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BMC infectious diseases
Jun 24, 2019;19 (1): 553.

Genomic characterization of MDR/XDR-TB in Kazakhstan by a combination of high-throughput methods predominantly shows the ongoing transmission of L2/Beijing 94-32 central Asian/Russian clusters.

B J Klotoe, S Kacimi, E Costa-Conceicão, H M Gomes, R B Barcellos, S Panaiotov, D Haj Slimene, N Sikhayeva, S Sengstake, A R Schuitema, M Akhalaia, A Alenova, E Zholdybayeva, P Tarlykov, R Anthony, G Refrégier, C Sola
Author Information
  1. B J Klotoe: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  2. S Kacimi: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  3. E Costa-Conceicão: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  4. H M Gomes: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  5. R B Barcellos: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  6. S Panaiotov: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  7. D Haj Slimene: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  8. N Sikhayeva: National Centre for Biotechnology, Astana, Kazakhstan.
  9. S Sengstake: Royal Tropical Institute (KIT), Amsterdam, The Netherlands.
  10. A R Schuitema: Royal Tropical Institute (KIT), Amsterdam, The Netherlands.
  11. M Akhalaia: Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland.
  12. A Alenova: National Centre for Tuberculosis Problems, Almaty, Kazakhstan.
  13. E Zholdybayeva: National Centre for Biotechnology, Astana, Kazakhstan.
  14. P Tarlykov: National Centre for Biotechnology, Astana, Kazakhstan.
  15. R Anthony: Royal Tropical Institute (KIT), Amsterdam, The Netherlands.
  16. G Refrégier: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
  17. C Sola: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France. christophe.sola@i2bc.paris-saclay.fr. ORCID
PMID: 31234780 DOI: 10.1186/s12879-019-4201-2

Abstract

BACKGROUND: Kazakhstan remains a high-burden TB prevalence country with a concomitent high-burden of multi-drug resistant tuberculosis. For this reason, we performed an in depth genetic diversity and population structure characterization of Mycobacterium tuberculosis complex (MTC) genetic diversity in Kazakhstan with both patient and community benefit.
METHODS: A convenience sample of 700 MTC DNA cultures extracts from 630 tuberculosis patients recruited from 12 out of 14 regions in Kazakhstan, between 2010 and 2015, was independently studied by high-throughput hybridization-based methods, TB-SPRINT (59-Plex, n = 700), TB-SNPID (50-Plex, n = 543). DNA from 391 clinical isolates was successfully typed by two methods. To resolve the population structure of drug-resistant clades in more detail two complementary assays were run on the L2 isolates: an IS6110-NTF insertion site typing assay and a SigE SNP polymorphism assay.
RESULTS: Strains belonged to L2/Beijing and L4/Euro-American sublineages; L2/Beijing prevalence totaled almost 80%. 50% of all samples were resistant to RIF and to INH., Subtyping showed that: (1) all L2/Beijing were "modern" Beijing and (2) most of these belonged to the previously described 94-32 sublineage (Central Asian/Russian), (3) at least two populations of the Central Asian/Russian sublineages are circulating in Kazakhstan, with different evolutionary dynamics.
CONCLUSIONS: For the first time, the global genetic diversity and population structure of M. tuberculosis genotypes circulating in Kazakhstan was obtained and compared to previous local studies. Results suggest a region-specific spread of a very limited number of L2/Beijing clonal complexes in Kazakhstan many strongly associated with an MDR phenotype.

Keywords

Genomics High-throughput diagnostics methods Kazakhstan MDR-TB Molecular evolution Public health Tuberculosis XDR-TB

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Grants

  1. AP05130238/Ministry of Research and Technology
  2. Priority area: 439 «Life Science» «Development of biomedicine and genetic engineering/Ministry of Research and Technology
  3. 2015-1177/Agence Nationale de la Recherche et de la Technologie

MeSH Term

Adult
Aged
Antitubercular Agents
DNA, Bacterial
Drug Resistance, Multiple, Bacterial
Evolution, Molecular
Genetic Variation
Genotype
Humans
Kazakhstan
Male
Middle Aged
Mycobacterium tuberculosis
Nucleic Acid Amplification Techniques
Nucleic Acid Hybridization
Phenotype
Prevalence
Tuberculosis, Multidrug-Resistant
Young Adult

Chemicals

Antitubercular Agents
DNA, Bacterial
Journal Article
Article has an altmetric score of 1

Word Cloud

Created with Highcharts 10.0.0KazakhstanL2/BeijingtuberculosismethodsgeneticdiversitypopulationstructuretwoAsian/Russianhigh-burdenprevalenceresistantcharacterizationMTCDNAhigh-throughputassaybelongedsublineages94-32CentralcirculatingBACKGROUND:remainsTBcountryconcomitentmulti-drugreasonperformeddepthMycobacteriumcomplexpatientcommunitybenefitMETHODS:conveniencesample700culturesextracts630patientsrecruited1214regions20102015independentlystudiedhybridization-basedTB-SPRINT59-Plexn = 700TB-SNPID50-Plexn = 543391clinicalisolatessuccessfullytypedresolvedrug-resistantcladesdetailcomplementaryassaysrunL2isolates:IS6110-NTFinsertionsitetypingSigESNPpolymorphismRESULTS:StrainsL4/Euro-Americantotaledalmost80%50%samplesRIFINHSubtypingshowedthat:1"modern"Beijing2previouslydescribedsublineage3leastpopulationsdifferentevolutionarydynamicsCONCLUSIONS:firsttimeglobalMgenotypesobtainedcomparedpreviouslocalstudiesResultssuggestregion-specificspreadlimitednumberclonalcomplexesmanystronglyassociatedMDRphenotypeGenomicMDR/XDR-TBcombinationpredominantlyshowsongoingtransmissioncentralclustersGenomicsHigh-throughputdiagnosticsMDR-TBMolecularevolutionPublichealthTuberculosisXDR-TB

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