Molecular Typing of Mycobacterium tuberculosis Strains with a Common Two-Band IS6110 Pattern

We conducted a population-based molecular typing of all Mycobacterium tuberculosis isolates obtained in Alabama since 1994. Of 2,452 isolates, 1,013 (41%) had fewer than 6 bands of IS6110; 348 (14%) had a single two-band pattern (JH2). With conventional epidemiologic methods, we identified three groups of related patients with JH2 isolates. Spoligotyping and pattern of variable number of tandem repeats identified 10 molecular groups; two found by conventional methods were subdivided

Molecular Differentiation of Mycobacterium tuberculosis Strains without IS6110 Insertions

By using standard restriction fragment length polymorphism, 6 zero-copy IS6110 Mycobacterium tuberculosis isolates were identified from 1,180 Maryland isolates as part of the National Tuberculosis Genotyping Surveillance Network Project. By using various genotyping methods, we demonstrated that this zero band cluster can be differentiated into six genotypes

Evaluation Method, Dataset Size or Dataset Content: How to Evaluate Algorithms for Image Matching?

Most vision papers have to include some evaluation work in order to demonstrate that the algorithm proposed is an improvement on existing ones. Generally, these evaluation results are presented in tabular or graphical forms. Neither of these is ideal because there is no indication as to whether any performance differences are statistically significant. Moreover, the size and nature of the dataset used for evaluation will obviously have a bearing on the results, and neither of these factors are usually discussed. This paper evaluates the effectiveness of commonly used performance characterization metrics for image feature detection and description for matching problems and explores the use of statistical tests such as McNemar’s test and ANOVA as better alternatives

Genetic Diversity of Mycobacterium tuberculosis Isolates from Tibetans in Tibet, China

BACKGROUND: Tuberculosis (TB) is a serious health problem in Tibet where Tibetans are the major ethnic group. Although genotyping of Mycobacterium tuberculosis (M. tuberculosis) isolates is a valuable tool for TB control, our knowledge of population structure of M. tuberculosis circulating in Tibet is limited. METHODOLOGY/PRINCIPAL FINDINGS: In our study, a total of 576 M. tuberculosis isolates from Tibetans in Tibet, China, were analyzed via spoligotyping and 24-locus MIRU-VNTR. The Beijing genotype was the most prevalent family (90.63%, n = 522). Shared-type (ST) 1 was the most dominant genotype (88.89%, n = 512). We found that there was no association between the Beijing genotype and sex, age and treatment status. In this sample collection, 7 of the 24 MIRU-VNTR loci were highly or moderately discriminative according to their Hunter-Gaston discriminatory index. An informative set of 12 loci had similar discriminatory power with 24 loci set. CONCLUSIONS/SIGNIFICANCE: The population structure of M. tuberculosis isolates in Tibetans is homogeneous and dominated by Beijing genotype. The analysis of 24-locus MIRU-VNTR data might be useful to select appropriate VNTR loci for the genotyping of M. tuberculosis

The Forest behind the Tree: Phylogenetic Exploration of a Dominant Mycobacterium tuberculosis Strain Lineage from a High Tuberculosis Burden Country

BACKGROUND: Genotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages. METHODOLOGY/PRINCIPAL FINDINGS: We tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission. CONCLUSIONS/SIGNIFICANCE: Standard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications

The Genome of Mycobacterium Africanum West African 2 Reveals a Lineage-Specific Locus and Genome Erosion Common to the M. tuberculosis Complex

Mycobacterium africanum, a close relative of M. tuberculosis, is studied for the following reasons: M. africanum is commonly isolated from West African patients with tuberculosis yet has not spread beyond this region, it is more common in HIV infected patients, and it is less likely to lead to tuberculosis after one is exposed to an infectious case. Understanding this organism's unique biology gets a boost from the decoding of its genome, reported in this issue. For example, genome analysis reveals that M. africanum contains a region shared with “ancient” lineages in the M. tuberculosis complex and other mycobacterial species, which was lost independently from both M. tuberculosis and M. bovis. This region encodes a protein involved in transmembrane transport. Furthermore, M. africanum has lost genes, including a known virulence gene and genes for vitamin synthesis, in addition to an intact copy of a gene that may increase its susceptibility to antibiotics that are insufficiently active against M. tuberculosis. Finally, the genome sequence and analysis reported here will aid in the development of new diagnostics and vaccines against tuberculosis, which need to take into account the differences between M. africanum and other species in order to be effective worldwide

Investigation on Mycobacterium tuberculosis Diversity in China and the Origin of the Beijing Clade

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