Table 3. List of primers sequences used to detect the virulence genes of Salmonella enteric serovar Typhi isolates.

Sr.#	Location	Gene	Primer Sequence 5`→3`	Annealing Temp°C	Amplicon size (bp)	Reference (Coordinatesa)
1	SPI-1	invA (STY3019)	GTGAAATTATCGCCACGTTCGGGCAA TCATCGCACCGTCAAAGGAACC	64	284	[51]
2	SPI-1	prig (STY2994)	CAGGTAACAGAGGCGCTGGATAAA TTACCGTGTTCGATTGCGCGTTAC	55	121	[52]
3	SPI-1	hilA/iagA	ACGGACAGGGTTATCGGTTTAAT AAAAGGAAGTATCGCCAATGTATGAG	50	92	[53]
4	SPI-1	sipA/sspA	GTTAAGTAATGTGCTGGACGGCCT ACCCGATCCACACCAGGTTTATTC	55	100	[52]
5	SPI-1	prgH	TCATAATCGCCCCTCGCTAA TCTATGTCGCTGCGCAAAAT	50	70	[53]
6	SPI-2	spiC	CCTGGATAATGACTATTGAT AGTTTATGGTGATTGCGTAT	50	301	[54]
7	SPI-2	sseB	ATATGGCGATCATGGGAAGCTGGA TCGGTATTCCGGTTGGCGTCATTA	55	84	[52]
8	SPI-3	mgtB	GGCAGGAGTTTCGCACTAAC GCGTACCCACAATGGATTTC	55	445	[55]
9	SPI-3	mgtC	TCGGCGTGTTATGCGGCTTA AGCCCTGTTCCTGAGCGGGG	55	264	[56]
10	SPI-3	nepI/gaiA (STY4008)	GTTGGCGCTGGGCGGATTCT CACCGGCACCAACGCAAACG	60	616	This study (3870217–3871410)
11	SPI-4	spi4D (STY4457)	GTTCATGGTCAGGGCGTTAT CTTAAAGAACGGGTGCCATC	55	275	[55]
12	SPI-4	orfL (STY4458)	GGAGTATCGATAAAGATGTT GCGCGTAACGTCAGAATCAA	50	332	[57]
13	SPI-5	pipB	TAAGAAGAAGCAATGAAAGATGGTT GGTTATAAGTGAATCAGGCTGTTGT	50	305	[58]
14	SPI-5	pipD	CGGCGATTCATGACTTTGAT CGTTATCATTCGGATCGTAA	50	399	[54]
15	SPI-5	sopB/sigD	CGGACCGCCCAGCAACAAAACAAGAAGAAG TAGTGATGCCCGTTATGCGTCAGTGTATT	55	220	[54]
16	SPI-6	tcf	CATTTATTCTCAGGGGGAGCG CATCCTCTTTATCTGTTGCCACG	57	1049	[59]
17	SPI-6	safC	TGTTCTGGCTCCTTGTTTGACG TTCTGTTTGACCTCCACCCGAG	57		[59]
18	SPI-7	pilS	GTATCAACATTAAATCCATGC CGTTACTTTCGCATCGGTGTG	50	502	[18]
19	SPI-7	tviA	GTTATTTCAGCATAAGGAG ACTTGTCCGTGTTTTACTC	50	599	[60]
20	SPI-7	tviB	CGAGTGAAACCGTTGGTACA CAATGATCGCATCGTAGTGG	50	846	[28]
21	SPI-7	tviD-E	TACCTAGCGAGCCAGTACAGAG CTGGAACCGTCATTCTTATCCCG	55	2500	[61]
22	SPI-7	sopE	GCTGACTTTGGTGCTGCTGCTCTCG CTGGCGTATGCGGGGTCTTTACTCG	50	2000/2425	[35]
23	SPI-8	STY3280	ATATGACTCGAATGAAATCAGG GGGGATTGTCTACATTGTAA	50	132	[62]
24	SPI-8	STY3282	AAAAAGAGGTCGAGCGCCTTACTCC TTTTAGGAGTGTTTATCATA	50	142	[62]
25	SPI-9	prtB (STY2877)	TAACCTGTGCGGCGTGCTGG GCCGGACAGGCCGTTACCAC	55	559	This study (2755839–2757995)
26	SPI-9	STY-2875	TGGCGACACTCTGCTTGGCG CCGTTGAGCGTCGGCTGTGT	50	276	This study (2743495–2754369)
27	SPI-10	sefC	GAAGAAAACCACAATTACTC CAACTGTTAGTTTGCTCTTT	50	668	[62]
28	SPI-10	sefB	AATATTATGGCCTAAGATTGGG GCTCAATATATCCATTTGGA	50	534	[62]
29	SPI-10	sefR	TGACATTCCTACGGCATATG TTACCATTAAGAACAAGTCAAAGCC	50	625	[62]
30	SPI-10	prpZ	CAATGGTGCGGTGCGAAAGATAAC TTCCCATAAGGGTCCCATAACTCT	57	115	[42]
31	SPI-10	prk-Y	AGCCATGACAAATATGCTCGACCG TTTCCATTCAGGACGAAGAGGGCA	57	104	[42]
32	SPI-10	prk-X	CGTCATGTCGGTCGCGTCAATAAT TTGTTGAGGTGTTTGGGTACCTCG	55	127	[42]
33	SPI-11	pagC	TTTAATGGTTGGGCCAGCCTATCG TTAAATGTCGCCTTTACCGTGCCG	55	87	[63]
34	SPI-11	msgA	GCCAGGCGCACGCGAAATCATCC GCGACCAGCCACATATCAGCCTCTTCAAAC	62	189	[64]
35	SPI-11	pagD(STY1880a)	TGGTAGTAAAACCCCGCAACCACC TGGGTTTTGCCGTCGGGCAG	60	89	This study (1782539–1782802)
36	SPI-11	cdtB	ACAACTGTCGCATCTCGCCCCGTCATT CAATTTGCGTGGGTTCTGTAGGTGCGAGT	58	268	[11]
37	SPI-12	sspH2 (STY2467)	GGGCTGCACCCGCAGAAGAG AGACCTCCAGCGTCCGCAGT	60	216	This study (c2300203-2297837)
38	SPI-16	gtrA (STY0607)	GCATCAGGCGCTGGCGAACT AGCGAAGCGTGGTGGTGCTG	60	104	This study (c609678-609316)
39	SPI-16	gtrB (STY0606)	CATGCAACCGGGGATGCGGT AATCGCCGGCAACACGCTCA	60	364	This study (c609319-608393)
40	SPI-17	STY-2629	TGGGACGGGTTTAATTGGCGCA GCCCATTGAAAAGAGCCGCCG	55	251	This study (2462589–42645111)
41	SPI-18	clay	GACCTTTGATGAAACCATAAAAGAG GCATCGATATCTTTATTCGCTTG	50	600	[65]
42	SPI-18	taiA	ATATCACCGATGCGGTGGGAATC ACTTTCACCATTCCATCTTCCGGC	55	141	[63]
43	Non-SPI	cgsA	TGCAAAGCGATGCCCGTAAATC TTAGCGTTCCACTGGTCGATGGTG	55	151	[66]
44	Non-SPI	staA/yadN	CTTTAGAAGCATCGGCACGAAC CGCAATGGTTATGGCTATGGG	57	505	[67]
45	Non-SPI	stgA	TGCCAGGTTACGCCACAAACC CGCTGTGGTATCAATCGTGC	60	354	[68]
46	Non-SPI	fimA	CCTTTCTCCATCGTCCTGAA TGGTGTTATCTGCCTGACCA	58	85	[69]
47	Non-SPI	fliA (STY2164)	ACGCCCCAGTTCCTGCTCCA ACCGCTGGTGCGTCACGAAG	60	277	This study (2008974–2009693)
48	Non-SPI	rpoS (STY3049)	CCGCACTCGGTTCGTGGTCC GTCGCGCACTGCGTGGAGAT	60	345	This study (2915077–2916069)
49	Non-SPI	phoP	ATGCAAAGCCCGACCATGACG GTATCGACCACCACGATGGTT	62	299	[70]
50	Non-SPI	tolC	TACCCAGGCGCAAAAAGAGGCTATC CCGCGTTATCCAGGTTGTTGC	60	161	[64]
51	Non-SPI	SsifA	TTTGCCGAACGCGCCCCCACACG GTTGCCTTTTCTTGCGCTTTCCACCCATCT	55	449	[54]
52	Non-SPI	STY1460	TACCGGGGTGGATGCGCTGA GCGACAGGCCTGCGAACAGT	60	322	This study 1410094–1412058
53	pRST98	spvB	ATGTTGATACTAAATGGTTTTTCA CTATGAGTTGAGTACCCTCATGTT	55	1776	[71]
54	pRST98	spvR	ATGGATTTCATTAATAAAAAATTA TCAGAAGGTGGACTGTTTCAGTTT	55	894	[71]
55	R27, pHCM1	trhW	ACTGGCCAGGTTCCCGCAGA CTGACCGCTGCCAAGACGCT	60	109	This study
56	Non-SPI	eno(STY3081)	GCTCCGTCAGGTGCTTCTAC GCGTCTTTGCCAAGAATAGC	60	143	[72]

^aGenome coordinates of the location of the genes for which primers have been designed in this study based on S. enterica Typhi CT8 reference genome [26]