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Maitre T, Baulard A, Aubry A, Veziris N. Optimizing the use of current antituberculosis drugs to overcome drug resistance in Mycobacterium tuberculosis. Infect Dis Now 2024; 54:104807. [PMID: 37839674 DOI: 10.1016/j.idnow.2023.104807] [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: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Antibiotic-resistant tuberculosis continues to be one of the major threats to global tuberculosis control. After a hiatus of over 40 years in antituberculosis drug development, the last decade has seen a resurgence of research, yielding a number of promising compounds in the tuberculosis drug pipeline, with some that are now game changers in the treatment of MDRTB. Despite this progress, there are still obstacles restricting the use of these molecules as first-line drugs. The quick appearance of bacteria resistant to these new treatments highlights a continuing need to fuel the discovery and development of new molecules. With this in mind, alternative strategies aimed at optimizing the utilization of existing antituberculosis agents are currently under evaluation. They are focused on enhancing the efficacy of antibiotics against their bacterial targets, primarily by augmenting the quantity of antibiotic that engages with these targets. This objective can be achieved through two primary approaches: (1) Provided that toxicity concerns are not a limiting factor, increased dosing is a viable avenue, as demonstrated by rifampicin, isoniazid, and fluoroquinolones, for which escalated dosing has been effective; and (2) Employing enhancers such as drug activator boosters (ethionamide), efflux pump inhibitors, or hydrolytic enzyme inhibitors (kanamycin) can elevate the concentration of antibiotics in bacterial cells. These strategies offer the potential to mitigate antibiotic obsolescence and complement the discovery of new antibiotics.
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Affiliation(s)
- Thomas Maitre
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; Service de Pneumologie et d'Oncologie Thoracique, Centre constitutif maladies rares, Hôpital Tenon, AP-HP, Sorbonne-Université, Paris, France.
| | - Alain Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Alexandra Aubry
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Universite, Hôpital Pitié Salpêtrière, Laboratoire de Bactériologie-Hygiene, Centre National de Référence des Mycobactéries, Paris France
| | - Nicolas Veziris
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Université, Hôpital Saint-Antoine, Département de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Hôpital Pitié-Salpêtrière, Paris, France
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2
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Yurtseven A, Buyanova S, Agrawal AA, Bochkareva OO, Kalinina OV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiol 2023; 23:404. [PMID: 38124060 PMCID: PMC10731705 DOI: 10.1186/s12866-023-03147-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. RESULTS In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models' performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. CONCLUSIONS Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.
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Affiliation(s)
- Alper Yurtseven
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany.
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany.
| | - Sofia Buyanova
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
| | - Amay Ajaykumar Agrawal
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
| | - Olga O Bochkareva
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Djerassiplatz 1 A, Wien, 1030, Austria
| | - Olga V Kalinina
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
- Faculty of Medicine, Saarland University, Homburg, 66421, Saarland, Germany
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3
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Wang S, Zhang J, Hameed HMA, Ding J, Guan P, Fang X, Peng J, Su B, Ma S, Tan Y, M. Cook G, Zhang G, Lin Y, Zhong N, Hu J, Liu J, Zhang T. Amino acid 17 in QRDR of Gyrase A plays a key role in fluoroquinolones susceptibility in mycobacteria. Microbiol Spectr 2023; 11:e0280923. [PMID: 37831477 PMCID: PMC10715211 DOI: 10.1128/spectrum.02809-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/27/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Fluoroquinolones (FQs) play a key role in the treatment regimens against tuberculosis and non-tuberculous mycobacterial infections. However, there are significant differences in the sensitivities of different mycobacteria to FQs. In this study, we proved that this is associated with the polymorphism at amino acid 17 of quinolone resistance-determining region of Gyrase A by gene editing. This is the first study using CRISPR-associated recombination for gene editing in Mycobacterium abscessus to underscore the contribution of the amino acid substitutions in GyrA to FQ susceptibilities in mycobacteria.
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Affiliation(s)
- Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Jingran Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - H. M. Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Jie Ding
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Xiange Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Jiacong Peng
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Biyi Su
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Shangming Ma
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Gregory M. Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland, New Zealand
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Shenzhen, China
| | - Yongping Lin
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
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4
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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.
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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.)
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5
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Thapa J, Chizimu JY, Kitamura S, Akapelwa ML, Suwanthada P, Miura N, Toyting J, Nishimura T, Hasegawa N, Nishiuchi Y, Gordon SV, Nakajima C, Suzuki Y. Characterization of DNA Gyrase Activity and Elucidation of the Impact of Amino Acid Substitution in GyrA on Fluoroquinolone Resistance in Mycobacterium avium. Microbiol Spectr 2023; 11:e0508822. [PMID: 37067420 PMCID: PMC10269562 DOI: 10.1128/spectrum.05088-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
Mycobacterium avium, a member of the M. avium complex (MAC), is the major pathogen contributing to nontuberculous mycobacteria (NTM) infections worldwide. Fluoroquinolones (FQs) are recommended for the treatment of macrolide-resistant MACs. The association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA of M. avium is not yet clearly understood, as many FQ-resistant clinical M. avium isolates do not have such mutations. This study aimed to elucidate the role of amino acid substitution in the QRDR of M. avium GyrA in the development of FQ resistance. We found four clinical M. avium subsp. hominissuis isolates with Asp-to-Gly change at position 95 (Asp95Gly) and Asp95Tyr mutations in gyrA that were highly resistant to FQs and had 2- to 32-fold-higher MICs than the wild-type (WT) isolates. To clarify the contribution of amino acid substitutions to FQ resistance, we produced recombinant WT GyrA, GyrB, and four GyrA mutant proteins (Ala91Val, Asp95Ala, Asp95Gly, and Asp95Tyr) to elucidate their potential role in FQ resistance, using them to perform FQ-inhibited DNA supercoiling assays. While all the mutant GyrAs contributed to the higher (1.3- to 35.6-fold) FQ 50% inhibitory concentration (IC50) than the WT, Asp95Tyr was the most resistant mutant, with an IC50 15- to 35.6-higher than that of the WT, followed by the Asp95Gly mutant, with an IC50 12.5- to 17.6-fold higher than that of the WT, indicating that these amino acid substitutions significantly reduced the inhibitory activity of FQs. Our results showed that amino acid substitutions in the gyrA of M. avium contribute to FQ resistance. IMPORTANCE The emergence of fluoroquinolone (FQ) resistance has further compounded the control of emerging Mycobacterium avium-associated nontuberculous mycobacteria infections worldwide. For M. avium, the association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA is not yet clearly understood. Here, we report that four clinical M. avium isolates with a mutation in the QRDR of gyrA were highly resistant to FQs. We further clarified the impact of mutations in the QRDR of GyrA proteins by performing in vitro FQ-inhibited DNA supercoiling assays. These results confirmed that, like in Mycobacterium tuberculosis, mutations in the QRDR of gyrA also strongly contribute to FQ resistance in M. avium. Since many FQ-resistant M. avium isolates do have these mutations, the detailed molecular mechanism of FQ resistance in M. avium needs further exploration.
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Affiliation(s)
- Jeewan Thapa
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Joseph Yamweka Chizimu
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Zambian National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - Soyoka Kitamura
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Mwangala Lonah Akapelwa
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Pondpan Suwanthada
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Nami Miura
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jirachaya Toyting
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
- Office of Academic Research and Industry-Government Collaboration, Section of Microbial Genomics and Ecology, Hiroshima University, Higashi-Hiroshima, Japan
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
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Halim SA, Abdel-Rahman MA. First-principles density functional theoretical study on the structures, reactivity and spectroscopic properties of (NH) and (OH) Tautomer's of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one. Sci Rep 2023; 13:8909. [PMID: 37264069 DOI: 10.1038/s41598-023-35933-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 05/25/2023] [Indexed: 06/03/2023] Open
Abstract
The tautomerizations mechanism of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one were inspected in the gas phase and ethanol using density function theory (DFT) M06-2X and B3LYP methods. Thermo-kinetic features of different conversion processes were estimated in temperature range 273-333 K using the Transition state theory (TST) accompanied with one dimensional Eckert tunneling correction (1D-Eck). Acidity and basicity were computed as well, and the computational results were compared against the experimental ones. Additionally, NMR, global descriptors, Fukui functions, NBO charges, and electrostatic potential (ESP) were discussed. From thermodynamics analysis, the keto form of 4-(methylsulfanyl)-3-[(1Z)-1-(2 phenylhydrazinylidene) quinoline-2(1H)-one is the most stable form in the gas phase and ethanol and the barrier heights required for tautomerization process were found to be high in the gas phase and ethanol ~ 38.80 and 37.35 kcal/mol, respectively. DFT methods were used for UV-Vis electronic spectra simulation and the time-dependent density functional theory solvation model (TDDFT-SMD) in acetonitrile compounds.
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Affiliation(s)
- Shimaa Abdel Halim
- Chemistry Department, Faculty of Education, Ain Shams University, Roxy, Cairo, 11711, Egypt.
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Anjos TRD, Castro VS, Machado Filho ES, Suffys PN, Gomes HM, Duarte RS, Figueiredo EEDS, Carvalho RCT. Genomic analysis of Mycobacterium tuberculosis variant bovis strains isolated from bovine in the state of Mato Grosso, Brazil. Front Vet Sci 2022; 9:1006090. [DOI: 10.3389/fvets.2022.1006090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
The species Mycobacterium tuberculosis variant bovis (M. tuberculosis var. bovis) is associated with tuberculosis, mainly in cattle and buffaloes. This pathogen has the potential to infect other mammals, including humans. Tuberculosis caused by M. tuberculosis var. bovis is a zoonosis clinically identical to tuberculosis caused by Mycobacterium tuberculosis, and the recommended treatment in humans results in the use of antibiotics. In this study, we used the whole genome sequencing (WGS) methodology Illumina NovaSeq 6000 System platform to characterize the genome of M. tuberculosis var. bovis in cattle circulating in Mato Grosso, identify mutations related to drug resistance genes, compare with other strains of M. tuberculosis var. bovis brazilian and assess potential drug resistance. Four isolates of M. tuberculosis var. bovis of cattle origin representing the main livestock circuits, which had been more prevalent in previous studies in the state of Mato Grosso, were selected for the genomic study. The genome sizes of the sequenced strains ranged from 4,306,423 to 4,332,964 bp, and the GC content was 65.6%. The four strains from Mato Grosso presented resistance genes to pncA (pyrazinamide), characterized as drug-resistant strains. In addition to verifying several point mutations in the pncA, rpsA, rpsL, gid, rpoB, katG, gyrB, gyrA, tlyA, embA, embB, embC, fgd, fbiB, and fbiC genes, these genes were similar to antibiotic resistance in more than 92% of the Brazilian strains. Therefore, our results indicated a high genetic diversity between our isolates and other M. tuberculosis var. bovis isolated in Brazil. Thus, multiple transmission routes of this pathogen may be present in the production chain. So, to achieve a bovine tuberculosis-free health status, the use of the WGS as a control and monitoring tool will be crucial to determine these transmission routes.
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8
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Singh A, Zhao X, Drlica K. Fluoroquinolone heteroresistance, antimicrobial tolerance, and lethality enhancement. Front Cell Infect Microbiol 2022; 12:938032. [PMID: 36250047 PMCID: PMC9559723 DOI: 10.3389/fcimb.2022.938032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
With tuberculosis, the emergence of fluoroquinolone resistance erodes the ability of treatment to interrupt the progression of MDR-TB to XDR-TB. One way to reduce the emergence of resistance is to identify heteroresistant infections in which subpopulations of resistant mutants are likely to expand and make the infections fully resistant: treatment modification can be instituted to suppress mutant enrichment. Rapid DNA-based detection methods exploit the finding that fluoroquinolone-resistant substitutions occur largely in a few codons of DNA gyrase. A second approach for restricting the emergence of resistance involves understanding fluoroquinolone lethality through studies of antimicrobial tolerance, a condition in which bacteria fail to be killed even though their growth is blocked by lethal agents. Studies with Escherichia coli guide work with Mycobacterium tuberculosis. Lethal action, which is mechanistically distinct from blocking growth, is associated with a surge in respiration and reactive oxygen species (ROS). Mutations in carbohydrate metabolism that attenuate ROS accumulation create pan-tolerance to antimicrobials, disinfectants, and environmental stressors. These observations indicate the existence of a general death pathway with respect to stressors. M. tuberculosis displays a variation on the death pathway idea, as stress-induced ROS is generated by NADH-mediated reductive stress rather than by respiration. A third approach, which emerges from lethality studies, uses a small molecule, N-acetyl cysteine, to artificially increase respiration and additional ROS accumulation. That enhances moxifloxacin lethality with M. tuberculosis in culture, during infection of cultured macrophages, and with infection of mice. Addition of ROS stimulators to fluoroquinolone treatment of tuberculosis constitutes a new direction for suppressing the transition of MDR-TB to XDR-TB.
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Affiliation(s)
- Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- *Correspondence: Amit Singh, ; Karl Drlica,
| | - Xilin Zhao
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Karl Drlica
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- *Correspondence: Amit Singh, ; Karl Drlica,
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Monir BB, Sultana SS, Tarafder S. 24 loci MIRU-VNTR analysis and pattern of drug resistance in pre-extensively drug resistant pulmonary tuberculosis in Bangladesh. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105304. [PMID: 35595025 DOI: 10.1016/j.meegid.2022.105304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Phylogenetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis (MTB) contribute to regional differences in drug resistance. The emergence of pre-extensively drug resistant tuberculosis (Pre-XDR-TB) becomes obstacles to achieve End TB strategy in Bangladesh. This cross-sectional study was conducted to identify the strains of different lineages of MTB, their variations of distribution among Pre-XDR-TB cases and to observe the linkage of particular strains of MTB with drug resistance. A total of 33 Pre-XDR-TB isolates were enrolled in this study. All isolates were confirmed as MTB by MPT 64 antigen detection and genotyped by 24 loci Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeats (MIRU-VNTR) analysis. Drug resistance was detected by second line Line probe assay (LPA). Beijing was the predominant strain 16 (48.48%), followed by Delhi/CAS 5(15.15%), LAM 4 (12.12%) and Harlem 3(9.10%), EAI 2(6.06%), Cameroon 2(6.06%) and NEW-1 1(3.03%). There were 31 different genotypes consisting of 2 clusters and 29 singletons. All the clustered strains were belonged to Beijing lineage. Recent transmission occurred manly by Beijing strains, showed low transmission rate (12.1%). Of 33 isolates 30(90.90%) were Fluoroquinolones resistant, the mutations involved was Asp94Gly in gyr A MUT 3C gene 13(39.39%) in quinolone resistance determining region (QRDR) followed by 11 (33.33%) in gyr A MUT 1. Three (9.10%) isolates showed resistant to injectable 2nd line drugs and all mutation occurs in G1484T of rrs MUT 2. Beijing lineage was predominant in treatment failure and relapse cases. Levofloxacin was resistant to all Pre-XDR-TB cases, but moxifloxacin showed low level resistance. QUB 26 was the most discriminatory locus (0.85) among 24 loci whereas MIRU 2 was the least (0.03). 24 loci MIRU-VNTR analysis shows high discriminatory index (0.71), found to be powerful tool for genotyping of Pre-XDR-TB, which is the first study in Bangladesh that enhanced the current TB control policy.
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Affiliation(s)
- Bayzid Bin Monir
- National Institute of Laboratory Medicine and Referral Centre, Dhaka, Bangladesh
| | - Sabia Shahin Sultana
- Department of Microbiology, Shaheed Suhrawardy Medical College, Dhaka, Bangladesh
| | - Shirin Tarafder
- Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka 1000, Bangladesh.
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10
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Ngabonziza JCS, Rigouts L, Torrea G, Decroo T, Kamanzi E, Lempens P, Rucogoza A, Habimana YM, Laenen L, Niyigena BE, Uwizeye C, Ushizimpumu B, Mulders W, Ivan E, Tzfadia O, Muvunyi CM, Migambi P, Andre E, Mazarati JB, Affolabi D, Umubyeyi AN, Nsanzimana S, Portaels F, Gasana M, de Jong BC, Meehan CJ. Multidrug-resistant tuberculosis control in Rwanda overcomes a successful clone that causes most disease over a quarter century. J Clin Tuberc Other Mycobact Dis 2022; 27:100299. [PMID: 35146133 PMCID: PMC8802117 DOI: 10.1016/j.jctube.2022.100299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
SUMMARY BACKGROUND Multidrug-resistant (MDR) tuberculosis (TB) poses an important challenge in TB management and control. Rifampicin resistance (RR) is a solid surrogate marker of MDR-TB. We investigated the RR-TB clustering rates, bacterial population dynamics to infer transmission dynamics, and the impact of changes to patient management on these dynamics over 27 years in Rwanda. METHODS We analysed whole genome sequences of a longitudinal collection of nationwide RR-TB isolates. The collection covered three important periods: before programmatic management of MDR-TB (PMDT; 1991-2005), the early PMDT phase (2006-2013), in which rifampicin drug-susceptibility testing (DST) was offered to retreatment patients only, and the consolidated phase (2014-2018), in which all bacteriologically confirmed TB patients had rifampicin DST done mostly via Xpert MTB/RIF assay. We constructed clusters based on a 5 SNP cut-off and resistance conferring SNPs. We used Bayesian modelling for dating and population size estimations, TransPhylo to estimate the number of secondary cases infected by each patient, and multivariable logistic regression to assess predictors of being infected by the dominant clone. RESULTS Of 308 baseline RR-TB isolates considered for transmission analysis, the clustering analysis grouped 259 (84.1%) isolates into 13 clusters. Within these clusters, a single dominant clone was discovered containing 213 isolates (82.2% of clustered and 69.1% of all RR-TB), which we named the "Rwanda Rifampicin-Resistant clone" (R3clone). R3clone isolates belonged to Ugandan sub-lineage 4.6.1.2 and its rifampicin and isoniazid resistance were conferred by the Ser450Leu mutation in rpoB and Ser315Thr in katG genes, respectively. All R3clone isolates had Pro481Thr, a putative compensatory mutation in the rpoC gene that likely restored its fitness. The R3clone was estimated to first arise in 1987 and its population size increased exponentially through the 1990s', reaching maximum size (∼84%) in early 2000 s', with a declining trend since 2014. Indeed, the highest proportion of R3clone (129/157; 82·2%, 95%CI: 75·3-87·8%) occurred between 2000 and 13, declining to 64·4% (95%CI: 55·1-73·0%) from 2014 onward. We showed that patients with R3clone detected after an unsuccessful category 2 treatment were more likely to generate secondary cases than patients with R3clone detected after an unsuccessful category 1 treatment regimen. CONCLUSIONS RR-TB in Rwanda is largely transmitted. Xpert MTB/RIF assay as first diagnostic test avoids unnecessary rounds of rifampicin-based TB treatment, thus preventing ongoing transmission of the dominant R3clone. As PMDT was intensified and all TB patients accessed rifampicin-resistance testing, the nationwide R3clone burden declined. To our knowledge, our findings provide the first evidence supporting the impact of universal DST on the transmission of RR-TB.
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Affiliation(s)
- Jean Claude S. Ngabonziza
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Center, Kigali, Rwanda
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Clinical Biology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Gabriela Torrea
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tom Decroo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Research Foundation Flanders, Brussels, Belgium
| | - Eliane Kamanzi
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Center, Kigali, Rwanda
| | - Pauline Lempens
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Aniceth Rucogoza
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Center, Kigali, Rwanda
| | - Yves M. Habimana
- Tuberculosis and Other Respiratory Diseases Division, Institute of HIV/AIDS Disease Prevention and Control, Rwanda Biomedical Center, Kigali, Rwanda
| | - Lies Laenen
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Belamo E. Niyigena
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Center, Kigali, Rwanda
| | - Cécile Uwizeye
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bertin Ushizimpumu
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Center, Kigali, Rwanda
| | - Wim Mulders
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emil Ivan
- National Reference Laboratory Division, Department of Biomedical Services, Rwanda Biomedical Center, Kigali, Rwanda
| | - Oren Tzfadia
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Claude Mambo Muvunyi
- Department of Clinical Biology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | | | - Emmanuel Andre
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, Leuven, Belgium
| | | | | | | | | | - Françoise Portaels
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michel Gasana
- Tuberculosis and Other Respiratory Diseases Division, Institute of HIV/AIDS Disease Prevention and Control, Rwanda Biomedical Center, Kigali, Rwanda
| | - Bouke C. de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- School of Chemistry and Biosciences, University of Bradford, UK
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Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:7588033. [PMID: 35386470 PMCID: PMC8979720 DOI: 10.1155/2022/7588033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/27/2022] [Accepted: 03/14/2022] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis antimicrobial resistance has been continually reported and is a major public health issue worldwide. Rapid prediction of drug resistance is important for selecting appropriate antibiotic treatments, which significantly increases cure rates. Gene sequencing technology has proven to be a powerful strategy for identifying relevant drug resistance information. This study established a sequencing method and bioinformatics pipeline for resistance gene analysis using an Oxford Nanopore Technologies sequencer. The pipeline was validated by Sanger sequencing and exhibited 100% concordance with the identified variants. Turnaround time for the nanopore sequencing workflow was approximately 12 h, facilitating drug resistance prediction several weeks earlier than that of traditional phenotype drug susceptibility testing. This study produced a customized gene panel assay for rapid bacterial identification via nanopore sequencing, which improves the timeliness of tuberculosis diagnoses and provides a reliable method that may have clinical application.
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12
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Molecular characterization of Mycobacterium ulcerans DNA gyrase and identification of mutations reduced susceptibility against quinolones in vitro. Antimicrob Agents Chemother 2022; 66:e0190221. [PMID: 35041504 PMCID: PMC9017346 DOI: 10.1128/aac.01902-21] [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] [Indexed: 12/02/2022] Open
Abstract
Buruli ulcer disease is a neglected necrotizing and disabling cutaneous tropical illness caused by Mycobacterium ulcerans. Fluoroquinolone (FQ), used in the treatment of this disease, has been known to act by inhibiting the enzymatic activities of DNA gyrase. However, the detailed molecular basis of these characteristics and the FQ resistance mechanisms in M. ulcerans remains unknown. This study investigated the detailed molecular mechanism of M. ulcerans DNA gyrase and the contribution of FQ resistance in vitro using recombinant proteins from the M. ulcerans subsp. shinshuense and Agy99 strains with reduced sensitivity to FQs. The IC50 of FQs against Ala91Val and Asp95Gly mutants of M. ulcerans shinshuense and Agy99 GyrA subunits were 3.7- to 42.0-fold higher than those against wild-type (WT) enzyme. Similarly, the quinolone concentrations required to induce 25% of the maximum DNA cleavage (CC25) was 10- to 210-fold higher than those for the WT enzyme. Furthermore, the interaction between the amino acid residues of the WT/mutant M. ulcerans DNA gyrase and FQ side chains were assessed by molecular docking studies. This was the first elaborative study demonstrating the contribution of mutations in M. ulcerans DNA GyrA subunit to FQ resistance in vitro.
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Zhang X, Chen X, Wang B, Fu L, Huo F, Gao T, Pang Y, Lu Y, Li Q. Molecular Characteristic of Both Levofloxacin and Moxifloxacin Resistance in Mycobacterium tuberculosis from Individuals Diagnosed with Preextensive Drug-Resistant Tuberculosis. Microb Drug Resist 2021; 28:280-287. [PMID: 34981969 DOI: 10.1089/mdr.2021.0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aim: Fluoroquinolones (FQs) are the cornerstone in treating drug-resistant tuberculosis (TB); the prevalence of TB among the population is diverse in different regions, understanding the relationship between resistance pattern and molecular characteristic of FQs in preextensive drug-resistant (pre-XDR) clinical isolates is limited in China. Methods: A total of 141 pre-XDR clinical isolates from different individuals stored at the National Clinical Centre were collected from the Beijing Chest Hospital, minimal inhibitory concentrations of levofloxacin (Lfx) and moxifloxacin (Mfx) as well as sequences of quinolone-resistant determining regions in gyrA and gyrB genes were examined. Results: One hundred twelve pre-XDR clinical isolates were resistant to both Lfx and Mfx, molecular analyses showed that 87.50%, 0.89%, and 6.25% of the pre-XDR clinical isolates harbored FQ resistance mutations in gyrA, gyrB, and in both. We found five amino acid mutation positions in gyrA and four in gyrB, The mutation position in gyrA included codons 94, 91, 90, 88, and 74, and in gyrB included codons 504, 500, 512, and 501. Codon 94 of gyrA was the most prevalent mutation (83.04%), containing the Asp amino acid substitution with Gly (50.89%), Asn (15.17%), Ala (8.93%), Tyr (6.25%), and His (1.79%). Conclusions: The mutations of gyrA were most common and the frequency of Asp94Gly was the highest in pre-XDR clinical isolates in Beijing, China. The mutations at codon 94 significantly contributed to the resistance to both Lfx and Mfx in pre-XDR clinical isolates and may cause a high resistance level.
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Affiliation(s)
- Xiaofu Zhang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xi Chen
- Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Bin Wang
- Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Lei Fu
- Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Tianhui Gao
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yu Pang
- Biobank of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yu Lu
- Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Li
- Clinical Center on Tuberculosis Control, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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Rahman SMM, Nasrin R, Rahman A, Ahmed S, Khatun R, Uddin MKM, Rahman MM, Banu S. Performance of GenoType MTBDRsl assay for detection of second-line drugs and ethambutol resistance directly from sputum specimens of MDR-TB patients in Bangladesh. PLoS One 2021; 16:e0261329. [PMID: 34914803 PMCID: PMC8675706 DOI: 10.1371/journal.pone.0261329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
Background Rapid and early detection of drug susceptibility among multidrug-resistant tuberculosis (MDR-TB) patients could guide the timely initiation of effective treatment and reduce transmission of drug-resistant TB. In the current study, we evaluated the diagnostic performance of GenoType MTBDRsl (MTBDRsl) ver1.0 assay for detection of resistance to ofloxacin (OFL), kanamycin (KAN) and ethambutol (EMB), and additionally the XDR-TB among MDR-TB patients in Bangladesh. Methods The MTBDRsl assay was performed directly on 218 smear-positive sputum specimens collected from MDR-TB patients and the results were compared with the phenotypic drug susceptibility testing (DST) performed on solid Lowenstein-Jensen (L-J) media. We also analyzed the mutation patterns of gyrA, rrs, and embB genes for detection of resistance to OFL, KAN and EMB, respectively. Results The sensitivity and specificity of the MTBDRsl compared to phenotypic L-J DST were 81.8% (95% CI, 69.1–90.9) and 98.8% (95% CI, 95.6–99.8), respectively for OFL (PPV: 95.7% & NPV: 94.1%); 65.1% (95% CI, 57.5–72.2) and 86.7% (95% CI, 73.2–94.9), respectively for EMB (PPV: 94.9% & NPV: 39.4%); and 100% for KAN. The diagnostic accuracy of KAN, OFL and EMB were 100, 94.5 and 69.6%, respectively. Moreover, the sensitivity, specificity and diagnostic accuracy of MtBDRsl for detection of XDR-TB was 100%. The most frequently observed mutations were at codon D94G (46.8%) of gyrA gene, A1401G (83.3%) of rrs gene, and M306V (41.5%) of the embB gene. Conclusion Considering the excellent performance in this study we suggest that MTBDRsl assay can be used as an initial rapid test for detection of KAN and OFL susceptibility, as well as XDR-TB directly from smear-positive sputum specimens of MDR-TB patients in Bangladesh.
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Affiliation(s)
| | - Rumana Nasrin
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Arfatur Rahman
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Shahriar Ahmed
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Razia Khatun
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | | | - Md. Mojibur Rahman
- Department of Epidemiology, Bangladesh University of Health Sciences, Darus Salam, Mirpur, Dhaka, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
- * E-mail:
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15
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Bi J, Guo Q, Fu X, Liang J, Zeng L, Ou M, Zhang J, Wang Z, Sun Y, Liu L, Zhang G. Characterizing the gene mutations associated with resistance to gatifloxacin in Mycobacterium tuberculosis through whole-genome sequencing. Int J Infect Dis 2021; 112:189-194. [PMID: 34547490 DOI: 10.1016/j.ijid.2021.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/02/2021] [Accepted: 09/15/2021] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES Gatifloxacin (GAT), a fourth-generation fluoroquinolone (FQ), is used to treat drug-resistant tuberculosis. Although DNA gyrase mutations are the leading cause of FQ resistance, mutations conferring resistance to GAT remain inadequately characterized. METHODS GAT-resistant mutants were selected from 7H10 agar plates containing 0.5 mg/L GAT (critical concentration). Mutations involved in GAT resistance were identified through whole-genome sequencing. RESULTS In total, 123 isolates demonstrated resistance to GAT. Among these isolates, 55.3% (68/123) had gyrA gene mutations [G280A (D94N), A281G (D94G), G280T (D94Y) and G262T (G88C)]. The remainder (44.7%, 55/123) harboured gyrB gene mutations [A1495G (N499D), C1497A (N499K), C1497G (N499K) and A1503C (E501D)]. CONCLUSIONS Mutations in the gyrA and gyrB genes are the main mechanisms of GAT resistance. These findings provide new insight into GAT resistance, and contribute to molecular diagnosis of GAT resistance in the clinical setting.
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Affiliation(s)
- Jing Bi
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Qinglong Guo
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Xiangdong Fu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Juan Liang
- Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Lidong Zeng
- GeneMind Biosciences Co. Ltd, Shenzhen, China
| | - Min Ou
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Juanjuan Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Zhaoqin Wang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Yicheng Sun
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China.
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Chauffour A, Morel F, Reibel F, Petrella S, Mayer C, Cambau E, Aubry A. A systematic review of Mycobacterium leprae DNA gyrase mutations and their impact on fluoroquinolone resistance. Clin Microbiol Infect 2021; 27:1601-1612. [PMID: 34265461 DOI: 10.1016/j.cmi.2021.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The fact that Mycobacterium leprae does not grow in vitro remains a challenge in the survey of its antimicrobial resistance (AMR). Mainly molecular methods are used to diagnose AMR in M. leprae to provide reliable data concerning mutations and their impact. Fluoroquinolones (FQs) are efficient for the treatment of leprosy and the main second-line drugs in case of multidrug resistance. OBJECTIVES This study aimed at performing a systematic review (a) to characterize all DNA gyrase gene mutations described in clinical isolates of M. leprae, (b) to distinguish between those associated with FQ resistance or susceptibility and (c) to delineate a consensus numbering system for M. leprae GyrA and GyrB. DATA SOURCES Data source was PubMed. STUDY ELIGIBILITY CRITERIA Publications reporting genotypic susceptibility-testing methods and gyrase gene mutations in M. leprae clinical strains. RESULTS In 25 studies meeting our inclusion criteria, 2884 M. leprae isolates were analysed (2236 for gyrA only (77%) and 755 for both gyrA and gyrB (26%)): 3.8% of isolates had gyrA mutations (n = 110), mostly at position 91 (n = 75, 68%) and 0.8% gyrB mutations (n = 6). Since we found discrepancies regarding the location of substitutions associated with FQ resistance, we established a consensus numbering system to properly number the mutations. We also designed a 3D model of the M. leprae DNA gyrase to predict the impact of mutations whose role in FQ-susceptibility has not been demonstrated previously. CONCLUSIONS Mutations in DNA gyrase are observed in 4% of the M. leprae clinical isolates. To solve discrepancies among publications and to distinguish between mutations associated with FQ resistance or susceptibility, the consensus numbering system we proposed as well as the 3D model of the M. leprae gyrase for the evaluation of the impact of unknown mutations in FQ resistance, will provide help for resistance surveillance.
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Affiliation(s)
- Aurélie Chauffour
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Paris, France
| | - Florence Morel
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Paris, France; AP-HP, Sorbonne-Université, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Florence Reibel
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Paris, France; AP-HP, Sorbonne-Université, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France; Laboratoire de Biologie, Groupe Hospitalier Nord-Essonne, Site de Longjumeau, Longjumeau, France
| | - Stéphanie Petrella
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Claudine Mayer
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Emmanuelle Cambau
- AP-HP GHU Nord, Service de Mycobactériologie Spécialisée et de Référence, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France; Université de Paris, Paris Diderot, INSERM, IAME UMR1137, Paris, France
| | - Alexandra Aubry
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Paris, France; AP-HP, Sorbonne-Université, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France.
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Sheikh BA, Bhat BA, Mehraj U, Mir W, Hamadani S, Mir MA. Development of New Therapeutics to Meet the Current Challenge of Drug Resistant Tuberculosis. Curr Pharm Biotechnol 2021; 22:480-500. [PMID: 32600226 DOI: 10.2174/1389201021666200628021702] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is a prominent infective disease and a major reason of mortality/ morbidity globally. Mycobacterium tuberculosis causes a long-lasting latent infection in a significant proportion of human population. The increasing burden of tuberculosis is mainly caused due to multi drug-resistance. The failure of conventional treatment has been observed in large number of cases. Drugs that are used to treat extensively drug-resistant tuberculosis are expensive, have limited efficacy, and have more side effects for a longer duration of time and are often associated with poor prognosis. To regulate the emergence of multidrug resistant tuberculosis, extensively drug-resistant tuberculosis and totally drug resistant tuberculosis, efforts are being made to understand the genetic/molecular basis of target drug delivery and mechanisms of drug resistance. Understanding the molecular approaches and pathology of Mycobacterium tuberculosis through whole genome sequencing may further help in the improvement of new therapeutics to meet the current challenge of global health. Understanding cellular mechanisms that trigger resistance to Mycobacterium tuberculosis infection may expose immune associates of protection, which could be an important way for vaccine development, diagnostics, and novel host-directed therapeutic strategies. The recent development of new drugs and combinational therapies for drug-resistant tuberculosis through major collaboration between industry, donors, and academia gives an improved hope to overcome the challenges in tuberculosis treatment. In this review article, an attempt was made to highlight the new developments of drug resistance to the conventional drugs and the recent progress in the development of new therapeutics for the treatment of drugresistant and non-resistant cases.
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Affiliation(s)
- Bashir A Sheikh
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Basharat A Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Umar Mehraj
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Wajahat Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Suhail Hamadani
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Manzoor A Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
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Park JH, Yamaguchi T, Ouchi Y, Koide K, Pachanon R, Chizimu JY, Mori S, Kim H, Mukai T, Nakajima C, Suzuki Y. Interaction of Quinolones Carrying New R1 Group with Mycobacterium leprae DNA Gyrase. Microb Drug Resist 2021; 27:1616-1623. [PMID: 34077282 DOI: 10.1089/mdr.2020.0408] [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: 11/12/2022] Open
Abstract
Background: Leprosy is a chronic infectious disease caused by Mycobacterium leprae and the treatment of choice is ofloxacin (OFX). Specific amino acid substitutions in DNA gyrase of M. leprae have been reported leading to resistance against the drug. In our previous study, WQ-3810, a fluoroquinolone with a new R1 group (6-amino-3,5-difluoropyridin-2-yl) was shown to have a strong inhibitory activity on OFX-resistant DNA gyrases of M. leprae, and the structural characteristics of its R1 group was predicted to enhance the inhibitory activity. Methodology/Principal Finding: To further understand the contribution of the R1 group, WQ-3334 with the same R1 group as WQ-3810, WQ-4064, and WQ-4065, but with slightly modified R1 group, were assessed on their activities against recombinant DNA gyrase of M. leprae. An in silico study was conducted to understand the molecular interactions between DNA gyrase and WQ compounds. WQ-3334 and WQ-3810 were shown to have greater inhibitory activity against M. leprae DNA gyrase than others. Furthermore, analysis using quinolone-resistant M. leprae DNA gyrases showed that WQ-3334 had greater inhibitory activity than WQ-3810. The R8 group was shown to be a factor for the linkage of the R1 groups with GyrB by an in silico study. Conclusions/Significance: The inhibitory effect of WQ compounds that have a new R1 group against M. leprae DNA gyrase can be enhanced by improving the binding affinity with different R8 group molecules. The information obtained by this work could be applied to design new fluoroquinolones effective for quinolone-resistant M. leprae and other bacterial pathogens.
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Affiliation(s)
- Jong-Hoon Park
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Tomoyuki Yamaguchi
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yuki Ouchi
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Kentaro Koide
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Ruttana Pachanon
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Joseph Yamweka Chizimu
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - Shigetarou Mori
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hyun Kim
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsu Mukai
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
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Hänel I, Müller E, Santamarina BG, Tomaso H, Hotzel H, Busch A. Antimicrobial Susceptibility and Genomic Analysis of Aliarcobacter cibarius and Aliarcobacter thereius, Two Rarely Detected Aliarcobacter Species. Front Cell Infect Microbiol 2021; 11:532989. [PMID: 33816322 PMCID: PMC8010192 DOI: 10.3389/fcimb.2021.532989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 01/19/2021] [Indexed: 01/06/2023] Open
Abstract
Aliarcobacter cibarius and Aliarcobacter thereius are two rarely detected Aliarcobacter species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic Campylobacter species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide. The genus Aliarcobacter is part of the Campylobacteraceae family and includes the species Aliarcobacter butzleri, Aliarcobacter cryaerophilus, Aliarcobacter skirrowii, and the rarely described Aliarcobacter cibarius, Aliarcobacter faecis, Aliarcobacter lanthieri, Aliarcobacter thereius, and Acrobarter trophiarum. Aliarcobacter are emergent enteropathogens and potential zoonotic agents. Here, we generated, analyzed, and characterized whole-genome sequences of Aliarcobacter cibarius and Aliarcobacter thereius. They were isolated from water poultry farms in Germany, cultured and identified by MALDI-TOF MS. With PCR the identity was verified. Antibiotic susceptibility testing was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, streptomycin, ampicillin, and cefotaxime using the gradient strip method (E-test). Whole-genome sequences were generated including those of reference strains. Complete genomes for six selected strains are reported. These provide detailed insights into the genotype. With these, we predicted in silico known AMR genes, virulence-associated genes, and plasmid replicons. Phenotypic analysis of resistance showed differences between the presence of resistance genes and the prediction of phenotypic resistance profiles. In Aliarcobacter butzleri, the nucleotide sequence of the gyrA gene (DQ464331) can show a signature mutation resulting in an amino acid change T85>I. Acrobarter cibarius and Acrobarter thereius showed the same gene as assessed by similarity annotation of the mutations 254C>G. Most of the isolates were found to be sensitive to ciprofloxacin. The ciprofloxacin-resistant Aliarcobacter thereius isolate was associated with the amino acid change T85>I. But this was not predicted with antibiotic resistance databases, before. Ultimately, a phylogenetic analysis was done to facilitate in future outbreak analysis.
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Affiliation(s)
- Ingrid Hänel
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany
| | - Eva Müller
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany
| | | | | | - Helmut Hotzel
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany
| | - Anne Busch
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany.,Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Jena, Germany
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20
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Vázquez-Chacón CA, Rodríguez-Gaxiola FDJ, López-Carrera CF, Cruz-Rivera M, Martínez-Guarneros A, Parra-Unda R, Arámbula-Meraz E, Fonseca-Coronado S, Vaughan G, López-Durán PA. Identification of drug resistance mutations among Mycobacterium bovis lineages in the Americas. PLoS Negl Trop Dis 2021; 15:e0009145. [PMID: 33591982 PMCID: PMC7886168 DOI: 10.1371/journal.pntd.0009145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/14/2021] [Indexed: 01/25/2023] Open
Abstract
Identifying the Mycobacterium tuberculosis resistance mutation patterns is of the utmost importance to assure proper patient's management and devising of control programs aimed to limit spread of disease. Zoonotic Mycobacterium bovis infection still represents a threat to human health, particularly in dairy production regions. Routinary, molecular characterization of M. bovis is performed primarily by spoligotyping and mycobacterial interspersed repetitive units (MIRU) while next generation sequencing (NGS) approaches are often performed by reference laboratories. However, spoligotyping and MIRU methodologies lack the resolution required for the fine characterization of tuberculosis isolates, particularly in outbreak settings. In conjunction with sophisticated bioinformatic algorithms, whole genome sequencing (WGS) analysis is becoming the method of choice for advanced genetic characterization of tuberculosis isolates. WGS provides valuable information on drug resistance and compensatory mutations that other technologies cannot assess. Here, we performed an analysis of the most frequently identified mutations associated with tuberculosis drug resistance and their genetic relationship among 2,074 Mycobacterium bovis WGS recovered primarily from non-human hosts. Full-length gene sequences harboring drug resistant associated mutations and their phylogenetic relationships were analyzed. The results showed that M. bovis isolates harbor mutations conferring resistance to both first- and second-line antibiotics. Mutations conferring resistance for isoniazid, fluoroquinolones, streptomycin, and aminoglycosides were identified among animal strains. Our findings highlight the importance of molecular surveillance to monitor the emergence of mutations associated with multi and extensive drug resistance in livestock and other non-human mammals.
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Affiliation(s)
- Carlos Arturo Vázquez-Chacón
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, México
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | | | | | - Mayra Cruz-Rivera
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Armando Martínez-Guarneros
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | - Ricardo Parra-Unda
- Unidad de Investigaciones en Salud Pública, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Eliakym Arámbula-Meraz
- Laboratorio de Genética y Biología Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Salvador Fonseca-Coronado
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
| | - Gilberto Vaughan
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
| | - Paúl Alexis López-Durán
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
- * E-mail:
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21
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Hu Y, Liu J, Shen J, Feng X, Liu W, Zhu D, Zheng H, Hu D. Genotyping and Molecular Characterization of Fluoroquinolone's Resistance Among Multidrug-Resistant Mycobacterium tuberculosis in Southwest of China. Microb Drug Resist 2020; 27:865-870. [PMID: 33305990 DOI: 10.1089/mdr.2019.0339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although fluoroquinolones (FQs) are the backbone drugs for the treatment of multidrug-resistant tuberculosis (MDR-TB), the knowledge about the resistance pattern and molecular characterization of new-generation FQs in Chongqing is limited. This study aimed to investigate the resistance rate and mutation types of later-generation FQs against MDR-TB in Chongqing, and further to explore the relationship between different genotypes and phenotypes. A total of 967 clinical strains were characterized using multilocus sequence typing and drug susceptibility testing, followed by analysis of genotype/phenotype association. The 229 (23.7%, 229/967) isolates were identified as MDR-TB. The most effective agent against MDR-TB was gatifloxacin (GFX) (20.1%, 46/229), and the highest resistant rate was observed in ofloxacin (OFX) (41.0%, 94/229). Of the 190 strains (83.0%) identified as Beijing genotype, 111 isolates were modern Beijing genotype (58.4%) and 79 isolates were ancient Beijing genotype (41.6%). By analyzing 94 OFX-resistant isolates, 13 isolates were clustered with the cumulative clustering rate of 13.8% (13/94). Of the 91 isolates (39.7%, 91/229) with a mutation in gyrA gene, mutation in codon 94 was the most prevalent. Only 15 isolates (6.6%, 15/229) harbored a mutation in gyrB gene. There was no significant difference in the mutation rate of gyrA gene between Beijing and non-Beijing genotype, clustered isolates, and nonclustered isolates (p > 0.05).
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jie Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jing Shen
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Xin Feng
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Wenguo Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Damian Zhu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Huiwen Zheng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Daiyu Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
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22
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Sayadi M, Zare H, Jamedar SA, Hashemy SI, Meshkat Z, Soleimanpour S, Hoffner S, Ghazvini K. Genotypic and phenotypic characterization of Mycobacterium tuberculosis resistance against fluoroquinolones in the northeast of Iran. BMC Infect Dis 2020; 20:390. [PMID: 32487030 PMCID: PMC7268510 DOI: 10.1186/s12879-020-05112-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 05/20/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Fluoroquinolones are broad-spectrum antibiotics that are recommended, and increasingly important, for the treatment of multidrug-resistant tuberculosis (MDR-TB). Resistance to fluoroquinolones is caused by mutations in the Quinolone Resistance Determining Region (QRDR) of gyrA and gyrB genes of Mycobacterium tuberculosis. In this study, we characterized the phenotypic and genotypic resistance to fluoroquinolones for the first time in northeast Iran. METHODS A total of 123 Mycobacterium tuberculosis isolates, including 111 clinical and 12 collected multidrug-resistant isolates were studied. Also, 19 WHO quality control strains were included in the study. The phenotypic susceptibility was determined by the proportion method on Löwenstein-Jensen medium. The molecular cause of resistance to the fluoroquinolone drugs ofloxacin and levofloxacin was investigated by sequencing of the QRDR region of the gyrA and gyrB genes. RESULTS Among 123 isolates, six (4.8%) were fluoroquinolone-resistant according to phenotypic methods, and genotypically three of them had a mutation at codon 94 of the gyrA gene (Asp→ Gly) which was earlier reported to cause resistance. All three remaining phenotypically resistant isolates had a nucleotide change in codon 95. No mutations were found in the gyrB gene. Five of the 19 WHO quality control strains, were phenotypically fluoroquinolone-resistant, four of them were genotypically resistant with mutations at codon 90, 91 of the gyrA gene and one resistant strain had no detected mutation. CONCLUSIONS Mutation at codon 94 of the gyrA gene, was the main cause of fluoroquinolone resistance among M. tuberculosis isolates in our region. In 3/6 fluoroquinolone-resistant isolates, no mutations were found in either gyrA or gyrB. Therefore, it can be concluded that various other factors may lead to fluoroquinolone resistance, such as active efflux pumps, decreased cell wall permeability, and drug inactivation.
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Affiliation(s)
- Mahdieh Sayadi
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hosna Zare
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Amel Jamedar
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Isaac Hashemy
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sven Hoffner
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Umar FF, Husain DR, Hatta MM, Natzir RR, Sjahril RS, Dwiyanti RR, Junita AR, Primaguna MR. Molecular characterisation of mutations associated with resistance to first- and second-line drugs among Indonesian patients with tuberculosis. J Taibah Univ Med Sci 2020; 15:54-58. [PMID: 32110183 PMCID: PMC7033412 DOI: 10.1016/j.jtumed.2019.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 12/25/2019] [Accepted: 12/27/2019] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES This study aimed to determine molecular characteristics of rpoB, katG, rrs, and gyrA genes in Mycobacterium tuberculosis isolated from a cohort of Indonesian patients with tuberculosis. METHODS Fifty isolates of M. tuberculosis were analysed by testing (DST) for susceptibility to first- and second-line drugs using the proportional method in a liquid medium. The genomic material was extracted to perform multiplex polymerase chain reaction (PCR) for identification and gene sequencing of rpoB, katG, rrs, and gyrA. RESULTS Approximately 80% (40/50) of the rpoB mutations that were detected outside the hot-spot region (S450L, H445D, D435V, S441L, I491F, and Q432P) conferred rifampicin-resistance on M. tuberculosis. Approximately 11.42% (4/35) of isolates with S315T mutation in katG led to rifampicin-resistance instead of isoniazid-resistance. The mutation in katG gene was found at various locations (P280P, G279R, E340Q, T271I, E340*stop codon, R373G, and S315N). Streptomycin-resistance was detected in 42% (21/50) of the strains, but only two strains had rrs gene mutations (G878A and/or S514R). Approximately 14% (7/50) of M. tuberculosis isolates were kanamycin- and capreomycin-resistant but did not harbour mutations in the rrs gene, while 80% (40/50) of the strains had mutations in the quinolone-resistance determining region (QRDR) of the gyrA gene (S95T, D94V, A90V, and S91P) including the pan-susceptible strain. CONCLUSIONS Of the 50 strains analysed, most of the mutations in the rpoB gene associated with rifampicin-resistance were also detected in the katG and gyrA genes. Molecular characterisation using DNA sequencing techniques is a highly sensitive approach for detecting mutations.
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Affiliation(s)
- Faiqah F. Umar
- Post Graduate of Medical Science, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia
| | - Dirayah R. Husain
- Department of Biology, Faculty of Science, University of Hasanuddin, Makassar, Indonesia
| | - Mochammad M. Hatta
- Molecular Biology and Immunology Laboratory, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia
| | - Rosdiana R. Natzir
- Department of Biochemistry, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia
| | - Rizalinda S. Sjahril
- Department of Medical Microbiology, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia
| | - Ressy R. Dwiyanti
- Department of Medical Microbiology, Faculty of Medicine, Tadulako University, Palu, Indonesia
| | - Ade R. Junita
- Post Graduate of Medical Science, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia
| | - Muhammad R. Primaguna
- Department of Internal Medicine, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
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WQ-3810 inhibits DNA gyrase activity in ofloxacin-resistant Mycobacterium leprae. J Infect Chemother 2019; 26:335-342. [PMID: 31839561 DOI: 10.1016/j.jiac.2019.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 11/21/2022]
Abstract
BACKGROUND Mycobacterium leprae causes leprosy and ofloxacin is used to control this bacterium. However, specific amino acid substitutions in DNA gyrases of M. leprae interferes with the effect of ofloxacin. METHODOLOGY/PRINCIPAL FINDINGS Here we tested the inhibitory effect of WQ-3810 on DNA gyrases in M. leprae, using recombinant gyrases. We theorized that WQ-3810 and DNA gyrases interacted, which was tested in silico. Compared with control drugs like ofloxacin, WQ-3810 showed a better inhibitory effect on ofloxacin-resistant DNA gyrases. The in-silico study showed that, unlike control drugs, a specific linkage between a R1 group in WQ-3810 and aspartic acid at position 464 in the subunit B of DNA gyrases existed, which would enhance the inhibitory effect of WQ-3810. This linkage was confirmed in a further experiment, using recombinant DNA gyrases with amino acid substitutions in subunits B instead. CONCLUSIONS/SIGNIFICANCE The inhibitory effect of WQ-3810 was likely enhanced by the specific linkage between a R1 group residue in its structure and DNA gyrases. Using interactions like the one found in the present work may help design new fluoroquinolones that contribute to halt the emergence of antibiotic-resistant pathogens.
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WQ-3810: A new fluoroquinolone with a high potential against fluoroquinolone-resistant Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 120:101891. [PMID: 31778929 DOI: 10.1016/j.tube.2019.101891] [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: 09/11/2019] [Revised: 11/06/2019] [Accepted: 11/17/2019] [Indexed: 11/23/2022]
Abstract
Fluoroquinolone (FQ) resistance in Mycobacterium tuberculosis (Mtb), caused by amino acid substitutions in DNA gyrase, has been increasingly reported worldwide. WQ-3810 is a newly developed FQ that is highly active against FQ-resistant pathogens; however, its activity against Mtb has not been evaluated. Herein we examined the efficacy of WQ-3810 against Mtb through the use of recombinant Mtb DNA gyrases. In addition, in vitro antimycobacterial activity of WQ-3810 was evaluated against recombinant Mtb var. bovis Bacille Calmette-Guérin strains in which gyrase-coding genes were replaced with Mtb variants containing resistance-conferring mutations. WQ-3810 showed a higher inhibitory activity than levofloxacin against most recombinant DNA gyrases with FQ-resistance mutations. Furthermore, WQ-3810 showed inhibition even against a DNA gyrase variant harboring a G88C mutation which is thought to confer the highest resistance against FQs in clinical Mtb isolates. In contrast, the FQ susceptibility test showed that WQ-3810 had relatively weak mycobactericidal activity compared with moxifloxacin. However, the combination of WQ-3810 and ethambutol showed the greatest degree of synergistic activity against recombinant strains. Since FQs and ethambutol have been used in multi-drug therapy for tuberculosis, WQ-3810 might represent a new, potent anti-tuberculosis drug that can be effective even against FQ-resistant Mtb strains.
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Yoshida M, Nakata N, Miyamoto Y, Fukano H, Ato M, Hoshino Y. A rapid and non-pathogenic assay for association of Mycobacterium tuberculosis gyrBA mutations and fluoroquinolone resistance using recombinant Mycobacterium smegmatis. FEMS Microbiol Lett 2019; 365:5173037. [PMID: 30418577 DOI: 10.1093/femsle/fny266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/07/2018] [Indexed: 12/13/2022] Open
Abstract
We developed a method involving recombinant Mycobacterium bovis bacillus Calmette-Guérin (BCG) and recombinant Mycobacterium smegmatis to determine which mutations in Mycobacterium tuberculosis (Mtb) gyrBA are associated with fluoroquinolone (FQ) resistance. The minimal inhibitory concentration (MIC) for FQ for recombinant strains with wild-type Mtb gyrBA was equivalent to that for strains with intrinsic gyrBA. Among 27 gyrBA mutations, the fold-changes in FQ MIC for M. smegmatis and M. bovis BCG backgrounds were comparable and were in part equivalent to those previously reported for recombinant Mtb strains. Mutations at position 90 or 94 of gyrA conferred strong and synergistic FQ resistance, which may be associated with the clinical observation that isolates carrying these mutations are the most or second most frequent. Sitafloxacin hydrate had the lowest MIC among the FQs tested in this study, which is similar to findings from a previous in vivo animal study. Most gyrBA mutations detected in clinical Mtb isolates could confer FQ resistance, but several mutations reduced bacterial growth rates. Overall, recombinant M. smegmatis appears to be a beneficial surrogate system to evaluate FQ susceptibility of virulent mycobacteria.
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Affiliation(s)
- Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noboru Nakata
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuji Miyamoto
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Yathursan S, Wiles S, Read H, Sarojini V. A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity. J Pept Sci 2019; 25:e3213. [PMID: 31515916 DOI: 10.1002/psc.3213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.
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Affiliation(s)
- Sutharsana Yathursan
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Hannah Read
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140, New Zealand
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28
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Kateete DP, Kamulegeya R, Kigozi E, Katabazi FA, Lukoye D, Sebit SI, Abdi H, Arube P, Kasule GW, Musisi K, Dlamini MG, Khumalo D, Joloba ML. Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014-2016). BMC Pulm Med 2019; 19:124. [PMID: 31291943 PMCID: PMC6617586 DOI: 10.1186/s12890-019-0891-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/03/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pulmonary tuberculosis is a leading cause of morbidity and mortality in developing countries. Drug resistance, a huge problem in this contagious disease, is driven by point mutations in the Mycobacterium tuberculosis genome however, their frequencies vary geographically and this affects applicability of molecular diagnostics for rapid detection of resistance. Here, we report the frequency and patterns of mutations associated with resistance to second-line anti-TB drugs in multidrug-resistant (MDR) M. tuberculosis isolates from eSwatini, Somalia and Uganda that were resistant to a second-line anti-TB drug. METHODS The quinolone resistance determining region (QRDR) of gyrA/gyrB genes and the drug resistance associated fragment of rrs gene from 80 isolates were sequenced and investigated for presence of drug resistance mutations. Of the 80 isolates, 40 were MDR, of which 28 (70%) were resistant to a second-line anti-TB injectable drug, 18 (45%) were levofloxacin resistant while 12 (30%) were extensively drug resistant (XDR). The remaining 40 isolates were susceptible to anti-TB drugs. MIRU-VNTR analysis was performed for M/XDR isolates. RESULTS We successfully sub-cultured 38 of the 40 M/XDR isolates. The gyrA resistance mutations (Gly88Ala/Cys/Ala, Ala90Val, Ser91Pro, Asp94Gly/Asn) and gyrB resistance mutations (Asp500His, Asn538Asp) were detected in 72.2% (13/18) and 22.2% (4/18) of the MDR and levofloxacin resistant isolates, respectively. Overall, drug resistance mutations in gyrA/gyrB QRDRs occurred in 77.8% (14/18) of the MDR and levofloxacin resistant isolates. Furthermore, drug resistance mutations a1401g and g1484 t in rrs occurred in 64.3% (18/28) of the MDR isolates resistant to a second-line anti-TB injectable drug. Drug resistance mutations were not detected in drug susceptible isolates. CONCLUSIONS The frequency of resistance mutations to second-line anti-TB drugs in MDR-TB isolates resistant to second line anti-TB drugs from eSwatini, Somalia and Uganda is high, implying that rapid molecular tests are useful in detecting second-line anti-TB drug resistance in those countries. Relatedly, the frequency of fluoroquinolone resistance mutations in gyrB/QRDR is high relative to global estimates, and they occurred independently of gyrA/QRDR mutations implying that their absence in panels of molecular tests for detecting fluoroquinolone resistance may yield false negative results in our setting.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rogers Kamulegeya
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Deus Lukoye
- National Tuberculosis/Leprosy Program, Ministry of Health Uganda, Kampala, Uganda
| | | | - Hergeye Abdi
- Ministry of Health, Hargeisa, Somaliland Somalia
| | | | | | - Kenneth Musisi
- National Tuberculosis Reference Laboratory, Kampala, Uganda
| | - Myalo Glen Dlamini
- National TB Reference Laboratory / eSwatini Health Laboratory Services, Ministry of Health, Hospital Hill Mbabane, Mbabane, eSwatini
| | - Derrick Khumalo
- National TB Reference Laboratory / eSwatini Health Laboratory Services, Ministry of Health, Hospital Hill Mbabane, Mbabane, eSwatini
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
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Mahmood N, Abbas SN, Faraz N, Shahid S. Mutational analysis of gyrB at amino acids: G481A & D505A in multidrug resistant (MDR) tuberculosis patients. J Infect Public Health 2019; 12:496-501. [PMID: 30738756 DOI: 10.1016/j.jiph.2019.01.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 01/03/2019] [Accepted: 01/15/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The MDR (multidrug resistance) tuberculosis is a serious public health concern. Fluoroquinolones are in use to treat tuberculosis, but M. tuberculosis strains have now become resistant due to several mutations in different genes. We evaluated mutations in gyrB gene at amino acid positions G481A and D505A of M. tuberculosis by semi-multiplex allele specific (MAS) PCR. METHODS The information on gender, age, type of tuberculosis (TB), positive/negative for MDR-TB and HIV infection was gathered. The genomic DNA isolation from sputum culture samples (n=53) was carried out by non-column based method. The gyrB mutations were investigated by using self-designed primers in semi MAS-PCR, at mentioned amino acid positions. RESULTS There were 38% male patients and 62% were female patients. Most of MDR-TB patients (58.5%) were in the age between 16-30years. There were 90.5% cases of pulmonary TB and 9.4% cases of extra pulmonary TB. Only 1.8% patients were co-infected with HIV. The 24 samples had mutation in gyrB gene out of 53 (45.28%), on both of positions of amino acids Gly481Ala and Asp505Ala. All samples had mutations at Gly481Ala, whereas, 24 samples (45.28%) had mutations at Asp505Ala. CONCLUSION Mutations at amino acids positions 481 and 505 were involved in MDR-TB, which could further develop into an extensively-drug resistance (XDR) TB. Therefore, there is a need to explore all mutations in gyrB gene in MDR-TB, because it can result in a Fluoroquinolones resistance.
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Affiliation(s)
- Nasir Mahmood
- Department of Biochemistry & Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan; Department of Cell and Systems Biology, University of Toronto, Canada.
| | - Shahzada N Abbas
- Department of Biology, Lahore Garrison University, Lahore, Pakistan
| | - Neelam Faraz
- Department of Biology, Lahore Garrison University, Lahore, Pakistan
| | - Saman Shahid
- Department of Sciences and Humanities, National University of Computer & Emerging Sciences (NUCES), Foundation for Advancement of Science and Technology (FAST), Lahore, Pakistan
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Rode HB, Lade DM, Grée R, Mainkar PS, Chandrasekhar S. Strategies towards the synthesis of anti-tuberculosis drugs. Org Biomol Chem 2019; 17:5428-5459. [DOI: 10.1039/c9ob00817a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this report, we reviewed the strategies towards the synthesis of anti-tuberculosis drugs. They include semisynthetic approaches, resolution based strategies, microbial transformations, solid phase synthesis, and asymmetric synthesis.
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Affiliation(s)
- Haridas B. Rode
- Department of Organic Synthesis and Process Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Dhanaji M. Lade
- Department of Organic Synthesis and Process Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - René Grée
- University of Rennes
- CNRS
- ISCR (Institut des Sciences Chimiques de Rennes)
- UMR 6226
- F-35000 Rennes
| | - Prathama S. Mainkar
- Department of Organic Synthesis and Process Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Srivari Chandrasekhar
- Department of Organic Synthesis and Process Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
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Marimani M, Ahmad A, Duse A. The role of epigenetics, bacterial and host factors in progression of Mycobacterium tuberculosis infection. Tuberculosis (Edinb) 2018; 113:200-214. [PMID: 30514504 DOI: 10.1016/j.tube.2018.10.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/21/2018] [Accepted: 10/23/2018] [Indexed: 12/29/2022]
Abstract
Tuberculosis (TB) infection caused by Mycobacterium tuberculosis (Mtb) is still a persistent global health problem, particularly in developing countries. The World Health Organization (WHO) reported a mortality rate of about 1.8 million worldwide due to TB complications in 2015. The Bacillus Calmette-Guérin (BCG) vaccine was introduced in 1921 and is still widely used to prevent TB development. This vaccine offers up to 80% protection against various forms of TB; however its efficacy against lung infection varies among different geographical settings. Devastatingly, the development of various forms of drug-resistant TB strains has significantly impaired the discovery of effective and safe anti-bacterial agents. Consequently, this necessitated discovery of new drug targets and novel anti-TB therapeutics to counter infection caused by various Mtb strains. Importantly, various factors that contribute to TB development have been identified and include bacterial resuscitation factors, host factors, environmental factors and genetics. Furthermore, Mtb-induced epigenetic changes also play a crucial role in evading the host immune response and leads to bacterial persistence and dissemination. Recently, the application of GeneXpert MTB/RIF® to rapidly diagnose and identify drug-resistant strains and discovery of different molecular markers that distinguish between latent and active TB infection has motivated and energised TB research. Therefore, this review article will briefly discuss the current TB state, highlight various mechanisms employed by Mtb to evade the host immune response as well as to discuss some modern molecular techniques that may potentially target and inhibit Mtb replication.
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Affiliation(s)
- Musa Marimani
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, South Africa.
| | - Adriano Duse
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, South Africa
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32
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Drug targets exploited in Mycobacterium tuberculosis: Pitfalls and promises on the horizon. Biomed Pharmacother 2018; 103:1733-1747. [PMID: 29864964 DOI: 10.1016/j.biopha.2018.04.176] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 01/10/2023] Open
Abstract
Tuberculosis is an ever evolving infectious disease that still claims about 1.8 million human lives each year around the globe. Although modern chemotherapy has played a pivotal role in combating TB, the increasing emergence of drug-resistant TB aligned with HIV pandemic threaten its control. This highlights both the need to understand how our current drugs work and the need to develop new and more effective drugs. TB drug discovery is revisiting the clinically validated drug targets in Mycobacterium tuberculosis using whole-cell phenotypic assays in search of better therapeutic scaffolds. Herein, we review the promises of current TB drug regimens, major pitfalls faced, key drug targets exploited so far in M. tuberculosis along with the status of newly discovered drugs against drug resistant forms of TB. New antituberculosis regimens that use lesser number of drugs, require shorter duration of treatment, are equally effective against susceptible and resistant forms of disease, have acceptable toxicity profiles and behave friendly with anti-HIV regimens remains top most priority in TB drug discovery.
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33
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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.
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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
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34
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Chawla K, Kumar A, Shenoy VP, Chakrabarty S, Satyamoorthy K. Genotypic detection of fluoroquinolone resistance in drug-resistant Mycobacterium tuberculosis at a tertiary care centre in south Coastal Karnataka, India. J Glob Antimicrob Resist 2018; 13:250-253. [DOI: 10.1016/j.jgar.2018.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Accepted: 01/29/2018] [Indexed: 11/16/2022] Open
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35
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Farhat MR, Jacobson KR, Franke MF, Kaur D, Murray M, Mitnick CD. Fluoroquinolone Resistance Mutation Detection Is Equivalent to Culture-Based Drug Sensitivity Testing for Predicting Multidrug-Resistant Tuberculosis Treatment Outcome: A Retrospective Cohort Study. Clin Infect Dis 2018; 65:1364-1370. [PMID: 29017248 DOI: 10.1093/cid/cix556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/10/2017] [Indexed: 11/12/2022] Open
Abstract
Background Molecular diagnostics that rapidly and accurately predict fluoroquinolone (FQ) resistance promise to improve treatment outcomes for individuals with multidrug-resistant (MDR) tuberculosis (TB). Mutations in the gyr genes, though, can cause variable levels of in vitro FQ resistance, and some in vitro resistance remains unexplained by gyr mutations alone, but the implications of these discrepancies for treatment outcome are unknown. Methods We performed a retrospective cohort study of 172 subjects with MDR/extensively drug-resistant TB subjects and sequenced the full gyrA and gyrB open reading frames in their respective sputum TB isolates. The gyr mutations were classified into 2 categories: a set of mutations that encode high-level FQ resistance and a second set that encodes intermediate resistance levels. We constructed a Cox proportional model to assess the effect of the gyr mutation type on the time to death or treatment failure and compared this with in vitro FQ resistance, controlling for host and treatment factors. Results Controlling for other host and treatment factors and compared with patients with isolates without gyr resistance mutations, "high-level" gyr mutations significantly predict poor treatment outcomes with a hazard ratio of 2.6 (1.2-5.6). We observed a hazard of death and treatment failure with "intermediate-level" gyr mutations of 1.3 (0.6-3.1), which did not reach statistical significance. The gyr mutations were not different than culture-based FQ drug susceptibility testing in predicting the hazard of death or treatment failure and may be superior. Conclusions FQ molecular-based diagnostic tests may better predict treatment response than traditional drug susceptibility testing and open avenues for personalizing TB therapy.
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Affiliation(s)
- Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School.,Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine
| | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School
| | - Devinder Kaur
- University of Massachusetts Medical School, Massachusetts Supranational Tuberculosis Reference Laboratory
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School.,Department of Epidemiology, Harvard School of Public Health
| | - Carole D Mitnick
- Department of Global Health and Social Medicine, Harvard Medical School.,Department of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts
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Dookie N, Rambaran S, Padayatchi N, Mahomed S, Naidoo K. Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care. J Antimicrob Chemother 2018; 73:1138-1151. [PMID: 29360989 PMCID: PMC5909630 DOI: 10.1093/jac/dkx506] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant TB (DR-TB) remains a significant challenge in TB treatment and control programmes worldwide. Advances in sequencing technology have significantly increased our understanding of the mechanisms of resistance to anti-TB drugs. This review provides an update on advances in our understanding of drug resistance mechanisms to new, existing drugs and repurposed agents. Recent advances in WGS technology hold promise as a tool for rapid diagnosis and clinical management of TB. Although the standard approach to WGS of Mycobacterium tuberculosis is slow due to the requirement for organism culture, recent attempts to sequence directly from clinical specimens have improved the potential to diagnose and detect resistance within days. The introduction of new databases may be helpful, such as the Relational Sequencing TB Data Platform, which contains a collection of whole-genome sequences highlighting key drug resistance mutations and clinical outcomes. Taken together, these advances will help devise better molecular diagnostics for more effective DR-TB management enabling personalized treatment, and will facilitate the development of new drugs aimed at improving outcomes of patients with this disease.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Santhuri Rambaran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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Luo T, Yuan J, Peng X, Yang G, Mi Y, Sun C, Wang C, Zhang C, Bao L. Double mutation in DNA gyrase confers moxifloxacin resistance and decreased fitness of Mycobacterium smegmatis. J Antimicrob Chemother 2018; 72:1893-1900. [PMID: 28387828 DOI: 10.1093/jac/dkx110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 03/13/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives Ofloxacin and moxifloxacin are the most commonly used fluoroquinolones (FQs) for the treatment of tuberculosis. As a new generation FQ, moxifloxacin has been recommended for the treatment of ofloxacin-resistant TB. However, the mechanism by which ofloxacin-resistant Mycobacterium tuberculosis further gains resistance to moxifloxacin remains unclear. Methods We used Mycobacterium smegmatis as a model for studying FQ resistance in M. tuberculosis . Moxifloxacin-resistant M. smegmatis was selected in vitro based on strains with primary ofloxacin resistance. The gyrA and gyrB genes of the resistant strains were sequenced to identify resistance-associated mutations. An in vitro competition assay was applied to explore the influence of gyrA / gyrB mutations on bacterial fitness. Finally, we evaluated the clinical relevance of our findings by analysing the WGS data of 1984 globally collected M. tuberculosis strains. Results A total of 57 moxifloxacin-resistant M. smegmatis strains based on five ofloxacin-resistant strains were obtained. Sequencing results revealed that all moxifloxacin-resistant strains harboured second-step mutations in gyrA or gyrB . The relative fitnesses of the double-mutation strains varied from 0.65 to 0.93 and were mostly lower than those of their mono-mutation parents. From the genomic data, we identified 37 clinical M. tuberculosis strains harbouring double mutations in gyrA and/or gyrB and 36 of them carried at least one low-level FQ-resistance mutation. Conclusions Double mutation in DNA gyrase leads to moxifloxacin resistance and decreased fitness in M. smegmatis . Under current dosing of moxifloxacin, double mutations mainly happened in M. tuberculosis strains with primary low-level resistance mutations.
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Affiliation(s)
- Tao Luo
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Jinning Yuan
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Xuan Peng
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Guoping Yang
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Youjun Mi
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Changfeng Sun
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Chuhan Wang
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Chunxi Zhang
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Lang Bao
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
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Hameed HMA, Islam MM, Chhotaray C, Wang C, Liu Y, Tan Y, Li X, Tan S, Delorme V, Yew WW, Liu J, Zhang T. Molecular Targets Related Drug Resistance Mechanisms in MDR-, XDR-, and TDR- Mycobacterium tuberculosis Strains. Front Cell Infect Microbiol 2018; 8:114. [PMID: 29755957 PMCID: PMC5932416 DOI: 10.3389/fcimb.2018.00114] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/23/2018] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB) is a formidable infectious disease that remains a major cause of death worldwide today. Escalating application of genomic techniques has expedited the identification of increasing number of mutations associated with drug resistance in Mycobacterium tuberculosis. Unfortunately the prevalence of bacillary resistance becomes alarming in many parts of the world, with the daunting scenarios of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and total drug-resistant tuberculosis (TDR-TB), due to number of resistance pathways, alongside some apparently obscure ones. Recent advances in the understanding of the molecular/ genetic basis of drug targets and drug resistance mechanisms have been steadily made. Intriguing findings through whole genome sequencing and other molecular approaches facilitate the further understanding of biology and pathology of M. tuberculosis for the development of new therapeutics to meet the immense challenge of global health.
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Affiliation(s)
- H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Institute of Health Sciences, Anhui University, Hefei, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Vincent Delorme
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Wing W Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
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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.
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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
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Lee YS, Lee BY, Jo KW, Shim TS. Performance of the GenoType MTBDRsl assay for the detection second-line anti-tuberculosis drug resistance. J Infect Chemother 2017; 23:820-825. [PMID: 29066216 DOI: 10.1016/j.jiac.2017.08.010] [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] [Received: 06/06/2017] [Revised: 08/09/2017] [Accepted: 08/15/2017] [Indexed: 10/18/2022]
Abstract
The rapid detection of drug-resistant tuberculosis (TB) is important to improve treatment outcomes and prevent disease transmission. The GenoType MTBDRsl assay (MTBDRsl assay) was developed to detect fluoroquinolone (FQ) and second-line injectable drug (SLID) resistance. The aim of this study was to evaluate the performance and clinical utility of MTBDRsl assay. We retrospectively reviewed patient medical records with MTBDRsl assay data between December 2011 and February 2017. MTBDRsl assay results were compared with that of phenotypic drug susceptibility testing. In addition, treatment outcomes were analyzed to evaluate the clinical utility of the MTBDRsl assay. Among 107 clinical isolates (84 cultured isolates and 23 sputum specimens), 85 (79.4%) were multidrug-resistant TB and 9 (8.4%) were extensively drug-resistant TB (XDR-TB). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of MTBDRsl assay for detecting FQ resistance was 87.5%, 94.7%, 87.5%, 94.7%, and 92.5%, respectively. The sensitivity, specificity, PPV, NPV, and accuracy of MTBDRsl assay for detecting SLID resistance was 88.9%, 98.9%, 94.1%, 97.8%, and 97.2%, respectively. Novel drugs such as bedaquiline and linezolid were more commonly used in patients with FQ or SLID resistance detected by the MTBDRsl assay and, probably therefore, the treatment outcome was favorable irrespective of FQ or SLID resistance. The MTBDRsl assay could be used as a rule-in test to detect FQ and SLID resistance. By detecting FQ- and SLID-drug resistance rapidly, novel or repurposed drugs could be initiated earlier, suggesting that better treatment outcomes would be expected in patients with pre-XDR- and XDR-TB.
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Affiliation(s)
- Young Seok Lee
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Korea University Medical Center, Guro Hospital, Seoul, South Korea
| | - Bo Young Lee
- Division of Allergy and Respiratory Diseases, SoonChunHyang University Hospital, Seoul, South Korea
| | - Kyung-Wook Jo
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Tae Sun Shim
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
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Gupta SK, Drancourt M, Rolain JM. In Silico Prediction of Antibiotic Resistance in Mycobacterium ulcerans Agy99 through Whole Genome Sequence Analysis. Am J Trop Med Hyg 2017; 97:810-814. [PMID: 28749770 DOI: 10.4269/ajtmh.16-0478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Buruli ulcer is an emerging infectious disease caused by Mycobacterium ulcerans that has been reported from 33 countries. Antimicrobial agents either alone or in combination with surgery have been proved to be clinically relevant and therapeutic strategies have been deduced mainly from the empirical experience. The genome sequences of M. ulcerans strain AGY99, M. ulcerans ecovar liflandii, and three Mycobacterium marinum strains were analyzed to predict resistance in these bacteria. Fourteen putative antibiotic resistance genes from different antibiotics classes were predicted in M. ulcerans and mutation in katG (R431G) and pncA (T47A, V125I) genes were detected, that confer resistance to isoniazid and pyrazinamide, respectively. No mutations were detected in rpoB, gyrA, gyrB, rpsL, rrs, emb, ethA, 23S ribosomal RNA genes and promoter region of inhA and ahpC genes associated with resistance. Our results reemphasize the usefulness of in silico analysis for the prediction of antibiotic resistance in fastidious bacteria.
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Affiliation(s)
- Sushim Kumar Gupta
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278-IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278-IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278-IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
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Ahamad S, Rahman S, Khan FI, Dwivedi N, Ali S, Kim J, Imtaiyaz Hassan M. QSAR based therapeutic management of M. tuberculosis. Arch Pharm Res 2017; 40:676-694. [PMID: 28456911 DOI: 10.1007/s12272-017-0914-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/06/2017] [Indexed: 01/09/2023]
Abstract
Mycobacterium tuberculosis is responsible for severe mortality and morbidity worldwide but, under-developed and developing countries are more prone to infection. In search of effective and wide-spectrum anti-tubercular agents, interdisciplinary approaches are being explored. Of the several approaches used, computer based quantitative structure activity relationship (QSAR) have gained momentum. Structure-based drug design and discovery implies a combined knowledge of accurate prediction of ligand poses with the good prediction and interpretation of statistically validated models derived from the 3D-QSAR approach. The validated models are generally used to screen a small combinatorial library of potential synthetic candidates to identify hits which further subjected to docking to filter out compounds as novel potential emerging drug molecules to address multidrug-resistant tuberculosis. Several newer models are integrated to QSAR methods which include different types of chemical and biological data, and simultaneous prediction of pharmacological activities including toxicities and/or other safety profiles to get new compounds with desired activity. In the process, several newer molecules have been identified which are now being assessed for their clinical efficacy. Present review deals with the advances made in the field highlighting overall future prospects of the development of anti-tuberculosis drugs.
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Affiliation(s)
- Shahzaib Ahamad
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, 450001, China.,Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa
| | - Neeraja Dwivedi
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India.
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Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDR sl Assays. Antimicrob Agents Chemother 2017; 61:AAC.02169-16. [PMID: 28137812 PMCID: PMC5365657 DOI: 10.1128/aac.02169-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/16/2017] [Indexed: 11/20/2022] Open
Abstract
In this study, using the Hain GenoType MTBDRsl assays (versions 1 and 2), we found that some nonsynonymous and synonymous mutations in gyrA in Mycobacterium tuberculosis result in systematic false-resistance results to fluoroquinolones by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings.
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Viñuelas-Bayón J, Vitoria MA, Samper S. Rapid diagnosis of tuberculosis. Detection of drug resistance mechanisms. Enferm Infecc Microbiol Clin 2017; 35:520-528. [PMID: 28318570 DOI: 10.1016/j.eimc.2017.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 11/16/2022]
Abstract
Tuberculosis is still a serious public health problem, with 10.8 million new cases and 1.8 million deaths worldwide in 2015. The diversity among members of the Mycobacterium tuberculosis complex, the causal agent of tuberculosis, is conducive to the design of different methods for rapid diagnosis. Mutations in the genes involved in resistance mechanisms enable the bacteria to elude the treatment. We have reviewed the methods for the rapid diagnosis of M. tuberculosis complex and the detection of susceptibility to drugs, both of which are necessary to prevent the onset of new resistance and to establish early, appropriate treatment.
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Affiliation(s)
- Jesús Viñuelas-Bayón
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, España
| | - María Asunción Vitoria
- Servicio de Microbiología, Hospital Universitario Lozano Blesa, CIBERES, Zaragoza, España
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, IIS Aragón, CIBERES, Zaragoza, España.
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Su KY, Yan BS, Chiu HC, Yu CJ, Chang SY, Jou R, Liu JL, Hsueh PR, Yu SL. Rapid Sputum Multiplex Detection of the M. tuberculosis Complex (MTBC) and Resistance Mutations for Eight Antibiotics by Nucleotide MALDI-TOF MS. Sci Rep 2017; 7:41486. [PMID: 28134321 PMCID: PMC5278408 DOI: 10.1038/srep41486] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/21/2016] [Indexed: 01/29/2023] Open
Abstract
The increasing incidence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) adds further urgency for rapid and multiplex molecular testing to identify the MTB complex and drug susceptibility directly from sputum for disease control. A nucleotide matrix-assisted-laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based assay was developed to identify MTB (MTBID panel) and 45 chromosomal mutations for resistance to eight antibiotics (MTBDR panel). We conducted a 300 case trial from outpatients to evaluate this platform. An MTBID panel specifically identified MTB with as few as 10 chromosome DNA copies. The panel was 100% consistent with an acid-fast stain and culture for MTB, nontuberculous mycobacteria, and non-mycobacteria bacteria. The MTBDR panel was validated using 20 known MDR-MTB isolates. In a 64-case double-blind clinical isolates test, the sensitivity and specificity were 83% and 100%, respectively. In a 300-case raw sputum trial, the MTB identification sensitivity in smear-negative cases using MALDI-TOF MS was better than the COBAS assay (61.9% vs. 46.6%). Importantly, the failure rate of MALDI-TOF MS was better than COBAS (11.3% vs. 26.3%). To the best of our knowledge, the test described herein is the only multiplex test that predicts resistance for up to eight antibiotics with both sensitivity and flexibility.
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Affiliation(s)
- Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Bo-Shiun Yan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hao-Chieh Chiu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - So-Yi Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruwen Jou
- Centers for Disease Control, Taipei, Taiwan
| | - Jia-Long Liu
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Pathology and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Center for Optoelectronic Biomedicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, Taiwan
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Minovski N, Novič M. Integrated in Silico Methods for the Design and Optimization of Novel Drug Candidates. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although almost fully automated, the discovery of novel, effective, and safe drugs is still a long-term and highly expensive process. Consequently, the need for fleet, rational, and cost-efficient development of novel drugs is crucial, and nowadays the advanced in silico drug design methodologies seem to effectively meet these issues. The aim of this chapter is to provide a comprehensive overview of some of the current trends and advances in the in silico design of novel drug candidates with a special emphasis on 6-fluoroquinolone (6-FQ) antibacterials as potential novel Mycobacterium tuberculosis DNA gyrase inhibitors. In particular, the chapter covers some of the recent aspects of a wide range of in silico drug discovery approaches including multidimensional machine-learning methods, ligand-based and structure-based methodologies, as well as their proficient combination and integration into an intelligent virtual screening protocol for design and optimization of novel 6-FQ analogs.
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Evolution of Phenotypic and Molecular Drug Susceptibility Testing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:221-246. [PMID: 29116638 DOI: 10.1007/978-3-319-64371-7_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Drug Resistant Tuberculosis (DRTB) is an emerging problem world-wide. In order to control the disease and decrease the number of cases overtime a prompt diagnosis followed by an appropriate treatment should be provided to patients. Phenotypic DST based on liquid automated culture has greatly reduced the time needed to generate reliable data but has the drawback to be expensive and prone to contamination in the absence of appropriate infrastructures. In the past 10 years molecular biology tools have been developed. Those tools target the main mutations responsible for DRTB and are now globally accessible in term of cost and infrastructures needed for the implementation. The dissemination of the Xpert MTB/rif has radically increased the capacity to perform the detection of rifampicin resistant TB cases. One of the main challenges for the large scale implementation of molecular based tests is the emergence of conflicting results between phenotypic and genotypic tests. This mines the confidence of clinicians in the molecular tests and delays the initiation of an appropriate treatment. A new technique is revolutionizing the genotypic approach to DST: the WGS by Next-Generation Sequencing technologies. This methodology promises to become the solution for a rapid access to universal DST, able indeed to overcome the limitations of the current phenotypic and genotypic assays. Today the use of the generated information is still challenging in decentralized facilities due to the lack of automation for sample processing and standardization in the analysis.The growing knowledge of the molecular mechanisms at the basis of drug resistance and the introduction of high-performing user-friendly tools at peripheral level should allow the very much needed accurate diagnosis of DRTB in the near future.
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DC-159a Shows Inhibitory Activity against DNA Gyrases of Mycobacterium leprae. PLoS Negl Trop Dis 2016; 10:e0005013. [PMID: 27681932 PMCID: PMC5040261 DOI: 10.1371/journal.pntd.0005013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/30/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Fluoroquinolones are a class of antibacterial agents used for leprosy treatment. Some new fluoroquinolones have been attracting interest due to their remarkable potency that is reportedly better than that of ofloxacin, the fluoroquinolone currently recommended for treatment of leprosy. For example, DC-159a, a recently developed 8-methoxy fluoroquinolone, has been found to be highly potent against various bacterial species. Nonetheless, the efficacy of DC-159a against Mycobacterium leprae is yet to be examined. METHODOLOGY/PRINCIPAL FINDINGS To gather data that can support highly effective fluoroquinolones as candidates for new remedies for leprosy treatment, we conducted in vitro assays to assess and compare the inhibitory activities of DC-159a and two fluoroquinolones that are already known to be more effective against M. leprae than ofloxacin. The fluoroquinolone-inhibited DNA supercoiling assay using recombinant DNA gyrases of wild type and ofloxacin-resistant M. leprae revealed that inhibitory activities of DC-159a and sitafloxacin were at most 9.8- and 11.9-fold higher than moxifloxacin. Also the fluoroquinolone-mediated cleavage assay showed that potencies of those drugs were at most 13.5- and 9.8-fold higher than moxifloxacin. In addition, these two drugs retained their inhibitory activities even against DNA gyrases of ofloxacin-resistant M. leprae. CONCLUSIONS/SIGNIFICANCE The results indicated that DC-159a and sitafloxacin are more effective against wild type and mutant M. leprae DNA gyrases than moxifloxacin, suggesting that these antibacterial drugs can be good candidates that may supersede current fluoroquinolone remedies. DC-159a in particular is very promising because it is classified in a subgroup of fluoroquinolones that is known to be less likely to cause adverse effects. Our results implied that DC-159a is well worth further investigation to ascertain its in vivo effectiveness and clinical safety for humans.
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Sequence Analysis of Fluoroquinolone Resistance-Associated Genes gyrA and gyrB in Clinical Mycobacterium tuberculosis Isolates from Patients Suspected of Having Multidrug-Resistant Tuberculosis in New Delhi, India. J Clin Microbiol 2016; 54:2298-305. [PMID: 27335153 DOI: 10.1128/jcm.00670-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/17/2016] [Indexed: 11/20/2022] Open
Abstract
Fluoroquinolones (FQs) are broad-spectrum antibiotics recommended for the treatment of multidrug-resistant tuberculosis (MDR-TB) patients. FQ resistance, caused by mutations in the gyrA and gyrB genes of Mycobacterium tuberculosis, is increasingly reported worldwide; however, information on mutations occurring in strains from the Indian subcontinent is scarce. Hence, in this study, we aimed to characterize mutations in the gyrA and gyrB genes of acid-fast bacillus (AFB) smear-positive sediments or of M. tuberculosis isolates from AFB smear-negative samples from patients in India suspected of having MDR-TB. A total of 152 samples from patients suspected of having MDR-TB were included in the study. One hundred forty-six strains detected in these samples were characterized by sequencing of the gyrA and gyrB genes. The extracted DNA was subjected to successive amplifications using a nested PCR protocol, followed by sequencing. A total of 27 mutations were observed in the gyrA genes of 25 strains, while no mutations were observed in the gyrB genes. The most common mutations occurred at amino acid position 94 (13/27 [48.1%]); of these, the D94G mutation was the most prevalent. The gyrA mutations were significantly associated with patients with rifampin (RIF)-resistant TB. Heterozygosity was seen in 4/27 (14.8%) mutations, suggesting the occurrence of mixed populations with different antimicrobial susceptibilities. A high rate of FQ-resistant mutations (17.1%) was obtained among the isolates of TB patients suspected of having MDR-TB. These observations emphasize the need for accurate and rapid molecular tests for the detection of FQ-resistant mutations at the time of MDR-TB diagnosis.
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50
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Description of compensatorygyrAmutations restoring fluoroquinolone susceptibility inMycobacterium tuberculosis. J Antimicrob Chemother 2016; 71:2428-31. [DOI: 10.1093/jac/dkw169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 04/11/2016] [Indexed: 11/14/2022] Open
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