CORE Metadata, citation and similar papers at core.ac.uk Provided by ResearchSpace@UKZN J Antimicrob Chemother 2018; 73: 1138–1151 doi:10.1093/jac/dkx506 Advance Access publication 19 January 2018 Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care Navisha Dookie1*, Santhuri Rambaran1, Nesri Padayatchi1,2, Sharana Mahomed1 and Kogieleum Naidoo1,2 1Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; 2South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa *Corresponding author. CAPRISA, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Private Bag X7, Congella, 4013 South Africa. Tel: !27 31 260 4703; Fax: !27 31 260 4549; E-mail: [email protected] Drug-resistant TB (DR-TB) remains a significant challenge in TB treatment and control programmes worldwide. Advances in sequencing technology have significantly increased our understanding of the mechanisms of resistance to anti-TB drugs. This review provides an update on advances in our understanding of drug resistance mechanisms to new, existing drugs and repurposed agents. Recent advances in WGS technology hold promise as a tool for rapid diagnosis and clinical management of TB. Although the standard approach to WGS of Mycobacterium tuberculosis is slow due to the requirement for organism culture, recent attempts to sequence directly from clinical specimens have improved the potential to diagnose and detect resistance within days. The introduction of new databases may be helpful, such as the Relational Sequencing TB Data Platform, which contains a collection of whole-genome sequences highlighting key drug resistance mutations and clinical outcomes. Taken together, these advances will help devise better molecular diagnostics for more effective DR-TB management enabling personalized treatment, and will facilitate the development of new drugs aimed at improving outcomes of patients with this disease. Introduction including treatment failure and mortality. The management of DR- TB is further compounded by the high cost, long duration and debili- Resistance to anti-TB drugs is an escalating global health crisis. tating toxicity of currently available second-line drugs.3 Current The global burden of TB remains alarmingly high, with 10.4 mil- treatment guidelines indicate standardized fixed dose 6 month reg- lion incident cases and 1.5 million deaths reported by the WHO imens for new treatment and re-treatment of drug-susceptible TB in 2015.1 Mycobacterium tuberculosis (MTB) strains displaying (DS-TB). In the case of DR-TB, the conventional 18–24 month treat- in vitro resistance to isoniazid and rifampicin accounted for ment regimen has been redesigned and now ranges between 9 480000 incident cases and 250000 deaths in 2015.1 XDR-TB and 24 months based on individual patient eligibility such as pre- strains display additional resistance to both the fluoroquinolones vious TB history and drug exposure. In addition to duration, complex and second-line injectable agents, and have been reported to 1,2 multidrug regimens and optimal medication adherence are cause disease in 106 countries to date. With high mortality 9,10 rates, XDR-TB poses a dire threat to public health, exacerbated by required for effective treatment of TB infection. Challenges its deadly interaction with the HIV/AIDS epidemic. of adherence are linked to complex dosing strategies, serious and Additional resistance beyond XDR has been described as totally often life-threatening drug side effects, and drug–drug interactions. drug-resistant TB, which displays further resistance to drugs used This review provides an update on scientific advances in under- to treat XDR-TB, resulting in programmatically untreatable forms standing drug resistance mechanisms in MTB, to new, existing and of TB.3 This, coupled with estimates from published studies that repurposed drugs. We also highlight developments in sequencing suggest that current treatment options for XDR-TB fail to cure technology and bioinformatics that enable personalized therapy 30%–75% of patients with XDR-TB, contributes to an emerging for DR-TB. public health crisis.4–8 New drugs such as bedaquiline and delama- nid, and repurposed drugs such as linezolid, have been introduced Implications for personalized therapy into drug-resistant TB (DR-TB) treatment regimens. Despite the for DR-TB availability of new drugs, limited access to these agents and/or the inability to construct an effective regimen containing at least four The diagnosis of DR-TB remains a challenge. Currently, the front- active drugs, contribute to ongoing poor outcomes in DR-TB, line molecular diagnostic assay for the detection of drug resistance VC The Author(s) 2018. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] 1138 Review JAC is the Cepheid Xpert MTB/RIF (GeneXpert), which detects the pres- that the rate of mutations causing drug resistance varies according ence of MTB bacilli and simultaneously detects rifampicin resist- to the lineage to which the strain belongs. The Beijing strain family, ance.11 Whilst rapidly identifying patients eligible for MDR-TB which is strongly associated with DR-TB in many settings, has treatment, the test is limited to the detection of rifampicin resist- demonstrated increased mutation rates in vitro.32–34 ance. In addition to the GeneXpert, the WHO endorsed the use of The following section details the mutations mediating resist- the Hain line probe assay.12 Current versions include the Genotype ance to each of the anti-TB drugs. Table 1 summarizes the genes MTBDRplus and Genotype MTBDRsl-v2.0, which collectively detect associated with resistance, MICs and mutation frequencies to resistance to isoniazid, rifampicin, fluoroquinolones and second- existing anti-TB agents and new/repurposed agents, respectively. line injectable agents.13,14 However, analysis of published perform- 15,16 ance data of the tests shows suboptimal sensitivities. Thus, Mechanisms of resistance to first-line drugs WGS remains the most desirable platform to perform follow-on testing on rifampicin-resistant TB, which can accelerate the initia- Isoniazid tion of effective treatment. Isoniazid is a prodrug activated by the catalase/peroxidase The current gold standard for MTB drug susceptibility testing enzyme encoded by the katG gene. Once activated, isoniazid inhib- (DST) is culture on solid media, which takes several weeks to months its mycolic acid synthesis via the NADH-dependent enoyl-acyl owing to the slow growth rate of TB in vitro.Treatmentistherefore carrier protein reductase, encoded by the inhA gene.23,24 The often empirical, based on factors such as past medical or social his- molecular basis of isoniazid resistance is mediated by mutations in tory, or local prevalence of resistance. This results in delays in the ini- the katG, inhA gene or within the promoter region of the inhA gene. tiation of appropriate treatment.17 The use of empirical treatment The most common resistance mechanism has been identified as regimens often leads to overprescribing of drugs with adverse the katG S315T mutation, which leads to an inefficient isoniazid– effects including irreversible hearing loss, renal toxicity and hepato- NAD product inhibiting the antimicrobial action of isoniazid. This toxicity. In contrast, suboptimal treatment increases the potential mechanism is associated with high-level isoniazid resistance in for the development of drug resistance.18,19 MDR isolates.35–38 Mutations of the inhA promoter region, the most An additional challenge is the misdiagnosis of infection by non- common being found at position #15, result in an overexpression TB mycobacteria (NTM) as TB. Pulmonary infections caused by NTM of inhA. This mechanism is associated with low-level resistance in are gaining recognition for increasing isolation in clinical settings isoniazid monoresistant isolates and has been implicated in cross- worldwide.20 The presence of NTM as commensals in pulmonary resistance to a structural analogue, ethionamide. Mutations in the samples confounds MTB diagnosis, particularly in patients with a active region of the inhA gene result in a decreased affinity of the previous TB history and other chronic pulmonary conditions. isoniazid–NAD product. Such mutations are less frequent.38,39 Furthermore, the clinical signs and symptoms of NTM infection are clinically and radiologically indistinguishable from MTB infection, A recent study reported that mutations occurring in the inhA regu- 21 latory region and coding region resulted in high-level isoniazid underscoring the need for a reliable molecular-based diagnostic. 40 These factors clearly underscore the urgent need to detect rap- resistance and cross-resistance to ethionamide. Mutations in the idly the drug resistance and initiate personalized treatment for dfrA gene have recently been implicated in resistance to isoniazid. every patient presenting with DR-TB to prevent ongoing DR-TB