Table 1.
Strains Sequenced in This Study: Sources, Sequencing Data and tetA(C) Presence
| Isolatea | Farm # | Treatment | Mean Cov | Plasmid Cov | Pl:Chr | Suspected Mixed | # Contigs | Draft Length (bp) | TetRb | tetA(C) PCR | Tet-island |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 9-1 a | 1 | None | 20 | 66 | 4 | Only plasmid | 2 | 1082098 | S | N | N |
| 9-1 b | 1 | None | 134 | 462 | 4 | N | 1 | 1082175 | S | N | N |
| 1-25 a | 25 | None | 31 | 183 | 7 | Some read heterogeneity | 2 | 1088920 | S | N | N |
| 1-25 b | 25 | None | 75 | 536 | 8 | N | 2 | 1088751 | S | N | N |
| 3-25 a | 25 | None | 73 | 388 | 6 | Y – one dominant | 3 | 1092018 | S | N | N |
| 3-25 b | 25 | None | 28 | 146 | 6 | N | 1 | 1075010 | S | N | N |
| 9-25 a | 25 | None | 154 | 755 | 5 | N | 5 | 1093713 | S | N | N |
| 2-26 b | 26 | TSS | 27 | 134 | 6 | Y – one dominant | 1 | 1083861 | S | Y | N |
| 10-26 b | 26 | TSS | 29 | 109 | 4 | N | 1 | 1080931 | S | N | N |
| 14-23 b | 23 | TSS | 12 | 39 | 4 | Low coverage | 23 | 1081871 | S | N | N |
| 5-27 b | 27 | CTS | 45 | 326 | 8 | N | 1 | 1101914 | R | Y | Y |
| 1-28 a | 28 | Unknown | 119 | 633 | 6 | N | 2 | 1084542 | S | N | N |
| 1-28 b | 28 | Unknown | 129 | 872 | 7 | N | 2 | 1096577 | I | Y | Y, TetRfusion |
| 8-29 b | 29 | CTS | 93 | 427 | 5 | N | 1 | 1098010 | R | Y | Y |
| 6-17 a | 17 | CTS | 32.3 | 171 | 5 | Y – one dominant | 3 | 1072079 | S | N | N |
| 8-17 a | 17 | CTS | 16.5 | 135 | 8 | N | 2 | 1079515 | S | N | N |
| 11-17 a | 17 | CTS | 19.1 | 129 | 7 | N | 3 | 1106365 | R | Y | Y |
| 11-17 b | 17 | CTS | 24 | 123 | 5 | N | 3 | 1107636 | R | Y | Y |
| 5-22 b | 22 | CTS | 45 | 188 | 4 | Only plasmid | 1 | 1094277 | R | Y | Y |
| 22-22 b | 22 | CTS | 14.4 | 91 | 6 | Y – one dominant | 8 | 1092471 | R | Y | Y |
| 30-22 b | 22 | CTS | 37.6 | 213 | 6 | Y – one dominant | 2 | 1095150 | R | Y | Y |
| 15-27 b | 27 | CTS | 29.5 | 145 | 5 | N | 3 | 1103721 | R | Y | Y |
| 17-23 a | 23 | TSS | 12.3 | 66 | 6 | N | 5 | 1102774 | R | Y | Y |
| 17-23 b | 23 | TSS | 13.8 | 83 | 6 | N | 9 | 1072633 | S | Y | N |
| 19-23 a | 23 | TSS | 13.3 | 76 | 6 | N | 8 | 1099448 | R | Y | Y |
| 19-23 b | 23 | TSS | 6.1 | 21 | 3 | N | 344 | 1045494 | S | N | N |
| 3-29 b | 29 | CTS | 20.3 | 103 | 5 | N | 2 | 1096059 | R | Y | Y |
| 4-29 b | 29 | CTS | 15.7 | 67 | 4 | N | 1 | 1094002 | R | Y | Y |
| 9-29 b | 29 | CTS | 65.9 | 266 | 4 | Only plasmid | 5 | 1092041 | R | Y | Y |
| mean 5 |
a
Isolate refers to the pig ID followed by either: a, indicating first sample at beginning of fattening period, before antibiotic treatment; or b, indicating second sample at end of fattening period, after antibiotic treatment. Paired samples from the same pig at these timepoints are shaded together. Cov = coverage. bR, resistant; S, sensitive; I, intermediate. Anomalous tetA(C) PCR results are shown with a grey background.