Strain | Origin | Farm | Production system | 266_07 | VNTR | 346_06 | VNTR | 360_06 | VNTR | 854_08 | VNTR |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | Guanajuato | 1 | Extensive | 955 | 27 | 1092 | 73 | 1187 | 40 | 1101 | 11 |
2 | Guanajuato | 1 | Extensive | 955 | 27 | 1166 | 78 | 1156 | 39 | 301 | 3 |
3 | Guanajuato | 1 | Extensive | 963 | 27 | 1153 | 77 | 1183 | 39 | 1101 | 11 |
4 | Guanajuato | 1 | Extensive | 953 | 26 | 1161 | 77 | 1181 | 39 | 1077 | 11 |
5 | Guanajuato | 1 | Extensive | 952 | 26 | 1159 | 77 | 1181 | 39 | 1210 | 13 |
6 | Guanajuato | 1 | Extensive | 936 | 26 | 1164 | 78 | 1175 | 39 | 1201 | 13 |
7 | Querétaro | 2 | Intensive | 453 | 13 | 1181 | 79 | 1175 | 39 | 329 | 3 |
8 | Querétaro | 2 | Intensive | 453 | 13 | 1177 | 78 | 1177 | 39 | 329 | 3 |
9 | Querétaro | 2 | Intensive | 1075 | 30 | 1176 | 78 | 1176 | 39 | 1221 | 13 |
10 | Querétaro | 2 | Intensive | 1080 | 30 | 1178 | 79 | 1182 | 39 | 1229 | 13 |
11 | Querétaro | 3 | Intensive | 384 | 11 | 1155 | 77 | 1176 | 39 | 329 | 3 |
12 | Querétaro | 3 | Intensive | 383 | 11 | 1157 | 77 | 1178 | 39 | 329 | 3 |
13 | Querétaro | 3 | Intensive | 385 | 11 | 1156 | 77 | 1172 | 39 | 329 | 3 |
14 | Querétaro | 3 | Intensive | 382 | 11 | 1164 | 78 | 1181 | 39 | 204 | 2 |
15 | Querétaro | 3 | Intensive | 382 | 11 | 1150 | 77 | 1181 | 39 | 329 | 3 |
16 | Querétaro | 3 | Intensive | 382 | 11 | 1155 | 77 | 1183 | 39 | 330 | 3 |
17 | Querétaro | 3 | Intensive | 385 | 11 | 1178 | 79 | 1181 | 39 | 329 | 3 |
18 | Querétaro | 3 | Intensive | 989 | 27 | 1158 | 77 | 1181 | 39 | 329 | 3 |
19 | Querétaro | 3 | Intensive | 384 | 11 | 1156 | 77 | 1178 | 39 | 329 | 3 |
20 | Querétaro | 3 | Semi-intensive | 383 | 11 | 1168 | 78 | 1186 | 40 | 328 | 3 |
21 | Querétaro | 3 | Semi-intensive | 386 | 11 | 1163 | 78 | 1186 | 40 | 205 | 2 |
22 | Querétaro | 3 | Semi-intensive | 872 | 24 | 1192 | 79 | 1185 | 40 | 329 | 3 |
23 | Querétaro | 3 | Semi-intensive | 0 | 0 | 1187 | 79 | 1186 | 40 | 329 | 3 |
Locus | Size [bp] | Simpson index | Confidence intervals 95% | Hunter-gaston index | Confidence intervals 95% |
---|---|---|---|---|---|
266_07 | 36 | 0.87 | 0.803–0.936 | 0.909 | 0.843–0.975 |
346_06 | 15 | 0.926 | 0.896–0.957 | 0.968 | 0.938–0.999 |
360_06 | 30 | 0.756 | 0.650–0.862 | 0.791 | 0.684–0.897 |
854_08 | 96 | 0.654 | 0.449–0.859 | 0.684 | 0.479–0.888 |
Primer | Sequence (5’-3’) | Conditions | Size [bp] |
---|---|---|---|
266_07 | F’- ATTCTGGATTTTGCACAGC | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 266 |
346_06 | F’- CAAAACAACGATATCTGTATCTGA | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 346 |
360_06 | F’- CAAGTGCATAACCGTTATTCC | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 360 |
854_08 | F’- GAAGCACTTACACTTTCGGAG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 854 |
638_07 | F’- TGAGGTCTCCGCTGTAGG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 638 |
613_12 | F’- AGTAGCTAACCATTTTGTTAATTGC | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 613 |
The gen coding for | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
+/total | % | +/total | % | +/total | % | +/total | % | +/total | % | |
Aureolysin | 23/23 | 100 | 5/18 | 27.78 | 4/9 | 44.44 | 2/2 | 100 | 0/1 | 0 |
Hemolysin | 23/23 | 100 | 2/18 | 11.11 | 0/9 | 0 | 0/2 | 0 | 0/1 | 0 |
Extracellular protein | 23/23 | 100 | 18/18 | 100 | 9/9 | 100 | 2/2 | 100 | 1/1 | 100 |
Zin metaloprotease | 23/23 | 100 | 18/18 | 100 | 9/9 | 100 | 2/2 | 100 | 1/1 | 100 |
Surface protein SasH | 23/23 | 100 | 18/18 | 100 | 6/9 | 66.67 | 2/2 | 100 | 0/1 | 0 |
TRAP | 23/23 | 100 | 3/18 | 16.67 | 3/9 | 33.33 | 2/2 | 100 | 0/1 | 0 |
B Antigen | 23/23 | 100 | 2/18 | 11.11 | 0/9 | 0 | 0/2 | 0 | 0/1 | 0 |
Virulence B factor | 22/23 | 95.65 | 0/18 | 0 | 3/9 | 33.33 | 2/2 | 100 | 1/1 | 100 |
FemA protein | 23/23 | 100 | 18/18 | 100 | 9/9 | 100 | 2/2 | 100 | 0/1 | 0 |
Primers | Sequence (5’-3’) | Conditions | Size [bp] |
---|---|---|---|
16S rRNA | F’- CCTATAAGACTGGGATAACTTCGGG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 791 |
F’- CAAAGCAGATGCGATAG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 56°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 1200 | |
Aureolysin | F’- GCATTAAACGAAASCTTYTCWG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 247 |
Hemolysin | F’- ATGAATATTGGAATAACTTTAGTCAG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 600 |
Extracelular protein | F’- ACGTGAGCAATATATGAACGC | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 133 |
Zin Metaloprotease | F’- ATTTGCAATCGGGATGG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 250 |
Surface protein SasH | F’- GGCWAAAGCRATGAATGC | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, | 201 |
R’- ACCGATAATKCCRTAACG | 72°C/1 m/1 cycle 72°C/5 m. | ||
TRAP (Transduction signal protein) | F’-AACTCTATTCACTTATGGAACATATGG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 529 |
B antigen | F’- CAAAAACACTATTAGCGACTGG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 488 |
Virulence B factor | F’- ATGTCTTTTAAAGAAAATGAAATCG | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 905 |
FemA protein | F’- GTGTGCTTRTACCWYTAGC | 1 cycle 95°C/5 m, 30 cycles 95°C/1 m, 50°C/1 m, 72°C/1 m/1 cycle 72°C/5 m. | 250 |
Strain | Origin | Goat id | Farm | Production system | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Guanajuato | A | 1 | Extensive | + | + | + | + | + | + | − | − | − | + | + | − | − | − | + | − | + | + | + | R | S | S | S | S |
2 | Guanajuato | B | 1 | Extensive | + | + | + | − | + | + | − | − | − | + | + | − | − | − | + | − | + | + | + | S | S | S | S | S |
3 | Guanajuato | C | 1 | Extensive | + | + | + | − | + | + | − | − | − | + | + | − | − | − | + | − | + | + | + | S | S | S | S | S |
4 | Guanajuato | D | 1 | Extensive | + | + | + | + | + | + | − | − | − | + | + | − | − | − | + | − | + | + | + | S | R | S | S | S |
5 | Guanajuato | E | 1 | Extensive | + | + | + | − | − | + | + | − | − | + | + | − | − | − | + | − | − | + | + | S | S | S | S | S |
6 | Guanajuato | F | 1 | Extensive | + | + | + | − | + | + | − | − | − | + | + | − | − | − | + | − | − | + | + | S | R | S | S | S |
7 | Querétaro | G-105R | 2 | Intensive | + | + | + | + | + | + | − | − | − | + | + | − | − | − | + | − | + | + | + | S | R | S | S | S |
8 | Querétaro | H-105R | 2 | Intensive | + | − | + | + | + | + | − | − | − | − | + | − | − | − | + | − | + | + | + | S | R | S | S | S |
9 | Querétaro | G-60L | 2 | Intensive | + | + | − | − | + | + | + | − | − | + | + | − | − | − | + | − | + | + | − | S | S | S | S | S |
10 | Querétaro | G-150R | 2 | Intensive | + | + | − | − | + | + | + | − | − | + | + | − | + | − | + | − | + | + | − | S | S | S | S | S |
11 | Querétaro | I-15R | 3 | Intensive | + | + | + | + | + | + | − | − | − | − | + | − | − | − | + | − | + | + | + | R | R | S | S | S |
12 | Querétaro | J-15R | 3 | Intensive | + | + | + | + | + | + | − | − | − | − | + | − | − | − | + | − | + | + | + | R | R | S | S | S |
13 | Querétaro | K-15L | 3 | Intensive | + | + | + | + | + | + | − | − | − | − | + | − | − | − | + | − | + | + | + | R | R | S | S | S |
14 | Querétaro | J-60R | 3 | Intensive | + | + | + | + | + | + | − | − | − | − | + | − | − | − | + | − | + | + | + | S | R | S | S | S |
15 | Querétaro | K-15L1 | 3 | Intensive | + | + | + | + | + | + | − | − | − | + | + | − | − | − | + | − | + | + | + | R | R | S | S | S |
16 | Querétaro | K-15L2 | 3 | Intensive | + | + | − | + | + | + | − | − | − | + | + | − | − | − | + | − | − | + | + | R | R | S | S | S |
17 | Querétaro | K-15R3 | 3 | Intensive | + | + | + | + | + | + | − | − | − | + | + | + | − | − | + | − | − | + | + | S | R | S | S | S |
18 | Querétaro | L-15R | 3 | Intensive | + | + | + | + | + | + | − | − | − | − | + | − | − | − | + | − | + | + | + | I | R | S | S | S |
19 | Querétaro | J-195R | 3 | Intensive | + | + | + | + | + | + | − | − | − | − | + | − | − | − | + | − | + | + | + | I | R | S | S | S |
20 | Querétaro | M-15L | 3 | Semiintensive | + | + | + | + | + | + | − | − | − | + | + | − | − | − | + | − | − | + | + | R | R | S | S | S |
21 | Querétaro | N-60R | 3 | Semiintensive | + | + | + | + | + | + | − | − | − | + | + | + | − | − | + | − | − | + | + | S | R | S | S | S |
22 | Querétaro | O-150L | 3 | Semiintensive | + | + | + | + | + | + | − | − | − | + | + | + | − | − | + | − | − | + | + | I | R | S | S | S |
23 | Querétaro | O-150R | 3 | Semiintensive | + | + | + | + | + | + | − | − | − | + | + | − | − | − | + | − | − | + | + | R | R | S | S | S |