TABLE 1.

Primers and probes used for PCR amplification and detection of drug-resistant M. tuberculosis strains

Target	Primer or probe	Sequence (5′-3′)h	Nucleotides within targeta	Product size (bp)	Annealing temp (°C)	Tm (°C)
rpoB	TR9	TCGCCGCGATCAAGGAGTb	2335-2352	158	62	61.0
	TR8	GTGCACGTCGCGGACCTCCAb	2492-2473			68.4
	rpo sensorc	640-ACCCACAAGCGCCGACTGCTGG-Pd	2412-2432			70.4
	rpo anchorc	TTCATGGACCAGAACAACCCGCTGTCGGT-F	2379-2407			73.8
	RPO1 sensore	CAGCTGAGCCAATTCATGGACC-F	2367-2388			65.2
	RPO1 sensore	640-AACAACCCGCTGTCGGGG	2390-2407			65.2
katG	TB86	GAAACAGCGGCGCTGATCGTb	2759-2778	209	67	64.3
	TB87	GTTGTCCCATTTCGTCGGGGb	2968-2948			62.8
	TB sensorc	640-TCACCAGCGGCATCGAGGTCGT-Pd	2916-1937			69.4
	TB anchorc	CGTATGGCACCGGAACCGGTAAGGACGC-F	2886-2913			75.3
	TaqMan MGB probes	FAM-ACCAGCGGCATCG-Q	2918-2930			66.3
		VIC-TCACCACAGGCATCG-Q	2916-2930			65.1
		VIC-ACCACCGGCATCG-Q	2918-2930			64.9
inhA	TB92	CCTCGCTGCCCAGAAAGGGAf	56-75	248	64	65.2
	TB93	ATCCCCCGGTTTCCTCCGGTf	303-284			66.5
	TB ATTg	640-CCCGACAACCTATCATCTCGCC-Pd	223-202			63.1
	TB anchorg	CCCCTTCAGTGGCTGTGGCAGTC-F	248-226			68.1

^aThe positions of the primers and probes correspond to GenBank accession numbers L27989, X68081, and U66801 for the rpoB gene, the katG gene, and the inhA locus, respectively.

^bPrimer sequence described by Telenti et al. (23).

^cProbe sequence described by Torres et al. (25).

^dP, phosphorylation of the 3′ end of the probe to prevent extension during PCR.

^eProbe sequence described by Garcia de Viedma et al. (7).

^fPrimer sequence described by Gonzalez et al. (8).

^gProbe sequence described by Torres et al. (26).

^hFluorophores were as follows: 640, Red 640; F, fluorescein; FAM, 6-carboxy-fluorescein; Q, quencher (TAMRA [6-carboxy-N,N,N′,N′-tetramethylrhodamine]); VIC, fluorescent reporter. For TaqMan MGB probes, designed to detect wt codon 315 of katG (AGC) and two mutations (ACA and ACC), these sequences are underlined.