TABLE 1.
Salmonella enterica strains isolated from stream sediment and poultry litter in the Shenandoah Valley of Virginia from October 2016 through September 2018.
| Isolate | SRR number | Collection date | Sourcea | Source type | Serotype | MLSTb | cgMLSTc |
| HJ-01 | SRR5886281 | 2016/10/02 | MC | Sediment | Give | 654 | 97788 |
| HJ-02 | SRR5886286 | 2016/10/02 | MC | Sediment | Give | 654 | 80760 |
| HJ-03 | SRR5886299 | 2016/10/02 | PR | Sediment | Uganda | 684 | 80845 |
| HJ-04 | SRR5886298 | 2016/10/02 | PR | Sediment | Uganda | 684 | 70491 |
| HJ-05 | SRR5886283 | 2016/10/16 | CC11 | Sediment | Litchfield | 214 | 80915 |
| HJ-06 | SRR5886290 | 2016/10/16 | CC11 | Sediment | Schwarzengrund | 96 | 80849 |
| HJ-07 | SRR5886279 | 2016/10/16 | PR | Sediment | Muenster | 321 | 80796 |
| HJ-08 | SRR5886351 | 2016/10/16 | PR | Sediment | Muenster | 321 | 80796 |
| HJ-09 | SRR5886350 | 2016/10/16 | CC704 | Sediment | Mbandaka | 413 | 80794 |
| HJ-10 | SRR5884063 | 2016/12/05 | MC | Sediment | Anatum | 64 | 80537 |
| HJ-11 | SRR5884068 | 2016/12/05 | CC704 | Sediment | Schwarzengrund | 96 | 80539 |
| HJ-12 | SRR5884053 | 2016/12/05 | CC704 | Sediment | Senftenberg | 14 | 80536 |
| HJ-13 | SRR5884069 | 2017/01/15 | CC11 | Sediment | Hadar | 33 | 80533 |
| HJ-14 | SRR5884070 | 2017/01/15 | CC11 | Sediment | Hadar | 33 | 80527 |
| HJ-15 | SRR5884058 | 2017/01/15 | CC11 | Sediment | Hadar | 33 | 80538 |
| HJ-16 | SRR5884066 | 2017/02/01 | L | Litter | Cerro | 367 | 80542 |
| HJ-17 | SRR5884067 | 2017/02/01 | L | Litter | Typhimurium | 19 | 80529 |
| HJ-18 | SRR5884056 | 2017/02/01 | L | Litter | Typhimurium | 19 | 80535 |
| HJ-19 | SRR5884062 | 2017/02/01 | L | Litter | Typhimurium | 19 | 80530 |
| HJ-20 | SRR5884079 | 2017/02/01 | L | Litter | Typhimurium | 19 | 80534 |
| HJ-21 | SRR5884080, SRR13268785d | 2017/02/05 | CC11 | Sediment | Typhimurium | 19 | 80528 |
| HJ-22 | SRR5884077 | 2017/02/26 | CC704 | Sediment | Muenchen | 112 | 80532 |
| HJ-23 | SRR5884081 | 2017/02/26 | CC704 | Sediment | Muenchen | 112 | 80526 |
| HJ-24 | SRR6832866, SRR13268782d | 2017/09/10 | PR | Sediment | Montevideo | 138 | 111799 |
| HJ-25 | SRR6832877 | 2017/09/10 | PR | Sediment | Montevideo | 138 | 169196 |
| HJ-26 | SRR6832873 | 2017/09/10 | MC | Sediment | Senftenberg | 14 | 111800 |
| HJ-27 | SRR6366729 | 2017/10/22 | CC704 | Sediment | Cerro | 367 | 101373 |
| HJ-28 | SRR6367403 | 2017/10/22 | CC704 | Sediment | Cerro | 367 | 101373 |
| HJ-29 | SRR6369106, SRR13268783d | 2017/10/22 | CC704 | Sediment | Anatum | 64 | 11895 |
| HJ-30 | SRR6367413 | 2017/10/22 | CCP | Sediment | Braenderup | 22 | 4601 |
| HJ-31 | SRR6367404 | 2017/10/22 | CCP | Sediment | Braenderup | 22 | 101420 |
| HJ-32 | SRR6367414 | 2017/10/22 | CCP | Sediment | Braenderup | 22 | 4601 |
| HJ-33 | SRR6367467 | 2017/10/22 | MC | Sediment | Montevideo | 138 | 101411 |
| HJ-34 | SRR6832876 | 2018/01/21 | CCP | Sediment | Braenderup | 22 | 113399 |
| HJ-35 | SRR6832896 | 2018/01/21 | CCP | Sediment | Braenderup | 22 | 4601 |
| HJ-36 | SRR6832925 | 2018/01/21 | CCP | Sediment | Typhimurium | 19 | 113353 |
| HJ-37 | SRR6832911 | 2018/01/21 | CCP | Sediment | Typhimurium | 19 | 111797 |
| HJ-38 | SRR6832904, SRR13268784d | 2018/01/21 | CCP | Sediment | Typhimurium | 19 | 111798 |
| HJ-39 | SRR6832916 | 2018/01/21 | CCP | Sediment | Typhimurium | 19 | 111391 |
| FHS-01 | SRR6832910 | 2018/01/23 | CC704 | Sediment | Montevideo | 138 | 166542 |
| FHS-02 | SRR6832913, SRR13268786d | 2018/01/23 | CC704 | Sediment | Infantis | 32 | 111896 |
| FHS-04 | SRR6832912 | 2018/01/23 | CC704 | Sediment | Montevideo | 138 | 152383 |
| DG-01 | SRR8360264 | 2018/05/20 | PR | Sediment | Muenchen | 112 | 131452 |
| DG-02 | SRR8360271 | 2018/05/20 | PR | Sediment | Montevideo | 138 | 131598 |
| DG-03 | SRR8104581 | 2018/05/20 | PR | Sediment | Montevideo | 138 | 131599 |
| DG-04 | SRR8104579 | 2018/05/20 | CC11 | Sediment | Hadar | 33 | 131627 |
| DG-05 | SRR8104582 | 2018/05/20 | CC11 | Sediment | Hadar | 33 | 131627 |
| DG-06 | SRR7504390 | 2018/05/20 | CC11 | Sediment | Hadar | 33 | 131627 |
| DG-07 | SRR7506701 | 2018/05/20 | CC11 | Sediment | Hadar | 33 | 136579 |
| DG-08 | SRR7506695 | 2018/05/20 | CC704 | Sediment | Typhimurium | 19 | 136587 |
| DG-09 | SRR7506699 | 2018/05/20 | CC704 | Sediment | Typhimurium | 19 | 131813 |
| DG-10 | SRR8360260 | 2018/05/20 | CC704 | Sediment | Typhimurium | 19 | 153131 |
| DG-11 | SRR7504359 | 2018/05/20 | CC704 | Sediment | Typhimurium | 19 | 153155 |
| DG-12 | SRR7506710 | 2018/05/20 | CC704 | Sediment | Typhimurium | 19 | 153158 |
| DG-13 | SRR7499244 | 2018/05/20 | CC704 | Sediment | Typhimurium | 19 | 153152 |
| DG-14 | SRR7499253 | 2018/05/20 | MC | Sediment | Meleagridis | 463 | 135814 |
| DG-15 | SRR7499245 | 2018/05/20 | MC | Sediment | Meleagridis | 463 | 135813 |
| DG-16 | SRR7499272 | 2018/05/20 | MC | Sediment | Cerro | 367 | 135849 |
| DG-17 | SRR7499280 | 2018/05/20 | MC | Sediment | Meleagridis | 463 | 135804 |
| DG-18 | SRR7499278 | 2018/05/20 | MC | Sediment | Meleagridis | 463 | 135809 |
| DG-19 | SRR7889322 | 2018/05/20 | CC11 | Sediment | Schwarzengrund | 96 | 144617 |
| DG-20 | SRR7878396 | 2018/05/20 | CC704 | Sediment | Alachua | 1298 | 144057 |
| DG-21 | SRR7889352 | 2018/05/20 | CCP | Sediment | Mbandaka | 413 | 144638 |
| DG-22 | SRR7878395 | 2018/05/20 | BR | Sediment | Mbandaka | 413 | 144059 |
| AP-01 | SRR8179982 | 2018/09/03 | CC11 | Sediment | Bareilly | 2553 | 153210 |
| AP-02 | SRR8179943 | 2018/09/03 | CC11 | Sediment | Bareilly | 2553 | 153210 |
| AP-03 | SRR8179958 | 2018/09/03 | CC11 | Sediment | Bareilly | 2553 | 153210 |
| AP-04 | SRR8179911 | 2018/09/03 | CC11 | Sediment | Bareilly | 2553 | 153210 |
| BES-01 | SRR8179966 | 2018/09/03 | CC704 | Sediment | Reading | 412 | 153206 |
| BES-02 | SRR8179907 | 2018/09/03 | CC11 | Sediment | Reading | 412 | 153208 |
| PPL-01 | SRR8179980 | 2018/09/03 | CC11 | Sediment | Braenderup | 22 | 4601 |
| PPL-02 | SRR8179892 | 2018/09/03 | CC11 | Sediment | Braenderup | 22 | 4601 |
| WEK-01 | SRR8179901 | 2018/09/03 | CC704 | Sediment | Montevideo | 138 | 153130 |
| WEK-02 | SRR8179936 | 2018/09/03 | CC11 | Sediment | Mbandaka | 413 | 153196 |
| WEK-03 | SRR8179927 | 2018/09/03 | CC11 | Sediment | Braenderup | 22 | 4601 |
| WEK-04 | SRR8179981 | 2018/09/03 | CC11 | Sediment | Mbandaka | 413 | 153188 |
| WMD-01 | SRR8570270 | 2018/09/30 | PR | Sediment | Muenchen | 112 | 164635 |
| WMD-02 | SRR8570265 | 2018/09/30 | CC11 | Sediment | Give | 654 | 169281 |
| WMD-03 | SRR8570271 | 2018/09/30 | MC | Sediment | Montevideo | 138 | 164641 |
| WMD-04 | SRR8570267 | 2018/09/30 | MC | Sediment | Montevideo | 138 | 164640 |
| WMD-05 | SRR8570264 | 2018/09/30 | CCA | Sediment | Muenster | 321 | 164639 |
| WMD-07 | SRR8573695 | 2018/09/30 | PR | Sediment | Montevideo | 138 | 164637 |
| WMD-08 | SRR8570269 | 2018/09/30 | CCA | Sediment | Montevideo | 138 | 164636 |
| WMD-09 | SRR8570273 | 2018/09/30 | MC | Sediment | Montevideo | 138 | 164643 |
| WMD-10 | SRR8570263 | 2018/09/30 | CCA | Sediment | Cerro | 367 | 164638 |
| WMD-11 | SRR8570268 | 2018/09/30 | MC | Sediment | Typhimurium | 19 | 164642 |
| WMD-12 | SRR8570266 | 2018/09/30 | BR | Sediment | Give | 654 | 164644 |
| WMD-13 | SRR8570272 | 2018/09/30 | CCA | Sediment | Cerro | 367 | 164645 |
aPR: Pleasant Run, CC11: Cook’s Creek Rt. 11, CC704: Cook’s Creek Rt. 704, CCP: Cook’s Creek Park, CCA: Cook’s Creek Arboretum, MC: Muddy Creek, BR: Black’s Run, and L: poultry litter.
bMLST: 7-gene multilocus sequence type.
ccgMLST: core-genome multilocus sequence type, Enterobase scheme (Zhou et al., 2018).
dOxford Nanopore fastq SRR numbers.