Table 1. Proposed clade-defining single nucleotide polymorphisms for the previously reported EUSeqMyTB snpCL[1], EU/EEA, 2017–2019 (n = 34 clades).
| SNP | snpCLa | Gene product | Locus tag | Amino acid change (codon)b | Size of snpCL | Isolates containing the proposed SNPc | Genotype (Coll clade) |
|---|---|---|---|---|---|---|---|
| 1157317_T | 1 | Two component sensor histidine kinase TrcS | Rv1032c | Leu213Leu (ctg/ctA) | 29 | 32 | Mainly T (4.8) |
| 4327088_C | 2 | Monooxygenase EthA | Rv3854c | Leu129Arg (ctc/cGc) | 20 | 20 | Ural (4.2.1) |
| 130881_G | 3 | NA | 16 | 16 | Euro-American (4.6.2) | ||
| 1485300_G | 4 | NA | 14 | 15 | Mainly T (4.8) | ||
| 1208477_G | 5 | Hypothetical protein | Rv1084 | Ala281Gly (gcg/gGg) | 13 | 15 | Ural (4.2.1) |
| 1547828_C | 6 | NA | 13 | 14 | Mainly T (4.8) | ||
| 2971513_G | 7 | Integrase | Rv2646 | Asp321Glu (gac/gaG) | 12 | 17 | Beijing (2.2.1) |
| 1039921_G | 8 | NA | 12 | 12 | Euro-American (4.2.2) | ||
| No SNP | 9 | NA | 12 | NA | Mainly T (4.8) | ||
| 211015_A | 10 | Transmembrane protein | Rv0180c | His412His (cac/caT) | 12 | 12 | Haarlem (4.1.2.1) |
| 1895566_G | 11 | NA | 10 | 10 | LAM (4.3.3) | ||
| 1914071_A | 12 | Tyrosine-tRNA ligase | Rv1689 | Arg157Gln (cgg/cAg) | 10 | 10 | Euro-American (4.2.2) |
| 1810244_A | 13 | Indole-3-glycerol phosphate synthase | Rv1611 | Ser2Asn (agt/aAt) | 9 | 9 | Beijing (2.2.1) |
| 4155977_A | 14 | DNA polymerase III subunit epsilon | Rv3711c | Val251Val (gtc/gtT) | 7 | 7 | Beijing (2.2.1) |
| 2399093_A | 15 | Dihydroorotate dehydrogenase | Rv2139 | Arg125Gln (cgg/cAg) | 7 | 7 | Beijing (2.2.1) |
| 1008074_A | 16 | Acetyl-CoA carboxylase carboxyl transferase beta | Rv0904c | Ala36Val (gcg/gTg) | 7 | 8 | Beijing (2.2.1) |
| 4284172_T | 17 | Hypothetical protein | Rv3819 | Asp59Asp (gac/gaT) | 5 | 9 | LAM (4.3.3) |
| 766707_G | 18 | DNA-directed RNA polymerase subunit beta | Rv0668 | Glu1113Gly (gaa/gGa) | 5 | 5 | Beijing (2.2.1) |
| 3169491_A | 19 | Aldehyde dehydrogenase | Rv2858c | Ser411Ser (tcg/tcT) | 5 | 5 | Mainly T (4.8) |
| 996197_C | 20 | S-adenosylmethionine-dependent methyltransferase | Rv0893c | Asp33Glu (gat/gaG) | 5 | 5 | LAM (4.3.3) |
| No SNP | 21 | NA | 5 | NA | TUR (4.2.2.1) | ||
| 1231934_G | 22 | NA | 5 | 6 | Haarlem (4.1.2.1) | ||
| 1398622_A | 23 | Hypothetical protein | Rv1251c | Arg207Cys (cgc/Tgc) | 4 | 4 | LAM (4.3.3) |
| No SNP | 24 | NA | 4 | NA | Beijing (2.2.1) | ||
| 1068731_C | 25 | Formyltransferase/inosine monophosphate cyclohydrolase | Rv0957 | Arg176Thr (agg/aCg) | 3 | 3 | Beijing (2.2.1) |
| No SNP | 26 | NA | 3 | NA | Beijing (2.2.1) | ||
| 3031515_C | 27 | Membrane protein | Rv2719c | His8Arg (cat/cGt) | 3 | 3 | Beijing (2.2.1) |
| 1028437_T | 28 | Transposase | Rv0922 | Arg251Arg (cgc/cgT) | 3 | 3 | Mainly T (4.7) |
| 3640351_T | 29 | NA | 3 | 3 | Mainly T (4.8) | ||
| 3223901_A | 30 | NA | 3 | 3 | Mainly T (4.8) | ||
| 1946519_T | 31 | NA | 3 | 3 | Euro-American (4.2.2) | ||
| 3088899_A | 32 | Oxidoreductase | Rv2781c | Ala29Val (gcg/gTg) | 3 | 3 | X-type (4.1.1.1) |
| 1921877_A | 33 | Hypothetical protein | Rv1697 | Gly112Gly (ggg/ggA) | 3 | 3 | Haarlem (4.1.2.1) |
| 1760095_G | 34 | Fumarate reductase iron-sulphur subunit | Rv1553 | Pro221Ala (cct/Gct) | 3 | 3 | Haarlem (4.1.2.1) |
EU/EEA: European Union/European Economic Area; NA: not applicable; SNP: single nucleotide polymorphism.
a The snpCL1 was expanded by 3 isolates to identify a characteristic SNP and one isolate was missed because of a mixed genotype. SNP 3640351 c > T, which defines snpCL29, is within 4 bp of a second SNP 3640354 c > G.
b A capital letter is used to indicate the changed base.
c The total number of isolates from the 2,218 isolates in the EUSeqMyTB database containing the proposed SNP.