Table 1.

Oligonucleotide Primers for Multiplex and Single Polymerase Chain Reaction Assays

Primer mix	Primer sequence	Primer name	Gene target	PCR Size (bp)	Pathotype	Plasmid controla
M1b	5′-GAGCGAAATAATTTATATGTG-3′	VT.F	VT	518	STEC	pOG401
	5′-TGATGATGGCAATTCAGTAT-3′	VT.R
	5′-CTGAACGGCGATTACGCGAA-3′	eae.F	eae	917	STEC, EPEC	pOG390
	5′-CGAGACGATACGATCCAG-3′	eae.R
	5′-AATGGTGCTTGCGCTTGCTGC-3′	bfpA.F	bfpA	326	EPEC	pOG394
	5′-GCCGCTTTATCCAACCTGGTA-3′	bfpA.R
	5′-GTATACACAAAAGAAGGAAGC-3′	aggR.F	aggR	254	EAEC	pOG395
	5′-ACAGAATCGTCAGCATCAGC-3′	aggR.F
M2b	5′-GCACACGGAGCTCCTCAGTC-3′	LT.F	LT	218	ETEC	pWD299
	5′-TCCTTCATCCTTTCAATGGCTTT-3′	LT.R
	5′-GCTAAACCAGTAGAG(C)TCTTCAAAA-3′	ST.F	ST	147	ETEC	pSLm004
	5′-CCCGGTACAG(A)GCAGGATTACAACA-3′	ST.R
	5′-GAACGTTGGTTAATGTGGGGTAA-3′	daaE.F	daaE	542	DAEC	pOG391
	5′-TATTCACCGGTCGGTTATCAGT-3′	daaE.R
	5′-AGCTCAGGCAATGAAACTTTGAC-3′	virF.F	virF	618	EIEC	pOG392
	5′-TGGGCTTGATATTCCGATAAGTC-3′	virF.R
	5′-CTCGGCACGTTTTAATAGTCTGG-3′	ipaH.F	ipaH	933	EIEC	pOG393
	5′-GTGGAGAGCTGAAGTTTCTCTGC-3′	IpaH.R
Pc	5′-GACGAACCAACGGTCAGGAT-3′	chuA.F	chuA	279	NA	-
	5′-TGCCGCCAGTACCAAAGACA-3′	chuA.R
	5′-TGAAGTGTCAGGAGACGCTG-3′	yiaA.F	yiaA	211	NA	-
	5′-ATGGAGAATGCGTTCCTCAAC-3′	yiaA.R
	5′-GAGTAATGTCGGGGCATTCA-3′	TspE4C2.F	TspE4C2	152	NA	-
	5′-CGCGCCAACAAAGTATTACG-3′	TspE4C2.R
VT1	5′-CAGTTAATGTGGTGGCGAAGG-3	VT1.F	VT1	348	STEC	-
	5′CACCAGACAATGTAACCGCTG-3′	VT1.R
VT2	5′-ACCGTTTTTCAGATTTT(G/A)CACATA-3′	VT2.F	VT2	298	STEC	-
	5′-TACACAGGAGCAGTTTCAGACAGT-3′	VT2.R
uigA	5′-GCGTCTGTTGACTGGCAGGTGGTGG-3′	uidA.F	uidA	503	NA	-
	5′-GTTGCCCGCTTCGAAACCAATGCCT-3′	uidA.R

^aM1 and M2 are primer mixes to be used for the two-sample multiplex PCR assay for detection of Escherichia coli pathotypes.

^bPlasmids carrying each one of the E. coli pathotype gene targets. Plasmids are used as template DNA control for the two-sample multiplex PCR assay as previously described (Gomez-Duarte et al., 2009).

^cP is the primer mix to be used for a single-multiplex PCR for identification of phylogenetic group (Clermont et al., 2000).

PCR, polymerase chain reaction; EPEC, enteropathogenic Escherichia coli; STEC, shiga-toxin producing E. coli; EAEC, enteroaggregative E. coli; ETEC, enterotoxigenic E. coli; DAEC, diffuse adherent E. coli; EIEC, enteroinvasive E. coli; NA, not applicable.