Dataset Information

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.

ABSTRACT:

Background

The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database.

Results

The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network.

Conclusion

Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

SUBMITTER: Brudey K

PROVIDER: S-EPMC1468417 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature

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Publications

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.

Brudey Karine K Driscoll Jeffrey R JR Rigouts Leen L Prodinger Wolfgang M WM Gori Andrea A Al-Hajoj Sahal A SA Allix Caroline C Aristimuño Liselotte L Arora Jyoti J Baumanis Viesturs V Binder Lothar L Cafrune Patricia P Cataldi Angel A Cheong Soonfatt S Diel Roland R Ellermeier Christopher C Evans Jason T JT Fauville-Dufaux Maryse M Ferdinand Séverine S Garcia de Viedma Dario D Garzelli Carlo C Gazzola Lidia L Gomes Harrison M HM Guttierez M Cristina MC Hawkey Peter M PM van Helden Paul D PD Kadival Gurujaj V GV Kreiswirth Barry N BN Kremer Kristin K Kubin Milan M Kulkarni Savita P SP Liens Benjamin B Lillebaek Troels T Ho Minh Ly ML Martin Carlos C Martin Christian C Mokrousov Igor I Narvskaïa Olga O Ngeow Yun Fong YF Naumann Ludmilla L Niemann Stefan S Parwati Ida I Rahim Zeaur Z Rasolofo-Razanamparany Voahangy V Rasolonavalona Tiana T Rossetti M Lucia ML Rüsch-Gerdes Sabine S Sajduda Anna A Samper Sofia S Shemyakin Igor G IG Singh Urvashi B UB Somoskovi Akos A Skuce Robin A RA van Soolingen Dick D Streicher Elisabeth M EM Suffys Philip N PN Tortoli Enrico E Tracevska Tatjana T Vincent Véronique V Victor Tommie C TC Warren Robin M RM Yap Sook Fan SF Zaman Khadiza K Portaels Françoise F Rastogi Nalin N Sola Christophe C

BMC microbiology 20060306

<h4>Background</h4>The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable num ...[more]

PMID: 16519816

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Project description:BackgroundThe control of tuberculosis in densely populated cities is complicated by close human-to-human contacts and potential transmission of pathogens from multiple sources. We conducted a molecular epidemiologic analysis of 356 Mycobacterium tuberculosis (MTB) isolates from patients presenting pulmonary tuberculosis in metropolitan Taipei. Classical antibiogram studies and genetic characterization, using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping, were applied after culture.MethodsA total of 356 isolates were genotyped by standard spoligotyping and the strains were compared with in the international spoligotyping database (SpolDB4). All isolates were also categorized using the 15 loci MIRU-VNTR typing method and combin with NTF locus and RD deletion analyses.ResultsOf 356 isolates spoligotyped, 290 (81.4%) displayed known spoligotypes and 66 were not identified in the database. Major spoligotypes found were Beijing lineages (52.5%), followed by Haarlem lineages (13.5%) and EAI plus EAI-like lineages (11%). When MIRU-VNTR was employed, 140 patterns were identified, including 36 clusters by 252 isolates and 104 unique patterns, and the largest cluster comprised 95 isolates from the Beijing family. The combination of spoligotyping and MIRU-VNTR revealed that 236 (67%) of the 356 isolates were clustered in 43 genotypes. Strains of the Beijing family was more likely to be of modern strain and a higher percentage of multiple drug resistance than other families combined (P = 0.08). Patients infected with Beijing strains were younger than those with other strains (mean 58.7 vs. 64.2, p = 0.02). Moreover, 85.3% of infected persons younger than 25 years had Beijing modern strain, suggesting a possible recent spread in the young population by this family of TB strain in Taipei.ConclusionOur data on MTB genotype in Taipei suggest that MTB infection has not been optimally controlled. Control efforts should be reinforced in view of the high prevalence of the Beijing strain in young population and association with drug resistance.

Project description:Understanding the types of strains and lineages of Mycobacterium tuberculosis (M. tuberculosis) circulating in a country is of paramount importance for tuberculosis (TB) control program of that country. The main aim of this study was to review and compile the results of studies conducted on strains and lineages of M. tuberculosis in Ethiopia.A systematic search and review of articles published on M. tuberculosis strains and lineages in Ethiopia were made. PubMed and Google Scholar databases were considered for the search while the keywords used were M. tuberculosis, molecular epidemiology, molecular typing spoligotyping and Ethiopia.Twenty-one studies were considered in this review and a total of 3071 M. tuberculosis isolates and 3067 strains were included. These studies used spoligotyping and identified five lineages including Indo-Ocean, East Asian/Beijing, East African-Indian, Euro-American and Ethiopian in a proportion of 7.1%, 0.2%, 23.0%, 64.8%, and 4.1%, respectively. Thus, Euro-American was the most frequently (64.8%) occurring Lineage while East Asian was the least (0.2%) frequently occurring Lineage in the country. Surprisingly, the Ethiopian Lineage seemed to be localized to northeastern Ethiopia. In addition, the top five clades identified by this review were T, CAS, H, Manu and Ethiopian comprising of 48.0%, 23.0%, 11.0%, 6.0% and 4.1% of the strains, respectively. Furthermore, predominant shared types (spoligotype patterns) identified were SIT149, SIT53, SIT25, SIT37, and SIT21, each consisting of 420, 343, 266, 162 and 102 isolates, respectively, while, on the other hand, 15% of the strains were orphan.According to the summary of the results of this review, diversified strains and lineages of M. tuberculosis were found in Ethiopia, and the frequencies of occurrence of these strains and lineages were variable in different regions of the country. This systematic review is registered in the PRISMA with the registration number of 42017059263.

Dataset Information

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.

Background

Results

Conclusion

Publications

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.

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