Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 26, Number 3—March 2020
Research

Multidrug- and Extensively Drug-Resistant Mycobacterium tuberculosis Beijing Clades, Ukraine, 2015

Matthias MerkerComments to Author , Elena Nikolaevskaya, Thomas A. Kohl, Barbara Molina-Moya, Olha Pavlovska, Patrik Brännberg, Andrii Dudnyk, Valentyna Stokich, Ivan Barilar, Iryna Marynova, Tetiana Filipova, Cristina Prat, Anders Sjöstedt, Jose Dominguez, Olena RzhepishevskaComments to Author , and Stefan Niemann
Author affiliations: Research Center Borstel, Borstel, Germany (M. Merker, T.A. Kohl, I. Barilar, S. Niemann); Odessa Regional TB Hospital, Odessa, Ukraine (E. Nikolaevskaya, O. Pavlovska, V. Stokich); Institut d'Investigació Germans Trias i Pujol, Badalona, Spain (B. Molina-Moya, C. Prat, J. Dominguez); Centro de Investigación Biomédica en Red (CIBERES), Badalona (B. Molina-Moya, C. Prat, J. Dominguez); Universitat Autònoma de Barcelona, Barcelona, Spain (B. Molina-Moya, C. Prat, J. Dominguez); Umeå University, Umea, Sweden (P. Brännberg, A. Sjöstedt, O. Rzhepishevska); National Pirogov Memorial Medical University, Vinnytsia, Ukraine (A. Dudnyk); Odessa I.I. Mechnikov National University, Odessa (I. Marynova, T. Filipova); German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany (S. Niemann)

Main Article

Figure 2

Maximum-likelihood phylogeny based on 10,339 SNPs, and employing general time-reversible substitution model for 177 clinical MDR/XDR and non-MDR Mycobacterium tuberculosis complex isolates from southern Ukraine. Branches are color-coded according the phylogenetic classification from Coll et al. (22). Resistance profile bars represent drug resistance classifications based on drug resistance mediating mutations. Scale bar indicates substitutions per site. MDR, multidrug resistant; XDR, extensively

Figure 2. Maximum-likelihood phylogeny based on 10,339 SNPs, and employing general time-reversible substitution model for 177 clinical MDR/XDR and non-MDR Mycobacterium tuberculosis complex isolates from southern Ukraine. Branches are color-coded according to the phylogenetic classification from Coll et al. (22). Resistance profile bars represent drug resistance classifications based on drug resistance mediating mutations. Scale bar indicates substitutions per site. MDR, multidrug resistant; XDR, extensively drug-resistant.

Main Article

References
  1. World Health Organization. Global tuberculosis report 2017. Geneva: The Organization; 2017.
  2. World Health Organization. Global tuberculosis report 2018: Geneva: The Organization; 2018.
  3. Walker  TM, Merker  M, Knoblauch  AM, Helbling  P, Schoch  OD, van der Werf  MJ, et al.; MDR-TB Cluster Consortium. A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study. Lancet Infect Dis. 2018;18:43140. DOIPubMedGoogle Scholar
  4. Lange  C, Abubakar  I, Alffenaar  JW, Bothamley  G, Caminero  JA, Carvalho  AC, et al.; TBNET. Management of patients with multidrug-resistant/extensively drug-resistant tuberculosis in Europe: a TBNET consensus statement. Eur Respir J. 2014;44:2363. DOIPubMedGoogle Scholar
  5. Günther  G, Gomez  GB, Lange  C, Rupert  S, van Leth  F; TBNET. Availability, price and affordability of anti-tuberculosis drugs in Europe: a TBNET survey. Eur Respir J. 2015;45:10818. DOIPubMedGoogle Scholar
  6. Matteelli  A, Rendon  A, Tiberi  S, Al-Abri  S, Voniatis  C, Carvalho  ACC, et al. Tuberculosis elimination: where are we now? Eur Respir Rev. 2018;27:27. DOIPubMedGoogle Scholar
  7. European Centre for Disease Prevention and Control/WHO Regional Office for Europe. Tuberculosis surveillance and monitoring in Europe, 2018, 2016 data. 2018 [cited 2019 Dec 31]. https://www.ecdc.europa.eu/en/publications-data/tuberculosis-surveillance-and-monitoring-europe-2018
  8. Merker  M, Blin  C, Mona  S, Duforet-Frebourg  N, Lecher  S, Willery  E, et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet. 2015;47:2429. DOIPubMedGoogle Scholar
  9. Cohen  KA, Abeel  T, Manson McGuire  A, Desjardins  CA, Munsamy  V, Shea  TP, et al. Evolution of extensively drug-resistant tuberculosis over four decades: whole-genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal. PLoS Med. 2015;12:e1001880. DOIPubMedGoogle Scholar
  10. Casali  N, Nikolayevskyy  V, Balabanova  Y, Harris  SR, Ignatyeva  O, Kontsevaya  I, et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet. 2014;46:27986. DOIPubMedGoogle Scholar
  11. Comas  I, Coscolla  M, Luo  T, Borrell  S, Holt  KE, Kato-Maeda  M, et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet. 2013;45:117682. DOIPubMedGoogle Scholar
  12. Kendall  EA, Fofana  MO, Dowdy  DW. Burden of transmitted multidrug resistance in epidemics of tuberculosis: a transmission modelling analysis. Lancet Respir Med. 2015;3:96372. DOIPubMedGoogle Scholar
  13. Eldholm  V, Monteserin  J, Rieux  A, Lopez  B, Sobkowiak  B, Ritacco  V, et al. Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain. Nat Commun. 2015;6:7119. DOIPubMedGoogle Scholar
  14. Lalor  MK, Casali  N, Walker  TM, Anderson  LF, Davidson  JA, Ratna  N, et al. The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak. Eur Respir J. 2018;51:1702313. DOIPubMedGoogle Scholar
  15. Nikolayevskyy  V, Kranzer  K, Niemann  S, Drobniewski  F. Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review. Tuberculosis (Edinb). 2016;98:7785.https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=27156621&dopt=Abstract DOIGoogle Scholar
  16. Public Health Center Ukraine. Tuberculosis in Ukraine [in Ukrainian]. 2018 [cited 2019 Dec 31]. http://aph.org.ua/wp-content/uploads/2018/09/proekt-dovidnika-TB-2018.pdf
  17. van Soolingen  D, Hermans  PW, de Haas  PE, Soll  DR, van Embden  JD. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J Clin Microbiol. 1991;29:257886. DOIPubMedGoogle Scholar
  18. Li  H, Durbin  R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:175460. DOIPubMedGoogle Scholar
  19. McKenna  A, Hanna  M, Banks  E, Sivachenko  A, Cibulskis  K, Kernytsky  A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297303. DOIPubMedGoogle Scholar
  20. Li  H, Handsaker  B, Wysoker  A, Fennell  T, Ruan  J, Homer  N, et al.; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:20789. DOIPubMedGoogle Scholar
  21. Price  MN, Dehal  PS, Arkin  AP. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490. DOIPubMedGoogle Scholar
  22. Coll  F, McNerney  R, Guerra-Assunção  JA, Glynn  JR, Perdigão  J, Viveiros  M, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun. 2014;5:4812. DOIPubMedGoogle Scholar
  23. Walker  TM, Ip  CL, Harrell  RH, Evans  JT, Kapatai  G, Dedicoat  MJ, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2013;13:13746. DOIPubMedGoogle Scholar
  24. Coll  F, McNerney  R, Preston  MD, Guerra-Assunção  JA, Warry  A, Hill-Cawthorne  G, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 2015;7:51. DOIPubMedGoogle Scholar
  25. Feuerriegel  S, Köser  CU, Niemann  S. Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex. J Antimicrob Chemother. 2014;69:120510. DOIPubMedGoogle Scholar
  26. Mayer  D, Zeileis  AKH. Visualizing independence using extended association plots. Presented at: Third International Workshop on Distributed Statistical Computing (DSC 2003); March 20–22, 2003; Vienna, Austria.
  27. The R Core Team. R: a language and environment for statistical computing. Reference index. 2019 [cited 2019 Dec 31]. https://cran.r-project.org/manuals.html
  28. Daum  LT, Konstantynovska  OS, Solodiankin  OS, Liashenko  OO, Poteiko  PI, Bolotin  VI, et al. Next-generation sequencing for characterizing drug resistance-conferring Mycobacterium tuberculosis genes from clinical isolates in the Ukraine. J Clin Microbiol. 2018;56:e0000900018. DOIPubMedGoogle Scholar
  29. Nikolayevskyy  VV, Brown  TJ, Bazhora  YI, Asmolov  AA, Balabanova  YM, Drobniewski  FA. Molecular epidemiology and prevalence of mutations conferring rifampicin and isoniazid resistance in Mycobacterium tuberculosis strains from the southern Ukraine. Clin Microbiol Infect. 2007;13:12938. DOIPubMedGoogle Scholar
  30. World Health Organization. Review of the national tuberculosis programme in Ukraine. Copenhagen, Denmark: The Organization; 2011.
  31. A unified clinical protocol of primary, secondary (specialized) and tertiary (highly specialized) medical care for adults [in Ukrainian]. Tuberculosis. 2014 [cited 2020 Jan 8]. https://www.phc.org.ua/sites/default/files/uploads/files/%D0%9F%D1%80%D0%BE%D1%82%D0%BE%D0%BA%D0%BE%D0%BB%20%D0%A2%D0%91%20%D1%83%20%D0%B2%D0%B7%D1%80%D0%BE%D1%81%D0%BB%D1%8B%D1%85%20620%20%D0%BE%D1%82%20%2004%2009%2014.pdf
  32. Nikolayevskyy  V, Kontsevaya  I, Nikolaevskaya  E, Surkova  E, Samchenko  S, Esipenko  S. Diagnostic performance and impact of routinely implemented Xpert® MTB/RIF assay in a setting of high incidence of drug-resistant TB in Odessa Oblast, Ukraine. Clin Microbiol Infect. 2019;25:1040.e16. DOIPubMedGoogle Scholar
  33. Manson  AL, Cohen  KA, Abeel  T, Desjardins  CA, Armstrong  DT, Barry  CE III, et al.; TBResist Global Genome Consortium. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet. 2017;49:395402. DOIPubMedGoogle Scholar
  34. Lange  C, Duarte  R, Fréchet-Jachym  M, Guenther  G, Guglielmetti  L, Olaru  ID, et al.; European MDR-TB database collaboration *. European MDR-TB database collaboration. Limited benefit of the new shorter multidrug-resistant tuberculosis regimen in Europe. Am J Respir Crit Care Med. 2016;194:102931. DOIPubMedGoogle Scholar
  35. Balabanova  Y, Fiebig  L, Ignatyeva  O, Riekstina  V, Danilovits  M, Jaama  K, et al. Multidrug-resistant TB in Eastern region of the EU: is the shorter regimen an exception or a rule? Thorax. 2017;72:8502. DOIPubMedGoogle Scholar
  36. Konstantynovska  O, Rekrotchuk  M, Hrek  I, Rohozhyn  A, Rudova  N, Poteiko  P, et al. Severe clinical outcomes of tuberculosis in Kharkiv Region, Ukraine, are associated with Beijing strains of Mycobacterium tuberculosis. Pathogens. 2019;8:8. DOIPubMedGoogle Scholar
  37. Pavlenko  E, Barbova  A, Hovhannesyan  A, Tsenilova  Z, Slavuckij  A, Shcherbak-Verlan  B, et al. Alarming levels of multidrug-resistant tuberculosis in Ukraine: results from the first national survey. Int J Tuberc Lung Dis. 2018;22:197205. DOIPubMedGoogle Scholar
  38. Hoffmann  H, Kohl  TA, Hofmann-Thiel  S, Merker  M, Beckert  P, Jaton  K, et al. Delamanid and bedaquiline resistance in Mycobacterium tuberculosis ancestral Beijing genotype causing extensively drug-resistant tuberculosis in a Tibetan refugee. Am J Respir Crit Care Med. 2016;193:33740. DOIPubMedGoogle Scholar

Main Article

Page created: February 20, 2020
Page updated: February 20, 2020
Page reviewed: February 20, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external