Table 2.

Primer pair sequences, concentration, amplicon size, and T_m value for each SYBR® Green qPCR assay

Targeted genus	Targeted pathotype	Targeted gene	Primer pair name	Primer name	Primer sequence, 5′- > 3′	Primer concentration	Product size (bp)	Reference	Average Tm value specificity (°C)
Escherichia	All	β-Glucuronidase (uidA)	uidA-3	uidA-3-F-tronc	GCAGTTTCATCAATCACCAC	250 nM	87	This study	78.4
				uidA-3-R	CTCCTACCGTACCTCGCATTAC	250 nM
			uidA-7	uidA-7-F	GGGATAGTCTGCCAGTTCAGTT	250 nM	83	This study	77.2
				uidA-7-R-deg	GATGTCACDCCGTATGTTATTG	250 nM
Shigella/ Escherichia	All/ EIEC	Invasion plasmid antigen H (ipaH)	ipaH-569	ipaH-569-F	CCTTTTCCGCGTTCCTTGA	1000 nM	64	Thiem et al. (2004)	78.5
				ipaH-569-R	CGGAATCCGGAGGTATTGC	1000 nM
			ipaH-3	ipaH-3-F	ACAGGTGATGCGTGAGACTG	500 nM	101	This study	80.5
				ipaH-3-R-deg	ATGAATGGTGCAGTYGTGAG	500 nM
Escherichia	EHEC	Intimin (eae)	eae-185	eae-185-F	CATTGATCAGGATTTTTCTGGTGATA	1000 nM	102	Nielsen et al. (2003)	75.9
				eae-185-R	CTCATGCGGAAATAGCCGTTA	1000 nM
			eae-EBP1	eae-EBP-1F	CGTCATGGTACGGGTAAT	1000 nM	83	This study	74
				eae-EBP-1Rdeg	ATTTGCTGAGACCACGRTTT	1000 nM
	VTEC	Shiga toxins 1 and 2 (stx1 & stx2 (except 2f))	stx1&2–4	stx1&2–4-F-deg	TTTGTYACTGTSACRGCWGAAGCYTTACG	1000 nM	131–128	Degenerated from Perelle et al. (2004)	stx1: 77.2, stx2: 78.1
				stx1&2–4-R	CCCCAGTTCARWGTRAGRTCMACRTC	1000 nM		Perelle et al. (2004)
	stx1 containing VTEC	Shiga toxins 1 (stx1) (all variants)	stx1–185	stx1–185-F	GTCACAGTAACAAACCGTAACA	250 nM	95	Jothikumar et al. (2002)	77.1
				stx1–185-R	TCGTTGACTACTTCTTATCTGGA	250 nM
	stx2 containing VTEC	Shiga toxins 2 (stx2) (all variants)	stx2–81-mix	stx2–81-deg-F	GTTTCCATGACRACGGACAGCAG	250 nM	122	Pavlovic et al. (2010)	78.5 (variant “f”) other variants 79.5–80
				stx2–81-alt-R	CTGAACTCCATTAAMKCCAGATATG	250 nM		This study
	Typical EAEC	Transcriptional activator of the aggregative adherence fimbriae (aggR)	aggR-185	aggR-185-F	CAGAATCGTCAGCATCAGCTACA	1000 nM	97	Fukushima et al. (2009)	74.5
				aggR-185-R	GATGCCCTGATGATAATATACGGAA	1000 nM
			aggR-2	aggR-F2	AACCAGATCCTTATGCAATCAA	500 nM	61	This study	73.5
				aggR-R2	ATGAGTTATCAAGCAACAGCAA	500 nM
	EAEC	aggR-Activated island C (aaiC)	aaiC-EBP1	aaiC-EBP1-F	TTATCAGGGGTGTCGTATGC	250 nM	92	This study	74
				aaiC-EBP1-Rdeg	CACTCTCTTCTGSGGTAAACG	250 nM
			aaiC-EBP2	aaiC-EBP2-Ftronc	GCTCTTAGCAGGGAGTTTG	250 nM	113	This study	75
				aaiC-EBP2-R	TGAAATGCCTGAGGACAATG	250 nM

In bold and italics are degenerated nucleotides: D = A or G or T, Y = C or T, S = C or G, R = A or G, W = A or T, M = A or C, K = G or T