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Rukmana A, Nurfadillah M, Gozali C, Kiranasari A. Genome sequencing analysis of the pncA, rpsA and panD genes responsible for pyrazinamide resistance of Mycobacterium tuberculosis from Indonesian isolates. Trop Med Int Health 2024. [PMID: 39397216 DOI: 10.1111/tmi.14051] [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] [Indexed: 10/15/2024]
Abstract
BACKGROUND Developing the most suitable treatment against tuberculosis based on resistance profiles is imperative to effectively cure tuberculosis patients. Whole-genome sequencing is a molecular method that allows for the rapid and cost-effective detection of mutations in multiple genes associated with anti-tuberculosis drug resistance. This sequencing approach addresses the limitations of culture-based methods, which may not apply to certain anti-TB drugs, such as pyrazinamide, because of their specific culture medium requirements, potentially leading to biased resistance culture results. METHODS Thirty-four M. tuberculosis isolates were subcultured on a Lowenstein-Jensen medium. The genome of these bacteria was subsequently isolated using cetyltrimethylammonium bromide. Genome sequencing was performed with Novaseq Illumina 6000 (Illumina), and the data were analysed using the GenTB and Mykrobe applications. We also conducted a de novo analysis to compare the two methods and performed mutation analysis of other genes encoding pyrazinamide resistance, namely rpsA and panD. RESULTS The results revealed mutations in the pncA gene, which were identified based on the databases accessed through GenTB and Mykrobe. Two discrepancies between the drug susceptibility testing and sequencing results may suggest potential instability in the drug susceptibility testing culture, specifically concerning PZA. Meanwhile, the results of the de novo analysis showed the same result of pncA mutation to the GenTB or Mykrobe; meanwhile, there were silent mutations in rpsA in several isolates and a point mutation; no mutations were found in the panD gene. However, the mutations in the genes encoding pyrazinamide require further and in-depth study to understand their relationship to the phenotypic profile. CONCLUSIONS Compared to the conventional culture method, the whole-genome sequencing method has advantages in determining anti-tuberculosis resistance profiles, especially in reduced time and bias.
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Affiliation(s)
- Andriansjah Rukmana
- Department of Microbiology, Medical Faculty, Universitas Indonesia, Jakarta, Indonesia
- National Referral Laboratory for Molecular, Serology, MOTT, and Operational Research, Jakarta, Indonesia
| | - Mifa Nurfadillah
- Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Cynthia Gozali
- Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Ariyani Kiranasari
- Department of Microbiology, Medical Faculty, Universitas Indonesia, Jakarta, Indonesia
- National Referral Laboratory for Molecular, Serology, MOTT, and Operational Research, Jakarta, Indonesia
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Che Y, Lu Y, Zhu Y, He T, Li X, Gao J, Gao J, Wang X, Liu Z, Tong F. Surveillance of fluoroquinolones resistance in rifampicin-susceptible tuberculosis in eastern China with whole-genome sequencing-based approach. Front Microbiol 2024; 15:1413618. [PMID: 39050625 PMCID: PMC11266052 DOI: 10.3389/fmicb.2024.1413618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Background Leveraging well-established DNA-level drug resistance mechanisms, whole-genome sequencing (WGS) has emerged as a valuable methodology for predicting drug resistance. As the most effective second-line anti-tuberculosis (anti-TB) drugs, fluoroquinoloness (FQs) are generally used to treat multidrug-resistant tuberculosis (MDR-TB, defined as being resistant to resistant to rifampicin and isoniazid) or rifampicin-resistant tuberculosis (RR-TB). However, FQs are also commonly used in the management of other bacterial infections. There are few published data on the rates of FQs resistance among rifampicin-susceptible TB. The prevalence of FQs resistance among TB patients who are rifampicin-susceptible has not been studied in Zhejiang Province, China. The goal of this study was to provide a baseline characterization of the prevalence of FQs resistance, particularly among rifampicin-susceptible TB in Zhejiang Province, China. Methods Based on WGS, we have investigated the prevalence of FQs resistance among rifampicin-susceptible TB in Zhejiang Province. All pulmonary TB patients with positive cultures who were identified in Zhejiang area during TB drug resistance surveillance from 2018 to 2019 have enrolled in this population-based retrospective study. Results The rate of FQs resistance was 4.6% (32/698) among TB, 4.0% (27/676) among rifampicin-susceptible TB, and 22.7% (5/22) among RR-TB. According to WGS, strains that differ within 12 single-nucleotide polymorphisms (SNPs) were considered to be transmission of FQ-resistant strains. Specifically, 3.7% (1/27) of FQs resistance was caused by the transmission of FQs-resistant strains among the rifampicin-susceptible TB and 40.7% (11/27) of FQs resistance was identified as hetero-resistance. Conclusion The prevalence of FQs resistance among TB patients who were rifampicin-susceptible was severe in Zhejiang. The emergence of FQs resistance in TB isolates that are rifampicin-susceptible was mainly caused by the selection of drug-resistant strains. In order to prevent the emergence of FQs resistance, the WGS-based surveillance system for TB should be urgently established, and clinical awareness of the responsible use of FQs for respiratory infections should be enhanced.
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Affiliation(s)
- Yang Che
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Yelei Zhu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Tianfeng He
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Junli Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Junshun Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Xiaomeng Wang
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhengwei Liu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Feng Tong
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
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Torres-Fernandez D, Dalsuco J, Bramugy J, Bassat Q, Varo R. Innovative strategies for the surveillance, prevention, and management of pediatric infections applied to low-income settings. Expert Rev Anti Infect Ther 2024; 22:413-422. [PMID: 38739471 DOI: 10.1080/14787210.2024.2354839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION Infectious diseases still cause a significant burden of morbidity and mortality among children in low- and middle-income countries (LMICs). There are ample opportunities for innovation in surveillance, prevention, and management, with the ultimate goal of improving survival. AREAS COVERED This review discusses the current status in the use and development of innovative strategies for pediatric infectious diseases in LMICs by focusing on surveillance, diagnosis, prevention, and management. Topics covered are: Minimally Invasive Tissue Sampling as a technique to accurately ascertain the cause of death; Genetic Surveillance to trace the pathogen genomic diversity and emergence of resistance; Artificial Intelligence as a multidisciplinary tool; Portable noninvasive imaging methods; and Prognostic Biomarkers to triage and risk stratify pediatric patients. EXPERT OPINION To overcome the specific hurdles in child health for LMICs, some innovative strategies appear at the forefront of research. If the development of these next-generation tools remains focused on accessibility, sustainability and capacity building, reshaping epidemiological surveillance, diagnosis, and treatment in LMICs, can become a reality and result in a significant public health impact. Their integration with existing healthcare infrastructures may revolutionize disease detection and surveillance, and improve child health and survival.
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Affiliation(s)
- David Torres-Fernandez
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Jessica Dalsuco
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Justina Bramugy
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Pg. Lluís Companys, Barcelona, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosauro Varo
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
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Pitaloka DAE, Arfan A, Ramadhan DSF, Chaidir L. Insights from the molecular mechanism of pyrazinamide to mutated pyrazinamidase linked to the pncA gene in clinical isolates of Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:759-765. [PMID: 37096659 DOI: 10.1080/07391102.2023.2195002] [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: 10/27/2022] [Accepted: 03/18/2023] [Indexed: 04/26/2023]
Abstract
This study aims to conduct a comprehensive molecular dynamics strategy to evaluate whether mutations found in pyrazinamide monoresistant (PZAMR) strains of Mycobacterium tuberculosis (MTB) can potentially reduce the effectiveness of pyrazinamide (PZA) for tuberculosis (TB) treatment. Five single point mutations of pyrazinamidase (PZAse), an enzyme which is responsible for the activation of prodrug PZA into pyrazinoic acid, found in MTB clinical isolates, namely His82Arg, Thr87Met, Ser66Pro, Ala171Val, and Pro62Leu, were analyzed by the dynamics simulations both in the apo state (unbound state) and in the PZA bound state. The results showed that the mutation of His82 to Arg, Thr87 to Met, and Ser66 to Pro in PZAse affects the coordination state of the Fe2+ ion, which is a cofactor required for enzyme activity. These mutations change the flexibility, stability, and fluctuation of His51, His57, and ASP49 amino acid residues around the Fe2+ ion, culminating in an unstable complex and dissociation of PZA from the PZAse binding site. However, mutations of Ala171 to Val and Pro62 to Leu were found to have no effect on the complex's stability. Based on the results, PZAse mutations of His82Arg, Thr87Met, and Ser66Pro culminated in weak binding affinity for PZA and caused significant structural deformations that led to PZA resistance. Future structural and functional studies, as well as investigations into other aspects of drug resistance in PZAse, will require experimental clarification.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, Indonesia
| | - Arfan Arfan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Universitas Halu Oleo, Kendari, Indonesia
| | - Dwi Syah Fitra Ramadhan
- Department of Pharmaceutical Chemistry, Sekolah Tinggi Ilmu Kesehatan Mandala Waluya, Kendari, Indonesia
| | - Lidya Chaidir
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, Indonesia
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Wang Z, Tang Z, Heidari H, Molaeipour L, Ghanavati R, Kazemian H, Koohsar F, Kouhsari E. Global status of phenotypic pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates: an updated systematic review and meta-analysis. J Chemother 2023; 35:583-595. [PMID: 37211822 DOI: 10.1080/1120009x.2023.2214473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Pyrazinamide (PZA) is an essential first-line tuberculosis drug for its unique mechanism of action active against multidrug-resistant-TB (MDR-TB). Thus, the aim of updated meta-analysis was to estimate the PZA weighted pooled resistance (WPR) rate in M. tuberculosis isolates based on publication date and WHO regions. We systematically searched the related reports in PubMed, Scopus, and Embase (from January 2015 to July 2022). Statistical analyses were performed using STATA software. The 115 final reports in the analysis investigated phenotypic PZA resistance data. The WPR of PZA was 57% (95% CI 48-65%) in MDR-TB cases. According to the WHO regions, the higher WPRs of PZA were reported in the Western Pacific (32%; 95% CI 18-46%), South East Asian region (37%; 95% CI 31-43%), and the Eastern Mediterranean (78%; 95% CI 54-95%) among any-TB patients, high risk of MDR-TB patients, and MDR-TB patients, respectively. A negligible increase in the rate of PZA resistance were showed in MDR-TB cases (55% to 58%). The rate of PZA resistance has been rising in recent years among MDR-TB cases, underlines the essential for both standard and novel drug regimens development.
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Affiliation(s)
- Zheming Wang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Zhihua Tang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Hamid Heidari
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | | | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Faramarz Koohsar
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
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Rostamian M, Kooti S, Abiri R, Khazayel S, Kadivarian S, Borji S, Alvandi A. Prevalence of Mycobacterium tuberculosis mutations associated with isoniazid and rifampicin resistance: A systematic review and meta-analysis. J Clin Tuberc Other Mycobact Dis 2023; 32:100379. [PMID: 37389010 PMCID: PMC10302537 DOI: 10.1016/j.jctube.2023.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
Tuberculosis (TB) is still one of the leading causes of worldwide death, especially following the emergence of strains resistant to isoniazid (INH) and rifampicin (RIF). This study aimed to systematically review published articles focusing on the prevalence of INH and/or RIF resistance-associated mutations of Mycobacterium tuberculosis isolates in recent years. Literature databases were searched using appropriate keywords. The data of the included studies were extracted and used for a random-effects model meta-analysis. Of the initial 1442 studies, 29 were finally eligible to be included in the review. The overall resistance to INH and RIF was about 17.2% and 7.3%, respectively. There was no difference between the frequency of INH and RIF resistance using different phenotypic or genotypic methods. The INH and/or RIF resistance was higher in Asia. The S315T mutation in KatG (23.7 %), C-15 T in InhA (10.7 %), and S531L in RpoB (13.5 %) were the most prevalent mutations. Altogether, the results showed that due to S531L in RpoB, S315T in KatG, and C-15 T in InhA mutations INH- and RIF-resistant M. tuberculosis isolates were widely distributed. Thus, it would be diagnostically and epidemiologically beneficial to track these gene mutations among resistant isolates.
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Affiliation(s)
- Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sara Kooti
- Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Ramin Abiri
- Fertility and Infertility Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saeed Khazayel
- Deupty of Research and Technology Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepide Kadivarian
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soroush Borji
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Medical Technology Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Siahaan AMP, Tandean S, Indharty RS, Nainggolan BWM, Susanto M. Paroxysmal sympathetic hyperactivity syndrome in tuberculous meningitis with paradoxical reaction. Int J Surg Case Rep 2022; 99:107619. [PMID: 36096085 PMCID: PMC9568713 DOI: 10.1016/j.ijscr.2022.107619] [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: 08/13/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION AND IMPORTANCE Paroxysmal sympathetic hyperactivity syndrome is frequently reported in traumatic brain injury. However, it may occur in non-traumatic brain injury, such as tuberculous meningitis with hydrocephalus. CASE PRESENTATION We reported a 38-year-old male who presented with acute decrease of consciousness and hemiparesis that was developed during antitubercular drugs therapy. CT Scan showed hydrocephalus and granuloma lesion. Emergency ventriculoperitoneal shunting were performed. During treatment, the patient developed paroxysmal sympathetic syndrome during treatment that was controlled based on symptom elimination and prevention. CLINICAL DISCUSSION Brain tuberculosis remains a difficult problem for clinicians. Even when antitubercular drugs are administered according to protocol, paradoxical reactions can occur. If hydrocephalus develops, ventriculoperitoneal shunting is one of the options for lowering intracranial pressure. Paroxysmal sympathetic hyperactivity may occur in brain tuberculosis and should be detected as soon as possible to avoid serious morbidity. CONCLUSION Paroxysmal sympathetic hyperactivity may be developed in brain tuberculosis. Early identification and treatment are mandatory.
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Affiliation(s)
| | - Steven Tandean
- Department of Neurosurgery, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Rr Suzy Indharty
- Department of Neurosurgery, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
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Che Y, Lin Y, Yang T, Chen T, Sang G, Chen Q, He T. Evaluation of whole-genome sequence to predict drug resistance of nine anti- tuberculosis drugs and characterize resistance genes in clinical rifampicin-resistant Mycobacterium tuberculosis isolates from Ningbo, China. Front Public Health 2022; 10:956171. [PMID: 36062095 PMCID: PMC9433565 DOI: 10.3389/fpubh.2022.956171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/28/2022] [Indexed: 01/24/2023] Open
Abstract
Setting Controlling drug-resistant tuberculosis in Ningbo, China. Objective Whole-genome sequencing (WGS) has not been employed to comprehensively study Mycobacterium tuberculosis isolates, especially rifampicin-resistant tuberculosis, in Ningbo, China. Here, we aim to characterize genes involved in drug resistance in RR-TB and create a prognostic tool for successfully predicting drug resistance in patients with TB. Design Drug resistance was predicted by WGS in a "TB-Profiler" web service after phenotypic drug susceptibility tests (DSTs) against nine anti-TB drugs among 59 clinical isolates. A comparison of consistency, sensitivity, specificity, and positive and negative predictive values between WGS and DST were carried out for each drug. Results The sensitivities and specificities for WGS were 95.92 and 90% for isoniazid (INH), 100 and 64.1% for ethambutol (EMB), 97.37 and 100% for streptomycin (SM), 75 and 100% for amikacin (AM), 80 and 96.3%for capreomycin (CAP), 100 and 97.22% for levofloxacin (LFX), 93.33 and 90.91% for prothionamide (PTO), and 70 and 97.96% for para-aminosalicylic acid (PAS). Around 53 (89.83%) and 6 (10.17%) of the isolates belonged to lineage two (East-Asian) and lineage four (Euro-American), respectively. Conclusion Whole-genome sequencing is a reliable method for predicting resistance to INH, RIF, EMB, SM, AM, CAP, LFX, PTO, and PAS with high consistency, sensitivity, and specificity. There was no transmission that occurred among the patients with RR-TB in Ningbo, China.
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Affiliation(s)
- Yang Che
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Yi Lin
- Center for Health Economics, Faculty of Humanities and Social Sciences, University of Nottingham, Ningbo, China
| | - Tianchi Yang
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Tong Chen
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Guoxin Sang
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Qin Chen
- Department of Disease Prevention and Health Promotion, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China,*Correspondence: Qin Chen
| | - Tianfeng He
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China,Tianfeng He
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Use of Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Complex Drug Resistance from Early Positive Liquid Cultures. Microbiol Spectr 2022; 10:e0251621. [PMID: 35311541 PMCID: PMC9045259 DOI: 10.1128/spectrum.02516-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Our objective was to evaluate the performance of whole-genome sequencing (WGS) from early positive liquid cultures for predicting Mycobacterium tuberculosis complex (MTBC) drug resistance. Clinical isolates were obtained from tuberculosis patients at Shanghai Pulmonary Hospital (SPH). Antimicrobial susceptibility testing (AST) was performed, and WGS from early Bactec mycobacterial growth indicator tube (MGIT) 960-positive liquid cultures was performed to predict the drug resistance using the TB-Profiler informatics platform. A total of 182 clinical isolates were enrolled in this study. Using phenotypic AST as the gold standard, the overall sensitivity and specificity for WGS were, respectively, 97.1% (89.8 to 99.6%) and 90.4% (83.4 to 95.1%) for rifampin, 91.0% (82.4 to 96.3%) and 95.2% (89.1 to 98.4%) for isoniazid, 100.0% (89.4 to 100.0%) and 87.3% (80.8 to 92.1%) for ethambutol, 96.6% (88.3 to 99.6%) and 61.8% (52.6 to 70.4%) for streptomycin, 86.8% (71.9 to 95.6%) and 95.8% (91.2 to 98.5%) for moxifloxacin, 86.5% (71.2 to 91.5%) and 95.2% (90.3 to 98.0%) for ofloxacin, 100.0% (54.1 to 100.0%) and 67.6% (60.2 to 74.5%) for amikacin, 100.0% (63.1 to 100.0%) and 67.2% (59.7 to 74.2%) for kanamycin, 62.5% (24.5 to 91.5%) and 88.5% (82.8 to 92.8%) for ethionamide, 33.3% (4.3 to 77.7%) and 98.3% (95.1 to 99.7%) for para-aminosalicylic acid, and 0.0% (0.0 to 12.3%) and 100.0% (97.6 to 100.0%) for cycloserine. The concordances of WGS-based AST and phenotypic AST were as follows: rifampin (92.9%), isoniazid (93.4%), ethambutol (89.6%), streptomycin (73.1%), moxifloxacin (94.0%), ofloxacin (93.4%), amikacin (68.7%), kanamycin (68.7%), ethionamide (87.4%), para-aminosalicylic acid (96.2%) and cycloserine (84.6%). We conclude that WGS could be a promising approach to predict MTBC resistance from early positive liquid cultures. IMPORTANCE In this study, we used whole-genome sequencing (WGS) from early positive liquid (MGIT) cultures instead of solid cultures to predict drug resistance of 182 Mycobacterium tuberculosis complex (MTBC) clinical isolates to predict drug resistance using the TB-Profiler informatics platform. Our study indicates that WGS may be a promising method for predicting MTBC resistance using early positive liquid cultures.
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Xu G, Liu H, Jia X, Wang X, Xu P. Mechanisms and detection methods of Mycobacterium tuberculosis rifampicin resistance: The phenomenon of drug resistance is complex. Tuberculosis (Edinb) 2021; 128:102083. [PMID: 33975262 DOI: 10.1016/j.tube.2021.102083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/30/2021] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease that poses a serious threat to human health. Rifampin (RIF) is an important first-line anti-TB drug, and rifampin resistance (RIF-R) is a key factor in formulating treatment regimen and evaluating the prognosis of TB. Compared with other drugs resistance, the RIF-R mechanism of Mycobacterium tuberculosis (M. tuberculosis) is one of the clearest, which is mainly caused by RIF resistance-related mutations in the rpoB gene. This provides a convenient condition for developing rapid detection methods, and also an ideal object for studying the general drug resistance mechanisms of M. tuberculosis. This review focuses on the mechanisms that influence the RIF resistance of M. tuberculosis and related detection methods. Besides the mutations in rpoB, M. tuberculosis can decrease the amount of drugs entering the cells, enhance the drugs efflux, and be heterogeneous RIF susceptibility to resist drug pressure. Based on the results of current researches, many genes participate in influencing the susceptibility to RIF, which indicates the phenomenon of M. tuberculosis drug resistance is very complex.
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Affiliation(s)
- Ge Xu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Hangchi Liu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Xudong Jia
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Xiaomin Wang
- Department of Microbiology, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China.
| | - Peng Xu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China.
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Supo-Escalante RR, Médico A, Gushiken E, Olivos-Ramírez GE, Quispe Y, Torres F, Zamudio M, Antiparra R, Amzel LM, Gilman RH, Sheen P, Zimic M. Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors. PLoS One 2020; 15:e0235643. [PMID: 32735615 PMCID: PMC7394417 DOI: 10.1371/journal.pone.0235643] [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: 03/30/2020] [Accepted: 06/19/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pyrazinamide is an important drug against the latent stage of tuberculosis and is used in both first- and second-line treatment regimens. Pyrazinamide-susceptibility test usually takes a week to have a diagnosis to guide initial therapy, implying a delay in receiving appropriate therapy. The continued increase in multi-drug resistant tuberculosis and the prevalence of pyrazinamide resistance in several countries makes the development of assays for prompt identification of resistance necessary. The main cause of pyrazinamide resistance is the impairment of pyrazinamidase function attributed to mutations in the promoter and/or pncA coding gene. However, not all pncA mutations necessarily affect the pyrazinamidase function. OBJECTIVE To develop a methodology to predict pyrazinamidase function from detected mutations in the pncA gene. METHODS We measured the catalytic constant (kcat), KM, enzymatic efficiency, and enzymatic activity of 35 recombinant mutated pyrazinamidase and the wild type (Protein Data Bank ID = 3pl1). From all the 3D modeled structures, we extracted several predictors based on three categories: structural stability (estimated by normal mode analysis and molecular dynamics), physicochemical, and geometrical characteristics. We used a stepwise Akaike's information criterion forward multiple log-linear regression to model each kinetic parameter with each category of predictors. We also developed weighted models combining the three categories of predictive models for each kinetic parameter. We tested the robustness of the predictive ability of each model by 6-fold cross-validation against random models. RESULTS The stability, physicochemical, and geometrical descriptors explained most of the variability (R2) of the kinetic parameters. Our models are best suited to predict kcat, efficiency, and activity based on the root-mean-square error of prediction of the 6-fold cross-validation. CONCLUSIONS This study shows a quick approach to predict the pyrazinamidase function only from the pncA sequence when point mutations are present. This can be an important tool to detect pyrazinamide resistance.
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Affiliation(s)
- Rydberg Roman Supo-Escalante
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Aldhair Médico
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gustavo E. Olivos-Ramírez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Yaneth Quispe
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Fiorella Torres
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Zamudio
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert H. Gilman
- International Health Department, Johns Hopkins School of Public Health, Baltimore, MD, United States of America
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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Dusthackeer A, Saadhali SA, Thangam M, Hassan S, Balasubramanian M, Balasubramanian A, Ramachandran G, Kumar AKH, Thiruvenkadam K, Shanmugam G, Nirmal CR, Rajadas SE, Mohanvel SK, Mondal R. Wild-Type MIC Distribution for Re-evaluating the Critical Concentration of Anti-TB Drugs and Pharmacodynamics Among Tuberculosis Patients From South India. Front Microbiol 2020; 11:1182. [PMID: 32695072 PMCID: PMC7338667 DOI: 10.3389/fmicb.2020.01182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/08/2020] [Indexed: 11/13/2022] Open
Abstract
The World Health Organization (WHO) has developed specific guidelines for critical concentrations (CCs) of antibiotics used for tuberculosis (TB) treatment, which is universally followed for drug susceptibility testing (DST) of clinical specimens. However, the CC of drugs can differ significantly among the mycobacterial species based on the population, geographic location, and the prevalence of the infecting strain in a particular area. The association between CC and the minimal inhibitory concentration (MIC) of anti-TB drugs is poorly understood. In this study, we assessed the MICs of anti-TB drugs, including isoniazid (INH), rifampicin (RMP), moxifloxacin (MXF), ethambutol (ETH), and p-aminosalicylic acid (PAS) on drug-sensitive Mtb isolates from pulmonary TB patients in South India. The MIC assays performed using solid- and liquid-growth media showed changes in the CC of a few of the tested antibiotics compared with the WHO-recommended levels. Our observation suggests that the WHO guidelines could potentially lead to overdiagnosis of drug-resistant cases, which can result in inappropriate therapeutic decisions. To evaluate the correlation between drug-resistance and CC, we performed the whole-genome sequencing for 16 mycobacterial isolates, including two wild-type and 14 resistant isolates. Our results showed that two of the isolates belonged to the W-Beijing lineage, while the rest were of the East-African-Indian type. We identified a total of 74 mutations, including five novel mutations, which are known to be associated with resistance to anti-TB drugs in these isolates. In our previous study, we determined the serum levels of INH and RMP among the same patients recruited in the current study and estimated the MICs of the corresponding infected isolates in these cases. Using these data and the CCs for INH and RMP from the present study, we performed pharmacodynamics (PD) evaluation. The results show that the PD of RMP was subtherapeutic. Together, these observations emphasize the need for optimizing the drug dosage based on the PD of large-scale studies conducted in different geographical settings.
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Affiliation(s)
- Azger Dusthackeer
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - Shainaba A Saadhali
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Sameer Hassan
- Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | | | | | - Geetha Ramachandran
- Department of Biochemistry, National Institute for Research in Tuberculosis, Chennai, India
| | - A K Hemanth Kumar
- Department of Biochemistry, National Institute for Research in Tuberculosis, Chennai, India
| | - Kannan Thiruvenkadam
- Department of Epidemiology, National Institute for Research in Tuberculosis, Chennai, India
| | - Govindarajan Shanmugam
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Sam Ebenezer Rajadas
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Rajesh Mondal
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
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13
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Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China. Int J Infect Dis 2020; 96:48-53. [DOI: 10.1016/j.ijid.2020.04.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 11/19/2022] Open
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14
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Solo ES, Nakajima C, Kaile T, Bwalya P, Mbulo G, Fukushima Y, Chila S, Kapata N, Shah Y, Suzuki Y. Mutations in rpoB and katG genes and the inhA operon in multidrug-resistant Mycobacterium tuberculosis isolates from Zambia. J Glob Antimicrob Resist 2020; 22:302-307. [PMID: 32169686 DOI: 10.1016/j.jgar.2020.02.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/26/2019] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES It is established that resistance to rifampicin (RIF) in 90% of RIF-resistant Mycobacterium tuberculosis isolates is attributable to point mutations in the rpoB gene, whilst 50-95% of M. tuberculosis resistance to isoniazid (INH) is caused by mutations in the katG gene. However, the patterns and frequencies of mutations vary by geographical region. In Zambia, the genetic mechanisms of resistance of M. tuberculosis to RIF and INH were unreported before this study. METHODS Using gene sequencing, the rpoB, katG and inhA genes of 99 multidrug-resistant M. tuberculosis (MDR-TB) and 49 pan-susceptible M. tuberculosis isolates stored at a tuberculosis reference laboratory from 2013 to 2016 were analysed and were compared with published profiles from other African countries. RESULTS Of the 99 MDR-TB isolates, 95 (96.0%) carried mutations in both rpoB and katG. No mutations were detected among the pan-susceptible isolates. The most common mutations among RIF- and INH-resistant isolates were in codon 531 of the rpoB gene (55.6%; 55/99) and codon 315 of the katG gene (94.9%; 94/99), respectively. Distinctly, katG mutations were predominantly high among Zambian isolates (96.0%) compared with other countries in the region. CONCLUSION Resistance-associated mutations to RIF and INH circulating in Zambia are similar to those reported globally, therefore these data validate the applicability of molecular diagnostic tools in Zambia. However, katG mutations were predominantly high among M. tuberculosis isolates in this study compared with other regional countries and might distinguish cross-boundary transmission of MDR-TB from other African nations.
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Affiliation(s)
- Eddie S Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan
| | - Trevor Kaile
- University of Zambia, School of Medicine, Lusaka, Zambia
| | - Precious Bwalya
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Grace Mbulo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | | | | | - Yogendra Shah
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
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Cao Z, Lan Y, Chen L, Xiang M, Peng Z, Zhang J, Zhang H. Resistance To First-Line Antituberculosis Drugs And Prevalence Of pncA Mutations In Clinical Isolates Of Mycobacterium tuberculosis From Zunyi, Guizhou Province Of China. Infect Drug Resist 2019; 12:3093-3102. [PMID: 31686870 PMCID: PMC6777635 DOI: 10.2147/idr.s222943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
Background China is one of the high-burden countries for multidrug-resistant tuberculosis (MDR-TB), and pyrazinamide is one of the anti-TB drugs used for the shorter MDR-TB treatment regimen. The aim of this study was to determine the correlation between pncA gene mutations and resistance to four first-line anti-TB drugs as well as treatment history in clinical isolates of Mycobacterium tuberculosis. Patients and methods M. tuberculosis clinical isolates were collected from 318 in-patients with smear-positive TB between October 2008 and September 2016 at a major hospital in Zunyi, Guizhou Province of China, and used for drug susceptibility testing against four first-line anti-TB drugs. Genomic DNA extracted from clinical isolates was used for PCR amplification and DNA sequencing of the pncA gene. Results Among 318 clinical isolates, 129 (40.6%), 170 (53.5%), 66 (20.8%) and 109 (34.3%) were resistant to rifampicin, isoniazid, ethambutol and streptomycin respectively. In addition, 124 clinical isolates were MDR-TB and 71.8% of them were previously treated cases. Sequencing results showed that 46.8% of MDR-TB and 2.2% of drug susceptible isolates harbored a pncA mutation, and 52 types of pncA mutations were detected from 64 isolates. The prevalence of pncA mutations in isolates resistant to first-line anti-TB drugs and previously treated TB cases was significantly higher than that in drug-susceptible isolates and new cases of TB. Conclusion High prevalence of pncA mutations in clinical isolates of M. tuberculosis from Zunyi, Guizhou Province of China, is correlated with resistance to four first-line anti-TB drugs, MDR-TB and previously treated TB cases.
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Affiliation(s)
- Zhimin Cao
- Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China
| | - Yuanbo Lan
- Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China
| | - Ling Chen
- Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China
| | - Min Xiang
- Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China
| | - Zhiyuan Peng
- Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China
| | - Jianyong Zhang
- Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China
| | - Hong Zhang
- Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China.,Department of R & D, Z-BioMed, Inc, Rockville, MD, 20855, USA
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