Table 4.
Possible epidemiological associations between BCA dairies based on isolates with a difference of ≤3 SNP.
| Dairies with closely related isolates (≤3 SNP) | Total matches within 3 SNPs | Total genomes per dairy | |
|---|---|---|---|
| Dairy001* | Dairy003*, Dairy004, Dairy005*, Dairy007*, Dairy011, Dairy047, Dairy050*, Dairy057 | 8 | 29 |
| Dairy002 | Dairy062 | 1 | 2 |
| Dairy003 | Dairy001, Dairy004, Dairy025 | 3 | 3 |
| Dairy004 | Dairy001, Dairy003, Dairy015, Dairy037 | 4 | 22 |
| Dairy005* | Dairy001*, Dairy014* | 2 | 7 |
| Diary006* | Dairy064* | 1 | 12 |
| Dairy007* | Dairy001* | 1 | 6 |
| Dairy009 | Dairy039, Dairy053 | 2 | 7 |
| Dairy010 | Dairy037 | 1 | 3 |
| Dairy011 | Dairy001, Dairy039 | 2 | 3 |
| Dairy012 | Dairy028, Dairy044 | 2 | 5 |
| Dairy014 | Dairy005 | 1 | 6 |
| Dairy015 | Dairy004, Dairy026 | 2 | 19 |
| Dairy016 | Dairy039 | 1 | 8 |
| Dairy023 | Dairy025 | 1 | 7 |
| Dairy025* | Dairy003, Dairy023, Dairy039*, Dairy040 | 4 | 23 |
| Dairy026 | Dairy015, Dairy037 | 2 | 4 |
| Dairy028* | Dairy012* | 1 | 3 |
| Dairy029* | Dairy037* | 1 | 3 |
| Dairy033 | Dairy041 | 1 | 8 |
| Dairy037* | Dairy004, Dairy010, Dairy026, Dairy029* | 4 | 18 |
| Dairy039 | Diary006, Dairy009, Dairy011, Dairy016, Dairy025, Dairy053 | 6 | 24 |
| Dairy040 | Dairy025 | 1 | 9 |
| Dairy041 | Dairy033 | 1 | 1 |
| Dairy044 | Dairy012 | 1 | 11 |
| Dairy047 | Dairy001 | 1 | 11 |
| Dairy050 | Dairy001 | 1 | 2 |
| Dairy053 | Dairy009, Dairy039 | 2 | 1 |
| Dairy055 | Unknown | 1 | 6 |
| Dairy057 | Dairy001 | 1 | 1 |
| Dairy062 | Dairy002 | 1 | 1 |
| Dairy064* | Diary006* | 1 | 4 |
| Unknown | Dairy055 | 1 | 4 |
Total associations found for each dairy and total number of high-quality genomes for the specific dairy are indicated. An asterisk indicates associations based on a 0 SNP difference (identical SNP profiles).