Molecular Typing of Mycobacterium intracellulare Using Pulsed-Field Gel Electrophoresis, Variable-Number Tandem-Repeat Analysis, Mycobacteria Interspersed Repetitive-Unit-Variable-Number Tandem Repeat Typing, and Multilocus Sequence Typing: Molecular Characterization and Comparison of Each Typing Methods

Abstract

ObjectivesMycobacterium intracellulare is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of M. intracellulare is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods.MethodsAntibiotic susceptibility testing, hsp65 and rpoB sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria interspersed repetitive-unit-variable-number tandem-repeat analysis (MIRU-VNTR), and VNTR assay targeting 44 M. intracellulare isolates obtained from patients with pulmonary infections were performed.ResultsAll the antibiotic susceptibility patterns had no association with the molecular and sequence types tested in this study; however, the molecular and sequence types were related with each other. PFGE gave best results for discriminatory capacity, followed by VNTR, MLST, and MIRU-VNTR.ConclusionThe high discriminatory power of PFGE, VNTR, and MLST is enough for differentiating between reinfection and relapse, as well as for other molecular epidemiological usages. The MLST could be regarded as a representative classification method, because it showed the clearest relation with the sequence types.

Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis

“…The overall discriminatory power of the 17-locus typing assay was calculated at 0.66. This was somewhat lower than what was reported for VNTR typing schemes in other NTM, including M. abscessus (13–18 loci, HGDI = 0.96–0.98) 29 , 49 , 50 , M. avium (5–8 loci, HGDI from 0.74 to 0.95) 44 , 51 – 53 or M. intracellulare (15–16 loci, 0.98–0.99) 27 , 45 , 54 , 55 . At the same time, the genetic diversity of the population studied, measured by the number of different VNTR profiles identified per study sample, was found to be rather moderate when compared to other VNTR-typed NTM (GDI = 0.35 vs 0.1–0.84) 25 , 27 , 29 , 44 , 54 – 56 .…”

“…The clustering rate, often used as a proxy for transmission or an outbreak, exceeded, with our method, 80%. This was higher than the analogous rate for M. abscessus (34.2–48.2%) 29 , 49 or M. intracellulare (31–55%) 27 , 54 , 56 and lower than for M. avium (95.6–95.9%) 25 , 44 . Given a long collection time of the study sample (16 years) and the fact that the isolates were of different origins (both environmental and clinical), and from different geographical locales, the overall high CR reflects genome homoplasy, which is a product of convergent evolution, rather than ongoing active transmission.…”

Comparative Evaluation of Band-Based Genotyping Methods for Mycobacterium intracellulare and Its Application for Epidemiological Analysis

“…The second MST analysis was conducted to reconfirm the characteristics of the strains from Gyeongnam, Korea (n = 99), and the comparison with the strains from Seoul, Korea (n = 45; [ 25 ]), was conducted more precisely using 21 loci of VNTR and VNTR-MIRU excluding VNTR 11 and MIRU3 ( Figure 5 ; see also Table S2 in the Supplemental Materials ). As a result, the Gyeongnam-derived strains were found to form genetic clusters (red, green) different from those of Seoul (purple cluster) ( Figure 5 ).…”

Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology

“…The patterns 22 of the two analyses were similar, suggesting that VNTR may be a suitable alternative to PFGE for use in distinguishing recurrence [63]. In addition, M. intracellulare was subjected to antibiotic susceptibility testing, sequencing of the hsp65 and rpoB genes, PFGE, Multilocus sequence typing (MLST), MIRU-VNTR, and VNTR [64]. The discrimination power for M. intracellulare was found to be higher in order of PFGE, VNTR, MLST.…”

“…The discrimination power for M. intracellulare was found to be higher in order of PFGE, VNTR, MLST. Furthermore, it was reported to be useful for distinguishing recurrence [64].…”