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Deshpande A, Likhar R, Khan T, Omri A. Decoding drug resistance in Mycobacterium tuberculosis complex: genetic insights and future challenges. Expert Rev Anti Infect Ther 2024:1-17. [PMID: 39219506 DOI: 10.1080/14787210.2024.2400536] [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: 03/25/2024] [Revised: 06/02/2024] [Accepted: 08/31/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Tuberculosis (TB), particularly its drug-resistant forms (MDR-TB and XDR-TB), continues to pose a significant global health challenge. Despite advances in treatment and diagnosis, the evolving nature of drug resistance in Mycobacterium tuberculosis (MTB) complicates TB eradication efforts. This review delves into the complexities of anti-TB drug resistance, its mechanisms, and implications on healthcare strategies globally. AREAS COVERED We explore the genetic underpinnings of resistance to both first-line and second-line anti-TB drugs, highlighting the role of mutations in key genes. The discussion extends to advanced diagnostic techniques, such as Whole-Genome Sequencing (WGS), CRISPR-based diagnostics and their impact on identifying and managing drug-resistant TB. Additionally, we discuss artificial intelligence applications, current treatment strategies, challenges in managing MDR-TB and XDR-TB, and the global disparities in TB treatment and control, translating to different therapeutic outcomes and have the potential to revolutionize our understanding and management of drug-resistant tuberculosis. EXPERT OPINION The current landscape of anti-TB drug resistance demands an integrated approach combining advanced diagnostics, novel therapeutic strategies, and global collaborative efforts. Future research should focus on understanding polygenic resistance and developing personalized medicine approaches. Policymakers must prioritize equitable access to diagnosis and treatment, enhancing TB control strategies, and support ongoing research and augmented government funding to address this critical public health issue effectively.
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Affiliation(s)
- Amey Deshpande
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth's College of Pharmacy, Navi Mumbai, India
| | - Rupali Likhar
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
- Department of Pharmaceutical Chemistry, LSHGCT's Gahlot Institute of Pharmacy, Navi Mumbai, India
| | - Tabassum Khan
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
| | - Abdelwahab Omri
- The Novel Drug & Vaccine Delivery Systems Facility, Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
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2
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Dakhave M, Rale T, Suryawanshi H, Patil N, Suryawanshi A, Kumar R, Gadekar S, Bhatnagar P, Khaire A, Wankhede G. Advanced integrative molecular platform for high-throughput screening of drug-resistant tuberculosis. Diagn Microbiol Infect Dis 2024; 109:116373. [PMID: 38815365 DOI: 10.1016/j.diagmicrobio.2024.116373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
A real time-polymerase chain reaction-based test in lyophilized form, was developed to simultaneously identify Mycobacterium tuberculosis complex (MTC) by targeting IS6110, rrs as dual markers, as well as mutations causing rifampicin and isoniazid resistance. The test was evaluated for pulmonary and non-pulmonary specimens from sample isolation to PCR analysis. The test demonstrated limit of detection of 25 CFU/mL for MTB, 200 CFU/mL for rpoB and inhA/katG targets with >95 % CI. The specificity for MTC was supported by a comprehensive clinical validation (n = 100). This load-and-go molecular platform, with features of high throughput, long shelf-life, room temperature storage provides simultaneous detection of MTC and its drug-resistant mutations in minimal time. The test named "PathoDetect TM MTB-RIF and INH resistance detection kit" has been approved by Central Drugs Standard Control Organisation, Indian Council of Medical Research and would have implications for tuberculosis elimination programs.
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Affiliation(s)
- Minal Dakhave
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India.
| | - Trupti Rale
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | | | - Nikita Patil
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | | | - Raju Kumar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Shruti Gadekar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Payal Bhatnagar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Amrita Khaire
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Gautam Wankhede
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
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3
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Vasanthaiah S, Verma R, Kumar A, Bandari AK, George J, Rastogi M, Manjunath GK, Sharma J, Kumar A, Subramani J, Chawla K, Pandey A. Culture-Free Whole Genome Sequencing of Mycobacterium tuberculosis Using Ligand-Mediated Bead Enrichment Method. Open Forum Infect Dis 2024; 11:ofae320. [PMID: 38957687 PMCID: PMC11218775 DOI: 10.1093/ofid/ofae320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Background Direct whole genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) can be used as a tool to study drug resistance, mixed infections, and within-host diversity. However, WGS is challenging to obtain from clinical samples due to low number of bacilli against a high background. Methods We prospectively collected 34 samples (sputum, n = 17; bronchoalveolar lavage, n = 13; and pus, n = 4) from patients with active tuberculosis (TB). Prior to DNA extraction, we used a ligand-mediated magnetic bead method to enrich Mtb from clinical samples and performed WGS on Illumina platform. Results Mtb was definitively identified based on WGS from 88.2% (30/34) of the samples, of which 35.3% (12/34) were smear negative. The overall median genome coverage was 15.2% (interquartile range [IQR], 7.7%-28.2%). There was a positive correlation between load of bacilli on smears and genome coverage (P < .001). We detected 58 genes listed in the World Health Organization mutation catalogue in each positive sample (median coverage, 85% [IQR, 61%-94%]), enabling the identification of mutations missed by routine diagnostics. Mutations causing resistance to rifampicin, isoniazid, streptomycin, and ethambutol were detected in 5 of 34 (14.7%) samples, including the rpoB S441A mutation that confers resistance to rifampicin, which is not covered by Xpert MTB/RIF. Conclusions We demonstrate the feasibility of magnetic bead-based enrichment for culture-free WGS of Mtb from clinical specimens, including smear-negative samples. This approach can also be integrated with low-cost sequencing workflows such as targeted sequencing for rapid detection of Mtb and drug resistance.
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Affiliation(s)
- Shruthi Vasanthaiah
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Renu Verma
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Ajay Kumar
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Aravind K Bandari
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - John George
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mona Rastogi
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Gowrang Kasaba Manjunath
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Jyoti Sharma
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Abhishek Kumar
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | | | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Akhilesh Pandey
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India
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Ogunlade B, Tadesse LF, Li H, Vu N, Banaei N, Barczak AK, Saleh AAE, Prakash M, Dionne JA. Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy. Proc Natl Acad Sci U S A 2024; 121:e2315670121. [PMID: 38861604 PMCID: PMC11194509 DOI: 10.1073/pnas.2315670121] [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: 09/08/2023] [Accepted: 04/02/2024] [Indexed: 06/13/2024] Open
Abstract
Tuberculosis (TB) is the world's deadliest infectious disease, with over 1.5 million deaths and 10 million new cases reported anually. The causative organism Mycobacterium tuberculosis (Mtb) can take nearly 40 d to culture, a required step to determine the pathogen's antibiotic susceptibility. Both rapid identification and rapid antibiotic susceptibility testing of Mtb are essential for effective patient treatment and combating antimicrobial resistance. Here, we demonstrate a rapid, culture-free, and antibiotic incubation-free drug susceptibility test for TB using Raman spectroscopy and machine learning. We collect few-to-single-cell Raman spectra from over 25,000 cells of the Mtb complex strain Bacillus Calmette-Guérin (BCG) resistant to one of the four mainstay anti-TB drugs, isoniazid, rifampicin, moxifloxacin, and amikacin, as well as a pan-susceptible wildtype strain. By training a neural network on this data, we classify the antibiotic resistance profile of each strain, both on dried samples and on patient sputum samples. On dried samples, we achieve >98% resistant versus susceptible classification accuracy across all five BCG strains. In patient sputum samples, we achieve ~79% average classification accuracy. We develop a feature recognition algorithm in order to verify that our machine learning model is using biologically relevant spectral features to assess the resistance profiles of our mycobacterial strains. Finally, we demonstrate how this approach can be deployed in resource-limited settings by developing a low-cost, portable Raman microscope that costs <$5,000. We show how this instrument and our machine learning model enable combined microscopy and spectroscopy for accurate few-to-single-cell drug susceptibility testing of BCG.
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Affiliation(s)
- Babatunde Ogunlade
- Department of Materials Science and Engineering, Stanford University, Stanford, CA94305
| | - Loza F. Tadesse
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, CA94305
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
- The Ragon Institute of Mass General, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
- Jameel Clinic for AI & Healthcare, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Hongquan Li
- Department of Electrical Engineering, Stanford University, Stanford, CA94305
| | - Nhat Vu
- Pumpkinseed Technologies, Inc., Palo Alto, CA94306
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Amy K. Barczak
- The Ragon Institute of Mass General, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA02114
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Amr A. E. Saleh
- Department of Materials Science and Engineering, Stanford University, Stanford, CA94305
- Department of Engineering Mathematics and Physics, Cairo University, Faculty of Engineering, Giza12613, Egypt
| | - Manu Prakash
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, CA94305
| | - Jennifer A. Dionne
- Department of Materials Science and Engineering, Stanford University, Stanford, CA94305
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA94035
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5
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Elrashedy A, Nayel M, Salama A, Zaghawa A, Abdelsalam NR, Hasan ME. Phylogenetic Analysis and Comparative Genomics of Brucella abortus and Brucella melitensis Strains in Egypt. J Mol Evol 2024; 92:338-357. [PMID: 38809331 PMCID: PMC11169049 DOI: 10.1007/s00239-024-10173-0] [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: 01/18/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Brucellosis is a notifiable disease induced by a facultative intracellular Brucella pathogen. In this study, eight Brucella abortus and eighteen Brucella melitensis strains from Egypt were annotated and compared with RB51 and REV1 vaccines respectively. RAST toolkit in the BV-BRC server was used for annotation, revealing genome length of 3,250,377 bp and 3,285,803 bp, 3289 and 3323 CDS, 48 and 49 tRNA genes, the same number of rRNA (3) genes, 583 and 586 hypothetical proteins, 2697 and 2726 functional proteins for B. abortus and B. melitensis respectively. B. abortus strains exhibit a similar number of candidate genes, while B. melitensis strains showed some differences, especially in the SRR19520422 Faiyum strain. Also, B. melitensis clarified differences in antimicrobial resistance genes (KatG, FabL, MtrA, MtrB, OxyR, and VanO-type) in SRR19520319 Faiyum and (Erm C and Tet K) in SRR19520422 Faiyum strain. Additionally, the whole genome phylogeny analysis proved that all B. abortus strains were related to vaccinated animals and all B. melitensis strains of Menoufia clustered together and closely related to Gharbia, Dameitta, and Kafr Elshiek. The Bowtie2 tool identified 338 (eight B. abortus) and 4271 (eighteen B. melitensis) single nucleotide polymorphisms (SNPs) along the genomes. These variants had been annotated according to type and impact. Moreover, thirty candidate genes were predicted and submitted at GenBank (24 in B. abortus) and (6 in B. melitensis). This study contributes significant insights into genetic variation, virulence factors, and vaccine-related associations of Brucella pathogens, enhancing our knowledge of brucellosis epidemiology and evolution in Egypt.
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Affiliation(s)
- Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Ahmed Zaghawa
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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J A, R M, Chinnakali P. Isoniazid monoresistant tuberculosis treatment outcomes in Puducherry, South India - A mixed methods study. Indian J Tuberc 2024; 71 Suppl 1:S91-S96. [PMID: 39067963 DOI: 10.1016/j.ijtb.2024.05.013] [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: 01/18/2024] [Revised: 01/29/2024] [Accepted: 05/31/2024] [Indexed: 07/30/2024]
Abstract
SETTING On a programmatic basis, a new regimen was introduced in the National Tuberculosis Elimination Programme for isoniazid monoresistant tuberculosis in a few states in India. OBJECTIVE To describe the clinical attributes and treatment outcomes of isoniazid mono-resistant tuberculosis patients on the new 6-month levofloxacin-containing regimen in Puducherry, India. DESIGN The study is designed as a convergent parallel mixed-methods study: a retrospective cohort study and a descriptive qualitative study. A total of 180 Hr-TB patient health records were reviewed, and in-depth interviews with 35 participants were conducted. (20 Hr-TB patients and 15 HCWs). RESULTS Of the total 180 Hr-TB patients included, we documented unfavourable outcomes in 26.1% of cases, and the KatG gene mutation was the most common mutation observed (63.9%). A significant risk of unfavourable outcomes was associated with low adherence and positive sputum at the third-month culture report. In interviewing the stakeholders, major challenges observed were the increased pill burden, delay in diagnosis, shortage of drugs, and lack of staff. CONCLUSION Hr-TB patients have difficulty in adhering to the 6-month levofloxacin regimen, with the need for rigorous early 3-month follow-up and assessment.
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Affiliation(s)
- Arifunhera J
- Department of Pharmacology, JIPMER, Puducherry, India
| | - Mirunalini R
- Department of Pharmacology, JIPMER, Puducherry, India.
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7
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Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. PLoS Comput Biol 2024; 20:e1011408. [PMID: 38768228 PMCID: PMC11104602 DOI: 10.1371/journal.pcbi.1011408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.
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Affiliation(s)
- Sanjeevani Choudhery
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Aarthi Srinivasan
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
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8
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Datta D, Jamwal S, Jyoti N, Patnaik S, Kumar D. Actionable mechanisms of drug tolerance and resistance in Mycobacterium tuberculosis. FEBS J 2024. [PMID: 38676952 DOI: 10.1111/febs.17142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/23/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
The emergence of antimicrobial resistance (AMR) across bacterial pathogens presents a serious threat to global health. This threat is further exacerbated in tuberculosis (TB), mainly due to a protracted treatment regimen involving a combination of drugs. A diversity of factors contributes to the emergence of drug resistance in TB, which is caused by the pathogen Mycobacterium tuberculosis (Mtb). While the traditional genetic mutation-driven drug resistance mechanisms operate in Mtb, there are also several additional unique features of drug resistance in this pathogen. Research in the past decade has enriched our understanding of such unconventional factors as efflux pumps, bacterial heterogeneity, metabolic states, and host microenvironment. Given that the discovery of new antibiotics is outpaced by the emergence of drug resistance patterns displayed by the pathogen, newer strategies for combating drug resistance are desperately needed. In the context of TB, such approaches include targeting the efflux capability of the pathogen, modulating the host environment to prevent bacterial drug tolerance, and activating the host anti-mycobacterial pathways. In this review, we discuss the traditional mechanisms of drug resistance in Mtb, newer understandings and the shaping of a set of unconventional approaches to target both the emergence and treatment of drug resistance in TB.
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Affiliation(s)
- Dipanwita Datta
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Shaina Jamwal
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nishant Jyoti
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Ogunlade B, Tadesse LF, Li H, Vu N, Banaei N, Barczak AK, Saleh AAE, Prakash M, Dionne JA. Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy. ARXIV 2024:arXiv:2306.05653v2. [PMID: 37332564 PMCID: PMC10274949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Tuberculosis (TB) is the world's deadliest infectious disease, with over 1.5 million deaths annually and 10 million new cases reported each year1. The causative organism, Mycobacterium tuberculosis (Mtb) can take nearly 40 days to culture2,3, a required step to determine the pathogen's antibiotic susceptibility. Both rapid identification of Mtb and rapid antibiotic susceptibility testing (AST) are essential for effective patient treatment and combating antimicrobial resistance. Here, we demonstrate a rapid, culture-free, and antibiotic incubation-free drug susceptibility test for TB using Raman spectroscopy and machine learning. We collect few-to-single-cell Raman spectra from over 25,000 cells of the MtB complex strain Bacillus Calmette-Guérin (BCG) resistant to one of the four mainstay anti-TB drugs, isoniazid, rifampicin, moxifloxacin and amikacin, as well as a pan-susceptible wildtype strain. By training a neural network on this data, we classify the antibiotic resistance profile of each strain, both on dried samples and in patient sputum samples. On dried samples, we achieve >98% resistant versus susceptible classification accuracy across all 5 BCG strains. In patient sputum samples, we achieve ~79% average classification accuracy. We develop a feature recognition algorithm in order to verify that our machine learning model is using biologically relevant spectral features to assess the resistance profiles of our mycobacterial strains. Finally, we demonstrate how this approach can be deployed in resource-limited settings by developing a low-cost, portable Raman microscope that costs <$5000. We show how this instrument and our machine learning model enables combined microscopy and spectroscopy for accurate few-to-single-cell drug susceptibility testing of BCG.
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Affiliation(s)
- Babatunde Ogunlade
- Department of Materials Science and Engineering, Stanford University; Stanford, 94305, CA, USA
| | - Loza F. Tadesse
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering; Stanford, 94305, CA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology; Cambridge, 02142, MA, USA
- The Ragon Institute, Massachusetts General Hospital; Cambridge, 02139, MA, USA
| | - Hongquan Li
- Department of Applied Physics, Stanford University; Stanford, 94305, CA, USA
| | - Nhat Vu
- Pumpkinseed Technologies, Inc; Palo Alto, 94306, CA, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine; Stanford, 94305, CA, USA
| | - Amy K. Barczak
- The Ragon Institute, Massachusetts General Hospital; Cambridge, 02139, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital; Boston, 02114, MA, USA
- Department of Medicine, Harvard Medical School; Boston, 02115, MA, USA
| | - Amr. A. E. Saleh
- Department of Materials Science and Engineering, Stanford University; Stanford, 94305, CA, USA
- Department of Engineering Mathematics and Physics, Cairo University; Giza, 12613, Egypt
| | - Manu Prakash
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering; Stanford, 94305, CA, USA
| | - Jennifer A. Dionne
- Department of Materials Science and Engineering, Stanford University; Stanford, 94305, CA, USA
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine; Stanford, 94035, CA, USA
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Tafess K, Ng TTL, Tam KKG, Leung KSS, Leung JSL, Lee LK, Lao HY, Chan CTM, Yam WC, Wong SSY, Lau TCK, Siu GKH. Genetic mechanisms of co-emergence of INH-resistant Mycobacterium tuberculosis strains during the standard course of antituberculosis therapy. Microbiol Spectr 2024; 12:e0213323. [PMID: 38466098 PMCID: PMC10986572 DOI: 10.1128/spectrum.02133-23] [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: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
The incidence of isoniazid (INH) resistant Mycobacterium tuberculosis is increasing globally. This study aimed to identify the molecular mechanisms behind the development of INH resistance in M. tuberculosis strains collected from the same patients during the standard course of treatment. Three M. tuberculosis strains were collected from a patient before and during antituberculosis (anti-TB) therapy. The strains were characterized using phenotypic drug susceptibility tests, Mycobacterial Interspersed Repeated Unit-Variable-Number Tandem Repeats (MIRU-VNTR), and whole-genome sequencing (WGS) to identify mutations associated with INH resistance. To validate the role of the novel mutations in INH resistance, the mutated katG genes were electroporated into a KatG-deleted M. tuberculosis strain (GA03). Three-dimensional structures of mutated KatG were modeled to predict their impact on INH binding. The pre-treatment strain was susceptible to INH. However, two INH-resistant strains were isolated from the patient after anti-TB therapy. MIRU-VNTR and WGS revealed that the three strains were clonally identical. A missense mutation (P232L) and a nonsense mutation (Q461Stop) were identified in the katG of the two post-treatment strains, respectively. Transformation experiments showed that katG of the pre-treatment strain restored INH susceptibility in GA03, whereas the mutated katG genes from the post-treatment strains rendered negative catalase activity and INH resistance. The protein model indicated that P232L reduced INH-KatG binding affinity while Q461Stop truncated gene transcription. Our results showed that the two katG mutations, P232L and Q461Stop, accounted for the co-emergence of INH-resistant clones during anti-TB therapy. The inclusion of these mutations in the design of molecular assays could increase the diagnostic performance.IMPORTANCEThe evolution of drug-resistant strains of Mycobacterium tuberculosis within the lung lesions of a patient has a detrimental impact on treatment outcomes. This is particularly concerning for isoniazid (INH), which is the most potent first-line antimycobacterial drug. However, the precise genetic factors responsible for drug resistance in patients have not been fully elucidated, with approximately 15% of INH-resistant strains harboring unknown genetic factors. This raises concerns about the emergence of drug-resistant clones within patients, further contributing to the global epidemic of resistance. In this study, we revealed the presence of two novel katG mutations, which emerged independently due to the stress exerted by antituberculosis (anti-TB) treatment on a parental strain. Importantly, we experimentally demonstrated the functional significance of both mutations in conferring resistance to INH. Overall, this research sheds light on the genetic mechanisms underlying the evolution of INH resistance within patients and provides valuable insights for improving diagnostic performance by targeting specific mutations.
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Affiliation(s)
- Ketema Tafess
- Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, Adama, Ethiopia
- Institute of Pharmaceutical Sciences, Adama Science and Technology University, Adama, Ethiopia
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Samson Sai Yin Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Terrence Chi-Kwong Lau
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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11
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Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.03.551759. [PMID: 37577548 PMCID: PMC10418283 DOI: 10.1101/2023.08.03.551759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.
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Affiliation(s)
- Sanjeevani Choudhery
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Aarthi Srinivasan
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
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12
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Girase R, Ahmad I, Oh JM, Kim H, Mathew B, Vagolu SK, Tønjum T, Desai NC, Sriram D, Kumari J, Patel HM. Repurposing Azoles to Resolve Serotogenic Toxicity Associated with Linezolid to Combat Multidrug-Resistant Tuberculosis. ACS Med Chem Lett 2023; 14:1754-1759. [PMID: 38116435 PMCID: PMC10726462 DOI: 10.1021/acsmedchemlett.3c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 12/21/2023] Open
Abstract
Serotogenic toxicity is a major hurdle associated with Linezolid in the treatment of drug-resistant tuberculosis (TB) due to the inhibition of monoamine oxidase (MAO) enzymes. Azole compounds demonstrate structural similarities to the recognized anti-TB drug Linezolid, making them intriguing candidates for repurposing. Therefore, we have repurposed azoles (Posaconazole, Itraconazole, Miconazole, and Clotrimazole) for the treatment of drug-resistant TB with the anticipation of their selectivity in sparing the MAO enzyme. The results of repurposing revealed that Clotrimazole showed equipotent activity against the Mycobacterium tuberculosis (Mtb) H37Rv strain compared to Linezolid, with a minimal inhibitory concentration (MIC) of 2.26 μM. Additionally, Clotrimazole exhibited reasonable MIC50 values of 0.17 μM, 1.72 μM, 1.53 μM, and 5.07 μM against the inhA promoter+, katG+, rpoB+, and MDR clinical Mtb isolates, respectively, compared to Linezolid. Clotrimazole also exhibited 3.90-fold less inhibition of MAO-A and 50.35-fold less inhibition of MAO-B compared to Linezolid, suggesting a reduced serotonergic toxicity burden.
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Affiliation(s)
- Rukaiyya
T. Girase
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra India, 4254
| | - Iqrar Ahmad
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra India, 4254
| | - Jong Min Oh
- Department
of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Hoon Kim
- Department
of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Bijo Mathew
- Department
of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi 690525, India
| | - Siva K. Vagolu
- Department
of Microbiology, University of Oslo, N-0316 Oslo, Norway
| | - Tone Tønjum
- Department
of Microbiology, University of Oslo, N-0316 Oslo, Norway
- Department
of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Nisheeth C. Desai
- Division
of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Maharaja Krishnakumarsinhji Bhavnagar University, Mahatma Gandhi Campus, Bhavnagar 364 002, India
| | - Dharmarajan Sriram
- Department
of Pharmacy, Birla Institute of Technology
and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Jyothi Kumari
- Department
of Pharmacy, Birla Institute of Technology
and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Harun M. Patel
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra India, 4254
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13
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Bielenica A, Głogowska A, Augustynowicz-Kopeć E, Orzelska-Górka J, Kurpios-Piec D, Struga M. In vitro antimycobacterial activity and interaction profiles of diarylthiourea-copper (II) complexes with antitubercular drugs against Mycobacterium tuberculosis isolates. Tuberculosis (Edinb) 2023; 143:102412. [PMID: 37774599 DOI: 10.1016/j.tube.2023.102412] [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: 07/04/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
The activity of several halogenated copper (II) complexes of 4-chloro-3-nitrophenylthiourea derivatives has been tested against Mycobacterium tuberculosis strains and strains of non-tuberculous mycobacteria. The compounds were 2-16 times more potent than current TB-drugs against multidrug-resistant M. tuberculosis 210. The 3,4-dichlorophenylthiourea complex (5) was equipotent to ethambutol (EMB) towards M. tuberculosis H37Rv and 192 strains. All derivatives acted 2-8 times stronger than isoniazid (INH) against nontuberculous isolates. In the presence of chosen coordinates, the 2-64 times reduction of MIC values of standard drugs was denoted. The synergistic interaction was found between the complex 4 and rifampicin (RMP), and additivity of 1-5, 8 in pairs with EMB and/or streptomycin (SM) against M. tuberculosis 800 was established. All coordination compounds in combination with at least one drug showed additive activity towards both H37Rv and 192 isolates. In 67% incidences of indifference, the individual MIC of a drug decreased 2-16-fold. One can conclude that the novel thiourea chelates described here are potent hits for further developments of new agents against tuberculosis.
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Affiliation(s)
- Anna Bielenica
- Department of Biochemistry, Medical University of Warsaw, 02-097, Warsaw, Poland.
| | - Agnieszka Głogowska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138, Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138, Warsaw, Poland
| | - Jolanta Orzelska-Górka
- Department of Pharmacology and Pharmacodynamics, Medical University of Lublin, Lublin, Poland
| | - Dagmara Kurpios-Piec
- Department of Biochemistry, Medical University of Warsaw, 02-097, Warsaw, Poland
| | - Marta Struga
- Department of Biochemistry, Medical University of Warsaw, 02-097, Warsaw, Poland
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14
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Lale Ngema S, Dookie N, Perumal R, Nandlal L, Naicker N, Peter Letsoalo M, O'Donnell M, Khan A, Padayatchi N, Naidoo K. Isoniazid resistance-conferring mutations are associated with highly variable phenotypic resistance. J Clin Tuberc Other Mycobact Dis 2023; 33:100387. [PMID: 37554582 PMCID: PMC10405055 DOI: 10.1016/j.jctube.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023] Open
Abstract
Background High-dose isoniazid is recommended in the 9-12 months short-course regimen for multidrug-resistant tuberculosis with inhA mutation. However, there is insufficient evidence to support the assumption of genotypic-phenotypic concordance. This study aimed to identify the genetic mutations associated with high-level phenotypic isoniazid resistance. Methods Clinical isolates from patients with drug-resistant tuberculosis were profiled by whole-genome sequencing and subjected to minimum inhibitory concentration (MIC) testing using MGIT based-method. MICs were performed in concentration ranges based on the mutation present: isolates with no isoniazid resistance-conferring mutations and H37Rv, 0.016-0.256 µg/ml; inhA, 0.256-4.0 µg/ml, katG 1.0-16.0 µg/ml; and inhA + katG, 4.0-64.0 µg/ml. Isolates demonstrating resistance at the upper limit of the concentration range were tested up to the maximum of 64.0 µg/ml. Bootstrap of the mean MICs was performed to increase the robustness of the estimates and an overlap index was used to compare the distributions of the MICs for each mutation profile. Results A total of 52 clinical isolates were included in this analysis. Bootstrap MIC means for inhA, katG and inhA + katG were 33.64 (95% CI, 9.47, 56.90), 6.79 (4.45, 9.70) and 52.34 (42.750, 61.66) µg/ml, respectively. There was high overlap between inhA and inhA + katG mutations (eta = 0.45) but not with inhA and katG (eta = 0.19). Furthermore, katG showed poor overlap with inhA + katG mutations (eta = 0.09). Unexpectedly, 4/8 (50.0%) of all InhA mutants demonstrated high-level resistance, while 20/24 (83.3%) of katG mutants demonstrated moderate-level resistance. Conclusions InhA mutations demonstrated unexpectedly high MICs and showed high overlap with inhA + katG. Contrary to the common belief that katG mutants are associated with high-level resistance, this mutation primarily showed moderate-level resistance.
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Affiliation(s)
- Senamile Lale Ngema
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Rubeshan Perumal
- 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, University of KwaZulu-Natal, Durban, South Africa
| | - Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nikita Naicker
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Marothi Peter Letsoalo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Max O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, & Department of Epidemiology, Columbia University Medical Center, New York City, NY, United States
| | - Azraa Khan
- 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
| | - 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, University of KwaZulu-Natal, Durban, South Africa
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15
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Gopi Reji J, K Edison L, Raghunandanan S, Pushparajan AR, Kurthkoti K, Ajay Kumar R. Rv1255c, a dormancy-related transcriptional regulator of TetR family in Mycobacterium tuberculosis, enhances isoniazid tolerance in Mycobacterium smegmatis. J Antibiot (Tokyo) 2023; 76:720-727. [PMID: 37821540 DOI: 10.1038/s41429-023-00661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Mycobacterium tuberculosis is exposed to diverse stresses inside the host during dormancy. Meanwhile, many metabolic and transcriptional regulatory changes occur, resulting in physiological modifications that help M. tuberculosis to adapt to these stresses. The same physiological changes also cause antibiotic tolerance in dormant M. tuberculosis. However, the transcriptional regulatory mechanism of antibiotic tolerance during dormancy remains unclear. Here, we showed that the expression of Rv1255c, an uncharacterised member of the tetracycline repressor family of transcriptional regulators, is upregulated during different stresses and hypoxia-induced dormancy. Antibiotic tolerance and efflux activities of Mycobacterium smegmatis constitutively expressing Rv1255c were analysed, and interestingly, it showed increased isoniazid tolerance and efflux activity. The intrabacterial isoniazid concentrations were found to be low in M. smegmatis expressing Rv1255c. Moreover, orthologs of the M. tuberculosis katG, gene of the enzyme which activates the first-line prodrug isoniazid, are overexpressed in this strain. Structural analysis of isoforms of KatG enzymes in M. smegmatis identified major amino acid substitutions associated with isoniazid resistance. Thus, we showed that Rv1255c helps M. smegmatis tolerate isoniazid by orchestrating drug efflux machinery. In addition, we showed that Rv1255c also causes overexpression of katG isoform in M. smegmatis which has amino acid substitutions as found in isoniazid-resistant katG in M. tuberculosis.
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Affiliation(s)
- Jijimole Gopi Reji
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Lakshmi K Edison
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Sajith Raghunandanan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Akhil Raj Pushparajan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Krishna Kurthkoti
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Ramakrsihnan Ajay Kumar
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
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16
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N MP, C GPD, R M. Exploring natural products library to identify potential inhibitors targeting isoniazid-resistant tuberculosis. J Biomol Struct Dyn 2023:1-15. [PMID: 37993985 DOI: 10.1080/07391102.2023.2283159] [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: 07/13/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Mycobacterium tuberculosis (MTB) causing tuberculosis (TB) infection is a leading source of illness and death in developing nations, and the emergence of drug-resistant TB remains a significant global threat and a challenge in treating the disease. Mutations in the inhA and katG genes are connected to the principal molecular mechanism of isoniazid (INH) resistance, and continuous treatment of INH for more than a decade led to the evolution of INH resistant-TB (inhR-TB). Structure-based drug discovery approaches on traditional natural compounds are the contemporary source to identify significant lead molecules. This work focuses on discovering effective small compounds from natural compound libraries and applying pharmacophore-based virtual screening to filter out the molecules. The best-identified hit complexes were used for molecular dynamics simulations (MDS) to observe their stability and compactness. A three-dimensional e-pharmacophore hypothesis and screening generated 62 hits based on phase fitness scores from the pharmacophore-based virtual screening. Molecular docking experiments in Maestro's GLIDE module indicated that ZINC000002383126 and ASN22022 may be potential inhibitors of inhA and katG (native, inhA mutants S94A, Y158A, Y158F and Y158S and D137S, Y229F, S315T, W321F, and R418L mutants of katG). In addition, MDS analysis indicated that the native and mutant docked complexes of inhA and katG had good stability and remained compact in the binding pocket of the targets. In vitro studies can further validate the compounds that can act as INH competitive inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhana Priya N
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Magesh R
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
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17
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Sachan RK, Mistry V, Dholaria M, Rana A, Devgon I, Ali I, Iqbal J, Eldin SM, Mohammad Said Al-Tawaha AR, Bawazeer S, Dutta J, Karnwal A. Overcoming Mycobacterium tuberculosis Drug Resistance: Novel Medications and Repositioning Strategies. ACS OMEGA 2023; 8:32244-32257. [PMID: 37720746 PMCID: PMC10500578 DOI: 10.1021/acsomega.3c02563] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023]
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is a global health concern, affecting millions worldwide. This bacterium has earned a reputation as a formidable adversary due to its multidrug-resistant nature, allowing it to withstand many antibiotics. The development of this drug resistance in Mycobacterium tuberculosis is attributed to innate and acquired mechanisms. In the past, rifampin was considered a potent medication for treating tuberculosis infections. However, the rapid development of resistance to this drug by the bacterium underscores the pressing need for new therapeutic agents. Fortunately, several other medications previously overlooked for tuberculosis treatment are already available in the market. Moreover, several innovative drugs are under clinical investigation, offering hope for more effective treatments. To enhance the effectiveness of these drugs, it is recommended that researchers concentrate on identifying unique target sites within the bacterium during the drug development process. This strategy could potentially circumvent the issues presented by Mycobacterium drug resistance. This review primarily focuses on the characteristics of novel drug resistance mechanisms in Mycobacterium tuberculosis. It also discusses potential medications being repositioned or sourced from novel origins. The ultimate objective of this review is to discover efficacious treatments for tuberculosis that can successfully tackle the hurdles posed by Mycobacterium drug resistance.
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Affiliation(s)
| | - Vyoma Mistry
- C.
G. Bhakta Institute of Biotechnology, Uka
Tarsadia University, Bardoli 394350, Surat, India
| | - Mayuri Dholaria
- Naran
Lala College of Professional and Applied Sciences, Navsari 396450, Gujarat, India
| | - Abhishek Rana
- Jindal
Global Law School, OP Jindal Global University, Sonepat 131001, Haryana, India
| | - Inderpal Devgon
- Lovely
Professional University, Phagwara 144411, Punjab, India
| | - Iftikhar Ali
- Center
for Plant Science and Biodiversity, University
of Swat, Charbagh 19120, Pakistan
- Department
of Genetics and Development, Columbia University
Irving Medical Center, New York, New York 10032, United States
| | - Javed Iqbal
- Department
of Botany, Bacha Khan University, Charsadda, 24420 Khyber Pakhtunkhwa, Pakistan
| | - Sayed M. Eldin
- Center
of Research, Faculty of Engineering, Future
University in Egypt, New Cairo 11835, Egypt
| | | | - Sami Bawazeer
- Faculty
of Pharmacy, Department of Pharmacognosy, Umm Al-Qura University, Makkah 4041-4152, Kingdom of Saudi Arabia
| | - Joydeep Dutta
- Lovely
Professional University, Phagwara 144411, Punjab, India
| | - Arun Karnwal
- Lovely
Professional University, Phagwara 144411, Punjab, India
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18
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Tilahun M, Wegayehu T, Wondale B, Gebresilase TT, Gebreyohannes T, Tekola A, Alemu M, Neway S, Adnew B, Nassir MF, Kassahun Y, Aseffa A, Bobosha K. Phenotypic and genotypic drug susceptibility patterns of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Central and Southern Ethiopia. PLoS One 2023; 18:e0285063. [PMID: 37682820 PMCID: PMC10491001 DOI: 10.1371/journal.pone.0285063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
INTRODUCTION The persistence of tuberculosis (TB) infection in some patients after treatment has highlighted the importance of drug susceptibility testing (DST). This study aimed to determine the drug susceptibility patterns of Mycobacterium tuberculosis (M. tuberculosis) isolates from pulmonary TB (PTB) patients in Central and Southern Ethiopia. METHODS A health institution-based cross-sectional study was conducted between July 2021 and April 2022. Sputum samples were collected from newly diagnosed smear microscopy and/or Xpert MTB/RIF-positive PTB patients. The samples were processed and cultivated in Lowenstein-Jensen (LJ) pyruvate and glycerol medium. M. tuberculosis isolates were identified using polymerase chain reaction (PCR) based region of difference 9 (RD9) deletion typing. Phenotypic DST patterns of the isolates were characterized using the BACTEC MGIT™ 960 instrument with SIRE kit. Isoniazid (INH) and Rifampicin (RIF) resistant M. tuberculosis isolates were identified using the GenoType® MTBDRplus assay. RESULTS Sputum samples were collected from 350 PTB patients, 315 (90%) of which were culture-positive, and phenotypic and genotypic DST were determined for 266 and 261 isolates, respectively. Due to invalid results and missing data, 6% (16/266) of the isolates were excluded, while 94% (250/266) were included in the paired analysis. According to the findings, 14.4% (36/250) of the isolates tested positive for resistance to at least one anti-TB drug. Gene mutations were observed only in the rpoB and katG gene loci, indicating RIF and high-level INH resistance. The GenoType® MTBDRplus assay has a sensitivity of 42% and a specificity of 100% in detecting INH-resistant M. tuberculosis isolates, with a kappa value of 0.56 (95%CI: 0.36-0.76) compared to the BACTEC MGIT™ DST. The overall discordance between the two methods was 5.6% (14/250) for INH alone and 0% for RIF resistance and MDR-TB (resistance to both INH and RIF) detection. CONCLUSION This study reveals a higher prevalence of phenotypic and genotypic discordant INH-resistant M. tuberculosis isolates in the study area. The use of whole-genome sequencing (WGS) is essential for gaining a comprehensive understanding of these discrepancies within INH-resistant M. tuberculosis strains.
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Affiliation(s)
- Melaku Tilahun
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Teklu Wegayehu
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Biniam Wondale
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
| | | | | | - Abraham Tekola
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Mekdes Alemu
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Sebsib Neway
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Bethlehem Adnew
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | | | - Yonas Kassahun
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Kidist Bobosha
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
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Wang J, Yu C, Xu Y, Chen Z, Qiu W, Chen S, Pei H, Zhong Y. Analysis of Drug-Resistance Characteristics and Genetic Diversity of Multidrug-Resistant Tuberculosis Based on Whole-Genome Sequencing on the Hainan Island, China. Infect Drug Resist 2023; 16:5783-5798. [PMID: 37692467 PMCID: PMC10487742 DOI: 10.2147/idr.s423955] [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: 06/22/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose Given the high burden of Tuberculosis (TB) in China, the prevalence of multidrug-resistant tuberculosis (MDR-TB) is significant. Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) enables the identification of lineages, drug-resistant mutations, and transmission patterns, offering valuable insights for TB control, clinical diagnosis, and treatment. Methods We collected 202 MDR-MTB strains from 3519 suspected pulmonary TB patients treated at The Second Affiliated Hospital of Hainan Medical University between July 2019 and June 2021. Proportional drug-susceptibility testing was performed using 8 common anti-tuberculosis drugs. Subsequently, the genotypic drug resistance and genetic characteristics were analyzed by the WGS. Results Lineages are identified by TB-profiler revealed 202 MDR-MTB strains, showcasing three predominant lineages, with lineage 2 being the most prevalent. Close genomic relatedness analysis and evidence of MTB transmission led to the formation of 15 clusters comprising 42 isolates, resulting in a clustering rate of 20.8%. Novelty, lineage 2.1 (non-Beijing) accounted for 27.2% of the MDR-MTB strains, which is rare in China and Neighboring countries. Regarding first-line anti-TB drugs, genes associated with rifampicin resistance, primarily the rpoB gene, were detected in 200 strains (99.0%). Genes conferring resistance to isoniazid, ethambutol, and streptomycin were identified in 191 (94.5%), 125 (61.9%), and 100 (49.5%) strains, respectively. Among the second-line drugs, 97 (48.0%) strains exhibited genes encoding resistance to fluoroquinolones. Comparing the results to phenotypic drug susceptibility-based testing, the sensitivity of WGS for detecting resistance to each of the six drugs (rifampicin, isoniazid, ethambutol, ofloxacin, kanamycin, capreomycin) was 90% or higher. With the exception of ethambutol, the specificity of WGS prediction for the remaining drugs exceeded 88%. Conclusion Our study provides crucial insights into genetic mutation types, genetic diversity, and transmission of MDR-MTB on Hainan Island, serving as a significant reference for MDR-MTB surveillance and clinical decision-making.
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Affiliation(s)
- Jieying Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Chunchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yuni Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Zhuolin Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Wenhua Qiu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Shaowen Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yeteng Zhong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
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Rostamian M, Kooti S, Abiri R, Khazayel S, Kadivarian S, Borji S, Alvandi A. Prevalence of Mycobacterium tuberculosis mutations associated with isoniazid and rifampicin resistance: A systematic review and meta-analysis. J Clin Tuberc Other Mycobact Dis 2023; 32:100379. [PMID: 37389010 PMCID: PMC10302537 DOI: 10.1016/j.jctube.2023.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
Tuberculosis (TB) is still one of the leading causes of worldwide death, especially following the emergence of strains resistant to isoniazid (INH) and rifampicin (RIF). This study aimed to systematically review published articles focusing on the prevalence of INH and/or RIF resistance-associated mutations of Mycobacterium tuberculosis isolates in recent years. Literature databases were searched using appropriate keywords. The data of the included studies were extracted and used for a random-effects model meta-analysis. Of the initial 1442 studies, 29 were finally eligible to be included in the review. The overall resistance to INH and RIF was about 17.2% and 7.3%, respectively. There was no difference between the frequency of INH and RIF resistance using different phenotypic or genotypic methods. The INH and/or RIF resistance was higher in Asia. The S315T mutation in KatG (23.7 %), C-15 T in InhA (10.7 %), and S531L in RpoB (13.5 %) were the most prevalent mutations. Altogether, the results showed that due to S531L in RpoB, S315T in KatG, and C-15 T in InhA mutations INH- and RIF-resistant M. tuberculosis isolates were widely distributed. Thus, it would be diagnostically and epidemiologically beneficial to track these gene mutations among resistant isolates.
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Affiliation(s)
- Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sara Kooti
- Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Ramin Abiri
- Fertility and Infertility Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saeed Khazayel
- Deupty of Research and Technology Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepide Kadivarian
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soroush Borji
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Medical Technology Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Faye LM, Hosu MC, Oostvogels S, Dippenaar A, Warren RM, Sineke N, Vasaikar S, Apalata T. The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province. Infect Dis Rep 2023; 15:403-416. [PMID: 37489395 PMCID: PMC10366782 DOI: 10.3390/idr15040041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mutations and the genotyping of DR-TB in the rural Eastern Cape Province; hence, we aimed to identify DR-TB mutations, genetic diversity, and allocated lineages among patients in this area. Using Xpert® MTB/RIF, we assessed the rifampin resistance of sputum samples collected from 1157 patients suspected of having tuberculosis. GenoType MTBDR plus VER 2.0 was used for the detection of mutations causing resistance to anti-TB medications. The next step was to spoligotype 441 isolates. The most prevalent rifampin resistance-conferring mutations were in rpoB codon S531L in INH-resistant strains; the katG gene at codon S315TB and the inhA gene at codon C-15TB had the most mutations; 54.5% and 24.7%, respectively. In addition, 24.6% of strains showed mutations in both the rpoB and inhA genes, while 69.9% of strains showed mutations in both the katG and rpoB genes. Heteroresistance was seen in 17.9% of all cases in the study. According to spoligotyping analysis, Beijing families predominated. Investigation of the evolutionary lineages of M. tuberculosis isolates can be carried out using the information provided by the study's diversity of mutations. In locations wherein these mutations have been discovered, decision-making regarding the standardization of treatment regimens or individualized treatment may be aided by the detection frequency of rpoB, katG, and inhA mutations in various study areas.
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Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council, Parowvallei, Cape Town 7505, South Africa
- Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Ncomeka Sineke
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
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Kumar S, Rout SS, Kar S, Bal HB, Turuk J, Das D, Hota PK, Pati S, Giri S. Pattern of InhA and KatG mutations in isoniazid mono resistant Mycobacterium tuberculosis isolates from Odisha. Indian J Med Microbiol 2023; 44:100373. [PMID: 37356845 DOI: 10.1016/j.ijmmb.2023.100373] [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: 05/17/2022] [Revised: 12/30/2022] [Accepted: 04/05/2023] [Indexed: 06/27/2023]
Abstract
We conducted a retrospective analysis of the line probe assay (LPA) data during January to December 2019, from 8 districts of Odisha. The prevalence of Hr-TB (isoniazid resistance only) was 1.53% (50/3272) with a range of 0-3.4% in the 8 districts. Of the 50 Hr-TB strains, katG mutation and inhA mutations were seen in 74% (37/50) and 26% (13/50) strains respectively. S315T1 and C15T were common mutations in katG and inhA respectively. Since these mutations are closely related to high- or low degree resistance to INH, it has therapeutic implications.
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Affiliation(s)
- Sujeet Kumar
- National Reference Laboratory for TB, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Sunil Swick Rout
- National Reference Laboratory for TB, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Sarita Kar
- National Reference Laboratory for TB, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Himadri Bhusan Bal
- National Reference Laboratory for TB, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Jyotirmayee Turuk
- ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Dasarathi Das
- ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | | | - Sanghamitra Pati
- ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Sidhartha Giri
- ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India.
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Sundar S. In-silico transcriptome analysis of antibiotic-treated Mycobacterium tuberculosis identifies novel antibiotic resistance factors. Indian J Tuberc 2023; 71 Suppl 1:S29-S36. [PMID: 39067951 DOI: 10.1016/j.ijtb.2023.06.010] [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: 06/23/2022] [Accepted: 06/20/2023] [Indexed: 07/30/2024]
Abstract
The emergence of drug resistant Mycobacterium tuberculosis strains increases the burden on the treatment of tuberculosis. In this study, through in-silico transcriptome analysis of drug-treated M. tuberculosis samples, novel drug targets for the treatment of drug resistance in tuberculosis were identified. Gene expression datasets of tuberculosis patients samples treated with different antibiotics (Isoniazid, Rifampicin, Pyrazinamide, Bedaquiline and Linezolid) were considered in this study. DESeq2 was used to identify the differentially regulated genes. Novel genes which were up-regulated during antibiotic treatment were identified which could be antibiotic resistance factors. Further, to understand the resistance mechanism of the novel genes, we performed gene ontology and gene network analysis for the differentially up-regulated genes. Thus, the in-silico transcriptome analysis paves way for a deeper understanding of the antibiotic resistance in M. tuberculosis.
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Affiliation(s)
- Shobana Sundar
- Department of Biotechnology, PSG College of Technology, Coimbatore, India.
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Cao B, Mijiti X, Deng LL, Wang Q, Yu JJ, Anwaierjiang A, Qian C, Li M, Fang DA, Jiang Y, Zhao LL, Zhao X, Wan K, Liu H, Li G, Yuan X. Genetic Characterization Conferred Co-Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis Isolates from Southern Xinjiang, China. Infect Drug Resist 2023; 16:3117-3135. [PMID: 37228658 PMCID: PMC10204763 DOI: 10.2147/idr.s407525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023] Open
Abstract
Background Ethionamide (ETH), a structural analogue of isoniazid (INH), is used for treating multidrug-resistant tuberculosis (MDR-TB). Due to the common target InhA, INH and ETH showed cross-resistance in M. tuberculosis. This study aimed to explore the INH and ETH resistant profiles and genetic mutations conferring independent INH- or ETH-resistance and INH-ETH cross-resistance in M. tuberculosis circulating in south of Xinjiang, China. Methods From Sep 2017 to Dec 2018, 312 isolates were included using drug susceptibility testing (DST), spoligotyping, and whole genome sequencing (WGS) to analyze the resistance characteristics for INH and/or ETH. Results Among the 312 isolates, 185 (58.3%) and 127 (40.7%) belonged to the Beijing family and non-Beijing family, respectively; 90 (28.9%) were INH-resistant (INHR) with mutation rates of 74.4% in katG, 13.3% in inhA and its promoter, 11.1% in ahpC and its upstream region, 2.2% in ndh, 0.0% in mshA, whilst 34 (10.9%) were ETH-resistant (ETHR) with mutation rates of 38.2% in ethA, 26.2% in inhA and its promoter, and 5.9% in ndh, 0.0% in ethR or mshA; and 25 (8.0%) were INH-ETH co-resistant (INHRETHR) with mutation rates of 40.0% in inhA and its promoter, and 8% in ndh. katG mutants tended to display high-level resistant to INH; and more inhA and its promoter mutants showed low-level of INH and ETH resistance. The optimal gene combinations by WGS for the prediction of INHR, ETHR, and INHRETHR were, respectively, katG+inhA and its promoter (sensitivity: 81.11%, specificity: 90.54%), ethA+inhA and its promoter+ndh (sensitivity: 61.76%, specificity: 76.62%), and inhA and its promoter+ndh (sensitivity: 48.00%, specificity: 97.65%). Conclusion This study revealed the high diversity of genetic mutations conferring INH and/or ETH resistance among M. tuberculosis isolates, which would facilitate the study on INHR and/or ETHR mechanisms and provide clues for choosing ETH for MDR treatment and molecular DST methods in south of Xinjiang, China.
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Affiliation(s)
- Bin Cao
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830000, People’s Republic of China
| | - Le-Le Deng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830000, People’s Republic of China
| | - Jin-Jie Yu
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | | | - Chengyu Qian
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Dan-Ang Fang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Yuan
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
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Biswas B, Kumar Misra T, Ray D, Majumder T, Kanti Bandyopadhyay T, Kumar Bhowmick T. Current Therapeutic Delivery Approaches Using Nanocarriers for the Treatment of Tuberculosis Disease. Int J Pharm 2023; 640:123018. [PMID: 37149113 DOI: 10.1016/j.ijpharm.2023.123018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/04/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023]
Abstract
Tuberculosis is a major health issue globally and a leading cause of death due to the infective microorganism Mycobacterium tuberculosis. Treatment of drug resistance tuberculosis requires longer treatment with multiple daily doses of drugs. Unfortunately, these drugs are often associated with poor patient compliance. In this situation, a need has been felt for the less toxic, shorter, and more effective treatment of the infected tuberculosis patients. Current research to develop novel anti-tubercular drugs shows hope for better management of the disease. Research on drug targeting and precise delivery of the old anti-tubercular drugs with the help of nanotechnology is promising for effective treatment. This review has discussed the status currently available treatments for tuberculosis patients infected with Mycobacterium alone or in comorbid conditions like diabetes, HIV and cancer. This review also highlighted the challenges in the current treatment and research on the novel anti-tubercular drugs to prevent multi-drug-resistant tuberculosis. It presents the research highlights on the targeted delivery of anti-tubercular drugs using different nanocarriers for preventing multi-drug resistant tuberculosis. Report has shown the importance and development of the research on nanocarriers mediated anti-tubercular delivery of the drugs to overcome the current challenges in tuberculosis treatment.
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Affiliation(s)
- Bhabatush Biswas
- Department of Bioengineering, National Institute of Technology Agartala, West Tripura - 799046, India
| | - Tarun Kumar Misra
- Department of Chemistry, National Institute of Technology Agartala, West Tripura - 799046, India
| | - Debasish Ray
- Agartala Govt. Medical College, Agartala, 799006, Tripura - 799006, India
| | - Tapan Majumder
- Agartala Govt. Medical College, Agartala, 799006, Tripura - 799006, India
| | - Tarun Kanti Bandyopadhyay
- Department of Bioengineering, National Institute of Technology Agartala, West Tripura - 799046, India
| | - Tridib Kumar Bhowmick
- Department of Bioengineering, National Institute of Technology Agartala, West Tripura - 799046, India.
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Aung YW, Faksri K, Sangka A, Tomanakan K, Namwat W. Heteroresistance of Mycobacterium tuberculosis in the Sputum Detected by Droplet Digital PCR. BIOLOGY 2023; 12:biology12040525. [PMID: 37106726 PMCID: PMC10136199 DOI: 10.3390/biology12040525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Heteroresistance in MTB refers to the presence of distinct subpopulations of bacteria with varying levels of antibiotic susceptibility within a population. Multidrug-resistant and rifampicin-resistant TB are serious global health concerns. In this study, we aimed to determine the prevalence of heteroresistance in MTB from sputum samples of new TB cases using Droplet Digital PCR mutation detection assays for katG and rpoB genes, which are commonly associated with resistance to isoniazid and rifampicin, respectively. We found that out of 79 samples, 9 (11.4%) exhibited mutations in katG and rpoB genes. INH mono-resistant TB, RIF mono-resistant TB, and MDR-TB samples constituted 1.3%, 6.3%, and 3.8% of new TB cases, respectively. Heteroresistance in katG, rpoB, and both genes were found in 2.5%, 5%, and 2.5% of total cases, respectively. Our results suggest that these mutations may have arisen spontaneously, as the patients had not yet received anti-TB drugs. ddPCR is a valuable tool for the early detection and management of DR-TB, as it can detect both mutant and wild-type strains in a population, enabling the detection of heteroresistance and MDR-TB. Overall, our findings highlight the importance of early detection and management of DR-TB for effective TB control (in katG, rpoB, and katG/rpoB).
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Affiliation(s)
- Ye Win Aung
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Arunnee Sangka
- Faculty of Associated Medical Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kanchana Tomanakan
- Department of Medical Laboratory, Khon Kaen Hospital, Khon Kaen 40000, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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Koçak Aslan E, Han Mİ, Krishna VS, Tamhaev R, Dengiz C, Doğan ŞD, Lherbet C, Mourey L, Tønjum T, Gündüz MG. Isoniazid Linked to Sulfonate Esters via Hydrazone Functionality: Design, Synthesis, and Evaluation of Antitubercular Activity. Pharmaceuticals (Basel) 2022; 15:ph15101301. [PMID: 36297413 PMCID: PMC9609273 DOI: 10.3390/ph15101301] [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: 09/09/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 01/24/2023] Open
Abstract
Isoniazid (INH) is one of the key molecules employed in the treatment of tuberculosis (TB), the most deadly infectious disease worldwide. However, the efficacy of this cornerstone drug has seriously decreased due to emerging INH-resistant strains of Mycobacterium tuberculosis (Mtb). In the present study, we aimed to chemically tailor INH to overcome this resistance. We obtained thirteen novel compounds by linking INH to in-house synthesized sulfonate esters via a hydrazone bridge (SIH1-SIH13). Following structural characterization by FTIR, 1H NMR, 13C NMR, and HRMS, all compounds were screened for their antitubercular activity against Mtb H37Rv strain and INH-resistant clinical isolates carrying katG and inhA mutations. Additionally, the cytotoxic effects of SIH1-SIH13 were assessed on three different healthy host cell lines; HEK293, IMR-90, and BEAS-2B. Based on the obtained data, the synthesized compounds appeared as attractive antimycobacterial drug candidates with low cytotoxicity. Moreover, the stability of the hydrazone moiety in the chemical structure of the final compounds was confirmed by using UV/Vis spectroscopy in both aqueous medium and DMSO. Subsequently, the compounds were tested for their inhibitory activities against enoyl acyl carrier protein reductase (InhA), the primary target enzyme of INH. Although most of the synthesized compounds are hosted by the InhA binding pocket, SIH1-SIH13 do not primarily show their antitubercular activities by direct InhA inhibition. Finally, in silico determination of important physicochemical parameters of the molecules showed that SIH1-SIH13 adhered to Lipinski's rule of five. Overall, our study revealed a new strategy for modifying INH to cope with the emerging drug-resistant strains of Mtb.
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Affiliation(s)
- Ebru Koçak Aslan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara 06100, Turkey
| | - Muhammed İhsan Han
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Vagolu Siva Krishna
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
| | - Rasoul Tamhaev
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France
| | - Cagatay Dengiz
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
- Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara 06100, Turkey
- Correspondence:
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Keleş Atıcı R, Doğan ŞD, Gündüz MG, Krishna VS, Chebaiki M, Homberset H, Lherbet C, Mourey L, Tønjum T. Urea derivatives carrying a thiophenylthiazole moiety: Design, synthesis, and evaluation of antitubercular and InhA inhibitory activities. Drug Dev Res 2022; 83:1292-1304. [PMID: 35769019 DOI: 10.1002/ddr.21958] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/05/2022]
Abstract
The recent emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) has complicated and significantly slowed efforts to eradicate and/or reduce the worldwide incidence of life-threatening acute and chronic cases of tuberculosis. To overcome this setback, researchers have increased the intensity of their work to identify new small-molecule compounds that are expected to remain efficacious antimicrobials against Mtb. Here, we describe our effort to apply the principles of molecular hybridization to synthesize 16 compounds carrying thiophene and thiazole rings beside the core urea functionality (TTU1-TTU16). Following extensive structural characterization, the obtained compounds were initially evaluated for their antimycobacterial activity against Mtb H37Rv. Subsequently, three derivatives standing out with their anti-Mtb activity profiles and low cytotoxicity (TTU5, TTU6, and TTU12) were tested on isoniazid-resistant clinical isolates carrying katG and inhA mutations. Additionally, due to their pharmacophore similarities to the well-known InhA inhibitors, the molecules were screened for their enoyl acyl carrier protein reductase (InhA) inhibitory potentials. Molecular docking studies were performed to support the experimental enzyme inhibition data. Finally, drug-likeness of the selected compounds was established by theoretical calculations of physicochemical descriptors.
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Affiliation(s)
- Rüveyde Keleş Atıcı
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Vagolu Siva Krishna
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Melina Chebaiki
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, Oslo, Norway
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Xie NG, Zhang K, Song P, Li R, Luo J, Zhang DY. High-Throughput Variant Detection Using a Color-Mixing Strategy. J Mol Diagn 2022; 24:878-892. [PMID: 35718091 PMCID: PMC9379672 DOI: 10.1016/j.jmoldx.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/04/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Many diseases are related to multiple genetic alterations along a single gene. Probing for highly multiple (>10) variants in a single quantitative PCR tube is not possible because of a limited number of fluorescence channels and one variant per channel, so many more tubes are needed. Herein, a novel color-mixing strategy that uses fluorescence combinations as digital color codes to probe multiple variants simultaneously was experimentally validated. The color-mixing strategy relies on a simple intratube assay that can probe for 15 variants as part of an intertube assay that can probe for an exponentially increased number of variants. This strategy is achieved by using multiplex double-stranded toehold probes modified with fluorophores and quenchers; the probes are designed to be quenched or luminous after binding to wild-type or variant templates. The color-mixing strategy was used to probe for 21 pathogenic variants in thalassemia and to distinguish between heterozygous and homozygous variants in six tubes, with a specificity of 99% and a sensitivity of 94%. To support tuberculosis diagnosis, the same strategy was applied to simultaneously probe in Mycobacterium tuberculosis for rifampicin-resistance mutations occurring within one 81-bp region and one 48-bp region in the rpoB gene, plus five isoniazid-resistance mutations in the inhA and katG genes.
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Affiliation(s)
- Nina Guanyi Xie
- Department of Bioengineering, Rice University, Houston, Texas
| | - Kerou Zhang
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, Texas
| | | | | | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas.
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Panova AE, Vinokurov AS, Shemetova AA, Burmistrova IA, Shulgina MV, Samoilova AG, Vasilyeva IA, Vakhrusheva DV, Umpeleva TV, Eremeeva NI, Lavrenchuk LS, Golubeva LA, Danilova TI, Vasilyeva TB, Ugol'kova VA, Sosova NV, Lekhlyaider MV, Gorshkova IA, Romanova TA. Molecular characteristics of Mycobacterium tuberculosis drug-resistant isolates from HIV- and HIV+ tuberculosis patients in Russia. BMC Microbiol 2022; 22:138. [PMID: 35590243 PMCID: PMC9118847 DOI: 10.1186/s12866-022-02553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background High burden of drug-resistant (DR) tuberculosis (TB) is a significant threat to national TB control programs all over the world and in the Russian Federation. Different Mycobacterium tuberculosis (MTB) genotypes are hypothesized to have specific characteristics affecting TB control programs. For example, Beijing strains are supposed to have higher mutation rates compared to strains of other genotypes and subsequently higher capability to develop drug-resistance. Results Clinical MTB isolates from HIV- and HIV+ patients from four regions of Russia were analyzed for genotypes and mutations conferring resistance to Isoniazid, Rifampicin, Ethambutol, aminoglycosides, and fluoroquinolones. Analysis of genotypes and polymorphism of genomic loci according to the HIV status of the patients – sources of MTB isolates were performed. Studied MTB isolates from HIV- TB patients belonged to 15 genotypes and from HIV + TB patients – to 6 genotypes. Beijing clinical isolates dominated in HIV- (64,7%) and HIV+ (74,4%) groups. Other isolates were of LAM (including LAM1 and LAM9), Ural, and 4 minor groups of genotypes (including 5 subclones T). The spectrum of genotypes in the HIV- group was broader than in the HIV+ group. PR of B0/W148 Beijing was significantly lower than of other Beijing genotypes in susceptible and MDR-XDR isolates. Rates of isolates belonging to non-Beijing genotypes were higher than Beijing in susceptible isolates from HIV- patients. Conclusions Beijing genotype isolates prevailed in clinical isolates of all drug susceptibility profiles both from HIV- and HIV+ patients, although B0/W148 Beijing genotype did not dominate in this study. Genome loci and mutations polymorphisms were more pronounced in clinical isolates from HIV- patients, than from HIV+.
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Affiliation(s)
- Anna E Panova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anatoliy S Vinokurov
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anastasiya A Shemetova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Burmistrova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Marina V Shulgina
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation.
| | - Anastasiya G Samoilova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Vasilyeva
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Diana V Vakhrusheva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana V Umpeleva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Nataliya I Eremeeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Leonid S Lavrenchuk
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Lyudmila A Golubeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana I Danilova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Tatiana B Vasilyeva
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Vera A Ugol'kova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Nataliya V Sosova
- Regional TB dispensary of Stavropolskiy kray, Stavropol, Russian Federation
| | - Marina V Lekhlyaider
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Irina A Gorshkova
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Tatiana A Romanova
- Regional TB dispensary of Kemerovskaya oblast, Kemerovo, Russian Federation
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Koçak Aslan E, Krishna VS, Armaković SJ, Armaković S, Şahin O, Tønjum T, Gündüz MG. Linking azoles to isoniazid via hydrazone bridge: Synthesis, crystal structure determination, antitubercular evaluation and computational studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Use of Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Complex Drug Resistance from Early Positive Liquid Cultures. Microbiol Spectr 2022; 10:e0251621. [PMID: 35311541 PMCID: PMC9045259 DOI: 10.1128/spectrum.02516-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Our objective was to evaluate the performance of whole-genome sequencing (WGS) from early positive liquid cultures for predicting Mycobacterium tuberculosis complex (MTBC) drug resistance. Clinical isolates were obtained from tuberculosis patients at Shanghai Pulmonary Hospital (SPH). Antimicrobial susceptibility testing (AST) was performed, and WGS from early Bactec mycobacterial growth indicator tube (MGIT) 960-positive liquid cultures was performed to predict the drug resistance using the TB-Profiler informatics platform. A total of 182 clinical isolates were enrolled in this study. Using phenotypic AST as the gold standard, the overall sensitivity and specificity for WGS were, respectively, 97.1% (89.8 to 99.6%) and 90.4% (83.4 to 95.1%) for rifampin, 91.0% (82.4 to 96.3%) and 95.2% (89.1 to 98.4%) for isoniazid, 100.0% (89.4 to 100.0%) and 87.3% (80.8 to 92.1%) for ethambutol, 96.6% (88.3 to 99.6%) and 61.8% (52.6 to 70.4%) for streptomycin, 86.8% (71.9 to 95.6%) and 95.8% (91.2 to 98.5%) for moxifloxacin, 86.5% (71.2 to 91.5%) and 95.2% (90.3 to 98.0%) for ofloxacin, 100.0% (54.1 to 100.0%) and 67.6% (60.2 to 74.5%) for amikacin, 100.0% (63.1 to 100.0%) and 67.2% (59.7 to 74.2%) for kanamycin, 62.5% (24.5 to 91.5%) and 88.5% (82.8 to 92.8%) for ethionamide, 33.3% (4.3 to 77.7%) and 98.3% (95.1 to 99.7%) for para-aminosalicylic acid, and 0.0% (0.0 to 12.3%) and 100.0% (97.6 to 100.0%) for cycloserine. The concordances of WGS-based AST and phenotypic AST were as follows: rifampin (92.9%), isoniazid (93.4%), ethambutol (89.6%), streptomycin (73.1%), moxifloxacin (94.0%), ofloxacin (93.4%), amikacin (68.7%), kanamycin (68.7%), ethionamide (87.4%), para-aminosalicylic acid (96.2%) and cycloserine (84.6%). We conclude that WGS could be a promising approach to predict MTBC resistance from early positive liquid cultures. IMPORTANCE In this study, we used whole-genome sequencing (WGS) from early positive liquid (MGIT) cultures instead of solid cultures to predict drug resistance of 182 Mycobacterium tuberculosis complex (MTBC) clinical isolates to predict drug resistance using the TB-Profiler informatics platform. Our study indicates that WGS may be a promising method for predicting MTBC resistance using early positive liquid cultures.
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Review of advances in diagnosis and treatment of pulmonary tuberculosis. Indian J Tuberc 2021; 68:510-515. [PMID: 34752322 DOI: 10.1016/j.ijtb.2021.07.002] [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: 12/11/2020] [Accepted: 07/01/2021] [Indexed: 11/20/2022]
Abstract
There has been a substantial leap in our understanding and the management of tuberculosis over the past couple of decades. New diagnostic tests, regimens and drugs have emerged. With a background of milestones in the management of tuberculosis, we review the advances made in the diagnosis and treatment of pulmonary tuberculosis. Since India accounts for 27% of word's burden of tuberculosis, the changes in RNTCP have been highlighted.
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Khurana P, Saigal K, Ghosh A. Drug resistance pattern and mutation pattern in pediatric tuberculosis: Study from north India. Indian J Tuberc 2021; 68:481-484. [PMID: 34752317 DOI: 10.1016/j.ijtb.2021.02.014] [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: 10/01/2020] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND The emergence of multidrug-resistant MDR-TB and extensively drug-resistant XDR-TB are serious threats to global TB control. Molecular tests like GenoType MTBDRplus has revolutionized MDR-TB diagnosis by rapid detection of resistance, leading to early and appropriate management of DR-TB. Information about common mutations imparting resistance to RIF and INH, helps in understanding the disease epidemiology in various regions. The study was conducted to determine the genetic mutation in drug resistant tuberculosis in children less than 12 years with pulmonary or extrapulmonary tuberculosis. MATERIALS/METHODS Retrospective analysis was done over a period of 54 months from January 2015 to June 2019 to study the resistance pattern and mutations present in DR-TB in children less than 12 years with suspected pulmonary or extrapulmonary tuberculosis using Hain's GenoType MTBDRplus VER 2.0. RESULTS Over a period of 54 months, samples from 3461 patients with suspected TB were received for MGIT culture, out of which, 347 were positive for Mycobacterium tuberculosis. 250 of these 347 isolated were tested for drug resistance by Hain's GenoType MTBDRplus VER 2.0.61.1% were sensitive to isoniazid and rifampicin while 15.2% were DR-TB (38 out of 250). Out of these 38, 22 were MDR TB, 13 were isoniazid monoresistant (34.2%) and 3 were rifampicin monoresistant. The most common genotypic resistance for rifampicin was absence of rpoB WT8 band and presence of rpoB MUT 3 band (88%). 84.6% of the INH monoresistant isolates showed high level isoniazid resistant. All these isolates showed presence of katG MUT 1 band. On comparing Hain's GenoType MTBDRplus VER 2.0 with Xpert MTB/Rif Assay, most common mutation for rifampicin resistance at S531L which can be detected by Xpert MTB/Rif Assay (probe E). However, two cases with rifampicin resistance had mutation in codon region 509-513 and 513-519 which could be missed by Xpert MTB/Rif Assay. CONCLUSIONS We cannot solely rely on Xpert MTB/Rif Assay for detection of drug resistance due to the risk of missing the isoniazid monoresistance. GenoType MTBDRplus has revolutionized MDR-TB diagnosis by substantially reducing turn around time and leading to early management of DR-TB cases.
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Affiliation(s)
- Prerna Khurana
- Department of Clinical Microbiology and Infectious Diseases, Chacha Nehru Bal Chikitsalaya, Delhi, India
| | - Karnika Saigal
- Department of Clinical Microbiology and Infectious Diseases, Chacha Nehru Bal Chikitsalaya, Delhi, India.
| | - Arnab Ghosh
- Department of Clinical Microbiology and Infectious Diseases, Chacha Nehru Bal Chikitsalaya, Delhi, India
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Sarin R, Bhalla M, Kumar G, Singh A, Myneedu VP, Singhal R. Correlation of inhA mutations and ethionamide susceptibility: Experience from national reference center for tuberculosis. Lung India 2021; 38:520-523. [PMID: 34747732 PMCID: PMC8614619 DOI: 10.4103/lungindia.lungindia_120_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background: Detection of ethionamide (ETH) resistance is crucial as it is part of antitubercular regime. It is crucial to examine the role of inhA gene mutations as a surrogate marker for the detection of ETH resistance, in the Indian context. The present retrospective study was designed with this objective. Subjects and Methods: The study was conducted in National Reference Laboratory within the tertiary care institute from January 1, 2018, to June 30, 2019, over 18 months duration. A total of 6612 sputum samples from presumptive multidrug-resistant tuberculosis (TB) patients were received from four districts of Delhi, outdoor and inpatients. Line probe assay (LPA) was performed for smear-positive or culture-positive samples for Mycobacterium tuberculosis. All isolates found to be INH resistant by LPA were cultured and phenotypic susceptibility to ETH was conducted for selected isolates as per the guidelines. Results: A total of 246 isolates were analyzed, for which phenotypic susceptibility to ETH and mutations in inhA were available. ETH resistance was detected among 87/108 (80.5%) isolates with inhA mutation. Sensitivity and specificity of inhA mutation for detection of ETH resistance were 80.5% and 83.8%, respectively. No inhA mutation was detected in 29/116 (25%) ETH-resistant isolates in our study, whereas ETH was found to be phenotypically susceptible in spite of the presence of inhA mutation among 21/130 (16.1%) isolates. Conclusions: Mutations in inhA gene in LPA predict ETH resistance with fairly good sensitivity and specificity. However, it is imperative to perform phenotypic detection of ETH resistance at proper concentration, in addition to detecting inhA mutation.
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Affiliation(s)
- Rohit Sarin
- Department of Tuberculosis and Chest, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Manpreet Bhalla
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Gavish Kumar
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Anjali Singh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Vithal Prasad Myneedu
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Mugumbate G, Nyathi B, Zindoga A, Munyuki G. Application of Computational Methods in Understanding Mutations in Mycobacterium tuberculosis Drug Resistance. Front Mol Biosci 2021; 8:643849. [PMID: 34651013 PMCID: PMC8505691 DOI: 10.3389/fmolb.2021.643849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 08/16/2021] [Indexed: 11/23/2022] Open
Abstract
The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) impedes the End TB Strategy by the World Health Organization aiming for zero deaths, disease, and suffering at the hands of tuberculosis (TB). Mutations within anti-TB drug targets play a major role in conferring drug resistance within Mtb; hence, computational methods and tools are being used to understand the mechanisms by which they facilitate drug resistance. In this article, computational techniques such as molecular docking and molecular dynamics are applied to explore point mutations and their roles in affecting binding affinities for anti-TB drugs, often times lowering the protein’s affinity for the drug. Advances and adoption of computational techniques, chemoinformatics, and bioinformatics in molecular biosciences and resources supporting machine learning techniques are in abundance, and this has seen a spike in its use to predict mutations in Mtb. This article highlights the importance of molecular modeling in deducing how point mutations in proteins confer resistance through destabilizing binding sites of drugs and effectively inhibiting the drug action.
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Affiliation(s)
- Grace Mugumbate
- Department of Chemical Sciences, Midlands State University, Gweru, Zimbabwe
| | - Brilliant Nyathi
- Department of Chemistry, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Albert Zindoga
- Department of Chemistry, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Gadzikano Munyuki
- Department of Chemistry, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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TREASURE: Text Mining Algorithm Based on Affinity Analysis and Set Intersection to Find the Action of Tuberculosis Drugs against Other Pathogens. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11156834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tuberculosis (TB) is one of the top causes of death in the world. Though TB is known as the world’s most infectious killer, it can be treated with a combination of TB drugs. Some of these drugs can be active against other infective agents, in addition to TB. We propose a framework called TREASURE (Text mining algoRithm basEd on Affinity analysis and Set intersection to find the action of tUberculosis dRugs against other pathogEns), which particularly focuses on the extraction of various drug–pathogen relationships in eight different TB drugs, namely pyrazinamide, moxifloxacin, ethambutol, isoniazid, rifampicin, linezolid, streptomycin and amikacin. More than 1500 research papers from PubMed are collected for each drug. The data collected for this purpose are first preprocessed, and various relation records are generated for each drug using affinity analysis. These records are then filtered based on the maximum co-occurrence value and set intersection property to obtain the required inferences. The inferences produced by this framework can help the medical researchers in finding cures for other bacterial diseases. Additionally, the analysis presented in this model can be utilized by the medical experts in their disease and drug experiments.
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The frequency of point mutations associated with resistance to isoniazid and rifampin among clinical isolates of multidrug-resistant Mycobacterium tuberculosis in the west of Iran. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.100981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Systematic Review of Mutations Associated with Isoniazid Resistance Points to Continuing Evolution and Subsequent Evasion of Molecular Detection, and Potential for Emergence of Multidrug Resistance in Clinical Strains of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:AAC.02091-20. [PMID: 33361298 DOI: 10.1128/aac.02091-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/13/2020] [Indexed: 01/24/2023] Open
Abstract
Molecular testing is rapidly becoming an integral component of global tuberculosis (TB) control. Uncommon mechanisms of resistance escape detection by these platforms and undermine our ability to contain outbreaks. This article is a systematic review of published articles that reported isoniazid (INH) resistance-conferring mutations between September 2013 and December 2019. The genes katG, inhA, and fabG1, and the intergenic region oxyR'-ahpC were considered in this review. Fifty-two articles were included that described 9,306 clinical isolates (5,804 INH resistant [INHr] and 3,502 INH susceptible [INHs]) from 31 countries. The three most frequently mutated loci continue to be locus 315 of katG (katG315; n = 4,271), locus -15 of inhA (inhA-15; n = 787), and locus -8 of inhA (inhA-8; 106). However, the diagnostic value of inhA-8 is far lower than previously thought, as it only appears in 25 (0.4%) of the INHr isolates lacking the first two mutations. I catalogued 45 new loci (29 katG, nine inhA, and seven ahpC) associated with INH resistance and identified 59 loci (common to this and previous reviews) as a reliable basis for molecular diagnostics. Including all observed mutations provides a cumulative sensitivity of 85.6%. In 14.4% of resistant isolates, no mechanism of resistance was detected, making them likely to escape molecular detection, and in the case of INH monoresistance, likely to convert to multidrug-resistant TB (MDR-TB). Integrating the information cataloged in this study into current diagnostic tools is essential for combating the emergence of MDR-TB, and its exclusion can lead to an unintended selection against common mechanisms and to diversifying evolution. Observation of many low-frequency resistance-conferring mutations points to an advantage of whole-genome sequencing (WGS) for diagnostics. Finally, I provide five recommendations for future diagnostic platforms.
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Jayaraman M, Ramadas K. An integrated computational investigation to unveil the structural impacts of mutation on the InhA structural gene of Mycobacterium tuberculosis. J Mol Graph Model 2020; 101:107768. [DOI: 10.1016/j.jmgm.2020.107768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 10/23/2022]
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A retrospective cohort study of isoniazid-resistant tuberculosis treatment outcomes and isoniazid resistance-associated mutations in eastern China from 2013 to 2018. J Glob Antimicrob Resist 2020; 22:847-853. [PMID: 32739538 DOI: 10.1016/j.jgar.2020.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/25/2020] [Accepted: 07/14/2020] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES The current situation of isoniazid-resistant, rifampicin-susceptible tuberculosis (Hr-TB) and associated genetic factors is not clear in China. METHODS A retrospective cohort study was conducted from 2013 to 2018 in Jiangsu Province, China. Phenotypic Hr-TB were identified by drug susceptibility testing on Lowenstein-Jensen medium and using a Mycobacterium Growth Indicator Tube 960 (MGIT 960) system, and mutations in the katG 315 codon and inhA promoter nucleotides -8, -15 and -16 were determined by GenoType MTBDRplus and sequencing. All of the Hr-TB patients enrolled were followed up until June 2019. RESULTS A total of 1416 smear-positive sputum samples were collected, of which 57 were excluded due to the presence of nontuberculous mycobacteria. Finally, 63/1359 (4.6%) were determined as Hr-TB. After follow-up, 11 Hr-TB patients (17.5%) showed an unfavourable outcome, of whom 5 (7.9%) relapsed, 4 (6.3%) had treatment failure and 2 (3.2%) died. A total of 52 isolates (82.5%) were detected with either katG 315 or inhA promoter nucleotide -8, -15 or -16 mutations, whereas no canonical mutations were found in 8 isolates (12.7%); 3 isolates failed in mutation detection. TB history was found to be associated with unfavourable outcomes for Hr-TB (odds ratio = 6.13, 95% confidence interval 1.05-35.82; P = 0.04). However, mutations in katG 315 and the inhA promoter region were not found to be associated with Hr-TB unfavourable outcomes (P = 0.15). CONCLUSION Unfavourable outcomes for Hr-TB are serious in eastern China, especially for previously treated patients. Meanwhile, current genetic determination of Hr-TB is inadequate.
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Chong SMS, Kamariah N, Grüber G. Residues of helix ɑ2 are critical for catalytic efficiency of mycobacterial alkylhydroperoxide reductase subunit C. FEBS Lett 2020; 594:2829-2839. [PMID: 32557576 DOI: 10.1002/1873-3468.13864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/05/2022]
Abstract
The ability of Mycobacteria to overcome oxidative stress is of paramount importance for its survival within the host. One of the key enzymes that are involved in protecting the bacterium from reactive oxygen species is the catalase-peroxidase (KatG). However, in strains resistant to the antibiotic isoniazid, KatG is rendered ineffective, which is associated with an increased expression of alkylhydroperoxide reductase subunit C (AhpC). Mycobacterial AhpC possesses a unique helical displacement when compared to its bacterial counterparts. Here, via mutagenesis studies, we demonstrate the importance of this helix for redox modulation of the catalytic activity of AhpC. Along with structural insights from crystallographic data, the impact of critical residues on the structure and flexibility of the helix and on AhpC oligomerization is described.
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Affiliation(s)
- Shi Min Sherilyn Chong
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Republic of Singapore.,Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Republic of Singapore
| | - Neelagandan Kamariah
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
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Yang M, Zhang L, Tao HL, Sun YC, Lou ZZ, Jia WZ, Hu LH, Gao CH. OxiR specifically responds to isoniazid and regulates isoniazid susceptibility in mycobacteria. FEMS Microbiol Lett 2020; 366:5498298. [PMID: 31125044 DOI: 10.1093/femsle/fnz109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/23/2019] [Indexed: 02/06/2023] Open
Abstract
The bacteria drug resistance is not only associated with the gain of drug resistance gene but also relied on the adaptation of bacterial cells to antibiotics by transcriptional regulation. However, only a few transcription factors that regulate drug resistance have been characterized in mycobacteria. In this study, a TetR family transcriptional factor (OxiR), encoded by Rv0067c in Mycobacterium tuberculosis, was found to be an isoniazid (INH) resistance regulator. Comparing with the wild-type strain, the oxiR overexpressing strain is four times resistant to INH, whereas the oxiR knockout strain is eight times sensitive to INH. However, the rifamycin and ethambutol resistance were not influenced by oxiR. OxiR can bind to self-promoter at a 66 bp imperfect palindromic motifs. Interestingly, OxiR directly binds to INH, and thereby alleviate the self-repression. Furthermore, OxiR negatively regulated an oxidoreductase encoded by Rv0068. And the susceptibility of the Rv0068-overexpressing and oxiR knockout strains to all the three above-mentioned anti-tuberculosis drugs was equivalent, suggesting that the effect of oxiR to INH susceptibility is attributed to the derepression of Rv0068. In conclusion, we showed that OxiR can specifically modulate INH susceptibility by regulating an oxidoreductase encoding gene, both of which have not been associated with drug-resistance previously.
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Affiliation(s)
- Min Yang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1, Shizishan Road, Hongshan District, Wuhan, China (430070)
| | - Li Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1, Shizishan Road, Hongshan District, Wuhan, China (430070)
| | - Hui-Ling Tao
- International Agricultural Institute, Yunnan Academy of Agricultural Sciences, No. 2338, Beijing China Road, Panlong District, Kunming, China (650000)
| | - Yuan-Chao Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1, Shizishan Road, Hongshan District, Wuhan, China (430070)
| | - Zhong-Zi Lou
- The State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1, Xujiaping, Chengguan District, Lanzhou, China (730046)
| | - Wan-Zhong Jia
- The State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1, Xujiaping, Chengguan District, Lanzhou, China (730046)
| | - Li-Hua Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1, Shizishan Road, Hongshan District, Wuhan, China (430070)
| | - Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, No. 1, Shizishan Road, Hongshan District, Wuhan, China (430070)
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Ong RYL, Chan SWB, Chew SJ, Liew WK, Thoon KC, Chong CY, Yung CF, Sng LH, Tan AM, Bhattacharyya R, Jamuar SS, Lim JY, Li J, Nadua KD, Kam KQ, Tan NWH. DISSEMINATED BACILLUS-CALMETTE-GUÉRIN INFECTIONS AND PRIMARY IMMUNODEFICIENCY DISORDERS IN SINGAPORE: A SINGLE CENTER 15-YEAR RETROSPECTIVE REVIEW. Int J Infect Dis 2020; 97:117-125. [PMID: 32497805 DOI: 10.1016/j.ijid.2020.05.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Disseminated Bacillus Calmette-Guérin (BCG) disease (BCGosis) is a classical feature of children with primary immunodeficiency disorders (PIDs). METHODS A 15-year retrospective review was conducted in KK Women's and Children's Hospital in Singapore, from January 2003 to October 2017. RESULTS Ten patients were identified, the majority male (60.0%). The median age at presentation of symptoms of BCG infections was 3.8 (0.8 - 7.4) months. All the patients had likely underlying PIDS - four with Severe Combined Immunodeficiency (SCID), three with Mendelian Susceptibility to Mycobacterial Diseases (MSMD), one with Anhidrotic Ectodermal Dysplasia with Primary Immunodeficiency (EDA-ID), one with combined immunodeficiency (CID), and one with STAT-1 gain-of-function mutation. Definitive BCGosis was confirmed in all patients by the identification of Mycobacterium bovis subsp BCG from microbiological cultures. The susceptibility profiles of Mycobacterium bovis subsp BCG are as follows: Rifampicin (88.9%), Isoniazid (44.47%), Ethambutol (100.0%), Streptomycin (100.0%), Kanamycin (100.0%), Ethionamide (25.0%), and Ofloxacin (100.0%). Four patients (40.0%) received a three-drug regimen. Five patients (50.0%) underwent hematopoietic stem cell transplant (HSCT), of which three (60%) have recovered. Overall mortality was 50.0%. CONCLUSION Disseminated BCG disease (BCGosis) should prompt immunology evaluation to determine the diagnosis of the immune defect. A three-drug regimen is adequate for treatment if the patient undergoes early HSCT.
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Affiliation(s)
- Rina Yue Ling Ong
- Department of Pharmacy, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore.
| | - Su-Wan Bianca Chan
- Rheumatology and Immunology Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Siu Jun Chew
- Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Woei Kang Liew
- Rheumatology and Immunology Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Koh Cheng Thoon
- Infectious Disease Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore 117597, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Lee Kong Chian School of Medicine, National Technological University, 59 Nanyang Drive, Experimental Medicine Building, Singapore 636921, Singapore
| | - Chia-Yin Chong
- Infectious Disease Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore 117597, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Lee Kong Chian School of Medicine, National Technological University, 59 Nanyang Drive, Experimental Medicine Building, Singapore 636921, Singapore
| | - Chee Fu Yung
- Infectious Disease Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Lee Kong Chian School of Medicine, National Technological University, 59 Nanyang Drive, Experimental Medicine Building, Singapore 636921, Singapore
| | - Li-Hwei Sng
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Division of Pathology, Department of Microbiology, Singapore General Hospital
| | - Ah Moy Tan
- Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore 117597, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Haematology/Oncology Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Rajat Bhattacharyya
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Haematology/Oncology Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Saumya Shekhar Jamuar
- Genetics Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiin Ying Lim
- Genetics Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Jiahui Li
- Infectious Disease Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Karen Donceras Nadua
- Infectious Disease Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Kai-Qian Kam
- Infectious Disease Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore
| | - Natalie Woon-Hui Tan
- Infectious Disease Service, Department of Pediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore 229899, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore 117597, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Lee Kong Chian School of Medicine, National Technological University, 59 Nanyang Drive, Experimental Medicine Building, Singapore 636921, Singapore
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Charan AS, Gupta N, Dixit R, Arora P, Patni T, Antony K, Singh M. Pattern of InhA and KatG mutations in isoniazid monoresistant Mycobacterium tuberculosis isolates. Lung India 2020; 37:227-231. [PMID: 32367844 PMCID: PMC7353940 DOI: 10.4103/lungindia.lungindia_204_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aims and Objectives: The aim of the study is to detect the pattern of genetic mutation, i.e., InhA or KatG or both (InhA and katG) in isoniazid (INH) monoresistant mycobacteria and to correlate with the pattern in multidrug-resistant (MDR) isolates. Materials and Methods: In this study, a quantitative research approach was used. The research design was descriptive observational study. The study was conducted at the Department of Respiratory Medicine, JLN Medical College, Ajmer, Rajasthan, and Intermediate Referral Laboratory, State TB Demonstration Centre, Ajmer. A total of 298 samples found to have resistant strains of Mycobacterium tuberculosis were enrolled with purposive sampling. Results: The mean age of patients was 40.27 ± 13.82 years. There were 250 (83.9%) males, while 48 (16.1%) were females. One hundred ninety-two (64.4%) were resistant for INH only, while the rest were resistant to both INH as well as rifampicin (MDR-tuberculosis). The most common mutation in INH monoresistance was katG (125; 65.1%) as compared to inhA (54; 28.1%) and both inhA and katG (13; 6.7%). Among katG mutations, the most common gene pattern was the absence of WT (S315T) and the presence of MUT1 (S315T1). Conclusion: Knowledge about mutation patterns of different INH resistant strains is important in the present era where there is a provision of separate regimens for INH monoresistant TB. Since these mutations are very closely related to high- or low-degree resistance to INH, the therapeutic regimens cannot be generalized.
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Affiliation(s)
- Ashok Singh Charan
- Department of Respiratory Medicine, JLN Medical College, Ajmer, Rajasthan, India
| | - Neeraj Gupta
- Department of Respiratory Medicine, JLN Medical College, Ajmer, Rajasthan, India
| | - Ramakant Dixit
- Department of Respiratory Medicine, JLN Medical College, Ajmer, Rajasthan, India
| | - Piyush Arora
- Department of Respiratory Medicine, JLN Medical College, Ajmer, Rajasthan, India
| | - Tarun Patni
- State TB Demonstration Centre, Ajmer, Rajasthan, India
| | - Kalliath Antony
- Department of Respiratory Medicine, JLN Medical College, Ajmer, Rajasthan, India
| | - Manisha Singh
- Department of Psychiatry, JLN Medical College, Ajmer, Rajasthan, India
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Mourenza Á, Gil JA, Mateos LM, Letek M. Oxidative Stress-Generating Antimicrobials, a Novel Strategy to Overcome Antibacterial Resistance. Antioxidants (Basel) 2020; 9:antiox9050361. [PMID: 32357394 PMCID: PMC7278815 DOI: 10.3390/antiox9050361] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance is becoming one of the most important human health issues. Accordingly, the research focused on finding new antibiotherapeutic strategies is again becoming a priority for governments and major funding bodies. The development of treatments based on the generation of oxidative stress with the aim to disrupt the redox defenses of bacterial pathogens is an important strategy that has gained interest in recent years. This approach is allowing the identification of antimicrobials with repurposing potential that could be part of combinatorial chemotherapies designed to treat infections caused by recalcitrant bacterial pathogens. In addition, there have been important advances in the identification of novel plant and bacterial secondary metabolites that may generate oxidative stress as part of their antibacterial mechanism of action. Here, we revised the current status of this emerging field, focusing in particular on novel oxidative stress-generating compounds with the potential to treat infections caused by intracellular bacterial pathogens.
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Kukhtin AV, Norville R, Bueno A, Qu P, Parrish N, Murray M, Chandler DP, Holmberg RC, Cooney CG. A Benchtop Automated Sputum-to-Genotype System Using a Lab-on-a-Film Assembly for Detection of Multidrug-Resistant Mycobacterium tuberculosis. Anal Chem 2020; 92:5311-5318. [PMID: 32142258 PMCID: PMC7354060 DOI: 10.1021/acs.analchem.9b05853] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Automated genotyping of drug-resistant Mycobacterium tuberculosis (MTB) directly from sputum is challenging for three primary reasons. First, the sample matrix, sputum, is highly viscous and heterogeneous, posing a challenge for sample processing. Second, acid-fast MTB bacilli are difficult to lyse. And third, there are hundreds of MTB mutations that confer drug resistance. An additional constraint is that MTB is most prevalent where test affordability is paramount. We address the challenge of sample homogenization and cell lysis using magnetic rotation of an external magnet, at high (5000) rpm, to induce the rotation of a disposable stir disc that causes chaotic mixing of glass beads ("MagVor"). Nucleic acid is purified using a pipet tip with an embedded matrix that isolates nucleic acid ("TruTip"). We address the challenge of cost and genotyping multiple mutations using 203 porous three-dimensional gel elements printed on a film substrate and enclosed in a microfluidic laminate assembly ("Lab-on-a-Film"). This Lab-on-a-Film assembly (LFA) serves as a platform for amplification, hybridization, washing, and fluorescent imaging, while maintaining a closed format to prevent amplicon contamination of the workspace. We integrated and automated MagVor homogenization, TruTip purification, and LFA amplification in a multisample, sputum-to-genotype system. Using this system, we report detection down to 43 cfu/mL of MTB bacilli from raw sputum.
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Affiliation(s)
- Alexander V Kukhtin
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Ryan Norville
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Arial Bueno
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Peter Qu
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Nicole Parrish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Darrell P Chandler
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Rebecca C Holmberg
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
| | - Christopher G Cooney
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, Maryland 21701, United States
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Solo ES, Nakajima C, Kaile T, Bwalya P, Mbulo G, Fukushima Y, Chila S, Kapata N, Shah Y, Suzuki Y. Mutations in rpoB and katG genes and the inhA operon in multidrug-resistant Mycobacterium tuberculosis isolates from Zambia. J Glob Antimicrob Resist 2020; 22:302-307. [PMID: 32169686 DOI: 10.1016/j.jgar.2020.02.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/26/2019] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES It is established that resistance to rifampicin (RIF) in 90% of RIF-resistant Mycobacterium tuberculosis isolates is attributable to point mutations in the rpoB gene, whilst 50-95% of M. tuberculosis resistance to isoniazid (INH) is caused by mutations in the katG gene. However, the patterns and frequencies of mutations vary by geographical region. In Zambia, the genetic mechanisms of resistance of M. tuberculosis to RIF and INH were unreported before this study. METHODS Using gene sequencing, the rpoB, katG and inhA genes of 99 multidrug-resistant M. tuberculosis (MDR-TB) and 49 pan-susceptible M. tuberculosis isolates stored at a tuberculosis reference laboratory from 2013 to 2016 were analysed and were compared with published profiles from other African countries. RESULTS Of the 99 MDR-TB isolates, 95 (96.0%) carried mutations in both rpoB and katG. No mutations were detected among the pan-susceptible isolates. The most common mutations among RIF- and INH-resistant isolates were in codon 531 of the rpoB gene (55.6%; 55/99) and codon 315 of the katG gene (94.9%; 94/99), respectively. Distinctly, katG mutations were predominantly high among Zambian isolates (96.0%) compared with other countries in the region. CONCLUSION Resistance-associated mutations to RIF and INH circulating in Zambia are similar to those reported globally, therefore these data validate the applicability of molecular diagnostic tools in Zambia. However, katG mutations were predominantly high among M. tuberculosis isolates in this study compared with other regional countries and might distinguish cross-boundary transmission of MDR-TB from other African nations.
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Affiliation(s)
- Eddie S Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan
| | - Trevor Kaile
- University of Zambia, School of Medicine, Lusaka, Zambia
| | - Precious Bwalya
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Grace Mbulo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | | | | | - Yogendra Shah
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
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Antibiotic resistance of Mycobacterium tuberculosis complex in Africa: A systematic review of current reports of molecular epidemiology, mechanisms and diagnostics. J Infect 2019; 79:550-571. [DOI: 10.1016/j.jinf.2019.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 12/11/2022]
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50
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Pharmacoinformatics-based identification of anti-bacterial catalase-peroxidase enzyme inhibitors. Comput Biol Chem 2019; 83:107136. [DOI: 10.1016/j.compbiolchem.2019.107136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/28/2019] [Accepted: 09/29/2019] [Indexed: 11/17/2022]
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