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Infection, Genetics and Evolution :... Aug 2022Phylogenetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis (MTB) contribute to regional differences in drug resistance. The emergence...
Phylogenetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis (MTB) contribute to regional differences in drug resistance. The emergence of pre-extensively drug resistant tuberculosis (Pre-XDR-TB) becomes obstacles to achieve End TB strategy in Bangladesh. This cross-sectional study was conducted to identify the strains of different lineages of MTB, their variations of distribution among Pre-XDR-TB cases and to observe the linkage of particular strains of MTB with drug resistance. A total of 33 Pre-XDR-TB isolates were enrolled in this study. All isolates were confirmed as MTB by MPT 64 antigen detection and genotyped by 24 loci Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeats (MIRU-VNTR) analysis. Drug resistance was detected by second line Line probe assay (LPA). Beijing was the predominant strain 16 (48.48%), followed by Delhi/CAS 5(15.15%), LAM 4 (12.12%) and Harlem 3(9.10%), EAI 2(6.06%), Cameroon 2(6.06%) and NEW-1 1(3.03%). There were 31 different genotypes consisting of 2 clusters and 29 singletons. All the clustered strains were belonged to Beijing lineage. Recent transmission occurred manly by Beijing strains, showed low transmission rate (12.1%). Of 33 isolates 30(90.90%) were Fluoroquinolones resistant, the mutations involved was Asp94Gly in gyr A MUT 3C gene 13(39.39%) in quinolone resistance determining region (QRDR) followed by 11 (33.33%) in gyr A MUT 1. Three (9.10%) isolates showed resistant to injectable 2nd line drugs and all mutation occurs in G1484T of rrs MUT 2. Beijing lineage was predominant in treatment failure and relapse cases. Levofloxacin was resistant to all Pre-XDR-TB cases, but moxifloxacin showed low level resistance. QUB 26 was the most discriminatory locus (0.85) among 24 loci whereas MIRU 2 was the least (0.03). 24 loci MIRU-VNTR analysis shows high discriminatory index (0.71), found to be powerful tool for genotyping of Pre-XDR-TB, which is the first study in Bangladesh that enhanced the current TB control policy.
Topics: Bangladesh; Cross-Sectional Studies; Drug Resistance, Multiple, Bacterial; Extensively Drug-Resistant Tuberculosis; Genotype; Humans; Minisatellite Repeats; Mycobacterium tuberculosis; Phylogeny; Tuberculosis, Multidrug-Resistant; Tuberculosis, Pulmonary
PubMed: 35595025
DOI: 10.1016/j.meegid.2022.105304 -
Nucleic Acids Research May 2021Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole...
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.
Topics: Alleles; Datasets as Topic; Enhancer Elements, Genetic; Gene Expression Regulation; Genome, Human; Humans; Minisatellite Repeats; Polymorphism, Genetic; Population; Transcription Initiation Site; Whole Genome Sequencing
PubMed: 33849068
DOI: 10.1093/nar/gkab224 -
Veterinary Microbiology Oct 2020Mycoplasma hyorhinis is a swine pathogen bacterium, which causes significant economic losses. The infection spreads through direct contact between the animals. Powerful...
Mycoplasma hyorhinis is a swine pathogen bacterium, which causes significant economic losses. The infection spreads through direct contact between the animals. Powerful genotyping methods like PCR based multi-locus sequence typing (MLST) and multiple-locus variable-number tandem-repeat analysis (MLVA) are necessary to monitor the infections and to conduct epidemiological investigations; hence supporting the control of the disease. The aims of the present study were to examine M. hyorhinis isolates originating mainly from Hungary with MLST and MLVA developed in the study, and to compare the results of the two typing methods. To characterize 39 M. hyorhinis isolates and the type strain (NCTC 10,130), six house-keeping genes were selected for MLST and six tandem-repeat regions were chosen for MLVA. We were able to differentiate 31 sequence types and 37 genotypes within the 40 analyzed isolates by the MLST and the MLVA, respectively. With the combination of the two newly developed assays all examined isolates were distinguished with the exception of the ones originating from the same animal. The developed MLST assay provided a robust and high resolution phylogenetic tree, while the MLVA system is suitable for the differentiation of closely related isolates from the same farm, hence the assay is appropriate for epidemiologic studies.
Topics: Animals; Genotype; Minisatellite Repeats; Multilocus Sequence Typing; Mycoplasma Infections; Mycoplasma hyorhinis; Phylogeny; Swine; Swine Diseases
PubMed: 32956967
DOI: 10.1016/j.vetmic.2020.108836 -
BMC Microbiology Sep 2021The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal...
BACKGROUND
The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal samples, cow's milk, cattle beef, human urine, and ear discharge were screened for 12 virulence genes, phenotypic and genotypic antimicrobial resistance, and multiple-locus variable-number tandem-repeat analysis (MLVA).
RESULTS
The majority of strains harbored Shiga toxin 1 (stx) and stx, stx and stx, and ehxA genes, while a minority harbored stx subtype and eaeA. We identified 10 stx gene combinations; most of strains 31/60 (51.7%) exhibited four copies of stx genes, namely the stx, stx, stx, and stx, and the strains exhibited a high range of multiple antimicrobial resistance indices. The resistance genes blaCTX-M-1 and blaTEM were detected. For the oxytetracycline resistance genes, most of strains contained tetA, tetB, tetE, and tetG while the tetC was present at low frequency. MLVA genotyping resolved 26 unique genotypes; genotype 21 was highly prevalent. The six highly discriminatory loci DI = 0.9138 are suitable for the preliminary genotyping of STEC from animals and humans.
CONCLUSIONS
The STEC isolated from animals are virulent, resistant to antimicrobials, and genetically diverse, thus demands greater attention for the potential risk to human.
Topics: Animals; Cattle; Chickens; Drug Resistance, Bacterial; Egypt; Escherichia coli Infections; Farmers; Feces; Genes, Bacterial; Genotype; Humans; Minisatellite Repeats; Serogroup; Shiga-Toxigenic Escherichia coli; Virulence
PubMed: 34556033
DOI: 10.1186/s12866-021-02308-w -
Biomedica : Revista Del Instituto... Mar 2022Fusarium is a very heterogeneous group of fungi, difficult to classify, with a wide range of living styles, acting as saprophytes, parasites of plants, or pathogens for...
INTRODUCTION
Fusarium is a very heterogeneous group of fungi, difficult to classify, with a wide range of living styles, acting as saprophytes, parasites of plants, or pathogens for humans and animals. Prevalence of clinical fusariosis and lack of effective treatments have increased the interest in the precise diagnosis, which implies a molecular characterization of Fusarium populations.
OBJECTIVE
We compared different genotyping markers in their assessment of the genetic variability and molecular identification of clinical isolates of Fusarium.
MATERIALS AND METHODS
We evaluated the performance of the fingerprinting produced by two random primers: M13, which amplifies a minisatellite sequence, and (GACA)4, which corresponds to a simple repetitive DNA sequence. Using the Hunter Gaston Discriminatory Index (HGDI), an analysis of molecular variance (AMOVA), and a Mantel test, the resolution of these markers was compared to the reference sequencing-based and PCR genotyping methods.
RESULTS
The highest HGDI value was associated with the M13 marker followed by (GACA)4. AMOVA and the Mantel tests supported a strong correlation between the M13 classification and the reference method given by the partial sequencing of the transcription elongation factor 1-alpha (TEF1-α) and rDNA 28S.
CONCLUSION
The strong correlation between the M13 classification and the sequencingbased reference together with its higher resolution demonstrates its adequacy for the characterization of Fusarium populations.
Topics: Animals; Biomarkers; Colombia; DNA Primers; Fusarium; Genotype; Microsatellite Repeats
PubMed: 35471167
DOI: 10.7705/biomedica.5869 -
Nature Communications Sep 2023Markedly expanded tandem repeats (TRs) have been correlated with ~60 diseases. TR diversity has been considered a clue toward understanding missing heritability....
Markedly expanded tandem repeats (TRs) have been correlated with ~60 diseases. TR diversity has been considered a clue toward understanding missing heritability. However, haplotype-resolved long TRs remain mostly hidden or blacked out because their complex structures (TRs composed of various units and minisatellites containing >10-bp units) make them difficult to determine accurately with existing methods. Here, using a high-precision algorithm to determine complex TR structures from long, accurate reads of PacBio HiFi, an investigation of 270 Japanese control samples yields several genome-wide findings. Approximately 322,000 TRs are difficult to impute from the surrounding single-nucleotide variants. Greater genetic divergence of TR loci is significantly correlated with more events of younger replication slippage. Complex TRs are more abundant than single-unit TRs, and a tendency for complex TRs to consist of <10-bp units and single-unit TRs to be minisatellites is statistically significant at loci with ≥500-bp TRs. Of note, 8909 loci with extended TRs (>100b longer than the mode) contain several known disease-associated TRs and are considered candidates for association with disorders. Overall, complex TRs and minisatellites are found to be abundant and diverse, even in genetically small Japanese populations, yielding insights into the landscape of long TRs.
Topics: Humans; Genome, Human; Tandem Repeat Sequences; Minisatellite Repeats; Algorithms; Genetic Drift
PubMed: 37709751
DOI: 10.1038/s41467-023-41262-1 -
Frontiers in Cellular and Infection... 2022Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences,...
SETTING
Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi.
OBJECTIVES
We aimed to identify the distribution of various genotypes of among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital.
PATIENTS AND METHODS
Genotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed.
RESULTS
A total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance.
CONCLUSION
The Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.
Topics: Humans; Mycobacterium tuberculosis; Minisatellite Repeats; Genetic Variation; Genotype; Tuberculosis, Lymph Node; Nontuberculous Mycobacteria
PubMed: 36310875
DOI: 10.3389/fcimb.2022.953443 -
Nature Communications Apr 2021Variable number tandem repeats (VNTRs) account for significant genetic variation in many organisms. In humans, VNTRs have been implicated in both Mendelian and complex...
Variable number tandem repeats (VNTRs) account for significant genetic variation in many organisms. In humans, VNTRs have been implicated in both Mendelian and complex disorders, but are largely ignored by genomic pipelines due to the complexity of genotyping and the computational expense. We describe adVNTR-NN, a method that uses shallow neural networks to genotype a VNTR in 18 seconds on 55X whole genome data, while maintaining high accuracy. We use adVNTR-NN to genotype 10,264 VNTRs in 652 GTEx individuals. Associating VNTR length with gene expression in 46 tissues, we identify 163 "eVNTRs". Of the 22 eVNTRs in blood where independent data is available, 21 (95%) are replicated in terms of significance and direction of association. 49% of the eVNTR loci show a strong and likely causal impact on the expression of genes and 80% have maximum effect size at least 0.3. The impacted genes are involved in diseases including Alzheimer's, obesity and familial cancers, highlighting the importance of VNTRs for understanding the genetic basis of complex diseases.
Topics: Alleles; Cerebral Cortex; Cohort Studies; Gene Expression Regulation; Genetic Loci; Genotype; Humans; Minisatellite Repeats; Reproducibility of Results
PubMed: 33824302
DOI: 10.1038/s41467-021-22206-z -
European Journal of Human Genetics :... Mar 2021The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal...
The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.
Topics: Chromosomes, Human, Y; Evolution, Molecular; Haplotypes; Human Migration; Humans; Male; Minisatellite Repeats; Pedigree; Polymorphism, Single Nucleotide; Scandinavian and Nordic Countries; United Kingdom
PubMed: 33139852
DOI: 10.1038/s41431-020-00747-z -
PloS One 2019Recurrent tuberculosis (TB) is one of the main challenges in TB control. Genotyping based on Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats...
INTRODUCTION
Recurrent tuberculosis (TB) is one of the main challenges in TB control. Genotyping based on Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) has been widely used to differentiate between relapse and reinfection, which are the two main causes of recurrent TB. There is a lack of data regarding the causes of TB recurrence in Georgia, and while differentiating between relapse and reinfection plays a key role in defining appropriate interventions, the required genotyping methodologies have not been implemented. The objective of this study was to implement MIRU-VNTR genotyping at the National Center for Tuberculosis and Lung Diseases (NCTBLD) and differentiate between relapse and reinfection in multidrug resistant (MDR-) TB patients from Tbilisi, Georgia.
METHODS
Recurrent MDR tuberculosis cases from 2014-2016 diagnosed at NCTLD were included in the study when bacterial samples from both episodes were available. Genotyping based on the MIRU-VNTR 24 loci was implemented and used for differentiating between relapse and reinfection. Paired samples showing the same MIRU-VNTR pattern or one locus difference were classified as relapse, while two and more loci differences were treated as reinfection. Exact logistic regression was used to identify predictors of recurrence.
RESULTS
Thirty two MDR-TB patients (64 samples) were included and MIRU-VNTR 24 typing was performed on the corresponding paired samples. Of the 32 patients, 25 (83.3%) were identified as relapse while 5 (16.7%) were due to re-infection. Patients with a history of incarceration were significantly associated with TB reinfection (p< 0.05).
CONCLUSION
Recurrent TB in MDR patients in Georgia are mainly caused by relapse, raising concerns on the efficacy of the TB control program. An association between incarceration and reinfection likely reflects high levels of ongoing TB transmission in prisons, indicating the need for better TB infection control measures in these settings. Our results add to the rationale for implementing genotypic surveillance of TB more broadly to support TB control in Georgia.
Topics: Adult; DNA, Bacterial; Female; Georgia (Republic); Humans; Male; Middle Aged; Minisatellite Repeats; Molecular Typing; Mycobacterium tuberculosis; Odds Ratio; Public Health Surveillance; Recurrence; Tuberculosis
PubMed: 31626647
DOI: 10.1371/journal.pone.0223610