Molecular typing of Mycobacterium intracellulare using multilocus variable-number of tandem-repeat analysis: identification of loci and analysis of clinical isolates

Ichikawa, Kazuya; Yagi, Tetsuya; Inagaki, Takayuki; Moriyama, Makoto; Nagao, Taku; Uchiya, Kei-ichi; Nikai, Toshiaki; Ogawa, Kenji

doi:10.1099/mic.0.030684-0

Cited by 25 publications

(47 citation statements)

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“…Studies have shown the ability of VNTR analysis to meet the criteria for discrimination from the closely related species M. intracellulare (11)(12)(13), and preliminary studies have shown VNTR analysis to be feasible with M. avium (8,9). Thus, we undertook a study on the use of VNTR analysis in the clinical setting of U.S. patients with nodular bronchiectasis and M. avium.…”

Section: Methodsmentioning

confidence: 99%

“…Such studies include the use of mycobacterial interspersed repetitive unit (MIRU) loci (8) and M. avium tandem-repeat (MATR) loci (some of which recognize the same tandem repeat) (9). VNTR analysis has been used for strain comparisons and population studies of other species of mycobacteria, including M. intracellulare, Mycobacterium ulcerans, and Mycobacterium tuberculosis (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). Studies on the use of VNTR analysis for M. intracellulare isolates were reported from Japan and France in 2009 and 2010 (11,13), respectively, and from the United States in 2013 (12).…”

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confidence: 99%

“…VNTR analysis has been used for strain comparisons and population studies of other species of mycobacteria, including M. intracellulare, Mycobacterium ulcerans, and Mycobacterium tuberculosis (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). Studies on the use of VNTR analysis for M. intracellulare isolates were reported from Japan and France in 2009 and 2010 (11,13), respectively, and from the United States in 2013 (12). Similar studies on the use of VNTR analysis for M. avium isolates have also been reported, but none of those studies evaluated isolates from the United States (9,15,18).…”

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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: Methodsmentioning

confidence: 99%

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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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“…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). Those studies looked at approximate VNTR sizes based on sequencing of M. intracellulare populations from the two countries.…”

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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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“…Wallace et al (1998Wallace et al ( , 2002 used PFGE to determine that recurrences occurred more commonly from reinfection by new MAC isolates than endogenous reactivation of the initial MAC isolate if patients had completed 10-12 months of negative cultures during therapy. Ichikawa et al (2010) developed a VNTR analysis method for Mycobacterium intracellulare infection and showed that isolate genotypes were stable for up to 4 years. They also reported a patient with an M. intracellulare infection that recurred 1 year after treatment; VNTR analysis showed that isolates collected from the patient before and after recurrence were genetically identical.…”

Section: Discussionmentioning

confidence: 99%

Recurrence of pulmonary Mycobacterium avium complex disease due to endogenous reactivation

et al. 2014

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statement has shown that patients with pulmonary Mycobacterium avium complex (MAC) disease who complete 10-12 months of negative cultures on therapy but then have either single or multiple positive MAC cultures are more likely to have reinfection with a new MAC strain.Case presentation: A 63-year-old woman was diagnosed with pulmonary disease caused by clarithromycin (CAM)-susceptible MAC. Before initiating chemotherapy using a four-drug regimen containing CAM, an investigation of the patient's residential bathroom was conducted and one of the M. avium isolates recovered from the bathtub inlet was found to be genetically identical to sputum-derived isolates by variable number tandem repeats analysis using M. avium tandem repeat loci (MATR-VNTR). A second investigation of the bathroom during chemotherapy showed no M. avium isolates, and five consecutive sputum cultures were negative for 12 months until chemotherapy was discontinued. A recurrence occurred 3 months after the end of chemotherapy (at age 65 years). A third investigation of the bathroom was performed and MATR-VNTR analysis revealed that the VNTR profile of the M. avium isolates recovered from the sputum at recurrence was identical to that of the isolates recovered from the sputum at initial diagnosis and the bathroom at the first investigation. Conclusion:The recurrence occurred due to endogenous reactivation of the initial M. avium isolate despite drug treatment for 12 months after sputum culture conversion. Further genetic analyses of MAC isolates recovered from patients and environments should be encouraged.

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Molecular typing of Mycobacterium intracellulare using multilocus variable-number of tandem-repeat analysis: identification of loci and analysis of clinical isolates

Cited by 25 publications

References 20 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

Recurrence of pulmonary Mycobacterium avium complex disease due to endogenous reactivation

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