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

, 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 Rzhepishevska

, 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)
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Figure 2
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.
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References
World Health Organization. Global tuberculosis report 2017. Geneva: The Organization; 2017.
World Health Organization. Global tuberculosis report 2018: Geneva: The Organization; 2018.
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:
431–
40.
DOIPubMed 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:
23–
63.
DOIPubMed 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:
1081–
8.
DOIPubMed 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.
DOIPubMed 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:
242–
9.
DOIPubMed 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.
DOIPubMed 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:
279–
86.
DOIPubMed 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:
1176–
82.
DOIPubMed Kendall EA,
Fofana MO,
Dowdy DW.
Burden of transmitted multidrug resistance in epidemics of tuberculosis: a transmission modelling analysis. Lancet Respir Med.
2015;
3:
963–
72.
DOIPubMed 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.
DOIPubMed 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.
DOIPubMed 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:
2578–
86.
DOIPubMed Li H,
Durbin R.
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics.
2009;
25:
1754–
60.
DOIPubMed 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:
1297–
303.
DOIPubMed 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:
2078–
9.
DOIPubMed Price MN,
Dehal PS,
Arkin AP.
FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One.
2010;
5:
e9490.
DOIPubMed 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.
DOIPubMed 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:
137–
46.
DOIPubMed 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.
DOIPubMed Feuerriegel S,
Köser CU,
Niemann S.
Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex. J Antimicrob Chemother.
2014;
69:
1205–
10.
DOIPubMed 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.
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:
e00009–
00018.
DOIPubMed 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:
129–
38.
DOIPubMed World Health Organization. Review of the national tuberculosis programme in Ukraine. Copenhagen, Denmark: The Organization; 2011.
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.e1–
6.
DOIPubMed 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:
395–
402.
DOIPubMed 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:
1029–
31.
DOIPubMed 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:
850–
2.
DOIPubMed 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.
DOIPubMed 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:
197–
205.
DOIPubMed 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:
337–
40.
DOIPubMed
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