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Online Tools

Globally Genotyping markers Lineages Drug Resistance HIV Sex/Age Potential evolution of genotypes Connection with other databases

Global Distribution of M. tuberculosis complex (MTBC) strains in SITVIT2


  • Map representing the total number of strains by country of isolation:
  • Table representing the total number of strains by country of isolation: here
  • Map representing the total number of strains by country of origin of patient:
  • Table representing the total number of strains by country of origin of patient: here


Global Incidence of TB as reported by the World Health Organization (WHO) in 2018


sitvit2

Distribution of clustered patterns (International Types)

Enter a short list of ITs (one per line) Retrieve Origin Data
SIT
12-MIT
15-MIT
24-MIT
VIT



Cartographies of International Types

Enter a SIT, a 12- 15- or 24-MIT or a VIT SIT 12-MIT 15-MIT 24-MIT VIT    

Another tool which displays the distribution of a given IT by Region of Isolation

Select a Region of Isolation SIT 12-MIT 15-MIT 24-MIT VIT    

Another tool which displays the distribution of a given IT by Region of Origin of patient

Select a Region of Origin SIT 12-MIT 15-MIT 24-MIT VIT    

Another tool which displays the distribution of a given IT by Country of Isolation

Select a Country of Isolation SIT 12-MIT 15-MIT 24-MIT VIT    

Another tool which displays the distribution of a given IT by Country of Origin of Patient

Select a Country of Origin SIT 12-MIT 15-MIT 24-MIT VIT    

Another tool which displays the distribution of a given IT by City of Isolation

Select a City of Isolation (Country Code) SIT 12-MIT 15-MIT 24-MIT VIT    


Distribution of combined International Types

Enter a short list of couples SIT/MIRU-VNTR-IT (separated by "/" e.g: 1/16) Retrieve Origin Data

SIT/12-MIT
SIT/15-MIT
SIT/24-MIT
SIT/VIT



Highlighting Rare Genotypes

This tool provides a list of genotypes (SITs, VITs or MITs) containing a given minimal number of strains, and isolated in a given maximal number of sub-regions of isolation.
Enter the minimum number of strains and a maximum number of sub-regions Nb of Strains ≥
Nb of Subregions ≤ 		SIT 12-MIT 15-MIT 24-MIT VIT    

Distribution of Lineages

This tool shows the geographic distribution of a given Lineage.

Select a Lineage

This tool shows the Distribution of Lineage in a given region of isolation

Select a Region of Isolation

This tool shows the Distribution of Lineage in a given region of origin

Select a Region of Origin of patient

This tool shows the Distribution of Lineage in a given Country of Isolation

Select a Country of Isolation

This tool shows the Distribution of Lineage in a given Country of Origin of patient

Select a Country of Origin of patient

This tool shows the Distribution of Lineage in a given City of Isolation

Select a City of Isolation

Global Distribution of Drug resistant strains by Country of Isolation

Select a Code of Drug Resistance:

Select a Country of Isolation:


Global Distribution of Drug resistant strains by Country of Origin of patient

Select a Code of Drug Resistance:

Select a Country of Origin of patient:

Global Distribution of HIV serology by Country of Isolation

Select the HIV serology:

Select a Country of Isolation:


Global Distribution of HIV serology by Country of Origin of patient

Select the HIV serology:

Select a Country of Origin of patient:

Global Distributions of HIV serology in function of other parameters

Excel file of Global distribution of HIV serology of patients in function of the Age groups

Excel file of Global distribution of HIV serology of patients in function of the Mean Age

Excel file of Global distribution of HIV serology of patients in function of the Male/Female sex ratio

Global Distribution of Sex and Age groups of patients by Country of Isolation

Select the Sex:

Select the Age group:

Select a Country of Isolation:


Global Distribution of Sex and Age groups of patients by Country of Origin of patient

Select the Sex:

Select the Age group:

Select a Country of Origin of patient:

SpoligoLogos (performed with WebLogo application) of all sublineages of SITVIT2


Select a sublineage:


Phylogenetic Analyses based on Spoligotyping and MIRU-VNTRs typing


Spoligoforests trees using a Hierachical Layout and the Fruchterman-Reingold algorithm (drawn using the SpolTools software)

Hierarchical Layout of Spoligotyping prototypes (spoligotyping patterns of the main sublineages)

Spoligoforest tree using the Fruchterman-Reingold algorithm (with Spoligotyping patterns representing 10 or more isolates in database)


Minimum Spanning Trees (MST) drawn using BioNumerics version 6.6 (Applied Maths, Sint-Martens-Latem, Belgium)

MST tree based on Spoligotypes of SITVIT2

MST tree based on 12-loci MIRU-VNTRs

MST tree based on 15-loci MIRU-VNTRs

MST tree based on 24-loci MIRU-VNTRs


Minimum Spanning Trees (MST) drawn using MLVA Compare version 1.02 (developed by Ridom and Genoscreen)

Legends are available on Figures

12-loci MIRU-VNTRs International Types (12-MITs)

MST tree based on 12-MITs and representing MIRU-VNTRplus MTBC lineages

MST tree based on 12-MITs and representing SITVIT2 MTBC lineages

15-loci MIRU-VNTRs International Types (15-MITs)

MST tree based on 15-MITs and representing MIRU-VNTRplus MTBC lineages

MST tree based on 15-MITs and representing SITVIT2 MTBC lineages

24-loci MIRU-VNTRs International Types (24-MITs)

MST tree based on 24-MITs and representing MIRU-VNTRplus MTBC lineages

MST tree based on 24-MITs and representing SITVIT2 MTBC lineages


Spoligotyping and MIRU-VNTRs typing patterns associated with Drug resistance information

Meaning of Codes of Drug Resistance: Code 1 (Pansusceptible or non-resistant); Code 2 (multiple drug resistant or MDR); Code 3 (drug resistant); Code 4 (extensively drug resistant or XDR)

MST tree based on Spoligotype International Types (SITs) vs. Drug Resistance


MST tree based on 12-MITs vs. Drug Resistance

MST tree based on combined SITs and 12-MITs vs. Drug Resistance (the SIT number appears first, followed by the 12-MIT number)


MST tree based on 15-MITs vs. Drug Resistance

MST tree based on combined SITs and 15-MITs vs. Drug Resistance (the SIT number appears first, followed by the 15-MIT number)


MST tree based on 24-MITs vs. Drug Resistance

MST tree based on combined SITs and 24-MITs vs. Drug Resistance (the SIT number appears first, followed by the 24-MIT number)

Connection with other databases and/or Web tools


Connection with SITVIT-KBBN

The SITVIT-KBBN tool was developed to better define the spoligotyping based isolates, and to improve our expert-based classification of the genotypes, using a Bayesian network. This project was conjointly performed by Rensselaer Polytechnic Institute (RPI) and Institut Pasteur de la Guadeloupe, and is consultable Here (selecting the option "SITVIT Clade by KBBN").


The Excel File of KBBN tool applied to spoligotyping patterns present in SITVIT2 on March 2013, is downloadable Here.

Connection with MIRU-VNTRplus

All our 15- and 24-loci MIRU-VNTRs patterns (having a MIT number) have been entered in MIRU-VNTRplus database, and they have bee assigned an identifier based on MtbC15-9 Nomenclature.


Download the Excel file of the MtbC15-9 Nomenclature applied to our 15-MITs patterns

Download the Excel file of the MtbC15-9 Nomenclature applied to our 24-MITs patterns

Supervisor & Web Content Manager: Dr. Nalin RASTOGI

Validation & Development: Dr. Thierry ZOZIO & Dr. David COUVIN (Assisted by Ms. Audrey DAVID)


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