1
|
Xu JT, Lin Y, Cheng T, Deng JY. The rv2820c K114N mutation is related with capreomycin tolerance. Tuberculosis (Edinb) 2024; 148:102551. [PMID: 39084000 DOI: 10.1016/j.tube.2024.102551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/17/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
As one of the factors affecting the treatment outcomes, drug tolerance in mycobacteriosis has not been paid due attention. Genome-wide association studies on 607 Mycobacterium tuberculosis clinical isolates with phenotypic drug susceptibility test data revealed that a K114N mutation on the rv2820c gene was highly enriched in capreomycin-resistant isolates (32/213, 15.02%). However, the mutation was also observed in capreomycin-sensitive isolates (10/394, 2.53%). In most cases (31/42, 73.81%), the rv2820c K114N mutation occurred in isolates with the known capreomycin resistance conferring mutation rrs A1401G. In contrast, the general frequency of the rv2820c K114N mutation was low in 7061 genomes downloaded from the National Center for Biotechnology Information database. To determine the impact of this mutation on the antimycobacterial activity of capreomycin, the intact rv2820c gene and the rv2820c K114N mutant were over-expressed in Mycobacterium smegmatis (Ms), and the results of susceptibility tests showed that the rv2820c K114N mutation did not affect the minimum inhibition concentration (MIC) of capreomycin. Subsequently, the data of time-kill assays showed that, it took only 2 h of capreomycin treatment (40 μg/ml, 5 × MIC) to kill 99.9% bacterial cells of Ms MC2155 pMV261::rv2820cH37Rv, while it took 6 h to achieve that for Ms MC2155 pMV261::rv2820cK114N. Taken together, these data suggested that the rv2820c K114N mutation is related with capreomycin tolerance, which merits further investigation.
Collapse
Affiliation(s)
- Jin-Tian Xu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Lin
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Cheng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiao-Yu Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
2
|
Datta D, Jamwal S, Jyoti N, Patnaik S, Kumar D. Actionable mechanisms of drug tolerance and resistance in Mycobacterium tuberculosis. FEBS J 2024. [PMID: 38676952 DOI: 10.1111/febs.17142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/23/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
The emergence of antimicrobial resistance (AMR) across bacterial pathogens presents a serious threat to global health. This threat is further exacerbated in tuberculosis (TB), mainly due to a protracted treatment regimen involving a combination of drugs. A diversity of factors contributes to the emergence of drug resistance in TB, which is caused by the pathogen Mycobacterium tuberculosis (Mtb). While the traditional genetic mutation-driven drug resistance mechanisms operate in Mtb, there are also several additional unique features of drug resistance in this pathogen. Research in the past decade has enriched our understanding of such unconventional factors as efflux pumps, bacterial heterogeneity, metabolic states, and host microenvironment. Given that the discovery of new antibiotics is outpaced by the emergence of drug resistance patterns displayed by the pathogen, newer strategies for combating drug resistance are desperately needed. In the context of TB, such approaches include targeting the efflux capability of the pathogen, modulating the host environment to prevent bacterial drug tolerance, and activating the host anti-mycobacterial pathways. In this review, we discuss the traditional mechanisms of drug resistance in Mtb, newer understandings and the shaping of a set of unconventional approaches to target both the emergence and treatment of drug resistance in TB.
Collapse
Affiliation(s)
- Dipanwita Datta
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Shaina Jamwal
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nishant Jyoti
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| |
Collapse
|
3
|
Xiong XS, Zhang XD, Yan JW, Huang TT, Liu ZZ, Li ZK, Wang L, Li F. Identification of Mycobacterium tuberculosis Resistance to Common Antibiotics: An Overview of Current Methods and Techniques. Infect Drug Resist 2024; 17:1491-1506. [PMID: 38628245 PMCID: PMC11020249 DOI: 10.2147/idr.s457308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is an essential cause of tuberculosis treatment failure and death of tuberculosis patients. The rapid and reliable profiling of Mycobacterium tuberculosis (MTB) drug resistance in the early stage is a critical research area for public health. Then, most traditional approaches for detecting MTB are time-consuming and costly, leading to the inappropriate therapeutic schedule resting on the ambiguous information of MTB drug resistance, increasing patient economic burden, morbidity, and mortality. Therefore, novel diagnosis methods are frequently required to meet the emerging challenges of MTB drug resistance distinguish. Considering the difficulty in treating MDR-TB, it is urgently required for the development of rapid and accurate methods in the identification of drug resistance profiles of MTB in clinical diagnosis. This review discussed recent advances in MTB drug resistance detection, focusing on developing emerging approaches and their applications in tangled clinical situations. In particular, a brief overview of antibiotic resistance to MTB was present, referred to as intrinsic bacterial resistance, consisting of cell wall barriers and efflux pumping action and acquired resistance caused by genetic mutations. Then, different drug susceptibility test (DST) methods were described, including phenotype DST, genotype DST and novel DST methods. The phenotype DST includes nitrate reductase assay, RocheTM solid ratio method, and liquid culture method and genotype DST includes fluorescent PCR, GeneXpert, PCR reverse dot hybridization, ddPCR, next-generation sequencing and gene chips. Then, novel DST methods were described, including metabolism testing, cell-free DNA probe, CRISPR assay, and spectral analysis technique. The limitations, challenges, and perspectives of different techniques for drug resistance are also discussed. These methods significantly improve the detection sensitivity and accuracy of multidrug-resistant tuberculosis (MRT) and can effectively curb the incidence of drug-resistant tuberculosis and accelerate the process of tuberculosis eradication.
Collapse
Affiliation(s)
- Xue-Song Xiong
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Xue-Di Zhang
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Jia-Wei Yan
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Ting-Ting Huang
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Zhan-Zhong Liu
- Department of Pharmacy, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Zheng-Kang Li
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Liang Wang
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fen Li
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| |
Collapse
|
4
|
Jeon SM, Park S, Lim NR, Lee N, Jung J, Sung N, Kim S. Molecular Analysis of Anti-Tuberculosis Drug Resistance of Mycobacterium tuberculosis Isolated in the Republic of Korea. Antibiotics (Basel) 2023; 12:1324. [PMID: 37627744 PMCID: PMC10451913 DOI: 10.3390/antibiotics12081324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid and accurate detection of tuberculosis (TB) drug resistance is critical for the successful treatment and control of TB. Here, we investigated resistance to anti-TB drugs and genetic variations in 215 drug-resistant Mycobacterium tuberculosis isolates in Korea. Genetic variations were observed in rpoB Ser531Leu, katG Ser315Thr, and gyrA Asp94Gly; however, the minimum inhibitory concentrations varied, which can be attributed to other resistance mechanisms. Examination of genetic relatedness among drug-resistant isolates revealed that the cluster size of resistant bacteria was less than six strains, suggesting no evidence of a large-scale epidemic caused by a specific strain. However, rpoC mutants of the rifampicin-resistant isolates were composed of five types of clusters, suggesting that these compensatory mutations advance propagation. In the present study, more than 90% of the resistance mechanisms to major anti-TB drugs were identified, and the effect of each mutation on drug resistance was estimated. With the clinical application of recent next-generation sequencing-based susceptibility testing, the present study is expected to improve the clinical utilization of genotype-based drug susceptibility testing for the diagnosis and treatment of patients with drug-resistant TB.
Collapse
Affiliation(s)
- Se-Mi Jeon
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Sanghee Park
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Na-Ra Lim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Noori Lee
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Jihee Jung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Nackmoon Sung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Seonghan Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| |
Collapse
|
5
|
Robbins L, Balaram A, Dejneka S, McMahon M, Najibi Z, Pawlowicz P, Conrad WH. Heterologous production of the D-cycloserine intermediate O-acetyl-L-serine in a human type II pulmonary cell model. Sci Rep 2023; 13:8551. [PMID: 37237156 DOI: 10.1038/s41598-023-35632-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Tuberculosis (TB) is the second leading cause of death by a single infectious disease behind COVID-19. Despite a century of effort, the current TB vaccine does not effectively prevent pulmonary TB, promote herd immunity, or prevent transmission. Therefore, alternative approaches are needed. We seek to develop a cell therapy that produces an effective antibiotic in response to TB infection. D-cycloserine (D-CS) is a second-line antibiotic for TB that inhibits bacterial cell wall synthesis. We have determined D-CS to be the optimal candidate for anti-TB cell therapy due to its effectiveness against TB, relatively short biosynthetic pathway, and its low-resistance incidence. The first committed step towards D-CS synthesis is catalyzed by the L-serine-O-acetyltransferase (DcsE) which converts L-serine and acetyl-CoA to O-acetyl-L-serine (L-OAS). To test if the D-CS pathway could be an effective prophylaxis for TB, we endeavored to express functional DcsE in A549 cells as a human pulmonary model. We observed DcsE-FLAG-GFP expression using fluorescence microscopy. DcsE purified from A549 cells catalyzed the synthesis of L-OAS as observed by HPLC-MS. Therefore, human cells synthesize functional DcsE capable of converting L-serine and acetyl-CoA to L-OAS demonstrating the first step towards D-CS production in human cells.
Collapse
Affiliation(s)
- Laurel Robbins
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Ariane Balaram
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Stefanie Dejneka
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Matthew McMahon
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Zarina Najibi
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Peter Pawlowicz
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - William H Conrad
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA.
| |
Collapse
|
6
|
Gautam S, Qureshi KA, Jameel Pasha SB, Dhanasekaran S, Aspatwar A, Parkkila S, Alanazi S, Atiya A, Khan MMU, Venugopal D. Medicinal Plants as Therapeutic Alternatives to Combat Mycobacterium tuberculosis: A Comprehensive Review. Antibiotics (Basel) 2023; 12:antibiotics12030541. [PMID: 36978408 PMCID: PMC10044459 DOI: 10.3390/antibiotics12030541] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Tuberculosis (TB) is a serious infectious disease caused by Mycobacterium tuberculosis (MTB) and a significant health concern worldwide. The main threat to the elimination of TB is the development of resistance by MTB to the currently used antibiotics and more extended treatment methods, which is a massive burden on the health care system. As a result, there is an urgent need to identify new, effective therapeutic strategies with fewer adverse effects. The traditional medicines found in South Asia and Africa have a reservoir of medicinal plants and plant-based compounds that are considered another reliable option for human beings to treat various diseases. Abundant research is available for the biotherapeutic potential of naturally occurring compounds in various diseases but has been lagging in the area of TB. Plant-based compounds, or phytoproducts, are being investigated as potential anti-mycobacterial agents by reducing bacterial burden or modulating the immune system, thereby minimizing adverse effects. The efficacy of these phytochemicals has been evaluated through drug delivery using nanoformulations. This review aims to emphasize the value of anti-TB compounds derived from plants and provide a summary of current research on phytochemicals with potential anti-mycobacterial activity against MTB. This article aims to inform readers about the numerous potential herbal treatment options available for combatting TB.
Collapse
Affiliation(s)
- Silvi Gautam
- Department of Microbiology, Graphic Era Deemed to be University, Dehradun 248002, India
| | - Kamal A. Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah 51911, Saudi Arabia
- Correspondence: (K.A.Q.); (D.V.)
| | | | - Sugapriya Dhanasekaran
- Department of Molecular Analytics, Institute of Bioinformatics, SSE-SIMATS, Chennai 602105, India
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Samyah Alanazi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger, Abha 62529, Saudi Arabia
| | - Mohd Masih Uzzaman Khan
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Unaizah 51911, Saudi Arabia
| | - Divya Venugopal
- Department of Microbiology, Graphic Era Deemed to be University, Dehradun 248002, India
- Correspondence: (K.A.Q.); (D.V.)
| |
Collapse
|
7
|
Gaglani P, Dwivedi M, Upadhyay TK, Kaushal RS, Ahmad I, Saeed M. A pro-oxidant property of vitamin C to overcome the burden of latent Mycobacterium tuberculosis infection: A cross-talk review with Fenton reaction. Front Cell Infect Microbiol 2023; 13:1152269. [PMID: 37153159 PMCID: PMC10155705 DOI: 10.3389/fcimb.2023.1152269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/17/2023] [Indexed: 05/09/2023] Open
Abstract
Tuberculosis (TB), caused by the bacillus M. tuberculosis, is one of the deadliest infectious illnesses of our day, along with HIV and malaria.Chemotherapy, the cornerstone of TB control efforts, is jeopardized by the advent of M. tuberculosis strains resistant to many, if not all, of the existing medications.Isoniazid (INH), rifampicin (RIF), pyrazinamide, and ethambutol are used to treat drug-susceptible TB for two months, followed by four months of INH and RIF, but chemotherapy with potentially harmful side effects is sometimes needed to treat multidrug-resistant (MDR) TB for up to two years. Chemotherapy might be greatly shortened by drugs that kill M. tuberculosis more quickly while simultaneously limiting the emergence of drug resistance.Regardless of their intended target, bactericidal medicines commonly kill pathogenic bacteria (gram-negative and gram-positive) by producing hydroxyl radicals via the Fenton reaction.Researchers have concentrated on vitamins with bactericidal properties to address the rising cases globally and have discovered that these vitamins are effective when given along with first-line drugs. The presence of elevated iron content, reactive oxygen species (ROS) generation, and DNA damage all contributed to VC's sterilizing action on M. tb in vitro. Moreover, it has a pleiotropic effect on a variety of biological processes such as detoxification, protein folding - chaperons, cell wall processes, information pathways, regulatory, virulence, metabolism etc.In this review report, the authors extensively discussed the effects of VC on M. tb., such as the generation of free radicals and bactericidal mechanisms with existing treatments, and their further drug development based on ROS production.
Collapse
Affiliation(s)
- Pratikkumar Gaglani
- Department of Life Sciences, Parul Institute of Applied Sciences and Biophysics and Structural Biology Laboratory, Center of Research for Development, Parul University, Vadodara, Gujarat, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, India
| | - Tarun Kumar Upadhyay
- Department of Life Sciences, Parul Institute of Applied Sciences and Animal Cell Culture and Immunobiochemistry Lab, Center of Research for Development, Parul University, Vadodara, Gujarat, India
| | - Radhey Shyam Kaushal
- Department of Life Sciences, Parul Institute of Applied Sciences and Biophysics and Structural Biology Laboratory, Center of Research for Development, Parul University, Vadodara, Gujarat, India
- *Correspondence: Radhey Shyam Kaushal, ; Mohd Saeed,
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, Hail, Saudi Arabia
- *Correspondence: Radhey Shyam Kaushal, ; Mohd Saeed,
| |
Collapse
|
8
|
Ali W, Jamal S, Grover A, Grover S. Insights into the mutations leading to capreomycin resistance in S-adenosyl-L-methionine binding motif in TlyA from Mycobacterium tuberculosis. J Biomol Struct Dyn 2022; 40:12239-12247. [PMID: 34463210 DOI: 10.1080/07391102.2021.1969284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Capreomycin is a second line antibiotic used for the treatment of drug resistant Tuberculosis (TB), primary reason of death from a solo infectious organism, Mycobacterium tuberculosis (M.tb). Capreomycin targets the ribosome of bacteria and is known to bind at the interface where the large and small ribosomal subunits interact in M.tb using an S-Adenosyl Methionine (SAM) dependent methyltransferase, TlyA (Rv1794). Besides the methyltransferase activity, TlyA has also been found to show substantial haemolytic activity. The dual activity of TlyA highlights its crucial role in pathogenesis and virulence of M.tb. In the present study, docking and molecular dynamics (MD) simulations were carried out to explore the impact of mutations in a conserved SAM binding motif, 90GASTG94, on the affinity of TlyA enzyme for SAM. Two already reported mutations, A91E and S92L, and the remaining wild type residues, Gly90, Thr93, Gly94 mutated to alanine were taken into consideration resulting in a total of six systems, wild type + SAM, G90A + SAM, A91E + SAM, S92L + SAM, T93A + SAM and G94A + SAM that were subjected to 100 ns MD simulations. Docking scores and MD simulations analyses revealed that in contrast to wild type, mutants reduced the affinity of SAM for TlyA with most prominent effect observed in case of alanine mutants. Mutations also led to the loss of hydrogen bond and hydrophobic interactions and large-scale movement of atoms evident from the principal component analyses indicating their destabilizing impact on TlyA. The present study gives insights into influence of mutations on binding of SAM to TlyA in M.tb and promoting capreomycin resistance.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Waseem Ali
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Salma Jamal
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Sonam Grover
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
| |
Collapse
|
9
|
Wu SH, Xiao YX, Hsiao HC, Jou R. Development and Assessment of a Novel Whole-Gene-Based Targeted Next-Generation Sequencing Assay for Detecting the Susceptibility of Mycobacterium tuberculosis to 14 Drugs. Microbiol Spectr 2022; 10:e0260522. [PMID: 36255328 PMCID: PMC9769975 DOI: 10.1128/spectrum.02605-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as an alternative method for detecting drug-resistant tuberculosis (DR-TB). To provide comprehensive drug susceptibility information and to address mutations missed by available commercial molecular diagnostics, we developed and evaluated a tNGS panel with 22 whole-gene targets using the Ion Torrent platform to predict drug resistance to 14 drugs, namely, rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide (PZA), moxifloxacin (MFX), levofloxacin (LFX), amikacin (AMK), capreomycin (CM), kanamycin (KM), streptomycin (SM), bedaquiline (BDQ), clofazimine (CFZ), linezolid (LZD), and delamanid (DLM). We selected 50 and 35 Mycobacterium tuberculosis isolates with various DR profiles as the training set and the challenge set, respectively. Comparative variant analyses of the DR genes were performed using Sanger sequencing and whole-genome sequencing (WGS). Phenotypic drug susceptibility testing (pDST) results were used as gold standards. Regarding the limit of detection, the tNGS assay detected 2.9 to 3.8% minority variants in 4% mutant mixtures. The sensitivity and specificity of tNGS were 97.0% (95% confidence interval [CI] = 93.1 to 98.7%) and 99.1% (95% CI = 97.7 to 99.7%), respectively. The concordance of tNGS with pDST was 98.5% (95% CI = 97.2 to 99.2%), which was comparable to that of WGS (98.7%, 95% CI = 97.4 to 99.3%) and better than that of Sanger sequencing (96.9%, 95% CI = 95.3 to 98.0%). The agreement between tNGS and pDST was almost perfect for RIF, INH, EMB, MFX, LFX, AMK, CM, KM, SM, BDQ, and LZD (kappa value = 0.807 to 1.000) and substantial for PZA (kappa value = 0.791). Our customized novel whole-gene-based tNGS panel is highly consistent with pDST and WGS for comprehensive and accurate prediction of drug resistance in a strengthened and streamlined DR-TB laboratory program. IMPORTANCE We developed and validated a tNGS assay that was the first to target 22 whole genes instead of regions of drug resistance genes and comprehensively detected susceptibility to 14 anti-TB drugs, with great flexibility to include new or repurposed drugs. Notably, we demonstrated that our custom-designed Ion AmpliSeq TB research panel platform had high concordance with pDST and could significantly reduce turnaround time (by approximately 70%) to meet a clinically actionable time frame. Our tNGS assay is a promising DST solution for providing needed clinical information for precision medicine-guided therapies for DR-TB and allows the rollout of active pharmacovigilance.
Collapse
Affiliation(s)
- Sheng-Han Wu
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Xin Xiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hseuh-Chien Hsiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| |
Collapse
|
10
|
Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms. PLoS Biol 2022; 20:e3001755. [PMID: 35944070 PMCID: PMC9363015 DOI: 10.1371/journal.pbio.3001755] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.
Collapse
|
11
|
Evaluation of Susceptibility of the Human Pathogen Helicobacter pylori to the Antibiotic Capreomycin. ScientificWorldJournal 2022; 2022:8924023. [PMID: 35958801 PMCID: PMC9357814 DOI: 10.1155/2022/8924023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
Helicobacter pylori infection causes gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue lymphoma, and gastric cancer and can also promote thrombosis. It is estimated that approximately 4.5 billion individuals are infected, thus rendering H. pylori the most prevalent microbial pathogen. Currently established regimes for antibiotic treatment are massively challenged by increasing drug resistance and the development of novel antimicrobial therapies is urgently required. The antibiotic capreomycin is clinically used against multiple drug-resistant strains of Mycobacterium tuberculosis. It targets the complex between TlyA, a hemolysin- and RNA-binding protein, and the bacterial rRNA. In this study we have explored the possible antibacterial effects of capreomycin against several strains of H. pylori and found only moderate activity which was comparable to metronidazole-resistant strains. Molecular docking of capreomycin to TlyA proteins from H. pylori and M. tuberculosis identified several residues within TlyA which interact with the drug; however, binding affinities of H. pylori– TlyA for capreomycin appear to be higher than those of Mycobacterium– TlyA. The data suggest that capreomycin may warrant further investigations into its potential use as antibiotic against H. pylori.
Collapse
|
12
|
Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study. Antimicrob Agents Chemother 2022; 66:e0207521. [PMID: 35532237 DOI: 10.1128/aac.02075-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Point mutations in the rrs gene and the eis promoter are known to confer resistance to the second-line injectable drugs (SLIDs) amikacin (AMK), capreomycin (CAP), and kanamycin (KAN). While mutations in these canonical genes confer the majority of SLID resistance, alternative mechanisms of resistance are not uncommon and threaten effective treatment decisions when using conventional molecular diagnostics. In total, 1,184 clinical Mycobacterium tuberculosis isolates from 7 countries were studied for genomic markers associated with phenotypic resistance. The markers rrs:A1401G and rrs:G1484T were associated with resistance to all three SLIDs, and three known markers in the eis promoter (eis:G-10A, eis:C-12T, and eis:C-14T) were similarly associated with kanamycin resistance (KAN-R). Among 325, 324, and 270 AMK-R, CAP-R, and KAN-R isolates, 274 (84.3%), 250 (77.2%), and 249 (92.3%) harbored canonical mutations, respectively. Thirteen isolates harbored more than one canonical mutation. Canonical mutations did not account for 103 of the phenotypically resistant isolates. A genome-wide association study identified three genes and promoters with mutations that, on aggregate, were associated with unexplained resistance to at least one SLID. Our analysis associated whiB7 5'-untranslated-region mutations with KAN resistance, supporting clinical relevance for this previously demonstrated mechanism of KAN resistance. We also provide evidence for the novel association of CAP resistance with the promoter of the Rv2680-Rv2681 operon, which encodes an exoribonuclease that may influence the binding of CAP to the ribosome. Aggregating mutations by gene can provide additional insight and therefore is recommended for identifying rare mechanisms of resistance when individual mutations carry insufficient statistical power.
Collapse
|
13
|
Heidary M, Shirani M, Moradi M, Goudarzi M, Pouriran R, Rezaeian T, Khoshnood S. Tuberculosis challenges: Resistance, co-infection, diagnosis, and treatment. Eur J Microbiol Immunol (Bp) 2022; 12:1-17. [PMID: 35420996 PMCID: PMC9036649 DOI: 10.1556/1886.2021.00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/10/2022] [Indexed: 01/23/2023] Open
Abstract
Early diagnosis of tuberculosis (TB), followed by effective treatment, is the cornerstone of global TB control efforts. An estimated 3 million cases of TB remain undetected each year. Early detection and effective management of TB can prevent severe disease and reduce mortality and transmission. Intrinsic and acquired drug resistance of Mycobacterium tuberculosis (MTB) severely restricted the anti-TB therapeutic options, and public health policies are required to preserve the new medications to treat TB. In addition, TB and HIV frequently accelerate the progression of each other, and one disease can enhance the other effect. Overall, TB-HIV co-infections show an adverse bidirectional interaction. For HIV-infected patients, the risk of developing TB disease is approximately 22 times higher than for persons with a protective immune response. Analysis of the current TB challenges is critical to meet the goals of the end TB strategy and can go a long way in eradicating the disease. It provides opportunities for global TB control and demonstrates the efforts required to accelerate eliminating TB. This review will discuss the main challenges of the TB era, including resistance, co-infection, diagnosis, and treatment.
Collapse
Affiliation(s)
- Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Maryam Shirani
- Toxicology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Melika Moradi
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ramin Pouriran
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayebe Rezaeian
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| |
Collapse
|
14
|
Laughlin ZT, Nandi S, Dey D, Zelinskaya N, Witek MA, Srinivas P, Nguyen HA, Kuiper EG, Comstock LR, Dunham CM, Conn GL. 50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA. Proc Natl Acad Sci U S A 2022; 119:e2120352119. [PMID: 35357969 PMCID: PMC9168844 DOI: 10.1073/pnas.2120352119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single methyltransferase that acts on one nucleotide target and rRNA methylation directly prevents drug binding, thereby conferring drug resistance. Loss of intrinsic methylation can also result in antibiotic resistance. For example, Mycobacterium tuberculosis becomes sensitized to tuberactinomycin antibiotics, such as capreomycin and viomycin, due to the action of the intrinsic methyltransferase TlyA. TlyA is unique among antibiotic resistance-associated methyltransferases as it has dual 16S and 23S rRNA substrate specificity and can incorporate cytidine-2′-O-methylations within two structurally distinct contexts. Here, we report the structure of a mycobacterial 50S subunit-TlyA complex trapped in a postcatalytic state with a S-adenosyl-L-methionine analog using single-particle cryogenic electron microscopy. Together with complementary functional analyses, this structure reveals critical roles in 23S rRNA substrate recognition for conserved residues across an interaction surface that spans both TlyA domains. These interactions position the TlyA active site over the target nucleotide C2144, which is flipped from 23S Helix 69 in a process stabilized by stacking of TlyA residue Phe157 on the adjacent A2143. Base flipping may thus be a common strategy among rRNA methyltransferase enzymes, even in cases where the target site is accessible without such structural reorganization. Finally, functional studies with 30S subunit suggest that the same TlyA interaction surface is employed to recognize this second substrate, but with distinct dependencies on essential conserved residues.
Collapse
Affiliation(s)
- Zane T. Laughlin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Suparno Nandi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Natalia Zelinskaya
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Marta A. Witek
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Pooja Srinivas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Ha An Nguyen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Department of Chemistry Graduate Program, Emory University, Atlanta, GA 30322
| | - Emily G. Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Christine M. Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Emory Antibiotic Resistance Center, Emory University, Atlanta, GA 30322
| | - Graeme L. Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Emory Antibiotic Resistance Center, Emory University, Atlanta, GA 30322
| |
Collapse
|
15
|
Salaikumaran MR, Badiger VP, Burra VLSP. 16S rRNA Methyltransferases as Novel Drug Targets Against Tuberculosis. Protein J 2022; 41:97-130. [PMID: 35112243 DOI: 10.1007/s10930-021-10029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is an airborne infectious disease caused by Mycobacterium tuberculosis (M.tb) whose natural history traces back to 70,000 years. TB remains a major global health burden. Methylation is a type of post-replication, post-transcriptional and post-translational epi-genetic modification involved in transcription, translation, replication, tissue specific expression, embryonic development, genomic imprinting, genome stability and chromatin structure, protein protein interactions and signal transduction indicating its indispensable role in survival of a pathogen like M.tb. The pathogens use this epigenetic mechanism to develop resistance against certain drug molecules and survive the lethality. Drug resistance has become a major challenge to tackle and also a major concern raised by WHO. Methyltransferases are enzymes that catalyze the methylation of various substrates. None of the current TB targets belong to methyltransferases which provides therapeutic opportunities to develop novel drugs through studying methyltransferases as potential novel targets against TB. Targeting 16S rRNA methyltransferases serves two purposes simultaneously: a) translation inhibition and b) simultaneous elimination of the ability to methylate its substrates hence stopping the emergence of drug resistance strains. There are ~ 40 different rRNA methyltransferases and 13 different 16S rRNA specific methyltransferases which are unexplored and provide a huge opportunity for treatment of TB.
Collapse
Affiliation(s)
- M R Salaikumaran
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India
| | - Veena P Badiger
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India
| | - V L S Prasad Burra
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India.
| |
Collapse
|
16
|
Keith BA, Harding JCS, Loewen ME. Mutational analysis of TlyA from Brachyspira hampsonii reveals two key residues conserved in pathogenic bacteria responsible for oligomerization and hemolytic activity. Biochim Biophys Acta Gen Subj 2022; 1866:130045. [PMID: 34715264 DOI: 10.1016/j.bbagen.2021.130045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/07/2021] [Accepted: 10/22/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND TlyA proteins are expressed in a variety of pathogenic bacteria and possess dual hemolytic and ribosomal RNA methyltransferase functions. While the mechanism of TlyA mediated rRNA methylation is well understood, relatively little is known about the mechanism of TlyA induced hemolysis. METHODS TlyA protein from the pig pathogen Brachyspira hampsonii was heterologously expressed and purified from an E. coli host. Hemolytic activity and rRNA methylation were assessed in vitro. Site-directed mutagenesis was used to mutate amino acids believed to be involved in TlyA mediated hemolysis. RESULTS Purified TlyA-His protein exhibited both hemolytic and rRNA methyltransferase activities in vitro, with partial inhibition of hemolysis observed under reducing conditions. Mutation of cysteine 80 to alanine impaired hemolytic activity. A C27A/C93A mutant was capable of dimerizing under non-reducing conditions, indicating that a C80-C80 disulfide bond is involved in TlyA oligomerization. A mutation conserved in several avirulent Brachyspira species (S9K) completely abolished hemolytic activity of TlyA. This loss of activity was attributed to impaired oligomerization in the S9K mutant, as assessed by ITC and size-exclusion chromatography experiments. CONCLUSIONS Oligomeric assembly and hemolytic activity of TlyA from Brachyspira hampsonii is dependent on the formation of an intermolecular C80-C80 disulfide bond and noncovalent interactions involving serine 9. The conservation of these amino acids in TlyA proteins from pathogenic bacteria suggests a correlation between tlyA gene mutations and bacterial virulence. GENERAL SIGNIFICANCE Our results further elucidate the mechanisms underlying TlyA mediated hemolysis and provide evidence of a conserved mechanism of oligomerization for TlyA family proteins.
Collapse
Affiliation(s)
- Brandon A Keith
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Matthew E Loewen
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada.
| |
Collapse
|
17
|
Akpobolokemi T, Martinez-Nunez RT, Raimi-Abraham BT. Tackling the global impact of substandard and falsified and unregistered/unlicensed anti-tuberculosis medicines. MEDICINE ACCESS @ POINT OF CARE 2022; 6:23992026211070406. [PMID: 36204519 PMCID: PMC9413333 DOI: 10.1177/23992026211070406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Substandard and falsified (SF) medicines are a global health challenge with the
World Health Organization (WHO) estimating that 1 in 10 of medicines in low- and
middle-income countries (LMICs) are SF. Antimicrobials (i.e. antimalarials,
antibiotics) are the most commonly reported SF medicines. SF medicines
contribute significantly to the global burden of infectious diseases and
antimicrobial resistance (AMR). This article discusses the challenges associated
with the global impact of SF and unregistered/unlicensed antimicrobials with a
focus on anti-TB medicines. Tuberculosis (TB) is the 13th leading cause of death
worldwide, and is currently the second leading cause of death from a single
infectious agent, ranking after COVID-19 and above HIV/AIDS. Specifically in the
case of TB, poor quality of anti-TB medicines is among the drivers of the
emergence of drug-resistant TB pathogens. In this article, we highlight and
discuss challenges including the emergence of SF associated AMR, patient
mistrust and lack of relevant data. We also present study reports to inform
meaningful change. Recommended solutions involve the adaptation of interventions
from high-income countries (HICs) to LMICS, the need for improvement in the
uptake of medication authentication tools in LMICs, increased stewardship, and
the need for global and regional multidisciplinary legal and policy cooperation,
resulting in improved legal sanctions.
Collapse
Affiliation(s)
- Tamara Akpobolokemi
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, UK
| | - Rocio Teresa Martinez-Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, Faculty of Life Sciences & Medicine, King’s College London, Guy’s Hospital, London, UK
| | - Bahijja Tolulope Raimi-Abraham
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, UK
| |
Collapse
|
18
|
Sharma M, Singh P. Role of TlyA in the Biology of Uncultivable Mycobacteria. Comb Chem High Throughput Screen 2022; 25:1587-1594. [PMID: 35021968 DOI: 10.2174/1386207325666220111150923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022]
Abstract
TlyA proteins are related to distinct functions in a diverse spectrum of bacterial pathogens including mycobacterial spp. There are several annotated proteins function as hemolysin or pore forming molecules that play an important role in the virulence of pathogenic organisms. Many studies reported the dual activity of mycobacterial TlyA as 'hemolysin' and 'S-adenosylmethionine dependent rRNA methylase'. To act as a hemolysin, a sequence must have a signal sequence and transmembrane segment which helps the protein to enter the extracellular environment. Interestingly, the mycobacterial tlyA has neither a traditional signal sequences of general/sec/tat pathways nor any transmembrane segments are present. Still it can reach the extracellular milieu with the help of non-classical signal mechanisms. Also, retention of tlyA in cultivable mycobacterial pathogens (such as Mycobacterium tuberculosis and M. marinum) as well as uncultivated mycobacterial pathogens despite their extreme reductive evolution (such as M. leprae, M. lepromatosis and M. uberis) suggests its crucial role in evolutionary biology of pathogenic mycobacteria. Numerous virulence factors have been characterised from the uncultivable mycobacteria but the information of TlyA protein is still limited in terms of molecular and structural characterisation. The genomic insights offered by comparative analysis of TlyA sequences and its conserved domains reveal its pore forming activity which further confirms its role as a virulence protein, particularly in uncultivable mycobacteria. Therefore, this review presents a comparative analysis of mycobacterial TlyA family by sequence homology and alignment to improve our understanding of this unconventional hemolysin and RNA methyltransferase TlyA of uncultivable mycobacteria.
Collapse
Affiliation(s)
- Mukul Sharma
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Pushpendra Singh
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| |
Collapse
|
19
|
Ponnusamy N, Arumugam M. Interaction of Host Pattern Recognition Receptors (PRRs) with Mycobacterium Tuberculosis and Ayurvedic Management of Tuberculosis: A Systemic Approach. Infect Disord Drug Targets 2022; 22:e130921196420. [PMID: 34517809 DOI: 10.2174/1871526521666210913110834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/15/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (Mtb), infects the lungs' alveolar surfaces through aerosol droplets. At this stage, the disease progression may have many consequences, determined primarily by the reactions of the human immune system. However, one approach will be to more actively integrate the immune system, especially the pattern recognition receptor (PRR) systems of the host, which notices pathogen-associated molecular patterns (PAMPs) of Mtb. Several types of PRRs are involved in the detection of Mtb, including Toll-like receptors (TLRs), C-type lectin receptors (CLRs), Dendritic cell (DC) -specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN), Mannose receptor (MR), and NOD-like receptors (NLRs) related to inflammasome activation. In this study, we focus on reviewing the Mtb pathophysiology and interaction of host PPRs with Mtb as well as adverse drug effects of anti-tuberculosis drugs (ATDs) and systematic TB treatment via Ayurvedic medicine.
Collapse
Affiliation(s)
- Nirmaladevi Ponnusamy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Mohanapriya Arumugam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| |
Collapse
|
20
|
Osterman IA, Dontsova OA, Sergiev PV. rRNA Methylation and Antibiotic Resistance. BIOCHEMISTRY (MOSCOW) 2021; 85:1335-1349. [PMID: 33280577 DOI: 10.1134/s000629792011005x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Methylation of nucleotides in rRNA is one of the basic mechanisms of bacterial resistance to protein synthesis inhibitors. The genes for corresponding methyltransferases have been found in producer strains and clinical isolates of pathogenic bacteria. In some cases, rRNA methylation by housekeeping enzymes is, on the contrary, required for the action of antibiotics. The effects of rRNA modifications associated with antibiotic efficacy may be cooperative or mutually exclusive. Evolutionary relationships between the systems of rRNA modification by housekeeping enzymes and antibiotic resistance-related methyltransferases are of particular interest. In this review, we discuss the above topics in detail.
Collapse
Affiliation(s)
- I A Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - O A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - P V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia. .,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
21
|
Assessment of the GenoType MTBDRsl VER 2.0 compared to the phenotypic drug susceptibility testing and whole genome sequencing for the rapid detection of resistance to fluoroquinolone and second-line injectable drugs among rifampicin-resistant Mycobacterium tuberculosis isolates. Arch Microbiol 2021; 203:3989-3996. [PMID: 34032874 DOI: 10.1007/s00203-021-02387-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 04/23/2021] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
Molecular techniques have considerable advantages for rapid detection, a reduction of infectiousness, prevention of further resistance development and surveillance of drug-resistant TB. MTBDRsl VER 2.0 was used to detect resistance to second-line anti-tuberculosis drugs on 35 rifampicin-resistant M. tuberculosis (RR-MTB) isolates compared to the minimum inhibitory concentrations (MICs) and whole genome sequencing (WGS). The MTBDRsl VER 2.0 (Hain Life Science, Nehren, Germany) and WGS (San Diego, CA, USA) were performed for tracing mutations in resistant-related genes involved in resistance to fluoroquinolone (FLQ) and second-line injectable drugs. The broth microdilution method using 7H9 Middlebrook media supplemented with OADC was used to determine the MICs. The MTBDRsl VER 2.0 correctly detected 5/6 (83.3%) of FLQ-resistant strains. The MUT1 A1401G (seven strains) and MUT2 G1484T (one strain) mutations in rrs gene were detected in eight AMK/KAN/CAP-resistant strains. Four low-level KAN-resistant strains with the G-10A/C-12T (three strains) and eis C-14T (one strain) mutations in eis gene was diagnosed using MTBDRsl VER 2.0. Five errors were found in detecting resistance to kanamycin and capreomycin compared to the phenotypic drug susceptibility testing and WGS. Failling wild-type bands without improved mutant bands did not indicate a reliable resistance. WGS could efficiently resolve the discrepancies of the results. MTBDRsl showed better performance in detecting XDR strains than pre-XDR.
Collapse
|
22
|
Momen G, Aainouss A, Lamaammal A, Chettioui F, Blaghen M, Messoudi M, Belghmi K, Mouslim J, El Mzibri M, El Messaoudi MD, Khyatti M, Chaoui I. Molecular characterization of mutations associated with resistance to second line drugs in Mycobacterium tuberculosis patients from Casablanca, Morocco. Rev Inst Med Trop Sao Paulo 2021; 63:e19. [PMID: 33787739 PMCID: PMC7997671 DOI: 10.1590/s1678-9946202163019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/22/2021] [Indexed: 12/02/2022] Open
Abstract
The emergence and spread of extensively drug-resistant tuberculosis (XDR-TB) is a
serious threat to global health. Therefore, its rapid diagnosis is crucial. The
present study aimed to characterize mutations conferring resistance to second
line drugs (SLDs) within multidrug Mycobacterium tuberculosis
(MDR-MTB) isolates and to estimate the occurrence of XDR-TB in Casablanca,
Morocco. A panel of 200 MDR-TB isolates was collected at the Pasteur Institute
between 2015-2018. Samples were subjected to drug susceptibility testing to
Ofloxacin (OFX), Kanamycin (KAN) and Amikacin (AMK). The mutational status of
gyrA, gyrB, rrs,
tlyA and eis was assessed by sequencing
these target genes. Drug susceptibility testing for SLDs showed that among the
200 MDR strains, 20% were resistant to OFX, 2.5% to KAN and 1.5% to AMK.
Overall, 14.5% of MDR strains harbored mutations in gyrA,
gyrB, rrs and tlyA genes.
From the 40 OFXR isolates, 67.5% had mutations in QRDR of
gyrA and gyrB genes, the most frequent one
being Ala90Val in gyrA gene. Of note, none of the isolates
harbored simultaneously mutations in gyrA and
gyrB genes. In eight out of the 200 MDR-TB isolates
resistant either to KAN or AMK, only 25% had A1401G or Lys89Glu change in
rrs and tlyA genes respectively. This
study is very informative and provides data on the alarming rate of
fluoroquinolone resistance which warrants the need to implement appropriate drug
regimens to prevent the emergence and spread of more severe forms of
Mycobacterium tuberculosis drug resistance.
Collapse
Affiliation(s)
- Ghizlane Momen
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco.,Faculté des Sciences, Laboratoire de Microbiologie, Pharmacologie, Biotechnologie et Environnement, Casablanca, Morocco
| | - Achraf Aainouss
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco.,Faculté des Sciences Ben M'Sik, Laboratoire d'Ecologie et Environment, Casablanca, Morocco
| | | | - Fouad Chettioui
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Mohamed Blaghen
- Faculté des Sciences, Laboratoire de Microbiologie, Pharmacologie, Biotechnologie et Environnement, Casablanca, Morocco
| | - Malika Messoudi
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Khalid Belghmi
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Jamal Mouslim
- Faculté des Sciences Ben M'Sik, Laboratoire d'Ecologie et Environment, Casablanca, Morocco
| | - Mohammed El Mzibri
- Centre National de l'Energie, des Sciences et Techniques Nucléaires, Département des Sciences du Vivant, Unité de Recherches Médicales et Biologiques, Rabat, Morocco
| | | | - Meriem Khyatti
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Imane Chaoui
- Centre National de l'Energie, des Sciences et Techniques Nucléaires, Département des Sciences du Vivant, Unité de Recherches Médicales et Biologiques, Rabat, Morocco
| |
Collapse
|
23
|
Khawbung JL, Nath D, Chakraborty S. Drug resistant Tuberculosis: A review. Comp Immunol Microbiol Infect Dis 2020; 74:101574. [PMID: 33249329 DOI: 10.1016/j.cimid.2020.101574] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) was announced as a global emergency in 1993. There was an alarming counter attack of TB worldwide. However, when it was known that TB can be cured completely, the general public became ignorant towards the infection. The pathogenic organism Mycobacterium tuberculosis continuously evolved to resist the antagonist drugs. This has led to the outbreak of resistant strain that gave rise to "Multi Drug Resistant-Tuberculosis" and "Extensively Drug Resistant Tuberculosis" that can still be cured with a lower success rate. While the mechanism of resistance proceeds further, it ultimately causes unmanageable totally drug resistant TB (TDR-TB). Studying the molecular mechanisms underlying the resistance to drugs would help us grasp the genetics and pathophysiology of the disease. In this review, we present the molecular mechanisms behind Mycobacterium tolerance to drugs and their approach towards the development of multi-drug resistant, extremely drug resistant and totally drug resistant TB.
Collapse
Affiliation(s)
| | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
| |
Collapse
|
24
|
Loss of U1498 methylation in 16S rRNA by RsmE methyltransferase associates its role with aminoglycoside resistance in mycobacteria. J Glob Antimicrob Resist 2020; 23:359-369. [PMID: 33186785 DOI: 10.1016/j.jgar.2020.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/28/2020] [Accepted: 10/06/2020] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Modulation of methylation pattern through mutations in ribosomal methyltransferases is a key mechanism of bacterial drug resistance. However, RsmG (GidB), which specifically methylates G527 in 16S rRNA, remains the only conserved methyltransferase known to be associated with low-level drug resistance in mycobacterial isolates. The mycobacterial RsmE homologue methylates U1498 in 16S rRNA in a highly specific manner. U1498 lies in the vicinity of the binding site for various aminoglycosides in the ribosome. However, the association of methylation at U1498 with altered drug response remains poorly understood. METHODS A deletion mutant of the RsmE homologue in Mycobacterium smegmatis was generated by a suicidal vector strategy and drug susceptibility assays were performed on wild-type, knockout and complemented strains with varying concentrations of ribosomal- and non-ribosomal-targeting drugs. RESULTS Deletion of the RsmE homologue of M. smegmatis led to an at least two-fold increase in the minimum inhibitory concentrations (MICs) of aminoglycosides that bind in the decoding centre proximal to U1498 in the 30S subunit. The change in MICs was highly specific and reproducible and did not show any cross-resistance to other drug classes. Surprisingly, Rv2372c, the RsmE homologue of Mycobacterium tuberculosis, has the largest number of mutations among conserved ribosomal methyltransferases, after gidB, highlighting the role of mutations in RsmE methyltransferase as a key emerging mechanism of resistance in clinical strains. CONCLUSION We present the first evidence of an association of methylation of U1498 in 16S rRNA with development of low-level resistance in mycobacteria that must be tackled in a timely manner.
Collapse
|
25
|
Li G, Guo Q, Liu H, Wan L, Jiang Y, Li M, Zhao LL, Zhao X, Liu Z, Wan K. Detection of Resistance to Fluoroquinolones and Second-Line Injectable Drugs Among Mycobacterium tuberculosis by a Reverse Dot Blot Hybridization Assay. Infect Drug Resist 2020; 13:4091-4104. [PMID: 33204126 PMCID: PMC7666996 DOI: 10.2147/idr.s270209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/07/2020] [Indexed: 01/23/2023] Open
Abstract
Background Reliable and timely determination of second-line drug resistance is essential for early initiation effective anti-tubercular treatment among multi-drug resistant (MDR) patients and blocking the spread of MDR and extensively drug-resistant tuberculosis. Molecular methods have the potency to provide accurate and rapid drug susceptibility results. We aimed to establish and evaluate the accuracy of a reverse dot blot hybridization (RDBH) assay to simultaneously detect the resistance of fluoroquinolones (FQs), kanamycin (KN), amikacin (AMK), capreomycin (CPM) and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis. Methods We established and evaluated the accuracy of the RDBH assay by comparing to the phenotypic drug susceptibility testing (DST) and sequencing in 170 M. tuberculosis, of which 94 and 27 were respectively resistant to ofloxacin (OFX) and SLIDs. Results The results show that, compared to phenotypic DST, the sensitivity and specificity of the RDBH assay for resistance detection were 63.8% and 100.0% for OFX, 60.0% and 100.0% for KN, 61.5% and 98.1% for AMK, 50.0% and 99.3% for CPM, and 55.6% and 100% for SLIDs, respectively; compared to sequencing, the sensitivity and specificity of the RDBH assay were 95.2% and 100.0% for OFX, 93.8% and 100.0% for SLIDs or KN (both based on mutations in rrs 1400 region and eis promoter), and 91.6% and 100.0% for AMK or CPM (both based on mutations in rrs 1400 region), respectively. The turnaround time of the RDBH assay was 7 h for testing 42 samples. Conclusion Our data suggested that compared to sequencing, the RDBH assay could serve as a rapid and reliable method for testing the resistance of M. tuberculosis against OFX and SLIDs, enabling early administration of appropriate treatment regimens among MDR tuberculosis patients.
Collapse
Affiliation(s)
- Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Qian Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.,Department of Molecular Biology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Zhiguang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| |
Collapse
|
26
|
Antibiotic Resistance by Enzymatic Modification of Antibiotic Targets. Trends Mol Med 2020; 26:768-782. [PMID: 32493628 DOI: 10.1016/j.molmed.2020.05.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 11/21/2022]
Abstract
Antibiotic resistance remains a significant threat to modern medicine. Modification of the antibiotic target is a resistance strategy that is increasingly prevalent among pathogens. Examples include resistance to glycopeptide and polymyxin antibiotics that occurs via chemical modification of their molecular targets in the cell envelope. Similarly, many ribosome-targeting antibiotics are impaired by methylation of the rRNA. In these cases, the antibiotic target is subjected to enzymatic modification rather than genetic mutation, and in many instances the resistance enzymes are readily mobilized among pathogens. Understanding the enzymes responsible for these modifications is crucial to combat resistance. Here, we review our current understanding of enzymatic modification of antibiotic targets as well as discuss efforts to combat these resistance mechanisms.
Collapse
|
27
|
Tafess K, Ng TTL, Lao HY, Leung KSS, Tam KKG, Rajwani R, Tam STY, Ho LPK, Chu CMK, Gonzalez D, Sayada C, Ma OCK, Nega BH, Ameni G, Yam WC, Siu GKH. Targeted-Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis Cultures Using Two Commercial Sequencing Platforms: Comparison of Analytical and Diagnostic Performance, Turnaround Time, and Cost. Clin Chem 2020; 66:809-820. [DOI: 10.1093/clinchem/hvaa092] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 03/11/2020] [Indexed: 12/16/2022]
Abstract
Abstract
Background
The emergence of Mycobacterium tuberculosis with complex drug resistance profiles necessitates a rapid and comprehensive drug susceptibility test for guidance of patient treatment. We developed two targeted-sequencing workflows based on Illumina MiSeq and Nanopore MinION for the prediction of drug resistance in M. tuberculosis toward 12 antibiotics.
Methods
A total of 163 M. tuberculosis isolates collected from Hong Kong and Ethiopia were subjected to a multiplex PCR for simultaneous amplification of 19 drug resistance-associated genetic regions. The amplicons were then barcoded and sequenced in parallel on MiSeq and MinION in respective batch sizes of 24 and 12 samples. A web-based bioinformatics pipeline, BacterioChek-TB, was developed to translate the raw datasets into clinician-friendly reports.
Results
Both platforms successfully sequenced all samples with mean read depths of 1,127× and 1,649×, respectively. The variant calling by MiSeq and MinION could achieve 100% agreement if variants with an allele frequency of <40% reported by MinION were excluded. Both workflows achieved a mean clinical sensitivity of 94.8% and clinical specificity of 98.0% when compared with phenotypic drug susceptibility test (pDST). Turnaround times for the MiSeq and MinION workflows were 38 and 15 h, facilitating the delivery of treatment guidance at least 17–18 days earlier than pDST, respectively. The higher cost per sample on the MinION platform ($71.56) versus the MiSeq platform ($67.83) was attributed to differences in batching capabilities.
Conclusion
Our study demonstrates the interchangeability of MiSeq and MinION platforms for generation of accurate and actionable results for the treatment of tuberculosis.
Collapse
Affiliation(s)
- Ketema Tafess
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
- Department of Medical Laboratory, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Timothy Ting Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kenneth Siu Sing Leung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kingsley King Gee Tam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Rahim Rajwani
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sarah Tsz Yan Tam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lily Pui Ki Ho
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Corey Mang Kiu Chu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | | | - Chalom Sayada
- Advanced Biological Laboratories (ABL), Metz, France
| | - Oliver Chiu Kit Ma
- KingMed Diagnostics, Science Park, Hong Kong Special Administrative Region, China
| | - Belete Haile Nega
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wing Cheong Yam
- Department of Medical Laboratory, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Gilman Kit Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| |
Collapse
|
28
|
The structural basis for inhibition of ribosomal translocation by viomycin. Proc Natl Acad Sci U S A 2020; 117:10271-10277. [PMID: 32341159 DOI: 10.1073/pnas.2002888117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubunit rotation. The mechanism by which viomycin stabilizes this state remains unexplained. To address this, we have determined cryo-EM and X-ray crystal structures of Escherichia coli 70S ribosome complexes trapped in a rotated state by viomycin. The 3.8-Å resolution cryo-EM structure reveals a ribosome trapped in the hybrid state with 8.6° intersubunit rotation and 5.3° rotation of the 30S subunit head domain, bearing a single P/E state transfer RNA (tRNA). We identify five different binding sites for viomycin, four of which have not been previously described. To resolve the details of their binding interactions, we solved the 3.1-Å crystal structure of a viomycin-bound ribosome complex, revealing that all five viomycins bind to ribosomal RNA. One of these (Vio1) corresponds to the single viomycin that was previously identified in a complex with a nonrotated classical-state ribosome. Three of the newly observed binding sites (Vio3, Vio4, and Vio5) are clustered at intersubunit bridges, consistent with the ability of viomycin to inhibit subunit dissociation. We propose that one or more of these same three viomycins induce intersubunit rotation by selectively binding the rotated state of the ribosome at dynamic elements of 16S and 23S rRNA, thus, blocking conformational changes associated with molecular movements that are required for translocation.
Collapse
|
29
|
Sałamaszyńska-Guz A, Serafińska I, Bącal P, Douthwaite S. Virulence properties of Campylobacter jejuni are enhanced by displaying a mycobacterial TlyA methylation pattern in its rRNA. Cell Microbiol 2020; 22:e13199. [PMID: 32134554 PMCID: PMC7317525 DOI: 10.1111/cmi.13199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/24/2020] [Accepted: 02/23/2020] [Indexed: 01/18/2023]
Abstract
Campylobacter jejuni is a bacterial pathogen that is generally acquired as a zoonotic infection from poultry and animals. Adhesion of C. jejuni to human colorectal epithelial cells is weakened after loss of its cj0588 gene. The Cj0588 protein belongs to the type I group of TlyA (TlyAI) enzymes, which 2′‐O‐methylate nucleotide C1920 in 23S rRNA. Slightly longer TlyAII versions of the methyltransferase are found in actinobacterial species including Mycobacterium tuberculosis, and methylate not only C1920 but also nucleotide C1409 in 16S rRNA. Loss of TlyA function attenuates virulence of both M. tuberculosis and C. jejuni. We show here that the traits impaired in C. jejuni null strains can be rescued by complementation not only with the original cj0588 (tlyAI) but also with a mycobacterial tlyAII gene. There are, however, significant differences in the recombinant phenotypes. While cj0588 restores motility, biofilm formation, adhesion to and invasion of human epithelial cells and stimulation of IL‐8 production in a C. jejuni null strain, several of these properties are further enhanced by the mycobacterial tlyAII gene, in some cases to twice the original wild‐type level. These findings strongly suggest that subtle changes in rRNA modification patterns can affect protein synthesis in a manner that has serious consequences for bacterial pathogenicity.
Collapse
Affiliation(s)
- Agnieszka Sałamaszyńska-Guz
- Division of Microbiology, Department of Pre-Clinical Sciences, Institute of Veterinary Medicine, Warsaw University of Live Sciences - SGGW, Warsaw, Poland
| | - Izabela Serafińska
- Division of Microbiology, Department of Pre-Clinical Sciences, Institute of Veterinary Medicine, Warsaw University of Live Sciences - SGGW, Warsaw, Poland
| | - Paweł Bącal
- Laboratory of Theory and Applications of Electrodes, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,Nałęcz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw, Poland
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| |
Collapse
|
30
|
Wollenberg K, Harris M, Gabrielian A, Ciobanu N, Chesov D, Long A, Taaffe J, Hurt D, Rosenthal A, Tartakovsky M, Crudu V. A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status. BMC Infect Dis 2020; 20:17. [PMID: 31910804 PMCID: PMC6947865 DOI: 10.1186/s12879-019-4739-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/27/2019] [Indexed: 12/01/2022] Open
Abstract
Background Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions present unique challenges in determining recurrence status for effective disease management and treatment. In the Republic of Moldova the burden of DR-TB is exceptionally high, with many cases presenting as recurrent. Methods We performed a retrospective analysis of Mycobacterium tuberculosis from Moldova to better understand the genomic basis of drug resistance and its effect on the determination of recurrence status in a high DR-burden environment. To do this we analyzed genomes from 278 isolates collected from 189 patients, including 87 patients with longitudinal samples. These pathogen genomes were sequenced using Illumina technology, and SNP panels were generated for each sample for use in phylogenetic and network analysis. Discordance between genomic resistance profiles and clinical drug-resistance test results was examined in detail to assess the possibility of mixed infection. Results There were clusters of multiple patients with 10 or fewer differences among DR-TB samples, which is evidence of person-to-person transmission of DR-TB. Analysis of longitudinally collected isolates revealed that many infections exhibited little change over time, though 35 patients demonstrated reinfection by divergent (number of differences > 10) lineages. Additionally, several same-lineage sample pairs were found to be more divergent than expected for a relapsed infection. Network analysis of the H3/4.2.1 clade found very close relationships among 61 of these samples, making differentiation of reactivation and reinfection difficult. There was discordance between genomic profile and clinical drug sensitivity test results in twelve samples, and four of these had low level (but not statistically significant) variation at DR SNPs suggesting low-level mixed infections. Conclusions Whole-genome sequencing provided a detailed view of the genealogical structure of the DR-TB epidemic in Moldova, showing that reinfection may be more prevalent than currently recognized. We also found increased evidence of mixed infection, which could be more robustly characterized with deeper levels of genomic sequencing.
Collapse
Affiliation(s)
- Kurt Wollenberg
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Michael Harris
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrei Gabrielian
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nelly Ciobanu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisnau, Moldova
| | - Dumitru Chesov
- Department of Pneumology and Allergology, Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Moldova.,Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Alyssa Long
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Taaffe
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Darrell Hurt
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael Tartakovsky
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Valeriu Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisnau, Moldova
| |
Collapse
|
31
|
Gómez-Tangarife VJ, Gómez-Restrepo AJ, Robledo-Restrepo J, Hernández-Sarmiento JM. [Drug resistance in Mycobacterium tuberculosis: contribution of constituent and acquired mechanisms]. ACTA ACUST UNITED AC 2019; 20:491-497. [PMID: 30843986 DOI: 10.15446/rsap.v20n4.50575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/12/2018] [Indexed: 11/09/2022]
Abstract
Due to the emergence of multi-drug resistant (MDR-MTB) and extensively drug-resistant (XDR-MTB) Mycobacterium tuberculosis (MTB) isolates, the failure rates of standard treatment regimens are high, thus becoming a major public health challenge worldwide. Resistance to anti-tuberculous (anti-TB) drugs is attributed mainly to specific mutations in target genes; however, a proportion of drug-resistant MTB isolates do not have mutations in these genes, which suggests the involvement of other mechanisms, such as the low permeability of the mycobacterial cell wall, enzymatic modification and/or efflux pumps. Clinical drug resistance to anti-TB drugs occurs largely as a result of the selection of resistant mutants caused by poor patient adherence to treatment, inappropriate follow-ups and prescriptions, suboptimal doses of drugs and poor access to health services and treatment. Major advances in molecular biology tools and the availability of the complete genome sequences of MTB have contributed to improve understanding of the mechanisms of resistance to the main anti-TB drugs. Better knowledge of the drug-resistance of MTB will contribute to the identification of new therapeutic targets to design new drugs, develop new diagnostic tests and/or improve methods currently available for the rapid detection of drug-resistant TB. This article presents an updated review of the mechanisms and molecular basis of drug resistance in MTB.
Collapse
Affiliation(s)
- Verónica J Gómez-Tangarife
- VG: Bacterióloga y Laboratorista. Clínico. M. Sc. Ciencias Médicas -Microbiología Corporación para Investigaciones Biológicas. Medellín, Colombia.
| | - Alex J Gómez-Restrepo
- AG: Bibliotecólogo. M. Sc. Bibliotecología y Ciencias de la Información, Medellín, Colombia. Institución: Corporación para Investigaciones Biológicas.
| | - Jaime Robledo-Restrepo
- JR: MD. Ph. D. Ciencias Médicas. - Microbiología, Institución: Universidad Pontificia Bolivariana y Corporación para Investigaciones Biológicas. Medellín, Colombia.
| | - José M Hernández-Sarmiento
- JH: MD. M. Sc.; Ph. D. Ciencias Médicas - Microbiología., Institución: Universidad Pontificia Bolivariana. Medellín, Colombia.
| |
Collapse
|
32
|
Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
Collapse
Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
| |
Collapse
|
33
|
Zhao J, Wei W, Yan H, Zhou Y, Li Z, Chen Y, Zhang C, Zeng J, Chen T, Zhou L. Assessing capreomycin resistance on tlyA deficient and point mutation (G695A) Mycobacterium tuberculosis strains using multi-omics analysis. Int J Med Microbiol 2019; 309:151323. [PMID: 31279617 DOI: 10.1016/j.ijmm.2019.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/26/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022] Open
Abstract
Capreomycin (CAP), a cyclic peptide antibiotic, is considered to be an ideal second-line drug for tuberculosis (TB). However, in the past few years, the emergence of more CAP-resistant (CAPr) TB patients has limited its use. Although it has been reported that CAP resistance to Mycobacterium tuberculosis (Mtb) is associated with rrs or tlyA mutation, the exact mechanism of CAPr Mtb strains, especially the mechanism associated with tlyA deficient or mutation, is not fully understood. Herein, we utilized a multi-omics (genome, proteome, and metabolome) approach to assess CAP resistance on tlyA deficient CAPr Mtb strains (CAPr1) and tlyA point mutation CAPr Mtb strains (CAPr2) that we established for the first time in vitro to investigate the CAP-resistant mechanism. Our results showed that the CAPr1 strains (> 40 μg/ml) was more resistant to CAP than the CAPr2 strains (G695A, 10 μg/ml). Furthermore, multi-omics analysis indicated that the CAPr1 strains exhibited greater drug tolerance than the CAPr2 strains may be associated with the weakening of S-adenosyl-L-methionine-dependent methyltransferase (AdoMet-MT) activity and abnormal membrane lipid metabolism such as suppression of fatty acid metabolism, promotion of glycolipid phospholipid and glycerolipid metabolism. As a result, these studies reveal a new mechanism for CAP resistance to tlyA deficient or mutation Mtb strains, and may be helpful in developing new therapeutic approaches to prevent Mtb resistance to CAP.
Collapse
Affiliation(s)
- Jiao Zhao
- Jinan University, Guangzhou 510632, China
| | - Wenjing Wei
- Center for Tuberculosis Control of Guangdong Province, Key Laboratory of Translational Medicine of Guangdong, Guangzhou 510630, China
| | - Huimin Yan
- Dongguang Key Laboratory of Medical Bioactive Molecular Development and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Ying Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, Guangdong, 528000, China
| | - Zhenyan Li
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Yanmei Chen
- Center for Tuberculosis Control of Guangdong Province, Key Laboratory of Translational Medicine of Guangdong, Guangzhou 510630, China
| | - Chenchen Zhang
- Center for Tuberculosis Control of Guangdong Province, Key Laboratory of Translational Medicine of Guangdong, Guangzhou 510630, China
| | - Jincheng Zeng
- Dongguang Key Laboratory of Medical Bioactive Molecular Development and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, 523808, China.
| | - Tao Chen
- Center for Tuberculosis Control of Guangdong Province, Key Laboratory of Translational Medicine of Guangdong, Guangzhou 510630, China; South China Institute of Biomedicine, Guangzhou 510530, China.
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Key Laboratory of Translational Medicine of Guangdong, Guangzhou 510630, China; Jinan University, Guangzhou 510632, China.
| |
Collapse
|
34
|
Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
Collapse
|
35
|
Chen CY, Weng JY, Huang HH, Yen WC, Tsai YH, Cheng TC, Jou R. A new oligonucleotide array for the detection of multidrug and extensively drug-resistance tuberculosis. Sci Rep 2019; 9:4425. [PMID: 30872613 PMCID: PMC6418274 DOI: 10.1038/s41598-019-39339-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/21/2019] [Indexed: 11/23/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a global crisis and a threat to health security. Since conventional drug susceptibility testing (DST) takes several weeks, we herein described a molecular assay to rapidly identify multidrug-resistant (MDR) and extensively drug-resistant (XDR) and reveal transmission associated-mutations of Mycobacterium tuberculosis complex (MTBC) isolates in 6 to 7 hours. An array was designed with 12 pairs of primers and 60 single nucleotide polymorphisms of 9 genes: rpoB, katG, inhA, ahpC, embB, rpsL, gyrA, rrs and eis. We assessed the performance of the array using 176 clinical MTBC isolates. The results of culture-based DST were used as the gold standard, the GenoType MTBDRplus and MTBDRsl tests were used for parallel comparison, and gene sequencing was performed to resolve the discordance. The sensitivities and specificities of the array are comparable to those of the MTBDRplus test for resistance to isoniazid (INH) (100.0%, 96.7%) and rifampicin (RIF) (99.4%, 96.7%) and of the MTBDRsl test for resistance to fluoroquinolones (FQs) (100%, 100%) and second-line injectable drugs (SLIDs) (98.3%, 100%). The sensitivities of the array for detecting resistance to ethambutol and streptomycin were 79.3% and 64.9%, respectively. The array has potential as a powerful tool for clinical diagnosis and epidemiological investigations.
Collapse
Affiliation(s)
- Ching-Yu Chen
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, 115, Taiwan
| | - Jui-Yun Weng
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, 115, Taiwan
| | - Hsin-Hui Huang
- Department of Medical Laboratory and Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wen-Chun Yen
- Department of Medical Laboratory and Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Han Tsai
- Department of Medical Laboratory and Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Tsung Chain Cheng
- Department of Medical Laboratory and Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, 115, Taiwan. .,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 112, Taiwan.
| |
Collapse
|
36
|
Moreno-Molina M, Comas I, Furió V. The Future of TB Resistance Diagnosis: The Essentials on Whole Genome Sequencing and Rapid Testing Methods. Arch Bronconeumol 2019; 55:421-426. [PMID: 30795867 DOI: 10.1016/j.arbres.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/25/2022]
Abstract
Tuberculosis resistance diagnostics have vastly improved in recent years thanks to the development of standardised phenotypic and molecular testing methods. However, these methods are either slow or limited in the number of resistant genotypes they can detect. With the advent of next-generation sequencing (NGS) we can sidestep all those problems, as we can sequence whole tuberculosis genomes at increasingly smaller costs and requiring less and less DNA. In this review, we explain how accumulated knowledge in the field has allowed us to go from phenotypic testing to molecular methods to Whole Genome Sequencing (WGS) for resistance diagnostics. We compare current diagnostic methods with WGS as to their efficacy in detecting resistant cases, and show how forthcoming advances in NGS technologies will be crucial in widespread implementation of WGS as a diagnostic tool.
Collapse
Affiliation(s)
| | - Iñaki Comas
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain; CIBER in Epidemiology and Public Health, Spain
| | - Victoria Furió
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain.
| |
Collapse
|
37
|
Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
Collapse
|
38
|
Miotto P, Zhang Y, Cirillo DM, Yam WC. Drug resistance mechanisms and drug susceptibility testing for tuberculosis. Respirology 2018; 23:1098-1113. [PMID: 30189463 DOI: 10.1111/resp.13393] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/03/2018] [Accepted: 08/12/2018] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is the deadliest infectious disease and the associated global threat has worsened with the emergence of drug resistance, in particular multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Although the World Health Organization (WHO) End-TB Strategy advocates for universal access to antimicrobial susceptibility testing, this is not widely available and/or it is still underused. The majority of drug resistance in clinical MTB strains is attributed to chromosomal mutations. Resistance-related mutations could also exert certain fitness cost to the drug-resistant MTB strains and growth fitness could be restored by the presence of compensatory mutations. Understanding these underlying mechanisms could provide an important insight into TB pathogenesis and predict the future trend of MDR-TB global pandemic. This review covers the mechanisms of resistance in MTB and provides a comprehensive overview of current phenotypic and molecular approaches for drug susceptibility testing, with particular attention to the methods endorsed and recommended by the WHO.
Collapse
Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Wing Cheong Yam
- Department of Microbiology, Queen Mary Hospital Compound, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
39
|
Kirpekar F, Hansen LH, Mundus J, Tryggedsson S, Teixeira Dos Santos P, Ntokou E, Vester B. Mapping of ribosomal 23S ribosomal RNA modifications in Clostridium sporogenes. RNA Biol 2018; 15:1060-1070. [PMID: 29947286 DOI: 10.1080/15476286.2018.1486662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
All organisms contain RNA modifications in their ribosomal RNA (rRNA), but the importance, positions and exact function of these are still not fully elucidated. Various functions such as stabilizing structures, controlling ribosome assembly and facilitating interactions have been suggested and in some cases substantiated. Bacterial rRNA contains much fewer modifications than eukaryotic rRNA. The rRNA modification patterns in bacteria differ from each other, but too few organisms have been mapped to draw general conclusions. This study maps 23S ribosomal RNA modifications in Clostridium sporogenes that can be characterized as a non-toxin producing Clostridium botulinum. Clostridia are able to sporulate and thereby survive harsh conditions, and are in general considered to be resilient to antibiotics. Selected regions of the 23S rRNA were investigated by mass spectrometry and by primer extension analysis to pinpoint modified sites and the nature of the modifications. Apparently, C. sporogenes 23S rRNA contains few modifications compared to other investigated bacteria. No modifications were identified in domain II and III of 23S rRNA. Three modifications were identified in domain IV, all of which have also been found in other organisms. Two unusual modifications were identified in domain V, methylated dihydrouridine at position U2449 and dihydrouridine at position U2500 (Escherichia coli numbering), in addition to four previously known modified positions. The enzymes responsible for the modifications were searched for in the C. sporogenes genome using BLAST with characterized enzymes as query. The search identified genes potentially coding for RNA modifying enzymes responsible for most of the found modifications.
Collapse
Affiliation(s)
- Finn Kirpekar
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Lykke H Hansen
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Julie Mundus
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Stine Tryggedsson
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | | | - Eleni Ntokou
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Birte Vester
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| |
Collapse
|
40
|
Man DKW, Kanno T, Manzo G, Robertson BD, Lam JKW, Mason AJ. Rifampin- or Capreomycin-Induced Remodeling of the Mycobacterium smegmatis Mycolic Acid Layer Is Mitigated in Synergistic Combinations with Cationic Antimicrobial Peptides. mSphere 2018; 3:e00218-18. [PMID: 30021876 PMCID: PMC6052339 DOI: 10.1128/msphere.00218-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/24/2018] [Indexed: 01/15/2023] Open
Abstract
The mycobacterial cell wall affords natural resistance to antibiotics. Antimicrobial peptides (AMPs) modify the surface properties of mycobacteria and can act synergistically with antibiotics from differing classes. Here, we investigate the response of Mycobacterium smegmatis to the presence of rifampin or capreomycin, either alone or in combination with two synthetic, cationic, α-helical AMPs that are distinguished by the presence (D-LAK120-HP13) or absence (D-LAK120-A) of a kink-inducing proline. Using a combination of high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) metabolomics, diphenylhexatriene (DPH) fluorescence anisotropy measurements, and laurdan emission spectroscopy, we show that M. smegmatis responds to challenge with rifampin or capreomycin by substantially altering its metabolism and, in particular, by remodeling the cell envelope. Overall, the changes are consistent with a reduction of trehalose dimycolate and an increase of trehalose monomycolate and are associated with increased rigidity of the mycolic acid layer observed following challenge by capreomycin but not rifampin. Challenge with D-LAK120-A or D-LAK120-HP13 induced no or modest changes, respectively, in mycomembrane metabolites and did not induce a significant increase in the rigidity of the mycolic acid layer. Furthermore, the response to rifampin or capreomycin was significantly reduced when these were combined with D-LAK120-HP13 and D-LAK120-A, respectively, suggesting a possible mechanism for the synergy of these combinations. The remodeling of the mycomembrane in M. smegmatis is therefore identified as an important countermeasure deployed against rifampin or capreomycin, but this can be mitigated and the efficacy of rifampin or capreomycin potentiated by combining the drug with AMPs.IMPORTANCE We have used a combined NMR metabolomics/biophysical approach to better understand differences in the mechanisms of two closely related antimicrobial peptides, as well as the response of the model organism Mycobacterium smegmatis to challenge with first- or second-line antibiotics used against mycobacterial pathogens. We show that, in addition to membrane damage, the triggering of oxidative stress may be an important part of the mechanism of action of one AMP. The metabolic shift that accompanied rifampin and, particularly, capreomycin challenge was associated with modest and more dramatic changes, respectively, in the mycomembrane, providing a rationale for how the response to one antibiotic may affect bacterial penetration and, hence, the action of another. This study presents the first insights into how antimicrobial peptides may operate synergistically with existing antibiotics whose efficacy is waning or sensitize MDR mycobacteria and/or latent mycobacterial infections to them, prolonging the useful life of these drugs.
Collapse
Affiliation(s)
- DeDe Kwun-Wai Man
- Institute of Pharmaceutical Sciences, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
- Department of Pharmacology & Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tokuwa Kanno
- Institute of Pharmaceutical Sciences, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Giorgia Manzo
- Institute of Pharmaceutical Sciences, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, United Kingdom
| | - Jenny K W Lam
- Department of Pharmacology & Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - A James Mason
- Institute of Pharmaceutical Sciences, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
| |
Collapse
|
41
|
Zeng X, Kwok JSL, Yang KY, Leung KSS, Shi M, Yang Z, Yam WC, Tsui SKW. Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance. BMC Genomics 2018; 19:365. [PMID: 29769016 PMCID: PMC5956929 DOI: 10.1186/s12864-018-4734-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has focused on the relationship between insertions / deletions (indels) and drug resistance. Results Here, we retrieved whole genome sequencing data of 743 drug-resistant MTB strains and 367 pan-susceptible strains from TB patients from the public domain to identify novel genomic markers of drug resistance. A total of 20 region markers containing genes and intergenic regions (IGRs) with significant statistical correlation with antibiotic resistance were revealed, four of which have been previously reported to be associated with drug resistance. In addition, 83 point markers containing frameshift (FS) mutations and IGR indels were also identified independently based on differences in their incidence rates between drug-sensitive and -resistant strains. Among the 83 point markers, eight indels were detected in known drug-associated genes or IGRs. Furthermore, the overlap between 20 region markers and 83 point markers further indicated their associations with drug resistance. The markers identified were involved in essential bacterial metabolic functions, including cell wall and transmembrane transporter functions. A strong correlation between FS mutations and mutations in DNA repair genes including I21V in alkA, R48G in mutT4 and P2R in nth was also found. Conclusions This study identified a set of novel genetic markers with FS mutations and IGR indels associated with MTB drug resistance, which greatly broadens the pool of mutations related to MTB drug resistance. This insight may be important in identifying novel mechanisms of drug resistance in MTB. Electronic supplementary material The online version of this article (10.1186/s12864-018-4734-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xi Zeng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jamie Sui-Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhiyuan Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
42
|
Hentschel J, Burnside C, Mignot I, Leibundgut M, Boehringer D, Ban N. The Complete Structure of the Mycobacterium smegmatis 70S Ribosome. Cell Rep 2018; 20:149-160. [PMID: 28683309 DOI: 10.1016/j.celrep.2017.06.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/03/2017] [Accepted: 06/10/2017] [Indexed: 11/24/2022] Open
Abstract
The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
Collapse
Affiliation(s)
- Jendrik Hentschel
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Chloe Burnside
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Ingrid Mignot
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Marc Leibundgut
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland.
| |
Collapse
|
43
|
Oudghiri A, Karimi H, Chetioui F, Zakham F, Bourkadi JE, Elmessaoudi MD, Laglaoui A, Chaoui I, El Mzibri M. Molecular characterization of mutations associated with resistance to second-line tuberculosis drug among multidrug-resistant tuberculosis patients from high prevalence tuberculosis city in Morocco. BMC Infect Dis 2018; 18:98. [PMID: 29486710 PMCID: PMC5830342 DOI: 10.1186/s12879-018-3009-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 02/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of extensively drug-resistant tuberculosis (XDR-TB) has raised public health concern for global TB control. Although multi drug-resistant tuberculosis (MDR- TB) prevalence and associated genetic mutations in Morocco are well documented, scarce information on XDR TB is available. Hence, the evaluation of pre-XDR and XDR prevalence, as well as the mutation status of gyrA, gyrB, rrs, tlyA genes and eis promoter region, associated with resistance to second line drugs, is of great value for better management of M/XDR TB in Morocco. OBJECTIVES To evaluate pre-XDR and XDR prevalence, as well as the mutation status of gyrA, gyrB, rrs, tlyA genes and eis promoter region, associated with resistance to second line drug resistance, in 703 clinical isolates from TB patients recruited in Casablanca, and to assess the usefulness of molecular tools in clinical laboratories for better management of M/XDR TB in Morocco. METHODS Drug susceptibility testing (DST) was performed by the proportional method for first line drugs, and then the selected MDR isolates were tested for second line drugs (Ofloxacin, Kanamycin, Amikacin and Capreomycin). Along with DST, all samples were subjected to rpoB, katG and p-inhA mutation analysis by PCR and DNA sequencing. MDR isolates as well as 30 pan-susceptible strains were subjected to PCR and DNA sequencing of gyrA, gyrB, rrs, tlyA genes and eis promoter, associated with resistance to fluoroquinolones and injectable drugs. RESULTS Among the 703 analysed strains, 12.8% were MDR; Ser531Leu and Ser315Thr being the most common recorded mutations within rpoB and katG genes associated with RIF and INH resistance respectively. Drug susceptibility testing for second line drugs showed that among the 90 MDR strains, 22.2% (20/90) were resistant to OFX, 2.22% (2/90) to KAN, 3.33% (3/90) to AMK and 1.11% (1/90) to CAP. Genotypic analysis revealed that 19 MDR strains harbored mutations in the gyrA gene; the most recorded mutation being Asp91Ala accounting for 47.6% (10/21), and 2 isolates harbored mutations in the promoter region of eis gene. No mutation was found in gyrB, rrs and tlyA genes. Moreover, none of the pan-susceptible isolates displayed mutations in targeted genes. CONCLUSION Most of mutations associated with SLD resistance occurred in gyrA gene (codons 90-94) and eis promoter region. These findings highlight the impact of mutations in gyrA on the development of fluroquinolones resistance and provide the first estimates of the proportion of pre-XDR-TB among MDR-TB cases in Morocco.
Collapse
Affiliation(s)
- Amal Oudghiri
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco
- Equipe de Recherche en Biotechnologies et Génie des Biomolécules, Faculté des Sciences et Techniques de Tanger, Ancienne Route de l'Aéroport, Km 10, Ziaten, BP 416, Tanger, Morocco
| | - Hind Karimi
- Equipe de Recherche en Biotechnologies et Génie des Biomolécules, Faculté des Sciences et Techniques de Tanger, Ancienne Route de l'Aéroport, Km 10, Ziaten, BP 416, Tanger, Morocco
| | - Fouad Chetioui
- Laboratoire de la Tuberculose, Institut Pasteur du Maroc, Casablanca, 1 Place Louis Pasteur, Boulevard Abdelmoumen, 20250, Casablanca, Morocco
| | - Fathiah Zakham
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco
| | - Jamal Eddine Bourkadi
- Service de Pneumo-Phtisiologie, Hôpital Moulay Youssef, CHU Rabat, Avenue Sidi Mohamed Ben Abdallah, Al Akkari, Rabat, Morocco
| | - My Driss Elmessaoudi
- Laboratoire de la Tuberculose, Institut Pasteur du Maroc, Casablanca, 1 Place Louis Pasteur, Boulevard Abdelmoumen, 20250, Casablanca, Morocco
| | - Amin Laglaoui
- Equipe de Recherche en Biotechnologies et Génie des Biomolécules, Faculté des Sciences et Techniques de Tanger, Ancienne Route de l'Aéroport, Km 10, Ziaten, BP 416, Tanger, Morocco
| | - Imane Chaoui
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco.
| | - Mohammed El Mzibri
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco
| |
Collapse
|
44
|
Osei-Wusu S, Amo Omari M, Asante-Poku A, Darko Otchere I, Asare P, Forson A, Otu J, Antonio M, Yeboah-Manu D. Second-line anti-tuberculosis drug resistance testing in Ghana identifies the first extensively drug-resistant tuberculosis case. Infect Drug Resist 2018; 11:239-246. [PMID: 29503573 PMCID: PMC5825993 DOI: 10.2147/idr.s152720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Drug resistance surveillance is crucial for tuberculosis (TB) control. Therefore, our goal was to determine the prevalence of second-line anti-TB drug resistance among diverse primary drug-resistant Mycobacterium tuberculosis complex (MTBC) isolates in Ghana. MATERIALS AND METHODS One hundred and seventeen MTBC isolates with varying first-line drug resistance were analyzed. Additional resistance to second-line anti-TB drugs (streptomycin [STR], amikacin [AMK] and moxifloxacin [MOX]) was profiled using the Etest and GenoType MTBDRsl version 2.0. Genes associated with resistance to AMK and MOX (gyrA, gyrB, eis, rrs, tap, whiB7 and tlyA) were then analyzed for mutation. RESULTS Thirty-seven (31.9%) isolates had minimum inhibitory concentration (MIC) values ≥2 µg/mL against STR while 12 (10.3%) isolates had MIC values ≥1 µg/mL for AMK. Only one multidrug-resistant (MDR) isolate (Isolate ID: TB/Nm 919) had an MIC value of ≥0.125 µg/mL for MOX (MIC = 3 µg/mL). This isolate also had the highest MIC value for AMK (MIC = 16 µg/mL) and was confirmed as resistant to AMK and MOX by the line probe assay GenoType MTBDRsl version 2.0. Mutations associated with the resistance were: gyrA (G88C) and rrs (A514C and A1401G). CONCLUSION Our findings suggest the need to include routine second-line anti-TB drug susceptibility testing of MDR/rifampicin-resistant isolates in our diagnostic algorithm.
Collapse
Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West Africa Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Michael Amo Omari
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Jacob Otu
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| |
Collapse
|
45
|
Heyckendorf J, Andres S, Köser CU, Olaru ID, Schön T, Sturegård E, Beckert P, Schleusener V, Kohl TA, Hillemann D, Moradigaravand D, Parkhill J, Peacock SJ, Niemann S, Lange C, Merker M. What Is Resistance? Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis. Antimicrob Agents Chemother 2018; 62:e01550-17. [PMID: 29133554 PMCID: PMC5786814 DOI: 10.1128/aac.01550-17] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/26/2017] [Indexed: 12/29/2022] Open
Abstract
Rapid and accurate drug susceptibility testing (DST) is essential for the treatment of multi- and extensively drug-resistant tuberculosis (M/XDR-TB). We compared the utility of genotypic DST assays with phenotypic DST (pDST) using Bactec 960 MGIT or Löwenstein-Jensen to construct M/XDR-TB treatment regimens for a cohort of 25 consecutive M/XDR-TB patients and 15 possible anti-TB drugs. Genotypic DST results from Cepheid GeneXpert MTB/RIF (Xpert) and line probe assays (LPAs; Hain GenoType MTBDRplus 2.0 and MTBDRsl 2.0) and whole-genome sequencing (WGS) were translated into individual algorithm-derived treatment regimens for each patient. We further analyzed if discrepancies between the various methods were due to flaws in the genotypic or phenotypic test using MIC results. Compared with pDST, the average agreement in the number of drugs prescribed in genotypic regimens ranged from just 49% (95% confidence interval [CI], 39 to 59%) for Xpert and 63% (95% CI, 56 to 70%) for LPAs to 93% (95% CI, 88 to 98%) for WGS. Only the WGS regimens did not contain any drugs to which pDST showed resistance. Importantly, MIC testing revealed that pDST likely underestimated the true rate of resistance for key drugs (rifampin, levofloxacin, moxifloxacin, and kanamycin) because critical concentrations (CCs) were too high. WGS can be used to rule in resistance even in M/XDR strains with complex resistance patterns, but pDST for some drugs is still needed to confirm susceptibility and construct the final regimens. Some CCs for pDST need to be reexamined to avoid systematic false-susceptible results in low-level resistant isolates.
Collapse
Affiliation(s)
- Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Sönke Andres
- Division of Mycobacteriology (National Tuberculosis Reference Laboratory), Research Center Borstel, Borstel, Germany
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ioana D Olaru
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Thomas Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - Erik Sturegård
- Clinical Microbiology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Patrick Beckert
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Viola Schleusener
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Thomas A Kohl
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Doris Hillemann
- Division of Mycobacteriology (National Tuberculosis Reference Laboratory), Research Center Borstel, Borstel, Germany
| | | | | | - Sharon J Peacock
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Medicine, University of Namibia School of Medicine, Windhoek, Namibia
| | - Matthias Merker
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| |
Collapse
|
46
|
Sałamaszyńska-Guz A, Rose S, Lykkebo CA, Taciak B, Bącal P, Uśpieński T, Douthwaite S. Biofilm Formation and Motility Are Promoted by Cj0588-Directed Methylation of rRNA in Campylobacter jejuni. Front Cell Infect Microbiol 2018; 7:533. [PMID: 29404277 PMCID: PMC5778110 DOI: 10.3389/fcimb.2017.00533] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022] Open
Abstract
Numerous bacterial pathogens express an ortholog of the enzyme TlyA, which is an rRNA 2′-O-methyltransferase associated with resistance to cyclic peptide antibiotics such as capreomycin. Several other virulence traits have also been attributed to TlyA, and these appear to be unrelated to its methyltransferase activity. The bacterial pathogen Campylobacter jejuni possesses the TlyA homolog Cj0588, which has been shown to contribute to virulence. Here, we investigate the mechanism of Cj0588 action and demonstrate that it is a type I homolog of TlyA that 2′-O-methylates 23S rRNA nucleotide C1920. This same specific function is retained by Cj0588 both in vitro and also when expressed in Escherichia coli. Deletion of the cj0588 gene in C. jejuni or substitution with alanine of K80, D162, or K188 in the catalytic center of the enzyme cause complete loss of 2′-O-methylation activity. Cofactor interactions remain unchanged and binding affinity to the ribosomal substrate is only slightly reduced, indicating that the inactivated proteins are folded correctly. The substitution mutations thus dissociate the 2′-O-methylation function of Cj0588/TlyA from any other putative roles that the protein might play. C. jejuni strains expressing catalytically inactive versions of Cj0588 have the same phenotype as cj0588-null mutants, and show altered tolerance to capreomycin due to perturbed ribosomal subunit association, reduced motility and impaired ability to form biofilms. These functions are reestablished when methyltransferase activity is restored and we conclude that the contribution of Cj0588 to virulence in C. jejuni is a consequence of the enzyme's ability to methylate its rRNA.
Collapse
Affiliation(s)
- Agnieszka Sałamaszyńska-Guz
- Division of Microbiology, Department of Pre-Clinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - Simon Rose
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Claus A Lykkebo
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bartłomiej Taciak
- Division of Physiology, Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - Paweł Bącal
- Laboratory of Theory and Applications of Electrodes, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Tomasz Uśpieński
- Division of Microbiology, Department of Pre-Clinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
47
|
Gygli SM, Borrell S, Trauner A, Gagneux S. Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives. FEMS Microbiol Rev 2018; 41:354-373. [PMID: 28369307 DOI: 10.1093/femsre/fux011] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/17/2017] [Indexed: 11/12/2022] Open
Abstract
Antibiotic-resistant Mycobacterium tuberculosis strains are threatening progress in containing the global tuberculosis epidemic. Mycobacterium tuberculosis is intrinsically resistant to many antibiotics, limiting the number of compounds available for treatment. This intrinsic resistance is due to a number of mechanisms including a thick, waxy, hydrophobic cell envelope and the presence of drug degrading and modifying enzymes. Resistance to the drugs which are active against M. tuberculosis is, in the absence of horizontally transferred resistance determinants, conferred by chromosomal mutations. These chromosomal mutations may confer drug resistance via modification or overexpression of the drug target, as well as by prevention of prodrug activation. Drug resistance mutations may have pleiotropic effects leading to a reduction in the bacterium's fitness, quantifiable e.g. by a reduction in the in vitro growth rate. Secondary so-called compensatory mutations, not involved in conferring resistance, can ameliorate the fitness cost by interacting epistatically with the resistance mutation. Although the genetic diversity of M. tuberculosis is low compared to other pathogenic bacteria, the strain genetic background has been demonstrated to influence multiple aspects in the evolution of drug resistance. The rate of resistance evolution and the fitness costs of drug resistance mutations may vary as a function of the genetic background.
Collapse
Affiliation(s)
- Sebastian M Gygli
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| |
Collapse
|
48
|
A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study. THE LANCET. INFECTIOUS DISEASES 2018; 18:431-440. [PMID: 29326013 PMCID: PMC5864516 DOI: 10.1016/s1473-3099(18)30004-5] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/10/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023]
Abstract
Background The risk of tuberculosis outbreaks among people fleeing hardship for refuge in Europe is heightened. We describe the cross-border European response to an outbreak of multidrug-resistant tuberculosis among patients from the Horn of Africa and Sudan. Methods On April 29 and May 30, 2016, the Swiss and German National Mycobacterial Reference Laboratories independently triggered an outbreak investigation after four patients were diagnosed with multidrug-resistant tuberculosis. In this molecular epidemiological study, we prospectively defined outbreak cases with 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) profiles; phenotypic resistance to isoniazid, rifampicin, ethambutol, pyrazinamide, and capreomycin; and corresponding drug resistance mutations. We whole-genome sequenced all Mycobacterium tuberculosis isolates and clustered them using a threshold of five single nucleotide polymorphisms (SNPs). We collated epidemiological data from host countries from the European Centre for Disease Prevention and Control. Findings Between Feb 12, 2016, and April 19, 2017, 29 patients were diagnosed with multidrug-resistant tuberculosis in seven European countries. All originated from the Horn of Africa or Sudan, with all isolates two SNPs or fewer apart. 22 (76%) patients reported their travel routes, with clear spatiotemporal overlap between routes. We identified a further 29 MIRU-VNTR-linked cases from the Horn of Africa that predated the outbreak, but all were more than five SNPs from the outbreak. However all 58 isolates shared a capreomycin resistance-associated tlyA mutation. Interpretation Our data suggest that source cases are linked to an M tuberculosis clone circulating in northern Somalia or Djibouti and that transmission probably occurred en route before arrival in Europe. We hypothesise that the shared mutation of tlyA is a drug resistance mutation and phylogenetic marker, the first of its kind in M tuberculosis sensu stricto. Funding The Swiss Federal Office of Public Health, the University of Zurich, the Wellcome Trust, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), the Medical Research Council, BELTA-TBnet, the European Union, the German Center for Infection Research, and Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG).
Collapse
|
49
|
Tagliani E, Hassan MO, Waberi Y, De Filippo MR, Falzon D, Dean A, Zignol M, Supply P, Abdoulkader MA, Hassangue H, Cirillo DM. Culture and Next-generation sequencing-based drug susceptibility testing unveil high levels of drug-resistant-TB in Djibouti: results from the first national survey. Sci Rep 2017; 7:17672. [PMID: 29247181 PMCID: PMC5732159 DOI: 10.1038/s41598-017-17705-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/29/2017] [Indexed: 01/15/2023] Open
Abstract
Djibouti is a small country in the Horn of Africa with a high TB incidence (378/100,000 in 2015). Multidrug-resistant TB (MDR-TB) and resistance to second-line agents have been previously identified in the country but the extent of the problem has yet to be quantified. A national survey was conducted to estimate the proportion of MDR-TB among a representative sample of TB patients. Sputum was tested using XpertMTB/RIF and samples positive for MTB and resistant to rifampicin underwent first line phenotypic susceptibility testing. The TB supranational reference laboratory in Milan, Italy, undertook external quality assurance, genotypic testing based on whole genome and targeted-deep sequencing and phylogenetic studies. 301 new and 66 previously treated TB cases were enrolled. MDR-TB was detected in 34 patients: 4.7% of new and 31% of previously treated cases. Resistance to pyrazinamide, aminoglycosides and capreomycin was detected in 68%, 18% and 29% of MDR-TB strains respectively, while resistance to fluoroquinolones was not detected. Cluster analysis identified transmission of MDR-TB as a critical factor fostering drug resistance in the country. Levels of MDR-TB in Djibouti are among the highest on the African continent. High prevalence of resistance to pyrazinamide and second-line injectable agents have important implications for treatment regimens.
Collapse
Affiliation(s)
- Elisa Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | | | - Yacine Waberi
- National TB Reference Laboratory, Djibouti, Djibouti
| | - Maria Rosaria De Filippo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dennis Falzon
- World Health Organization/Global TB Programme, Geneva, Switzerland
| | - Anna Dean
- World Health Organization/Global TB Programme, Geneva, Switzerland
| | - Matteo Zignol
- World Health Organization/Global TB Programme, Geneva, Switzerland
| | | | | | - Hawa Hassangue
- Programme National de Lutte contre la Tuberculose, Djibouti, Djibouti
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
50
|
Lohrasbi V, Talebi M, Bialvaei AZ, Fattorini L, Drancourt M, Heidary M, Darban-Sarokhalil D. Trends in the discovery of new drugs for Mycobacterium tuberculosis therapy with a glance at resistance. Tuberculosis (Edinb) 2017; 109:17-27. [PMID: 29559117 DOI: 10.1016/j.tube.2017.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 12/19/2022]
Abstract
Despite the low expensive and effective four-drug treatment regimen (isoniazid, rifampicin, pyrazinamide and ethambutol) was introduced 40 years ago, TB continues to cause considerable morbidity and mortality worldwide. In 2015, the WHO estimated a total of 10.4 million new tuberculosis (TB) cases worldwide. Currently, the increased number of multidrug-resistant (MDR-TB), extensively-drug resistant (XDR-TB) and in some recent reports, totally drug-resistant TB (TDR-TB) cases raises concerns about this disease. MDR-TB and XDR-TB have lower cure rates and higher mortality levels due to treatment problems. Novel drugs and regimens for all forms of TB have emerged in recent years. Moreover, scientific interest has recently increased in the field of host-directed therapies (HDTs) in order to identify new treatments for MDR-TB. In this review, we offer an update on the discovery of new drugs for TB therapy with a glance at molecular mechanisms leading to drug resistance in Mycobacterium tuberculosis.
Collapse
Affiliation(s)
- Vahid Lohrasbi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abed Zahedi Bialvaei
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Lanfranco Fattorini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Michel Drancourt
- Institut Hospital-Universitaire (IHU) Mediterranée Infection, AP-HM, Marseille, France; Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Mohsen Heidary
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|