IS6110-based global phylogeny of Mycobacterium tuberculosis

Thorne, Nicola; Borrell, Sònia; Evans, Jonathan D.; Magee, Jeffrey C.; Viedma, Darío García de; Bishop, Chloe; González-Martín, Julià; Gharbia, Saheer E.; Arnold, Cath

doi:10.1016/j.meegid.2010.09.011

Cited by 21 publications

(22 citation statements)

References 34 publications

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“…Forty three samples (24.4%) grouped under "unassigned" group. Common fragments seen were exactly the same as the earlier published report by Thorne et al, (2011) except for an additional fragment, 78.4 G, for the CAS lineage. A dendrogram was generated using only the IS6110 FAFLP data ( Figure 2) confirming again the above mentioned lineages in relation to the PGGs.…”

Section: Analysis Of Data Using Bionumerics Software V61supporting

confidence: 78%

“…It has been demonstrated previously that IS6110 FAFLP PCR can be used to delineate the phylogeny of MTBC as shared common fragments can determine the different lineages in a geographical location by comparison with a reference database collection [7]. As limited lineage information is available from strains in Nepal, we have applied the IS6110 method published recently on mapping the IS6110 sites in H37Rv [9] and also carried out rpoB sequencing to further characterize strains from this important region.…”

Section: Discussionmentioning

confidence: 99%

“…Modification of the conventional IS6110 typing method, using differentially labelled primers has allowed characterisation of Mtb isolates into the key genetic lineages more rapidly than traditional methods [7]. This approach can be facilitated with automation, which enables this technique to be performed in a high throughput setting.…”

Section: Introductionmentioning

confidence: 99%

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Insertion Element IS6110 based characterisation of Nepalese tuberculosis strains into different genetic lineages

Moganeradj¹,

Rajendram²,

Khadge³

et al. 2016

Clin Microbiol Infect Dis

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Nepal is geographically located between India and China, a region containing significant Tuberculosis (TB) and Multi-Drug Resistance (MDR-TB) burdens. However, limited information is available on the phylogenetic diversity of Mycobacterium tuberculosis (Mtb) in Nepal. To gain further insight into the diversity of Mtb in Nepal, consecutive clinical samples from 176 newly diagnosed pulmonary tuberculosis patients were collected from two hospitals in Nepal. Insertion Site IS6110 Fluorescent Amplified Fragment Length Polymorphism (FAFLP) PCR and rpoB sequence analysis were carried out on genomic DNA extracts of cultured strains to assign them to accepted genetic lineages and identify MDR-TB. In this study, the IS6110 based characterisation showed a prevalence of 36.36% Central Asian Strain (CAS), 18.75% Beijing, 7.95% Haarlem, 3.97% X, 2.2% each of Latin American Mediterranean (LAM), T-Uganda and T, 1.7% S and 24.4% were unassigned. Further, 3.9% of total M. tuberculosis isolates were of rifampicin resistant genotypes thus indicating that the prevalence of MDR could be higher than the country wide prevalence of MDR among new TB cases (2.2%) as reported by the national drug resistance survey carried out in 2011/2012.

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Section: Analysis Of Data Using Bionumerics Software V61supporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

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Insertion Element IS6110 based characterisation of Nepalese tuberculosis strains into different genetic lineages

Moganeradj¹,

Rajendram²,

Khadge³

et al. 2016

Clin Microbiol Infect Dis

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“…In parallel, the discovery of the Direct Repeat (DR) locus polymorphism, based on the presence/absence of short spacer sequences connecting the DR sequences, and the development of the spacer oligonucleotide typing (spoligotyping) methodology [12], introduced a further tool for genetic analysis of the M. tuberculosis complex that soon became the most practiced typing system used in studies of genetic diversity [13]. In general, the polymorphisms probed by RD deletion analysis and spoligotyping turn out to be largely congruent, as they reflect the clonal population structure of the M. tuberculosis complex [5], [14]–[16], so that the spoligotype families are generally regarded as sublineages within the LSP-defined main lineages [17]; in certain cases, however, spoligotype homoplasy, i.e. identical molecular pattern of the DR locus in strains belonging to different evolutionary lineages, likely resulting from convergent evolution, has been reported [17]–[23].…”

Section: Introductionmentioning

confidence: 99%

Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

et al. 2014

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A sample of 260 Mycobacterium tuberculosis strains assigned to the Euro-American family was studied to identify phylogenetically informative genomic regions of difference (RD). Mutually exclusive deletions of regions RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 and RD761 were found in 202 strains; the RDRio deletion was detected exclusively among the RD174-deleted strains. Although certain deletions were found more frequently in certain spoligotype families (i.e., deletion RD115 in T and LAM, RD174 in LAM, RD182 in Haarlem, RD219 in T and RD726 in the “Cameroon” family), the RD-defined sublineages did not specifically match with spoligotype-defined families, thus arguing against the use of spoligotyping for establishing exact phylogenetic relationships between strains. Notably, when tested for katG463/gyrA95 polymorphism, all the RD-defined sublineages belonged to Principal Genotypic Group (PGG) 2, except sublineage RD219 exclusively belonging to PGG3; the 58 Euro-American strains with no deletion were of either PGG2 or 3. A representative sample of 197 isolates was then analyzed by standard 15-locus MIRU-VNTR typing, a suitable approach to independently assess genetic relationships among the strains. Analysis of the MIRU-VNTR typing results by using a minimum spanning tree (MST) and a classical dendrogram showed groupings that were largely concordant with those obtained by RD-based analysis. Isolates of a given RD profile show, in addition to closely related MIRU-VNTR profiles, related spoligotype profiles that can serve as a basis for better spoligotype-based classification.

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“…The insertion sequence “IS6110" is a transposable element which is present in the members of MTB complex in multiple copies (up to 25 copies), except M. bovis BCG which harbours a single copy and absent in other mycobacteria 13,14. For those reasons the insertion sequence “IS6110” has been reported as the most common target used for the MTB diagnosis in the clinical samples and demonstrated that the detection rate of MTB complex targeting “IS6110” was higher than that of microscopy or MTB culturing with a considerable time 7,12,15,16.…”

Section: Introductionmentioning

confidence: 99%

Comparison of a Dna Based PCR Approach With Conventional Methods for the Detection of Mycobacterium Tuberculosis in Morocco

Zakham¹,

Lahlou²,

Akrim³

et al. 2012

Mediterr J Hematol Infect Dis

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BackgroundWorldwide, tuberculosis (TB) is a major public health problem and the rapid diagnosis and appropriate chemotherapy become the first priority and a serious challenge to improve TB treatment. In the objective of early TB diagnosis and rapid detection of Mycobacterium tuberculosis (MTB) in the clinical specimens, the utility of the Polymerase Chain Reaction (PCR) using the Insertion Sequence 6110 “IS6110" as target was compared to conventional methods.MethodsOut of 305 patients with different clinical manifestations: suspected, new, drug relapse, drug failure and chronic cases were enrolled in this study and tested by mycobacteriological and PCR techniques for the investigation about the tubercle bacilli.ResultsThe results of the in house “IS6110" PCR showed a good sensitivity (92.4%) and high specificity (98.0%), the positive and negative predictive values were 96.4 % and 95.3 % respectively.ConclusionThis study showed clearly that the PCR testing using the “IS6110" in the routine analysis is a potential tool for the rapid TB diagnosis, especially for critical cases and would be of great interest to help the clinician in the misdiagnosed critical cases by the traditional radiology.

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IS6110-based global phylogeny of Mycobacterium tuberculosis

Cited by 21 publications

References 34 publications

Insertion Element IS6110 based characterisation of Nepalese tuberculosis strains into different genetic lineages

Insertion Element IS6110 based characterisation of Nepalese tuberculosis strains into different genetic lineages

Genomic Variability of Mycobacterium tuberculosis Strains of the Euro-American Lineage Based on Large Sequence Deletions and 15-Locus MIRU-VNTR Polymorphism

Comparison of a Dna Based PCR Approach With Conventional Methods for the Detection of Mycobacterium Tuberculosis in Morocco

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