Figures
- FIGURE 1
Percentage of multidrug-resistant (MDR)-tuberculosis (TB) coverage per European Union/European Economic Area country in 2018. The number of MDR-TB cases among all laboratory-confirmed TB cases notified to the European Centre for Disease Prevention and Control in 2018 was used as reference. The map was generated using the online tool available at www.mapchart.net/.
- FIGURE 2
a, b) Lineage distribution of the 2151 rifampicin-resistant (RR)/multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) isolates included in the EUSeqMyTB study. Lineages: 1: East-African Indian (EAI) (includes EAI and EAI Manila); 2: East-Asian (includes 2.2.1 Beijing and 2.1 East-Asian non-Beijing); 3: Delhi-CAS; 4.1: Euro-American (includes 4.1 and 4.1.2: Euro-American; 4.1.1: X-type; and 4.1.2.1: Haarlem); 4.2: Euro-American (includes 4.2 and 4.2.2: Euro-American; 4.2.1: Ural; and 4.2.2.1: TUR); 4.3: LAM; 4.4 (includes 4.4.1.1: S-type); 4.5: Euro-American; 4.6: Euro-American; 4.7: mainly T; 4.8: mainly T; 4.9: H37Rv-like; 5: West-Africa 1.
- FIGURE 3
Map showing the percentage of rifampicin-resistant/multidrug-resistant tuberculosis cases of foreign origin in cross-border clusters per European Union/European Economic Area country. The map was generated using the online tool available at www.mapchart.net/.
- FIGURE 4
Minimum spanning tree of a) snpCL1, b) snpCL3 and c) snpCL8. The numbers on the branches indicate the genetic distance in single nucleotide polymorphism (SNP) differences to the nearest isolate. SNP differences between distant isolates can be reconstituted by summing the number of SNPs on the branches. Different colours indicate the different European Union/European Economic Area countries where the strains were isolated.
Tables
- TABLE 1
Mycobacterium tuberculosis isolates submitted to the EUSeqMyTB consortium by year of isolation
Country Isolates submitted by year of isolation n Total n 2017 2018 2019 Austria 0 19 6 25 Belgium 5 8 6 19 Bulgaria 25 24 16 65 Croatia 0 2 1 3 Cyprus 0 0 0 0 Czech Republic 5 9 11 25 Denmark 0 4 4 8 Estonia 28 25 13 66 Finland 4 4 2 10 France 8 66 25 99 Germany 77 124 45 246 Hungary 5 13 4 22 Ireland 6 7 10 23 Italy 63 44 20 127 Latvia 18 33 34 85 Lithuania 77 60 42 179 Luxembourg 0 0 0 0 Malta 0 0 0 0 Netherlands 12 6 6 24 Norway 2 6 2 10 Poland 31 57 10 98 Portugal 12 19 6 37 Romania 335 336 195 866 Slovakia 2 4 2 8 Slovenia 0 1 0 1 Spain 17 37 12 66 Sweden 9 11 5 25 UK 27 30 24 81 Total per year 768 949 501 2218 - TABLE 2
Drug-resistance profile of the 2217 Mycobacterium tuberculosis isolates included in the database stratified by lineage
Lineage R H MDR-TB Z SLIDs FQs XDR-TB 1 (EAI) 32 (1.5) 31 (1.6) 30 (1.5) 13 (1.0) 0 (0.0) 1 (0.2 0 (0.0) 2 (Beijing/East-Asian non-Beijing) 638 (29.7) 632 (31.9) 630 (32.1) 443 (34.4) 337 (48.4) 257 (44.2) 179 (54.1) 3 (Delhi-CAS) 63 (2.9) 53 (2.7) 53 (2.7) 22 (1.7) 2 (0.3) 10 (1.7) 1 (0.3) 4.1 (Euro-American) 390 (18.1) 347 (17.5) 341 (17.4) 206 (16.0) 71 (10.2) 77 (13.3) 38 (11.5) 4.2 (Euro-American) 199 (9.3) 191 (9.6) 189 (9.6) 122 (9.5) 48 (6.9) 49 (8.4) 25 (7.6) 4.3 (LAM) 183 (8.5) 166 (8.4) 163 (8.3) 95 (7.4) 38 (5.5) 50 (8.6) 19 (5.7) 4.4, 4.5, 4.6 (Euro-American) 77 (3.6) 70 (3.5) 69 (3.5) 48 (3.7) 22 (3.2) 5 (0.9) 1 (0.3) 4.7, 4.8, 4.9 (Euro-American) 555 (25.8) 483 (24.3) 476 (24.3) 333 (25.9) 175 (25.1) 131 (22.5) 67 (20.2) 5 (West-Africa 1) 1 (0.0) 1 (0.1) 1 (0.1) 0 (0.0) 0 (0.0) 0 (0.0) 0 (0.0) Unknown 13 (0.6) 10 (0.5) 10 (0.5) 4 (0.3) 4 (0.6) 1 (0.2) 1 (0.3) Total 2151 (97.0) 1984 (89.5) 1962 (88.5) 1286 (58.0) 697 (31.4) 581 (26.8) 331 (15.4) Data are presented as n (%). R: rifampicin; H: isoniazid; MDR: multidrug resistant; TB: tuberculosis; Z: pyrazinamide; SLID: second-line injectable drug; FQ: fluoroquinolone; XDR: extensively drug resistant.
- TABLE 3
Cross-border clusters identified using an SNP-based approach
SNP-based cross-border clusters (≤5 SNPs threshold) Cross-border cluster name Isolates n Countries involved n Lineage classification snpCL 1 30 3 4.8 (mainly T) snpCL 2 20 2 4.2.1 (Ural) snpCL 3 16 4 4.6.2 (Euro-American) snpCL 4 14 2 4.8 (mainly T) snpCL 5 13 2 4.2.1 (Ural) snpCL 6 13 3 4.8 (mainly T) snpCL 7 12 3 2.2.1 (Beijing) snpCL 8 12 4 4.2.2 (Euro-American) snpCL 9 12 2 4.8 (mainly T) snpCL 10 12 2 4.1.2.1 (Haarlem) snpCL 11 10 2 4.3.3 (LAM) snpCL 12 10 5 4.2.2 (Euro-American) snpCL 13 9 6 2.2.1 (Beijing) snpCL 14 7 4 2.2.1 (Beijing) snpCL 15 7 5 2.2.1 (Beijing) snpCL 16 7 2 2.2.1 (Beijing) snpCL 17 5 4 4.3.3 (LAM) snpCL 18 5 2 2.2.1 (Beijing) snpCL 19 5 2 4.8 (mainly T) snpCL 20 5 2 4.3.3 (LAM) snpCL 21 5 2 4.2.2.1 (TUR) snpCL 22 5 2 4.1.2.1 (Haarlem) snpCL 23 4 3 4.3.3 (LAM) snpCL 24 4 3 2.2.1 (Beijing) snpCL 25–34# 3 2 to 3 snpCL 35–56¶ 2 2 A sequential number from 1 to 56 was assigned to each cross-border cluster identified by SNP-based analysis, based on the size of the cluster and starting from the largest one. SNP: single nucleotide polymorphism; snpCL: SNP-based cluster. #: 10 clusters comprising three isolates from three (n=1) and two (n=9) countries, with the lineage distribution comprising 2.2.1 Beijing (n=3), 4.8 mainly T (n=2), 4.7 mainly T (n=1), 4.1.2.1 Haarlem (n=2), 4.2.2 Euro-American (n=1) and 4.1.1.1 X-type (n=1); ¶: 22 clusters comprising two isolates from two countries, with the lineage distribution comprising 2.2.1 Beijing (n=7), 4.8 mainly T (n=3), 4.1.2.1 Haarlem (n=3), 4.2.1 Ural (n=2), 4.3.3 LAM (n=2), 4.3.1 LAM (n=1), 4.1.2 Euro-American (n=1), 4.2.2 Euro-American (n=1), 4.9, H37Rv-like (n=1) and 3 Delhi-CAS (n=1).
- TABLE 4
Country contribution to cross-border clusters#
Country RR/MDR-TB cases in cluster n Percentage among clustered isolates Percentage of clustered RR/MDR-TB cases among submitted ones¶ Austria 9 2.8 36.0 Belgium 5 1.6 26.3 Bulgaria 6 1.9 9.2 Croatia 0 – – Czech Republic 6 1.9 24.0 Denmark 0 – – Estonia 5 1.6 7.6 Finland 2 0.6 22.2 France 11 3.5 11.1 Germany 40 12.7 16.3 Hungary 2 0.6 9.1 Ireland 3 0.9 13.0 Italy 38 12.0 29.9 Latvia 3 0.9 3.5 Lithuania 43 13.6 24.0 Netherland 5 1.6 20.8 Norway 1 0.3 10 Poland 7 2.2 7.1 Portugal 0 – – Romania 101 32.0 11.7 Slovakia 2 0.6 25.0 Slovenia 0 – – Spain 9 2.8 13.6 Sweden 8 2.5 32.0 UK 10 3.2 12.3 Total 316 100 14.3 RR: rifampicin resistant; MDR: multidrug resistant; TB: tuberculosis. #: a cross-border cluster is defined as two or more RR/MDR Mycobacterium tuberculosis complex isolates having a single nucleotide polymorphism difference ≤5, and isolated in at least two different countries; ¶: n=2217.
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