.; Yates, M.D.; Iványi, Juraj

doi:10.1099/13500872-141-10-2739

Cited by 52 publications

(51 citation statements)

References 6 publications

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“…Amplicons were further sequenced using the forward primer Tb11 (5Ј-ACCAACGATGGTGTGTCCAT-3Ј) as described previously (28) after purification on a QIAGEN column as described by the supplier (QIAGEN, France). The 16S rRNA sequencing was performed as previously described (16), and the ITS sequencing was performed on purified amplicons made for Lipav1 and Lipav2 by Innogenetics (Ghent, Belgium) (6,20).…”

Section: Methodsmentioning

confidence: 99%

“…The digestion product separated by agarose gel electrophoresis appears as bands whose patterns are usually species specific. In addition to the hsp65 gene, the 16S-23S rRNA internal transcribed spacer (ITS) region has been shown to be more discriminative than the 16S rRNA itself (6,9,10). A detailed understanding of ITS data was developed for the heterogeneous MAIS group, allowing the separation and classification of species belonging to this group as sequevars, and for other mycobacteria, including the M. tuberculosis complex (11), leading to the development of a line probe assay (INNO-LiPA-MYCOBACTERIA).…”

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confidence: 99%

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Use of the INNO-LiPA-MYCOBACTERIA Assay (Version 2) for Identification of Mycobacterium avium - Mycobacterium intracellulare - Mycobacterium scrofulaceum Complex Isolates

et al. 2005

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Molecular biology has made a great impact on the diagnosis of mycobacterial infection, considerably reducing the delay of reporting results to clinicians (14). AccuProbe (Gen-Probe Inc./bioMérieux) was the first molecular test developed and commercialized for the rapid identification of mycobacteria from culture-positive specimens (21). Detection of 16S rRNA by a chemiluminescent species-specific probe allowed the identification of mycobacterial isolates belonging to the Mycobacterium tuberculosis complex, the Mycobacterium avium complex (MAC/MAIS) (including species-specific probes for M. avium and Mycobacterium intracellulare), Mycobacterium kansasii (29), and Mycobacterium gordonae. However, the need for rapid identification of more mycobacterial species in parallel has resulted in the development of several in-house PCRbased assays, consisting of the amplification of several conserved genes followed by the characterization of the amplicons ensured by restriction enzyme analysis or sequencing (4-6, 9, 15-17, 22-24, 28). The 16S rRNA sequence is often considered as a gold standard for bacterial identification but has demonstrated lower variability with several examples of species difficult to separate within the genus Mycobacterium (31). The 65-kDa heat shock protein gene is highly conserved in mycobacteria, with several polymorphic regions allowing its use for identification purposes. PCR restriction pattern analysis (PRA) of an hsp65 441-bp sequence has been developed, leading to catalogues of hsp65 PRA patterns (28). The digestion product separated by agarose gel electrophoresis appears as bands whose patterns are usually species specific. In addition to the hsp65 gene, the 16S-23S rRNA internal transcribed spacer (ITS) region has been shown to be more discriminative than the 16S rRNA itself (6, 9, 10). A detailed understanding of ITS data was developed for the heterogeneous MAIS group, allowing the separation and classification of species belonging to this group as sequevars, and for other mycobacteria, including the M. tuberculosis complex (11), leading to the development of a line probe assay (INNO-LiPA-MYCOBACTERIA). This assay has been the first commercial DNA probe test able to identify the most frequently isolated mycobacterial species in parallel (18,19,27,30). After amplification of the ITS, the biotinylated amplified DNA product is hybridized with 14 specific oligonucleotide probes immobilized as parallel lines on membrane strips. These include probes for the identification of strains belonging to the M. tuberculosis complex, M. kansasii (groups I, II, and III), Mycobacterium xenopi, M. gordonae, Mycobacterium chelonae (groups I, II, and III), and MAC

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Use of the INNO-LiPA-MYCOBACTERIA Assay (Version 2) for Identification of Mycobacterium avium - Mycobacterium intracellulare - Mycobacterium scrofulaceum Complex Isolates

et al. 2005

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“…The 16S rDNA sequence from the four isolates showed one single-nucleotide polymorphism (T instead of G at nucleotide 445) with the M. avium 104 strain sequence (GenBank accession CP000479). The ITS sequence obtained matched perfectly with the Mav-A sequevar described previously (6,12).…”

Section: Methodsmentioning

confidence: 52%

Genetic Diversity of Mycobacterium avium Isolates Recovered from Clinical Samples and from the Environment: Molecular Characterization for Diagnostic Purposes

et al. 2008

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“…The ITS region was amplified as described by De Smet et al (1995) and sequenced. To determine the sequevar of each strain, the ITS sequences were compared with the published sequevar sequences (Frothingham & Wilson, 1993;Mijs et al, 2002) following alignment using CLUSTALX (Thompson et al, 1997).…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of Mycobacterium avium strains inferred from glycopeptidolipid biosynthesis pathway genes

2004

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The Mycobacterium avium complex (MAC) encompasses two species, M. avium and Mycobacterium intracellulare, which are opportunistic pathogens of humans and animals. The standard method of MAC strain differentiation is serotyping based on a variation in the antigenic glycopeptidolipid (GPL) composition. To elucidate the relationships among M. avium serotypes a phylogenetic analysis of 13 reference and clinical M. avium strains from 8 serotypes was performed using as markers two genomic regions (890 bp of the gtfB gene and 2150 bp spanning the rtfA-mtfC genes) which are associated with the strains' serological properties. Strains belonging to three other known M. avium serotypes were not included in the phylogeny inference due to apparent lack of the marker sequences in their genomes, as revealed by PCR and Southern blot analysis. These studies suggest that serotypes prevalent in AIDS patients have multiple origins. In trees inferred from both markers, serotype 1 strains, known to have the simplest and shortest GPLs among all other serotypes, were polyphyletic. Likewise, comparisons of the inferred phylogenies with the molecular typing results imply that the existing tools used in epidemiological studies may be poor estimators of M. avium strain relatedness. Additionally, trees inferred from each marker had significantly incongruent topologies due to a well supported alternative placement of strain 2151, suggesting a complex evolutionary history of this genomic region.

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Ribosomal internal transcribed spacer sequences are identical among Mycobacterium avium-intracellulare complex isolates from AIDS patients, but vary among isolates from elderly pulmonary disease patients

Cited by 52 publications

References 6 publications

Use of the INNO-LiPA-MYCOBACTERIA Assay (Version 2) for Identification of Mycobacterium avium - Mycobacterium intracellulare - Mycobacterium scrofulaceum Complex Isolates

Use of the INNO-LiPA-MYCOBACTERIA Assay (Version 2) for Identification of Mycobacterium avium - Mycobacterium intracellulare - Mycobacterium scrofulaceum Complex Isolates

Genetic Diversity of Mycobacterium avium Isolates Recovered from Clinical Samples and from the Environment: Molecular Characterization for Diagnostic Purposes

Phylogeny of Mycobacterium avium strains inferred from glycopeptidolipid biosynthesis pathway genes

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