Table 3.
Phylogroups determined with gel-based PCR and phylogroups and sequence types determined via Enterobase.
| Sample ID | Trial | Timepoint (h) | Sampling site | Phylogroup FU1 | Phylogroup Enterobase | ST 7 gene MLST2 | ST cGMLST3 | HC1100 cgST4 | H-Antigen | O-Antigen |
|---|---|---|---|---|---|---|---|---|---|---|
| 7-1EP06 | Summer | 0 h | Barn | D/E | D | 2,309 | 86,589 | 5,033 | H6 | O15 |
| 7-1EP05 | Summer | 0 h | Barn | D/E | D | 2,309 | 86,626 | 5,033 | H6 | O15 |
| 7-1MP03 | Summer | 0 h | Surface | D/E | D | 2,309 | 86,616 | 5,033 | H6 | O15 |
| 7-1MP05 | Summer | 1 h | Depth | D/E | D | 2,309 | 86,618 | 5,033 | H6 | O15 |
| 7-1MP11 | Summer | 3 h | Depth | B1 | B1 | 162 | 86,592 | 138 | H10 | O9 |
| 7-1MP10 | Summer | 3 h | Surface | D/E | D | 2,309 | 86,619 | 5,033 | H6 | O15 |
| 7-1MP16 | Summer | 6 h | Surface | B1 | B1 | 1,304 | 86,593 | 152 | H7 | O91 |
| 7-1MP17 | Summer | 6 h | Depth | D/E | D | 2,309 | 86,608 | 5,033 | H6 | O15 |
| 7-1MP23 | Summer | 12 h | Depth | B1 | D | 2,309 | 86,590 | 5,033 | H6 | O15 |
| 7-1MP22 | Summer | 12 h | Surface | B1 | B1 | 162 | 86,622 | 138 | H10 | O88 |
| 7-1MP31 | Summer | 24 h | Depth | D/E | D | 2,309 | 86,580 | 5,033 | H6 | O15 |
| 7-1MP39 | Summer | 36 h | Depth | D/E | D | 2,309 | 86,577 | 5,033 | H6 | O15 |
| 7-1MP34 | Summer | 36 h | Surface | B1 | B1 | 1,304 | 86,593 | 152 | H7 | O91 |
| 7-1MP38 | Summer | 36 h | Surface | D/E | D | 2,309 | 86,614 | 5,033 | H6 | O15 |
| 7-1MP35 | Summer | 36 h | Depth | D/E | D | 2,309 | 86,620 | 5,033 | H6 | O15 |
| 7-1MP37 | Summer | 36 h | Depth | D/E | D | 2,309 | 86,617 | 5,033 | H6 | O15 |
| 7-1MP41 | Summer | 48 h | Depth | D/E | D | 2,309 | 86,580 | 5,033 | H6 | O15 |
| 7-1MP40 | Summer | 48 h | Surface | D/E | D | 2,309 | 86,601 | 5,033 | H6 | O15 |
| 7-1MP42 | Summer | 48 h | Surface | D/E | D | 2,309 | 86,623 | 5,033 | H6 | O15 |
| 7-1MP43 | Summer | 48 h | Depth | D/E | D | 2,309 | 86,623 | 5,033 | H6 | O15 |
| 7-1MP44 | Summer | 48 h | Surface | D/E | D | 2,309 | 86,580 | 5,033 | H6 | O15 |
| 7-1MP46 | Summer | 72 h | Surface | B1 | B1 | 162 | 86,615 | 138 | H10 | O88 |
| 7-1MP48 | Summer | 72 h | Surface | D/E | D | 2,309 | 86,625 | 5,033 | H6 | O15 |
| 7-1MP56 | Summer | 96 h | Surface | B1 | B1 | 1,304 | 86,593 | 152 | H7 | O91 |
| 7-1MP54 | Summer | 96 h | Surface | D/E | D | 2,309 | 86,624 | 5,033 | H6 | O15 |
| 5-2EP02 | Winter | 0 h | Barn | F | F | 117 | 86,591 | 50 | H4 | O8 |
| 5-2EP01 | Winter | 0 h | Barn | F | F | 117 | 86,578 | 50 | H4 | O8 |
| 5-2MP32 | Winter | 24 h | Surface | A/C | A | 10 | 86,613 | 13 | H48 | O12 |
| 5-2MP33 | Winter | 24 h | Depth | F | F | 117 | 86,579 | 50 | H4 | O8 |
| 5-2MP35 | Winter | 36 h | Depth | F | F | 117 | 86,599 | 50 | H4 | O8 |
| 5-2MP34 | Winter | 36 h | Surface | F | F | 117 | 86,653 | 50 | H4 | O8 |
| 5-2MP41 | Winter | 48 h | Depth | F | F | 117 | 86,647 | 50 | H4 | O8 |
| 5-2MP43 | Winter | 48 h | Depth | F | F | 117 | 86,600 | 50 | H4 | O8 |
| 5-2MP44 | Winter | 48 h | Surface | F | F | 117 | 86,621 | 50 | H4 | O8 |
| 5-2MP42 | Winter | 48 h | Surface | F | F | 117 | 86,632 | 50 | H4 | O8 |
| 5-2MP49 | Winter | 72 h | Depth | F | F | 117 | 86,578 | 50 | H4 | O8 |
| 5-2MP50 | Winter | 72 h | Surface | F | F | 117 | 86,578 | 50 | H4 | O8 |
| 5-2MP48 | Winter | 72 h | Surface | F | F | 117 | 86,578 | 50 | H4 | O8 |
| 5-2MP46 | Winter | 72 h | Surface | F | F | 117 | 86,578 | 50 | H4 | O8 |
| 5-2MP55 | Winter | 96 h | Depth | F | F | 117 | 86,578 | 50 | H4 | O8 |
| 5-2MP54 | Winter | 96 h | Surface | F | F | 117 | 86,627 | 50 | H4 | O8 |
| 5-2MP57 | Winter | 96 h | Depth | F | F | 117 | 86,579 | 50 | H4 | O8 |
| 5-2MP56 | Winter | 96 h | Surface | F | F | 117 | 86,578 | 50 | H4 | O8 |
| 5-2MP52 | Winter | 96 h | Surface | F | F | 117 | 86,612 | 50 | H4 | O8 |
1
Freie Universität Berlin.
2
Sequence type 7 gene multilocus sequence type.
3
Sequence type core genome multilocus sequence type.
4
Hierarchical cluster 1,100 core genome sequence type.