TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex

Shabbeer, Amina; Cowan, Lauren S.; Ozcaglar, Cagri; Rastogi, Nalin; Vandenberg, Scott; Yener, Bülent; Bennett, Kristin P.

doi:10.1016/j.meegid.2012.02.010

Cited by 90 publications

(71 citation statements)

References 29 publications

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“…Web tools that allow extracting knowledge contained within huge international databases are becoming increasingly important to visualize epidemiological and demographic characteristics of TB in order to control and monitor global TB epidemic [4,[13][14][15][16]33,35,43]. Algorithms of Artificial Intelligence and Bayesian networks have already proved their efficiency in TB research [44,45].…”

Section: Discussionmentioning

confidence: 99%

“…Throughout in this paper, the order of MIRU loci is as follows: 12-loci MIRU patterns: MIRU 2,4,10,16,20,23,24,26,27, …”

Section: Genotypingmentioning

confidence: 99%

“…http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE) and its earlier version SpolDB4 [14]; MIRU-VNTRplus ( [15]; http:// www.miru-vntrplus.org/MIRU/index.faces); and TB-Lineage ( [16]; http://tbinsight.cs.rpi.edu/run_tb_lineage.html).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Tuberculosis – A global emergency: Tools and methods to monitor, understand, and control the epidemic with specific example of the Beijing lineage

Couvin

Rastogi

2015

Tuberculosis

Self Cite

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Section: Discussionmentioning

confidence: 99%

“…Throughout in this paper, the order of MIRU loci is as follows: 12-loci MIRU patterns: MIRU 2,4,10,16,20,23,24,26,27, …”

Section: Genotypingmentioning

confidence: 99%

See 1 more Smart Citation

Tuberculosis – A global emergency: Tools and methods to monitor, understand, and control the epidemic with specific example of the Beijing lineage

Couvin

Rastogi

2015

Tuberculosis

Self Cite

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“…These spoligotypes were in addition compared in binary code format with the international spoligotyping database of the Pasteur Institute of Guadeloupe (http://www.pasteur-guadeloupe.fr: 8081/SITVIT_ONLINE/) to assign phylogenetic lineages. Isolates which were orphaned, those with contiguous deletion of spacers 33 to 36 and spacer 40 or 43 or both spacer 40 and spacer 43 missing, and those undesignated with the same signature were grouped as T2-Uganda using visual rules (23).…”

Section: Methodsmentioning

confidence: 99%

The T2 Mycobacterium tuberculosis Genotype, Predominant in Kampala, Uganda, Shows Negative Correlation with Antituberculosis Drug Resistance

Lukoye¹,

Katabazi²,

Musisi³

et al. 2014

Antimicrob Agents Chemother

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e Surveillance of the circulating Mycobacterium tuberculosis complex (MTC) strains in a given locality is important for understanding tuberculosis (TB) epidemiology. We performed molecular epidemiological studies on sputum smear-positive isolates that were collected for anti-TB drug resistance surveillance to establish the variability of MTC lineages with anti-TB drug resistance and HIV infection. Spoligotyping was performed to determine MTC phylogenetic lineages. We compared patients' MTC lineages with drug susceptibility testing (DST) patterns and HIV serostatus. , 5.0; 95% CI, 2.0 to 11.9; P < 0.001) and CAS (OR adj , 2.9; 95% CI, 1.4.0 to 6.3; P ‫؍‬ 0.006) families were more likely to show any resistance than was T2. All other MTC lineages combined were more likely to be resistant to any of the anti-TB drugs than were the T2 strains (OR adj , 1.7; 95% CI, 1.0 to 2.9; P ‫؍‬ 0.040). There were no significant associations between multidrug resistance and MTC lineages, but numbers of multidrug-resistant TB strains were small. No association was established between MTC lineages and HIV status. In conclusion, the T2 MTC lineage negatively correlates with anti-TB drug resistance, which might partly explain the reported low levels of anti-TB drug resistance in Kampala, Uganda. Patients' HIV status plays no role with respect to the MTC lineage distribution.

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“…Genotypic definitions-Four major phylogenetic lineages for M. tuberculosis [East African Indian, East Asian (i.e., Beijing strains), Euro-American, Indo-Oceanic], along with speciation of Mycobacterium africanum, were assigned using a set of rules correlating spoligotype with lineages defined by large sequence polymorphisms (LSP) (Click et al, 2012b;Supply et al, 2006). In cases that did not meet the full requirement for phylogenetic lineage assignment based on spoligotype, 12-locus MIRU-VNTR results was used in addition to spoligotype to assign lineage, as described elsewhere (Click et al, 2012b;Shabbeer et al, 2012). We excluded patients with M. africanum or Mycobacterium bovis isolates.…”

Section: Genotyping Methodsmentioning

confidence: 99%

Allopatric tuberculosis host–pathogen relationships are associated with greater pulmonary impairment

Pasipanodya

Moonan

Vecino

et al. 2013

Infection, Genetics and Evolution

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Background-Host pathogen relationships can be classified as allopatric, when the pathogens originated from separate, non-overlapping geographic areas from the host; or sympatric, when host and pathogen shared a common ancestral geographic location. It remains unclear if hostpathogen relationships, as defined by phylogenetic lineage, influence clinical outcome. We sought to examine the association between allopatric and sympatric phylogenetic Mycobacterium tuberculosis lineages and pulmonary impairment after tuberculosis (PIAT).

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TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex

Cited by 90 publications

References 29 publications

Tuberculosis – A global emergency: Tools and methods to monitor, understand, and control the epidemic with specific example of the Beijing lineage

Tuberculosis – A global emergency: Tools and methods to monitor, understand, and control the epidemic with specific example of the Beijing lineage

The T2 Mycobacterium tuberculosis Genotype, Predominant in Kampala, Uganda, Shows Negative Correlation with Antituberculosis Drug Resistance

Allopatric tuberculosis host–pathogen relationships are associated with greater pulmonary impairment

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