TABLE 3.

MIRU-VNTR phylogenetic codes for each lineage based on panel 1

Lineage (n)aMIRU-VNTR codeb (no. of isolates with correct repeat no./total isolates [%])Combined MIRU-VNTRc
CodeNo. of isolates with correct combined repeat no./total isolates (%)
I (20)39-3 (19/20 [95])39-318/20 (90)
A-4 (19/20 [95])A-4
C-4 (20/20 [100])C-4
II (168)16-1,2,3 (164/167 [98.2])16-1,2,3153/166 (92.7)
39-2 (160/167 [95.8])39-2
B-1,2 (162/166 [97.6])B-1,2
III (62)23-5 (61/62 [98.4])23-561/62 (98.4)
C-2 (62/62 [100])C-2
IV (62)24-2 (61/61 [100])24-259/61 (96.7)
26-2 (60/62 [98.8])26-2
M. bovis (4)10-2 (4/4 [100])10-24/4 (100)
40-2 (4/4 [100])40-2
C-5 (4/4 [100])C-5
  • a Some loci would not amplify; therefore, two isolates from lineage II and one isolate from lineage IV were excluded from the analyses, leaving a total of 309 M. tuberculosis isolates in panel 1.

  • b Each code consists of the MIRU (numbers) or ETR (letters) designation followed by a dash and the number of copies. For example, 16-1,2,3 indicates 1, 2, or 3 copies of MIRU-16; A-4 indicates 4 copies of ETR-A.

  • c Combination of MIRU-VNTR producing the most unambiguous definition of each lineage. The number and percentage of isolates tested that were correctly identified using this combination are given.