Table 2.

Primer pairs and amplicon size for each SYBR®Green qPCR assay

Targeted genus	Targeted species	Targeted subspecies	Targeted sequence	qPCR assay name	Prime name	Primer sequence (5' - > 3')	Position on the S. Enteritidis genome (AM933172)	Primer concentration (nM)	Product Size (bp)	Tm amplicon	References
Salmonella	All	All	Sigma factor (rpoD)	rpoD-20	rpoD-20-F	ACATGGGTATTCAGGTAATGGAAGA	3,264,501–3,264,525	250	75	77–78 °C	Adapted from Botteldoorn et al. 2006
					rpoD-20-R	CRGTGCTGGTGGTATTTTCA	3,264,574–3,264,555	1000
			Invasine gene (invA)	invA-5	invA-5-deg-F	GATYTGAARGCCGGTATTATTG	2,924,646–2,924,625	250	107	80–82 °C	This study
					invA-5-R	ATAAACTTCATCGCACCGTCA	2,924,540–2,924,560	250
	enterica	All	C-glycosyltransferase (iro-B)	iroB-192	iroB-192-F	CCAAGAGATCTGGCGTGGATAG	2,801,780–2,801,101	250	86	78 °C (S. enterica salamae- 79 °C (S. enterica enterica and S. enterica arizonae) - 80 °C (S. enterica doutenae and S. enterica diarizonae)	Adapted from Murphy et al. 2007
					iroB-192-R	TATTGCATGGAGATAACCGGCT	2,801,865–2,801,844	250
				iroB-12	iroB-12-deg-F	GGRACAAAAATGGGGMACTTCT	2,801,531–2,801,552	500	105	80.5–83 °C	This study
					iroB-12-R	AAGGGGAGGRTAGACGATGA	2,801,635–2,801,616	500
		enterica	Outer membrane usher protein (safC)	safC-10	safC-10-F	CACTAAAAAGTCGTCTGACTCTGG	323,795–323,818	250	72	75–76 °C	This study
					safC-10-R	CGGTAAATGGCACACTATCAAAT	323,866–323,844	250
				safC-13	safC-13-F	ATGATGACAGCTACGGACTGAGTT	324,665–324,688	250	76	77–78 °C	This study
					safC-13-R	CTGTTTTGATTCCAGTTCAATGAC	324,740–324,717	250
			STM0296 (Acc n: AAL19253)	STM0296	STM0296-F	AMGCCCATCCCTTCAATACAG	320,053–320,073	500	56	76–78 °C	This study
					STM0296-R	GTGATYACGCCGCAGCATACCC	320,108–320,087	500

Degenerated nucleotides: R=A or G, Y=C or T, M=A or C