SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology
| Autor: | Julie Millet, Thomas Burguière, Véronique Hill, David Couvin, Igor Mokrousov, Christophe Sola, Thierry Zozio, Benjamin Liens, Christophe Demay, Nalin Rastogi |
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| Rok vydání: | 2012 |
| Předmět: |
DNA
Bacterial Microbiology (medical) Genotype Minisatellite Repeats computer.software_genre Microbiology Tandem repeat Genetics Humans Tuberculosis Typing Molecular Biology Genotyping Ecology Evolution Behavior and Systematics Internet Genetic diversity Database Molecular epidemiology biology Computational Biology Genetic Variation Mycobacterium tuberculosis biology.organism_classification Bacterial Typing Techniques Phylogeography Infectious Diseases Mycobacterium tuberculosis complex Multilocus sequence typing Databases Nucleic Acid computer Software Multilocus Sequence Typing |
| Zdroj: | Infection, Genetics and Evolution. 12:755-766 |
| ISSN: | 1567-1348 |
| DOI: | 10.1016/j.meegid.2012.02.004 |
| Popis: | Among various genotyping methods to study Mycobacterium tuberculosis complex (MTC) genotypic polymorphism, spoligotyping and mycobacterial interspersed repetitive units-variable number of DNA tandem repeats (MIRU-VNTRs) have recently gained international approval as robust, fast, and reproducible typing methods generating data in a portable format. Spoligotyping constituted the backbone of a publicly available database SpolDB4 released in 2006; nonetheless this method possesses a low discriminatory power when used alone and should be ideally used in conjunction with a second typing method such as MIRU-VNTRs for high-resolution epidemiological studies. We hereby describe a publicly available international database named SITVITWEB which incorporates such multimarker data allowing to have a global vision of MTC genetic diversity worldwide based on 62,582 clinical isolates corresponding to 153 countries of patient origin (105 countries of isolation). We report a total of 7105 spoligotype patterns (corresponding to 58,180 clinical isolates) - grouped into 2740 shared-types or spoligotype international types (SIT) containing 53,816 clinical isolates and 4364 orphan patterns. Interestingly, only 7% of the MTC isolates worldwide were orphans whereas more than half of SITed isolates (n=27,059) were restricted to only 24 most prevalent SITs. The database also contains a total of 2379 MIRU patterns (from 8161 clinical isolates) from 87 countries of patient origin (35 countries of isolation); these were grouped in 847 shared-types or MIRU international types (MIT) containing 6626 isolates and 1533 orphan patterns. Lastly, data on 5-locus exact tandem repeats (ETRs) were available on 4626 isolates from 59 countries of patient origin (22 countries of isolation); a total of 458 different VNTR patterns were observed - split into 245 shared-types or VNTR International Types (VIT) containing 4413 isolates) and 213 orphan patterns. Datamining of SITVITWEB further allowed to update rules defining MTC genotypic lineages as well to have a new insight into MTC population structure and worldwide distribution at country, sub-regional and continental levels. At evolutionary level, the data compiled may be useful to distinguish the occasional convergent evolution of genotypes versus specific evolution of sublineages essentially influenced by adaptation to the host. This database is publicly available at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE. |
| Databáze: | OpenAIRE |
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