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Chand AB, Basnet A, Maharjan B, Rai G, Joshi YP, Bhatt LR, Sen B, Rai SK. Drug-resistant Mycobacterium tuberculosis among Nepalese patients at a tuberculosis referral center. PLoS One 2024; 19:e0301210. [PMID: 38709710 PMCID: PMC11073693 DOI: 10.1371/journal.pone.0301210] [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: 09/21/2023] [Accepted: 03/12/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB), characterized by isoniazid and rifampicin resistance, is caused by chromosomal mutations that restrict treatment options and complicate tuberculosis management. This study sought to investigate the prevalence of pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR) tuberculosis, as well as mutation pattern, in Nepalese patients with MDR/rifampicin-resistant (RR)-TB strains. METHODS A cross-sectional study was conducted on MDR/RR-TB patients at the German Nepal Tuberculosis Project from June 2017 to June 2018. The MTBDRsl line probe assay identified pre-XDR-TB and XDR-TB. Pre-XDR-TB included MDR/RR-TB with resistance to any fluoroquinolone (FLQ), while XDR-TB included MDR/RR-TB with resistance to any FLQ and at least one additional group A drug. Mutation status was determined by comparing bands on reaction zones [gyrA and gyrB for FLQ resistance, rrs for SILD resistance, and eis for low-level kanamycin resistance, according to the GenoType MTBDRsl VER 2.0, Hain Lifescience GmbH, Nehren, Germany definition of pre-XDR and XDR] to the evaluation sheet. SPSS version 17.0 was used for data analysis. RESULTS Out of a total of 171 patients with MDR/RR-TB, 160 had (93.57%) had MTBC, of whom 57 (35.63%) had pre-XDR-TB and 10 (6.25%) had XDR-TB. Among the pre-XDR-TB strains, 56 (98.25%) were FLQ resistant, while 1 (1.75%) was SLID resistant. The most frequent mutations were found at codons MUT3C (57.14%, 32/56) and MUT1 (23.21%, 13/56) of the gyrA gene. One patient had SLID resistant genotype at the MUT1 codon of the rrs gene (100%, 1/1). XDR-TB mutation bands were mostly detected on MUT1 (30%, 3/10) of the gyrA and rrs, MUT3C (30%, 3/10) of the gyrA, and MUT1 (30%, 3/10) of the rrs. CONCLUSIONS Pre-XDR-TB had a significantly higher likelihood than XDR-TB, with different specific mutation bands present in gyrA and rrs genes.
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Affiliation(s)
- Arun Bahadur Chand
- Department of Microbiology, KIST Medical College and Teaching Hospital, Lalitpur, Nepal
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
- German Nepal Tuberculosis Project, Kathmandu, Nepal
| | - Ajaya Basnet
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | | | - Ganesh Rai
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Yadav Prasad Joshi
- Department of Public Health, Manmohan Memorial Institute of Health Sciences, Kathmandu, Nepal
| | - Lok Raj Bhatt
- Department of Microbiology, KIST Medical College and Teaching Hospital, Lalitpur, Nepal
| | - Bindu Sen
- Department of Dentistry, KIST Medical College and Teaching Hospital, Lalitpur, Nepal
| | - Shiba Kumar Rai
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
- Department of Microbiology, Nepal Medical College Teaching Hospital, Kathmandu, Nepal
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Teng T, Chen S, Huo F, Jia J, Zhao L, Jiang G, Wang F, Chu N, Huang H. Efflux pump effects on levofloxacin resistance in Mycobacterium abscessus. Antimicrob Agents Chemother 2024; 68:e0134823. [PMID: 38572960 PMCID: PMC11064541 DOI: 10.1128/aac.01348-23] [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: 10/20/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Mycobacterium abscessus (M. abscessus) inherently displays resistance to most antibiotics, with the underlying drug resistance mechanisms remaining largely unexplored. Efflux pump is believed to play an important role in mediating drug resistance. The current study examined the potential of efflux pump inhibitors to reverse levofloxacin (LFX) resistance in M. abscessus. The reference strain of M. abscessus (ATCC19977) and 60 clinical isolates, including 41 M. abscessus subsp. abscessus and 19 M. abscessus subsp. massilense, were investigated. The drug sensitivity of M. abscessus against LFX alone or in conjunction with efflux pump inhibitors, including verapamil (VP), reserpine (RSP), carbonyl cyanide 3-chlorophenylhydrazone (CCCP), or dicyclohexylcarbodiimide (DCC), were determined by AlarmarBlue microplate assay. Drug-resistant regions of the gyrA and gyrB genes from the drug-resistant strains were sequenced. The transcription level of the efflux pump genes was monitored using qRT-PCR. All the tested strains were resistant to LFX. The drug-resistant regions from the gyrA and gyrB genes showed no mutation associated with LFX resistance. CCCP, DCC, VP, and RSP increased the susceptibility of 93.3% (56/60), 91.7% (55/60), 85% (51/60), and 83.3% (50/60) isolates to LFX by 2 to 32-fold, respectively. Elevated transcription of seven efflux pump genes was observed in isolates with a high reduction in LFX MIC values in the presence of efflux pump inhibitors. Efflux pump inhibitors can improve the antibacterial activity of LFX against M. abscessus in vitro. The overexpression of efflux-related genes in LFX-resistant isolates suggests that efflux pumps are associated with the development of LFX resistance in M. abscessus.
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Affiliation(s)
- Tianlu Teng
- Department of Respiratory and Critical Care Medicine, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Suting Chen
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Junnan Jia
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Liping Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Fen Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Naihui Chu
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
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Maringolo Ribeiro C, Augusto Roque-Borda C, Carolina Franzini M, Fernanda Manieri K, Manaia Demarqui F, Leite Campos D, Temperani Amaral Machado R, Cristiane da Silva I, Tavares Luiz M, Delello Di Filippo L, Bento da Silva P, Cristina Oliveira da Rocha M, Nair Báo S, Masci D, Fernandes GFS, Castagnolo D, Chorilli M, Rogério Pavan F. Liposome-siderophore conjugates loaded with moxifloxacin serve as a model for drug delivery against Mycobacterium tuberculosis. Int J Pharm 2024; 655:124050. [PMID: 38537924 DOI: 10.1016/j.ijpharm.2024.124050] [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: 11/29/2023] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
Tuberculosis (TB) is an infectious disease that annually affects millions of people, and resistance to available antibiotics has exacerbated this situation. Another notable characteristic of Mycobacterium tuberculosis, the primary causative agent of TB, is its ability to survive inside macrophages, a key component of the immune system. In our quest for an effective and safe treatment that facilitates the targeted delivery of antibiotics to the site of infection, we have proposed a nanotechnology approach based on an iron chelator. Iron chelators are the primary mechanism by which bacteria acquire iron, a metal essential for their metabolism. Four liposomes were synthesized and characterized using the dynamic light scattering technique (DLS), nanoparticle tracking analysis (NTA), and transmission electron microscopy (TEM). All of these methods revealed the presence of spherical particles, approximately 200 nm in size. NTA indicated a concentration of around 1011 particles/mL. We also developed and validated a high-performance liquid chromatography method for quantifying Moxifloxacin to determine encapsulation efficiency (EE) and release profiles (RF). The EE was 51.31 % for LipMox and 45.76 % for LipIchMox. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) confirmed the phagocytosis of liposomal vesicles by macrophages. Functionalizing liposomes with iron chelators can offer significant benefits for TB treatment, such as targeted drug delivery to intracellular bacilli through the phagocytosis of liposomal particles by cells like macrophages.
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Affiliation(s)
- Camila Maringolo Ribeiro
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | | | - Maria Carolina Franzini
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Karyn Fernanda Manieri
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Fernanda Manaia Demarqui
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Débora Leite Campos
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Rachel Temperani Amaral Machado
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Isabel Cristiane da Silva
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Marcela Tavares Luiz
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Leonardo Delello Di Filippo
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Patrícia Bento da Silva
- Cell Biology Department, Institute of Biological Sciences, University of Brasilia, Brasília, Brazil
| | | | - Sônia Nair Báo
- Cell Biology Department, Institute of Biological Sciences, University of Brasilia, Brasília, Brazil
| | - Domiziana Masci
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, 150 Stamford Street, SE1 9NH London, United Kingdom
| | - Guilherme F S Fernandes
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, 150 Stamford Street, SE1 9NH London, United Kingdom; Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Daniele Castagnolo
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, 150 Stamford Street, SE1 9NH London, United Kingdom; Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Marlus Chorilli
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Fernando Rogério Pavan
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil.
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Singha B, Murmu S, Nair T, Rawat RS, Sharma AK, Soni V. Metabolic Rewiring of Mycobacterium tuberculosis upon Drug Treatment and Antibiotics Resistance. Metabolites 2024; 14:63. [PMID: 38248866 PMCID: PMC10820029 DOI: 10.3390/metabo14010063] [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: 12/25/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge, further compounded by the issue of antimicrobial resistance (AMR). AMR is a result of several system-level molecular rearrangements enabling bacteria to evolve with better survival capacities: metabolic rewiring is one of them. In this review, we present a detailed analysis of the metabolic rewiring of Mtb in response to anti-TB drugs and elucidate the dynamic mechanisms of bacterial metabolism contributing to drug efficacy and resistance. We have discussed the current state of AMR, its role in the prevalence of the disease, and the limitations of current anti-TB drug regimens. Further, the concept of metabolic rewiring is defined, underscoring its relevance in understanding drug resistance and the biotransformation of drugs by Mtb. The review proceeds to discuss the metabolic adaptations of Mtb to drug treatment, and the pleiotropic effects of anti-TB drugs on Mtb metabolism. Next, the association between metabolic changes and antimycobacterial resistance, including intrinsic and acquired drug resistance, is discussed. The review concludes by summarizing the challenges of anti-TB treatment from a metabolic viewpoint, justifying the need for this discussion in the context of novel drug discovery, repositioning, and repurposing to control AMR in TB.
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Affiliation(s)
- Biplab Singha
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA;
| | - Sumit Murmu
- Regional Centre of Biotechnology, Faridabad 121001, India;
| | - Tripti Nair
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA;
| | - Rahul Singh Rawat
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, New Delhi 110067, India;
| | - Aditya Kumar Sharma
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
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Ansari MA, Shoaib S, Alomary MN, Ather H, Ansari SMA, Hani U, Jamous YF, Alyahya SA, Alharbi JN, Imran MA, Wahab S, Ahmad W, Islam N. Deciphering the emerging role of phytocompounds: Implications in the management of drug-resistant tuberculosis and ATDs-induced hepatic damage. J Infect Public Health 2023; 16:1443-1459. [PMID: 37523915 DOI: 10.1016/j.jiph.2023.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/05/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Tuberculosis is a disease of poverty, discrimination, and socioeconomic burden. Epidemiological studies suggest that the mortality and incidence of tuberculosis are unacceptably higher worldwide. Genomic mutations in embCAB, embR, katG, inhA, ahpC, rpoB, pncA, rrs, rpsL, gyrA, gyrB, and ethR contribute to drug resistance reducing the susceptibility of Mycobacterium tuberculosis to many antibiotics. Additionally, treating tuberculosis with antibiotics also poses a serious risk of hepatotoxicity in the patient's body. Emerging data on drug-induced liver injury showed that anti-tuberculosis drugs remarkably altered levels of hepatotoxicity biomarkers. The review is an attempt to explore the anti-mycobacterial potential of selected, commonly available, and well-known phytocompounds and extracts of medicinal plants against strains of Mycobacterium tuberculosis. Many studies have demonstrated that phytocompounds such as flavonoids, alkaloids, terpenoids, and phenolic compounds have antibacterial action against Mycobacterium species, inhibiting the bacteria's growth and replication, and sometimes, causing cell death. Phytocompounds act by disrupting bacterial cell walls and membranes, reducing enzyme activity, and interfering with essential metabolic processes. The combination of these processes reduces the overall survivability of the bacteria. Moreover, several phytochemicals have synergistic effects with antibiotics routinely used to treat TB, improving their efficacy and decreasing the risk of resistance development. Interestingly, phytocompounds have been presented to reduce isoniazid- and ethambutol-induced hepatotoxicity by reversing serum levels of AST, ALP, ALT, bilirubin, MDA, urea, creatinine, and albumin to their normal range, leading to attenuation of inflammation and hepatic necrosis. As a result, phytochemicals represent a promising field of research for the development of new TB medicines.
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Affiliation(s)
- Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441 Dammam, Saudi Arabia.
| | - Shoaib Shoaib
- Department Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mohammad N Alomary
- Advanced Diagnostic and Therapeutic Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Hissana Ather
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | | | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Yahya F Jamous
- Vaccine and Bioprocessing Center, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Sami A Alyahya
- Wellness and Preventive Medicine Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Jameela Naif Alharbi
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441 Dammam, Saudi Arabia
| | - Mohammad Azhar Imran
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 120752, Republic of Korea
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - Wasim Ahmad
- Department of Pharmacy, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Najmul Islam
- Department Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India.
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An Q, Lin R, Yang Q, Wang C, Wang D. Evaluation of genetic mutations associated with phenotypic resistance to fluoroquinolones, bedaquiline, and linezolid in clinical Mycobacterium tuberculosis: A systematic review and meta-analysis. J Glob Antimicrob Resist 2023; 34:214-226. [PMID: 37172764 DOI: 10.1016/j.jgar.2023.05.001] [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: 12/28/2022] [Revised: 03/26/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
OBJECTIVES The aim of the study was to update the classification of drugs used in multidrug-resistant tuberculosis (MDR-TB) regimens. Group A drugs (fluoroquinolones, bedaquiline (BDQ), and linezolid (LZD)) are crucial drugs for the control of MDR-TB. Molecular drug resistance assays could facilitate the effective use of Group A drugs. METHODS We summarised the evidence implicating specific genetic mutations in resistance to Group A drugs. We searched PubMed, Embase, MEDLINE, and the Cochrane Library for studies published from the inception of each database until July 1, 2022. Using a random-effects model, we calculated the odds ratios and 95% confidence intervals as our measures of association. RESULTS A total of 5001 clinical isolates were included in 47 studies. Mutations in gyrA A90V, D94G, D94N, and D94Y were significantly associated with an increased risk of a levofloxacin (LFX)-resistant phenotype. In addition, mutations in gyrA G88C, A90V, D94G, D94H, D94N, and D94Y were significantly associated with an increased risk of a moxifloxacin (MFX)-resistant phenotype. In only one study, the majority of gene loci (n = 126, 90.65%) in BDQ-resistant isolates were observed to have unique mutations in atpE, Rv0678, mmpL5, pepQ, and Rv1979c. The most common mutations occurred at four sites in the rrl gene (g2061t, g2270c, g2270t, and g2814t) and at one site in rplC (C154R) in LZD-resistant isolates. Our meta-analysis demonstrated that there were no mutations associated with BDQ- or LZD-resistant phenotypes. CONCLUSION The mutations detected by rapid molecular assay were correlated with phenotypic resistance to LFX and MFX. The absence of mutation-phenotype associations for BDQ and LZD hindered the development of a rapid molecular assay.
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Affiliation(s)
- Qi An
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Rui Lin
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Qing Yang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Chuan Wang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China.
| | - Dongmei Wang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China.
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Jeon SM, Park S, Lim NR, Lee N, Jung J, Sung N, Kim S. Molecular Analysis of Anti-Tuberculosis Drug Resistance of Mycobacterium tuberculosis Isolated in the Republic of Korea. Antibiotics (Basel) 2023; 12:1324. [PMID: 37627744 PMCID: PMC10451913 DOI: 10.3390/antibiotics12081324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid and accurate detection of tuberculosis (TB) drug resistance is critical for the successful treatment and control of TB. Here, we investigated resistance to anti-TB drugs and genetic variations in 215 drug-resistant Mycobacterium tuberculosis isolates in Korea. Genetic variations were observed in rpoB Ser531Leu, katG Ser315Thr, and gyrA Asp94Gly; however, the minimum inhibitory concentrations varied, which can be attributed to other resistance mechanisms. Examination of genetic relatedness among drug-resistant isolates revealed that the cluster size of resistant bacteria was less than six strains, suggesting no evidence of a large-scale epidemic caused by a specific strain. However, rpoC mutants of the rifampicin-resistant isolates were composed of five types of clusters, suggesting that these compensatory mutations advance propagation. In the present study, more than 90% of the resistance mechanisms to major anti-TB drugs were identified, and the effect of each mutation on drug resistance was estimated. With the clinical application of recent next-generation sequencing-based susceptibility testing, the present study is expected to improve the clinical utilization of genotype-based drug susceptibility testing for the diagnosis and treatment of patients with drug-resistant TB.
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Affiliation(s)
- Se-Mi Jeon
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Sanghee Park
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Na-Ra Lim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Noori Lee
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Jihee Jung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Nackmoon Sung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Seonghan Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
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Sharma RK, Kumari U, Kumari N, Kumar R. Characterization of Genetic Mutations in Multi-Drug-Resistant Isolates of Mycobacterium tuberculosis Bacilli Conferring Resistance to a Second-Line Anti-tuberculosis Drug. Cureus 2023; 15:e40442. [PMID: 37456413 PMCID: PMC10349655 DOI: 10.7759/cureus.40442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
INTRODUCTION Multi-drug-resistant tuberculosis (MDR-TB) has become a major public health concern globally. Mutations in first- and second-line drug targets such as katG, inhA, rpoB, rrs, eis, gyrA, and gyrB have been associated with drug resistance. Monitoring predominant mutations in the MDR-TB patient population is essential to monitor and devise future therapeutic regimes. The present study is aimed to characterize genetic mutations in MDR isolates of Mycobacterium tuberculosis (MTB) bacilli conferring resistance to a second-line anti-tuberculosis drug in the Eastern Indian population. METHODS This cross-sectional study was conducted in the Department of Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, Bihar, and in the Tuberculosis Demonstration & Training Centre, Agamkuan, Patna. A total of 3270 patients suspected to have MDR-TB were recruited in the study. Two sputum samples, one on the spot, and the other in the morning were collected from each patient and the diagnosis of rifampicin-sensitive (RS)/rifampicin-resistant (RR/MDR) TB was done by Gene-Xpert test. One hundred fifty RS-TB samples and 150 RR/MDR-TB samples were considered for line probe assay (LPA). RS samples were subjected to first-line LPA using Genotype® MTBDR Plus ver 2.0 and RR/MDR samples were considered for second-line LPA using Genotype® MTBDRsl ver 2.0. All sputum samples were subjected to sputum smear microscopy using the Ziehl-Neelsen staining method. Statistical analysis was done using Statistical Package for Social Sciences (SPSS) version 26.0 (IBM Corp. Armonk, NY) and R (version 4.1; R Core Team 2021). RESULTS In the present study, out of 3270 patients, we detected RR/MDR-TB in 235 patients (7.19%), RS-TB in 812 patients (24.83%), the rest of the patients negative for MTB (2223, 67.98%). Out of 150 RR/MDR-TB sputum samples tested, resistance to fluoroquinolone (FQ) was observed in 41 samples. The selected patients had predominantly FQ resistance due to the gyrA gene mutations (97.56%, n=40) compared to the gyrB gene mutations (2.44%, n=1). We observed >60% of the mutations in the gyrA gene in codon 94 (MUT3C (D94G), MUT3A (D94A), and MUT3D (D94H). In addition, we found the mutations MUT1 (A90V) and MUT2 (S91P) in the codons 90 and 91 of the gyrA gene in the considered MTB patient population. CONCLUSION The identified genes can be further validated to be considered as therapeutic targets, but more therapeutics and advanced strategies should be applied in the management of MTB.
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Affiliation(s)
| | - Usha Kumari
- Biochemistry, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Namrata Kumari
- Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Rakesh Kumar
- Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, IND
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Stanley S, Liu Q, Fortune SM. Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine. Front Cell Infect Microbiol 2022; 12:1007958. [PMID: 36262182 PMCID: PMC9574059 DOI: 10.3389/fcimb.2022.1007958] [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] [Received: 07/31/2022] [Accepted: 09/14/2022] [Indexed: 01/27/2023] Open
Abstract
In the face of the unrelenting global burden of tuberculosis (TB), antibiotics remain our most effective tools to save lives and control the spread of Mycobacterium tuberculosis (Mtb). However, we confront a dual challenge in our use of antibiotics: simplifying and shortening the TB drug regimen while also limiting the emergence and propagation of antibiotic resistance. This task is now more feasible due to the increasing availability of bacterial genomic data at or near the point of care. These resources create an opportunity to envision how integration of bacterial genetic determinants of antibiotic response into treatment algorithms might transform TB care. Historically, Mtb drug resistance studies focused on mutations in genes encoding antibiotic targets and the resulting increases in the minimal inhibitory concentrations (MICs) above a breakpoint value. But recent progress in elucidating the effects of functional genetic diversity in Mtb has revealed various genetic loci that are associated with drug phenotypes such as low-level MIC increases and tolerance which predict the development of resistance and treatment failure. As a result, we are now poised to advance precision medicine approaches in TB treatment. By incorporating information regarding Mtb genetic characteristics into the development of drug regimens, clinical care which tailors antibiotic treatment to maximize the likelihood of success has come into reach.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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10
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Singh A, Zhao X, Drlica K. Fluoroquinolone heteroresistance, antimicrobial tolerance, and lethality enhancement. Front Cell Infect Microbiol 2022; 12:938032. [PMID: 36250047 PMCID: PMC9559723 DOI: 10.3389/fcimb.2022.938032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
With tuberculosis, the emergence of fluoroquinolone resistance erodes the ability of treatment to interrupt the progression of MDR-TB to XDR-TB. One way to reduce the emergence of resistance is to identify heteroresistant infections in which subpopulations of resistant mutants are likely to expand and make the infections fully resistant: treatment modification can be instituted to suppress mutant enrichment. Rapid DNA-based detection methods exploit the finding that fluoroquinolone-resistant substitutions occur largely in a few codons of DNA gyrase. A second approach for restricting the emergence of resistance involves understanding fluoroquinolone lethality through studies of antimicrobial tolerance, a condition in which bacteria fail to be killed even though their growth is blocked by lethal agents. Studies with Escherichia coli guide work with Mycobacterium tuberculosis. Lethal action, which is mechanistically distinct from blocking growth, is associated with a surge in respiration and reactive oxygen species (ROS). Mutations in carbohydrate metabolism that attenuate ROS accumulation create pan-tolerance to antimicrobials, disinfectants, and environmental stressors. These observations indicate the existence of a general death pathway with respect to stressors. M. tuberculosis displays a variation on the death pathway idea, as stress-induced ROS is generated by NADH-mediated reductive stress rather than by respiration. A third approach, which emerges from lethality studies, uses a small molecule, N-acetyl cysteine, to artificially increase respiration and additional ROS accumulation. That enhances moxifloxacin lethality with M. tuberculosis in culture, during infection of cultured macrophages, and with infection of mice. Addition of ROS stimulators to fluoroquinolone treatment of tuberculosis constitutes a new direction for suppressing the transition of MDR-TB to XDR-TB.
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Affiliation(s)
- Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- *Correspondence: Amit Singh, ; Karl Drlica,
| | - Xilin Zhao
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Karl Drlica
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- *Correspondence: Amit Singh, ; Karl Drlica,
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Salman M, Sharma P, Kumar M, Ethayathulla AS, Kaur P. Targeting novel sites in DNA gyrase for development of anti-microbials. Brief Funct Genomics 2022; 22:180-194. [PMID: 36064602 DOI: 10.1093/bfgp/elac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance in bacteria poses major challenges in selection of the therapeutic regime for managing the infectious disease. There is currently an upsurge in the appearance of multiple drug resistance in bacterial pathogens and a decline in the discovery of novel antibiotics. DNA gyrase is an attractive target used for antibiotic discovery due to its vital role in bacterial DNA replication and segregation in addition to its absence in mammalian organisms. Despite the presence of successful antibiotics targeting this enzyme, there is a need to bypass the resistance against this validated drug target. Hence, drug development in DNA gyrase is a highly active research area. In addition to the conventional binding sites for the novobiocin and fluoroquinolone antibiotics, several novel sites are being exploited for drug discovery. The binding sites for novel bacterial type II topoisomerase inhibitor (NBTI), simocyclinone, YacG, Thiophene and CcdB are structurally and biochemically validated active sites, which inhibit the supercoiling activity of topoisomerases. The novel chemical moieties with varied scaffolds have been identified to target DNA gyrase. Amongst them, the NBTI constitutes the most advanced DNA gyrase inhibitor which are in phase III trial of drug development. The present review aims to classify the novel binding sites other than the conventional novobiocin and quinolone binding pocket to bypass the resistance due to mutations in the DNA gyrase enzyme. These sites can be exploited for the identification of new scaffolds for the development of novel antibacterial compounds.
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Affiliation(s)
- Mohd Salman
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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12
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Finci I, Albertini A, Merker M, Andres S, Bablishvili N, Barilar I, Cáceres T, Crudu V, Gotuzzo E, Hapeela N, Hoffmann H, Hoogland C, Kohl TA, Kranzer K, Mantsoki A, Maurer FP, Nicol MP, Noroc E, Plesnik S, Rodwell T, Ruhwald M, Savidge T, Salfinger M, Streicher E, Tukvadze N, Warren R, Zemanay W, Zurek A, Niemann S, Denkinger CM. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study. THE LANCET. MICROBE 2022; 3:e672-e682. [PMID: 35907429 PMCID: PMC9436784 DOI: 10.1016/s2666-5247(22)00116-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce. METHODS In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS. FINDINGS Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations. INTERPRETATION The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background). FUNDING Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.
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Affiliation(s)
- Iris Finci
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; Evolution of the Resistome, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Nino Bablishvili
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Tatiana Cáceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeriu Crudu
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Nchimunya Hapeela
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Harald Hoffmann
- SYNLAB Gauting, SYNLAB MVZ Dachau, Gauting, Germany; Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | | | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Katharina Kranzer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Biomedical Research and Training Institute, Harare, Zimbabwe
| | | | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark P Nicol
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Ecaterina Noroc
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Sara Plesnik
- Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | - Timothy Rodwell
- FIND, Geneva, Switzerland; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Theresa Savidge
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA; Alaska State Public Health Laboratories, Anchorage, AK, USA
| | - Max Salfinger
- College of Public Health, University of South Florida, Tampa, FL, USA; Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Elizabeth Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nestani Tukvadze
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Robin Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Widaad Zemanay
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna Zurek
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Claudia M Denkinger
- FIND, Geneva, Switzerland; German Center for Infection Research, Heidelberg, Germany; Division of Clinical Tropical Medicine and German Centre for Infection Research, Heidelberg University Hospital, Heidelberg, Germany.
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Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms. PLoS Biol 2022; 20:e3001755. [PMID: 35944070 PMCID: PMC9363015 DOI: 10.1371/journal.pbio.3001755] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.
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Shi Y, Kong W, Jiang H, Zhang W, Wang C, Wu L, Shen Y, Yao Q, Wang H. Molecular Surveillance of Antimicrobial Resistance of Mycobacterium leprae from Leprosy Patients in Zhejiang Province, China. Infect Drug Resist 2022; 15:4029-4036. [PMID: 35924023 PMCID: PMC9342246 DOI: 10.2147/idr.s368682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/06/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Reports on antimicrobial resistance (AMR) of Mycobacterium leprae (M. leprae) in Zhejiang Province are limited. Thus, this study aimed to investigate the drug resistance of new leprosy cases within several years and analyse the emergence of AMR mutations from Zhejiang Province. Methods This study enrolled 34 leprosy cases in Zhejiang Province, China, from 2018 to 2021. Gene mutation of WHO-recommended DRDRs (folP1, rpoB and gyrA) and genes of compensatory AMR-associated DRDRs, including nth, rpoA, rpoC, gyrB and 23S rRNA, were detected by amplification. Clinical data analysis was performed to investigate the epidemiological association of leprosy. Results Of the 34 samples, 2 (5.9%) strains showed drug resistance, which were mutated to dapsone and ofloxacin, separately. Two single mutations in gyrB were detected in different strains (5.9%), whereas one of the rpoC mutation was also detected in one strain each (2.9%), which were proved to be polymorphs. No correlation of drug resistance proportion was identified in male vs female, nerve vs no nerve involvement, deformity vs no deformity and reaction vs non-reaction cases. Conclusion Results showed well control of leprosy patients in Zhejiang Province. Gene mutations of WHO-recommended DRDRs folP1 and gyrA confirmed the resistance to dapsone and ofloxacin. Compensatory AMR-associated mutations confirmed to be polymorphs still require further study to determine their phenotypic outcomes in M. leprae. The results demonstrated that drug-resistant strains are not epidemic in this area. Given the few cases of leprosy, analysing the AMR of M. leprae in Zhejiang Province more comprehensively is difficult. However, regular MDT treatment and population management in the early stage may contribute to the low prevalence of leprosy.
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Affiliation(s)
- Ying Shi
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
| | - Wenming Kong
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
| | - Haiqin Jiang
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
| | - Wenyue Zhang
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
| | - Chen Wang
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Limei Wu
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
| | - Yunliang Shen
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
| | - Qiang Yao
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
- Correspondence: Qiang Yao, Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, St 61, Zhejiang, People’s Republic of China, Email
| | - Hongsheng Wang
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
- Centre for Global health, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
- Hongsheng Wang, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 12 Jiangwangmiao Street, Nanjing, People’s Republic of China, Tel: +86 025 8547 8953, Email
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Li H, Yuan J, Duan S, Pang Y. Resistance and tolerance of Mycobacterium tuberculosis to antimicrobial agents-How M. tuberculosis can escape antibiotics. WIREs Mech Dis 2022; 14:e1573. [PMID: 35753313 DOI: 10.1002/wsbm.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) poses a serious threat to public health worldwide since it was discovered. Until now, TB has been one of the top 10 causes of death from a single infectious disease globally. The treatment of active TB cases majorly relies on various anti-tuberculosis drugs. However, under the selection pressure by drugs, the continuous evolution of Mycobacterium tuberculosis (Mtb) facilitates the emergence of drug-resistant strains, further resulting in the accumulation of tubercle bacilli with multiple drug resistance, especially deadly multidrug-resistant TB and extensively drug-resistant TB. Researches on the mechanism of drug action and drug resistance of Mtb provide a new scheme for clinical management of TB patients, and prevention of drug resistance. In this review, we summarized the molecular mechanisms of drug resistance of existing anti-TB drugs to better understand the evolution of drug resistance of Mtb, which will provide more effective strategies against drug-resistant TB, and accelerate the achievement of the EndTB Strategy by 2035. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jinfeng Yuan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shujuan Duan
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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16
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Maringolo-Ribeiro C, Grecco JA, Bellato DL, Almeida AL, Baldin VP, Caleffi-Ferracioli KR, Pavan FR. Rescue of susceptibility to second-line drugs in resistant clinical isolates of Mycobacterium tuberculosis. Future Microbiol 2022; 17:511-527. [PMID: 35317616 DOI: 10.2217/fmb-2021-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Antibiotic resistance is one of the biggest threats to global health, and this study aimed better understand how the efflux pumps are related to this process in tuberculosis clinical isolates. Results: The combination of antibiotics plus efflux pumps (EP) inhibitors was able to restore the susceptibility of clinical isolates in 100% of aminoglycosides resistance and 33.3% of the fluoroquinolones resistance. The relative expression of EP genes in pre-extensively drug-resistant isolates showed an increase of up to 1000-times. Conclusion: The rescue of susceptibility in the presence of EP inhibitors, the increased of activity and expression of the EP genes alert that the inhibition of EP can reduce the selection of resistant strains and improve treatment.
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Affiliation(s)
- Camila Maringolo-Ribeiro
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Júlia A Grecco
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Débora L Bellato
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
| | - Aryadne L Almeida
- State University of Maringá (UEM), Department of Clinical Analysis & Biomedicine, Maringá, Paraná, Brazil
| | - Vanessa P Baldin
- State University of Maringá (UEM), Department of Clinical Analysis & Biomedicine, Maringá, Paraná, Brazil
| | | | - Fernando R Pavan
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, Araraquara, São Paulo, Brazil
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17
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Uddin MKM, Ather MF, Nasrin R, Rahman T, Islam ASMI, Rahman SMM, Ahmed S, Banu S. Correlation of gyr Mutations with the Minimum Inhibitory Concentrations of Fluoroquinolones among Multidrug-Resistant Mycobacterium tuberculosis Isolates in Bangladesh. Pathogens 2021; 10:1422. [PMID: 34832578 PMCID: PMC8623510 DOI: 10.3390/pathogens10111422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/30/2022] Open
Abstract
Fluoroquinolone (FQ) compounds-moxifloxacin (MOX), levofloxacin (LEV), and ofloxacin (OFL)-are used to treat multidrug-resistant tuberculosis (MDR-TB) globally. In this study, we investigated the correlation of gyr mutations among Mtb isolates with the MICs of MOX, LEV, and OFL in Bangladesh. A total of 50 MDR-TB isolates with gyr mutations, detected by the GenoType MTBDRsl assay, were subjected to drug susceptibility testing to determine the MICs of the FQs. Spoligotyping was performed to correlate the genetic diversity of the gyr mutant isolates with different MIC distributions. Among the 50 isolates, 44 (88%) had mutations in the gyrA gene, one (2%) had a mutation in the gyrB gene, and five (10%) isolates had unidentified mutations. The substitutions in the gyrA region were at A90V (n = 19, 38%), D94G (n = 16, 32%), D94A (n = 4, 8%), D94N/D94Y (n = 4, 8%), and S91P (n = 1, 2%), compared to the gyrB gene at N538D (n = 1.2%). D94G mutations showed the highest MICs for MOX, LEV, and OFL, ranging between 4.0 and 8.0 μg/mL, 4.0 and 16.0 μg/mL, and 16.0 and 32.0 μg/mL, respectively; while the most common substitution of A90V showed the lowest ranges of MICs (1.0-4.0 μg/mL, 2.0-8.0 μg/mL, and 4.0-32.0 μg/mL, respectively). Spoligotyping lineages demonstrated no significant differences regarding the prevalence of different gyr mutations. In conclusion, the substitutions of codon A90V and D94G in the gyr genes were mostly responsible for the FQs' resistance among Mtb isolates in Bangladesh. Low levels of resistance were associated with the substitutions of A90V, while the D94G substitutions were associated with a high level of resistance to all FQs.
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Affiliation(s)
| | | | | | | | | | | | | | - Sayera Banu
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh; (M.K.M.U.); (M.F.A.); (R.N.); (T.R.); (A.S.M.I.I.); (S.M.M.R.); (S.A.)
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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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19
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Maruri F, Guo Y, Blackman A, van der Heijden YF, Rebeiro PF, Sterling TR. Resistance-Conferring Mutations on Whole-Genome Sequencing of Fluoroquinolone-resistant and -Susceptible Mycobacterium tuberculosis Isolates: A Proposed Threshold for Identifying Resistance. Clin Infect Dis 2021; 72:1910-1918. [PMID: 32348473 PMCID: PMC8315129 DOI: 10.1093/cid/ciaa496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Fluoroquinolone resistance in Mycobacterium tuberculosis (Mtb) is conferred by DNA gyrase mutations, but not all fluoroquinolone-resistant Mtb isolates have mutations detected. The optimal allele frequency threshold to identify resistance-conferring mutations by whole-genome sequencing is unknown. METHODS Phenotypically ofloxacin-resistant and lineage-matched ofloxacin-susceptible Mtb isolates underwent whole-genome sequencing at an average coverage depth of 868 reads. Polymorphisms within the quinolone-resistance-determining region (QRDR) of gyrA and gyrB were identified. The allele frequency threshold using the Genome Analysis Toolkit pipeline was ~8%; allele-level data identified the predominant variant allele frequency and mutational burden (ie, sum of all variant allele frequencies in the QRDR) in gyrA, gyrB, and gyrA + gyrB for each isolate. Receiver operating characteristic (ROC) curves assessed the optimal measure of allele frequency and potential thresholds for identifying phenotypically resistant isolates. RESULTS Of 42 ofloxacin-resistant Mtb isolates, area under the ROC curve (AUC) was highest for predominant variant allele frequency, so that measure was used to evaluate optimal mutation detection thresholds. AUCs for 8%, 2.5%, and 0.8% thresholds were 0.8452, 0.9286, and 0.9069, respectively. Sensitivity and specificity were 69% and 100% for 8%, 86% and 100% for 2.5%, 91% and 91% for 0.8%. The sensitivity of the 2.5% and 0.8% thresholds were significantly higher than the 8% threshold (P = .016 and .004, respectively) but not significantly different between one another (P = .5). CONCLUSIONS A predominant mutation allele frequency threshold of 2.5% had the highest AUC for detecting DNA gyrase mutations that confer ofloxacin resistance, and was therefore the optimal threshold.
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Affiliation(s)
- Fernanda Maruri
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yan Guo
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Amondrea Blackman
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yuri F van der Heijden
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- The Aurum Institute, Johannesburg, South Africa
| | - Peter F Rebeiro
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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20
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Santos-Lazaro D, Gavilan RG, Solari L, Vigo AN, Puyen ZM. Whole genome analysis of extensively drug resistant Mycobacterium tuberculosis strains in Peru. Sci Rep 2021; 11:9493. [PMID: 33947918 PMCID: PMC8097007 DOI: 10.1038/s41598-021-88603-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/14/2021] [Indexed: 02/02/2023] Open
Abstract
Peru has the highest burden of multidrug-resistant tuberculosis in the Americas region. Since 1999, the annual number of extensively drug-resistant tuberculosis (XDR-TB) Peruvian cases has been increasing, becoming a public health challenge. The objective of this study was to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Peruvian patients with XDR-TB diagnosed from 2011 to 2015 in Peru. Whole genome sequencing (WGS) was performed on 68 XDR-TB strains from different regions of Peru. 58 (85.3%) strains came from the most populated districts of Lima and Callao. Concerning the lineages, 62 (91.2%) strains belonged to the Euro-American Lineage, while the remaining 6 (8.8%) strains belonged to the East-Asian Lineage. Most strains (90%) had high-confidence resistance mutations according to pre-established WHO-confident grading system. Discordant results between microbiological and molecular methodologies were caused by mutations outside the hotspot regions analysed by commercial molecular assays (rpoB I491F and inhA S94A). Cluster analysis using a cut-off ≤ 10 SNPs revealed that only 23 (34%) strains evidenced recent transmission links. This study highlights the relevance and utility of WGS as a high-resolution approach to predict drug resistance, analyse transmission of strains between groups, and determine evolutionary patterns of circulating XDR-TB strains in the country.
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Affiliation(s)
| | - Ronnie G. Gavilan
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru ,grid.441740.20000 0004 0542 2122Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Lely Solari
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru
| | - Aiko N. Vigo
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru
| | - Zully M. Puyen
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru ,grid.441917.e0000 0001 2196 144XEscuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
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21
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Singh P, Jamal S, Ahmed F, Saqib N, Mehra S, Ali W, Roy D, Ehtesham NZ, Hasnain SE. Computational modeling and bioinformatic analyses of functional mutations in drug target genes in Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:2423-2446. [PMID: 34025934 PMCID: PMC8113780 DOI: 10.1016/j.csbj.2021.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022] Open
Abstract
MycoTRAP-DB, a database of mutations and their impact on normal functionality of protein in M.tb genes. Several secondary mutations were identified with significant impact on protein structure and function. Comprehensive information gives insight for screening of suspected hotspots in advance to combat drug resistant TB.
Tuberculosis (TB) continues to be the leading cause of deaths due to its persistent drug resistance and the consequent ineffectiveness of anti-TB treatment. Recent years witnessed huge amount of sequencing data, revealing mutations responsible for drug resistance. However, the lack of an up-to-date repository remains a barrier towards utilization of these data and identifying major mutations-associated with resistance. Amongst all mutations, non-synonymous mutations alter the amino acid sequence of a protein and have a much greater effect on pathogenicity. Hence, this type of gene mutation is of prime interest of the present study. The purpose of this study is to develop an updated database comprising almost all reported substitutions within the Mycobacterium tuberculosis (M.tb) drug target genes rpoB, inhA, katG, pncA, gyrA and gyrB. Various bioinformatics prediction tools were used to assess the structural and biophysical impacts of the resistance causing non-synonymous single nucleotide polymorphisms (nsSNPs) at the molecular level. This was followed by evaluating the impact of these mutations on binding affinity of the drugs to target proteins. We have developed a comprehensive online resource named MycoTRAP-DB (Mycobacterium tuberculosis Resistance Associated Polymorphisms Database) that connects mutations in genes with their structural, functional and pathogenic implications on protein. This database is accessible at http://139.59.12.92. This integrated platform would enable comprehensive analysis and prioritization of SNPs for the development of improved diagnostics and antimycobacterial medications. Moreover, our study puts forward secondary mutations that can be important for prognostic assessments of drug-resistance mechanism and actionable anti-TB drugs.
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Affiliation(s)
- Pooja Singh
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Salma Jamal
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Faraz Ahmed
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Najumu Saqib
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Seema Mehra
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Waseem Ali
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Deodutta Roy
- Department of Environmental and Occupational Health, Florida International University, Miami 33029, USA
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201301, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110016, India
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22
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Al-Mutairi NM, Ahmad S, Mokaddas E. Increasing prevalence of resistance to second-line drugs among multidrug-resistant Mycobacterium tuberculosis isolates in Kuwait. Sci Rep 2021; 11:7765. [PMID: 33833390 PMCID: PMC8032671 DOI: 10.1038/s41598-021-87516-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/30/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular methods detect genetic mutations associated with drug resistance. This study detected resistance-conferring mutations in gyrA/gyrB for fluoroquinolones and rrs/eis genes for second-line injectable drugs (SLIDs) among multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates in Kuwait. Fifty pansusceptible M. tuberculosis and 102 MDR-TB strains were tested. Phenotypic susceptibility testing was performed by MGIT 960 system using SIRE drug kit. GenoType MTBDRsl version 1 (gMTBDRslv1) and GenoType MTBDRsl version 2 (gMTBDRslv2) tests were used for mutation detection. Results were validated by PCR-sequencing of respective genes. Fingerprinting was performed by spoligotyping. No mutations were detected in pansusceptible isolates. gMTBDRslv1 detected gyrA mutations in 12 and rrs mutations in 8 MDR-TB isolates. gMTBDRsl2 additionally detected gyrB mutations in 2 and eis mutation in 1 isolate. Mutations in both gyrA/gyrB and rrs/eis were not detected. gMTBDRslv1 also detected ethambutol resistance-conferring embB mutations in 59 isolates. Although XDR-TB was not detected, frequency of resistance-conferring mutations for fluoroquinolones or SLIDs was significantly higher among isolates collected during 2013–2019 versus 2006–2012. Application of both tests is warranted for proper management of MDR-TB patients in Kuwait as gMTBDRslv2 detected resistance to fluoroquinolones and/or SLIDs in 3 additional isolates while gMTBDRslv1 additionally detected resistance to ethambutol in 58% of MDR-TB isolates.
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Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.,Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
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23
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Hänel I, Müller E, Santamarina BG, Tomaso H, Hotzel H, Busch A. Antimicrobial Susceptibility and Genomic Analysis of Aliarcobacter cibarius and Aliarcobacter thereius, Two Rarely Detected Aliarcobacter Species. Front Cell Infect Microbiol 2021; 11:532989. [PMID: 33816322 PMCID: PMC8010192 DOI: 10.3389/fcimb.2021.532989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 01/19/2021] [Indexed: 01/06/2023] Open
Abstract
Aliarcobacter cibarius and Aliarcobacter thereius are two rarely detected Aliarcobacter species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic Campylobacter species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide. The genus Aliarcobacter is part of the Campylobacteraceae family and includes the species Aliarcobacter butzleri, Aliarcobacter cryaerophilus, Aliarcobacter skirrowii, and the rarely described Aliarcobacter cibarius, Aliarcobacter faecis, Aliarcobacter lanthieri, Aliarcobacter thereius, and Acrobarter trophiarum. Aliarcobacter are emergent enteropathogens and potential zoonotic agents. Here, we generated, analyzed, and characterized whole-genome sequences of Aliarcobacter cibarius and Aliarcobacter thereius. They were isolated from water poultry farms in Germany, cultured and identified by MALDI-TOF MS. With PCR the identity was verified. Antibiotic susceptibility testing was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, streptomycin, ampicillin, and cefotaxime using the gradient strip method (E-test). Whole-genome sequences were generated including those of reference strains. Complete genomes for six selected strains are reported. These provide detailed insights into the genotype. With these, we predicted in silico known AMR genes, virulence-associated genes, and plasmid replicons. Phenotypic analysis of resistance showed differences between the presence of resistance genes and the prediction of phenotypic resistance profiles. In Aliarcobacter butzleri, the nucleotide sequence of the gyrA gene (DQ464331) can show a signature mutation resulting in an amino acid change T85>I. Acrobarter cibarius and Acrobarter thereius showed the same gene as assessed by similarity annotation of the mutations 254C>G. Most of the isolates were found to be sensitive to ciprofloxacin. The ciprofloxacin-resistant Aliarcobacter thereius isolate was associated with the amino acid change T85>I. But this was not predicted with antibiotic resistance databases, before. Ultimately, a phylogenetic analysis was done to facilitate in future outbreak analysis.
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Affiliation(s)
- Ingrid Hänel
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany
| | - Eva Müller
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany
| | | | | | - Helmut Hotzel
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany
| | - Anne Busch
- IBIZ, Friedrich-Loeffler-Institut Jena, Jena, Germany.,Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Jena, Germany
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24
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Xpert MTB/XDR: a 10-Color Reflex Assay Suitable for Point-of-Care Settings To Detect Isoniazid, Fluoroquinolone, and Second-Line-Injectable-Drug Resistance Directly from Mycobacterium tuberculosis-Positive Sputum. J Clin Microbiol 2021; 59:JCM.02314-20. [PMID: 33298611 DOI: 10.1128/jcm.02314-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/22/2020] [Indexed: 11/20/2022] Open
Abstract
We describe the design, development, analytical performance, and a limited clinical evaluation of the 10-color Xpert MTB/XDR assay (CE-IVD only, not for sale in the United States). This assay is intended as a reflex test to detect resistance to isoniazid (INH), fluoroquinolones (FLQ), ethionamide (ETH), and second-line injectable drugs (SLIDs) in unprocessed sputum samples and concentrated sputum sediments which are positive for Mycobacterium tuberculosis The Xpert MTB/XDR assay simultaneously amplifies eight genes and promoter regions in M. tuberculosis and analyzes melting temperatures (Tm s) using sloppy molecular beacon (SMB) probes to identify mutations associated with INH, FLQ, ETH, and SLID resistance. Results can be obtained in under 90 min using 10-color GeneXpert modules. The assay can differentiate low- versus high-level resistance to INH and FLQ as well as cross-resistance versus individual resistance to SLIDs by identifying mutation-specific Tm s or Tm patterns generated by the SMB probes. The assay has a limit of detection comparable to that of the Xpert MTB/RIF assay and successfully detected 16 clinically significant mutations in a challenge set of clinical isolate DNA. In a clinical study performed at two sites with 100 sputum and 214 clinical isolates, the assay showed a sensitivity of 94% to 100% and a specificity of 100% for all drugs except for ETH compared to that of sequencing. The sensitivity and specificity were in the same ranges as those of phenotypic drug-susceptibility testing. Used in combination with a primary tuberculosis diagnostic test, this assay should expand the capacity for detection of drug-resistant tuberculosis near the point of care.
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25
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Vázquez-Chacón CA, Rodríguez-Gaxiola FDJ, López-Carrera CF, Cruz-Rivera M, Martínez-Guarneros A, Parra-Unda R, Arámbula-Meraz E, Fonseca-Coronado S, Vaughan G, López-Durán PA. Identification of drug resistance mutations among Mycobacterium bovis lineages in the Americas. PLoS Negl Trop Dis 2021; 15:e0009145. [PMID: 33591982 PMCID: PMC7886168 DOI: 10.1371/journal.pntd.0009145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/14/2021] [Indexed: 01/25/2023] Open
Abstract
Identifying the Mycobacterium tuberculosis resistance mutation patterns is of the utmost importance to assure proper patient's management and devising of control programs aimed to limit spread of disease. Zoonotic Mycobacterium bovis infection still represents a threat to human health, particularly in dairy production regions. Routinary, molecular characterization of M. bovis is performed primarily by spoligotyping and mycobacterial interspersed repetitive units (MIRU) while next generation sequencing (NGS) approaches are often performed by reference laboratories. However, spoligotyping and MIRU methodologies lack the resolution required for the fine characterization of tuberculosis isolates, particularly in outbreak settings. In conjunction with sophisticated bioinformatic algorithms, whole genome sequencing (WGS) analysis is becoming the method of choice for advanced genetic characterization of tuberculosis isolates. WGS provides valuable information on drug resistance and compensatory mutations that other technologies cannot assess. Here, we performed an analysis of the most frequently identified mutations associated with tuberculosis drug resistance and their genetic relationship among 2,074 Mycobacterium bovis WGS recovered primarily from non-human hosts. Full-length gene sequences harboring drug resistant associated mutations and their phylogenetic relationships were analyzed. The results showed that M. bovis isolates harbor mutations conferring resistance to both first- and second-line antibiotics. Mutations conferring resistance for isoniazid, fluoroquinolones, streptomycin, and aminoglycosides were identified among animal strains. Our findings highlight the importance of molecular surveillance to monitor the emergence of mutations associated with multi and extensive drug resistance in livestock and other non-human mammals.
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Affiliation(s)
- Carlos Arturo Vázquez-Chacón
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, México
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | | | | | - Mayra Cruz-Rivera
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Armando Martínez-Guarneros
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | - Ricardo Parra-Unda
- Unidad de Investigaciones en Salud Pública, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Eliakym Arámbula-Meraz
- Laboratorio de Genética y Biología Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Salvador Fonseca-Coronado
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
| | - Gilberto Vaughan
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
| | - Paúl Alexis López-Durán
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
- * E-mail:
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Borham M, Oreiby A, El-Gedawy A, Hegazy Y, Hemedan A, Al-Gaabary M. Abattoir survey of bovine tuberculosis in tanta, centre of the Nile delta, with in silico analysis of gene mutations and protein-protein interactions of the involved mycobacteria. Transbound Emerg Dis 2021; 69:434-450. [PMID: 33484233 DOI: 10.1111/tbed.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/18/2020] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
Bovine tuberculosis is a transboundary disease of high economic and public health burden worldwide. In this study, post-mortem examination of 750 cattle and buffalo in Tanta abattoir, Centre of the Nile Delta, revealed visible TB in 4% of animals and a true prevalence of 6.85% (95% CI: 5.3%-8.9%). Mycobacterial culture, histopathology and RT-PCR targeting all members of M. tuberculosis complex were performed, upon which 85%, 80% and 100% of each tested lesions were confirmed as TB, respectively. Mpb70-targeting PCR was conducted on ten RT-PCR positive samples for sequencing and identified nine Mycobacterium (M.) bovis strains and, interestingly, one M. tuberculosis (Mtb) strain from a buffalo. Bioinformatics tools were used for prediction of mutations, nucleotide polymorphisms, lineages, drug resistance and protein-protein interactions (PPI) of the sequenced strains. The Mtb strain was resistant to rifampicin, isoniazid and streptomycin, and to the best of our knowledge, this is the first report of multidrug resistant (MDR)-Mtb originating from buffaloes. Seven M. bovis strains were resistant to ethambutol and ethionamide. Such resistances were associated with KatG, rpoB, rpsL, embB and ethA genes mutations. Other mutations and nucleotide polymorphisms were also predicted, some are reported for the first time and require experimental work for validation. PPI revealed more interactions than what would be expected for a random set of proteins of similar size and had dense interactions between nodes that are biologically connected, as a group. Two M. bovis strains belonged to BOV AFRI lineage (Spoligotypes BOV 1; BOV 2) and eight strains belonged to East-Asian (Beijing) lineage. In conclusion, visible TB was prevalent in the study area, RT-PCR is the best to confirm the disease, MDR-Mtb is associated with buffalo TB, and mycobacteria of different lineages carry many resistance genes to chemotherapeutic agents used in treatment of human TB constituting a major public health risk.
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Affiliation(s)
- Mohamed Borham
- Bacteriology Department, Animal Health Research Institute Matrouh Lab, Matrouh, Egypt
| | - Atef Oreiby
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Attia El-Gedawy
- Bacteriology Department, Animal Health Research Institute, Cairo, Egypt
| | - Yamen Hegazy
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Ahmed Hemedan
- Bioinformatics Core, Luxembourg Centre For Systems Biomedicine, Luxembourg University, Luxembourg, Luxembourg
| | - Magdy Al-Gaabary
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
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27
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Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population. Sci Rep 2021; 11:1224. [PMID: 33441660 PMCID: PMC7806709 DOI: 10.1038/s41598-020-79621-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other infectious disease. Substantial challenges to disease eradication remain among vulnerable and underserved populations. The Guarani-Kaiowá people are an indigenous population in Paraguay and the Brazilian state of Mato Grosso do Sul. This community, marginalized in Brazilian society, experiences severe poverty. Like other South American indigenous populations, their TB prevalence is high, but the disease has remained largely unstudied in their communities. Herein, Mycobacterium tuberculosis isolates from local clinics were whole genome sequenced, and a population genetic framework was generated. Phylogenetics show M. tuberculosis isolates in the Guarani-Kaiowá people cluster away from selected reference strains, suggesting divergence. Most cluster in a single group, further characterized as M. tuberculosis sublineage 4.3.3. Closer analysis of SNPs showed numerous variants across the genome, including in drug resistance-associated genes, and with many unique changes fixed in each group. We report that local M. tuberculosis strains have acquired unique polymorphisms in the Guarani-Kaiowá people, and drug resistance characterization is urgently needed to inform public health to ensure proper care and avoid further evolution and spread of drug-resistant TB.
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Narain A, Dubey RK, Verma AK, Srivastava A, Kant S. Potential Role of Proteasome Accessory Factor-C in Resistance against Second Line Drugs in Mycobacteria. J Lab Physicians 2021; 12:250-262. [PMID: 33390674 PMCID: PMC7773444 DOI: 10.1055/s-0040-1722552] [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: 11/03/2022] Open
Abstract
Objectives Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), can survive inside the host granuloma courtesy the various extrinsic and intrinsic factors involved. Continuous use or misuse of the anti TB drugs over the years has led to the development of resistance in MTB against antibiotics. Drug-resistant TB in particular has been a menace since treating it requires exposing the patient to drugs for a prolonged period of time. Multidrug-resistant (MDR) and extensively drug resistant TB cases have increased over the years mostly due to the exposure of MTB to suboptimal levels of drug. Proteasomes provide MTB its pathogenicity and hence helps it to survive inside the host even in the presence of drugs. Materials and Methods The recombinantly expressed proteasome accessory factor-C (PafC) protein was purified via Ni-NTA affinity chromatography and overexpressed in the nonpathogenic strain of mycobacteria (Mycobacterium smegmatis) for the comparative analysis of minimum inhibitory concentrations of antimycobacterial drugs. The bacteria were subjected to various stress conditions. Secretory nature of PafC was analyzed by probing the purified protein against patient sera. Quantitative mRNA analysis of paf C, lex A, and rec A was performed to check for their level under fluoroquinolone (FQ) presence. The data were validated in clinical samples of pulmonary TB patients. Results pafC , that forms one part of paf operon, is involved in providing MTB its resistance against FQs. Through a series of experiments, we established the fact that PafC is upregulated in mycobacteria upon exposure to FQs and it leads to the increased intracellular survival of mycobacteria under the stresses generated by FQs. The study also refers to the correlation of pafC to deoxyribonucleic acid (DNA) damage repair enzymes lexA and recA at transcriptional level. The results obtained in vitro corroborated when the pulmonary TB patients' samples were subjected to the same molecular analysis. Statistical Analysis All experiments were conducted at least in triplicate. p -Value of <0.05 was considered to be statistically significant Conclusion PafC plays a significant role in providing resistance to mycobacteria against FQ class of drugs by increasing its intracellular survival through increased drug efflux and getting involved with DNA damage repair machinery.
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Affiliation(s)
- Apoorva Narain
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rikesh K Dubey
- Department of Microbiology, Central Drug Research Institute (CSIR), Lucknow, Uttar Pradesh, India
| | - Ajay Kumar Verma
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anand Srivastava
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Surya Kant
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
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Li G, Guo Q, Liu H, Wan L, Jiang Y, Li M, Zhao LL, Zhao X, Liu Z, Wan K. Detection of Resistance to Fluoroquinolones and Second-Line Injectable Drugs Among Mycobacterium tuberculosis by a Reverse Dot Blot Hybridization Assay. Infect Drug Resist 2020; 13:4091-4104. [PMID: 33204126 PMCID: PMC7666996 DOI: 10.2147/idr.s270209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/07/2020] [Indexed: 01/23/2023] Open
Abstract
Background Reliable and timely determination of second-line drug resistance is essential for early initiation effective anti-tubercular treatment among multi-drug resistant (MDR) patients and blocking the spread of MDR and extensively drug-resistant tuberculosis. Molecular methods have the potency to provide accurate and rapid drug susceptibility results. We aimed to establish and evaluate the accuracy of a reverse dot blot hybridization (RDBH) assay to simultaneously detect the resistance of fluoroquinolones (FQs), kanamycin (KN), amikacin (AMK), capreomycin (CPM) and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis. Methods We established and evaluated the accuracy of the RDBH assay by comparing to the phenotypic drug susceptibility testing (DST) and sequencing in 170 M. tuberculosis, of which 94 and 27 were respectively resistant to ofloxacin (OFX) and SLIDs. Results The results show that, compared to phenotypic DST, the sensitivity and specificity of the RDBH assay for resistance detection were 63.8% and 100.0% for OFX, 60.0% and 100.0% for KN, 61.5% and 98.1% for AMK, 50.0% and 99.3% for CPM, and 55.6% and 100% for SLIDs, respectively; compared to sequencing, the sensitivity and specificity of the RDBH assay were 95.2% and 100.0% for OFX, 93.8% and 100.0% for SLIDs or KN (both based on mutations in rrs 1400 region and eis promoter), and 91.6% and 100.0% for AMK or CPM (both based on mutations in rrs 1400 region), respectively. The turnaround time of the RDBH assay was 7 h for testing 42 samples. Conclusion Our data suggested that compared to sequencing, the RDBH assay could serve as a rapid and reliable method for testing the resistance of M. tuberculosis against OFX and SLIDs, enabling early administration of appropriate treatment regimens among MDR tuberculosis patients.
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Affiliation(s)
- Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Qian Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.,Department of Molecular Biology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Zhiguang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
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Abstract
Mycobacterium tuberculosis is a major global human pathogen, and new drugs and new drug targets are urgently required. Cell wall biosynthesis is a major target of current tuberculosis drugs and of new agents under development. Several new classes of molecules appear to have the same target, MmpL3, which is involved in the export and synthesis of the mycobacterial cell wall. However, there is still debate over whether MmpL3 is the primary or only target for these classes. We wanted to confirm the mechanism of resistance for one series. We identified mutations in MmpL3 which led to resistance to the spiral amine series. High-level resistance to these compounds and two other series was conferred by multiple mutations in the same protein (MmpL3). These mutations did not reduce growth rate in culture. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores. The Mycobacterium tuberculosis protein MmpL3 performs an essential role in cell wall synthesis, since it effects the transport of trehalose monomycolates across the inner membrane. Numerous structurally diverse pharmacophores have been identified as inhibitors of MmpL3 largely based on the identification of resistant isolates with mutations in MmpL3. For some compounds, it is possible there are different primary or secondary targets. Here, we have investigated resistance to the spiral amine class of compounds. Isolation and sequencing of resistant mutants demonstrated that all had mutations in MmpL3. We hypothesized that if additional targets of this pharmacophore existed, then successive rounds to generate resistant isolates might reveal mutations in other loci. Since compounds were still active against resistant isolates, albeit with reduced potency, we isolated resistant mutants in this background at higher concentrations. After a second round of isolation with the spiral amine, we found additional mutations in MmpL3. To increase our chance of finding alternative targets, we ran a third round of isolation using a different molecule scaffold (AU1235, an adamantyl urea). Surprisingly, we obtained further mutations in MmpL3. Multiple mutations in MmpL3 increased the level and spectrum of resistance to different pharmacophores but did not incur a fitness cost in vitro. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores. IMPORTANCEMycobacterium tuberculosis is a major global human pathogen, and new drugs and new drug targets are urgently required. Cell wall biosynthesis is a major target of current tuberculosis drugs and of new agents under development. Several new classes of molecules appear to have the same target, MmpL3, which is involved in the export and synthesis of the mycobacterial cell wall. However, there is still debate over whether MmpL3 is the primary or only target for these classes. We wanted to confirm the mechanism of resistance for one series. We identified mutations in MmpL3 which led to resistance to the spiral amine series. High-level resistance to these compounds and two other series was conferred by multiple mutations in the same protein (MmpL3). These mutations did not reduce growth rate in culture. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores.
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He G, Li Y, Chen X, Chen J, Zhang W. Prediction of treatment outcomes for multidrug-resistant tuberculosis by whole-genome sequencing. Int J Infect Dis 2020; 96:68-72. [PMID: 32339719 DOI: 10.1016/j.ijid.2020.04.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) has been proposed to be a powerful tool to predict drug resistance for antitubercular drugs. However, the feasibility of WGS in predicting final treatment outcomes for multidrug-resistant tuberculosis (MDR-TB) patients remains unclear PATIENTS AND METHODS: In this prospective observational study conducted from January 2014 to September 2016, MDR-TB patients were enrolled consecutively. Genotypic drug sensitivity testing was performed via WGS using culture isolates. Patients were followed for two years to determine the treatment outcomes. Multivariate analysis was used to identify the association between information provided by WGS and the final treatment outcomes RESULTS: A total of 123 patients with MDR-TB were included in this study. The overall favorable treatment outcome rate was 60.2%. Multivariate analysis showed that independent risk factors associated with unfavorable treatment outcome including high-level moxifloxacin phenotypic resistance (OR, 4.362; 95%CI, 1.364-13.950; p=0.013), cycloserine phenotypic resistance (OR, 7.457; 95%CI, 1.644-33.819; p=0.009), mutations causing high-level fluoroquinolones resistance (OR, 3.947; 95%CI, 1.195-13.034; p=0.024), and ethA mutation (OR, 3.817; 95% CI, 1.154-12.823; p=0.028). WGS costs for each patient are ¥450 ($63), and the average turnaround time was one week CONCLUSIONS: In summary, WGS showed promising feasibility in predicting treatment outcomes for MDR-TB patients within a clinically relevant time frame.
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Affiliation(s)
- Guiqing He
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yang Li
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xinchang Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China; State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China; Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Shibabaw A, Gelaw B, Gebreyes W, Robinson R, Wang SH, Tessema B. The burden of pre-extensively and extensively drug-resistant tuberculosis among MDR-TB patients in the Amhara region, Ethiopia. PLoS One 2020; 15:e0229040. [PMID: 32053661 PMCID: PMC7018133 DOI: 10.1371/journal.pone.0229040] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/28/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The emergence of pre-extensively and extensively drug-resistant tuberculosis (Pre-XDR/XDR-TB) is the major hurdle for TB prevention and care programs especially in developing countries like Ethiopia. The less emphasis on universal access to laboratory techniques for the rapid diagnosis of TB and drug susceptibility testing (DST) makes the management of MDR-TB a challenge. Early detection of second line anti-TB drugs resistance is essential to reduce transmission of Pre-XDR/XDR-TB strains and adjusting the treatment regimen in MDR-TB. OBJECTIVE To determine the prevalence and resistance pattern of Pre-XDR- and XDR-TB among MDR-TB patients in the Amhara region, Ethiopia. METHODS A cross sectional study was carried out in nine MDR-TB treatment centers in the Amhara region. Sputum samples were collected from all pulmonary rifampicin resistant (RR) or MDR-TB patients prior to anti-TB treatment. Lӧwenstein-Jensen (LJ) culture, Ziehl Neelsen (ZN) smear, MTBDRplus and MTBDRsl assays were performed according to the standard procedures. Data were analyzed using SPSS 20 software. Chi-square and/or Fishers exact test was employed. RESULTS Overall, 6.3% of MDR-TB isolates were resistant to at least one second line drugs. Pre-XDR-TB and XDR-TB isolates accounted 5.7% and 0.6% respectively. Moreover, 3.4% were resistant to FQs and 3.4% were resistant to second line injectable drugs. All isolates were susceptible for low level kanamycin. Almost all pre-XDR-TB strains (90%) were previously treated with anti-TB drugs. Drug resistant Mycobacterium tuberculosis isolates were disproportionately distributed in districts of the Amhara region and the majorities were concentrated in urban areas. CONCLUSIONS The high proportion of MDR-TB patients resistant to at least one second line drug is alarming. Strengthening the laboratory facilities to monitor pre-XDR and XDR-TB patients is crucial. The TB programs need to give emphasis on the effective and rational use of second line drugs for newly diagnosed MDR-TB patients to prevent the emergence of pre-XDR/XDR-TB strains.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, Ohio, United States of America
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Richard Robinson
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, Ohio, United States of America
- Department of Internal Medicine, Division of infectious diseases, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Belay Tessema
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Chokkakula S, Chen Z, Wang L, Jiang H, Chen Y, Shi Y, Zhang W, Gao W, Yang J, Li J, Li X, Shui T, He J, Shen L, Liu J, Wang D, Wang H, Chen H, Kuang Y, Li B, Chen Z, Wu A, Yu M, Yan L, Suryadevara NC, Vissa V, Liu W, Wang H. Molecular surveillance of antimicrobial resistance and transmission pattern of Mycobacterium leprae in Chinese leprosy patients. Emerg Microbes Infect 2020; 8:1479-1489. [PMID: 31621517 PMCID: PMC6818117 DOI: 10.1080/22221751.2019.1677177] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Reports on antimicrobial resistance (AMR) of Mycobacterium leprae, relationship with bacteriological index (BI), and transmission in China are limited. We investigated the emergence of AMR mutations, the relationship between BI and AMR in complete, moderate and lack of BI decline cases, and molecular epidemiological features of AMR cases by enrolling 290 leprosy cases from four endemic provinces. Seven (2.41%), one (0.34%), five (1.72%), one (0.34%), and one (0.34%) strains had single mutations in folP1, rpoC, gyrA, gyrB, and 23S rRNA, respectively. Double mutations in folP1 and gyrA, rpoB and gyrA, and gyrA and 23S rRNA were observed in one (0.34%) strain each. Mutated strains occurred in three out of 81 (95% CI-0.005-0.079, p = 0.083) cases with complete BI decline, in seven out of 103 (95% CI 0.018-0.117, p = 0.008) cases with moderate BI decline, and in four out of 34 (95% CI 0.003-0.231, p = 0.044) cases with lack of BI decline. Most of these mutated strains were geographically separated and diverged genotypically. AMR mutations may not be the main cause of the lack of BI decline. The low transmission of AMR strains at the county level indicates an ongoing transmission at close contact levels.
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Affiliation(s)
- Santosh Chokkakula
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Zhiming Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Le Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Haiqin Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Yanqing Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Ying Shi
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Wenyue Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Wei Gao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Jun Yang
- Yunnan Provincial CDC , Kunming , China
| | - Jinlan Li
- Guizhou Provincial CDC , Guiyang , China
| | - Xiong Li
- Yunnan Provincial CDC , Kunming , China
| | | | - Jun He
- Yunnan Provincial CDC , Kunming , China
| | - Limei Shen
- Guizhou Provincial CDC , Guiyang , China
| | - Jie Liu
- Guizhou Provincial CDC , Guiyang , China
| | - De Wang
- Guizhou Provincial CDC , Guiyang , China
| | - Hao Wang
- Sichuan Provincial People's Hospital , Chengdu , China
| | - Huan Chen
- Hunan Provincial CDC , Changsha , China
| | | | - Bin Li
- Hunan Provincial CDC , Changsha , China
| | - Ziyi Chen
- Suzhou Institute of Systems Medicine , Suzhou , China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine , Suzhou , China
| | - Meiwen Yu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | - Liangbin Yan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | | | - Varalakshmi Vissa
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China
| | - Weida Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | - Hongsheng Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China.,National Centre for STD and Leprosy Control, China CDC , Nanjing , China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs , Nanjing , China.,Centre for global health, School of Public Health, Nanjing Medical University , Nanjing , China
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WQ-3810: A new fluoroquinolone with a high potential against fluoroquinolone-resistant Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 120:101891. [PMID: 31778929 DOI: 10.1016/j.tube.2019.101891] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/06/2019] [Accepted: 11/17/2019] [Indexed: 11/23/2022]
Abstract
Fluoroquinolone (FQ) resistance in Mycobacterium tuberculosis (Mtb), caused by amino acid substitutions in DNA gyrase, has been increasingly reported worldwide. WQ-3810 is a newly developed FQ that is highly active against FQ-resistant pathogens; however, its activity against Mtb has not been evaluated. Herein we examined the efficacy of WQ-3810 against Mtb through the use of recombinant Mtb DNA gyrases. In addition, in vitro antimycobacterial activity of WQ-3810 was evaluated against recombinant Mtb var. bovis Bacille Calmette-Guérin strains in which gyrase-coding genes were replaced with Mtb variants containing resistance-conferring mutations. WQ-3810 showed a higher inhibitory activity than levofloxacin against most recombinant DNA gyrases with FQ-resistance mutations. Furthermore, WQ-3810 showed inhibition even against a DNA gyrase variant harboring a G88C mutation which is thought to confer the highest resistance against FQs in clinical Mtb isolates. In contrast, the FQ susceptibility test showed that WQ-3810 had relatively weak mycobactericidal activity compared with moxifloxacin. However, the combination of WQ-3810 and ethambutol showed the greatest degree of synergistic activity against recombinant strains. Since FQs and ethambutol have been used in multi-drug therapy for tuberculosis, WQ-3810 might represent a new, potent anti-tuberculosis drug that can be effective even against FQ-resistant Mtb strains.
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35
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Yoshida M, Nakata N, Miyamoto Y, Fukano H, Ato M, Hoshino Y. A rapid and non-pathogenic assay for association of Mycobacterium tuberculosis gyrBA mutations and fluoroquinolone resistance using recombinant Mycobacterium smegmatis. FEMS Microbiol Lett 2019; 365:5173037. [PMID: 30418577 DOI: 10.1093/femsle/fny266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/07/2018] [Indexed: 12/13/2022] Open
Abstract
We developed a method involving recombinant Mycobacterium bovis bacillus Calmette-Guérin (BCG) and recombinant Mycobacterium smegmatis to determine which mutations in Mycobacterium tuberculosis (Mtb) gyrBA are associated with fluoroquinolone (FQ) resistance. The minimal inhibitory concentration (MIC) for FQ for recombinant strains with wild-type Mtb gyrBA was equivalent to that for strains with intrinsic gyrBA. Among 27 gyrBA mutations, the fold-changes in FQ MIC for M. smegmatis and M. bovis BCG backgrounds were comparable and were in part equivalent to those previously reported for recombinant Mtb strains. Mutations at position 90 or 94 of gyrA conferred strong and synergistic FQ resistance, which may be associated with the clinical observation that isolates carrying these mutations are the most or second most frequent. Sitafloxacin hydrate had the lowest MIC among the FQs tested in this study, which is similar to findings from a previous in vivo animal study. Most gyrBA mutations detected in clinical Mtb isolates could confer FQ resistance, but several mutations reduced bacterial growth rates. Overall, recombinant M. smegmatis appears to be a beneficial surrogate system to evaluate FQ susceptibility of virulent mycobacteria.
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Affiliation(s)
- Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noboru Nakata
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuji Miyamoto
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Gómez-Tangarife VJ, Gómez-Restrepo AJ, Robledo-Restrepo J, Hernández-Sarmiento JM. [Drug resistance in Mycobacterium tuberculosis: contribution of constituent and acquired mechanisms]. ACTA ACUST UNITED AC 2019; 20:491-497. [PMID: 30843986 DOI: 10.15446/rsap.v20n4.50575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/12/2018] [Indexed: 11/09/2022]
Abstract
Due to the emergence of multi-drug resistant (MDR-MTB) and extensively drug-resistant (XDR-MTB) Mycobacterium tuberculosis (MTB) isolates, the failure rates of standard treatment regimens are high, thus becoming a major public health challenge worldwide. Resistance to anti-tuberculous (anti-TB) drugs is attributed mainly to specific mutations in target genes; however, a proportion of drug-resistant MTB isolates do not have mutations in these genes, which suggests the involvement of other mechanisms, such as the low permeability of the mycobacterial cell wall, enzymatic modification and/or efflux pumps. Clinical drug resistance to anti-TB drugs occurs largely as a result of the selection of resistant mutants caused by poor patient adherence to treatment, inappropriate follow-ups and prescriptions, suboptimal doses of drugs and poor access to health services and treatment. Major advances in molecular biology tools and the availability of the complete genome sequences of MTB have contributed to improve understanding of the mechanisms of resistance to the main anti-TB drugs. Better knowledge of the drug-resistance of MTB will contribute to the identification of new therapeutic targets to design new drugs, develop new diagnostic tests and/or improve methods currently available for the rapid detection of drug-resistant TB. This article presents an updated review of the mechanisms and molecular basis of drug resistance in MTB.
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Affiliation(s)
- Verónica J Gómez-Tangarife
- VG: Bacterióloga y Laboratorista. Clínico. M. Sc. Ciencias Médicas -Microbiología Corporación para Investigaciones Biológicas. Medellín, Colombia.
| | - Alex J Gómez-Restrepo
- AG: Bibliotecólogo. M. Sc. Bibliotecología y Ciencias de la Información, Medellín, Colombia. Institución: Corporación para Investigaciones Biológicas.
| | - Jaime Robledo-Restrepo
- JR: MD. Ph. D. Ciencias Médicas. - Microbiología, Institución: Universidad Pontificia Bolivariana y Corporación para Investigaciones Biológicas. Medellín, Colombia.
| | - José M Hernández-Sarmiento
- JH: MD. M. Sc.; Ph. D. Ciencias Médicas - Microbiología., Institución: Universidad Pontificia Bolivariana. Medellín, Colombia.
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Retrospective Analysis of Archived Pyrazinamide Resistant Mycobacterium tuberculosis Complex Isolates from Uganda-Evidence of Interspecies Transmission. Microorganisms 2019; 7:microorganisms7080221. [PMID: 31362370 PMCID: PMC6723201 DOI: 10.3390/microorganisms7080221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unknown. A retrospective study was undertaken on archived Mycobacterium tuberculosis complex (MTBC) isolates from a reference laboratory in Uganda to identify the prevalence of human M. bovis infection. A total of 5676 isolates maintained in this repository were queried and 136 isolates were identified as pyrazinamide resistant, a hallmark phenotype of M. bovis. Of these, 1.5% (n = 2) isolates were confirmed as M. bovis by using regions of difference PCR analysis. The overall size of whole genome sequences (WGSs) of these two M. bovis isolates were ~4.272 Mb (M. bovis Bz_31150 isolated from a captive chimpanzee) and 4.17 Mb (M. bovis B2_7505 from a human patient), respectively. Alignment of these genomes against 15 MTBC genome sequences revealed 7248 single nucleotide polumorphisms (SNPs). Theses SNPs were used for phylogenetic analysis that indicated a strong relationship between M. bovis and the chimpanzee isolate (Bz_31150) while the other M. bovis genome from the human patient (B2_7505) analyzed did not cluster with any M. bovis or M. tuberculosis strains. WGS analysis also revealed multidrug resistance genotypes; these genomes revealed pncA mutations at positions H57D in Bz_31150 and B2_7505. Phenotypically, B2_7505 was an extensively drug-resistant strain and this was confirmed by the presence of mutations in the major resistance-associated proteins for all anti-tuberculosis (TB) drugs, including isoniazid (KatG (S315T) and InhA (S94A)), fluoroquinolones (S95T), streptomycin (rrs (R309C)), and rifampin (D435Y, a rare but disputed mutation in rpoB). The presence of these mutations exclusively in the human M. bovis isolate suggested that these occurred after transmission from cattle. Genome analysis in this study identified M. bovis in humans and great apes, suggesting possible transmission from domesticated ruminants in the area due to a dynamic and changing interface, which has created opportunity for exposure and transmission.
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Kateete DP, Kamulegeya R, Kigozi E, Katabazi FA, Lukoye D, Sebit SI, Abdi H, Arube P, Kasule GW, Musisi K, Dlamini MG, Khumalo D, Joloba ML. Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014-2016). BMC Pulm Med 2019; 19:124. [PMID: 31291943 PMCID: PMC6617586 DOI: 10.1186/s12890-019-0891-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/03/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pulmonary tuberculosis is a leading cause of morbidity and mortality in developing countries. Drug resistance, a huge problem in this contagious disease, is driven by point mutations in the Mycobacterium tuberculosis genome however, their frequencies vary geographically and this affects applicability of molecular diagnostics for rapid detection of resistance. Here, we report the frequency and patterns of mutations associated with resistance to second-line anti-TB drugs in multidrug-resistant (MDR) M. tuberculosis isolates from eSwatini, Somalia and Uganda that were resistant to a second-line anti-TB drug. METHODS The quinolone resistance determining region (QRDR) of gyrA/gyrB genes and the drug resistance associated fragment of rrs gene from 80 isolates were sequenced and investigated for presence of drug resistance mutations. Of the 80 isolates, 40 were MDR, of which 28 (70%) were resistant to a second-line anti-TB injectable drug, 18 (45%) were levofloxacin resistant while 12 (30%) were extensively drug resistant (XDR). The remaining 40 isolates were susceptible to anti-TB drugs. MIRU-VNTR analysis was performed for M/XDR isolates. RESULTS We successfully sub-cultured 38 of the 40 M/XDR isolates. The gyrA resistance mutations (Gly88Ala/Cys/Ala, Ala90Val, Ser91Pro, Asp94Gly/Asn) and gyrB resistance mutations (Asp500His, Asn538Asp) were detected in 72.2% (13/18) and 22.2% (4/18) of the MDR and levofloxacin resistant isolates, respectively. Overall, drug resistance mutations in gyrA/gyrB QRDRs occurred in 77.8% (14/18) of the MDR and levofloxacin resistant isolates. Furthermore, drug resistance mutations a1401g and g1484 t in rrs occurred in 64.3% (18/28) of the MDR isolates resistant to a second-line anti-TB injectable drug. Drug resistance mutations were not detected in drug susceptible isolates. CONCLUSIONS The frequency of resistance mutations to second-line anti-TB drugs in MDR-TB isolates resistant to second line anti-TB drugs from eSwatini, Somalia and Uganda is high, implying that rapid molecular tests are useful in detecting second-line anti-TB drug resistance in those countries. Relatedly, the frequency of fluoroquinolone resistance mutations in gyrB/QRDR is high relative to global estimates, and they occurred independently of gyrA/QRDR mutations implying that their absence in panels of molecular tests for detecting fluoroquinolone resistance may yield false negative results in our setting.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rogers Kamulegeya
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Deus Lukoye
- National Tuberculosis/Leprosy Program, Ministry of Health Uganda, Kampala, Uganda
| | | | - Hergeye Abdi
- Ministry of Health, Hargeisa, Somaliland Somalia
| | | | | | - Kenneth Musisi
- National Tuberculosis Reference Laboratory, Kampala, Uganda
| | - Myalo Glen Dlamini
- National TB Reference Laboratory / eSwatini Health Laboratory Services, Ministry of Health, Hospital Hill Mbabane, Mbabane, eSwatini
| | - Derrick Khumalo
- National TB Reference Laboratory / eSwatini Health Laboratory Services, Ministry of Health, Hospital Hill Mbabane, Mbabane, eSwatini
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
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Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines. Sci Rep 2019; 9:9305. [PMID: 31243306 PMCID: PMC6594935 DOI: 10.1038/s41598-019-45566-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/10/2019] [Indexed: 11/08/2022] Open
Abstract
The Philippines has a high incidence of tuberculosis disease (TB), with an increasing prevalence of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains making its control difficult. Although the M. tuberculosis "Manila" ancient lineage 1 strain-type is thought to be prevalent in the country, with evidence of export to others, little is known about the genetic diversity of circulating strains. By whole genome sequencing (WGS) 178 isolates from the Philippines National Drug Resistance Survey, we found the majority (143/178; 80.3%) belonged to the lineage 1 Manila clade, with the minority belonging to lineages 4 (European-American; n = 33) and 2 (East Asian; n = 2). A high proportion were found to be multidrug-resistant (34/178; 19.1%), established through highly concordant laboratory drug susceptibility testing and in silico prediction methods. Some MDR-TB isolates had near identical genomic variation, providing potential evidence of transmission. By placing the Philippine isolates within a phylogeny of global M. tuberculosis (n > 17,000), we established that they are genetically similar to those observed outside the country, including a clade of Manila-like strain-types in Thailand. An analysis of the phylogeny revealed a set of ~200 SNPs that are specific for the Manila strain-type, and a subset can be used within a molecular barcode. Sixty-eight mutations known to be associated with 10 anti-TB drug resistance were identified in the Philippine strains, and all have been observed in other populations. Whilst nine putative streptomycin resistance conferring markers in gid (8) and rrs (1) genes appear to be novel and with functional consequences. Overall, this study provides an important baseline characterisation of M. tuberculosis genetic diversity for the Philippines, and will fill a gap in global datasets and aid the development of a nation-wide database for epidemiological studies and clinical decision making. Further, by establishing a molecular barcode for detecting Manila strains it will assist with the design of diagnostic tools for disease control activities.
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40
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Nimmo C, Shaw LP, Doyle R, Williams R, Brien K, Burgess C, Breuer J, Balloux F, Pym AS. Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture. BMC Genomics 2019; 20:389. [PMID: 31109296 PMCID: PMC6528373 DOI: 10.1186/s12864-019-5782-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Background Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture. Results DNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance. Conclusions Culture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating. Electronic supplementary material The online version of this article (10.1186/s12864-019-5782-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK. .,Africa Health Research Institute, Durban, South Africa.
| | - Liam P Shaw
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Nuffield Department of Clinical Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Ronan Doyle
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | - Carrie Burgess
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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Payne JL, Menardo F, Trauner A, Borrell S, Gygli SM, Loiseau C, Gagneux S, Hall AR. Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS Biol 2019; 17:e3000265. [PMID: 31083647 PMCID: PMC6532934 DOI: 10.1371/journal.pbio.3000265] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/23/2019] [Accepted: 04/26/2019] [Indexed: 11/21/2022] Open
Abstract
Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies of the rates and spectra of spontaneous mutations. However, demonstrating the role of transition bias in adaptive evolution remains challenging. In particular, it is unclear whether such biases direct the evolution of bacterial pathogens adapting to treatment. We addressed this challenge by analyzing adaptive antibiotic-resistance mutations in the major human pathogen Mycobacterium tuberculosis (MTB). We found strong evidence for transition bias in two independently curated data sets comprising 152 and 208 antibiotic-resistance mutations. This was true at the level of mutational paths (distinct adaptive DNA sequence changes) and events (individual instances of the adaptive DNA sequence changes) and across different genes and gene promoters conferring resistance to a diversity of antibiotics. It was also true for mutations that do not code for amino acid changes (in gene promoters and the 16S ribosomal RNA gene rrs) and for mutations that are synonymous to each other and are therefore likely to have similar fitness effects, suggesting that transition bias can be caused by a bias in mutation supply. These results point to a central role for transition bias in determining which mutations drive adaptive antibiotic resistance evolution in a key pathogen. Some types of mutations occur more frequently than expected. This study shows that such bias —an excess of transitions over transversions—influences the evolution of antibiotic resistance in a key global pathogen, Mycobacterium tuberculosis.
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Affiliation(s)
- Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastian M. Gygli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Chloe Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alex R. Hall
- Institute of Integrative Biology, ETH Zurich, Switzerland
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Moreno-Molina M, Comas I, Furió V. The Future of TB Resistance Diagnosis: The Essentials on Whole Genome Sequencing and Rapid Testing Methods. Arch Bronconeumol 2019; 55:421-426. [PMID: 30795867 DOI: 10.1016/j.arbres.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/25/2022]
Abstract
Tuberculosis resistance diagnostics have vastly improved in recent years thanks to the development of standardised phenotypic and molecular testing methods. However, these methods are either slow or limited in the number of resistant genotypes they can detect. With the advent of next-generation sequencing (NGS) we can sidestep all those problems, as we can sequence whole tuberculosis genomes at increasingly smaller costs and requiring less and less DNA. In this review, we explain how accumulated knowledge in the field has allowed us to go from phenotypic testing to molecular methods to Whole Genome Sequencing (WGS) for resistance diagnostics. We compare current diagnostic methods with WGS as to their efficacy in detecting resistant cases, and show how forthcoming advances in NGS technologies will be crucial in widespread implementation of WGS as a diagnostic tool.
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Affiliation(s)
| | - Iñaki Comas
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain; CIBER in Epidemiology and Public Health, Spain
| | - Victoria Furió
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain.
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Redefining MDR-TB: Comparison of Mycobacterium tuberculosis clinical isolates from Russia and Taiwan. INFECTION GENETICS AND EVOLUTION 2018; 72:141-146. [PMID: 30593924 DOI: 10.1016/j.meegid.2018.12.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 12/22/2022]
Abstract
Multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis are global challenges due to the limited number of effective drugs for treatment. Treatment with less than 4-5 effective drugs might lead to the further emergence of drug resistance and poor clinical outcomes. For better prediction of treatment outcomes, we compared drug-resistance profiles of consecutive clinical MDR Mycobacterium tuberculosis isolates from high- and low-burden settings. This was a retrospective cohort study. We analysed 225 and 229 MDR isolates from Moscow (Russia) and Taiwan, respectively, obtained between 2014 and 2015. Drug susceptibility testing was performed by the Bactec MGIT 960 automated system and the agar proportion method. Detection of resistance-associated mutations in the M. tuberculosis genome was carried out by an array and/or sequencing of selected loci. The principal differences between resistance profiles of MDR isolates in the two countries were the percentages of pre-XDR (40.9% vs. 14.8%) and XDR (34.7% vs. 1.7%) isolates, both of which were significantly higher in Moscow isolates. Forty-eight (33%) of 147 MDR and pre-XDR Russian isolates fall into a group with less than four effective drugs, which accounts for 40% (N = 120) of these isolates. The other 60% in this group were XDR strains (N = 72). Consequently, the average number of effective anti-tuberculosis drugs for MDR-TB treatment was lower for Russian isolates (3 vs. 7). Furthermore, a notable percentage (9%) of isolates resistant to kanamycin harboured mutations in the whiB7 locus, which was not detected by molecular tests targeting common mutations in the rrs and eis loci. We found that 98.2% and 45.9% of MDR isolates from Moscow and Taiwan, respectively, were resistant to streptomycin. Molecular tests for detecting resistance to drugs other than rifampicin, isoniazid, fluoroquinolones, and second-line injectable drugs are needed for individualized therapy. The conventional MDR treatment schemes most probably fail in these cases due to the limited number of effective drugs.
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Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Pettersson JOH, Kirkeleite I, Fandinho F, da Silva MA, Perdigao J, Portugal I, Viveiros M, Clark T, Caws M, Dunstan S, Thai PVK, Lopez B, Ritacco V, Kitchen A, Brown TS, van Soolingen D, O’Neill MB, Holt KE, Feil EJ, Mathema B, Balloux F, Eldholm V. Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. SCIENCE ADVANCES 2018; 4:eaat5869. [PMID: 30345355 PMCID: PMC6192687 DOI: 10.1126/sciadv.aat5869] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/11/2018] [Indexed: 05/23/2023]
Abstract
On the basis of population genomic and phylogeographic analyses of 1669 Mycobacterium tuberculosis lineage 4 (L4) genomes, we find that dispersal of L4 has been completely dominated by historical migrations out of Europe. We demonstrate an intimate temporal relationship between European colonial expansion into Africa and the Americas and the spread of L4 tuberculosis (TB). Markedly, in the age of antibiotics, mutations conferring antimicrobial resistance overwhelmingly emerged locally (at the level of nations), with minimal cross-border transmission of resistance. The latter finding was found to reflect the relatively recent emergence of these mutations, as a similar degree of local restriction was observed for susceptible variants emerging on comparable time scales. The restricted international transmission of drug-resistant TB suggests that containment efforts at the level of individual countries could be successful.
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Affiliation(s)
- Ola B. Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Caitlin S. Pepperell
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Philip Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Avenida Brasil 4365, C.P. 926, Manguinhos 21040-360, Rio de Janeiro, Brazil
| | - Louis Grandjean
- Department of Paediatric Infectious Diseases, Imperial College London, W2 1NY, London, UK
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Nadia Debech
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Jon Bohlin
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Kristian Alfsnes
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - John O.-H. Pettersson
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
- Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
| | - Ingerid Kirkeleite
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Fatima Fandinho
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Marcia Aparecida da Silva
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Joao Perdigao
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel Portugal
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Medica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Taane Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Maxine Caws
- Liverpool School of Tropical medicine, Department of Clinical Sciences, Liverpool, UK
- Birat-Nepal Medical Trust, Lazimpat, Kathmandu, Nepal
| | - Sarah Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA
| | - Tyler S. Brown
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dick van Soolingen
- Center for Infectious Disease Research, Diagnostics and Perinatal Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, Netherlands
| | - Mary B. O’Neill
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathryn E. Holt
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Biochemistry and Molecular Biology and Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Edward J. Feil
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
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Klotoe BJ, Molina-Moya B, Gomes HM, Gomgnimbou MK, Oliveira Suzarte L, Féres Saad MH, Ali S, Dominguez J, Pimkina E, Zholdybayeva E, Sola C, Refrégier G. TB-EFI, a novel 18-Plex microbead-based method for prediction of second-line drugs and ethambutol resistance in Mycobacterium tuberculosis complex. J Microbiol Methods 2018; 152:10-17. [PMID: 29913189 DOI: 10.1016/j.mimet.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
Abstract
Several diagnostic tests are being developed to detect drug resistance in tuberculosis. In line with previous developments detecting rifampicin and isoniazid resistance using microbead-based systems (spoligoriftyping and TB-SPRINT), we present here an assay called TB-EFI detecting mutations involved in resistance to ethambutol, fluoroquinolones and the three classical injectable drugs (kanamycin, amikacin and capreomycin) in Mycobacterium tuberculosis. The proposed test includes both wild-type and mutant probes for each targeted locus. Basic analysis can be performed manually. An upgraded interpretation is made available in Excel 2016®. Using a reference set of 61 DNA extracts, we show that TB-EFI provides perfect concordance with pyrosequencing. Concordance between genotypic resistance and phenotypic DST was relatively good (72 to 98% concordance), with lower efficiency for fluoroquinolones and ethambutol due to some untargeted mutations. When compared to phenotypical resistance, performances were similar to those obtained with Hain MTBDRsl assay, possibly thanks to the use of automatized processing of data although some mutations involved in fluoroquinolone resistance could not be included. When applied on three uncharacterized sets, phenotype could be predicted for 51% to 98% depending on the setting and the drug investigated, detecting one extensively drug-resistant isolate in each of a Pakistan and a Brazilian set of 91 samples, and 9 XDR among 43 multi-resistant Kazakhstan samples. By allowing high-throughput detection of second-line drugs resistance and of resistance to ethambutol that is often combined to second-line treatments, TB-EFI is a cost-effective assay for large-scale worldwide surveillance of resistant tuberculosis and XDR-TB control.
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Affiliation(s)
- Bernice J Klotoe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Barbara Molina-Moya
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Harrison Magdinier Gomes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France; Laboratório de Biologia Molecular Aplicada à Micobactérias, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Michel K Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France; Centre Muraz, Bobo-Dioulasso, Burkina Faso; Univ. Polytech, Bobo-Dioulasso, Burkina Faso
| | - Lorenna Oliveira Suzarte
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Maria H Féres Saad
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Av. Brasil, 4365 - 20245, Rio de Janeiro, Brazil
| | - Sajid Ali
- Microbiology Department, Quaid-i-Azam University, Islamabad, Pakistan
| | - José Dominguez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Edita Pimkina
- Infectious Diseases and Tuberculosis Hospital, Affiliate of Vilnius University Hospital Santariskiu klinikos, Vilnius, Lithuania
| | - Elena Zholdybayeva
- National Center for Biotechnology, Astana, Kazakhstan; Universitat Autònoma de Barcelona. CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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Chawla K, Kumar A, Shenoy VP, Chakrabarty S, Satyamoorthy K. Genotypic detection of fluoroquinolone resistance in drug-resistant Mycobacterium tuberculosis at a tertiary care centre in south Coastal Karnataka, India. J Glob Antimicrob Resist 2018; 13:250-253. [DOI: 10.1016/j.jgar.2018.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Accepted: 01/29/2018] [Indexed: 11/16/2022] Open
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McNerney R, Zignol M, Clark TG. Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert Rev Anti Infect Ther 2018; 16:433-442. [PMID: 29718745 DOI: 10.1080/14787210.2018.1472577] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The threat of resistance to anti-tuberculosis drugs is of global concern. Current efforts to monitor resistance rely on phenotypic testing where cultured bacteria are exposed to critical concentrations of the drugs. Capacity for such testing is low in TB endemic countries. Drug resistance is caused by mutations in the Mycobacterium tuberculosis genome and whole genome sequencing to detect these mutations offers an alternative means of assessing resistance. Areas covered: The challenges of assessing TB drug resistance are discussed. Progress in elucidating the M. tuberculosis resistome and evidence of the accuracy of next generation sequencing for detecting resistance is reviewed. Expert Commentary: There are considerable advantages to using next generation sequencing for TB drug resistance surveillance. Accuracy is high for detecting resistance to the major first-line drugs but is currently lower for the second-line drugs due to our incomplete knowledge regarding resistance causing mutations. With the advances in sequencing technology and the opportunity to replace phenotypic drug susceptibility testing with safer and more cost effective methods it would appear that the question is when to implement. Current bottlenecks are sample extraction to allow whole genome sequencing directly from sputum and the lack of bioinformatics expertise in some TB endemic countries.
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Affiliation(s)
- Ruth McNerney
- a Division of Pulmonary Medicine, Department of Medicine , University of Cape Town , Cape Town , South Africa
| | - Matteo Zignol
- b Global Tuberculosis Programme , World Health Organization , Geneva , Switzerland
| | - Taane G Clark
- c Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health , London School of Hygiene & Tropical Medicine , London , United Kingdom
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Luo T, Yuan J, Peng X, Yang G, Mi Y, Sun C, Wang C, Zhang C, Bao L. Double mutation in DNA gyrase confers moxifloxacin resistance and decreased fitness of Mycobacterium smegmatis. J Antimicrob Chemother 2018; 72:1893-1900. [PMID: 28387828 DOI: 10.1093/jac/dkx110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 03/13/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives Ofloxacin and moxifloxacin are the most commonly used fluoroquinolones (FQs) for the treatment of tuberculosis. As a new generation FQ, moxifloxacin has been recommended for the treatment of ofloxacin-resistant TB. However, the mechanism by which ofloxacin-resistant Mycobacterium tuberculosis further gains resistance to moxifloxacin remains unclear. Methods We used Mycobacterium smegmatis as a model for studying FQ resistance in M. tuberculosis . Moxifloxacin-resistant M. smegmatis was selected in vitro based on strains with primary ofloxacin resistance. The gyrA and gyrB genes of the resistant strains were sequenced to identify resistance-associated mutations. An in vitro competition assay was applied to explore the influence of gyrA / gyrB mutations on bacterial fitness. Finally, we evaluated the clinical relevance of our findings by analysing the WGS data of 1984 globally collected M. tuberculosis strains. Results A total of 57 moxifloxacin-resistant M. smegmatis strains based on five ofloxacin-resistant strains were obtained. Sequencing results revealed that all moxifloxacin-resistant strains harboured second-step mutations in gyrA or gyrB . The relative fitnesses of the double-mutation strains varied from 0.65 to 0.93 and were mostly lower than those of their mono-mutation parents. From the genomic data, we identified 37 clinical M. tuberculosis strains harbouring double mutations in gyrA and/or gyrB and 36 of them carried at least one low-level FQ-resistance mutation. Conclusions Double mutation in DNA gyrase leads to moxifloxacin resistance and decreased fitness in M. smegmatis . Under current dosing of moxifloxacin, double mutations mainly happened in M. tuberculosis strains with primary low-level resistance mutations.
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Affiliation(s)
- Tao Luo
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Jinning Yuan
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Xuan Peng
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Guoping Yang
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Youjun Mi
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Changfeng Sun
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Chuhan Wang
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Chunxi Zhang
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
| | - Lang Bao
- Laboratory of Infection and Immunity, West China Center of Medical Sciences, Sichuan University, Chengdu 610041, China
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