INT J TUBERC LUNG DIS 19(11):1276–1289 STATE OF THE ART Q 2015 The Union http://dx.doi.org/10.5588/ijtld.15.0389 Mechanisms of drug resistance in Mycobacterium tuberculosis: update 2015 Y. Zhang,* W-W. Yew† *Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA; †Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China SUMMARY Drug-resistant tuberculosis (DR-TB), including multi- resistance. However, further research is needed to and extensively drug-resistant TB, is posing a significant address the significance of newly discovered gene challenge to effective treatment and TB control world- mutations in causing drug resistance. Improved knowl- wide. New progress has been made in our understanding edge of drug resistance mechanisms will help understand of the mechanisms of resistance to anti-tuberculosis the mechanisms of action of the drugs, devise better drugs. This review provides an update on the major molecular diagnostic tests for more effective DR-TB advances in drug resistance mechanisms since the management (and for personalised treatment), and previous publication in 2009, as well as added informa- facilitate the development of new drugs to improve the tion on mechanisms of resistance to new drugs and treatment of this disease. repurposed agents. The recent application of whole KEY WORDS: antibiotics; drug resistance; mechanisms; genome sequencing technologies has provided new molecular diagnostics; new drugs insight into the mechanisms and complexity of drug The use of multiple-drug therapy, although defi- drug-resistant TB (DR-TB) epidemic thus remains nitely beneficial, is not an absolute guarantee an alarming problem, and is further aggravated by against the emergence of drug-resistant in- human immunodeficiency virus (HIV) coinfection.3 fections. Consequently, we cannot have confi- The present review is aimed at updating readers on dence that drug-resistant tubercle bacilli will not major advances in drug resistance mechanisms in emerge simply because multidrug therapy is Mycobacterium tuberculosis since the publication of employed.1 the previous article in 2009.4 Additional information ACCORDING TO the World Health Organization’s pertaining to newly developed drugs and repurposed (WHO’s) 2014 global tuberculosis report,2 there were agents have also been included. about 9.0 million new tuberculosis (TB) patients and 1.5 million deaths in 2013; 3.5% of newly diagnosed BASIC CONCEPTS IN THE DEVELOPMENT OF and 20.5% of previously treated patients had DRUG-RESISTANT TUBERCULOSIS multidrug-resistant TB (MDR-TB, defined as bacil- lary resistance to at least rifampicin [RMP] and There are two types of drug resistance in M. isoniazid (INH]). The highest levels of MDR-TB were tuberculosis: genetic resistance and phenotypic resis- found in Eastern Europe and Central Asia, with rates tance. Genetic drug resistance is due to mutations in reaching 20% and 50%, respectively. At least one chromosomal genes in growing bacteria, while case of extensively drug-resistant TB (XDR-TB, phenotypic resistance or drug tolerance is due to defined as MDR-TB with additional resistance to epigenetic changes in gene expression and protein fluoroquinolone[s] [FQs] and one or more of three modification that cause tolerance to drugs in non- second-line injectable drugs [SLIDs], namely capreo- growing persister bacteria. The two types of resis- mycin [CPM], kanamycin [KM] and amikacin tance have been responsible for a number of problems [AMK]) had been reported to the WHO from 92 in effective TB control, with genetic resistance (Yang countries by the end of 2012. An estimated 9% of resistance), as present in MDR-/XDR-TB, causing MDR-TB patients had XDR-TB. The worldwide problems worldwide, while the more subtle pheno- Correspondence to: Ying Zhang, Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA. Tel: (þ1) 410 614 2975. e-mail: [email protected] Article submitted 5 May 2015. Final version accepted 18 June 2015. [A version in French of this article is available from the Editorial Office in Paris and from the Union website www.theunion.org] Mechanisms of drug resistance: update 2015 1277 typic drug resistance, or tolerance (Yin resistance), as tant findings.17 Among over 1200 patients, 43.7% present in persisters, entails prolonged treatment and showed bacillary resistance to at least one SLD, 20% risk of post-treatment relapse.5,6 The situation in vivo to at least one SLID and 12.9% to at least one FQ, appears more complex, and the two types of with 6.7% of cases meeting the definition for XDR- resistance can overlap and interconvert. Prior stress TB. Previous treatment with SLDs was consistently or subinhibitory concentration of drugs may induce the strongest risk factor for resistance to these drugs, efflux pump expression,7,8 which causes phenotypic with a four-fold increased risk for XDR-TB. Bacillary resistance and may in turn facilitate the development resistance to FQs and XDR-TB were found more of more stable genetic drug resistance,8 while genetic frequently in women than men. Unemployment, resistance in growing organisms can develop persis- alcohol abuse and smoking were associated with tence or phenotypic resistance. There is increasing mycobacterial resistance to SLIDs across countries. In interest in understanding the biology of mycobacte- addition, in a study in the United States, the risk rial persisters and developing anti-tuberculosis drugs factors for bacillary acquired resistance to SLIDs that target them.5 included age 25–44 years, positive HIV status, MDR- M. tuberculosis drug-resistant strains develop TB at treatment initiation and treatment with any largely through the selection of genetic mutants. This SLD. However, the only predictor for bacillary is almost a wholly man-made phenomenon, resulting acquired resistance to FQs was MDR-TB at treatment from suboptimal physician prescription and/or poor initiation.18 A recent expanded analysis of these data patient adherence. However, there is some recent from the same group of researchers further showed evidence that pharmacokinetic-pharmacodynamic that mortality was significantly higher among TB variability scenarios related to the induction of the patients with bacillary acquired resistance to SLDs, mycobacterial drug efflux pump may also facilitate after controlling for age. MDR-TB at treatment the development of genetic mutations in M. tubercu- initiation, positive HIV status and extra-pulmonary losis.9 disease were also significantly associated with mor- The development of drug resistance as a result of tality.19 A meta-analysis on treatment outcomes of mutations in drug resistance genes in M. tuberculosis MDR-TB was undertaken in about 6700 patients may incur a cost in terms of fitness and virulence of from 26 centres using individual patient data the organism. Acquired resistance can also be analysis.20 Compared with treatment failure, relapse compounded by transmitted resistance. Recent sys- and death, treatment success was higher in MDR-TB tematic reviews have alluded to an association patients carrying bacilli without additional resistance between primary resistance in M. tuberculosis and or with additional resistance to SLIDs only than in HIV coinfection, suggesting transmitted DR-TB, as a those with resistance to FQs alone or to FQs plus significant challenge to the management of this SLIDs. In XDR-TB patients, treatment success was patient population.10,11 Furthermore, recent studies highest if at least six drugs were used in the intensive from China have indicated that a significant number phase and four in the continuation phase (odds ratios of MDR- and XDR-TB cases are due to the active 4.9 and 6.1, respectively). Likewise, in another transmission of (mainly) the Beijing genotype,12 and similar study focusing on XDR-TB, the odds of cure the same is true for Europe13 and Africa.14 This is a were significantly lower in XDR-TB patients with worrying development that requires more studies to additional bacillary resistance to CPM and KM/AMK better understand how such apparently virulent DR- than patients with only XDR-TB. The odds of failure TB strains evolve and adapt in the host, and and death were found to be higher in all XDR-TB highlights the need for more effective means to curtail patients with additional bacillary resistance, inclusive transmission. of groups with bacillary resistance to oral bacterio- static agents, with or without ethambutol (EMB) plus Clinical relevance of anti-tuberculosis drug resistance PZA.21 It was recently noted that combined resis- The clinical relevance of resistance to RMP and INH tance to FQ (high-level) and PZA was associated with has been amply discussed.4 Besides the known a poor treatment outcome in some MDR-TB patients negative impact of bacillary resistance to pyrazin- treated with the 9-month Bangladesh regimen.22 amide (PZA) on treatment outcomes among MDR- TB patients, including PZA in the treatment regimen MECHANISMS OF RESISTANCE TO FIRST- AND for MDR-TB as guided by drug susceptibility testing SECOND-LINE ANTI-TUBERCULOSIS DRUGS (DST) might substantially improve early sputum culture conversion and subsequent cure or treatment The mechanisms of resistance of the various drugs are completion.15,16 discussed below. Table 1 summarises the genetic basis A prospective cohort