Variable-number tandem repeat markers for Mycobacterium intracellulare genotyping: comparison to the 16S rRNA gene sequencing

Abstract

Introduction: Characterizing Mycobacterium intracellulare responsible for nontuberculous mycobacterial (NTM) infections may aid in controlling outbreaks. This study aimed to compare 16S ribosomal ribonucleic acid (rRNA) sequencing and variable-number tandem repeat (VNTR) genotyping of M. intracellulare strains isolated from clinical samples, and to characterize VNTR clusters associated with NTM infections or cavity formation. Methodology: Sputum samples were obtained from 77 HIV-negative patients with pulmonary disease between 2009 and 2013. One M. intracellulare strain was isolated from each patient and genotyped using 16S rRNA and eight loci VNTR sequencing. Results: Single nucleotide polymorphism (SNP) genotyping identified seven point mutations at nucleotide positions 101, 178, 190, 252, 382, 443, and 490 in 16S rRNA, and four SNP patterns were identified: type 1 (16 strains), 2 (41 strains), 3 (11 strains), and 4 (1 strain); 5 strains had unique SNP patterns. VNTR genotyping identified VNTR12 as the most discriminating marker (allelic diversity 0.692). VNTR3 was the most homogeneous marker (allelic diversity 0.518), but each locus had high discriminating ability. The 77 strains were clustered according to the unpaired group method using arithmetic averages: cluster 1 (17 strains), 2 (43 strains), 3 (9 strains), and 4 (4 strains); 4strains had unique SNP patterns. Overall, over 90% strains were matched to similar SNP and VNTR groupings. VNTR clusters were associated with NTM infection (p =0.007) and presence of a cavity (p =0.042). Both methods distinguished four subtypes of M. intracellulare, which corresponded. Conclusions: VNTRs may represent an effective, user-friendly, low-cost typing technique.

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

“…The study used a combination of MIRU and VNTR loci, and the association of VNTR clusters, which had clinical significance. NTM infection and the presence of cavity were also related to the VNTR type [77]. Additionally, the study confirmed the similarity between VNTR and PFGE profiling of M. intracellulare patient isolates using seven MIRU loci.…”

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 .…”