Table S1 Rank 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
“Top 100” serotypes of Salmonella (2002-2006)
Serotype Typhimurium Enteritidis Newport Heidelberg Javiana Montevideo Muenchen I 4,[5],12:i:Saintpaul Oranienburg Braenderup Infantis Mississippi Thompson Agona Paratyphi B var. L(+) tartrate+ Typhi Berta Hadar Stanley Poona Bareilly Anatum Hartford Mbandaka Panama Paratyphi B Litchfield Sandiego Schwarzengrund Derby Paratyphi A Tennessee Brandenburg Senftenberg Norwich Rubislaw Give Miami Gaminara Weltevreden Bovismorbificans Kentucky Virchow Muenster Dublin Manhattan Pomona Reading Adelaide
Subsp. I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I
O Group B D1 C2 B D1 C1 C2 B B C1 C1 C1 G C1 B B D1 D1 C2 B G C1 E1 C1 C1 D1 B C2 B B B A C1 B E4 C1 F E1 D1 I E1 C2 C2 C1 E1 D1 C2 M B O
O Antigen 4,[5],12 9,12 6,8,[20] 4,[5],12 9,12 6,7,[14] 6,8 4,[5],12 4,[5],12 6,7,[14] 6,7,[14] 6,7,[14] 13,23 6,7,[14] 4,[5],12 4,[5],12 9,12,[Vi] 9,12 6,8 4,[5],12,[27] 13,22 6,7,[14] 3,10[15][15,34 ] 6,7 6,7,[14] 9,12 4,[5],12 6,8 4,[5],12 4,12,[27] 4,[5],12 2,12 6,7,[14] 4,[5],12 1,3,19 6,7 11 3,10[15][15,34 ] 9,12 16 3,10[15] 6,8,[20] 8,[20] 6,7,[14] 3,10[15][15,34 ] 1,9,12,[Vi] 6,8 28 4,[5],12 35
H1 i g,m e,h r l,z28 g,m,s d i e,h m,t e,h r b k f,g,s b d f,g,t z10 d z y e,h y z10 l,v b l,v e,h d f,g a z29 l,v g,s,t e,h r l,v a d r r i r e,h g,p d y e,h f,g
H2 1,2 1,2 1,2 1,5 1,2 1,2 e,n,z15 1,5 1,5 1,5 1,2 e,n,x 1,2 1,6 1,5 1,6 e,n,x e,n,z15 1,5 1,2 1,2 e,n,z15 1,7 e,n,z15 1,6 e,n,x 1,7 1,5 1,7 z6 1,5 z6 1,2 1,5 1,5 1,7 1,5 -
Table S1 con’t Rank 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Serotype Ohio Blockley Kiambu Uganda Urbana I 4,[5],12:b:Minnesota Inverness Hvittingfoss Bardo Bredeney London Telelkebir Havana Johannesburg Cerro Albany Chester Worthington Indiana Istanbul Oslo Agbeni Grumpensis IV 48:g,z51:Alachua Cubana Haardt Eastbourne Lomalinda IV 50:z4,z23:Edinburg Baildon Ealing IV 50:g,z51:Monschaui IV 44:z4,z23:Choleraesuis Meleagridis Kottbus Kintambo Corvallis I 9,12:l,z28:Ibadan Rissen IIIa 18:z4,z23:Nima Irumu Pensacola Choleraesuis var. Kunzendorf
Subsp. I I I I I I I I I I I I I I I I I I I I I I I I IV I I I I I IV I I I IV I IV I I I I I I I I IIIa I I I I
O Group C1 C2 B E1 N B L P I C2 B E1 G G R K C2 B G B C2 C1 G G Y O G C2 D1 D1 Z C1 D2 O Z O V C1 E1 C2 G C2 D1 G C1 K M C1 D1 C1
O Antigen 6,7,[14] 6,8 4,12 3,10[15] 30 4,[5],12 21 38 16 8 4,12,[27] 3,10[15] 13,23 13,23 40 [6],[14],18 8,[20] 4,[5],12 13,23 4,12 8 6,7,[14] 13,23 13,23 48 35 13,23 8 9,12 9,12 50 6,7,[14] 9,46 35 50 35 44 6,7 3,10[15][15,34 ] 6,8 13,23 8,[20] 9,12 13,22 6,7,[14] 18 28 6,7 9,12 6,7
H1 b k z l,z13 b b b k b e,h l,v l,v d f,g,s b z4,z23 z4,z24 e,h z z z10 a g,m,[s],[t] d g,z51 z4,z23 z29 k e,h a z4,z23 b a g,m,s g,z51 m,t z4,z23 c e,h e,h m,t z4,z23 l,z28 b f,g z4,z23 y l,v m,t c
H2 l,w 1,5 1,5 1,5 e,n,x e,n,x 1,6 e,n,x 1,2 1,7 1,6 e,n,z15 e,n,x e,n,x l,w 1,7 e,n,x e,n,x 1,7 1,5 1,5 e,n,x 1,5 e,n,x 1,5 l,w 1,5 1,5 1,5 1,5 1,5
Fig. S1 H:1,5 lineages
fljB 1,5 Choleraesuis Decatur 04-0071 99 99
fljB 1,5 Choleraesuis Decatur 04-0073
fljB 1,5 Choleraesuis Decatur 04-0070 fljB 1,5 Infantis 1428
1
99 96 fljB 1,5 Nima 06-0205 100
fljB 1,5 Bovismorbificans 2201 fljB 1,5 Edinburg 05-0406
71
98
fljB 1,5 Edinburg 05-0436 fljB 1,5 Edinburg 05-0559 fljB 1,5 VI 11:a:1,5 2229
47
fljB 1,5 Choleraesuis Decatur 04 0074 99 fljB 1,5 Michigan 370 01
72
100
fljB 1,5 Choleraesuis Kunzendorf 04-0075 fljB 1,5 Choleraesuis Kunzendorf 04-0072
45
2
fljB 1,5 II 43:e,h:1,5 2532 76
fljB 1,5 Vanier 2205
63
fljB 1,5 Thompson 00-0342 100
fljB 1,5 Thompson 00-0476 fljB 1,5 Thompson 00-0499
100
fliC 1,5,7 II 17:e,n,x,z15:1,5,7 2157 fliC 1,5,7 II 40:e,n,x:1,5,7 2207 fliC 1,5 Cubana 1472
100
3
fliC 1,5 II 40:z6:1,5 1254 fljB 1,5,7 Hisingen 891 93
fljB 1,5 IIIb 60:z52:1,5,[7] Ar528
4
fljB 1,5 IIIb 47:l,v:1,5,(7) Ar251
96
fljB 1,5,7 IIIb 47:r:1,5,7 Ar467 10046 fljB 1,5 IIIb 61:c:1,5,(7) Ar222 fljB 1,5 IIIb 65:c:1,5,7 Ar418 77
fljB 1,5 IIIb 61:k:1,5,(7) 01-365 fljB 1,5,7 IIIb 48:l,v:1,5,(7) Ar209 74
fljB 1,5 IIIb 42:l,v:1,5,7 Ar208 fljB 1,5,7 IIIb 61:lv:1,5,7 02-0010
fljB 1,5 IIIb Rough:z10:15 02-0029
0.005
5
Fig. S2 H:a lineages 100 58 67
fliC a Paratyphi A 1
fliC a Paratyphi A 2
1
fliC a Damman 05-0035
57
fliC a Jangwani 05-427
fliC a IV 44:a:- 2639 72 fliC a IV 51:a:- 2642 96 100 fliC a IV 50:a:- 2575 67
100
fliC a Miami 427 fliC a Miami 198
76
2
3
fliC a I 40:a:1,7 05-390 fliC a II 13,23:a:1,5 2488
4
fliC a II 58:a:z6 05-327 93 52
fliC a II 47:a:1,5 05-473
5
fliC a II 6,7:a:z6 1225 fliC a VI 6,14,25:a:e,n,x 811 100
fliC a VI 6,14:a:e,n,x CNM 186
fliC a VI 11:a:1,5 2229
0.005
6
t-1 target region
Fig. S3
Majority
A A C T C A G G G G C G G T A G T A A C T G A C A C C A C T G C T C C A A C T G T T C C T
I_fliC_f,g,t 02-616 Berta.seq I_fliC_f,g,t 02-617 Berta.seq I_fliC_f,g,t 1544 Berta.seq I_fliC_g,s,t 672 Senftenberg v T1 I_fliC_g,t 520 Agodi II_fliC_g,t 548 16:g,t:[1,5] II_fliC_g,m,s,t 1055 Namib II_fliC_g,m,s,t 1432 Mosselbay II_fliC_g,m,t 1836 II 28:g,m,t:e,n,x II_fliC_g,m,t 2492 II 6,8:g,m,t:1,7 I_fliC_m,p,t,u 1229 Haelsingborg I_fliC_m,p,t,u 586 Haelsingborg I_fliC m,t_1109 California I_fliC_m,t_212 Monschaui I_fliC_m,t 2226 Oranienburg I_fliC_m,t 2410 Oranienburg I_fliC_g,s,t 2309 Missouri
A A A A A A A A A A A A A A A A A
640 A A A A A A A A A A A A A A A A A
C C C T T T T T T T C C C C C C T
T T T T T T T T T T T T T T T T T
C C C C C C C C C C C C C C C C C
A A A A C C A A A A A A A A A A A
G G G G G G G G G G G G G G G G G
G G G G G G G G G G G G G G G G G
G G G T T T T T T T G G G G G G T
G G G G G G G G G G G G G G G G G
650 C C C C C C C C C C C C C C C C C
G G G T T T T T T T G G G G G G T
G G G G G G G G G G G G G G G G G
T T T T T T T T T T T T T T T T T
G G G G G G G G G G G G G G G G G
T T T T T T T T T T T T T T T T T
A A A A G G A A A A A A A A A A A
A A A A A A A A A A A A A A A A A
C C C C C C C C C C C C C C C C C
660 T T T T T T T T T T T T T T T T T
G G G G G G G G G G G G G G G G G
A A A A A A A A A A A A A A A A A
C C C T T T T T T T C C C C C C T
A A A G G G G G G G A A A A A A G
C C C A C C A A C C C C C C C C A
I_fliC_d 59 Typhi I_fliC_d 189 Virginia I_fliC_d 1629 Schwarzengrund I_fliC_d 2668 Muenchen I_fliC_d 08_0185 Putten I_fliC_d 08_0464 Putten I_fliC_d 08_0589 Putten
A A A G G G G G G G A A A A A A G
C C C C C C C C C C C C C C C C C
T T T A A A A A A A T T T T T T A
670 G G G G G G G G G G G G G G G G G
C C C C C C C C C C C C C C C C C
T T T A A A A A C C T T T T T T A
C C C C C C C C C C C C C C C C C
C C C C C C C C C C C C C C C C C
A A A G G G G G G G A A A A A A G
A A A A A A A A A -
C C C C C C C C C -
T T T T T T T T T -
G G G G G G G G G -
T T T T T T T T T -
T T T T T T T T T -
C C C C C C C C C -
C C C C C C C C C -
T T T T T T T T T -
675 675 675 666 666 666 666 666 666 666 675 675 675 675 675 675 666
C T A C A A A G A A A G T T A A T A T T G A T A C G A C T 760
I_fliC_d 57 Typhi
C C C T A A T T A A C C C C C C T
d probe target region
Fig. S4
Majority
A A A A A A A A A A A A A A A A A
C C C C C C C C
T T T T T T T T
A A A A A A A A
C C C C C C C C
A A A A A C C C
A A A A A A A A
A A A A A A A A
G G G G G G G G
A A A A A A A A
770 A A A A A A A A
A A A A A A A A
G G G G G G G G
T T T T T T T T
T T T T T T T T
A A A A A A A A
A A A A A G G G
T T T T T T T T
A A A A A A A A
T T T T T T T T
780 T T T T T A A A
G G G G G G G G
A A A A A A A A
T T T T T T T T
A A A A A A A A
C C C C C C C C
G G G G G A A A
A A A A A A A A
C C C C C C C C
T T T T T T T T
780 780 780 780 780 780 780 780
