• Using an example of the emerging multidrug-resistant strain of Mycobacterium tuberculosis , we showed the value of informed understanding when in silico prediction from NGS data achieved with available bioinformatics tools is placed within the context of the existing genotyping framework. (cdc.gov)
  • the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. (jci.org)
  • As repeatedly stated, one third of the world's population is latently infected with Mycobacterium tuberculosis and 10 % of these people will develop active disease at some point in their life. (tuberculosistextbook.com)
  • EBV DNA positivity was associated with younger age, shorter duration of HIV diagnosis, lower CSF glucose levels, higher CSF protein and white blood cell levels, and a positive CSF Mycobacterium tuberculosis result. (bvsalud.org)
  • Molecular screening of CSF for other possible causes of infection identified Mycobacterium tuberculosis in 30.1% and cytomegalovirus (CMV) in 10.5% of samples. (bvsalud.org)
  • Kolb J, Hillemann D, Möbius P, Reetz J, Lahiri A, Lewin A, Rüsch-Gerdes S, Richter E. Genetic characterization of German Mycobacterium avium strains isolated from different hosts and specimens by multilocus sequence typing. (fz-borstel.de)
  • As such, VNTRs can be used to distinguish strains of bacterial pathogens. (wikipedia.org)
  • Several molecular typing methods have been developed to differentiate between M. avium subspecies and strains, such as single nucleotide polymorphism (SNP) typing and mini-satellite sequence analysis-mycobacterial interspersed repetitive-unit variable-number tandem repeats (MIRU-VNTR) ( 5 ). (frontiersin.org)
  • In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains ofM. (9lib.org)
  • Although metagenomic tools exist to classify strains in a metagenomic sample, most tools have been developed for more divergent species, and therefore cannot provide the sensitivity required to disentangle strains within closely related bacterial species such asM. (9lib.org)
  • tuberculosis strains in whole genome sequencing data. (9lib.org)
  • On the basis of 24 mycobacterial interspersed repetitive unit variable number tandem repeats clustering and robust phylogenetic single-nucleotide polymorphisms, SIT264 and SIT266 isolates are assigned to the Latin American-Mediterranean lineage of M. tuberculosis ( 2 ). (cdc.gov)
  • Note that SITVITBovis also contains limited information on mycobacterial interspersed repetitive units-variable number of tandem repeats when available. (oup.com)
  • Bacterial DNA was subjected to macroarray-based spoligotyping ( 8 ) and whole-genome sequencing on the MiSeq platform (Illumina, San Diego, CA, USA). (cdc.gov)
  • The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. (jci.org)
  • Whole-genome sequencing (WGS) of M. tuberculosis and related mycobacteria is now routine, allowing comparisons across time and space. (jci.org)
  • The third report described Genetic Analysis and isolation from a child's hand with multibacterial synergistic Whole-Genome Sequencing gangrene ( 6 ). (cdc.gov)
  • A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. (wikipedia.org)
  • Repetitive DNA, representing over 40% of the human genome, is arranged in a bewildering array of patterns. (wikipedia.org)
  • The use of restriction enzymes showed that some repeat blocks were interspersed throughout the genome. (wikipedia.org)
  • MIRU-VNTR analysis, on the other hand, uses mini-satellite sequences (tandem repeats of 10-100 nucleotides) dispersed at multiple loci in the bacterial genome. (frontiersin.org)
  • At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. (jci.org)
  • While the genome sequence was already transformative at the time, the past 25 years of progress have substantially increased its impact on TB taxonomy, drug discovery, resistance mechanisms, epidemiology, vaccine development, and pathogenesis. (jci.org)
  • The M. tuberculosis genome has ushered in a quarter century of substantial clinical and public health advancements. (jci.org)
  • First, the complete genome sequence of the tubercle bacillus was deciphered. (tuberculosistextbook.com)
  • Management of patients with multidrug-resistant/extensively drug-resistant tuberculosis in Europe: a TBNET consensus statement. (fz-borstel.de)
  • Spoligotyping is a classical method of M. tuberculosis genotyping, and the SITVIT_WEB database contains data on 7,105 spoligotype patterns of 58,180 isolates from 153 countries ( http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE ). (cdc.gov)
  • We recovered 2 MDR M. tuberculosis isolates of SIT266 from pulmonary tuberculosis patients from northwestern Russia in 2014. (cdc.gov)
  • A phylogenetic for a case of multi-bacterial synergistic gangrene. (cdc.gov)
  • purification of antibodies to bacterial antigens by an immunoadsorbent and a method to quantify their reaction with insoluble bacterial targets. (liverpool.ac.uk)
  • All colonies, regardless of the nucleotide sequence of rpsA , were found to be sensitive to all of the drugs tested except for ethambutol. (frontiersin.org)
  • In this multiple-PI application, we propose to develop and analyze mathematical models of tuberculosis (TB) and HIV epidemics to examine whether targeted use of preventive therapy for latent TB infection (TLTBI) and active TB case-finding may prove more effective, and more cost-effective, than non-targeted use of interventions. (yale.edu)
  • DNA sequencing later showed that other repeats are clustered at specific locations, with tandem repeats being more common than inverted repeats (which may interfere with DNA replication). (wikipedia.org)
  • Minisatellites are a type of DNA tandem repeat sequence, meaning that the sequences repeat one after another without other sequences or nucleotides in between them. (wikipedia.org)
  • The two types of repeat sequences are both tandem but are specified by the length of the repeat sequence. (wikipedia.org)
  • VNTRs can vary in number of repeats from individual to individual, as where some non-VNTR minisatellites have repeat sequences that repeat the same number of times in all individuals containing the tandem repeats in their genomes. (wikipedia.org)
  • European Reference Laboratory Network for TB Members, Balabanova Y. Laboratory diagnosis of paediatric tuberculosis in the European Union/European Economic Area: analysis of routine laboratory data, 2007 to 2011. (fz-borstel.de)
  • Minisatellites are characterized by a repeat sequence of about ten to one hundred nucleotides, and the number of times the sequence repeats varies from about five to fifty times. (wikipedia.org)
  • The sequences of minisatellites are larger than those of microsatellites, in which the repeat sequence is generally 1 to 6 nucleotides. (wikipedia.org)
  • VNTRs, therefore, because they have repeat sequences of ten to one hundred nucleotides in which every repeat is exactly the same, are considered minisatellites. (wikipedia.org)
  • Background: Mixed infections ofMycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. (9lib.org)
  • M. tuberculosis NGS data were deposited in the National Center for Biotechnology Information Sequence Read Archive (project no. (cdc.gov)
  • It constitutes a substantial proportion of the population structure of M. tuberculosis in Belarus, a post-Soviet state in Eastern Europe ( 1 , 2 ), and has been described sporadically in the neighboring provinces in northwestern and central Russia ( 2 - 5 ) and in Latvia ( 6 ). (cdc.gov)
  • Spoligotyping targets a variation of the DR/CRISPR locus, whose evolution in M. tuberculosis occurs through deletion of single or multiple spacers. (cdc.gov)
  • The short sequencing reads were subjected to analysis by using the SpoTyping program ( https://github.com/xiaeryu/SpoTyping ) ( 9 ) and the TGS-TB online tool ( https://gph.niid.go.jp/tgs-tb/ ) ( 10 ) to deduce their spoligoprofile. (cdc.gov)
  • Flanking regions are segments of non-repetitive sequence (shown here as thin lines), allowing the VNTR blocks to be extracted with restriction enzymes and analyzed by RFLP, or amplified by the polymerase chain reaction (PCR) technique and their size determined by gel electrophoresis. (wikipedia.org)
  • The coding regions or exons are interspersed along with the introns in the primary transcript. (cox-inhibitors.com)
  • Electronic supplementary material Additional file 1: The sequences of PCR primers. (cox-inhibitors.com)