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Table 1 Polymorphic minisatellite markers for the M. tuberculosis complex

From: High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing

Locus name

"MIRU" alias [8]

"ETR" alias [7]

"QUB" alias [9, 11]

Other alias

Reference

TR location on H37Rv genome

Expected length in H37Rv (copy number)

Expected length in CDC1551 (copy number)

Expected length in M bovis AF2122 (copy number)

N° of strains

Size range observed (copy number)

N° of alleles observed

Polymorphism index

H37Rv_0024_18 bp

   

Mtub01

This report

24648

328 (10)

310 (9)

310 (9)

92

274–328 bp (7–10)

4

0.48

H37Rv_0079_9 bp

   

Mtub02

This report

79503

230 (6)

239 (7)

239 (7)

92

221–275 bp (5–11)

7

0.76

H37Rv_0154_53 bp

MIRU2

   

[8]

154111

508 (2)

508 (2)

508 (2)

92

455–561 bp (1–3)

3

0.09

H37Rv_0424_51 bp

   

Mtub04

This report

424010

269 (2.6)

371 (4.6)

269 (2.6)

28

218 – 320 (1.6–3.6)

3

0.52

H37Rv_0531_15 bp

   

MPTR-A

[7]

531430

328 (16)

328 (16)

328 (16)

48

(15–17)

3

0.23

H37Rv_0577_58 bp

 

ETR-C

  

[8]

577172

346 (4)

288 (3)

404 (5)

92

230–404 bp (2–5)

4

0.63

H37Rv_0580_77 bp

MIRU4

ETR-D

  

[7]

580546

353 (3.3)

330 (3)

483 (5)

92

253–715 bp (2–8)

7

0.35

H37Rv_0802_54 bp

MIRU40

   

[8]

802194

199 (1)

415 (5)

253 (2)

92

199–469 bp (1–6)

5

0.71

H37Rv_0959_53 bp

MIRU10

   

[8]

959868

643 (3)

750 (5)

590 (2)

92

537–1014 bp (1–10)

9

0.76

H37Rv_1121_15 bp

   

Mtub12

This report

1121658

215 (4)

230 (5)

215 (4)

92

200–230 bp (3–5)

3

0.19

H37Rv_1443_56 bp

   

Mtub16

This report

1443417

291 (1)

347 (2)

347 (2)

11

291–515 (1–5)

3

0.56

H37Rv_1451_57 bp

  

QUB-1451c

 

[9]

1451778

305 (3.8)

305 (3.8)

305 (3.8)

56

(2–4) (bovis)

2

0.12

H37Rv_1612_21 bp

  

QUB-23

 

[11]

1612529

141 (5)

162 (6)

162 (6)

20

141–203 (5–8)

3

0.18

H37Rv_1644_53 bp

MIRU16

   

[8]

1644026

671 (2)

724 (3)

671 (2)

92

618–777 bp (1–4)

4

0.59

H37Rv_1895_57 bp

  

QUB-1895

 

[9]

1895344

319 (4)

205 (2)

319 (4)

56

(2–4) (bovis)

3

0.35

H37Rv_1955_57 bp

   

Mtub21

This report

1955580

206 (2)

263 (3)

263 (3)

92

149–491 bp (1–7)

7

0.76

H37Rv_1982_78 bp

  

QUB-18

 

[11]

1982873

621 (5)

777 (7)

465 (3)

24

387–1167 (2–12)

9

0.74

H37Rv_2059_77 bp

MIRU20

   

[8]

2059429

591 (2)

591 (2)

591 (2)

53

(1–2)

2

0.29

H37Rv_2074_56 bp*

   

Mtub24

This report

2074431

805 (3.6)

693 (1.6)

693 (1.6)

44

637–749 (0.6–2.6)

3

0.52

H37Rv_2163_a_69 bp

  

QUB-11a

pUCD1

[11]

2163607

305 (3)

581 (7)

788 (10)

92

305–1832 bp (3–26)

15

0.88

H37Rv_2163_b_69 bp

  

QUB-11b

pUCD1

[11]

2163729

412 (5)

274 (3)

343 (4)

52

136–826 (1–11)

8

0.82

H37Rv_2165_75 pb

 

ETR-A

  

[7]

2165223

397 (3)

322 (2)

847 (9)

92

322–847 bp (2–9)

8

0.73

H37Rv_2347_57 bp

   

Mtub29

This report

2347393

350 (4)

292 (3)

293 (3)

92

236–350 bp (2–4)

3

0.55

H37Rv_2401_58 bp

   

Mtub30

This report

2401815

319 (2)

435 (4)

435 (4)

92

261–435 bp (1–4)

3

0.55

H37Rv_2461_57 bp

 

ETR-B

  

[7]

2461279

292 (3)

235 (2)

406 (5)

92

178–406 bp (1–5)

6

0.51

H37Rv_2531_53 bp

MIRU23

   

[8]

2531560

873 (6)

820 (5)

767 (4)

92

608–979 bp (1–8)

7

0.60

H37RV_2387_54 bp

MIRU24

   

[8]

2684427

447 (1)

447 (1)

447 (1)

53

(1–2)

2

0.24

H37Rv_2990_55 bp

   

Mtub31

This report

2990582

257 (2)

312 (3)

312 (3)

49

202–312 bp (1–3)

3

0.15

H37Rv_2996_51 bp

MIRU26

   

[8]

2996002

614 (3)

716 (5)

716 (5)

57

563–818 (2–7)

5

0.61

H37Rv_3006_53 bp

MIRU27

 

QUB-5

 

[8]

3006875

657 (3)

657 (3)

657 (3)

92

551–710 bp (1–4)

4

0.25

H37Rv_3171_54 bp

   

Mtub34

This report

3171465

279 (3)

225 (2)

279 (3)

11

171–225 (1–2)

2

0.3

H37Rv_3192_53 bp

MIRU31

ETR-E

  

[7]

3192168

651 (3)

651 (3)

651 (3)

92

545–810 bp (1–6)

6

0.67

H37Rv_3232_56 bp

  

QUB-3232

 

[9]

3232649

591 (3)

760 (6)

703 (5)

56

(4–22) (bovis)

10

0.65

H37Rv_3239_79 bp

 

ETR-F

  

[7]

3239469

476 (2.8)

476 (2.8)

421 (2.1)

48

(1–3)

3

0.49

H37Rv_3336_59 bp

  

QUB-3336

 

[9]

3336499

407 (5)

466 (6)

289 (3)

56

(3–21) (bovis)

8

0.55

H37Rv_3663_63 bp**

   

Mtub38

This report

3663751

373 (2.7)

310 (1.7)

310 (1.7)

92

247–400 bp (0.7–3.1)

5

0.35

H37Rv_3690_58 bp*

   

Mtub39

This report

3690947

341 (2.6)*

397 (3.6)

341 (2.6)

92

247–1349 bp (1–20)*

11

0.64

H37Rv_4052_111 bp

  

QUB-26

 

[11]

4052969

708 (5)

819 (6)

597 (4)

100

(4–14) (bovis)

5

0.41

H37Rv_4156_59 bp

  

QUB-4156c

 

[9]

4156797

224 (2)

283 (3)

165 (1)

52

106–283 (0–3)

4

0.69

H37Rv_4348_53 bp

MIRU39

   

[8]

4348401

646 (2)

646 (2)

646 (2)

92

593–699 bp (1–3)

3

0.31

  1. The markers are listed according to their position in the H37Rv genome. The proposed reference name includes the size of the repeat unit. The twenty-one markers used in the present report are italicised and underlined. Alias names identified in the literature are indicated. QUB11a, QUB11b, and ETR-A (position 2163–2165) are located within the gene PPE34 [19]. The expected length assumes that the primers listed in Table 2 were used. * : the observed size (Table 3) is not the expected size. ** : the repeat unit is not easily defined, size variations do not correspond to a multiple of 63 base-pairs. Polymorphism index is calculated as 1 - ∑ (allele frequency)2 among the 86 distinct genotypes. The values are deduced from the original report in nine cases (indicated by the absence of size range in the "size range" column). In some instances [9, 11], the population of strains used is biased (M. bovis strains).
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BMC Microbiology

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