Association between 16S-23S Internal Transcribed Spacer Sequence Groups of
            <i>Mycobacterium avium</i>
            Complex and Pulmonary Disease

Stout, Jason E.; Hopkins, Gregory; McDonald, Jay R.; Quinn, Anita; Hamilton, Carol; Reller, L. Barth; Frothingham, Richard

doi:10.1128/jcm.00719-08

Cited by 18 publications

(13 citation statements)

References 26 publications

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“…No consensus definition of copy numbers has been agreed upon for nontuberculous mycobacteria. The majority of VNTR types had the Mav-B and Mav-A ITS sequences (which differ by a single base pair), which has been noted in other studies (1,24,28). For multiple isolates of the same VNTR type from the same patient, only one was sequenced; the results for the rest were presumed.…”

Section: Discussionmentioning

confidence: 99%

“…This analysis revealed that 33 types or subtypes were Mav-B (58.9%), 18 were Mav-A (32.1%), 3 were Mav-F (5.4%), 1 was Mav-G (1.8%), and 1 did not amplify. Other previously described ITS sequences in isolates of M. avium (Mav C, Mav-D, and Mav-E sequences) were not encountered (1,24,28). Of the three reference strains of M. avium subsp.…”

Section: Pfgementioning

confidence: 99%

“…Sequencing of the ITS region (263 bp) was performed as described previously (23,24). Results were compared to ITS sequences in GenBank, including the Mav-A (GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

“…Isolates for study initially were identified as MAC using a commercial hybridization assay (AccuProbe MAC probe; Hologic Inc.) and then were identified as M. avium, M. intracellulare/Mycobacterium chimaera, or MAC X using the multiplex 16S rRNA gene PCR technique described by Wilton and Cousins (21) or hsp65 PCR-restriction analysis (PRA) (22). To confirm the species identification, sequencing of the internal transcribed spacer (ITS) region was performed (23,24).…”

Section: Methodsmentioning

confidence: 99%

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Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database

et al. 2016

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d"Mycobacterium avium subsp. hominissuis" is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandemrepeat (VNTR) analysis. Clinical and household biofilm M. avium isolates underwent molecular identification. Testing for IS901 was done to separate M. avium subsp. avium from M. avium subsp. hominissuis. VNTR types were defined using VNTR loci, and subtyping was performed using 3= hsp65 and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes of M. avium subsp. hominissuis (IS901 negative) were identified among 416 isolates of M. avium from 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included >4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3= hsp65 sequence code (sequevar). A total of 44 isolates belonging to four M. avium subsp. hominissuis VNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901 PCR primers. By sequencing, all 44 amplicons were not IS901 but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis of M. avium subsp. hominissuis isolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates of M. avium subsp. avium were identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan. The species "Mycobacterium avium subsp. hominissuis" is an important cause of chronic lung disease in the setting of bronchiectasis and disseminated disease in patients with AIDS. The species is acquired from environmental sources, with recent studies focusing on household water. It is present worldwide, with all areas of the United States (especially the southern United States) being considered high-risk areas for the disease.Efforts to compare isolates of M. avium have been difficult. Three subspecies are currently recognized, namely, M. avium subsp. avium, M. avium subsp. paratuberculosis, and M. avium subsp. silvaticum. A fourth subspecies, M. avium subsp. hominissuis (including human isolates), has also been proposed (1, 2). IS901 is present in all isolates of M. avium subsp. avium but is not present in isolates of M. avium subsp. hominissuis (1); this difference has been used to separate the two subspecies (1, 2). Strain comparisons within M. avium (as well as with other members of the Mycobacterium avium complex [MAC], especially Mycobacterium intracellulare) have most frequently utilized pulsed-field gel electrophoresis (PFGE) (3, 4), which is expensive, technically difficult, time-consuming, and useful only fo...

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Section: Discussionmentioning

confidence: 99%

Section: Pfgementioning

confidence: 99%

“…Sequencing of the ITS region (263 bp) was performed as described previously (23,24). Results were compared to ITS sequences in GenBank, including the Mav-A (GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database

et al. 2016

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“…Variable-number tandem (i.e., consecutive) repeats (VNTR) of the minisatellite class (10 to 100 bp) were identified. VNTR typing has been used for strain comparison and population studies of other species of mycobacteria, including Mycobacterium ulcerans, Mycobacterium avium, and Mycobacterium tuberculosis (8)(9)(10)(11)(12)(13)(14)(15). Subsequently, studies of the use of VNTR for M. intracellulare isolates were reported in 2009 and 2010 from Japan (16) and (Bordeaux) France (17), and the candidate markers were described as mycobacterial interspersed repetitive unit-variable-number tandem repeats (MIRU-VNTR) (17).…”

mentioning

confidence: 99%

Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat (MIRU-VNTR) Genotyping of Mycobacterium intracellulare for Strain Comparison with Establishment of a PCR-Based Database

et al. 2013

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Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the "gold standard" of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible.

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Mycobacterium avium Complex Disease

Holt¹,

Daley²

2018

Nontuberculous Mycobacterial Disease

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Association between 16S-23S Internal Transcribed Spacer Sequence Groups of Mycobacterium avium Complex and Pulmonary Disease

Cited by 18 publications

References 26 publications

Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database

Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database

Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat (MIRU-VNTR) Genotyping of Mycobacterium intracellulare for Strain Comparison with Establishment of a PCR-Based Database

Mycobacterium avium Complex Disease

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