|
Summary of SSH experiments. |
|||||
| SSH |
|||||
| 670 v 11168 |
504 v 11168 |
1967 v 11168 |
629 v 2 drivers |
961 v 2 drivers |
|
|
|
|||||
| Tester MLST group |
ST-21 |
ST-21 |
ST-42 |
ST-45 |
ST-61 |
| Tester source |
duck |
cattle |
cattle |
rabbit |
rabbit |
| SSH restriction enzymes |
AluI/DraI |
AluI/DraI |
AluI/DraI |
RsaI |
RsaI |
| clones sequenced |
75 |
92 |
98 |
98 |
145 |
| unsubtracted |
16 |
40 |
24 |
53 |
60 |
| %subtracted |
79% |
57% |
76% |
46% |
59% |
| repeats |
7 |
9 |
12 |
28 |
64 |
| %repeats |
12% |
17% |
16% |
53% |
75% |
| subtracted (SSH) sequences |
52 |
43 |
62 |
17 |
21 |
| SSH sequence length range |
|||||
| <200 bp |
21 |
22 |
14 |
0 |
1 |
| 200–400 bp |
28 |
20 |
37 |
4 |
5 |
| 400–600 bp |
3 |
1 |
9 |
4 |
2 |
| >600 bp |
0 |
0 |
2 |
9 |
13 |
| Best BLASTX match by strain |
|||||
| RM1221 (chicken) |
16 |
23 |
8 |
4 |
4 |
| 81–176 (human) |
16 |
1 |
39 |
4 |
0 |
| 11168 (human) |
2 |
2 |
1 |
1 |
0 |
| other C. jejuni |
11 |
16 |
12 |
5 |
17 |
| other Campylobacter sp. |
5 |
1 |
1 |
1 |
0 |
| other genera |
0 |
0 |
0 |
2 |
0 |
| no significant match |
2 |
0 |
1 |
0 |
0 |
| % Campylobacter |
96% |
100% |
98% |
88% |
100% |
| Campylobacter 50–80% ID |
2 |
0 |
2 |
0 |
1 |
| Campylobacter <50% ID |
0 |
0 |
0 |
1 |
2 |
| Best BLASTX by function |
|||||
| capsule |
0 |
1 |
6 |
3 |
2 |
| LOS |
0 |
0 |
6 |
1 |
6 |
| flagella/motility |
0 |
2 |
4 |
1 |
4 |
| restriction-modification |
1 |
1 |
4 |
0 |
0 |
| membrane/transport |
2 |
5 |
7 |
3 |
3 |
| metabolism/biosynthesis |
1 |
4 |
18 |
4 |
0 |
| plasmid |
24 |
0 |
1 |
0 |
0 |
| bacteriophage |
14 |
7 |
0 |
0 |
2 |
| hypothetical or unknown |
7 |
23 |
12 |
2 |
1 |
| others |
1 |
0 |
3 |
3 |
3 |
| no significant match |
2 |
0 |
1 |
0 |
0 |
|
The number of isolates fitting into each category is presented for each of the five subtractions. ID; protein sequence identity | |||||
Hepworth et al. BMC Genomics 2007 8:110 doi:10.1186/1471-2164-8-110 |
|||||