Table 5.

Different types of nucleic acid-based method approaches are used for the detection of food-borne pathogens.

Types of nucleic acid-based method	Pathogen name	Target site	Primer	Amplified product size (Base pair)	Probe	References
PCR	Escherichia coli	stx2b gene	Forward TATACGATGACACCGGAAGAAG Reverse CCTGCGATTCAGAAAAGCAGC	300	NA	[299]
	Salmonella typhimurium	MDH gene	Forward CGCATTCCACCACGCCCTTC Reverse TGCCAACGGAAGTTGAAGTG	261	NA	[300]
	Vibrio parahaemolyticus	VP1332 gene	Forward GTGCGTTGGGATTTGGTCT Reverse GGCGGTAAACTTCGTCAGG	352	NA	[301]
	Aspergillus flavus	Aflatoxin gene	Forward GTAGGGTTCCTAGCGAGCC Reverse GGAAAAAGATTGATTTGCG TTC	500	NA	[302]
Nested PCR	Yersinia enterocolitica	yadA gene	1st set primer Forward TAAGATCAGTGTCTCTGCGGCA Reverse TAGTTATTTGCGATCCCTAGCAC	747	NA	[303]
			2nd set primer Forward GCGTTGTTCTCATCTCCATATGC Reverse GGCTTTCATGACCATGGATACAC	529
	Salmonella enterica	fliC gene and stn gene	1st set primer Forward GGTCAAAATCCAGCGGTTTA Reverse TTGCTGCTAACGGCGAGA	1318	NA	[304]
			2nd set primer Forward GCCGGCTTTCAACGCCTCTAC Reverse GACCAAAGCTGACGGGACAG	450
Real-time PCR	E. coli O157:H7	stx2 gene	Forward ATTAACCACACCCCACCG Reverse GTCATGGAAACCGTTGTCAC	115	SensiFAST Probe	[305]
	Yersinia enterocolitica	ail gene	Forward ATGATAACTGGGGAGTAATAGGTTCG Reverse CCCAGTAATCCATAAAGGCTAACATAT		ail probe, Yc probe	[306]
	Campylobacter jejuni	hipO gene	Forward CAAAAAAATCCAAAATCCTCACTTG Reverse TGCACCAGTGACTATGAATAACGA	132	6-FAM and BHQ1 probe	[257]
	Bacillus cereus	ces gene	Forward CACGCCGAAAGTGATTATACCAA Reverse CACGATAAAACCACTGAGATAGTG	176	SYBR green I	[307]
Quantitative real time PCR	Escherichia coli	uidA gene	Forward CGGAAGCAACGCGTAAACTC Reverse TGAGCGTCGCAGAACATTACA	1300	Taq Man probe	[308]
	Listeria monocytogenes	hlyA gene	Forward GCAACAAACTGAAGCAAAGGAT Reverse CGATTGGCGTCTTAGGACTTGC	2000	hly specific probe	[309]
	Salmonella enterica	ssaN gene	Forward GCCAGAAGCGTGCTTTTCC Reverse GGGCAACGAGTGGGTATTTTT	–	IAC probe	[310]
Reverse transcriptase PCR	Vibrio spp.	16S rDNA	Forward ′-CGCCCGCCGCGCCCCGCGCCCGTCCCGCCGCCCCCGCCCGGGCGTAAAGCGCATGCAGGT Reverse GAATTCTACCCCCCTCTACAG	120	NA	[311]
	Escherichia coli	Shiga toxin(slt-II) operon	Forward TTAAATGGGTACTGTCCT Reverse CAGAGTGGTATAACTGCTGTC	401	NA	[312]
	Hepatitis A virus	capsid protein-coding region (VP1)	Forward CTCCAGAATCATCTCAAC Reverse CAGCACATCAGAAAGGTGAG	192	NA	[313]
Real-time reverse transcription PCR	Yeasts and molds	act gene	Forward CTGGGAYGAYATGGARAAGA Reverse GYTCRGCCAGGATCTTCAT	353	SYBR Green I	[314]
	Salmonella enterica	invA gene	Forward CACGCTCTTTCGTCTGGCA Reverse	154	SYBR Green I	[315]
	Listeria monocytogenes	hly gene	Forward ACTTCGGCGCAATCAGTGA Reverse TTGCAACTGCTCTTTAGTAACAGCTT	137	SYBR Green I	[316]
Multiplex PCR	Clostridium perfringens	cpa gene	Forward GCTAATGTTACTGCCGTTGA Reverse CCTCTGATACATCGTGTAAG	324	NA	[317]
		Cpb gene	Forward GCGAATATGCTGAATCATCTA Reverse GCAGGAACATTAGTATATCTTC	196
		Etx gene	Forward GCGGTGATATCCATCTATTC Reverse CCACTTACTTGTCCTACTAAC	655
		iA gene	Forward ACTACTCTCAGACAAGACAG Reverse CTTTCCTTCTATTACTATACG	446
		cpe gene	Forward GGAGATGGTTGGATATTAGG Reverse GGACCAGCAGTTGTAGATA	233
		cpb2 gene	Forward AGATTTTAAATATGATCCTAACC Reverse CAATACCCTTCACCAAATACTC	567
	Salmonella spp.	invA gene	Forward TTGTTACGGCTATTTTGACCA Reverse CTGACTGCTACCTTGCTGATG	521	NA	[318]
		sefA gene	Forward GCAGCGGTTACTATTGCAGC Reverse TGTGACAGGGACATTTAGCG	330
		pefA gene	Forward TTCCATTATTGCACTGGGTG Reverse GGCATCTTTCGCTGTGGCTT	497
	E. coli O157:H7	rfbE gene	Forward GCCACCCCCATTTTCGTTG Reverse TCCTCTCTTTCCTCTGCGGT	601	NA	[319]
	Staphylococcus aureus	nuc gene	Forward TACAGGTGACTGCGGGCTTATC Reverse CTTACCGGGCAATACACTCACTA	484
	Salmonella spp.	invA gene	Forward CTTTAGCCAAGCCTTGACGAAC Reverse AAAGGCAATACGCAAAGAGGT	284
	E. coli O157:H7	Stx1and stx2 gene	Forward GAGCGAAATAATTTATATGTG Reverse TGATGATGGCAATTCAGTAT	518	NA	[95]
	Salmonella spp.	invA gene	Forward ACAGTGCTCGTTTACGACCTGAAT Reverse AGACGACTGGTACTGATCGATAAT	284
	Listeria monocytogenes	hlyA gene	Forward CGCAACAAACTGAAGCAAAGG Reverse TTGGCGGCACATTTGTCAC	404
	Bacterial DNA	16S rRNA gene	Forward GTATTGAAAGCTCTGGCGG Reverse TCGCTTAGTCTCTGAACCC	654

PCR: polymerase chain reaction, NA: not applicable.