Background
Methods
Clinical specimen selection
Ethics
DNA Extraction and amplification
Primer selection for adaptation of MLST-7
Region | Locus tagb
| Format | Direction | Sequence (5′ to 3′) | 5′ positionc
| Fragment length (bp)d
|
---|---|---|---|---|---|---|
gatA
| CT0003 |
Outer
|
Forward
|
GCTTTAGAATTARSARAWGCT
| 2123 | 325 |
Outer
|
Reverse
|
GATCCTCCGGTATCYGATCC
| 2615 | |||
Inner + Seq | Forward | ATGACGAACAGATTGGAGC | 2186 | |||
Inner + Seq | Reverse | GGATTATTGGTAGGATGAA | 2532 | |||
oppA_3
| CT0198 |
Outer
|
Forward
|
ATGCGCAAGATATCAGTGGG
| 222438 | 480 |
Outer
|
Reverse
|
AAAGCTCCRSTWGMTATMGGWAG
| 223002 | |||
Inner + Seq | Forward | TCCTAGCATTAGCAACTTCT | 222469 | |||
Inner + Seq | Reverse | TCTTTCCGTATCTGATGCTGCG | 222970 | |||
hflX
| CT0379 |
Outer
|
Forward
|
GCTTCTARAGTACTTTTAAATG
| 432737 | 359 |
Outer
|
Reverse
|
TATTTRGAAATYTTTKCSAGYCG
| 432758 | |||
Inner + Seq | Forward | AAGTATGCGGAAGTTTGCG | 432768 | |||
Inner + Seq | Reverse | AATCAGGAGGTAGTGGTGGAGG | 433106 | |||
gidA
| CT0498 |
Outer
|
Forward
|
GGAGTCWCTACWAAAGAAGG
| 577352 | 389 |
Outer
|
Reverse
|
TCGTAYTGYACATCRAAAGG
| 577892 | |||
Inner + Seq | Forward | ACTTCTCTGGGGGACGATT | 577449 | |||
Inner + Seq | Reverse | GACCGTTCACATAAACTTCTTG | 577856 | |||
enoA
| CT0587 | Outer | Forward | GCAAATACTTTACAGAGACCTT | 662222 | 388 |
Outer | Reverse | CGTCACAAATAGGTCGTCTC | 662775 | |||
Inner + Seq
|
Forward
|
CCTATGATGAATCTKATCAATGG
| 662288 | |||
Inner + Seq
|
Reverse
|
TCTTCTTCGGCTAGCCCATCT
| 662698 | |||
hemN
| CT0746 | Outer | Forward | GAATCTTGCCTTTCACAGTTGC | 867674 | 448 |
Outer | Reverse | ACTTCCACATCCCATTCTGC | 868584 | |||
Inner + Seq
|
Forward
|
AGATCTTCTTCWGGRGGWAGAGA
| 867799 | |||
Inner + Seq
|
Reverse
|
TTCYTTCAKAACSTAGGTTTT
| 868269 | |||
fumC
| CT0855 |
Outer
|
Forward
|
ATTAAAAAATGTGCTGCT
| 1004691 | 451 |
Outer
|
Reverse
|
CCTTCAGGAACATTYAACCC
| 1005242 | |||
Inner + Seq | Forward | ATTAAAAAATGTGCTGCT | 1004691 | |||
Inner + Seq | Reverse | CCGCTCTAAACAATTATGCAACTG | 1005159 |
Nested PCR of MLST regions
Sequencing analysis
Minimum spanning tree analysis
Results
C. trachomatis typing using the MLST-7 scheme
Sequence type | Number of strains |
gatA
|
oppA_3
|
hflX
|
gidA
|
enoA
|
hemN
|
fumC
| Cluster |
ompA genovar (Number of strains) | Sexgroupa (number of strains) |
---|---|---|---|---|---|---|---|---|---|---|---|
8 | 1 | 2 | 1 | 1 | 2 | 4 | 2 | 3 | B | F (1) | Hetero (1) |
44 | 18 | 1 | 3 | 3 | 3 | 2 | 2 | 19 | C | L2 (1), L2b (17) | MSM (18) |
97 | 42 | 33 | 1 | 2 | 2 | 4 | 2 | 3 | B | D (24), E(1), F(17) | Hetero (17), MSM (25) |
106 | 1 | 2 | 3 | 2 | 5 | 3 | 2 | 3 | A | J (1) | Hetero (1) |
131 | 1 | 33 | 27 | 2 | 4 | 3 | 2 | 3 | A | G (1) | MSM (1) |
132 | 52 | 33 | 3 | 2 | 4 | 3 | 2 | 3 | A | G (26), H (1), I (10), J (13), K(2) | Hetero (13), MSM (39) |
133 | 26 | 33 | 1 | 1 | 2 | 4 | 2 | 3 | B | D (3), E (21), F (2) | Hetero (20), MSM (6) |
134 | 2 | 33 | 1 | 1 | 2 | 3 | 2 | 3 | B | F (2) | Hetero (1), MSM (1) |
135 | 19 | 33 | 4 | 1 | 2 | 4 | 2 | 3 | B | E (19) | Hetero (19) |
136 | 11 | 33 | 3 | 2 | 5 | 3 | 2 | 3 | A | B (1), D (2), G (4), J (4) | Hetero (11) |
137 | 1 | 33 | 3 | 2 | 40 | 3 | 2 | 3 | A | G (1) | Hetero (1) |
138 | 1 | 33 | 29 | 1 | 2 | 4 | 2 | 3 | B | E (1) | Hetero (1) |
139 | 1 | 33 | 1 | 1 | 2 | 32 | 2 | 3 | B | E (1) | Hetero (1) |
140 | 1 | 33 | 3 | 2 | 4 | 3 | 1 | 3 | A | G (1) | Hetero (1) |
141 | 4 | 33 | 3 | 2 | 5 | 3 | 1 | 3 | A | D (3), I (1) | Hetero (4) |
142 | 1 | 33 | 4 | 1 | 32 | 4 | 2 | 3 | B | E (1) | Hetero (1) |
143 | 1 | 33 | 3 | 2 | 5 | 3 | 25 | 3 | A | K (1) | Hetero (1) |
144 | 1 | 33 | 3 | 2 | 5 | 3 | 24 | 3 | A | G (1) | Hetero (1) |
145 | 1 | 33 | 3 | 2 | 4 | 24 | 2 | 3 | A | H (1) | Hetero (1) |
146 | 1 | 2 | 4 | 1 | 2 | 4 | 2 | 3 | B | F (1) | Hetero (1) |
147 | 1 | 33 | 28 | 2 | 4 | 3 | 2 | 3 | A | J (1) | MSM (1) |
C. trachomatis typing using hr-MLST-6 scheme
Sequence type | Number of strains |
ompA
| CT046 | CT058 | CT144 | CT172 | CT682 | Cluster |
ompA genovar (number of strains) | Sexgroupa (number of strains) |
---|---|---|---|---|---|---|---|---|---|---|
3 | 10 | 6 | 1 | 2 | 6 | 2 | 2 | VII | E (10) | Hetero (10) |
11 | 3 | 1 | 5 | 19 | 7 | 2 | 10 | D (3) | MSM (3) | |
16 | 1 | 6 | 7 | 19 | 14 | 2 | 1 | VI | E (1) | Hetero (1) |
27 | 1 | 9 | 10 | 6 | 10 | 1 | 6 | G (1) | Hetero (1) | |
30 | 1 | 12 | 10 | 7 | 1 | 3 | 8 | K (1) | MSM (1) | |
32 | 1 | 12 | 10 | 7 | 1 | 4 | 8 | K (1) | Hetero (1) | |
33 | 6 | 8 | 10 | 8 | 5 | 3 | 6 | II | G (6) | MSM (6) |
35 | 3 | 2 | 10 | 8 | 1 | 4 | 17 | D (3) | Hetero (3) | |
52 | 17 | 8 | 20 | 8 | 5 | 3 | 6 | II | G (17) | MSM (17) |
59 | 1 | 6 | 7 | 19 | 7 | 2 | 1 | VI | E (1) | Hetero (1) |
69 | 1 | 6 | 5 | 19 | 6 | 2 | 2 | E (1) | Hetero (1) | |
74 | 1 | 30 | 8 | 8 | 1 | 7 | 18 | B (1) | Hetero (1) | |
90 | 2 | 24 | 5 | 19 | 1 | 1 | 4 | IV | F (2) | Hetero (1), MSM (1) |
101 | 1 | 36 | 38 | 5 | 12 | 7 | 18 | III | I (1) | Hetero (1) |
109 | 18 | 1 | 5 | 20 | 5 | 2 | 34 | V | D (18) | MSM (18) |
110 | 1 | 24 | 1 | 2 | 7 | 2 | 4 | IV | F (1) | Hetero (1) |
137 | 1 | 8 | 10 | 8 | 22 | 4 | 6 | G (1) | Hetero (1) | |
143 | 1 | 28 | 44 | 13 | 17 | 13 | 28 | VIII | L2b (1) | MSM (1) |
153 | 2 | 6 | 35 | 19 | 7 | 2 | 1 | VI | E (2) | Hetero (2) |
165 | 1 | 35 | 12 | 5 | 1 | 9 | 8 | H (1) | Hetero (1) | |
171 | 2 | 6 | 49 | 19 | 7 | 2 | 1 | VI | E (2) | Hetero (2) |
172 | 1 | 6 | 1 | 2 | 7 | 2 | 2 | VII | E (1) | Hetero (1) |
194 | 3 | 1 | 5 | 6 | 5 | 2 | 34 | V | D (3) | MSM (3) |
232 | 2 | 20 | 5 | 19 | 1 | 4 | 18 | J (2) | Hetero (2) | |
240 | 1 | 24 | 5 | 19 | 12 | 1 | 4 | IV | F (1) | Hetero (1) |
265 | 1 | 10 | 10 | 4 | 1 | 3 | 7 | G (1) | Hetero (1) | |
270 | 1 | 8 | 10 | 5 | 12 | 3 | 8 | G (1) | Hetero (1) | |
272 | 1 | 36 | 10 | 5 | 12 | 24 | 18 | III | I (1) | Hetero (1) |
288 | 1 | 8 | 10 | 8 | 22 | 7 | 57 | G (1) | Hetero (1) | |
301 | 1 | 8 | 20 | 8 | 5 | 1 | 6 | II | G (1) | MSM (1) |
303 | 1 | 8 | 20 | 8 | 5 | 3 | 34 | II | G (1) | MSM (1) |
304 | 1 | 8 | 20 | 8 | 5 | 4 | 6 | II | G (1) | MSM (1) |
305 | 1 | 6 | 25 | 2 | 6 | 2 | 2 | VII | E (1) | Hetero (1) |
307 | 2 | 53 | 29 | 8 | 5 | 3 | 58 | I | J (2) | MSM (2) |
318 | 1 | 1 | 45 | 20 | 5 | 2 | 34 | V | D (1) | MSM (1) |
324 | 1 | 1 | 55 | 20 | 5 | 2 | 34 | V | D (1) | MSM (1) |
338 | 1 | 6 | 67 | 2 | 7 | 2 | 60 | E (1) | Hetero (1) | |
341 | 1 | 6 | 70 | 57 | 7 | 2 | 1 | E (1) | Hetero (1) | |
345 | 2 | 53 | 74 | 8 | 5 | 3 | 6 | I | J (2) | MSM (2) |
353 | 1 | 8 | 81 | 8 | 5 | 3 | 6 | II | G (1) | MSM (1) |
395 | 1 | 2 | 83 | 4 | 1 | 3 | 17 | D (1) | Hetero (1) | |
435 | 1 | 9 | 8 | 6 | 10 | 1 | 6 | G (1) | Hetero (1) | |
448 | 1 | 6 | 1 | 2 | 11 | 2 | 2 | VII | E (1) | Hetero (1) |
449 | 1 | 6 | 1 | 19 | 1 | 1 | 1 | E (1) | Hetero (1) | |
450 | 1 | 24 | 1 | 19 | 7 | 2 | 4 | IV | F (1) | Hetero (1) |
453 | 1 | 6 | 1 | 19 | 7 | 21 | 1 | VI | E (1) | Hetero (1) |
459 | 1 | 6 | 5 | 19 | 6 | 21 | 2 | E (1) | Hetero (1) | |
462 | 1 | 6 | 5 | 19 | 7 | 2 | 56 | E (1) | Hetero (1) | |
465 | 1 | 6 | 5 | 19 | 7 | 14 | 2 | E (1) | Hetero (1) | |
466 | 1 | 24 | 5 | 19 | 7 | 21 | 4 | IV | F (1) | Hetero (1) |
482 | 1 | 9 | 10 | 6 | 10 | 1 | 8 | G (1) | Hetero (1) | |
484 | 1 | 37 | 10 | 7 | 1 | 3 | 5 | I (1) | Hetero (1) | |
498 | 1 | 6 | 24 | 19 | 14 | 2 | 1 | VI | E (1) | Hetero (1) |
502 | 1 | 6 | 45 | 19 | 6 | 1 | 2 | E (1) | Hetero (1) | |
504 | 1 | 6 | 47 | 19 | 7 | 2 | 1 | VI | E (1) | Hetero (1) |
509 | 1 | 6 | 71 | 2 | 1 | 2 | 2 | VII | E (1) | Hetero (1) |
510 | 1 | 6 | 71 | 2 | 6 | 2 | 2 | VII | E (1) | Hetero (1) |
513 | 2 | 6 | 71 | 19 | 7 | 2 | 1 | VI | E (2) | Hetero (2) |
516 | 1 | 6 | 5 | 19 | 5 | 2 | 2 | E (1) | Hetero (1) | |
517 | 2 | 36 | 38 | 5 | 12 | 3 | 18 | III | I (2) | Hetero (2) |
100b | 3 | 36 | 10 | 5 | 12 | 7 | 18 | III | I (3) | Hetero (3) |
100c | 1 | 37 | 10 | 5 | 12 | 7 | 18 | III | I (1) | Hetero (1) |
108c | 9 | 53 | 29 | 8 | 5 | 3 | 6 | I | J (9) | MSM (9) |
12d | 13 | 24 | 5 | 19 | 7 | 1 | 4 | IV | F (13) | Hetero (12), MSM (1) |
135a | 1 | 20 | 10 | 5 | 12 | 4 | 18 | III | J (1) | Hetero (1) |
135b | 2 | 36 | 10 | 5 | 12 | 4 | 18 | III | I (2) | Hetero (2) |
13b | 1 | 24 | 5 | 19 | 15 | 1 | 4 | IV | F (1) | Hetero (1) |
148a | 2 | 24 | 5 | 19 | 7 | 2 | 4 | IV | F (2) | Hetero (1), MSM (1) |
205b | 1 | 20 | 10 | 6 | 22 | 4 | 8 | J (1) | Hetero (1) | |
20a | 1 | 2 | 10 | 4 | 1 | 4 | 17 | D (1) | Hetero (1) | |
220a | 1 | 12 | 10 | 4 | 1 | 3 | 8 | K (1) | Hetero (1) | |
281a | 1 | 20 | 10 | 8 | 1 | 4 | 18 | J (1) | Hetero (1) | |
281b | 1 | 63 | 10 | 8 | 1 | 4 | 18 | J (1) | Hetero (1) | |
56a | 9 | 6 | 1 | 19 | 7 | 2 | 1 | VI | E (9) | Hetero (7), MSM (2) |
58a | 1 | 22 | 27 | 13 | 17 | 13 | 28 | VIII | L2 (1) | MSM (1) |
58b | 16 | 28 | 27 | 13 | 17 | 13 | 28 | VIII | L2b (16) | MSM (16) |
77b | 1 | 31 | 5 | 19 | 7 | 2 | 37 | D (1) | Hetero (1) | |
91a | 1 | 24 | 5 | 19 | 5 | 2 | 4 | IV | F (1) | MSM (1) |
97b | 1 | 35 | 12 | 5 | 11 | 9 | 8 | H (1) | Hetero (1) |