The resistance of Mycobacterium tuberculosis to anti-tuberculotic drugs is mostly based on spontaneous random genetic mutations, typically occurring at a rate ranging from 3 × 10⁻⁷ to 1 × 10⁻⁸ per organism per generation for the first-line antituberculotic drugs (isoniazid, rifampicin, ethambutol, and streptomycin). From the molecular perspective, the resistance is based on gene mutations in mycobacteria, which frequently leads to a change in the target molecule making it functionally insensitive to the action of antituberculotic agents.

Telenti et al. (1993) described the molecular mechanism of rifampicin resistance in M. tuberculosis. Rifampicin acts by binding to a beta-subunit of the RNA polymerase (coded by the rpoB gene), inhibiting RNA transcription (Drobniewski and Wilson 1998). Subsequent DNA sequencing studies have shown that more than 95 % of rifampicin resistant strains have mutations in the 81-base pair region (codons 507–533) of the rpoB gene (Bartfai et al. 2001). More than 50 mutations within this region have been characterized by automated DNA sequencing; however, the majority are point mutations in codons 516, 526, or 531 (Gillespie 2002). Mutations in other regions of the rpoB gene have also been reported, but much less commonly. In addition, a few silent mutations infrequently occur which do not seem to confer rifampicin resistance.

Isoniazid inhibits InhA, enoyl-ACP-reductase, which is involved in the biosynthesis of mycolic acid (Gillespie 2002). Mutations causing isoniazid resistance are located in different regions of several genes. Isoniazid is a so-called ‘pro-drug’ which is converted to its active form by the catalase-peroxidase enzyme KatG. Therefore, resistance can be due to several factors, including the binding of the prodrug to its InhA target, the activation of the prodrug by KatG (encoded by the katG gene), or by increased expression of the target InhA (Miotto et al. 2008). Mutations in codon 315 of the katG gene have been found in 50–90 % of isoniazid resistant strains, while 20–35 % of isoniazid-resistant strains have been reported to have mutations in the inhA regulatory region, and 10–15 % of strains have mutations reported in the ahpC-oxyR intergenic region (Miotto et al. 2008; Brossier et al. 2006). Deficiency in catalase activity leads to high-level resistance to isoniazid. Most commonly, mutations in the katG gene are single point mutations at codon 315 involving a serine-to-threonine amino acid substitution. Other mutations in katG occur less commonly. Low-level resistance to isoniazid is mostly caused by inhA and ahpC-oxyR mutations (Miotto et al. 2008).

Ethambutol (EMB) is a narrow-spectrum antimycobacterial agent that is used for the treatment of tuberculosis. EMB is a first-line anti-tuberculosis agent that is especially important when used in drug combinations to prevent the emergence of drug resistance or to treat single drug-resistant tuberculosis (WHO 1997). Furthermore, streptomycin has been replaced by EMB as a key drug in the intensive phase of tuberculosis chemotherapy, as it is less expensive and patient compliance is better with this drug (Rabarijaona et al. 1999). This agent has been proposed to be an arabinose analog; the specific target is likely to be an arabinosyltransferase, presumably a functionally important site. A two-gene locus (embAB) that encodes arabinosyltransferase has been studied to elucidate a potential mechanism of EMB resistance (Alcaide et al. 1997; Telenti et al. 1997).

Fluoroquinolones are bactericidal antibiotics currently in use as second-line drugs in the treatment of TB. In M. tuberculosis, only type II topoisomerase (DNA gyrase) is present and thus is the only target for fluoroquinolone activity (Aubry et al. 2004). Type II topoisomerase is a tetramer composed of two A and B subunits, encoded by the genes gyrA and gyrB, respectively, which catalyses the supercoiling of DNA (Drlica 1999). Initial studies performed in laboratory strains of M. tuberculosis and M. smegmatis showed that resistance to fluoroquinolones is a result of aminoacid substitutions in the putative fluoroquinolone binding region in gyrA or gyrB.

Kanamycin and amikacin are aminoglycoside antibiotics, while capreomycin and viomycin are cyclic peptide antibiotics. All four are used as second-line drugs in the treatment of MDR-TB. Although belonging to two different antibiotic families, all exert their activity at the level of protein translation. Cross-resistance among kanamycin, capreomycin, and viomycin has been reported since the studies performed by Tsukamura and Mizuno (1975). The most common molecular mechanism of drug resistance has been associated with the A1401G mutation in the rrs gene coding for 16S rRNA. This mutation occurs more frequently in strains with high-level resistance to kanamycin and amikacin (Jugheli et al. 2009).

Traditionally, patients with MDR-TB are classified into two major groups: (1) those who acquired drug-resistant strain from community and (2) those with drug resistance developed due to previous therapy of tuberculosis. Only the cases of primary drug resistance are assumed to be due to transmission of drug-resistant strains (Van Rie et al. 2000). A person with fully susceptible TB may develop secondary (acquired) resistance during therapy. However, the clinical term ‘acquired’ drug resistance should be replaced with ‘drug resistance in previously treated cases’, which includes cases with drug resistance due to true acquisition as well as that due to transmitted drug-resistant strains (Van Rie et al. 2000).

Generally, the resistance to antituberculotic drugs can be classified as follows (van der Werf et al. 2012):

The terms ‘extremely drug resistant’ (XXDR-TB) and ‘totally drug-resistant TB’ (TDR-TB) are also used by some authors (Cegielski et al. 2012). Nevertheless, TDR-TB is yet to be clearly defined. While the concept of TDR-TB is easily understood in general terms. In practice, however, in vitro drug susceptibility testing (DST) is technically challenging and limitations on the use of results remain (Cegielski et al. 2012). Conventional DST for the drugs that define MDR-TB and XDR-TB has been thoroughly studied and a consensus has been reached on appropriate methods, critical drug concentrations that define resistance, and reliability and reproducibility of testing. Data on reproducibility and reliability of DST for the remaining second line drugs are either much more limited or have not been established, or the methodology for testing does not exist. Most importantly, correlation of DST results with clinical response to treatment has not yet been adequately established. Thus, a strain of TB showing resistance in in vitro DST could, in fact, turn out to be susceptible in the patient. The prognostic relevance of in vitro resistance to drugs without an internationally accepted and standardized drug susceptibility test remains unclear and the current WHO (1997) recommendations disadvise to rely on such results in treatment guiding.