Caroline Allix-Béguec

Publications of Caroline Allix-Béguec

• The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country.

  Authors: Maranibia Cardoso Oelemann, Harrison M Gomes, Eve Willery, Lia Possuelo, Karla Valéria Batista Lima, Caroline Allix-Béguec, Camille Locht, Yves-Olivier L Goguet de la Salmonière, Maria Cristina Gutierrez, Philip Suffys, Philip Supply

  PloS one. 01/2011; 6(3):e18256.

  Genotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing,Genotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages. We tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission. Standard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications.

• Genetic diversity of Mycobacterium tuberculosis isolates from a tertiary tuberculosis hospital in South Korea.

  Authors: Isdore Chola Shamputa, Jongseok Lee, Caroline Allix-Béguec, Eun-Jin Cho, Ji-Im Lee, Vignesh Rajan, Eun Gae Lee, Jin Hong Min, Matthew W. Carroll, Lisa C Goldfeder, Jin Hee Kim, Hyung Seok Kang, Soohee Hwang, Seok-Yong Eum, Seung Kyu Park, Hyeyoung Lee, Philip Supply, Sang-Nae Cho, Laura E Via, Clifton E Barry

  Journal of clinical microbiology. 12/2009;

  Tuberculosis (TB) remains an immense public health problem in the Republic of Korea despite more than a five fold decrease in the prevalence of the disease over the last three decades. The rise inTuberculosis (TB) remains an immense public health problem in the Republic of Korea despite more than a five fold decrease in the prevalence of the disease over the last three decades. The rise in drug resistant TB has compounded the situation. We analyzed 208 clinical isolates of M. tuberculosis from the National Masan Tuberculosis Hospital by spoligotyping, IS6110-Restriction Fragment Length Polymorphism (RFLP) and 24-locus based mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) to assess the diversity and transmission dynamics of the tubercle bacilli in the Republic of Korea. The majority of the isolates (97.1%) belonged to the Beijing genotype. Cluster analysis by MIRU-VNTR yielded a low clustering rate of 22.3% with most of the clusters comprising isolates with diverse drug resistance patterns. The discriminatory capacity of the typing methods was high for RFLP and MIRU-VNTR (h=0.99) but low for Spoligotyping (h=0.31). Although analysis of 19 MIRU-VNTR loci was needed to achieve maximum discrimination, an informative set of 8 loci (960, 1955, 2163b, 2165, 2996, 3192, 4052 and 4348) (h=0.98) that was able to differentiate most of the closely related strains was identified. These findings suggest that 24-locus based MIRU-VNTR typing is a likely suitable alternative to RFLP to differentiate clinical isolates in this setting dominated by M. tuberculosis Beijing strains. Within the study limits, our results also suggest that the problem of drug resistant TB in the Republic of Korea may be largely due to acquired resistance as opposed to transmission.

• Combined multilocus short sequence repeat and mycobacterial interspersed repetitive unit- variable-number tandem repeat typing of Mycobacterium avium subsp. paratuberculosis isolates.

  Authors: Virginie C Thibault, Maggy Grayon, Maria Laura Boschiroli, Eve Willery, Caroline Allix-Béguec, Karen Stevenson, Franck Biet, Philip Supply

  Journal of clinical microbiology. 11/2008;

  Short sequence repeat (SSR)-sequencing was applied to 127 Mycobacterium avium subsp. paratuberculosis isolates typed by mycobacterial interspersed repetitive unit-variable-number tandem repeatsShort sequence repeat (SSR)-sequencing was applied to 127 Mycobacterium avium subsp. paratuberculosis isolates typed by mycobacterial interspersed repetitive unit-variable-number tandem repeats (MIRU-VNTR) and IS900 restriction fragment length polymorphim (RFLP). Combined MIRU-VNTR and SSR typing followed by secondary IS900 RFLP typing is an improved approach to high-resolution genotyping of this pathogen.

• Origin, Spread and Demography of the Mycobacterium tuberculosis Complex.

  Authors: Thierry Wirth, Falk Hildebrand, Caroline Allix-Béguec, Florian Wölbeling, Tanja Kubica, Kristin Kremer, Dick van Soolingen, Sabine Rüsch-Gerdes, Camille Locht, Sylvain Brisse, Axel Meyer, Philip Supply, Stefan Niemann

  PLoS pathogens. 10/2008; 4(9):e1000160.

  The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterialThe evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates. The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of "modern" human populations out of Africa. Furthermore, coalescence analysis revealed a strong and recent demographic expansion in almost all M. tuberculosis lineages, which coincides with the human population explosion over the last two centuries. These findings thus unveil the dynamic dimension of the association between human host and pathogen populations.

• Evaluation and user-strategy of MIRU-VNTRplus, a multifunctional database for on-line analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates.

  Authors: Caroline Allix-Béguec, Dag Harmsen, Thomas Weniger, Philip Supply, Stefan Niemann

  Journal of clinical microbiology. 06/2008;

  Because of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing has become aBecause of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing has become a major method for epidemiological tracking of Mycobacterium tuberculosis complex (MTBC) clones. However, no public MIRU-VNTR database based on well-characterized reference strains was available hitherto for easy strain identification. Therefore, a collection of 186 reference strains representing the primary MTBC lineages was used to build up a database freely accessible at http://www.MIRU-VNTRplus.org. For each strain, geographical origin and drug-susceptibility profile was stored together with comprehensive genetic lineage information including 24-locus MIRU-VNTR profile, spoligotyping pattern, single nucleotide and large sequence polymorphism profile, and IS6110 restriction fragment length polymorphism fingerprint. Thanks to flexible import functions, single or multiple user strain(s) can be analyzed e.g. for lineage identification with or without using reference strains, by best-match or tree-based analyses employing single or combined marker datasets. Results can be easily exported. Here, we evaluated the database consistency and various analysis parameters, both by testing the reference collection against itself and by using an external population-based dataset comprising 629 different strains. In the optimal conditions found, lineage predictions based on 24-locus MIRU-VNTR-typing optionally combined with spoligotyping were verified in > 99% of the cases. Based on this evaluation, a user-strategy was defined, including best match analysis followed, if necessary, by tree-based analysis. The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification, which has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.

• Three-year population-based evaluation of standardized mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing of Mycobacterium tuberculosis.

  Authors: Caroline Allix-Béguec, Maryse Fauville-Dufaux, Philip Supply

  Journal of clinical microbiology. 05/2008; 46(4):1398-406.

  Standardized mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing based on 15 and 24 loci recently has been proposed for Mycobacterium tuberculosis genotyping.Standardized mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing based on 15 and 24 loci recently has been proposed for Mycobacterium tuberculosis genotyping. So far, this optimized system has been assessed in a single, 1-year population-based study performed in Germany (M. C. Oelemann, R. Diel, V. Vatin, W. Haas, S. Rusch-Gerdes, C. Locht, S. Niemann, and P. Supply, J. Clin. Microbiol. 45:691-697, 2007). Here, we evaluated these optimized formats in a much larger population-based study conducted during 39 months in the Brussels capital region of Belgium. Isolates from 807 patients were genotyped. The resolution power, cluster, and lineage identification by the standardized MIRU-VNTR sets were compared to those obtained using standardized IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, and a previous 12-MIRU-VNTR-locus set. On a subset representing 77% of the cases during a 16-month period, a high concordance was observed between unique isolates or strain clusters as defined by standardized MIRU-VNTR and IS6110-RFLP (i.e., more than five IS6110 bands). When extended to the entire population-based collection, the discriminatory subset of 15 loci decreased the strain-clustering rate by almost twofold compared to that of the old 12-locus set. The addition of the nine ancillary MIRU-VNTR loci and/or spoligotyping only slightly further decreased this strain-clustering rate. Familial, social, and/or geographic proximity links were found in 48% of the clusters identified, and well-known risk factors for tuberculosis transmission were identified. Finally, an excellent correspondence was determined between our MIRU-VNTR-spoligotyping strain identifications and external reference strain lineages included in the MIRU-VNTRplus database and identified by, e.g., large sequence polymorphisms. Our results reinforce the proposal of standardized MIRU-VNTR typing as a new reference genotyping method for the epidemiological and phylogenetic screening of M. tuberculosis strains.