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Coban AY. A novel agar base medium for drug susceptibility testing of Mycobacterium tuberculosis isolates. Future Microbiol 2021; 16:949-953. [PMID: 34384261 DOI: 10.2217/fmb-2021-0032] [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: 11/21/2022] Open
Abstract
Aim: In this study, it was aimed to evaluate AYC.2.2 agar for susceptibility testing of Mycobacterium tuberculosis clinical isolates against first-line drugs. Materials & methods: In the present study, 208 M. tuberculosis clinical isolates were tested on AYC.2.2 agar, which was previously validated for the first-line drugs isoniazid, rifampicin, streptomycin and ethambutol. Results: Specificity, sensitivity, positive predictive value, negative predictive value and agreement for isoniazid-rifampicin-ethambutol-streptomycin were 100-100-97.2-99.3%, 94.8-94.8-79.3-94.3%, 100-100-82.1-98.03%, 97.03-98.03-96.7-98.08%, 98.07-98.5-94.7-98.07%, respectively. Conclusion: Results had shown that the newly developed AYC.2.2 agar promises as an alternative medium that can be used to perform susceptibility testing of M. tuberculosis isolates. However, further multicenter studies are needed to be used in routine mycobacteriology laboratories.
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Affiliation(s)
- Ahmet Yilmaz Coban
- Akdeniz University Tuberculosis Research Center, Antalya, Turkey.,Department of Nutrition & Dietetics, Akdeniz University Faculty of Health Sciences, Antalya, Turkey.,Department of Medical Biotechnology, Akdeniz University Institute of Health Sciences, Antalya, Turkey
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Rakhmawatie MD, Wibawa T, Lisdiyanti P, Pratiwi WR, Mustofa. Evaluation of crystal violet decolorization assay and resazurin microplate assay for antimycobacterial screening. Heliyon 2019; 5:e02263. [PMID: 31497667 PMCID: PMC6722264 DOI: 10.1016/j.heliyon.2019.e02263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/28/2019] [Accepted: 08/06/2019] [Indexed: 11/29/2022] Open
Abstract
The main obstacle in antimycobacterial discovery is the extremely slow growth rates of pathogenic mycobacteria that lead to the long incubation times needed in antimycobacterial screening. Some in vitro testings has been developed and are currently available for antimycobacterial screening. The aim of the study was to compare Resazurin Microplate Assay (REMA) and Crystal Violet Decolorization Assay (CVDA) for testing mycobacteria susceptibility to isoniazid and rifampicin as well as for antimycobacterial screening of natural products (NP). Mycobacterium tuberculosis strain H37Rv and Mycobacterium smegmatis strain mc2 155 were used as tested mycobacteria. Serial two-fold dilutions from 0.0625 to 1.0 μg/mL for the isoniazid and rifampicin and from 6.25 to 100.0 μg/mL for the NP A and B were prepared. Tested mycobacteria were then incubated with tested drugs or NPs in each growth medium at 37 °C for 7 days for M. tuberculosis and 3 days for M. smegmatis. MIC values against M. tuberculosis were interpreted 24-48 h after adding resazurin or at least 72 h after adding crystal violet, whereas MIC values against M. smegmatis were interpreted 1 h after adding resazurin or 24 h after adding crystal violet. The MIC values against M. tuberculosis interpreted by REMA were 0.0625, 0.0625, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively, and those interpreted by CVDA were 0.0625, 0.0625, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively. Moreover, the MIC values against M. smegmatis interpreted by REMA were 0.0625, >1, 6.25, and 100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively, and those interpreted by CVDA were 0.125, >1, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, NP B respectively. In conclusion, REMA is faster and easier than CVDA to interpret MIC values, however CVDA produces higher MIC values than REMA for rifampicin and NP B in M. smegmatis susceptibility testing. Therefore, REMA and CVDA can be used for antimycobacterial screening.
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Affiliation(s)
- Maya Dian Rakhmawatie
- Doctoral Program in Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Muhammadiyah Semarang, Semarang, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences, Bogor, Indonesia
| | - Woro Rukmi Pratiwi
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mustofa
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Coban AY, Akbal AU, Ceyhan I, Uzun M, Sertel Selale D, Aslan G, Delialioglu N, Ozyurt M, Bektore B, Bicmen C, Aslanturk A, Ucarman N, Albay A, Sig AK, Ozkutuk N, Surucuoglu S. A new colorimetric method for rapid detection of ethambutol and streptomycin resistance in Mycobacterium tuberculosis: crystal violet decolorization assay (CVDA). Antonie van Leeuwenhoek 2018; 112:679-685. [PMID: 30417212 DOI: 10.1007/s10482-018-1198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/02/2018] [Indexed: 10/27/2022]
Abstract
Streptomycin (STR) and ethambutol (EMB) are important drugs used for the treatment of tuberculosis. There is a need for fast, reliable and inexpensive methods for detecting resistance to these drugs. The aim of this study was to evaluate the performance of the crystal violet decolorization assay (CVDA) for the detection of STR and EMB resistance that is important drugs in tuberculosis treatment. In this study, drug susceptibility testing was performed on 140 Mycobacterium tuberculosis isolates provided from nine centers. Three tubes were used for each isolate. One of the tubes had a concentration of 2 mg/L STR and the other 5 mg/L EMB. The third was drug-free control tube. Sensitivity, specificity, positive predictive value (PPD), negative predictive value (NPD) and agreement for STR were found to be 81.8%, 94.6%, 87.8%, 91.5% and 90.57%, respectively. For EMB, sensitivity, specificity, PPD, NPD, and agreement were found to be 76%, 98.23%, 90.47%, 94.87% and 94.2%, respectively. The results were obtained in 11.3 ± 2.7 days (8-21 days). CVDA is rapid, reliable, inexpensive, and easy to perform for rapid detection of STR and EMB resistance, and it could be adapted for drug susceptibility testing.
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Affiliation(s)
- Ahmet Yilmaz Coban
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Akdeniz University, Antalya, Turkey.
| | - Ahmet Ugur Akbal
- Department of Medical Microbiology, Ondokuz Mayis University Medical School, Samsun, Turkey
| | - Ismail Ceyhan
- Medical Microbiology Laboratory, Ataturk Chest Disease and Chest Surgery Training and Research Hospital, Ankara, Turkey
| | - Meltem Uzun
- Department of Medical Microbiology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Deniz Sertel Selale
- Department of Medical Microbiology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Gonul Aslan
- Department of Medical Microbiology, Mersin University Medical School, Mersin, Turkey
| | - Nuran Delialioglu
- Department of Medical Microbiology, Mersin University Medical School, Mersin, Turkey
| | - Mustafa Ozyurt
- Department of Medical Microbiology, Sultan Abdulhamit Han Training and Research Hospital, Gulhane Medical School, Health Sciences University, Istanbul, Turkey
| | - Beyhan Bektore
- Department of Medical Microbiology, Sultan Abdulhamit Han Training and Research Hospital, Gulhane Medical School, Health Sciences University, Istanbul, Turkey
| | - Can Bicmen
- Medical Microbiology Laboratory, University of Health Sciences, Dr. Suat Seren Chest Diseases and Surgery Training and Research Hospital, Izmir, Turkey
| | - Ahmet Aslanturk
- Tuberculosis Reference Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Nilay Ucarman
- Tuberculosis Reference Laboratory, Public Health Agency of Turkey, Ankara, Turkey
| | - Ali Albay
- Department of Medical Microbiology, Gulhane Medical School, Health Sciences University, Ankara, Turkey
| | - Ali Korhan Sig
- Department of Medical Microbiology, Gulhane Medical School, Health Sciences University, Ankara, Turkey
| | - Nuri Ozkutuk
- Department of Medical Microbiology, Celal Bayar University Medical School, Manisa, Turkey
| | - Suheyla Surucuoglu
- Department of Medical Microbiology, Celal Bayar University Medical School, Manisa, Turkey
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Chen L, Li H, Chen T, Yu L, Guo H, Chen Y, Chen M, Li Z, Wu Z, Wang X, Zhao J, Yan H, Wang X, Zhou L, Zhou J. Genome-wide DNA methylation and transcriptome changes in Mycobacterium tuberculosis with rifampicin and isoniazid resistance. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3036-3045. [PMID: 31938429 PMCID: PMC6958063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/11/2018] [Indexed: 06/10/2023]
Abstract
We investigated the genome-wide DNA methylation and transcriptome changes in M. tuberculosis with rifampicin or isoniazid resistance. Single-molecule real-time (SMRT) sequencing and microarray technology were performed to expound DNA methylation profiles and differentially expressed genes in rifampicin or isoniazid resistant M. tuberculosis. Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis and methylated regulatory network analysis were conducted by online forecasting databases. Integrated analysis of DNA methylation and transcriptome revealed that 335 differentially methylated genes (175 hypermethylated and 160 hypomethylated) and 132 significant differentially expressed genes (68 up-regulated and 63 down-regulated) were found to be regulated by both rifampicin and isoniazid in M. tuberculosis H37Rv. Correlation analysis showed that differential methylated genes were negatively correlated with their transcriptional levels in rifampicin or isoniazid resistant strains. KEGG pathway analysis indicated that nitrogen metabolism pathway is closely related to differentially methylated genes induced by rifampicin and isoniazid. KEGG also suggested that differentially expressed genes in rifampicin or isoniazid-resistant strains may play different roles in regulating signal transduction events. Furthermore, five differentially methylated candidate genes (Rv0840c, Rv2243, Rv0644c, Rv2386c and Rv1130) in rifampicin resistant strains and three genes (Rv0405, Rv0252 and Rv0908) in isoniazid-resistant strains were verified the existence of protein-protein interaction in STRING database. Integrated DNA methylation and transcriptome analyses provide an epigenetic overview of rifampicin and isoniazid-induced antibiotic resistance in M. tuberculosis H37Rv. Several interesting genes and regulatory pathways may provide valuable resources for epigenetic studies in M. tuberculosis antibiotic resistance.
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Affiliation(s)
- Liang Chen
- Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Haicheng Li
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Tao Chen
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Li Yu
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Huixin Guo
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Yuhui Chen
- Outpatient Office, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Mu Chen
- Department of Respiration, The Sixth Affiliated Hospital of SUN YAT-SEN UniversityGuangzhou 510655, China
| | - Zhenyan Li
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Zhuhua Wu
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Xuezhi Wang
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Jiao Zhao
- Medical College of Jinan UniversityGuangzhou, China
| | - Huimin Yan
- Guangdong Medical UniversityDongguan, China
| | - Xinchun Wang
- Reference Laboratory, Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Lin Zhou
- Centre for Tuberculosis Control of Guangdong ProvinceGuangzhou, China
| | - Jie Zhou
- The Forth People’s Hospital of FoshanFoshan, 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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Cunha MS, Ribeiro CEP, Corrêa CC, Diniz R. The Hirshfeld surface of three new isonicotinylhydrazine co-crystals: Comparison of hydrogen bonds and crystal structures. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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