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Zhang G, Sun X, Fleming J, Ran F, Luo J, Chen H, Ju H, Wang Z, Zhao H, Wang C, Zhang F, Dai X, Yang X, Li C, Liu Y, Wang Y, Zhang X, Jiang Y, Wu Z, Bi L, Zhang H. Genetic factors associated with acquired phenotypic drug resistance and its compensatory evolution during tuberculosis treatment. Clin Microbiol Infect 2024; 30:637-645. [PMID: 38286176 DOI: 10.1016/j.cmi.2024.01.016] [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: 08/31/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVES We elucidated the factors, evolution, and compensation of antimicrobial resistance (AMR) in Mycobacterium tuberculosis (MTB) isolates under dual pressure from the intra-host environment and anti-tuberculosis (anti-TB) drugs. METHODS This retrospective case-control study included 337 patients with pulmonary tuberculosis from 15 clinics in Tianjin, China, with phenotypic drug susceptibility testing results available for at least two time points between January 1, 2009 and December 31, 2016. Patients in the case group exhibited acquired AMR to isoniazid (INH) or rifampicin (RIF), while those in the control group lacked acquired AMR. The whole-genome sequencing (WGS) was conducted on 149 serial longitudinal MTB isolates from 46 patients who acquired or reversed phenotypic INH/RIF-resistance during treatment. The genetic basis, associated factors, and intra-host evolution of acquired phenotypic INH/RIF-resistance were elucidated using a combined analysis. RESULTS Anti-TB interruption duration of ≥30 days showed association with acquired phenotypic INH/RIF resistance (aOR = 2·2, 95% CI, 1·0-5·1) and new rpoB mutations (p = 0·024). The MTB evolution was 1·2 (95% CI, 1·02-1·38) single nucleotide polymorphisms per genome per year under dual pressure from the intra-host environment and anti-TB drugs. AMR-associated mutations occurred before phenotypic AMR appearance in cases with acquired phenotypic INH (10 of 16) and RIF (9 of 22) resistances. DISCUSSION Compensatory evolution may promote the fixation of INH/RIF-resistance mutations and affect phenotypic AMR. The TB treatment should be adjusted based on gene sequencing results, especially in persistent culture positivity during treatment, which highlights the clinical importance of WGS in identifying reinfection and AMR acquisition before phenotypic drug susceptibility testing.
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Affiliation(s)
- Guoqin Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Tianjin Center for Tuberculosis Control, Tianjin, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xianhui Sun
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fanlei Ran
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jianjun Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hanfang Ju
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Zhirui Wang
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Hui Zhao
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Chunhua Wang
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Fan Zhang
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Xiaowei Dai
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xinyu Yang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Chuanyou Li
- Biobank of Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumour Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yi Liu
- Biobank of Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumour Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | | | - Xilin Zhang
- Foshan Fourth People's Hospital, Foshan, China
| | - Yuan Jiang
- Shanghai Municipal Center for Disease Prevention and Control, Beijing, China
| | - Zhilong Wu
- Foshan Fourth People's Hospital, Foshan, China
| | - Lijun Bi
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Guangzhou National Laboratory, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hongtai Zhang
- Beijing Center for Disease Prevention and Control, Beijing, China.
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Vīksna A, Sadovska D, Berge I, Bogdanova I, Vaivode A, Freimane L, Norvaiša I, Ozere I, Ranka R. Genotypic and phenotypic comparison of drug resistance profiles of clinical multidrug-resistant Mycobacterium tuberculosis isolates using whole genome sequencing in Latvia. BMC Infect Dis 2023; 23:638. [PMID: 37770850 PMCID: PMC10540372 DOI: 10.1186/s12879-023-08629-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB) remains a major public health problem in many high tuberculosis (TB) burden countries. Phenotypic drug susceptibility testing (DST) take several weeks or months to result, but line probe assays and Xpert/Rif Ultra assay detect a limited number of resistance conferring gene mutations. Whole genome sequencing (WGS) is an advanced molecular testing method which theoretically can predict the resistance of M. tuberculosis (Mtb) isolates to all anti-TB agents through a single analysis. METHODS Here, we aimed to identify the level of concordance between the phenotypic and WGS-based genotypic drug susceptibility (DS) patterns of MDR-TB isolates. Overall, data for 12 anti-TB medications were analyzed. RESULTS In total, 63 MDR-TB Mtb isolates were included in the analysis, representing 27.4% of the total number of MDR-TB cases in Latvia in 2012-2014. Among them, five different sublineages were detected, and 2.2.1 (Beijing group) and 4.3.3 (Latin American-Mediterranean group) were the most abundant. There were 100% agreement between phenotypic and genotypic DS pattern for isoniazid, rifampicin, and linezolid. High concordance rate (> 90%) between phenotypic and genotypic DST results was detected for ofloxacin (93.7%), pyrazinamide (93.7%) and streptomycin (95.4%). Phenotypic and genotypic DS patterns were poorly correlated for ethionamide (agreement 56.4%), ethambutol (85.7%), amikacin (82.5%), capreomycin (81.0%), kanamycin (85.4%), and moxifloxacin (77.8%). For capreomycin, resistance conferring mutations were not identified in several phenotypically resistant isolates, and, in contrary, for ethionamide, ethambutol, amikacin, kanamycin, and moxifloxacin the resistance-related mutations were identified in several phenotypically sensitive isolates. CONCLUSIONS WGS is a valuable tool for rapid genotypic DST for all anti-TB agents. For isoniazid and rifampicin phenotypic DST potentially can be replaced by genotypic DST based on 100% agreement between the tests. However, discrepant results for other anti-TB agents limit their prescription based solely on WGS data. For clinical decision, at the current level of knowledge, there is a need for combination of genotypic DST with modern, validated phenotypic DST methodologies for those medications which did not showed 100% agreement between the methods.
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Affiliation(s)
- Anda Vīksna
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
- Rīga Stradiņš University, Riga, Latvia
| | - Darja Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia
| | - Iveta Berge
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
| | - Ineta Bogdanova
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
| | - Annija Vaivode
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia
| | - Lauma Freimane
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia
| | - Inga Norvaiša
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
| | - Iveta Ozere
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
- Rīga Stradiņš University, Riga, Latvia
| | - Renāte Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia.
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Srivastava S, Dey S, Mukhopadhyay S. Vaccines against Tuberculosis: Where Are We Now? Vaccines (Basel) 2023; 11:vaccines11051013. [PMID: 37243117 DOI: 10.3390/vaccines11051013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Tuberculosis (TB) is among the top 10 leading causes of death in low-income countries. Statistically, TB kills more than 30,000 people each week and leads to more deaths than any other infectious disease, such as acquired immunodeficiency syndrome (AIDS) and malaria. TB treatment is largely dependent on BCG vaccination and impacted by the inefficacy of drugs, absence of advanced vaccines, misdiagnosis improper treatment, and social stigma. The BCG vaccine provides partial effectiveness in demographically distinct populations and the prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB incidences demands the design of novel TB vaccines. Various strategies have been employed to design vaccines against TB, such as: (a) The protein subunit vaccine; (b) The viral vector vaccine; (c) The inactivation of whole-cell vaccine, using related mycobacteria, (d) Recombinant BCG (rBCG) expressing Mycobacterium tuberculosis (M.tb) protein or some non-essential gene deleted BCG. There are, approximately, 19 vaccine candidates in different phases of clinical trials. In this article, we review the development of TB vaccines, their status and potential in the treatment of TB. Heterologous immune responses generated by advanced vaccines will contribute to long-lasting immunity and might protect us from both drug-sensitive and drug-resistant TB. Therefore, advanced vaccine candidates need to be identified and developed to boost the human immune system against TB.
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Affiliation(s)
- Shruti Srivastava
- Research and Development Office, Ashoka University, Rajiv Gandhi Education City, Sonipat 131029, Haryana, India
| | - Sajal Dey
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, Telangana, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, Telangana, India
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Salina EG. Mycobacterium tuberculosis Infection: Control and Treatment. Microorganisms 2023; 11:microorganisms11041057. [PMID: 37110480 PMCID: PMC10146921 DOI: 10.3390/microorganisms11041057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 03/12/2023] [Indexed: 04/29/2023] Open
Abstract
Tuberculosis (TB) is the second leading infectious killer after COVID-19, causing 10 million new cases and claiming the lives of more than 1 [...].
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Affiliation(s)
- Elena G Salina
- Bach Institute of Biochemistry Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:ijms231810669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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