Supplemental Table S1. Salmonella isolates included in study Allelic type for b Isolate a Serotype Source fima mdh manb. manb Dupli- subtype
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1 Supplemental Table S1. Salmonella isolates included in study Allelic type for b Isolate a Serotype Source fima mdh manb Combined ST b ST/Serotype County c Farm fima Deletion e manb Dupli- subtype cation d S5-386 Thompson cattle AP Livingston 905 No No S5-387 Muenster cattle AQ Franklin 909 No No S5-419 Newport cattle O Cortland 910 No No S5-420 Newport cattle O Seneca 903 No No S5-424 Newport cattle O St. Lawrence 204 No No S5-425* Muenster cattle AQ Wyoming 259 No No S5-427 Oranienburg cattle AZ Oneida 61 Yes No S5-428 Rough o:i:1,2 cattle J Oswego 906 No No S5-429 Typhimurium cattle I Cortland 911 No No S5-430 T. Copenhagen cattle K Oswego 906 No No S5-431 Kentucky cattle R Erie 901 No No S5-432 Muenster cattle AQ Wyoming 907 No No S5-433 Typhimurium cattle I Ontario 820 No No S5-436 Newport cattle O Oneida 902 No No S5-437 Agona cattle B Tompkins 908 No No S5-544 Newport cattle O Oneida 228 No No S5-545 Newport cattle O Wyoming 260 No No S5-546* Muenster cattle AQ Wyoming 259 No No S5-547 Agona cattle A Lewis 54 No No S5-548 Newport cattle O Franklin, VT 303 No No S5-549 Havana cattle BP Rensselaer 120 Yes No S5-550* T. Copenhagen cattle K Cayuga 97 No No S5-551 Adelaide cattle BT Washington 186 No No S5-552 Newport cattle O Chittenden, VT 489 No No S5-553* Infantis cattle BG Saratoga 223 Yes No S5-554 T. Copenhagen cattle K Cayuga 97 No No S5-555 Typhimurium cattle I Tompkins 100 No No S5-556* Typhimurium cattle I St. Lawrence 208 No No S5-557* Newport cattle O Franklin, VT 303 No No S5-558* 4,5,12:i:- cattle G Wyoming 261 No No S5-559 Montevideo cattle M Wyoming 415 No No S5-560* Infantis cattle BG Saratoga 223 Yes No S5-561* Newport cattle O Franklin, VT 488 No No
2 S5-562 Newport cattle O Lamoille, VT 359 No No S5-564 Typhimurium cattle I St. Lawrence 208 No No S5-565 Newport cattle O Clinton 308 No No S5-566* Infantis cattle BG Saratoga 223 Yes No S5-567* Newport cattle O Franklin, VT 488 No No S5-570 Bardo cattle N Franklin, VT 488 No No S5-571* Infantis cattle BG Saratoga 223 Yes No S5-575* Infantis cattle BG Saratoga 223 Yes No S5-577* Newport cattle O Franklin, VT 320 No No S5-578 Newport cattle O Franklin, VT 320 No No S5-580* 4,5,12:i:- cattle G Wyoming 261 No No S5-582* Infantis cattle BG Saratoga 223 Yes No S5-584* Infantis cattle BG Saratoga 223 Yes No S5-590* Infantis cattle BG Saratoga 223 Yes No S5-591* Newport cattle O Chittenden, VT 490 No No S5-593* Infantis cattle BG Saratoga 223 Yes No S5-594 Newport cattle O Clinton 524 No No S ,5,12:i:- cattle G Clinton 524 No No S5-597* 4,5,12:i:- cattle G Wyoming 261 No No S5-601 Newport cattle O Franklin, VT 218 No No S5-602 Newport cattle O Franklin, VT 300 No No S5-605* Newport cattle O Clinton 524 No No S5-607 Typhimurium cattle I Rensselaer 584 No No S5-610 Newport cattle O Cayuga 163 No No S5-611 Newport cattle O Niagara 510 No No S5-612 Newport cattle O Erie 522 No No S5-615* 4,5,12:i:- cattle G Wyoming 261 No No S5-617* Infantis cattle BG Saratoga 223 Yes No S5-618* 4,5,12:i:- cattle G Wyoming 261 No No S5-619* Newport cattle O Onondaga 152 No No S5-620 Typhimurium cattle I Wyoming 415 No No S5-621 Newport cattle O Wyoming 791 No No S5-622* 4,5,12:i:- cattle G Wyoming 261 No No S5-623* Newport cattle O Onondaga 152 No No S5-624 Newport cattle O Franklin, VT 488 No No S5-625* Newport cattle O Clinton 524 No No S5-626* Newport cattle O Chittenden, VT 490 No No
3 S5-627* Newport cattle O Chittenden, VT 490 No No S5-628 Newport cattle O Chittenden, VT 490 No No S5-629* Newport cattle O Niagara 510 No No S5-630 Montevideo cattle M Washington 521 No No S5-631* Newport cattle O Onondaga 152 No No S5-715 Newport cattle O Lewis 438 No No S5-722* Newport cattle O Cayuga 163 No No S5-725* Infantis cattle BG Saratoga 223 Yes No S5-729 Typhimurium cattle I Washington 804 No No S5-730* Newport cattle O Niagara 510 No No S5-732 Newport cattle O Onondaga 152 No No S5-734 Infantis cattle BG Cayuga 163 Yes No S5-737* 4,5,12:i:- cattle G Wyoming 261 No No S5-739 Newport cattle O Niagara 827 No No S5-740* Newport cattle O Niagara 510 No No S5-743* Infantis cattle BG Saratoga 223 Yes No S5-744 Typhimurium cattle I Wyoming 261 No No S5-746* Newport cattle O Niagara 510 No No S5-747 Typhimurium cattle I Wyoming 691 No No S5-748* Agona cattle B Rensselaer 584 No No S5-750* Infantis cattle BG Saratoga 223 Yes No S5-752* Newport cattle O Niagara 510 No No S5-757 Montevideo cattle M Livingston 329 No No S5-758* Newport cattle O Niagara 510 No No S5-759* 4,5,12:i:- cattle G Wyoming 261 No No S5-760* Infantis cattle BG Saratoga 223 Yes No S5-761 Thompson cattle BI Niagara 679 Yes No S5-762* Newport cattle O Niagara 510 No No S5-765 Thompson cattle BI Livingston 329 Yes No S5-766* Newport cattle O Clinton 524 No No S5-776 Newport cattle O Niagara 637 No No S5-777* 4,5,12:i:- cattle G Wyoming 261 No No S5-780* Newport cattle O Niagara 510 No No S5-782* 4,5,12:i:- cattle G Wyoming 261 No No S5-784 Typhimurium cattle I Clinton 764 No No S5-785* 4,5,12:i:- cattle G Wyoming 261 No No S5-786 T. Copenhagen cattle K Washington 225 No No
4 S5-788 Typhimurium cattle AV Niagara 904 No No S5-789 Muenster cattle AQ Orleans 853 No No S ,12:i:- cattle F Cattaraugus 680 No No S5-796 Typhimurium cattle L Chenango 105 No No S5-797* Typhimurium cattle L Washington 186 No No S5-798* Muenster cattle AQ Livingston 329 No No S5-799 Typhimurium cattle I Genesee 821 No No S5-800 T. Copenhagen cattle K Washington 186 No No S5-805 Typhimurium cattle I Orleans 826 No No S5-808* Newport cattle O Niagara 510 No No S ,5,12:i:- cattle G Niagara 510 No No S5-820* 4,5,12:i:- cattle G Wyoming 261 No No S5-822* Kentucky cattle R Wyoming 261 No No S5-829* 4,5,12:i:- cattle G Wyoming 261 No No S5-831 Typhimurium cattle I Wyoming 837 No No S5-833* Newport cattle O Niagara 510 No No S5-836 Bardo cattle N Genesee 838 No No S5-838* Muenster cattle AQ Livingston 329 No No S5-839 Infantis cattle BG Saratoga 223 Yes No S5-840* Kentucky cattle R Wyoming 261 No No S5-841* 4,5,12:i:- cattle G Wyoming 261 No No S5-842 Newport cattle O Chenango 105 No No S5-845* Typhimurium cattle I Clinton 764 No No S5-846* Newport cattle O Niagara 510 No No S5-864* Kentucky cattle R Wyoming 261 No No S5-865* 4,5,12:i:- cattle G Wyoming 261 No No S5-867 Agona cattle B Allegany 599 No No S5-868 Muenster cattle AQ Wyoming 259 No No S5-872 Agona cattle B Rensselaer 584 No No S5-873* Kentucky cattle R Wyoming 261 No No S5-876* 4,5,12:i:- cattle G Wyoming 261 No No S5-879* Newport cattle O Niagara 510 No No S5-882* Newport cattle O Niagara 510 No No S5-887* Newport cattle O Niagara 510 No No S5-889 Kentucky cattle R Wyoming 261 No No S ,5,12:i:- cattle G Wyoming 261 No No S5-896 Typhimurium cattle I Rensselaer 318 No No
5 S5-903* Newport cattle O Niagara 510 No No S5-910* Newport cattle O Niagara 510 No No S5-914* Newport cattle O Niagara 510 No No S5-916 Typhimurium cattle L Washington 186 No No S5-917 Muenster cattle AQ Livingston 329 No No S5-920* Newport cattle O Niagara 510 No No S5-924* 4,5,12:i:- cattle G Wyoming 261 No No S5-931* Typhimurium cattle I Rensselaer 125 No No S5-933 Typhimurium cattle I Clinton 243 No No S5-936 Typhimurium cattle I Rensselaer 125 No No S5-938* Newport cattle O Niagara 510 No No S5-947 Mbandaka catlle BL Lewis 11 Yes No S5-369 Saintpaul human AK Monroe No No S5-370 Typhimurium human I Chautauqua No No S5-371 Enteritidis human Q Erie No No S5-373 Braenderup human BH Westchester Yes No S ,5,12:i:- human AM Monroe No No S5-375 Typhimurium human I Kings No No S5-376 Enteritidis human Q Nassau No No S5-377 Enteritidis human Q Nassau No No S ,7:-:1,5 human AO Nassau No No S5-379 Panama human AJ Suffolk No No S5-380 Litchfield human AC Niagara No No S5-381 Typhimurium human I Washington No No S5-382 Montevideo human BD Chautauqua Yes No S5-383 Heidelberg human D Dutchess No No S5-388 Urbana human AY Schenectady Yes No S ,5,12:i:- human G Erie No No S ,5,12:i:- human G Monroe No No S5-391 Kintambo human BF Westchester Yes No S5-392 Typhimurium human I Westchester No No S5-393 Newport human O Putnam No No S5-394 Typhimurium human I Dutchess No No S5-395 Javiana human T Richmond No No S5-396 Newport human O Suffolk No No S5-397 Typhimurium human I St. Lawrence No No S ,5,12:i:- human G Westchester No No
6 S5-399 Hadar human AN Tompkins No No S ,5,12:i:- human G Erie No No S5-401 Muenster human AQ Chemung No No S5-402 Enteritidis human Q Unknown No No S5-404 Paratyphi C human BY Monroe No Yes S5-405 Saintpaul human AK Monroe No No S5-406 Javiana human U Bronx No No S5-407 Dublin human V Orange No No S5-408 Stanley human CC Niagara No Yes S ,5,12:i:- human G Erie No No S5-410 Urbana human AY Schenectady Yes No S5-411 Thompson human BI Wayne Yes No S5-412 Thompson human BI Saratoga Yes No S5-413 Newport human O Chenango No No S5-414 Enteritidis human Q Erie No No S5-415 Enteritidis human Q Broome No No S5-416 Enteritidis human AH Albany No No S5-417 Agbeni human BJ Albany Yes No S5-438 Weltvreden human BX Monroe No Yes S5-439 Dublin human V Suffolk No No S5-440 Heidelberg human D Franklin No No S5-441 Abony human AR Monroe No No S5-442 Poona human BB Onondaga Yes No S5-443 Enteritidis human Q Dutchess No No S5-444 Enteritidis human AH Tompkins No No S5-445 Enteritidis human Q Suffolk No No S5-446 Newport human O Saratoga No No S5-447 Paratyphi B var. Java human AD Erie No No S5-448 Heidelberg human D Erie No No S5-449 Newport human O Unknown No No S5-450 Thompson human BI Ulster Yes No S5-451 Mbandaka human BK Oneida Yes No S5-452 Typhimurium human I Nassau No No S5-453 Arechavaleta human AI Nassau No No S5-454 Panama human AJ Chenango No No S5-455 Heidelberg human D Monroe No No S5-456 Schwarzengrund human E Orleans No No
7 S5-458 Schwarzengrund human E Orleans No No S5-459 Enteritidis human AH Erie No No S5-460 Enteritidis human Q Monroe No No S5-461 Enteritidis human AH Delaware No No S5-462 Typhimurium human I Suffolk No No S5-464 Stanley human AL Nassau No No S5-465 Poona human Z Nassau No No S ,12:r:- human C Nassau No No S5-467 Enteritidis human Q Kings No No S5-468 Paratyphi B var. Java human AD Bronx No No S5-469 Abony human AR Monroe No No S5-470 Montevideo human BN Nassau Yes No S5-472 Thompson human BI Nassau Yes No S5-473 Typhimurium human I Suffolk No No S5-474 Montevideo human BC Suffolk Yes No S5-475 Heidelberg human D Nassau No No S5-476 Typhimurium human I Suffolk No No S5-477 Rublislaw human BA Orleans Yes No S5-478 Montevideo human BC Suffolk Yes No S5-479 Muenchen human AG Suffolk No No S5-480 Heidelberg human D New York No No S5-481 Pomona human AA Erie No No S ,12:r:- human C Suffolk No No S5-483 Enteritidis human AH Westchester No No S5-484 Schwarzengrund human E Onondaga No No S5-485 Saintpaul human AK Erie No No S5-486 Enteritidis human Q Onondaga No No S5-487 Give human AB Unknown No No S5-488 Typhimurium human I Westchester No No S5-489 Newport human BU Suffolk No No S5-490 Worthington human BO Warren Yes No S5-491 Heidelberg human X Suffolk No No S5-492 Typhimurium human I Orange No No S5-493 Typhimurium human AT Suffolk No No S5-494 Typhimurium human I Bronx No No S5-495 Heidelberg human D Suffolk No No S5-496 Enteritidis human AH Monroe No No
8 S5-497 Enteritidis human Q Monroe No No S ,5,12:i:- human G Nassau No No S5-499 Paratyphi B human AU Nassau No No S5-500 Panama human CF Nassau No No S5-501 Typhimurium human I Nassau No No S5-502 Berta human CA Nassau No Yes S5-503 Newport human AE Genesee No No S5-504 Muenchen human BS Suffolk No No S5-505 Typhimurium human I Steuben No No S5-506 Infantis human BG Kings Yes No S5-507 Typhimurium human I Nassau No No S5-508 Enteritidis human AH Nassau No No S5-509 Typhimurium human I Washington No No S5-510 Hartford human BV Washington No No S5-511 Typhimurium human I Chemung No No S5-512 Saintpaul human BZ Monroe No Yes S5-513 Newport human AS Franklin No No S5-514 Enteritidis human Q Suffolk No No S5-515 Newport human O Niagara No No S5-516 Typhimurium human I Otsego No No S5-517 Agona human A Suffolk No No S5-518 Newport human O Wayne No No S5-519 Mbandaka human BR Erie No No S5-520 Typhimurium human I Steuben No No S5-521 Mbandaka human BR Erie No No S5-522 Enteritidis human Q Westchester No No S5-523 Thompson human AP Schenectady No No S5-524 Newport human BW Herkimer No Yes S5-525 Newport human O Westchester No No S ,5,12:i:- human G Suffolk No No S ,5,12:i:- human G Onondaga No No S5-528 Enteritidis human Q Erie No No S5-529 Anatum human W Erie No No S5-530 Anatum human W Erie No No S5-531 Typhimurium human CE Steuben No No S5-532 Typhimurium human I Cortland No No S5-533 Infantis human BG Saratoga Yes No
9 S5-534 Typhimurium human I Albany No No S5-535 Typhimurium human I Suffolk No No S5-536 Typhimurium human AV Jefferson No No S5-537 Newport human AE Erie No No S5-538 Enteritidis human Q Nassau No No S5-539 Enteritidis human Q Onondaga No No S5-540 Anatum human W Erie No No S5-541 Newport human O Ulster No No S ,7:-:1,5 human CG Dutchess No No S5-543 Hadar human AN Dutchess No No S5-632 Cubana human BQ Erie Yes No S5-633 Typhimurium human I Onondaga No No S ,5,12:i:- human G Suffolk No No S5-636 Muenchen human BS Saratoga No No S5-637 Berta human CB Oneida No Yes S5-639 Newport human BW Orange No Yes S5-640 Typhimurium human I Franklin No No S5-641 Enteritidis human Q Westchester No No S5-642 Oranienburg human AZ Nassau Yes No S5-643 Newport human P Nassau No No S5-645 Enteritidis human Q Orange No No S5-646 Adelaide human BT Albany No No S5-647 Agona human A Bronx No No S5-648 Blockley human Y Kings No No S5-649 Saintpaul human AK Bronx No No S5-650 Newport human AS Suffolk No No S5-651 Newport human BW Onondaga No Yes S5-652 Javiana human U Erie No No S5-653 Typhimurium human I Suffolk No No S5-654 Nyanza human BM Onondaga Yes No S5-655 Heidelberg human D Oneida No No S ,5,12:i:- human G Westchester No No S5-657 Mbandaka human BK Onondaga Yes No S5-658 Senftenberg human S Suffolk No No S5-659 Urbana human AY Clinton Yes No S5-660 Urbana human AY Clinton Yes No S5-661 Urbana human AY Schenectady Yes No
10 S ,7:-:1,5 human BE Allegany Yes No S5-663 Typhimurium human I Tompkins No No S5-664 Heidelberg human AW Suffolk No No S5-665 Javiana human T Nassau No No S ,5,12:i:- human G Warren No No S5-667 Agona human A Suffolk No No a Isolate designations followed by a * indicate bovine isolates not counted when calculating Chi square values and Fisher's exact test values. Only one representative isolate of each unique serotype/st combination per farm was used in the calculations b MLST and allelic types were assigned to be consistent with Alcaine et al. AAC : c All counties are in New York State, except for a small number of animal isolates from Vermont; for these isolates the county is followed by the state designation for Vermont (VT) d Indicates isolates which have two manb gene copies e Indicates isolates that have 3 bp or 5 bp deletions in the 3' region of the fima gene
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