Comprehensive and Rapid Real-Time PCR Analysis of 21 Foodborne Outbreaks

Table 2

22 pairs of specific primers for SYBR Green I PCR

Primer set for duplex PCR	Species and subgroups	Target gene		PCR primers			GenBank accession no.	location	Product size (bp)	𝑇𝑚 values^a	References
				Name	Forward or revers	primers' sequences (5' - 3')
First run	1 Escherichia coli	eaeA	∗^𝑏	eae	F2	CATTGATCAGGATTTTTCTGGTGATA	Z11541	899-924	106	83.2±0.2	[14]
	EPEC and EHEC				R	CTCATGCGGAAATAGCCGTTA		1000-979
	Staphylococcus aureus	femB	*	FemB	fw	AATTAACGAAATGGGCAGAAACA	AF106850	277-299	93	80.8±0.3	[15]
					rv	TGCGCAACACCCTGAACTT		370-351
	2 Campylobacter jejuni	C. jejuni- specific DNA	*	AB	F	CTGAATTTGATACCTTAAGTGCAGC	AL111168	381135	86	79.1±0.4	[8]
		DNA			R	AGGCACGCCTAAACCTATAGCT		381185
	EAEC	astA		EAST-1	S	GCCATCAACACAGTATATCC	L11241	63-82	106	84.9±0.6	[16]
					AS	GAGTGACGGCTTTGTAGTCC		168-148
	3 Vibrio parahaemoliticus	tdh		Tdh199	F	GGTACTAAATGGCTGACATC	X54341	601-582	251	81.6±0.3	[17]
					R	CCACTACCACTCTCATATGC		351-370
	Emetic Bacillus cereus	ces	*	ces-TM	F	GATGTTTGCGACGATGCAA	DQ360825	8689-8707	65	80.4±0.1	This study
					R	CTTTCGGCGTGATACCCATT		8793-8734
	4 Salmonella spp.	invA	*	Styinva	JHO-2-right	TCGTCATTCCATTACCTACC	M90846	167-186	119	81.3±0.4	[5]
					JHO-3-left	AAACGTTGAAAAACTGAGGA		285-234
	Clostridium perfringens	cpe		GAP	11	GGTTCATTAATTGAAACTGGTG	X81849	583-604	154	78.3±0.4	[18]
					12	AACGCCAATCATATAAATTACAGC		712-736
Second and third runs	5 ETEC (ST)	ST		STa	F	GCTAATGTTGGCAATTTTTATTTCTGTA	M25607	294-321	190	78.5±0.2	[19]
					R	AGGATTACAACAAAGTTCACAGCAGTAA		483-456
	Plesiomonas shigelloides	gyrB		PSG	237-F	TTCCAGTACGAGATCCTGGCTAA	AJ300545	237-259	68	83.1±0.2	[13]
					304-R	TGAATCGACACGCCAGAGTTC		304-284
	6 EAggEC	aggR	*	aggR-Z	F	CAGAATCGTCAGCATCAGCTACA	Z18751	432-454	97	79.5±0.3	This study
					R	GATGCCCTGATGATAATATACGGAA		358-382
	EIEC & Shigella spp.	virA		virA	F	CTGCATTCTGGCAATCTCTTCACA	D26468	1589-1622	215	82.4±0.3	[20]
					R	TGATGAGCTAACTTCGTAAGCCCTCC		1813-1788
	7 Aeromonas hydrophila	ahh1	*	AHH1	F	GCCGAGCGCCCAGAAGGTGAGTT	CP000462	1653360-82	133	89.8±0.4	[21]
					R	GAGCGGCTGGATGCGGTTGT		1653492-73
	ETEC (LT)	LT		LT	1	AGCAGGTTTCCCACCGGATCACCA	S60731	613-636	132	82.0±0.3	[22]
					2	GTGCTCAGATTCTGGGTCTC		744-725
	8 Providencia alcalifaciens	gyrB		PAG	38F	TCTGCACGGTGTGGGTGTT	AJ300547	38-56	73	81.0±0.2	[13]
					110R	ACCGTCACGGCGGATTACT		110-92
	Enterotoxigenic B. cereus	nheB	*	SG	F3	GCACTTATGGCAGTATTTGCAGC	DQ153257	2101-2123	152	82.7±0.4	[23]
					R3	GCATCTTTTAAGCCTTCTGGTC		2252-2231
	9 Yersinia enterocolitica	yadA	*	yadA-X	F	CCAGAACCAATTGCAATGCCT	X13882	1564-1543	100	81.6±0.2	This study
	Y. pseudotuberculosis				R	CTTTAAACAGCTTGTTCCAGCCA		1465-1487		81.1±0.3
	Campylobacter coli	ceuE	*	CCceuE	825F	ACGCGCACAAGGCATACTT	X88849	3513-3531	91	77.6±0.3	This study
					915R	CCAGTATTCAGGATCAAGATAAATGATTT		3603-3575
	10 Vibrio cholerae	hlyA		hlyA	2272-F	AGCAGCGTGTGGGACAAGA	X51746	2272-2291	71	82.4±0.1	[13]
					2272-F	GCGGACCCTAATGCATCAAT		2342-2323
	Vibrio parahaemoliticus	trh		Trh	250-F	GGCTCAAAATGGTTAAGCG	DQ359748	256-274	250	81.1±0.1	[17]
					251-R	CATTTCCGCTCTCATATGC		505-487
Singl PCR	EHEC (Stx 1)	Stx1		JMS1	F	GTCACAGTAACAAACCGTAACA	EF441598	509-488	95	81.1±1.0	[12]
					R	TCGTTGACTACTTCTTATCTGGA		415-437
Singl PCR	EHEC (Stx 2)	Stx2		JMS2	F	CGACCCCTCTTGAACATA	EF441616	140-157	108	81.7±0.3	[12]
					R	GATAGACATCAAGCCCTCGT		247-228

a: Average ± standard deviation of Tm values of 10 tests: b: *:new selected or designed primer