Table 2. Fragment/sequence analysis data for successful CP populations recovered from frozen or fresh caeca.
Fresh caecal samples were analysed immediately after necropsy; frozen caecal samples were stored at −20 °C prior to fragment or sequence analysis.
| Strain | Gene | Analysis | Caecal samples | Allele frequency | ||||
| CamR2 | Cj0685 | Fragment | 8C (−1) | 9C (ORF) | 10C (+1) | |||
| Frozen (CM3) | 43 % | 57 % | ||||||
| Fresh (CM1) | 48 % | 51 % | 1 % | |||||
| Cj1139 | Fragment | 7G (−1) | 8G (ORF) | |||||
| Frozen (CM3) | 55 % | 45 % | ||||||
| Fresh (CM1) | 55 % | 45 % | ||||||
| Cj1421 | Sequence | 8G (−1) | 9G (ORF) | 10G (+1) | 11G (+2) | |||
| Frozen (CM3) | 4 % | 35 % | 61 % | |||||
| Fresh (CM1) | 4 % | 50 % | 38 % | 8 % | ||||
| Cj1426 | Fragment | 9G (−1) | 10G (ORF) | 11G (+1) | ||||
| Frozen (CM3) | 57 % | 43 % | ||||||
| Fresh (CM1) | 55 % | 43 % | 2 % | |||||
| KanR4 | Cj0170 | Fragment | 8G (ORF) | 9G (+1) | 10G (+2) | |||
| Frozen (CM3) | 5 % | 72 % | 23 % | |||||
| Fresh (CM2) | 4 % | 76 % | 20 % | |||||
| Cj1422 | Sequence | 8G (−1) | 9G (ORF) | 10G (+1) | ||||
| Frozen (CM3) | 4 % | 87 % | 9 % | |||||
| Fresh (CM2) | 100 % | |||||||
| Cj1426 | Fragment | 9G (−1) | 10G (ORF) | 11G (+1) | ||||
| Frozen (CM3) | 12 % | 75 % | 13 % | |||||
| Fresh (CM2) | 8 % | 84 % | 8 % | |||||
| 33292 | Cj0045 | Fragment | <8G | 9G | 10G | 11G | 12G | |
| Frozen (CM3) | 4 % | 25 % | 66 % | 5 % | ||||
| Fresh (CM1) | 4 % | 26 % | 48 % | 21 % | 1 % | |||
| Cj1420 | Fragment | 8G (−1) | 9G (ORF) | |||||
| Frozen (CM3) | 85 % | 15 % | ||||||
| Fresh (CM1) | 84 % | 16 % | ||||||