. 2017 May 4;12(5):e0177167. doi: 10.1371/journal.pone.0177167

Table 1. Primers and probes used in the TB TAC v2.

Gene	Primers/Probes	Sequences	Assay region	Product size bp	References
inhA	Forward	`5’-GCTCGTGGACATACCGATTT-3’`	(-54)–codon 22	120	[6]
	Reverse	`5’-TCCGGTAACCAGGACTGAAC-3’`			[6]
	T(-8)C	`VIC-5’-CGAGACGATAGGCTG-3’-MGB`			[6]
	C(-15)T	`VIC-5’-ACCTATCATCTCGCC-3’-MGB`			[6]
	-8-15wt	`VIC-5'-ACAACCTATCGTCTCGC-3'-MGB`			This study
katG	Forward	`5’-CTCGTATGGCACCGGAAC-3’`	Codon 303–338	108	[6]
	Reverse	`5’-CCGTACAGGATCTCGAGGAA-3’`			[6]
	315 Thr^a	`HEX-5’-ATCA+CCA+CCG+GCA+TCG-3’`			[12]
	315wt	`VIC-5’-CGATGCCGCTGGT-3’-MGB`			This study
rpoB Amplicon 1	Forward	`5’-GCCGCGATCAAGGAGTTCT-3’`	Codon 500–543	130	[6]
	Reverse	`5’-CACGCTCACGTGACAGACC-3’`			[6]
	511Pro	`VIC-5’-AGCCAGCCGAGCC-3’-MGB`			[6]
	513Leu	`VIC-5’- CCAGCTGAGCCTAT-3’-MGB`			[6]
	513Glu	`VIC-5’-CTGAGCGAATTCA-3’-MGB`			[6]
	516Val^a	`HEX-5’-AATTCA+TGG+TCC+AGA+ACAA-3’`			[12]
	511wt	`VIC-5’-CAGCCAGCTGAGCC-3’-MGB`			This study
	513wt	`VIC-5’-CTGAGCCAATTCAT-3’-MGB`			This study
	513Lys	`NED-5’-CTGAGCAAATTCA-3’-MGB`			This study
	516wt^a	`HEX-5’-AATTCA+TGG+ACC+AGA+ACAA-3’`			This study
	516Tyr	`VIC-5’-CAATTCATGTACCAGAACA-3’-MGB`			This study
rpoB Amplicon 2	Forward	`5’-AGCCAGCTGAGCCAATTCAT-3’`	Codon 509–543	103	[6]
	Reverse	`5’-CACGCTCACGTGACAGACC-3’`			[6]
	526Tyr	`VIC-5’-CGGGGTTGACCTACA-3’-MGB`			[6]
	526Asp	`VIC-5’-GTTGACCGACAAGC-3’-MGB`			[6]
	526Leu^a	`HEX-5’-GT+TGA+CCC+TCA+AGC-3’`			[12]
	531Leu	`VIC-5’- CCGACTGTTGGCGC-3’-MGB`			[6]
	531Trp	`NED-5’-CCGACTGTGGGCG-3’-MGB`			[6]
	533Pro	`VIC-5’- ACTGTCGGCGCCGG-3’-MGB`			[6]
	526wt	`VIC-5’-TTGACCCACAAGCG-3’-MGB`			This study
	531wt	`VIC-5’-CGACTGTCGGCGCT-3’-MGB`			This study
	533wt	`VIC-5’-TGTCGGCGCTGGG-3’-MGB`			This study
rrs Amplicon 1	Forward	`5’-AAGTCGGAGTCGCTAGTAATCG-3’`	nt.1320-1427	104	[6]
	Reverse	`5’-TTCGGGTGTTACCGACTTTC-3’`			[6]
	A(1401)G	`VIC-5’-CCCGTCGCGTCAT-3’-MGB`			[13]
	1401wt	`VIC-5’-GCCCGTCACGTCAT-3’-MGB`			This study
rrs Amplicon 2	Forward	`5’-AAAGTCGGTAACACCCGAAG-3’`	nt.1409-1510	102	[6]
	Reverse	`5’-CCGGTACGGCTACCTTGTTA-3’`			[6]
	G(1484)T	`VIC-5’-CGATTGGGACTAAGTC-3’-MGB`			[6]
	1484wt	`NED-5’-ATTGGGACGAAGTCGT-3’-MGB`			This study
eis	Forward	`5’-TGATCCTTTGCCAGACACTG-3’`	(-73)—codon 10	103	[6]
	Reverse	`5’-CTCGGTCGGGCTACACAG-3’`			[6]
	C(-14)T	`VIC-5’- CGGCATATGCTACAGT-3’-MGB`			[6]
	G(-10)A	`NED-5’-TATGCCACAATCGGATT-3’-MGB`			[6]
	-10-15wt	`VIC-5'-ATATGCCACAGTCGGATT-3'-MGB`			This study
	C(-12)T	`VIC-5’- CATATGCCATAGTCGGATT-3’-MGB`			This study
gyrA	Forward	`5’-CCGGTCGGTTGCCGAGACC-3’`	Codon 75–109	107	[14]
	Reverse	`5’-CCAGCGGGTAGCGCAGCGACCAG-3’`			[14]
	90Val	`VIC-5’-AGATCGACACGTCGCC-3’-MGB`			[6]
	94Gly^b	`VIC-5’-CCAGGSTGCCGTAGATC-3’–MGB`			[6]
	94Tyr^b	`VIC-5’-TCGATCTACTACASCCT-3’-MGB`			[6]
	94Ala^b	`VIC-5’-ATCTACGCCASCCTG-3’-MGB`			[6]
	90wt	`VIC-5’-ATCGACGCGTCGCC-3’-MGB`			This study
	94wt	`VIC-5’-GATCTACGACAGCCTGG-3’-MGB`			This study
	94Asn^b	`VIC-5’-TCGATCTACAACASCCTG-3’-MGB`			This study
rplC	Forward	`5’-TCCAAGGGCAAAGGTTTCG-3’`	Codon 118–166	146	This study
	Reverse	`5’-ATCCGGGTGCCCTTGAAC-3’`			This study
	154wt	`NED-5’-CGTGGCACATCCG-3’-MGB`			This study
	154Arg	`VIC-5’-TGGCACGTCCGCCGA-3’-MGB`			This study
23S Amplicon 1	Forward	`5’-CAAGTCAAGCAGGGACGAAA-3’`	nt. 2359–2487	129	This study
	Reverse	`5’-TCCCGTCGATATGGACTCTTG-3’`			This study
	2447wt^c	`NED-5’-TACCCCGGGGATAACA-3’-MGB`			This study
	G(2447)T^c	`VIC-5’-GTACCCCGGGTATAACA-3’-MGB`			This study
23S Amplicon 2	Forward	`5’-ACCTCGATGTCGGCTCGT-3’`	nt. 2497–2617	124	This study
	Reverse	`5’-GGCGGATAGAGACCGAACTG-3’`			This study
	2576wt^c	`NED-5’-CCAGCTCGCGTGCC-3’-MGB`			This study
	G(2576)T^c	`VIC-5’-ACCCAGCTAGCGTGC-3’-MGB`			This study
pncA Amplicon 1	Forward	`5’-GCGTCGGTAGGCAAACTG-3’`	(-50)—codon 18	103	[6]
pncA Amplicon 1	Reverse	`5’-GAGCCACCCTCGCAGAAGT-3’`	(-50)—codon 18	103	[6]
pncA Amplicon 2	Forward	`5’-ATCATCGTCGACGTGCAGA-3’`	Codon 5–45	124	[6]
pncA Amplicon 2	Reverse	`5’-CCACGACGTGATGGTAGTCC-3’`	Codon 5–45	124	[6]
pncA Amplicon 3	Forward	`5’-CGCCATCAGCGACTACCT-3’`	Codon 30–66	113	[6]
	Reverse	`5’-ACGAGGAATAGTCCGGTGTG-3’`			[6]
	57Asp	`VIC-5’-CCGGGTGACGACT-3’-MGB`			[6]
pncA Amplicon 4	Forward	`5’-ACCCGGGTGACCACTTCT-3’`	Codon 53–86	102	[6]
	Reverse	`5’-TGTCCAGACTGGGATGGAA-3’`			[6]
	65Ser	`VIC-5’-CGGACTATTCTTCGTCGT-3’-MGB`			[6]
pncA Amplicon 5	Forward	`5’-CATTGCGTCAGCGGTACTC-3’`	Codon 71–113	128	[6]
pncA Amplicon 5	Reverse	`5’-CCGTTCTCGTCGACTCCTT-3’`	Codon 71–113	128	[6]
pncA Amplicon 6	Forward	`5’-AATCGAGGCGGTGTTCTACA-3’`	Codon 90–133	132	[6]
pncA Amplicon 6	Reverse	`5’-ATACCGACCACATCGACCTC-3’`	Codon 90–133	132	[6]
pncA Amplicon 7	Forward	`5’-CACGCCACTGCTGAATTG-3’`	Codon 114–149	109	[6]
pncA Amplicon 7	Reverse	`5’-ATTGCGTACCGCGTCCTC-3’`	Codon 114–149	109	[6]
pncA Amplicon 8	Forward	`5’-AGGTCGATGTGGTCGGTATT-3’`	Codon 128–162	107	[6]
pncA Amplicon 8	Reverse	`5’-ACCCGCTGTCAGGTCCAC-3’`	Codon 128–162	107	[6]
pncA Amplicon 9	Forward	`5’-GAGGACGCGGTACGCAAT-3’`	Codon 144–187	133	[6]
pncA Amplicon 9	Reverse	`5’-ATCAGGAGCTGCAAACCAAC-3’`	Codon 144–187	133	[6]
16S	Forward	`5’-GGATAAGCCTGGGAAACTGGGT-3’`	nt.142–259	118	[6] Modified
	Reverse	`5’-ACCCCACCAACAAGCTGATAGG-3’`			[6] Modified
	M.tb	`VIC-5’-ACCACGGGATGCATGT-3’-MGB`			[6] Modified

^a Locked nucleic acid bases are indicated by “+”,

^b a polymorphism at codon 95 Ser/Thr was included by using “S” G/C,

^c E. coli position number, underlined letters indicate the mutation position