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

Microbiology ◽  
2010 ◽  
Vol 156 (2) ◽  
pp. 496-504 ◽  
Author(s):  
Kazuya Ichikawa ◽  
Tetsuya Yagi ◽  
Takayuki Inagaki ◽  
Makoto Moriyama ◽  
Taku Nakagawa ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Variable Number ◽  
Clinical Isolates ◽  
Time Intervals ◽  
Mycobacterium Intracellulare ◽  
Epidemiological Tool ◽  
Disseminated Disease ◽  
Hiv Negative

In addition to its known status as a disseminated disease in HIV-positive patients, Mycobacterium avium complex (MAC) is increasingly recognized as a causative pathogen of respiratory disease in HIV-negative patients. MAC is divided into Mycobacterium avium, and the less-epidemiologically studied Mycobacterium intracellulare. Genetic typing for M. intracellulare using variable number of tandem repeats (VNTR) has not yet been developed. The aim of this study was to identify VNTR loci in the genome of M. intracellulare and apply them as an epidemiological tool to clinical isolates. Here, we identified 25 VNTR loci on the M. intracellulare genome, of which 16 showed variations among clinical isolates in the number of tandem repeat motifs. Among the 74 M. intracellulare isolates, 50 genotypes were distinguished using the 16 VNTR loci, resulting in a Hunter Gaston's discriminatory index of 0.988. Moreover, all 16 VNTR loci were stable in different sets of isolates recovered within time intervals ranging from 2 to 1551 days from 14 separate patients. These results indicate that for use as epidemiological markers of M. intracellulare, the loci in this VNTR assay are highly discriminating and stable over time.

scholarly journals Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1313-1320 ◽  
Author(s):  
John S Taylor ◽  
Felix Breden
Keyword(s):  
Tandem Repeat ◽  
Poecilia Reticulata ◽  
Tandem Repeats ◽  
Phylogenetic Reconstruction ◽  
Variable Number ◽  
Repeat Motif ◽  
Raw Material ◽  
Direct Repeats ◽  
Mt Dna ◽  
Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

Convenient PCR method for variable-number tandem-repeat typing of Mycobacterium tuberculosis clinical isolates

2017 ◽  
Vol 139 ◽  
pp. 12-14 ◽  
Author(s):  
Junji Seto ◽  
Takayuki Wada ◽  
Yu Suzuki ◽  
Tatsuya Ikeda ◽  
Katsumi Mizuta ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Clinical Isolates ◽  
Pcr Method

scholarly journals Moxifloxacin Pharmacokinetics/Pharmacodynamics and Optimal Dose and Susceptibility Breakpoint Identification for Treatment of Disseminated Mycobacterium avium Infection

2010 ◽  
Vol 54 (6) ◽  
pp. 2534-2539 ◽  
Author(s):  
Devyani Deshpande ◽  
Shashikant Srivastava ◽  
Claudia Meek ◽  
Richard Leff ◽  
Gerri S. Hall ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Critical Concentration ◽  
Optimal Dose ◽  
Clinical Isolates ◽  
Time Curve ◽  
Avium Infection ◽  
Mycobacterium Avium Intracellulare ◽  
Disseminated Disease ◽  
Susceptibility Breakpoint

ABSTRACT Organisms of the Mycobacterium avium-intracellulare complex (MAC) have been demonstrated to be susceptible to moxifloxacin. However, clinical data on how to utilize moxifloxacin to treat disseminated MAC are scanty. In addition, there have been no moxifloxacin pharmacokinetic-pharmacodynamic (PK/PD) studies performed for MAC infection. We utilized an in vitro PK/PD model of intracellular MAC to study moxifloxacin PK/PD for disseminated disease. Moxifloxacin doses, based on a serum half-life of 12 h, were administered, and the 0- to 24-h area under the concentration-time curve (AUC0-24) to MIC ratios associated with 1.0 log10 CFU/ml per week kill and 90% of maximal kill (EC90) were identified. The AUC0-24/MIC ratio associated with 1.0 log10 CFU/ml kill was 17.12, and that with EC90 was 391.56 (r 2 = 0.97). Next, the moxifloxacin MIC distribution in 102 clinical isolates of MAC was identified. The median MIC was 1 to 2 mg/liter. Monte Carlo simulations of 10,000 patients with disseminated MAC were performed to determine the probability that daily moxifloxacin doses of 400 and 800 mg/day would achieve or exceed 1.0 log10 CFU/ml per week kill or EC90. Doses of 400 and 800 mg/day achieved the AUC0-24/MIC ratio of 17.12 in 64% and 92% of patients, respectively. The critical concentration of moxifloxacin against MAC was identified as 0.25 mg/liter in Middlebrook media. The proposed susceptibility breakpoint means that a larger proportion of clinical isolates is resistant to moxifloxacin prior to therapy. For patients infected with susceptible isolates, however, 800 mg a day should be examined for safety and efficacy for disseminated M. avium disease.

Variable Number of Tandem Repeats in Zygosity Diagnosis in Twins

1990 ◽  
Vol 39 (4) ◽  
pp. 473-477 ◽  
Author(s):  
S. Costanzi Porrini ◽  
A. Sciarra ◽  
N. Sulli ◽  
M. Piane ◽  
R. Gualtieri ◽  
...  
Keyword(s):  
Population Genetics ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Variable Number ◽  
Hla Typing ◽  
Blood Group Antigens ◽  
Length Polymorphisms ◽  
Dna Restriction ◽  
Restriction Fragment Length

AbstractThe use of DNA restriction fragment length polymorphisms (RFLP) to analyze variable number of tandem repeat (VNTR) sequences dispersed in the human genome, has become a powerful tool for the study of population genetics due to the very substantial polymorphism involved. Because the markers usually employed for twin zygosity determination (such as sex combination, placentation, HLA typing, blood group antigens, etc) may not be uniformly informative, we propose the use of synthetic olygonucleotides, representing VNTR “core” sequences, for the determination of zygosity in twins.

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

2020 ◽  
Vol 8 (9) ◽  
pp. 1315
Author(s):  
Jeong-Ih Shin ◽  
Jong-Hun Ha ◽  
Dong-Hae Lee ◽  
Jeong-Gyu Choi ◽  
Kyu-Min Kim ◽  
...  
Keyword(s):  
Minimum Spanning Tree ◽  
Variable Number ◽  
Clinical Isolates ◽  
Epidemiological Analysis ◽  
Mycobacterium Intracellulare ◽  
Fundamental Information ◽  
Tandem Repetition ◽  
Comparative Results ◽  
Geographical Characteristics ◽  
Discriminatory Index

Mycobacterium intracellulare is a leading cause of nontuberculous mycobacterial pulmonary disease, with a rapidly increasing prevalence worldwide. This bacterium, commonly distributed in soil and water, is known to be transmitted through the environment rather than between people. Therefore, it is imperative to establish distinguishable genotyping methods to understand the clinical outcome, disease relapses, and epidemiology. Therefore, in this study, representative band-based genotyping methods were performed using M. intracellualre clinical isolates, and their Hunter–Gaston discriminatory index (HGDI) was 0.947, 0.994, and 1 for variable number tandem repetition (VNTR), VNTR-mycobacterial interspersed repetitive units, pulsed field gel electrophoresis, and repetitive sequence based-PCR, respectively. Although VNTR showed relatively low HGDI, co-infection with other M. intracellualre strains could be determined by loci showing allele diversity from 0 to 0.69. Additionally, genetic distance of clinical isolates from Gyeongnam/Korea, and other regions/countries were visualized by minimum spanning tree (MST) using the globally available VNTR profiles. The results of MST revealed that M. intracellulare isolated from patients in Gyeongnam/Korea had specific VNTR genotypes, which may be evidence of the geographic distribution of M. intracellulare specific genotypes. The comparative results of genotyping techniques and geographical characteristics in this study may provide fundamental information for the epidemiology of M. intracellulare.

scholarly journals Feature of Adhesins Produced by Human Clinical Isolates of Mycobacterium intracellulare, Mycobacterium intracellulare subsp. chimaera and Closely Related Species

2020 ◽  
Vol 8 (8) ◽  
pp. 1154
Author(s):  
Louise H. Lefrancois ◽  
Thierry Cochard ◽  
Maxime Branger ◽  
Olivia Peuchant ◽  
Cyril Conde ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Related Species ◽  
Fluorescent Protein ◽  
Severe Disease ◽  
A549 Cells ◽  
Clinical Isolates ◽  
Heparin Binding ◽  
Closely Related Species ◽  
Mycobacterium Intracellulare ◽  
Green Fluorescent

The Mycobacterium avium complex includes two closely related species, Mycobacterium avium and Mycobacterium intracellulare. They are opportunistic pathogens in humans and responsible for severe disease in a wide variety of animals. Yet, little is known about factors involved in their pathogenicity. Here, we identified, purified and characterized adhesins belonging to the heparin-binding hemagglutinin (HBHA) and laminin-binding protein (LBP) family from M. intracellulare ATCC13950 and examined clinical isolates from patients with different pathologies associated with M. intracellulare infection for the presence and conservation of HBHA and LBP. Using a recombinant derivative strain of M. intracellulare ATCC13950 producing green fluorescent protein and luciferase, we found that the addition of heparin inhibited mycobacterial adherence to A549 cells, whereas the addition of laminin enhanced adherence. Both HBHA and LBP were purified by heparin-Sepharose chromatography and their methylation profiles were determined by mass spectrometry. Patients with M. intracellulare infection mounted strong antibody responses to both proteins. By using PCR and immunoblot analyses, we found that both proteins were highly conserved among all 17 examined clinical M. intracellulare isolates from patients with diverse disease manifestations, suggesting a conserved role of these adhesins in M. intracellulare virulence in humans and their potential use as a diagnostic tool.

scholarly journals Human-specific tandem repeat expansion and differential gene expression during primate evolution

2019 ◽  
Vol 116 (46) ◽  
pp. 23243-23253 ◽  
Author(s):  
Arvis Sulovari ◽  
Ruiyang Li ◽  
Peter A. Audano ◽  
David Porubsky ◽  
Mitchell R. Vollger ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Variable Number ◽  
Specific Expression ◽  
Sequence Composition ◽  
Transcription Profiles ◽  
Long Read ◽  
Repeat Expansions ◽  
Human Specific

Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are important sources of natural and disease-causing variation, yet they have been problematic to resolve in reference genomes and genotype with short-read technology. We created a framework to model the evolution and instability of STRs and VNTRs in apes. We phased and assembled 3 ape genomes (chimpanzee, gorilla, and orangutan) using long-read and 10x Genomics linked-read sequence data for 21,442 human tandem repeats discovered in 6 haplotype-resolved assemblies of Yoruban, Chinese, and Puerto Rican origin. We define a set of 1,584 STRs/VNTRs expanded specifically in humans, including large tandem repeats affecting coding and noncoding portions of genes (e.g., MUC3A, CACNA1C). We show that short interspersed nuclear element–VNTR–Alu (SVA) retrotransposition is the main mechanism for distributing GC-rich human-specific tandem repeat expansions throughout the genome but with a bias against genes. In contrast, we observe that VNTRs not originating from retrotransposons have a propensity to cluster near genes, especially in the subtelomere. Using tissue-specific expression from human and chimpanzee brains, we identify genes where transcript isoform usage differs significantly, likely caused by cryptic splicing variation within VNTRs. Using single-cell expression from cerebral organoids, we observe a strong effect for genes associated with transcription profiles analogous to intermediate progenitor cells. Finally, we compare the sequence composition of some of the largest human-specific repeat expansions and identify 52 STRs/VNTRs with at least 40 uninterrupted pure tracts as candidates for genetically unstable regions associated with disease.

scholarly journals Mycobacterioses in dogs and cats from Buenos Aires, Argentina

2017 ◽  
Vol 29 (5) ◽  
pp. 729-732 ◽  
Author(s):  
Soledad Barandiaran ◽  
Marcela Martínez Vivot ◽  
Elvira Falzoni ◽  
María J. Marfil ◽  
Gabriela Pérez Tort ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Tandem Repeat ◽  
Potential Risk ◽  
Buenos Aires ◽  
Variable Number Tandem Repeat ◽  
Clinical Signs ◽  
Variable Number ◽  
Molecular Testing ◽  
Full Characterization

Mycobacterioses can produce nonspecific clinical signs in dogs and cats that make diagnosis difficult. Furthermore, the full characterization of mycobacterial agents is not always possible or practical. We characterized mycobacteria detected through cytology in 12 dogs and 7 cats with generalized clinical signs from the province of Buenos Aires in Argentina. In dogs, molecular testing confirmed the presence of Mycobacterium avium subsp. hominissuis (MAH) in 8 cases and M. fortuitum in 1 case. All dogs were Miniature Schnauzers, suggesting that this breed may be more susceptible to M. avium than other dog breeds. The cat isolates were 2 M. bovis, 1 M. fortuitum, and 1 MAH. Mycobacterial interspersed repetitive unit–variable-number tandem repeat patterns suggested possible links with cattle, swine, and humans studied previously in Argentina. The results show that pets may act as susceptible hosts with the potential risk of transmitting the infection to humans and other animals.

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