Table 2.

PCR primers and conditions used in this study

Primer designationNucleotide sequence of primersTargetPCR conditionsLength of PCR product (bp)Reference for PCR
DenaturingAnnealingExtension
TempaTb TempaTb TempaTb
KS7 5′-CCCGGATCCATGAAAAAAACATTATTAATAGC-3′ stx1B 94305260724028542
KS8 5′-CCCGAATTCAGCTATTCTGAGTCAACG-3′
GK3 5′-CCCGGATCCATGAAGAAGATGTTTATGGCG-3′ stx2B 94305260724026014
GK4 5′-CCCGAATTCTCAGTCATTTATTAAACTGCAC-3′ stx2c B
LP43 5′-ATCCTATTCCCGGGAGTTTACG-3′ stx2Aand variants94305760726058410
LP44 5′-GCGTCATCGTATACACAGGAGC-3′
VT2-cm 5′-AAGAAGATATTTGTAGCGG-3′ stx2d 94305560726025635
VT2-f 5′-TAAACTGCACTTCAGCAAAT-3′
SK1 5′-CCCGAATTCGGCACAAGCATAAGC-3′ eae 94305260726086343
SK2 5′-CCCGGATCCGTCTCGCCAGTATTCG-3′
Hly A1 5′-GGTGCAGCAGAAAAAGTTGTAG-3′ EHEChlyA 9430576072901,55145
Hly A4 5′-TCTCGCCTGATAGTGTTTGGTA-3′
asnU 5′-TTTCGCTGTTAAGATGTGCC-3′ asnU/int 9430536072601,500This studyc
int2 5′-TGCTTCCAGATAATCCGACCAC-3′
asnV 5′-GACAGCAAACAAACAAAAA-3′ asnV/int 9430536072601,500This study
int2 5′-TGCTTCCAGATAATCCGACCAC-3′
ybtEup 5′-GCAAGATAGACAAAAAACGCC-3′ ybtE/fyuA 946052607260359This study
fyuybtE (IX) 5′-GCTGACAACGGTAGACGAGA-3′
fyuA FP 5′-GCGACGGGAAGCGATTTA-3′ fyuA 94605760726078049
fyuA RP (X) 5′-CGCAGTAGGCACGATGTTGTA-3′
50A 5′-ATTGATCCACCGTTTTACTC-3′ IS100 946050607260100This study
50B (XI) 5′-CGAACGAAAGCATGAAACAA-3′
int5 5′-ATGGAATCGGGTTTATGGG-3′ int/ybtS 946054607260830This study
ybtSlp (XII) 5′-GCTATTGCTGAACTGGAGG-3′
ybtSup 5′-GAAACAGCACGGTAAACGCA-3′ ybtS/ybtQ 94305560721802,797This study
ybtQ3lp (XIII) 5′-ACGCGGCAGGAGGTAGAAG-3′
ybtQup 5′-GCCGCCAGTCTATCCACA-3′ ybtQ/ybtA 94305260721802,805This study
ybtA1lp (XIV) 5′-GAATCGGCCACAATAGGA-3′
ybtAup 5′-GGTATGGATATTTTGCTCTGG-3′ ybtA/irp2 9460546072601,340This study
irp2 RP (XV) 5′-TCGTCGGGCAGCGTTTCTTCT-3′
irp2-1up 5′-ACCTCTTCACCCACCCTTCT-3′ irp2/irp1 946054607260300This study
irp1-1lp (XVI) 5′-TTCAGGAAAATGGCAGGCGT-3′
irp1-1up 5′-TTCCGGTCCCCTGTCTCA-3′ irp1/ybtT 94305260721201,762This study
ybtTlp (XVII) 5′-ATCCGCCAATGTCTATCA-3′
asnT 5′-GACAGACAAGGTACCGCTAA-3′ asnT/int 9460526072601,500This study
int2 5′-TGCTTCCAGATAATCCGACCAC-3′
asnT1 5′-CACGATTCCTCTGTAGTTCA-3′ asnT/int 9460526072601,255This study
int3 (I) 5′-TCCTTTTTCGTGTCGTAACCC-3′
asnT1 5′-CACGATTCCTCTGTAGTTCA-3′ asnT/int 9460526072601,500This study
int2 (II) 5′-TGCTTCCAGATAATCCGACCAC-3′
int1 5′-TCCCTTACCGACGCAAAAATCC-3′ int 9460586072601,203This study
int2 (III) 5′-TGCTTCCAGATAATCCGACCAC-3′
ybtSup 5′-GAAACAGCACGGTAAACGCA-3′ ybtS 946052607260160This study
ybtSlp (IV) 5′-GCTATTGCTGAACTGGAGG-3′
ybtQup 5′-CGGGCGGCCTCTTCTACCT-3′ ybtQ 943059607290797This study
ybtQ1lp (V) 5′-GCGATGCGGCGACAAATGC-3′
ybtAup 5′-GGTATGGATATTTTGCTCTGG-3′ ybtA 946052607260233This study
ybtAlp (VI) 5′-GGTAATGCTCTCGAATCGG-3′
irp2 FP 5′-AAGGATTCGCTGTTACCGGAC-3′ irp2 94606060726028049
irp2 RP (VII) 5′-TCGTCGGGCAGCGTTTCTTCT-3′
irp1up 5′-TGAATCGCGGGTGTCTTATGC-3′ irp1 94605660726024034
irp1lp (VIII) 5′-TCCCTCAATAAAGCCCACGCT-3′
ybtTup 5′-TGCAAAAACAGCCCAGTA-3′ ybtT/fyuA 94305060721802,518This study
fyuA1lp (XVIII) 5′-CATTCCATCCCACATAGG-3′
  • a Temperature in degrees Celsius.

  • b Time in seconds.

  • c The primers asnU and asnV were designed according to DNA sequences published for the respective genes inE. coli K-12 (1); the primer pair asnT/int2 and the primer pairs targeting the regions I to VI, IX, and XI to XVIII were designed according to published sequences of Y. pestisHPI (13).