TABLE 1.

Primer and probe sequences used for detection of bacterial and viral pathogens

Target organism and gene	Primer	Sequence (5′→3′)a	Reference
V. parahaemolyticus
tlh	Forward	ACTCAACACAAGAAGAGATCGACAA	Nordstrom et al., 2007 (64)
	Reverse	GATGAGCGGTTGATGTCCAAA	Nordstrom et al., 2007 (64)
	Probe	TxRed-CGCTCGCGTTCACGAAACCGT-BHQ2	Nordstrom et al., 2007 (64)
tdh	Forward	TCCCTTTTCCTGCCCCC	Nordstrom et al., 2007 (64)
	Reverse	CGCTGCCATTGTATAGTCTTTATC	Nordstrom et al., 2007 (64)
	Probe	6FAM-TGACATCCTACATGACTGTG-MGBNFQ	Nordstrom et al., 2007 (64)
trh	Forward	TTGCTTTCAGTTTGCTATTGGCT	Nordstrom et al., 2007 (64)
	Reverse	TGTTTACCGTCATATAGGCGCTT	Nordstrom et al., 2007 (64)
	Probe	TET-AGAAATACAACAATCAAAACTGA-MGBNFQ	Nordstrom et al., 2007 (64)
Salmonella spp. (invA)	Forward	CAACGTTTCCTGCGGTACTGT	This study
	Reverse	CCCGAACGTGGCGATAATT	This study
	Probe	TxRed-CTCTTTCGTCTGGCATTATCGATCAGTACCA-BHQ2	This study
Toxigenic V. cholerae (ctx)	Forward	TTTGTTAGGCACGATGATGGAT	Blackstone et al., 2007 (8)
	Reverse	ACCAGACAATATAGTTTGACCCACTAAG	Blackstone et al., 2007 (8)
	Probe	6FAM-TGTTTCCACCTCAATTAGTTTGAGAAGTGCCC-BHQ1	Blackstone et al., 2007 (8)
Norovirus GI	Forward	CGYTGGATGCGNTTYCATGA	Kageyama et al., 2003 (47)
	Reverse	CTTAGACGCCATCATCATTYAC	Kageyama et al., 2003 (47)
	Probe	Cy5-AGATYGCGATCYCCTGTCCA-IBRQ	Kageyama et al., 2003 (47)
	Probe 2	Cy5-AGATCGCGGTCTCCTGTCCA-IBRQ	Kageyama et al., 2003 (47)
	Forward	TGGACICGYGGICCYAAYCA	Beuret et al., 2003 (6)
	Reverse	GAASCGCATCCARCGGAACAT	Beuret et al., 2003 (6)
Norovirus GII	Forward	CARGARBCNATGTTYAGRTGGATGAG	Kageyama et al., 2003 (47)
	Reverse	TCGACGCCATCTTCATTCACA	Kageyama et al., 2003 (47)
	Probe	Cy3-TGGGAGGGCGATCGCAATCT-IBRQ	Kageyama et al., 2003 (47)
	Forward	TGGACICGYGGICCYAAYCA	Beuret, et al., 2003 (6)
	Reverse	GAAYCTCATCCAYCTGAACAT	Beuret et al., 2003 (6)
Hepatitis A virus	Forward	ATAGGGTAACAGCGGCGGATAT	Gardner et al., 2003 (42)
	Reverse	AATGCATCCACTGGATGAG	Gardner et al., 2003 (42)
	Probe	Cy5-AGACAAAAACCATTCAACGCCGGAGG-IBRQ	Gardner et al., 2003 (42)
Calicivirus SMSV-17	Forward	AATCAATTGATATCCTCAGACACTTCAC	Burkhardt et al., 2004 (19)
	Reverse	CCGCAACCTTGAAAGCCACAC	Burkhardt et al., 2004 (19)
	Probe	Cy5-AATTGTTGATTCGGCCTGTGCACCAC-IBRQ	Burkhardt et al., 2004 (19)
Internal control	46Fb	GACATCGATATGGGTGCCG	Nordstrom et al., 2007 (64)
	186Rc	CGAGACGATGCAGCCATTC	Nordstrom et al., 2007 (64)
	185Rd	GAGACGATGCAGCCATTCG	Blackstone et al., 2007 (8)
	194Re	AATATTCGCGAGACGATGCAG	This study
	Probef	Cy5-TCTCATGCGTCTCCCTGGTGAATGTG-BHQ2	Nordstrom et al., 2007 (64)
	Probeg	TxRed-TCTCATGCGTCTCCCTGGTGAATGTG-IBRQ	This study

^aAll primers and probes for this study were purchased from Integrated DNA Technologies (Coralville, IA). TxRed, Texas Red-X N-hydroxysuccinimide ester; BHQ2, black hole quencher-2; 6FAM, 6-carboxyfluorescein; MGBNFQ, TaqMan minor groove binder/nonfluorescent quencher; TET, tetrachlorofluorescein; BHQ1, black hole quencher-1; Cy5, cyanine 5; IBRQ, Iowa black RQ; Cy3, cyanine 3.

^bIC primer 46F used for amplification of the internal control target DNA or RNA in all assays.

^cIC primer 186R used for amplification of the internal control target DNA in the V. parahaemolyticus assay.

^dIC primer 185R used for amplification of the internal control target DNA in the Salmonella and toxigenic V. cholerae assays.

^eIC primer 194R used for amplification of the internal control target RNA in the norovirus, HAV, and SMSV-17 assays.

^fCy5-labeled IC probe used in the V. parahaemolyticus, Salmonella, and toxigenic V. cholerae assays.

^gTxRed-labeled IC probe used in the norovirus, HAV, and SMSV-17 assays.