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Zhu Y, Feng Z, Xu Y, Luo S, Zhang R, Shi X, Wu X, Zhang H. Rapid detection of Mycobacterium tuberculosis based on cyp141 via real-time fluorescence loop-mediated isothermal amplification (cyp141-RealAmp). Front Cell Infect Microbiol 2024; 14:1349063. [PMID: 38938885 PMCID: PMC11208306 DOI: 10.3389/fcimb.2024.1349063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/06/2024] [Indexed: 06/29/2024] Open
Abstract
Background The rapid detection of Mycobacterium tuberculosis (MTB) is essential for controlling tuberculosis. Methods We designed a portable thermocycler-based real-time fluorescence loop-mediated isothermal amplification assay (cyp141-RealAmp) using six oligonucleotide primers derived from cyp141 to detect MTB. A combined number of 213 sputum samples (169 obtained from clinically diagnosed cases of pulmonary TB and 44 from a control group without tuberculosis) underwent Acid-fast bacillus (AFB) smear, culture, Xpert MTB/RIF assays, and cyp141-RealAmp assay. Results By targeting MTB cyp141, this technique could detect as low as 10 copies/reaction within 30 min, and it was successfully rejected by other mycobacteria and other bacterial species tested. Of the 169 patients, there was no statistical difference between the detection rate of cyp141-RealAmp (92.90%, 95% CI: 89.03-96.07) and that of Xpert MTB/RIF (94.67%, 95% CI: 91.28-98.06) (P > 0.05), but both were statistically higher than that of culture (65.68%, 95% CI: 58.52-72.84) (P< 0.05) and AFB (57.40%, 95% CI: 49.94-64.86) (P< 0.05). Both cyp141-RealAmp and Xpert MTB/RIF had a specificity of 100%. Furthermore, a high concordance between cyp141-RealAmp and Xpert MTB/RIF was found (Kappa = 0.89). Conclusion The cyp141-RealAmp assay was shown to be effective, responsive, and accurate in this study. This method offers a prospective strategy for the speedy and precise detection of MTB.
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Affiliation(s)
- Yinyin Zhu
- Department of Microbial Testing, Nanjing Center for Disease Control and Prevention Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zi Feng
- Department of Microbial Testing, Nanjing Center for Disease Control and Prevention Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yinfang Xu
- Department of Infectious Diseases, the Affiliated Zhongda Hospital of Southeast University, Nanjing, Jiangsu, China
| | - Sha Luo
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Ruixian Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xudong Shi
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xuping Wu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Hongying Zhang
- Department of Microbial Testing, Nanjing Center for Disease Control and Prevention Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
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Lu Y, Chen H, Shao Z, Sun L, Li C, Lu Y, You X, Yang X. Deletion of the Mycobacterium tuberculosis cyp138 gene leads to changes in membrane-related lipid composition and antibiotic susceptibility. Front Microbiol 2024; 15:1301204. [PMID: 38591032 PMCID: PMC10999552 DOI: 10.3389/fmicb.2024.1301204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/01/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction Mycobacterium tuberculosis (Mtb), the main cause of tuberculosis (TB), has brought a great burden to the world's public health. With the widespread use of Mtb drug-resistant strains, the pressure on anti-TB treatment is increasing. Anti-TB drugs with novel structures and targets are urgently needed. Previous studies have revealed a series of CYPs with important roles in the survival and metabolism of Mtb. However, there is little research on the structure and function of CYP138. Methods In our study, to discover the function and targetability of CYP138, a cyp138-knockout strain was built, and the function of CYP138 was speculated by the comparison between cyp138-knockout and wild-type strains through growth curves, growth status under different carbon sources, infection curves, SEM, MIC tests, quantitative proteomics, and lipidomics. Results and discussion The knockout of cyp138 was proven to affect the Mtb's macrophage infection, antibiotics susceptibility, and the levels of fatty acid metabolism, membrane-related proteins, and lipids such as triacylglycerol. We proposed that CYP138 plays an important role in the synthesis and decomposition of lipids related to the cell membrane structure as a new potential anti-tuberculosis drug target.
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Affiliation(s)
- Yun Lu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division for Medicinal Microorganisms-related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, China
| | - Hongtong Chen
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division for Medicinal Microorganisms-related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhiyuan Shao
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division for Medicinal Microorganisms-related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lang Sun
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division for Medicinal Microorganisms-related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Congran Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division for Medicinal Microorganisms-related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, China
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xuefu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division for Medicinal Microorganisms-related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division for Medicinal Microorganisms-related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing, China
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Díaz-Storani L, Clary AA, Moreno DM, Ballari MS, Porta EOJ, Bracca ABJ, Johnston JB, Labadie GR. Synthesis and interaction of terminal unsaturated chemical probes with Mycobacterium tuberculosis CYP124A1. Bioorg Med Chem 2021; 44:116304. [PMID: 34289431 DOI: 10.1016/j.bmc.2021.116304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022]
Abstract
A series of C15-C20 isoprenyl derivatives bearing terminal alkenyl and alkynyl groups were synthesized as possible substrates of the methyl-branched lipid ω-hydroxylase CYP124A1 from Mycobacterium tuberculosis. The interactions of each compound with the enzyme active site were characterized using UV-vis spectroscopy. We found that C10 and C15 analogs bind with similar affinity to the corresponding parent C10 and C15 substrates geraniol and farnesol, respectively. Three analogs (C10-ω-ene, C10-ω-yne, C15-ω-yne) interact with the proximal side of the heme iron by coordinating to the oxygen atom of the ferric heme, as judged by the appearance of typical Type-IA binding spectra. On the other hand, the C15-ω-ene analog interacts with the ferric heme by displacing the bound water that generates a typical Type I binding spectrum. We were unable to detect P450-mediated oxidation of these probes following extended incubations with CYP124A1 in our reconstituted assay system, whereas a control reaction containing farnesol was converted to ω-hydroxy farnesol under the same conditions. To understand the lack of detectable oxidation, we explored the possibility that the analogs were acting as mechanism-based inhibitors, but we were unable to detect time-dependent loss of enzymatic activity. In order to gain insight into the lack of detectable turnover or time-dependent inhibition, we examined the interaction of each compound with the CYP124A1 active site using molecular docking simulations. The docking studies revealed a binding mode where the terminal unsaturated functional groups were sequestered within the methyl-binding pocket, rather than positioned close to the heme iron for oxidation. These results aid in the design of specific inhibitors of Mtb-CYP124A1, an interesting enzyme that is implicated in the oxidation of methyl-branched lipids, including cholesterol, within a deadly human pathogen.
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Affiliation(s)
- Luz Díaz-Storani
- Instituto de Química Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Anaelle A Clary
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517, United States
| | - Diego M Moreno
- Instituto de Química Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - María Sol Ballari
- Instituto de Química Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Exequiel O J Porta
- Instituto de Química Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Andrea B J Bracca
- Instituto de Química Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Jonathan B Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517, United States.
| | - Guillermo R Labadie
- Instituto de Química Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina.
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Evaluating the Frequency of Resistance to Pyrazinamide Among Drug-resistant Strains of Mycobacterium tuberculosis in Isfahan, Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2021. [DOI: 10.5812/archcid.101092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background: Pyrazinamide is one of the most important first-line medications for the treatment of tuberculosis and an alternative intake for MDR-TB and XDR-TB patients. Objectives: The purpose of this study was to evaluate resistance to pyrazinamide in the isolates resistant to the Mycobacterium tuberculosis drug in patients in the city of Isfahan. Methods: In this study, the drug susceptibility test was performed with pyrazinamide using the proportion method and PZA assay on 47 isolates resistant to Mycobacterium tuberculosis. Then, the mutations of the pncA and rpsA genes of the isolates resistant to pyrazinamide were evaluated by the sequencing method. Results: According to the proportion method, 19 cases were resistant to pyrazinamide, 16 of which had mutations in their pncA and rpsA genes. Besides, five new mutations were recorded, and three isolates lacked mutations in the mentioned genes. Conclusions: Pyrazinamide resistance is high in MDR-TB and INH mono-resistant isolates. Therefore, evaluating the susceptibility to pyrazinamide in patients with MDR-TB before the initiation of treatment with pyrazinamide is considered essential.
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Performance of the Abbott RealTime MTB and RIF/INH resistance assays for the detection of Mycobacterium Tuberculosis and resistance markers in sputum specimens. PLoS One 2021; 16:e0251602. [PMID: 33979395 PMCID: PMC8115802 DOI: 10.1371/journal.pone.0251602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
Background The Abbott RealTime MTB is an assay for the detection of Mycobacterium tuberculosis (MTB) complex DNA from respiratory specimens in combination with the Abbott RealTime RIF/INH assay for the detection of genetic resistance markers for isoniazid (INH) and rifampicin (RIF) from MTB positive isolates. Hence, this study aimed to evaluate the performance of the Abbott RealTime MTB and RIF/INH assays. Methods A cross-sectional study was conducted on 289 study subjects presumptive to have pulmonary tuberculosis at Nigist Eleni Mohammed Memorial Hospital, South Ethiopia from April 2017 to June 2018. Two morning expectorated sputum specimens were collected from each study participant. One sample was tested directly by Xpert MTB/RIF assay at Nigist Eleni Mohammed Memorial Hospital and the other sample was used for smear microscopy, TB culture, Abbott RealTime MTB, and Abbott RealTime INH/RIF assays at International Clinical Laboratories, Addis Ababa, Ethiopia. The diagnostic performance of the Abbott RealTime MTB and INH/RIF assays were calculated against MGIT liquid culture and phenotypic drug susceptibility testing (DST) as the gold standard. Results For the detection of MTB the Abbott RealTime MTB assay exhibited sensitivity 92.4% (95% CI 83.6–96.9), specificity 95.4% (95% CI 91.1–97.7), PPV 89.0% (95% CI 79.7–94.5) and NPV 96.9% (95% CI 93.0–98.7). For the detection of RIF resistance MTB, Abbott RealTime MTB RIF/INH concurred with phenotypic DST and Xpert MTB/RIF, while for the detection of INH resistance MTB, the sensitivity, specificity, PPV and NPV of the Abbott MTB RIF/INH assay was 84.2% (95% CI 60.4–96.6), 100% (95% CI 89.7–100), 100% and 91.9% (95% CI 80.0–96.9), respectively. Conclusions The Abbott RTMTB and RIF/INH assays revealed high sensitivity and specificity in MTB diagnosis and provided reliable INH and RIF resistance profiles. This assay has a similar diagnostic performance to the Xpert MTB/RIF assay with the advantages of high-throughput.
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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Salehi M, Abdizadeh R, Pourgheysari B, Zamanzad B, Soltani A, Gholipour A, Heidari R. Evaluation of cellular immunogenicity of recombinant cytochrome p450 cyp141 protein of Mycobacterium tuberculosis in human and mouse model. Biologicals 2018; 52:25-29. [PMID: 29428196 DOI: 10.1016/j.biologicals.2018.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 09/11/2017] [Accepted: 01/29/2018] [Indexed: 11/28/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is still considered one of the unsolved problems for the World Health Organization Identifying and selecting an immunogenic antigen capable of generating specific immune responses is generally the goal of all studies being carried out in to designing new vaccines. Accordingly, the present study was conducted to evaluate the immunogenicity of a M. tuberculosis recombinant protein which exist in the regions of the bacterium genome and may be an immunogenic protein. Immunogenicity of purified proteins was measured by PBMC and mouse spleen lymphocytes culturing methods using ELISA after an appropriate amount of time of incubation with Recombinant cytochrome P450 CYP141 protein. Cellular immune responses were determined and compared by measuring IFN-γ and IL4 in human, and mouse groups. The results revealed a high level of IFN-γ in PPD + individuals and the mice immunized with protein and adjuvant. Recombinant cytochrome P450 CYP141 protein proved capable of generating an immune response in mice and people with a history of previous encounters with Mycobacterium tuberculosis bacteria. It, could be considered a tuberculosis vaccine candidate in order to induce a specific effective immune response in both mice and humans.
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Affiliation(s)
- Mahshid Salehi
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Sharekord University of Medical Sciences, Sharekord, IR, Iran; Department of Provincial Health Lab, Laboratory Regional Tuberculosis Reference, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Batoul Pourgheysari
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Behnam Zamanzad
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Sharekord University of Medical Sciences, Sharekord, IR, Iran.
| | - Amin Soltani
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Sharekord University of Medical Sciences, Sharekord, IR, Iran.
| | - Abolfazl Gholipour
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Sharekord University of Medical Sciences, Sharekord, IR, Iran.
| | - Reza Heidari
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Sharekord University of Medical Sciences, Sharekord, IR, Iran.
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Genotyping of Mycobacterium tuberculosis Isolates from Hormozgan Province of Iran Based on 15-Locus MIRU-VNTR and Spoligotyping. INTERNATIONAL JOURNAL OF BACTERIOLOGY 2016; 2016:7146470. [PMID: 27819023 PMCID: PMC5081880 DOI: 10.1155/2016/7146470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/25/2016] [Indexed: 11/17/2022]
Abstract
Background. Considering that Hormozgan province in Iran (southern part of Iran on the Persian Gulf) is among the areas with high prevalence of MDR-MTB and attracts so many sailors and tourists, genetic diversity of MTB isolates circulating in this part of Iran was evaluated. Pattern of TB transmission was also examined. Methods and Material. A total of 38 isolates of MTB were cultured from TB patients from Hormozgan province of Iran and standard MIRU-VNTR typing and spoligotyping were applied to genotype these isolates. Drug susceptibility testing was performed using proportion method. Results. There were 28 VNTR profiles comprising 5 clusters and 23 unique isolates compared to 21 spoligotyping profiles, which contained 9 clusters and 12 unique isolates. Latin American-Mediterranean (n = 9, 23.6%) was found to be the most predominant lineage. MIRU-VNTR analysis, with an HGDI of 0.975, was more discriminating than spoligotyping, which had an HGDI of 0.955. The estimated proportion of TB cases due to recent transmission was 26.3% and 44.7% by MIRU-VNTR and spoligotyping, respectively. The rates of monodrug resistance and MDR were 15.8% and 7.9%, respectively. Two of 3 MDR strains were found to be related to MIRU-VNTR and belonged to the same spoligotyping cluster characterized with T1/SIT53 genotype. Conclusions. The high genetic diversity among MTB isolates suggests that transmission occurred from different sources to this area. Reactivation of a priori, latent MTB infection was found to contribute mainly to TB cases in this geographic region.
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Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s. Sci Rep 2016; 6:33099. [PMID: 27616185 PMCID: PMC5018878 DOI: 10.1038/srep33099] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/19/2016] [Indexed: 12/27/2022] Open
Abstract
Since the initial identification of cytochrome P450 monooxygenases (CYPs/P450s), great progress has been made in understanding their structure-function relationship, diversity and application in producing compounds beneficial to humans. However, the molecular evolution of P450s in terms of their dynamics both at protein and DNA levels and functional conservation across kingdoms still needs investigation. In this study, we analyzed 17 598 P450s belonging to 113 P450 families (bacteria -42; fungi -19; plant -28; animal -22; plant and animal -1 and common P450 family -1) and found highly conserved and rapidly evolving P450 families. Results suggested that bacterial P450s, particularly P450s belonging to mycobacteria, are highly conserved both at protein and DNA levels. Mycobacteria possess the highest P450 diversity percentage compared to other microbes and have a high coverage of P450s (≥1%) in their genomes, as found in fungi and plants. Phylogenetic and functional analyses revealed the functional conservation of P450s despite belonging to different biological kingdoms, suggesting the adherence of P450s to their innate function such as their involvement in either generation or oxidation of steroids and structurally related molecules, fatty acids and terpenoids. This study's results offer new understanding of the dynamic structural nature of P450s.
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Darban-Sarokhalil D, Nasiri MJ, Fooladi AAI, Heidarieh P, Feizabadi MM. Rapid Detection of Rifampicin- and Isoniazid-Resistant Mycobacterium tuberculosis using TaqMan Allelic Discrimination. Osong Public Health Res Perspect 2016; 7:127-30. [PMID: 27169012 PMCID: PMC4850365 DOI: 10.1016/j.phrp.2016.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/27/2015] [Accepted: 01/06/2016] [Indexed: 11/04/2022] Open
Abstract
Objectives Multidrug-resistant tuberculosis (MDR-TB) is a global problem that many countries are challenged with. Rapid and accurate detection of MDR-TB is critical for appropriate treatment and controlling of TB. The aim of the present study was to evaluate the TaqMan allelic discrimination without minor groove binder (MGB) as a rapid, efficient, and low-cost method for detection of drug resistant strains of Mycobacterium tuberculosis. Methods A total of 112 M. tuberculosis isolates from cases with diagnosed TB were subjected to drug susceptibility testing (DST), using the proportion method. Resistant isolates were tested for characterization of mutations in the rpoB and KatG genes by TaqMan genotyping. Results Of 112 M. tuberculosis isolates for which DST was performed, three, one, and two isolates were MDR, rifampin (RIF) resistant, and isoniazid (INH) resistant, respectively. According to the threshold cycle (Ct) and curve pattern of mutants, TaqMan probes detect all of the mutations in the analyzed genes (katG 315, AGC→ACC, rpoB 531, TCG→TTG, and rpoB 531, TCG→TGG). Conclusion The present study suggests that drug-resistant strains of M. tuberculosis can be detected by pattern’s curve or Ct with TaqMan probes without MGB in real-time polymerase chain reaction (PCR).
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Affiliation(s)
- Davood Darban-Sarokhalil
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad J Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas A I Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Parvin Heidarieh
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad M Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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katG Ser315 and rpoB 81-bp hotspot region substitutions: Reliability for detection of drug-resistant strains of Mycobacterium tuberculosis. J Glob Antimicrob Resist 2015; 5:92-3. [PMID: 27436477 DOI: 10.1016/j.jgar.2015.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/24/2015] [Accepted: 12/01/2015] [Indexed: 11/21/2022] Open
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Functional analysis and crystallographic structure of clotrimazole bound OleP, a cytochrome P450 epoxidase from Streptomyces antibioticus involved in oleandomycin biosynthesis. Biochim Biophys Acta Gen Subj 2015; 1860:465-75. [PMID: 26475642 DOI: 10.1016/j.bbagen.2015.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/05/2015] [Accepted: 10/12/2015] [Indexed: 11/23/2022]
Abstract
BACKGROUND OleP is a cyt P450 from Streptomyces antibioticus carrying out epoxigenation of the antibiotic oleandomycin during its biosynthesis. The timing of its reaction has not been fully clarified, doubts remain regarding its substrate and catalytic mechanism. METHODS The crystal structure of OleP in complex with clotrimazole, an inhibitor of P450s used in therapy, was solved and the complex formation dynamics was characterized by equilibrium and kinetic binding studies and compared to ketoconazole, another azole differing for the N1-substituent. RESULTS Clotrimazole coordinates the heme and occupies the active site. Most of the residues interacting with clotrimazole are conserved and involved in substrate binding in MycG, the P450 epoxigenase with the highest homology with OleP. Kinetic characterization of inhibitor binding revealed OleP to follow a simple bimolecular reaction, without detectable intermediates. CONCLUSIONS Clotrimazole-bound OleP adopts an open form, held by a π-π stacking chain that fastens helices F and G and the FG loop. Affinity is affected by the interactions of the N1 substituent within the active site, given the one order of magnitude difference of the off-rate constants between clotrimazole and ketoconazole. Based on structural similarities with MycG, we propose a binding mode for both oleandomycin intermediates, that are the candidate substrates of OleP. GENERAL SIGNIFICANCE Among P450 epoxigenases OleP is the only one that introduces an epoxide on a non-activated C–C bond. The data here presented are necessary to understand the rare chemistry carried out by OleP, to engineer it and to design more selective and potent P450-targeted drugs.
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Heidari R, Rabiee-Faradonbeh M, Darban-Sarokhalil D, Alvandi A, Abdian N, Aryan E, Soleimani N, Gholipour A. Expression and Purification of the Recombinant Cytochrome P450 CYP141 Protein of Mycobacterium Tuberculosis as a Diagnostic Tool and Vaccine Production. IRANIAN RED CRESCENT MEDICAL JOURNAL 2015; 17:e23191. [PMID: 26380105 PMCID: PMC4568075 DOI: 10.5812/ircmj.23191v2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/27/2014] [Accepted: 03/15/2015] [Indexed: 12/02/2022]
Abstract
Background: Tuberculosis (TB) is regarded as a health problem worldwide, particularly in developing countries. Mycobacterium tuberculosis (M. tuberculosis) is the cause of this disease. Approximately two billion people worldwide are infected by M. tuberculosis and annually about two million individuals die in consequence. Forty million people are estimated to die because of M. tuberculosis over the next 25 years if the measures for controlling this infection are not extensively developed. In the vaccination field, BacillusCalmette–Guérin (BCG) is still the most effective vaccine but it shows no efficacy in adult pulmonary patients. One of the other problems regarding TB is its appropriate diagnosis. Objectives: In this experimental study, the recombinant cytochrome P450 CYP141 protein of M. tuberculosis was expressed and purified to be used as a vaccine candidate and diagnostic purpose in subsequent investigations. Materials and Methods: The optimization of the cytochrome P450 CYP141 protein expression was evaluated in different conditions. Then, this protein was purified with a resin column of nickel–nitrilotriacetic acid and investigated via Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) and Western Blotting. Results: The highest expression of the cytochrome P450 CYP141 protein was obtained by the addition of 1 mM of isopropyl β-D-1-thiogalactopyranoside (IPTG) to the bacterial culture grown to an optical density at 600 nm (OD600) of 0.6, 16 hours after induction. This protein was subsequently purified with a purification of higher than 80%. The results of Western Blotting indicated that the purified protein was specifically detected. Conclusions: In this experimental study, for the first time in Iran the expression and purification of this recombinant protein was done successfully. This recombinant protein could be used as a vaccine candidate and diagnostic purpose in subsequent investigations.
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Affiliation(s)
- Reza Heidari
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, IR Iran
| | | | - Davood Darban-Sarokhalil
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, IR Iran
| | - Amirhooshang Alvandi
- Department of Microbiology, Kermanshah University of Medical Sciences, Kermanshah, IR Iran
| | - Narges Abdian
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, IR Iran
| | - Ehsan Aryan
- Antimicrobial Resistance Research Center, Department of Medical Microbiology, Mashhad University of Medical Sciences, Mashhad, IR Iran
| | - Neda Soleimani
- Department of Pathology, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Abolfazl Gholipour
- Department of Microbiology and Immunology, Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, IR Iran
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Rabiee-Faradonbeh M, Darban-Sarokhalil D, Feizabadi MM, Alvandi A, Momtaz H, Soleimani N, Gholipour A. Cloning of the Recombinant Cytochrome P450 Cyp141 Protein of Mycobacterium tuberculosis as a Diagnostic Target and Vaccine Candidate. IRANIAN RED CRESCENT MEDICAL JOURNAL 2014; 16:e18001. [PMID: 25763215 PMCID: PMC4329965 DOI: 10.5812/ircmj.18001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/08/2014] [Accepted: 04/23/2014] [Indexed: 11/18/2022]
Abstract
Background: Tuberculosis has been announced as a global emergency by World Health Organization and the second infectious agent of mortality worldwide. The general policy in the development of new vaccines is to develop some vaccines with higher efficiency not only for infants but also for adults compared with the Bacillus Calmette-Guerin vaccine. Recently, cytochrome P450 cyp141 has been introduced as a new target for detecting Mycobacterium tuberculosis from clinical samples. Objectives: The aim of this study was to clone this gene in order to pave the way for more evaluation. Materials and Methods: M. tuberculosis H37Rv DNA was extracted by a standard phenol-chlorophorm protocol. After designing the specific primers, P450 cyp141 gene was replicated by PCR. The purified PCR products were then subcloned into the pTZ57R/T plasmid vector. After extraction, enzyme digestion, and recombinant pTZ57R/T-cyp141 plasmid vector sequencing, the aforementioned products were cloned into a pET-26b plasmid vector. Then, the recombinant pET26b-cyp141 plasmid molecules were transformed to Escherichia coli strain BL21 (DE3) using the transformation method. Next, the recombinant pET26b-cyp141 plasmids were purified and evaluated by the enzyme digestion analysis. Results: The cloning of P450 cyp141 gene was confirmed by the enzyme digestion and sequencing of the recombinant pTZ57R/T-cyp141 and pET26b-cyp141 plasmid vectors. Conclusions: The results of this study demonstrated that the P450 cyp141 gene was successfully cloned into a pET26b plasmid vector as an expression vector. In this paper, for the first time in Iran, this gene was cloned for more purposes, including the expression and purification of the recombinant cytochrome P450 cyp141 protein.
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Affiliation(s)
- Mohammad Rabiee-Faradonbeh
- Department of Microbiology and Immunology, Faculty of Medicine, Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, IR Iran
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord,IR Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology and Immunology, Faculty of Medicine, Alborz University of Medical Sciences, Karaj, IR Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Amirhooshang Alvandi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, IR Iran
| | - Hasan Momtaz
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord,IR Iran
| | - Neda Soleimani
- Department of Pathology, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Abolfazl Gholipour
- Department of Microbiology and Immunology, Faculty of Medicine, Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, IR Iran
- Corresponding Author: Abolfazl Gholipour, Department of Microbiology and Immunology, Cellular and Molecular Research Center, Faculty of Medicine, Shahrekord University of Medical Sciences, Rahmatiyeh, Shahrekord, IR Iran. Tel: +98-3813346732, E-mail:
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Comparison of cyp141 and IS6110 for detection of Mycobacterium tuberculosis from clinical specimens by PCR. J Infect Public Health 2014; 8:32-6. [PMID: 25304426 DOI: 10.1016/j.jiph.2014.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 04/23/2014] [Accepted: 08/24/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Tuberculosis is a major public health problem throughout the world. TB's worldwide patterns of prevalence coupled with the increase in incidence of HIV infection threaten the health and lives of humans worldwide. Rapid detection of TB and the rapidly initiation of the administration of medication are important strategies for stopping the transmission of this disease transmission and its resistance to anti-TB drugs. Molecular methods are advantageous relative to conventional techniques due to their greater speed and sensitivity in the detection of TB. METHODS In this study, we targeted the cyp141 gene for the detection of Mycobacterium tuberculosis from clinical specimens (n=123) by PCR and compared the sensitivity and specificity of this new target with those of IS6110 gene. RESULTS Targeting of the cyp141 gene is more sensitive (97.1% for cultured isolates and 85.7% for direct specimens) than the targeting of the commonly used IS6110 gene (95.1% for cultured isolates and 42.9% for direct specimens), and the specificities of these two target genes were equal (100%). CONCLUSIONS The cyp141 gene can be used as a new target for the direct detection of Mycobacterium tuberculosis that seems to be superior to IS6110.
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Drug resistance pattern of Mycobacterium tuberculosis isolates from patients of five provinces of Iran. ASIAN PAC J TROP MED 2014; 7:193-6. [PMID: 24507638 DOI: 10.1016/s1995-7645(14)60019-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/15/2014] [Accepted: 02/15/2014] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE To determine the patterns of resistance to first line anti-tuberculosis (TB) drugs among a collection of Mycobacterium tuberculosis (MTB) isolates from 5 provinces of Iran. METHODS A total of the 6 426 clinical specimens from patients suspected of active TB were collected from March 2010 to June 2012. All specimens were subjected for microscopy and culture tests in the TB centers of studies provinces. Drug susceptibility testing to the first line anti-TB drugs for culture positive MTB was performed on Löwenstein-Jensen (LJ) medium using proportion method. RESULTS Of 6 426 clinical specimens, 261 were culture positive for mycobacteria, of which 252 were MTB and 9 were MOTT (mycobacteria other than tuberculosis). Of 252 MTB isolates, 211 (83.7%) were pan-susceptible and 41 (16.3%) were resistant to at least one drug. Resistance was most common to streptomycin, 30 isolates (12.0%), followed by isoniazid, 20 isolates (8.0%), rifampin, 15 isolates (6.0%) and ethambutol, 14 isolates (5.5%). Sixteen (6.3%) MTB isolates were MDR. A clear evidence of heterogeneity amongst the 5 provinces in the proportions with resistance to one or more drugs was observed [χ(2); = 12.209 (4 degrees of freedom), P values = 0.015 9]. CONCLUSIONS The prevalence of drug resistance in this study area underscoring the need for further enforcement of TB control strategies in the Iran. Drug susceptibility testing for all TB cases to provide optimal treatment, establishing advanced diagnostic facilities for rapid detection of MDR-TB and continuous monitoring of drug resistance are recommended for prevention and control of drug-resistant TB.
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Darban-Sarokhalil D, Imani Fooladi AA, Maleknejad P, Bameri Z, Aflaki M, Nomanpour B, Yaslianifard S, Modarresi MH, Feizabadi MM. Comparison of smear microscopy, culture, and real-time PCR for quantitative detection of Mycobacterium tuberculosis in clinical respiratory specimens. ACTA ACUST UNITED AC 2012; 45:250-5. [PMID: 23113553 DOI: 10.3109/00365548.2012.727465] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND As a rapid diagnostic technique, the real-time polymerase chain reaction (PCR) can detect Mycobacterium tuberculosis with a high sensitivity and specificity. However, further studies are needed to confirm it as a standard method. In this study, we evaluated the cyp141 gene for the detection and quantification of M. tuberculosis in respiratory specimens and compared the results with direct microscopy and culture. METHODS Sputum samples (n = 247) were collected from patients of the different provinces of Iran. DNA was extracted from clinical specimens and H37Rv strain. After measuring the standard strain DNA concentration by NanoDrop and using the Avogadro number, the DNA was diluted 6 times in order to obtain 1 × 10(6) to 10 template copies. A Taqman probe was designed for detection of the target in a real-time PCR using the specific primers. RESULTS Of 247 samples, 135 (55%) were culture-negative. Of 112 (45%) culture-positive samples, 88 were positive by both smear and culture and 24 were smear-negative but culture-positive. The real-time PCR enumerated 1.5E + 02 to 4.3E+ 03, 8.5E + 03 to 5.5E + 04, 7.2E + 04 to 1.1E + 06, and 1.2E + 06 to 8.1E + 07 M. tuberculosis cells in the specimens with smear-negative, 1-plus, 2-plus, and 3-plus codes, respectively. The overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the real-time PCR were 90.2% (101/112), 97.8% (132/135), 97.1%, and 92.3%, respectively. CONCLUSIONS The overall sensitivity and specificity, the results in comparison with those of the Xpert MTB/RIF kit, and the good correlation with molecular and phenotypic methods, show that cyp141 could be a good target for the quantification of M. tuberculosis in sputum and possibly other clinical specimens.
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Affiliation(s)
- Davood Darban-Sarokhalil
- Department of Pathobiology, School of Medicine, Alborz university of Medical Sciences, Karaj, Iran
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Zamani S, Aflaki M, Fooladi AAI, Darban-Sarokhalil D, Bameri Z, Khazaee S, Nasiri MJ, Feizabadi MM. MIRU-VNTR analysis of the Mycobacterium tuberculosis isolates from three provinces of Iran. ACTA ACUST UNITED AC 2012; 45:124-30. [PMID: 22954102 DOI: 10.3109/00365548.2012.717233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Iran borders 2 high-burden tuberculosis (TB) countries to the east, and has the highest rates of TB in one of its eastern provinces. Limited information is available on the genetic diversity and transmission dynamics of Mycobacterium tuberculosis (MTB) in Iran. To examine the genetic diversity and transmission dynamics of MTB strains we genotyped a collection of isolates from different parts of Iran. METHODS Standard 15-locus variable number tandem repeat (VNTR) typing was applied to genotype 121 MTB clinical isolates collected from 3 provinces of Iran, including Tehran (the capital of Iran), Sistan-Baluchestan (southeast province of Iran, with the highest rate of TB), and Kermanshah (western part of Iran with high TB/human immunodeficiency virus cases). Antibiotic susceptibility for all isolates was determined using the proportion method. RESULTS Sixty-six distinct mycobacterial interspersed repetitive unit (MIRU)-VNTR patterns were detected among 121 isolates. Seventy-five strains grouped into 20 clusters, and 46 isolates were unique. The genetic diversity of strains from Sistan-Baluchestan was higher than that in the other provinces. All isolates from Tehran or Kermanshah that grouped into clusters shared identical patterns with Sistan-Baluchestan. The Hunter-Gaston discriminatory index (HGDI) was 0.972, indicating a high power of discrimination for MIRU-VNTR typing. The MIRU 16 and ETRA loci were designated as highly discriminative. The rates of monoresistance and multidrug resistance were 9.9% and 2.4%, respectively. CONCLUSIONS MIRU-VNTR typing revealed high genetic diversity and suggests the possibility of transmission from Sistan-Baluchestan to other provinces of Iran. This method has potential for genetic analysis and for studying the transmission routes of TB.
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Affiliation(s)
- Samin Zamani
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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