Molecular Epidemiology of Salmonella enterica in Poultry in South Africa Using the Farm-to-Fork Approach

Table 1

Primers used for the amplification of Salmonella virulence genes.

Gene	Primer sequence	Initial denaturation	# of cycles	Cycling conditions			Final extension	Product size (bp)	References
				Denaturation	Annealing	Extension
hilA	F: 5′ CGGAAGCTTATTTG; CGCCATGCTGAGGTAG 3′	94°C, 5 m	30	94°C, 1 m	65°C, 1 m	72°C, 1 m	72°C, 10 m	854	[26]
	R: 5′ GCATGGATCCCCG; CGGCGAGATTGTG 3′
spiC	F: 5′ CCTGGATAATGAC; TATTGAT 3′	94°C, 3 m	30	94°C, 1 m	55°C, 1 m	72°C, 1 m	72°C, 5 m	309	[21, 28]
	R: 5′ AGTTTATGGTG; ATTGCGTAT 3′
misL	F:5′ GTCGGCGAATGC; CGCGAATA 3′	94°C, 3 m	30	94°C, 1 m	55°C, 1 m	72°C, 1 m	72°C, 5 m	550	[21, 28]
	R: 5′ GCGCTGTTAAC; GCTAATAGT 3′
orfL	F: 5′ GGAGTATCGAT; AAAGATGTT 3′	94°C, 3 m	30	94°C, 1 m	55°C, 1 m	72°C, 1 m	72°C, 5 m	350	[21, 28]
	R: 5′ GCGCGTAACGTC; AGAATCAA 3′
pipD	F: 5′ CGGCGATTCATG; ACTTTGAT 3′	94°C, 5 m	34	94°C, 25°s	56°C, 30°s	72°C, 50°s	72°C, 5 m	400	[21, 28]
	R: 5′ CGTTATCATTCG; GATCGTAA 3′
sopB	F: 5′ TCAGAAGRCGTC; TAACCACTC 3′	94°C, 3 m	30	94°C, 1 m	55°C, 1 m	72°C, 1 m	72°C, 5 m	517	[27]
	R: 5′ TACCGTCCTCA; TGCACACTC 3′
stn	F: 5′TTGTGTCGCTATCA; CTGGCAACC 3′	94°C, 5 m	25	94°C, 1 m	59°C, 1 m	72°C, 1 m	72°C, 10 m	617	[26]
	R: 5′ ATTCGTAACCCG; CTCTCGTCC 3′
fliC	F: 5′ CGGTGTTGCCCA; GGTTGGTAAT 3′	94°C, 3 m	30	94°C, 1 m	55°C, 1 m	72°C, 1.5 m	72°C, 10 m	620	[26]
	R: 5′ ACTGGTAAAGAT; GGCT 3′
pefA	F: 5′ TGTTTCCGGGCT; TGTGCT 3′	94°C, 5 m	25	94°C, 55°s	55°C, 55°s	72°C, 55°s	72°C, 10 m	700	[26]
	R: 5′ CAGGGCATTTGC; TGATTCTTCC 3′
spvA	F: 5′GTCAGACCCGT; AAACAGT 3′	94°C, 5 m	30	94°C, 30°s	60°C, 30°s	72°C, 1 m	72°C, 5 m	604	[29]
	R: 5′ GCACGCAGAG; TACCCGCA 3′
spvB	F: 5′ ACGCCTCAGCG; ATCCGCA 3′	94°C, 5 m	30	94°C, 30 s	60°C, 30°s	72°C, 1 m	72°C, 5 m	1063	[29]
	R: 5′ GTACAACATCT; CCGAGTA 3′
spvC	F: 5′ CGGAAATACCA; TCAAATA 3′	94°C, 5 m	30	93°C, 1 m	42°C, 1 m	72°C, 2 m	72°C, 4°m	669	[26]
	R: 5′ CCCAAACCCAT; ACTTACTCTG 3′