A multiplex real-time PCR assay targeting virulence and resistance genes in Salmonella entericaserotype Typhimurium

Table 1 Primers and probes designed for the GeneDisc^® assay

Target sequence	Forward primer, reverse primer and probe sequences (5'-3')	GenBank accession number	Location within sequence
DT104	GGACCTGGCTGAGTTTATTTCG		1370 - 1391
16S-23S	GCATCGGCTGTGAGACCAA*	AF275268	1438 - 1420
spacer^a	FAM-TGGTTTCTGAAAGCGGAGCTAATGCG-BHQ		1393 - 1418
	TCTGCTGAGCGACAACAGATTT		1498146 - 1498167
ssaQ ^b	TGGCACCAGCCTGAATATACAG*	AE006468	1498213 - 1498192
	ROX-TCCTGCCCCTCCTGTGGTAGT -BHQ		1498169 - 1498189
	AAGAGGCCGCGATCTGTTTA*		3964669 - 3964650
mgtC ^c	CGAATTTCTTTATAGCCCTGTTCCT	AE006468	3964600 - 3964624
	ROX-AAGGGTTAGGTTCGGTCCCCG-BHQ *		3964648 - 3964628
	CGGCGGACTTACTTTTTGAAA		4482051 - 4482071
spi4_D ^d	TGGTCACGGTATTTGGGTAATATTT*	AE006468	4482132 - 4482108
	ROX-CCAAAAGTAAGGACTATGCTGGCCG-BHQ		4482077 - 4482101
	CTTATGAGGGAAAGGGCG*		1179300 - 1179283
sopB ^e	ATGCACACTCACCGTGG	AE006468	1179215 - 1179231
	ROX-TTGGGATACCAAGAATATTCATCACGCC-BHQ*		1179275 - 1179248
	AATGAACTACGAAGTGGGCG*		24307 - 24288
spvC ^f	TCAAACGATAAAACGGTTCCTC	FN432031	24232 - 24253
	FAM-ATGGTGGCGAAATGCAGAGACAGGC -BHQ*		24285 - 24261
	GGATTTTCTCCAGCTTCTGT		132 - 151
Left junction of SGI1^g	CTAACCATAAGAGAACTTCC*	AF261825	263 - 244
	FAM-TAAATCTCCTAAATTAAATTAAAACGAAGTAAAACC -BHQ		161 - 197
	TGGGCAGCAGCGAAGTC*		27686 - 27670
intI1 ^h	TGCGTGGAGACCGAAACC	AF261825	27617 - 27634
	FAM-AGGCATTTCTGTCCTGGCTGGCG-BHQ*		27668 - 27646
	CTGGATCTCAACAGCGG		270 - 286
bla _TEM ⁱ	CAACACGGGATAATACCGC*	AJ634602	378 - 360
	FAM- AGATCCTTGAGAGTTTTCGCCCCG-BHQ		289 - 312
	TCCTGACCCTGCGCTCTATC		29611 - 29630
sul1 ^j	TGCGCTGAGTGCATAACCA*	AF261825	29679 - 29661
	ROX-ATTGCTGAGGCGGACTGCAGGC -BHQ		29636 - 29657

FAM = 6-carboxylfluorescein; ROX = carboxy-X-rhodamine; BHQ = Black Hole Quencher. * complementary strand; ^a:marker of the phage type DT104 located in the 16S-to-23S spacer region of bacterial rRNA genes [4]; ^b: gene encoding SsaQ; ^c: gene encoding MgtC; ^d: gene encoding Spi4_D; ^e: gene encoding SopB; ^f: gene encoding SpvC; ^g: marker of the SGI1 left junction which is composed of the end of the thdF gene and the intergenic sequence between thdF and int genes [8]; ^h: marker targeting the gene encoding the integrase of the class 1 integron inside SGI1; ⁱ: gene encoding beta-lactam resistance; ^j:gene encoding sulphonamide resistance.

ISSN: 1471-2180