A method of detecting Mycobacterium tuberculosis resistant to rifampicin (MTB-RIF) and/or MTB resistant to isoniazid (MTB-INH) in a sample, the method comprising a multiplex real-time polymerase chain reaction assay comprising: - performing an amplifying step comprising contacting the sample with at least a set of rpo B primers, a set of inh A primers, and a set of kat G primers to produce one or more amplification products if any rpo B, inh A, and katG target nucleic acid is present in the sample; - performing a hybridizing step comprising contacting said one or more amplification products with a plurality of detectable rpoB probes, a plurality of detectable inh A probes, and a plurality of detectable kat G probes, at least comprising: - 17 rpo B probes for detection of one or more of 17 single nucleotide polymorphisms SNPs which confer rifampicin resistance to MTB; - 3 inh A probes for detection of one or more of 3 SNPs which confer isoniazid resistance to MTB; and - 4 katG probes for detection of one or more of 4 SNPs which confer isoniazid resistance to MTB; and - detecting the presence or absence of said one or more amplification products, wherein the presence of said one or more amplification products is indicative of the presence of MTB-RIF and/or MTB-INH in the sample and wherein the absence of said one or more amplification products is indicative of the absence of MTB-RIF and/or MTB-INH in the sample; wherein said plurality of rpo B probes comprise hydrolysis probes for detection of each of the 17 SNPs which confer rifampicin resistance to MTB, comprising rpo B 531L, rpo B 531W, rpo B 526L, rpo B 526Y, rpo B 526D, rpo B 526N, rpo B 513L, rpo B 513K, rpo B 513P, rpo B 522L, rpo B 522Q, rpo B 522W, rpo B 516V, rpo B 516Y, rpo B 533P, rpo B 511P, and rpo B 526R; wherein said plurality of inhA probes comprise hydrolysis probes for detection of each of the 3 SNPs which confer isoniazid resistance to MTB, comprising inh A-15T, inh A-8A, and inh A-8C; wherein said plurality of kat G probes comprise hydrolysis probes for detection of each of the 4 SNPs which confer isoniazid resistance to MTB, comprising kat G 3151, kat G 315N, kat G 315T, and kat G 315T2; and wherein: - the rpo B probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-289 and 437-438, or a complement thereof; - the inh A probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 344-409 and 436, or a complement thereof; and - the katG probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 290-343 and 434-435, or a complement thereof. - performing an amplifying step comprising contacting the sample with at least a set of rpo B primers, a set of inh A primers, and a set of kat G primers to produce one or more amplification products if any rpo B, inh A, and katG target nucleic acid is present in the sample; - performing a hybridizing step comprising contacting said one or more amplification products with a plurality of detectable rpoB probes, a plurality of detectable inh A probes, and a plurality of detectable kat G probes, at least comprising: - 17 rpo B probes for detection of one or more of 17 single nucleotide polymorphisms SNPs which confer rifampicin resistance to MTB; - 3 inh A probes for detection of one or more of 3 SNPs which confer isoniazid resistance to MTB; and - 4 katG probes for detection of one or more of 4 SNPs which confer isoniazid resistance to MTB; and - 17 rpo B probes for detection of one or more of 17 single nucleotide polymorphisms SNPs which confer rifampicin resistance to MTB; - 3 inh A probes for detection of one or more of 3 SNPs which confer isoniazid resistance to MTB; and - 4 katG probes for detection of one or more of 4 SNPs which confer isoniazid resistance to MTB; and - detecting the presence or absence of said one or more amplification products, - the rpo B probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-289 and 437-438, or a complement thereof; - the inh A probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 344-409 and 436, or a complement thereof; and - the katG probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 290-343 and 434-435, or a complement thereof.