Table S1: Primers used for multiplex and single PCR assays
Gene(s)
Description
Primer sequence (5´- 3´)
Size of
product
Primer
coordinates
GenBank
Acc.-No.
Source of
primer
afa/dra
Afimbrial/Dr-specific adhesin
s: TAAGGAAGTGAAGGAGCGTG
a: CCAGTAACTGTCCGTGACA
s: GATAAAACTGATACTGGGCAGC
a: AGTGACTGTTCGGGAAGCAC
s: ATGGCGCTAACTTGCCATGCTG
a: AGGGGGACATATAGCCCCCTTC
s: ACTCTGACTTGACTATTACC
a: AGATGCAGTCTGGTCAAC
s: GAATCTGTCCGAGAATATCA
a: GTTGGTACAGGTCTTAATGG
s: AATACTTGTTCAGGGAGAAA
a: AACTTTGTGGTTAACTTCCT
s: AAGTTACTGCCAGTCTATGC
a: GTAACTCCACCGTTTGTATC
a: TGGTAACGTATCAGCAACTA
s: ACTTACAGTGCTATTCGACG
s: AGTATCTGGTTCAGTGATGG
a. CCACTATAAGAGGTTGAAGC
s: GGGTAGAAAATGCCGATGGTG
a: CGTCATTTTGGGGGTAAGTGC
s: TGTTGGACCGTCTCAGGGCTC
a: CTCCCGGAACTCGCTGTTACT
s: TCACTTGCAGACCAGCGTTTC
a: GTAACTCACACTGCTGTCACCT
s: TAGTGCGTTGGGTTATCGCTC
a: AAGCCAGAGTGGTTATTCGC
s: TATACGCTGGACTGAGTCGTG
a: CAGGTAGCGTCGAACTGTA
810
1648-1667
2439-2457
2095-2116
2901-2920
79–100
562–583
276-295
458-475
94-113
573-592
488-507
698-717
705-724
1094-1115
24-43
317-336
299-318
891-910
4391-4411
4867-4887
111–131
1040–1060
136-156
651-672
44-64
633-652
499-519
1379-1397
AF325672
(Ewers, 2007)
bfp
Bundle forming pili
Z68186
(Mueller, 2006)
bmaE
Blood group M-specific adhesin
M15677
(Johnson, 2000)
csgA
Curli fibre gene
L04979
(Maurer, 1998)
faeG
F4 fimbrial adhesin
AJ610253.1
Z37500
(Moon et al.,
1999)
(Moon et al.,
1999)
(Moon et al.,
1999)
(Moon et al.,
1999)
(Moon et al.,
1999)
(Ewers, 2007)
fanA
F5 fimbrial adhesin
fasA
F6 fimbrial adhesin
fedA
F6 fimbrial adhesin
fimF41a
F41 fimbrial adhesin
fimC
Type 1 fimbriae
gafD
N-acetyl-D-glucosamine-specific
fimbrial lectin
Heat-resistant agglutinin
L33969
(Johnson, 2000)
AY040859
(Ewers, 2007)
AF401752
(Ewers, 2007)
AF325731
(Ewers, 2007)
s: GCTTACTGATTCTGGGATGGA
a: CGGTGGCCGAGTCATATGCCA
s: ATGGCAGTGGTGTCTTTTGGTG
557
S61970
(Johnson, 2000)
X61239
(Johnson, 2000)
Adhesins
hra
iha
mat
Iron-regulated-gene-homologueadhesin
Meningitis-associated and
temperature-regulated fimbriae
nfaE
Nonfimbrial adhesin
papA
Pyelonephritis associated pili
826
507
200
499
230
409
313
612
497
952
537
609
899
721
84–104
620–640
1796–1817
X05797.1
U50547.1
L26108.1
X14354.1
Gene(s)
Description
papC
Pyelonephritis associated pili
papEF
Pyelonephritis associated pili
papG II, III
Pyelonephritis associated pili
papG
allele II
allele III
Pyelonephritis associated pili
sfa/focDE
S-/F1C fimbrial adhesin
sfaS
Sialic acid-specific fimbrial
adhesin
F1C fimbrial adhesin
focG
tsh
Pyelonephritis associated pili
Temperature sensitive
hemagglutinin
Primer sequence (5´- 3´)
a: CGTCCCACCATACGTGCTCTTC
s: TGATATCACGCAGTCAGTAGC
a: CCGGCCATATTCACATAAC
s: GCAACAGCAACGCTGGTTGCATCAT
a: AGAGAGAGCCACTCTTATACGGACA
s: CTGTAATTACGGAAGTGATTTCTG
a: ACTATCCGGCTCCGGATAAACCAT
s: GGGATGAGCGGGCCTTTGAT
a: CGGGCCCCCAAGTAACTCG
s: GGCCTGCAATGGATTTACCTGG
a: CCACCAAATGACCATGCCAGAC
s: GTCCTGACTCATCTGAAACTGCA
a: CGGAGAACTGGGTGCATCTTA
s: GTGGATACGACGATTACTGTG
a: CCGCCAGCATTCCCTGTATTC
s: CAGCACAGGCAGTGGATACGA
a: GAATGTCGCCTGCCCATTGCT
s: ACTATTCTCTGCAGGAAGTC
a: CTTCCGATGTTCTGAACGT
Size of
product
501
336
1057
190
258
1243
242
359
824
Primer
coordinates
2495–2516
4313-4333
4795-4813
8025–8049
8336–8360
1198–1221
2230–2254
380-399
551-569
1420-1441
1656-1677
3618-3596
2376-2396
675–695
896–916
635–655
973–993
1499-1518
2304-2322
GenBank
Acc.-No.
Source of
primer
X61239
(Janßen, 2001)
X61239
M20181
X61238
AY212280
(Yamamoto,
1995)
(Marklund,
1992)
(Johnson, 2001)
X61238
(Johnson, 2001)
AY436351
(Ewers, 2007)
S53210
(Johnson, 2000)
S68237
(Johnson, 2000)
AJ223631
(Ewers, 2007)
U67920
(Clermont, 2000)
Z38064
(Schubert, 1998)
AF320691
(Ewers, 2007)
AF135597
(Ewers, 2007)
L18881
(Schubert, 1998)
M18968
(Janßen, 2001)
X05874
(Johnson, 1998)
AM072350
(Ewers, 2007)
Iron acquisition
chuA
Heme receptor gene
fyuA
Ferric yersinia uptake
ireA
Iron-responsive element
iroN
Catecholate siderophore receptor
irp2
Iron-repressible protein
iucD
Iron uptake chelate
iutA
Iron uptake transport
sit chr.
Salmonella iron transport system
s: GACGAACCAACGGTCAGGAT
a: TGCCGCCAGTACCAAAGACA
s: GCGACGGGAAGCGATGACTTA
a: CGCAGTAGGCACGATGTTGTA
s: ATTGCCGTGATGTGTTCTGC
a: CACGGATCACTTCAATGCGT
s: ATCCTCTGGTCGCTAACTG
a: CTGCACTGGAAGAACTGTTCT
s: AAGGATTCGCTGTTACCGGAC
a: TCGTCGGGCAGCGTTTCTTCT
s: ACAAAAAGTTCTATCGCTTCC
a: CCTGATCCAGATGATGCTC
s: GGCTGGACATCATGGGAACTGG
a: CGTCGGGAACGGGTAGAATCG
s: ACTCCCATACACAGGATCTG
279
774
385
847
413
693
300
554
735-754
994-1013
786-806
1539-1559
31-50
396-415
336-354
1162-1182
22-42
416-434
239-259
913-931
851–872
1132–1152
4118-4137
Gene(s)
Description
Primer sequence (5´- 3´)
Size of
product
Primer
coordinates
GenBank
Acc.-No.
Source of
primer
sit epis.
gene
Salmonella iron transport system
gene
a: CTGTCTGTGTCCGGAATGA
s: TTGAGAACGACAGCGACTTC
a: CTATCGAGCAGGTGAGGA
1052
4653-4671
4764343-24
1617-1634
CP000468
AY598030
(Ewers, 2007)
kpsMT
Group II capsule antigens
neuC
K1 capsular polysaccharide
ompA
Outer membrane protein
traT
Transfer protein
s: TCCAAGCGGACCCCTTATAG
a: CGCAGCATAGTTCCATGCT
s: ATCACATAGGATTCTGCCG
a: CAGCGGAGTATAGATGCCA
s: GCGCATTTGCTGATACTGTTG
a: CATCCAGACGATAAGCATGAGCA
s: GGTGGTACATTCCGGGATGTC
a: AGGTGAAAAGCCTGGTAGTGTG
s: AGCTATCGCGATTGCAGTG
a: GGTGTTGCCAGTAACCGG
s: GTGGTGCGATGAGCACAG
a: TAGTTCACATCTTCCACCATCG
598
iss
Structural genes of Colicin V
operon
Increased serum survival
X57525
(Ewers, 2007)
AF042279
(Ewers, 2005)
DQ242482
(Johnson, 2000)
M84026
(Watt, 2003)
V00307
(Ewers, 2007)
X06915
(Ewers, 2007)
s: TCGTTATAAAATCAAACAGTG
a: CTTTACAATATTGACATGCTG
446
X70670
(Ewers, 2004)
Protectins
cvi/cva
310
270
676
919
430
97-116
676-694
264-282
555-573
17100-17080
16831-16853
1314-1294
639-660
1048-1066
1949-1966
710-727
1118-1139
Toxins
cnf 1/2
Cytotoxic necrotising factor
EAST-1
Heat-stable cytotoxin
s: TGCCATCAACACAGTATATCC
a: TAGGATCCTCAGGTCGCGAGTGACGGC
111
eltB-Ip
Heat-labile enterotoxin
272
est-Ia
Heat-stable enterotoxin
est-II
Heat-stable enterotoxin
hlyA
Hemolysin A
sat
Secreted autotransporter toxin
a: GGCGTTACTATCCTCTCTAT
s: TGGTCTCGGTCAGATATGT
s: CAACTGAATCACTTGACTCTT
a: TTAATAACATCCAGCACAGG
s: TGCCTATGCATCTACACAAT
a: CTCCAGCAGTACCATCTCTA
s: GTCCATTGCCGATAAGTTT
a: AAGTAATTTTTGCCGTGTTTT
s: TGCTGGCTCTGGAGGAAC
a: TTGAACATTCAGAGTACCGGG
158
113
351
667
cnf1: 1817-1846
2241-2262
cnf2: 1073-1093
1498-1518
135-155
219-245
33-52
286-304
356-376
494-513
514-533
607-626
972-991
1302-1322
591-608
1237-1257
U01097
AF143819
M14107
(Yamamoto and
Echeverria,
1996)
(Moon et al.,
1999)
(Moon et al.,
1999)
(Moon et al.,
1999)
(Ewers, 2004)
AF289092
(Ewers, 2007)
FJ156281.1
M58746.1
AY028790.1
Gene(s)
Description
Primer sequence (5´- 3´)
Size of
product
Primer
coordinates
GenBank
Acc.-No.
Source of
primer
stx1A
Shigatoxin 1
s: GGCGTTCTTATGTAATGACTGC
a: ATCCCACGGACTCTTCCATC
s: CGTTTTGACCATCTTCGTCTG
a: AGCGTAAGGCTTCTGCTGTG
s: TCCTGGGACATAATGGCTAG
a: GTGTCAGAACGGAATTGTC
250
626-647
856-875
1947-1967
2252-2271
311997-982
311020-038
EU273279
(Mueller, 2006)
stx2A
Shigatoxin 2
AB290938
(Mueller, 2006)
vat
Vacuolating autotransporter toxin
CP000468
(Ewers and
Kießling, 2004)
s: TCCAGATTGAGCATATCCC
a: CCTGTAACATGTTGGCTTCA
s: TGGAACCCGCTCGTAATATAC
a: CTGCCTGTTCAAGCATTGCA
s: AGCGCTTCCGTCAGGACTT
a: ACCAGCATCCAGATAGCGAT
737
AJ810519
(Ewers, 2007)
AY248744
(Ewers, 2007)
U20318
(Ewers, 2007)
s: GGCTCTCTTCTTCTTTATGGCTG
a: CCTTTTACAAACTTCATCGCC
s: GGACATCCTGTTACAGCGCGCA
a: TCGCCACCAATCACAGCCGAAC
s: ACTGGATCTTAAGGCTCAGG
a: TGGAATATCAGGGTGCCACT
s: CGCTTCATCAACACGCTTTA
a: CCATCGCCTATCACCTCAAC
534
AF200363
(Mueller, 2006)
AF003742
(Johnson, 2000)
AF097644
(Ewers, 2007)
AM229678
Karch and Zhang
(personal
communication)
325
978
Invasins
gimB
Genetic island meningitis
ibeA
Invasion of brain endothelium
tia
Toxigenic invasion locus
342
512
369-387
1086-1105
55-75
377-396
143-161
635-654
Miscellaneous/Others
escv
Type III secretion system
malX
pic
Pathogenicity-associated island
marker CFT073
Serine protease autotransporter
pks
Polyketide megasynthase
922
411
290
15703-15725
16216-16236
1021-1042
1921-1942
2566-2585
2957-2976
29904-29923
30174-30193
Primer references
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Ewers, C., Janssen, T., Kiessling, S., Philipp, H.C., Wieler, L.H. (2005) Rapid detection of virulence-associated
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coli serogroup O78 strains isolated from diarrheal cases in bovines urge further investigations on their zoonotic
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