Database Interface and Implementation
The TB Strain Typing web interface help section is divided into the following categories:
- Remit of the National TB Strain Typing Strategy and database implementation
- 15 VNTR loci agreed for molecular typing of TB
- Data sharing policy
- Data download
- Data upload
- Report generation
National TB Database Remit
The aim of this project is to establish a National microbiological typing database for Mycobacterium tuberculosis, which holds molecular typing data and minimum clinical and epidemiological data as defined by the HPA TB Project Board group members.
The main function of the database is to provide rapid 'real time' assignation of genotypes by comparison with an accurate collated database of strains. This database will also allow the rapid comparison of strains nationally to allow the identifictaion of related cases/outbreaks to ensure that appropiate public health action can take place to controls the spread of tuberculosis.
The National TB Database is seen as an important resource to ensure the understanding of the prevalent strains within the UK and their evolutionary development. Variable Number of Tandem Repeats (VNTR) typing is carried out on all culture positive Mycobacterium tuberculosis isolates by Regional Mycobacteriology Units.
VNTR typing loci
Variable Number of Tandem Repeat (VNTR) typing can be applied to any living organism carrying repeat sequences within its genome. VNTR represents a locus that is hypervariable because of tandemly repeated DNA sequences. Exact Tandem Repeats (ETR) and Mycobacterium Intespersed Repetitive Units (MIRU) are specifically used in relation to typing Mycobacterium tuberculosis in humans. The ETR series or loci consists of five loci labelled A-E, which are represented as a five digit figure.
For the first release of the National TB Database, it has been agreed that 15 VNTR loci will be used to type TB isolates. These loci will be reviewed annually and amended if necessary. The loci agreed are ETR-A, ETR-B, ETR-C, ETR-D, ETR-E, MIRU-2, MIRU-10, MIRU-16, MIRU-20, MIRU-23, MIRU-24, MIRU-26, MIRU-27, MIRU-39 and MIRU-40. The twelve MIRU selected were used initially by Dr. Philippe (Supply 2001).
The VNTR profile is represented by 15 consecutive characters displayed which correspond to ETR numbers A-E and 10 MIRU loci (2, 10, 16, 20, 23, 24, 26, 27, 39, 40). ETR-E and MIRU-31 are equivalent and MIRU-4 can be calculated from ETR-D (MIRU-4 = ETR-D - 1). It has been agreed that any repeat numbers that are greater than 10 will be represented by alphanumeric charatacters such that 10=A, 11=B, 12=C etc. The first release of the National TB Database will store three experiment types for the rapid comparison of data and also to avoid any confusion with the existing lierature. These experiment types are be as follows:
- ETR (5 loci ETR-A to ETR-E)
- MIRU (12 loci MIRU-2 to MIRU-40 as defined by Supply)
- VNTR (15 loci, ETR-A to ETR-E and MIRU-2, MIRU-10, MIRU-16, MIRU-20, MIRU-23, MIRU-24, MIRU-26, MIRU-27, MIRU-39, MIRU-40)
Data Sharing Policy
The data sharing policy is in a draft format, which is under review. In the majority of cases, full access will only be given to those centres that are submitting data to the database. If you have any comments or queries regarding the data sharing policy please email Richard Myers at the Bioinformatics Unit in Colindale.
This database can be also accessed through a specialsed biological interface, Bionumerics. This software also allows data download and upload to the central database. However, this software is used only in regioanl and national centres. The web interface to the database allows those users who do not have Bionumerics to query, upload and download data to and from the central TB database. Data can be downloaded from the web as a comma seperated file (CSV), where by the maximum number of isolates downloaded per session is 10. Once downloaded, email(s) are sent to the owner(s) of the isolates records to inform them that some of their data has been downloaded.
The Regional Centres for Mycobacteriology (RCMs) will be able to upload their data via the Bionumerics platform. However, for those who do not contain this software, the possibility to upload data will br available through this web interface. However, for the interim, all centres will upload new data by emailing their results in a standardised XML format to Richard Myers at the Bioinformatics Unit in Colindale.
The web interface offers a numer of predefined dynamic reports, that can be used for a quick analysis of the database content.
- Supply,P., Lesjean,S., Savine,E., Kremer,K., van Soolingen,D. & Locht,C. (2001) Automated High-Throughput Genotyping for Study of Global Epidemiology of Mycobacterium tuberculosis on Mycobacterial Interspersed Repetitive Units. Journal of Clinical Microbiology 39, 3563-3571. Link
- Driscoll,J.R., Bifani,P.J., Mathema,B., McGarry,M.A., Zickas,G.M., Kreiswirth,B.N. & Taber,H.W. (2002) Spoligologos: A Bioinformatic Approach to Displaying and Analyzing Mycobacterium tuberculosis Data. Emerging Infectious Diseases 8, 1306-1309. Link