Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-64, Belonging to the INT1 Genotype

Kim, Byoung-Jun; Choi, Beom-Soon; Lim, Jong‐Sung; Choi, Ik‐Young; Kook, Yoon Hoh; Kim, Bumjoon J.

doi:10.1128/jb.00471-12

Cited by 19 publications

(13 citation statements)

References 8 publications

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“…Strain comparison of this species has been dependent upon pulsed-field gel electrophoresis (PFGE) [13,14], which is expensive, technically difficult, and time consuming, but its genome has been recently sequenced [15][16][17]. Now, sequence-based epidemiological characterization of M. intracellulare strains may be achieved [2].…”

Section: Introductionmentioning

confidence: 99%

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

Chen

Zhang

Peng

2017

J Infect Dev Ctries

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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.

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Section: Introductionmentioning

confidence: 99%

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

Chen

Zhang

Peng

2017

J Infect Dev Ctries

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“…Efforts to compare isolates of Mycobacterium intracellulare have been difficult, as the species has no known unique, multicopy insertional elements, and until recently the genome had not been sequenced (1)(2)(3). Strain comparison of this species has been dependent upon pulsed-field gel electrophoresis (PFGE) (4,5), which is expensive, technically difficult, and time-consuming.…”

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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“…CP003323.1), and MOTT-64 (GenBank accession no. CP003324.1)-the latter two were clinical isolates from Korean patients (2,3,4 Nucleotide sequence accession numbers. The whole-genome sequence of M.i.198 has been deposited in DDBJ/EMBL/GenBank under the accession numbers BAGQ01000001 to BAGQ01000149.…”

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Whole-Genome Sequence of the Hypervirulent Clinical Strain Mycobacterium intracellulare M.i.198

et al. 2012

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eWe report herein the draft genome sequence of Mycobacterium intracellulare clinical strain M.i.198, which consistently exhibits hypervirulence in human patients, human macrophages in vitro, and immunocompetent mice. N ontuberculous mycobacteria are of great clinical importance with respect to the recent increasing prevalence of nontuberculous mycobacterioses, such as Mycobacterium avium complex (MAC) disease, which is difficult to treat without specific antibiotics (1). However, the bacteriological etiology of nontuberculous mycobacteria remains to be elucidated. We identified a hypervirulent Mycobacterium intracellulare strain (M.i.198) from an immunocompetent patient with pulmonary MAC disease (5). To help understand the genetic background of the virulence, we performed whole-genome sequencing of strain M.i.198.We sequenced M. intracellulare M.i.198 genomic DNA on a Roche 454 FLX Titanium sequencer and assembled the reads using the software program Newbler v2.3. A total of 924,616 reads was generated, with an average read length of 246 bp, yielding a total sequence of 227,524,944 bp.The assembled sequences contained 149 contigs, and the length of all contigs combined was 5,406,664 bp, with a GϩC ratio of 68.0%. The average coverage depth was 42.1ϫ, the N 50 contig size was 90,025 bp, the average contig was 40,008 bp long, and the longest contig was 453,296 bp. The final assembly comprised 122 contigs in five scaffolds (99.7% of contig bases). We constructed an optical map (OpGen) of strain M.i.198 with the NheI restriction enzyme, yielding 311 ordered restriction fragments (average fragment size, 16 kb).

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Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-64, Belonging to the INT1 Genotype

Cited by 19 publications

References 8 publications

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

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

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

Whole-Genome Sequence of the Hypervirulent Clinical Strain Mycobacterium intracellulare M.i.198

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