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Tran BM, Larsson J, Grip A, Karempudi P, Elf J. Phenotypic drug susceptibility testing for Mycobacterium tuberculosis variant bovis BCG in 12 hours. Nat Commun 2025; 16:4366. [PMID: 40348759 PMCID: PMC12065818 DOI: 10.1038/s41467-025-59736-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 04/23/2025] [Indexed: 05/14/2025] Open
Abstract
Drug-resistant tuberculosis (DR-TB) kills ~200,000 people every year. A contributing factor is the slow turnaround time (TAT) associated with drug susceptibility diagnostics. The prevailing gold standard for phenotypic drug susceptibility testing (pDST) takes at least two weeks. Here we show that growth-based pDST for slow-growing mycobacteria can be conducted in 12 h. We use Mycobacterium tuberculosis variant bovis Bacillus Calmette-Guérin (BCG) and Mycobacterium smegmatis as the mycobacterial pathogen models and expose them to antibiotics used in (multidrug-resistant) tuberculosis (TB) treatment regimens - i.e., rifampicin (RIF), isoniazid (INH), ethambutol (EMB), linezolid (LZD), streptomycin (STR), bedaquiline (BDQ), and levofloxacin (LFX). The bacterial growth in a microfluidic chip is tracked by time-lapse phase-contrast microscopy. A deep neural network-based segmentation algorithm is used to quantify the growth rate and to determine how the strains responded to drug treatments. Most importantly, a panel of susceptible and resistant M. bovis BCG are tested at critical concentrations for INH, RIF, STR, and LFX. The susceptible strains could be identified in less than 12 h. These findings are comparable to what we expect for pathogenic M. tuberculosis as they share 99.96% genetic identity.
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Affiliation(s)
- Buu Minh Tran
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Jimmy Larsson
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Anastasia Grip
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Praneeth Karempudi
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden.
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Rajendran P, Giridaran P, Thomas SV, Nagaraj N, Thiruvengadam K, Radhika G, Samyuktha R, Selvaraju S, Frederick A, Padmapriyadarsini C, Shanmugam S. Characterisation of M. tuberculosis isolates obtained from Tamil Nadu prevalence survey by whole genome sequencing analysis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2025; 132:105763. [PMID: 40354869 DOI: 10.1016/j.meegid.2025.105763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Revised: 05/09/2025] [Accepted: 05/09/2025] [Indexed: 05/14/2025]
Abstract
Recent advances in whole genome sequencing have facilitated the understanding of drug resistance patterns and lineage distribution of M. tuberculosis worldwide. In this study, we aimed to determine the genetic diversity of MTB isolates from presumptive pulmonary TB patients obtained from a state prevalence survey. A total of 124 isolates were available for further characterisation, out of which 71 (57.2 %) and 47 (37.9 %) were subjected to sequencing and phenotypic DST, respectively. The phenotypic resistance profile revealed 3 isolates with multidrug resistance and 3 with mono-INH resistance. Out of 71 isolates, sequencing data were available for 61 (85.9 %), where the lineage distribution and drug resistance profile were analysed in comparison with phenotypic DST results. All the mutations were significant, accounting for one or the other resistance pattern. The concordance between pDST and gDST for the drugs was above 90 % except for ETH (77 %) and INH (87 %). The phylogenetic analysis of the lineage distribution revealed three clusters with MDR isolates belonging to lineage 1 and lineage 3. While lineage 2 is more frequently associated with MDR distribution both in India and worldwide, we did not find any lineage 2 MDR-TB isolates in our study. The use of WGS analysis improved our understanding of the genetic characteristics of MTB and its correlation with DR-TB transmission.
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Affiliation(s)
- Priya Rajendran
- ICMR, National Institute for Research in Tuberculosis, India
| | - Prathiksha Giridaran
- ICMR, National Institute for Research in Tuberculosis, India; ICMR, National Institute of Epidemiology, India
| | | | | | | | - Golla Radhika
- ICMR, National Institute for Research in Tuberculosis, India
| | - Roja Samyuktha
- ICMR, National Institute for Research in Tuberculosis, India
| | | | - Asha Frederick
- Directorate of Medical and Rural Health Services, Chennai, India
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Hong C, Ge J, Gui J, Che X, Li Y, Zhuo Z, Li M, Wang F, Tan W, Zhao Z. Cross-District Transmission of Tuberculosis in a High-Mobility City in China: Implications for Regional Collaboration in Infectious Disease Control. Infect Drug Resist 2025; 18:1551-1560. [PMID: 40123712 PMCID: PMC11930267 DOI: 10.2147/idr.s516162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 03/13/2025] [Indexed: 03/25/2025] Open
Abstract
Objective This study aims to elucidate the transmission dynamics of tuberculosis in a Chinese city with high population mobility and to identify the associated risk factors. Methods We included the data from ten city-level surveillance sites in Shenzhen between 2018 and 2023. Genomic clusters were defined as having a genomic distance of 12 single nucleotide polymorphisms based on whole-genome sequencing. Cross-district clusters were characterized as clusters containing patients from at least two districts, indicating cross-district transmission. Risk factors for clustering were identified using logistic regression. Results Of the 2,519 enrolled patients, 263 (10.4%) were grouped into 119 genomic clusters. Notably, 52.1% (62/119) of these clusters were cross-district clusters. We analyzed the data from Shenzhen's 10 districts separately and compared the results with a citywide combined analysis, finding that the combined analysis revealed significantly higher clustering rates across all districts (P<0.001). Furthermore, the risk of cross-district transmission was 3.41 times higher (95% CI: 1.49-7.80) among internal migrants than among residents. Multivariable logistic regression analysis identified significant risk factors for TB transmission, including age under 25 years (OR=3.07, 95% CI: 1.17-8.03), age 25-44 years (OR=2.86, 95% CI: 1.13-7.23), and drug-resistant TB (OR=1.57, 95% CI: 1.15-2.13). Conclusion Cross-district transmission is a key factor in the spread of tuberculosis in cities with high population mobility. TB control institutions at all levels must transcend regional boundaries and enhance collaboration to achieve more effective tuberculosis control.
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Affiliation(s)
- Chuangyue Hong
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Jinjin Ge
- National Clinical Research Center for Infectious Diseases, Shenzhen Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Shenzhen, 518112, People’s Republic of China
| | - Jing Gui
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Xiaoling Che
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Yilin Li
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Zhipeng Zhuo
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Mingzhen Li
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Feng Wang
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Weiguo Tan
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
| | - Zhiguang Zhao
- Department of Tuberculosis Prevention and Control, Shenzhen Center for Chronic Disease Control; Shenzhen Institute of Pulmonology, Shenzhen, 518020, People’s Republic of China
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Elton L, Aydin A, Stoker N, Rofael S, Wildner LM, Abdul JBPAA, Tembo J, Hamid MA, Claujens Chastel MM, Canseco JO, Doyle R, Satta G, O’Grady J, Witney A, Ntoumi F, Zumla A, McHugh TD. A pragmatic pipeline for drug resistance and lineage identification in Mycobacterium tuberculosis using whole genome sequencing. PLOS GLOBAL PUBLIC HEALTH 2025; 5:e0004099. [PMID: 39928651 PMCID: PMC11809915 DOI: 10.1371/journal.pgph.0004099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 12/03/2024] [Indexed: 02/12/2025]
Abstract
Delays in accurate diagnosis of drug resistant tuberculosis (DR-TB) can hinder treatment. Whole genome sequencing (WGS) provides more information than standard molecular and phenotypic testing, but commonly used platforms are expensive to implement, and data interpretation requires significant expertise. We aimed to optimise a TB WGS diagnostic pipeline balancing user-friendliness, cost-effectiveness and time to results, whilst ensuring accuracy. Growth conditions, DNA extraction protocols and Oxford Nanopore Technologies (ONT) library preparation kits were compared. ONT was compared with Illumina protocols. Software for basecalling and analysis were evaluated to find the most accurate resistance SNP and lineage predictor. Optimally, a spin-column CTAB DNA extraction method was combined with the RBK110.96 library preparation kit, high accuracy (HAC) basecalling and data analysis using TB-Profiler. Compared with Illumina, the pipeline was concordant for 16/17 (94%) isolates (lineage) and for 17/17 (100%) isolates (resistance SNPs). Our pipeline was 71% (12/17) concordant with phenotypic drug susceptibility test (DST) results. Time-to-diagnosis was around four weeks. This optimised TB sequencing pipeline requires less time and expertise to run and analyse than Illumina, takes less time than phenotypic DSTs and the results are comparable with Illumina. The cost per sample is comparable with other methods. These features make it an important tool for incorporating into routine DR-TB diagnostic pipelines and larger scale drug resistance surveillance in all settings.
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Affiliation(s)
- Linzy Elton
- Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Alp Aydin
- Oxford Nanopore Technologies plc. Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich, United Kingdom
| | - Neil Stoker
- Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Sylvia Rofael
- Centre for Clinical Microbiology, University College London, London, United Kingdom
- Faculty of Pharmacy, Alexandria University, Cairo, Egypt
| | | | | | - John Tembo
- HerpeZ, University Teaching Hospital, Lusaka, Zambia
| | | | - Mfoutou Mapanguy Claujens Chastel
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of Congo
- Université Marien Ngouabi, Brazzaville, Republic of Congo
| | | | - Ronan Doyle
- London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom
| | - Giovanni Satta
- Centre for Clinical Microbiology, University College London, London, United Kingdom
- University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Justin O’Grady
- Oxford Nanopore Technologies plc. Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich, United Kingdom
| | - Adam Witney
- St George’s, University of London, London, United Kingdom
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of Congo
- Université Marien Ngouabi, Brazzaville, Republic of Congo
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, University College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London, United Kingdom
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Couvin D, Allaguy AS, Ez-zari A, Jagielski T, Rastogi N. Molecular typing of Mycobacterium tuberculosis: a review of current methods, databases, softwares, and analytical tools. FEMS Microbiol Rev 2025; 49:fuaf017. [PMID: 40287399 PMCID: PMC12065434 DOI: 10.1093/femsre/fuaf017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Revised: 04/20/2025] [Accepted: 04/25/2025] [Indexed: 04/29/2025] Open
Abstract
Studies on the epidemiology and clinical relevance of Mycobacterium tuberculosis complex (MTBC) have immensely benefited from molecular typing methods, associated software applications, and bioinformatics tools. Over the last two decades, the Pasteur Institute of Guadeloupe has developed a range of bioinformatic resources, including databases and software, to advance understanding of TB epidemiology. Traditional methods, such as IS6110-RFLP, MIRU-VNTR typing, and spoligotyping, have been instrumental but are increasingly supplanted by more precise and high-throughput techniques. These typing methods offer relatively good discrimination and reproducibility, making them popular choices for epidemiological studies. However, the advent of whole-genome sequencing (WGS) has revolutionized Mycobacterium tuberculosis complex (MTBC) typing, providing unparalleled resolution and data analysis depth. WGS enables the identification of single nucleotide polymorphisms and other genetic variations, facilitating robust phylogenetic reconstructions, and detailed outbreak investigations. This review summarizes current molecular typing methods, as well as databases and software tools used for MTBC data analysis. A comprehensive comparison of available tools and databases is provided to guide future research on the epidemiology of TB and pathogen-associated variables (drug resistance or virulence) and public health initiatives.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory—TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, F-97139, Les Abymes, Guadeloupe, France
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, F-97154, Pointe-à-Pitre, Guadeloupe, France
| | - Anne-Sophie Allaguy
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, F-97154, Pointe-à-Pitre, Guadeloupe, France
| | - Ayoub Ez-zari
- Laboratory of Biology and Health (UAE/U06FS), Department of Biology, Faculty of Science, Abdelmalek Essaâdi University, BP 2121, 93002 Tetouan, Morocco
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory—TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, F-97139, Les Abymes, Guadeloupe, France
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Molla G, Bitew M. Revolutionizing Personalized Medicine: Synergy with Multi-Omics Data Generation, Main Hurdles, and Future Perspectives. Biomedicines 2024; 12:2750. [PMID: 39767657 PMCID: PMC11673561 DOI: 10.3390/biomedicines12122750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 10/05/2024] [Accepted: 10/07/2024] [Indexed: 01/11/2025] Open
Abstract
The field of personalized medicine is undergoing a transformative shift through the integration of multi-omics data, which mainly encompasses genomics, transcriptomics, proteomics, and metabolomics. This synergy allows for a comprehensive understanding of individual health by analyzing genetic, molecular, and biochemical profiles. The generation and integration of multi-omics data enable more precise and tailored therapeutic strategies, improving the efficacy of treatments and reducing adverse effects. However, several challenges hinder the full realization of personalized medicine. Key hurdles include the complexity of data integration across different omics layers, the need for advanced computational tools, and the high cost of comprehensive data generation. Additionally, issues related to data privacy, standardization, and the need for robust validation in diverse populations remain significant obstacles. Looking ahead, the future of personalized medicine promises advancements in technology and methodologies that will address these challenges. Emerging innovations in data analytics, machine learning, and high-throughput sequencing are expected to enhance the integration of multi-omics data, making personalized medicine more accessible and effective. Collaborative efforts among researchers, clinicians, and industry stakeholders are crucial to overcoming these hurdles and fully harnessing the potential of multi-omics for individualized healthcare.
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Affiliation(s)
- Getnet Molla
- College of Veterinary Medicine, Jigjiga University, Jigjiga P.O. Box 1020, Ethiopia
- Bio and Emerging Technology Institute (BETin), Addis Ababa P.O. Box 5954, Ethiopia;
| | - Molalegne Bitew
- Bio and Emerging Technology Institute (BETin), Addis Ababa P.O. Box 5954, Ethiopia;
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Roshdi Maleki M. Species and genetic diversity of nontuberculous mycobacteria in suspected tuberculosis cases in East Azerbaijan, Iran: a cross-sectional analysis. Front Cell Infect Microbiol 2024; 14:1477015. [PMID: 39512592 PMCID: PMC11540818 DOI: 10.3389/fcimb.2024.1477015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 10/01/2024] [Indexed: 11/15/2024] Open
Abstract
Introduction The incidence of nontuberculous mycobacterial (NTM) infections has increased worldwide, attracting attention in routine diagnostic settings, particularly among patients with suspected tuberculosis. This study aimed to acquire knowledge of NTM infections in patients with suspected tuberculosis and to evaluate the genetic diversity of the strains. Methods In this study, 230 clinical specimens were collected from suspected tuberculosis patients. Following decontamination with N-Acetyl-L-cysteine-sodium hydroxide (NALC-NaOH), the sediments of specimens were inoculated onto Löwenstein-Jensen medium and then incubated at 37°C for 8 weeks. The samples that yielded positive cultures were evaluated through the sequencing of conserved fragments of IS6110 and hsp65. For those samples that were not identified as part of the M. tuberculosis complex (MTC) by IS6110 PCR, further analysis was conducted via PCR to detect fragments of the hsp65 gene. Results Twenty-one NTM species were isolated from 230 clinical specimens (14 NTM from pulmonary specimens and 7 from extrapulmonary specimens). Among these, 12 (57.14%) were rapid-growing mycobacteria (RGM), and 9 (42.85%) were slow-growing mycobacteria (SGM). No M. avium complex (MAC) was identified in any of the specimens. Notably, the M. kansasii, M. gordonae, and M. abscessus strains presented significant genetic diversity. Conclusions The prevalence of infections attributed to nontuberculous species surpasses that attributed to tuberculosis. These findings underscore the importance of exploring NTM species in individuals suspected of having TB.
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Schwab TC, Perrig L, Göller PC, Guebely De la Hoz FF, Lahousse AP, Minder B, Günther G, Efthimiou O, Omar SV, Egger M, Fenner L. Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis. THE LANCET. INFECTIOUS DISEASES 2024; 24:1162-1176. [PMID: 38795712 PMCID: PMC11881551 DOI: 10.1016/s1473-3099(24)00263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 05/28/2024]
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) can rapidly and simultaneously detect mutations associated with resistance to tuberculosis drugs across multiple gene targets. The use of targeted NGS to diagnose drug-resistant tuberculosis, as described in publicly available data, has not been comprehensively reviewed. We aimed to identify targeted NGS assays that diagnose drug-resistant tuberculosis, determine how widely this technology has been used, and assess the diagnostic accuracy of these assays. METHODS In this systematic review and meta-analysis, we searched MEDLINE, Embase, Cochrane Library, Web of Science Core Collection, Global Index Medicus, Google Scholar, ClinicalTrials.gov, and the WHO International Clinical Trials Registry Platform for published and unpublished reports on targeted NGS for drug-resistant tuberculosis from Jan 1, 2005, to Oct 14, 2022, with updates to our search in Embase and Google Scholar until Feb 13, 2024. Studies eligible for the systematic review described targeted NGS approaches to predict drug resistance in Mycobacterium tuberculosis infections using primary samples, reference strain collections, or cultured isolates from individuals with presumed or confirmed tuberculosis. Our search had no limitations on study type or language, although only reports in English, German, and French were screened for eligibility. For the meta-analysis, we included test accuracy studies that used any reference standard, and we assessed risk of bias using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The primary outcomes for the meta-analysis were sensitivity and specificity of targeted NGS to diagnose drug-resistant tuberculosis compared to phenotypic and genotypic drug susceptibility testing. We used a Bayesian bivariate model to generate summary receiver operating characteristic plots and diagnostic accuracy measures, overall and stratified by drug and sample type. This study is registered with PROSPERO, CRD42022368707. FINDINGS We identified and screened 2920 reports, of which 124 were eligible for our systematic review, including 37 review articles and 87 reports of studies collecting samples for targeted NGS. Sequencing was mainly done in the USA (14 [16%] of 87), western Europe (ten [11%]), India (ten [11%]), and China (nine [10%]). We included 24 test accuracy studies in the meta-analysis, in which 23 different tuberculosis drugs or drug groups were assessed, covering first-line drugs, injectable drugs, and fluoroquinolones and predominantly comparing targeted NGS with phenotypic drug susceptibility testing. The combined sensitivity of targeted NGS across all drugs was 94·1% (95% credible interval [CrI] 90·9-96·3) and specificity was 98·1% (97·0-98·9). Sensitivity for individual drugs ranged from 76·5% (52·5-92·3) for capreomycin to 99·1% (98·3-99·7) for rifampicin; specificity ranged from 93·1% (88·0-96·3) for ethambutol to 99·4% (98·3-99·8) for amikacin. Diagnostic accuracy was similar for primary clinical samples and culture isolates overall and for rifampicin, isoniazid, ethambutol, streptomycin, and fluoroquinolones, and similar after excluding studies at high risk of bias (overall sensitivity 95·2% [95% CrI 91·7-97·1] and specificity 98·6% [97·4-99·3]). INTERPRETATION Targeted NGS is highly sensitive and specific for detecting drug resistance across panels of tuberculosis drugs and can be performed directly on clinical samples. There is a paucity of data on performance for some currently recommended drugs. The barriers preventing the use of targeted NGS to diagnose drug-resistant tuberculosis in high-burden countries need to be addressed. FUNDING National Institutes of Allergy and Infectious Diseases and Swiss National Science Foundation.
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Affiliation(s)
- Tiana Carina Schwab
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Lisa Perrig
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | - Beatrice Minder
- Public Health and Primary Care Library, University Library of Bern, University of Bern, Bern, Switzerland
| | - Gunar Günther
- Department of Pulmonology and Allergology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department of Medical Science, Faculty of Health Sciences, University of Namibia, Windhoek, Namibia
| | - Orestis Efthimiou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology & Research, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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Esteves LS, Gomes LL, Brites D, Fandinho FCO, Bhering M, Pereira MADS, Conceição EC, Salvato R, da Costa BP, Medeiros RFDM, Caldas PCDS, Redner P, Dalcolmo MP, Eldholm V, Gagneux S, Rossetti ML, Kritski AL, Suffys PN. Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing. Antibiotics (Basel) 2024; 13:496. [PMID: 38927163 PMCID: PMC11200758 DOI: 10.3390/antibiotics13060496] [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: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.
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Affiliation(s)
- Leonardo Souza Esteves
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Lia Lima Gomes
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Daniela Brites
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Fátima Cristina Onofre Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Marcela Bhering
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Márcia Aparecida da Silva Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
| | - Richard Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
| | - Bianca Porphirio da Costa
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Reginalda Ferreira de Melo Medeiros
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Redner
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Margareth Pretti Dalcolmo
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Vegard Eldholm
- Norwegian Institute of Public Health, 0213 Oslo, Norway;
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Maria Lucia Rossetti
- Laboratório de Biologia Molecular, Universidade Luterana do Brasil (ULBRA), Canoas 92425-020, RS, Brazil;
| | - Afrânio Lineu Kritski
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
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10
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Hu Y, Yu M, You G, Fan J, Zheng H. Evaluation of MeltPro Assay in Identification of Second-Line Injectable Drug Resistance in Multidrug-Resistant Tuberculosis Isolates. Infect Drug Resist 2024; 17:2069-2076. [PMID: 38807773 PMCID: PMC11131950 DOI: 10.2147/idr.s459142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Objective We compared the MeltPro assay to whole-genome sequencing (WGS) to investigate the molecular characterization of second-line injectable drug (SLID) resistance in multidrug-resistant tuberculosis (MDR-TB) isolates in Chongqing, China. Methods A total of 122 MDR-TB patient isolates were collected between March 2019 and June 2020 from Chongqing Municipality, China. Conventional drug-susceptibility testing was performed using the proportion method, followed to generate minimum inhibitory concentrations (MICs) of SLIDs determined by microplate alamarblue assay. All strains were subjected to both MeltPro and WGS assays. Results Among 122 MDR-TB isolates, 30 (24.6%), 22 (18.0%), and 14 (11.5%) were resistant to kanamycin (KM), amikacin (AM), and capreomycin (CM), respectively. Of the 31 SLID-resistant isolates, 24 (77.4%, 24/31) isolates harbored mutations in the rrs gene, with the most prevalent mutations in rrs A1401G (22/24, 91.7%). Mutation in rrs A1401G was associated with high levels of resistance to KM (MIC, ≥40 μg/mL) and AM (MIC, ≥64 μg/mL), but disparities in CM-resistance levels. Using phenotypic drug-susceptibility testing as gold standard, we found that the overall sensitivity of MeltPro and WGS was 87.1% and 90.32% and specificity 100% and 97.8%, respectively. Seven isolates had discordant results between phenotypic and genotypic resistance of SLIDs. Conclusion MeltPro is a promising diagnostic tool for accurate identification of SLID-resistant MTB isolates with mutations in the rrs and eis genes. There was a disparity between MeltPro with WGS results in the proportion of heterogeneous drug-resistant bacteria with rrs mutation and limited probes. Resistance mechanisms other than genetic mutations will affect the consistency of MeltPro and WGS with phenotypic drug-susceptibility results.
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Min Yu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Guoqing You
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Jun Fan
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Huiwen Zheng
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, People’s Republic of China
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11
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Tagami Y, Horita N, Kaneko M, Muraoka S, Fukuda N, Izawa A, Kaneko A, Somekawa K, Kamimaki C, Matsumoto H, Tanaka K, Murohashi K, Aoki A, Fujii H, Watanabe K, Hara Y, Kobayashi N, Kaneko T. Whole-Genome Sequencing Predicting Phenotypic Antitubercular Drug Resistance: Meta-analysis. J Infect Dis 2024; 229:1481-1492. [PMID: 37946558 DOI: 10.1093/infdis/jiad480] [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: 03/27/2023] [Revised: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND For simultaneous prediction of phenotypic drug susceptibility test (pDST) for multiple antituberculosis drugs, the whole genome sequencing (WGS) data can be analyzed using either a catalog-based approach, wherein 1 causative mutation suggests resistance, (eg, World Health Organization catalog) or noncatalog-based approach using complicated algorithm (eg, TB-profiler, machine learning). The aim was to estimate the predictive ability of WGS-based tests with pDST as the reference, and to compare the 2 approaches. METHODS Following a systematic literature search, the diagnostic test accuracies for 14 drugs were pooled using a random-effect bivariate model. RESULTS Of 779 articles, 44 with 16 821 specimens for meta-analysis and 13 not for meta-analysis were included. The areas under summary receiver operating characteristic curve suggested test accuracy was excellent (0.97-1.00) for 2 drugs (isoniazid 0.975, rifampicin 0.975), very good (0.93-0.97) for 8 drugs (pyrazinamide 0.946, streptomycin 0.952, amikacin 0.968, kanamycin 0.963, capreomycin 0.965, para-aminosalicylic acid 0.959, levofloxacin 0.960, ofloxacin 0.958), and good (0.75-0.93) for 4 drugs (ethambutol 0.926, moxifloxacin 0.896, ethionamide 0.878, prothionamide 0.908). The noncatalog-based and catalog-based approaches had similar ability for all drugs. CONCLUSIONS WGS accurately identifies isoniazid and rifampicin resistance. For most drugs, positive WGS results reliably predict pDST positive. The 2 approaches had similar ability. CLINICAL TRIALS REGISTRATION UMIN-ID UMIN000049276.
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Affiliation(s)
- Yoichi Tagami
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuyuki Horita
- Chemotherapy Center, Yokohama City University Hospital, Yokohama, Japan
| | - Megumi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Suguru Muraoka
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuhiko Fukuda
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ami Izawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ayami Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Somekawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Chisato Kamimaki
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Matsumoto
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Katsushi Tanaka
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kota Murohashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ayako Aoki
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroaki Fujii
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Keisuke Watanabe
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yu Hara
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuaki Kobayashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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12
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Zhang K, Potter RF, Marino J, Muenks CE, Lammers MG, Dien Bard J, Dingle TC, Humphries R, Westblade LF, Burnham CAD, Dantas G. Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus. mSystems 2023; 8:e0069723. [PMID: 38051037 PMCID: PMC10734486 DOI: 10.1128/msystems.00697-23] [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: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCCmec configurations as well as phage elements in S. saprophyticus, which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.
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Affiliation(s)
- Kailun Zhang
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Robert F. Potter
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jamie Marino
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carol E. Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Matthew G. Lammers
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tanis C. Dingle
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Romney Humphries
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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13
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Hazra D, Lam C, Chawla K, Sintchenko V, Dhyani VS, Venkatesh BT. Impact of Whole-Genome Sequencing of Mycobacterium tuberculosis on Treatment Outcomes for MDR-TB/XDR-TB: A Systematic Review. Pharmaceutics 2023; 15:2782. [PMID: 38140122 PMCID: PMC10747601 DOI: 10.3390/pharmaceutics15122782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence and persistence of drug-resistant tuberculosis is a major threat to global public health. Our objective was to assess the applicability of whole-genome sequencing (WGS) to detect genomic markers of drug resistance and explore their association with treatment outcomes for multidrug-resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB). METHODS Five electronic databases were searched for studies published in English from the year 2000 onward. Two reviewers independently conducted the article screening, relevant data extraction, and quality assessment. The data of the included studies were synthesized with a narrative method and are presented in a tabular format. RESULTS The database search identified 949 published articles and 8 studies were included. An unfavorable treatment outcome was reported for 26.6% (488/1834) of TB cases, which ranged from 9.7 to 51.3%. Death was reported in 10.5% (194/1834) of total cases. High-level fluoroquinolone resistance (due to gyrA 94AAC and 94GGC mutations) was correlated as the cause of unfavorable treatment outcomes and reported in three studies. Other drug resistance mutations, like kanamycin high-level resistance mutations (rrs 1401G), rpoB Ile491Phe, and ethA mutations, conferring prothionamide resistance were also reported. The secondary findings from this systematic review involved laboratory aspects of WGS, including correlations with phenotypic DST, cost, and turnaround time, or the impact of WGS results on public health actions, such as determining transmission events within outbreaks. CONCLUSIONS WGS has a significant capacity to provide accurate and comprehensive drug resistance data for MDR/XDR-TB, which can inform personalized drug therapy to optimize treatment outcomes.
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Affiliation(s)
- Druti Hazra
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| | - Connie Lam
- Sydney Institute for Infectious Diseases, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia;
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia;
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Vijay Shree Dhyani
- Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| | - Bhumika T. Venkatesh
- Public Health Evidence South Asia, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
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14
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [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: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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15
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Hemeg HA, Albulushi HO, Ozbak HA, Ali HM, Alahmadi EK, Almutawif YA, Alhuofie ST, Alaeq RA, Alhazmi AA, Najim MA, Hanafy AM. Evaluating the Sensitivity of Different Molecular Techniques for Detecting Mycobacterium tuberculosis Complex in Patients with Pulmonary Infection. Pol J Microbiol 2023; 72:421-431. [PMID: 37934050 PMCID: PMC10725165 DOI: 10.33073/pjm-2023-040] [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: 06/20/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023] Open
Abstract
This study aimed to evaluate the accuracy of detecting drug-resistant Mycobacterium tuberculosis complex (MTBC)-specific DNA in sputum specimens from 48 patients diagnosed with pulmonary tuberculosis. The presence of MTBC DNA in the specimens was validated using the GeneXpert MTB/RIF system and compared with a specific PCR assay targeting the IS6110 and the mtp40 gene sequence fragments. Additionally, the results obtained by multiplex PCR assays to detect the most frequently encountered rifampin, isoniazid, and ethambutol resistance-conferring mutations were matched with those obtained by GeneXpert and phenotypic culture-based drug susceptibility tests. Of the 48 sputum samples, 25 were positive for MTBC using the GeneXpert MTB/RIF test. Nevertheless, the IS6110 and mtp40 single-step PCR revealed the IS6110 in 27 of the 48 sputum samples, while the mtp40 gene fragment was found in only 17 of them. Furthermore, multiplex PCR assays detected drug-resistant conferring mutations in 21 (77.8%) of the 27 samples with confirmed MTBC DNA, 10 of which contained single drug-resistant conferring mutations towards ethambutol and two towards rifampin, and the remaining nine contained double-resistant mutations for ethambutol and rifampin. In contrast, only five sputum specimens (18.5%) contained drug-resistant MTBC isolates, and two contained mono-drug-resistant MTBC species toward ethambutol and rifampin, respectively, and the remaining three were designated as multi-drug resistant toward both drugs using GeneXpert and phenotypic culture-based drug susceptibility tests. Such discrepancies in the results emphasize the need to develop novel molecular tests that associate with phenotypic non-DNA-based assays to improve the detection of drug-resistant isolates in clinical specimens in future studies.
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Affiliation(s)
- Hassan A. Hemeg
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Hamzah O. Albulushi
- Biology Department, College of Science, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Hani A. Ozbak
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Hamza M. Ali
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Emad K. Alahmadi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Yahya A. Almutawif
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Sari T. Alhuofie
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Rana A. Alaeq
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Areej A. Alhazmi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Mustafa A. Najim
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Ahmed M. Hanafy
- Biology Department, College of Science, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
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Rao M, Wollenberg K, Harris M, Kulavalli S, Thomas L, Chawla K, Shenoy VP, Varma M, Saravu K, Hande HM, Shanthigrama Vasudeva CS, Jeffrey B, Gabrielian A, Rosenthal A. Lineage classification and antitubercular drug resistance surveillance of Mycobacterium tuberculosis by whole-genome sequencing in Southern India. Microbiol Spectr 2023; 11:e0453122. [PMID: 37671895 PMCID: PMC10580826 DOI: 10.1128/spectrum.04531-22] [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: 11/13/2022] [Accepted: 07/03/2023] [Indexed: 09/07/2023] Open
Abstract
IMPORTANCE Studies mapping genetic heterogeneity of clinical isolates of M. tuberculosis for determining their strain lineage and drug resistance by whole-genome sequencing are limited in high tuberculosis burden settings. We carried out whole-genome sequencing of 242 M. tuberculosis isolates from drug-sensitive and drug-resistant tuberculosis patients, identified and collected as part of the TB Portals Program, to have a comprehensive insight into the genetic diversity of M. tuberculosis in Southern India. We report several genetic variations in M. tuberculosis that may confer resistance to antitubercular drugs. Further wide-scale efforts are required to fully characterize M. tuberculosis genetic diversity at a population level in high tuberculosis burden settings for providing precise tuberculosis treatment.
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Affiliation(s)
- Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kurt Wollenberg
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Harris
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shrivathsa Kulavalli
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Vishnu Prasad Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavitha Saravu
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - H. Manjunatha Hande
- Department of Medicine, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Brendan Jeffrey
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrei Gabrielian
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alex Rosenthal
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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17
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Liang D, Song Z, Liang X, Qin H, Huang L, Ye J, Lan R, Luo D, Zhao Y, Lin M. Whole Genomic Analysis Revealed High Genetic Diversity and Drug-Resistant Characteristics of Mycobacterium tuberculosis in Guangxi, China. Infect Drug Resist 2023; 16:5021-5031. [PMID: 37554542 PMCID: PMC10405913 DOI: 10.2147/idr.s410828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 08/10/2023] Open
Abstract
Background Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a major public health issue in China. Nevertheless, the prevalence and drug resistance characteristics of isolates vary in different regions and provinces. In this study, we investigated the population structure, transmission dynamics and drug-resistant profiles of Mtb in Guangxi, located on the border of China. Methods From February 2016 to April 2017, 462 clinical M. tuberculosis isolates were selected from 5 locations in Guangxi. Drug-susceptibility testing was performed using 6 common anti-tuberculosis drugs. The genotypic drug resistance and transmission dynamics were analyzed by the whole genome sequence. Results Our data showed that the Mtb in Guangxi has high genetic diversity including Lineage 1 to Lineage 4, and mostly belong to Lineage 2 and Lineage 4. Novelty, 9.6% of Lineage 2 isolates were proto-Beijing genotype (L2.1), which is rare in China. About 12.6% of isolates were phylogenetically clustered and formed into 28 transmission clusters. We observed that the isolates with the high resistant rate of isoniazid (INH, 21.2%), followed by rifampicin (RIF, 13.2%), and 6.7%, 12.1%, 6.7% and 1.9% isolates were resistant to ethambutol (EMB), streptomycin (SM), ofloxacin (OFL) and kanamycin (KAN), respectively. Among these, 6.5% and 3.3% of isolates belong to MDR-TB and Pre-XDR, respectively, with a high drug-resistant burden. Genetic analysis identified the most frequently encountered mutations of INH, RIF, EMB, SM, OFL and KAN were katG_Ser315Thr (62.2%), rpoB_Ser450Leu (42.6%), embB_Met306Vol (45.2%), rpsL_Lys43Arg (53.6%), gyrA_Asp94Gly (29.0%) and rrs_A1401G (66.7%), respectively. Additionally, we discovered that isolates from border cities are more likely to be drug-resistant than isolates from non-border cities. Conclusion Our findings provide a deep analysis of the genomic population characteristics and drug-resistant of M. tuberculosis in Guangxi, which could contribute to developing effective TB prevention and control strategies.
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Affiliation(s)
- Dabin Liang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Zexuan Song
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiaoyan Liang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Huifang Qin
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Liwen Huang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Jing Ye
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Rushu Lan
- Department of Clinical Laboratory, Jiangbin Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, People’s Republic of China
| | - Dan Luo
- School of Public Health and Management, Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Mei Lin
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
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18
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Lee SH, Ferran E, Witney AA, Ryu S, Kang H, Storey N, McHugh TD, Satta G. A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea. JAC Antimicrob Resist 2023; 5:dlad056. [PMID: 37193005 PMCID: PMC10182733 DOI: 10.1093/jacamr/dlad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/07/2023] [Indexed: 05/18/2023] Open
Abstract
Background WGS has significant potential to help tackle the major public health problem of TB. The Republic of Korea has the third highest rates of TB of all Organisation for Economic Cooperation and Development countries but there has been very limited use of WGS in TB to date. Objectives A retrospective comparison of Mycobacterium tuberculosis (MTB) clinical isolates from 2015 to 2017 from two centres in the Republic of Korea using WGS to compare phenotypic drug susceptibility testing (pDST) and WGS drug susceptibility predictions (WGS-DSP). Methods Fifty-seven MTB isolates had DNA extracted and were sequenced using the Illumina HiSeq platform. The WGS analysis was performed using bwa mem, bcftools and IQ-Tree; resistance markers were identified using TB profiler. Phenotypic susceptibilities were carried out at the Supranational TB reference laboratory (Korean Institute of Tuberculosis). Results For first-line antituberculous drugs concordance for rifampicin, isoniazid, pyrazinamide and ethambutol was 98.25%, 92.98%, 87.72% and 85.96%, respectively. The sensitivity of WGS-DSP compared with pDST for rifampicin, isoniazid, pyrazinamide and ethambutol was 97.30%, 92.11%, 78.95% and 95.65%, respectively. The specificity for these first-line antituberculous drugs was 100%, 94.74%, 92.11% and 79.41%, respectively. The sensitivity and specificity for second-line drugs ranged from 66.67% to 100%, and from 82.98% to 100%, respectively. Conclusions This study confirms the potential role for WGS in drug susceptibility prediction, which would reduce turnaround times. However, further larger studies are needed to ensure current databases of drug resistance mutations are reflective of the TB present in the Republic of Korea.
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Affiliation(s)
- Seung Heon Lee
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | | | - Adam A Witney
- Institute for Infection and Immunity, St George’s University of London, London, UK
| | - Sungweon Ryu
- Clinical Research Centre, Masan National Tuberculosis Hospital, Changwon, South Korea
| | - Hyungseok Kang
- Clinical Research Centre, Masan National Tuberculosis Hospital, Changwon, South Korea
| | - Nathaniel Storey
- Great Ormond Street Hospital for Children NHS Foundation Trust, Microbiology, Virology and Infection Prevention and Control, London, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Department of Infection, University College London, London, UK
| | - Giovanni Satta
- Centre for Clinical Microbiology, Department of Infection, University College London, London, UK
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19
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Lin Y, Du Y, Shen H, Guo Y, Wang T, Lai K, Zhang D, Zheng G, Wu G, Lei Y, Liu J. Transmission of Mycobacterium tuberculosis in schools: a molecular epidemiological study using whole-genome sequencing in Guangzhou, China. Front Public Health 2023; 11:1156930. [PMID: 37250072 PMCID: PMC10219607 DOI: 10.3389/fpubh.2023.1156930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Background China is a country with a high burden of tuberculosis (TB). TB outbreaks are frequent in schools. Thus, understanding the transmission patterns is crucial for controlling TB. Method In this genomic epidemiological study, the conventional epidemiological survey data combined with whole-genome sequencing was used to assess the genotypic distribution and transmission characteristics of Mycobacterium tuberculosis strains isolated from patients with TB attending schools during 2015 to 2019 in Guangzhou, China. Result The TB incidence was mainly concentrated in regular secondary schools and technical and vocational schools. The incidence of drug resistance among the students was 16.30% (22/135). The phylogenetic tree showed that 79.26% (107/135) and 20.74% (28/135) of the strains belonged to lineage 2 (Beijing genotype) and lineage 4 (Euro-American genotype), respectively. Among the 135 isolates, five clusters with genomic distance within 12 single nucleotide polymorphisms were identified; these clusters included 10 strains, accounting for an overall clustering rate of 7.4% (10/135), which showed a much lower transmission index. The distance between the home or school address and the interval time of symptom onset or diagnosis indicated that campus dissemination and community dissemination may be existed both, and community dissemination is the main. Conclusion and recommendation TB cases in Guangzhou schools were mainly disseminated and predominantly originated from community transmission. Accordingly, surveillance needs to be strengthened to stop the spread of TB in schools.
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Affiliation(s)
- Ying Lin
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Yuhua Du
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Hongcheng Shen
- Department of Preventive Health Care, Guangzhou Chest Hospital, Guangzhou, China
| | - Yangfeng Guo
- Guangzhou Primary and Secondary School Health and Health Promotion Center, Guangzhou, China
| | - Ting Wang
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Keng Lai
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Danni Zhang
- Academy of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Guangmin Zheng
- Academy of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Guifeng Wu
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Yu Lei
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
| | - Jianxiong Liu
- Department of Tuberculosis Control, Guangzhou Chest Hospital, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou, China
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20
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Li M, Lu L, Guo M, Jiang Q, Xia L, Jiang Y, Zhang S, Qiu Y, Yang C, Chen Y, Hong J, Guo X, Takiff H, Shen X, Chen C, Gao Q. Discrepancy in the transmissibility of multidrug-resistant Mycobacterium tuberculosis in urban and rural areas in China. Emerg Microbes Infect 2023; 12:2192301. [PMID: 36924242 DOI: 10.1080/22221751.2023.2192301] [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: 03/18/2023]
Abstract
The fitness of multidrug-resistant tuberculosis (MDR-TB) is thought to be an important determinant of a strain's ability to be transmitted and cause outbreaks. Studies in the laboratory have demonstrated that MDR-TB strains have reduced fitness but the relative transmissibility of MDR-TB versus drug-susceptible (DS) TB strains in human populations remains unresolved. We used data on genomic clustering from our previous molecular epidemiological study in Songjiang (2011-2020) and Wusheng (2009-2020), China, to compare the relative transmissibility of MDR-TB versus DS-TB. Genomic clusters were defined with a threshold distance of 12-single-nucleotide-polymorphisms and the risk for MDR-TB clustering was analyzed by logistic regression. In total, 2212 culture-positive pulmonary TB patients were enrolled in Songjiang and 1289 in Wusheng. The clustering rates of MDR-TB and DS-TB strains were 19.4% (20/103) and 26.3% (509/1936), respectively in Songjiang, and 43.9% (29/66) and 26.0% (293/1128) in Wusheng. The risk of MDR-TB clustering was 2.34 (95% CI 1.38-3.94) times higher than DS-TB clustering in Wusheng and 0.64 (95% CI 0.38-1.06) times lower in Songjiang. Neither lineage 2, compensatory mutations nor rpoB S450L were significantly associated with MDR-TB transmission, and katG S315T increased MDR-TB transmission only in Wusheng (OR 5.28, 95% CI 1.42-19.21). MDR-TB was not more transmissible than DS-TB in either Songjiang or Wusheng. It appears that the different transmissibility of MDR-TB in Songjiang and Wusheng is likely due to differences in the quality of the local TB control programs. These results suggest that the most effective way to control MDR-TB is by improving local TB control programs.
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Affiliation(s)
- Meng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Liping Lu
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Mingcheng Guo
- Department of Tuberculosis Control, Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Qi Jiang
- School of Public Health, Renmin Hospital Public Health Research Institute, Wuhan University, Wuhan, China
| | - Lan Xia
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Yuan Jiang
- Tuberculosis Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Shu Zhang
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Yong Qiu
- Department of Tuberculosis Control, Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Chongguang Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yiwang Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Jianjun Hong
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoqin Guo
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Xin Shen
- Tuberculosis Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Chuang Chen
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
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21
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Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains. Tuberculosis (Edinb) 2023; 139:102324. [PMID: 36848710 DOI: 10.1016/j.tube.2023.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 02/15/2023]
Abstract
Whole-genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a rapidly growing tool to obtain results regarding the resistance and phylogeny of the strains. We evaluated the performances of two bioinformatics tools for the analysis of whole-genome sequences of MTBC strains. Two hundred and twenty-seven MTBC strains were isolated and whole-genome sequenced at the laboratory of Avicenne Hospital between 2015 and 2021. We investigated the resistance and susceptibility status of strains using two online tools, Mykrobe and PhyResSE. We compared the genotypic and phenotypic resistance results obtained by drug susceptibility testing. Unlike with the Mykrobe tool, sequencing quality data were obtained using PhyResSE: average coverage of 98% and average depth of 119X. We found a similar concordance between phenotypic and genotypic results when determining susceptibility to first-line anti-tuberculosis drugs (95%) with both tools. The sensitivity and specificity of each tool compared to the phenotypic method were respectively 72% [52-87] and 98% [96-99] for Mykrobe and 76% [57-90] and 97% [94-99] for PhyResSE. Mykrobe and PhyResSE were easy to use and efficient. These platforms are accessible to people not trained in bioinformatics and constitute a complementary approach to phenotypic methods for the study of MTBC strains.
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22
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Xiao YX, Liu KH, Lin WH, Chan TH, Jou R. Whole-genome sequencing-based analyses of drug-resistant Mycobacterium tuberculosis from Taiwan. Sci Rep 2023; 13:2540. [PMID: 36781938 PMCID: PMC9925824 DOI: 10.1038/s41598-023-29652-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) posed challenges to global TB control. Whole-genome sequencing (WGS) is recommended for predicting drug resistance to guide DR-TB treatment and management. Nevertheless, data are lacking in Taiwan. Phenotypic drug susceptibility testing (DST) of 12 anti-TB drugs was performed for 200 Mycobacterium tuberculosis isolates. WGS was performed using the Illumina platform. Drug resistance profiles and lineages were predicted in silico using the Total Genotyping Solution for TB (TGS-TB). Using the phenotypic DST results as a reference, WGS-based prediction demonstrated high concordance rates of isoniazid (95.0%), rifampicin (RIF) (98.0%), pyrazinamide (98.5%) and fluoroquinolones (FQs) (99.5%) and 96.0% to 99.5% for second-line injectable drugs (SLIDs); whereas, lower concordance rates of ethambutol (87.5%), streptomycin (88.0%) and ethionamide (84.0%). Furthermore, minimum inhibitory concentrations confirmed that RIF rpoB S450L, FQs gyrA D94G and SLIDs rrs a1401g conferred high resistance levels. Besides, we identified lineage-associated mutations in lineage 1 (rpoB H445Y and fabG1 c-15t) and predominant lineage 2 (rpoB S450L and rpsL K43R). The WGS-based prediction of drug resistance is highly concordant with phenotypic DST results and can provide comprehensive genetic information to guide DR-TB precision therapies in Taiwan.
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Affiliation(s)
- Yu-Xin Xiao
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Kuang-Hung Liu
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Wan-Hsuan Lin
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Tai-Hua Chan
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Ruwen Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C..
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C..
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23
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Li M, Guo M, Peng Y, Jiang Q, Xia L, Zhong S, Qiu Y, Su X, Zhang S, Yang C, Mijiti P, Mao Q, Takiff H, Li F, Chen C, Gao Q. High proportion of tuberculosis transmission among social contacts in rural China: a 12-year prospective population-based genomic epidemiological study. Emerg Microbes Infect 2022; 11:2102-2111. [PMID: 35950916 PMCID: PMC9448380 DOI: 10.1080/22221751.2022.2112912] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is more prevalent in rural than urban areas in China, and delineating TB transmission patterns in rural populations could improve TB control. We conducted a prospective population-based study of culture-positive pulmonary TB patients diagnosed between July 1, 2009 and December 31, 2020 in two rural counties in China. Genomic clusters were defined with a threshold distance of 12-single-nucleotide-polymorphisms, based on whole-genome sequencing. Risk factors for clustering were identified by logistic regression. Transmission links were sought through epidemiological investigation of genomic-clustered patients. Of 1517 and 751 culture-positive pulmonary TB patients in Wusheng and Wuchang counties, respectively, 1289 and 699 strains were sequenced. Overall, 624 (31.4%, 624/1988) patients were grouped into 225 genomic clusters. Epidemiological links were confirmed in 41.8% (196/469) of clustered isolates, including family (32.7%, 64/196) and social contacts (67.3%, 132/196). Social contacts were generally with relatives, within the community or in shared aggregated settings outside the community, but the proportion of clustered contacts in each category differed between the two sites. The time interval between diagnosis of student cases and contacts was significantly shorter than family and social contacts, probably due to enhanced student contact screening. Transmission of multidrug-resistant (MDR) strains was likely responsible for 81.4% (83/102) of MDR-TB cases, with minimal acquisition of additional resistance mutations. A large proportion of TB transmission in rural China occurred among social contacts, suggesting that active screening and aggressive contact tracing could benefit TB control, but contact screening should be tailored to local patterns of social interactions.
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Affiliation(s)
- Meng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,National Clinical Research Center for Infectious Diseases, Shenzhen, Guangdong, China
| | - Mingcheng Guo
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Ying Peng
- Heilongjiang Provincial Center for Tuberculosis Prevention and Control, Harbin, China
| | - Qi Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,School of Public Health, Wuhan University, Wuhan, China
| | - Lan Xia
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Sheng Zhong
- Wuchang City Center for Tuberculosis Control and Prevention, Harbin, China
| | - Yong Qiu
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Xin Su
- Wuchang City Center for Tuberculosis Control and Prevention, Harbin, China
| | - Shu Zhang
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Chongguang Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Peierdun Mijiti
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qizhi Mao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Fabin Li
- Heilongjiang Provincial Center for Tuberculosis Prevention and Control, Harbin, China
| | - Chuang Chen
- Institution for Tuberculosis Prevention and Control, Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.,National Clinical Research Center for Infectious Diseases, Shenzhen, Guangdong, China
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Use of Whole-Genome Sequencing to Explore Mycobacterium tuberculosis Complex Circulating in a Hotspot Department in France. Microorganisms 2022; 10:microorganisms10081586. [PMID: 36014004 PMCID: PMC9414808 DOI: 10.3390/microorganisms10081586] [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: 06/28/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
The Seine-Saint-Denis is the French metropolitan department with the highest incidence of tuberculosis (TB). Our aim was to explore epidemiological and phylogenetic characteristics of TB strains in this hotspot department. We performed WGS on 227 strains of Mycobacterium tuberculosis complex isolated from patients at the Avicenne Hospital from 2016 to 2021 and randomly selected to represent the clinical diversity of French TB localization. Clinical and demographic data were recorded for each TB patient. The mean age of patients was 36 years old. They came from Africa (44%), Asia (27%), Europe (26%) and America (3%). Strains isolated from extrapulmonary samples were associated with Asian patients, whereas strains isolated from pulmonary samples were associated with European patients. We observed a high level of lineage diversity in line with the known worldwide diversity. Interestingly, lineage 3 was associated with lymph node TB. Additionally, the sensitivity of WGS for predicting resistance was 100% for rifampicin, isoniazid and ethambutol and 66.7% for pyrazinamide. The global concordance with drug-susceptibility testing using the phenotypic approach was 97%. In microbiology laboratories, WGS turns out to be an essential tool for better understanding local TB epidemiology, with direct access to circulating lineage identification and to drug susceptibilities to first- and second-line anti-TB drugs.
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Yusoof KA, García JI, Schami A, Garcia-Vilanova A, Kelley HV, Wang SH, Rendon A, Restrepo BI, Yotebieng M, Torrelles JB. Tuberculosis Phenotypic and Genotypic Drug Susceptibility Testing and Immunodiagnostics: A Review. Front Immunol 2022; 13:870768. [PMID: 35874762 PMCID: PMC9301132 DOI: 10.3389/fimmu.2022.870768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022] Open
Abstract
Tuberculosis (TB), considered an ancient disease, is still killing one person every 21 seconds. Diagnosis of Mycobacterium tuberculosis (M.tb) still has many challenges, especially in low and middle-income countries with high burden disease rates. Over the last two decades, the amount of drug-resistant (DR)-TB cases has been increasing, from mono-resistant (mainly for isoniazid or rifampicin resistance) to extremely drug resistant TB. DR-TB is problematic to diagnose and treat, and thus, needs more resources to manage it. Together with+ TB clinical symptoms, phenotypic and genotypic diagnosis of TB includes a series of tests that can be used on different specimens to determine if a person has TB, as well as if the M.tb strain+ causing the disease is drug susceptible or resistant. Here, we review and discuss advantages and disadvantages of phenotypic vs. genotypic drug susceptibility testing for DR-TB, advances in TB immunodiagnostics, and propose a call to improve deployable and low-cost TB diagnostic tests to control the DR-TB burden, especially in light of the increase of the global burden of bacterial antimicrobial resistance, and the potentially long term impact of the coronavirus disease 2019 (COVID-19) disruption on TB programs.
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Affiliation(s)
- Kizil A. Yusoof
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Juan Ignacio García
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Alyssa Schami
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Andreu Garcia-Vilanova
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Holden V. Kelley
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Shu-Hua Wang
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine and Global One Health Initiative, The Ohio State University, Columbus, OH, United States
| | - Adrian Rendon
- Centro de Investigación, Prevención y Tratamiento de Infecciones Respiratorias (CIPTIR), Hospital Universitario de Monterrey Universidad Autónoma de Nuevo León (UANL), Monterrey, Mexico
| | - Blanca I. Restrepo
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Marcel Yotebieng
- Division of General Internal Medicine, Department of Medicine, Albert Einstein College of Medicine, New York City, NY, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Jordi B. Torrelles
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
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Dong B, He Z, Li Y, Xu X, Wang C, Zeng J. Improved Conventional and New Approaches in the Diagnosis of Tuberculosis. Front Microbiol 2022; 13:924410. [PMID: 35711765 PMCID: PMC9195135 DOI: 10.3389/fmicb.2022.924410] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
Tuberculosis (TB) is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). Timely diagnosis and effective treatment are essential in the control of TB. Conventional smear microscopy still has low sensitivity and is unable to reveal the drug resistance of this bacterium. The traditional culture-based diagnosis is time-consuming, since usually the results are available after 3–4 weeks. Molecular biology methods fail to differentiate live from dead M. tuberculosis, while diagnostic immunology methods fail to distinguish active from latent TB. In view of these limitations of the existing detection techniques, in addition to the continuous emergence of multidrug-resistant and extensively drug-resistant TB, in recent years there has been an increase in the demand for simple, rapid, accurate and economical point-of-care approaches. This review describes the development, evaluation, and implementation of conventional diagnostic methods for TB and the rapid new approaches for the detection of M. tuberculosis.
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Affiliation(s)
- Baoyu Dong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhiqun He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinyue Xu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chuan Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Liu Q, Qiu B, Li G, Yang T, Tao B, Martinez L, Zhu L, Wang J, Mao X, Lu W. Tuberculosis reinfection and relapse in eastern China: A prospective study using whole-genome sequencing. Clin Microbiol Infect 2022; 28:1458-1464. [PMID: 35700940 DOI: 10.1016/j.cmi.2022.05.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Tuberculosis recurrence after an initial successful treatment episode can occur from either reinfection or relapse. In a population-based sample and whole genome sequencing (WGS) in eastern China, we aimed to evaluate risk factors for tuberculosis recurrence, and assess the proportion of recurrence due to either reinfection or relapse. METHODS Successfully treated pulmonary tuberculosis patients with sputum culture positive results were recruited from five cities in Jiangsu Province from 2013-2015 and followed for two years for tuberculosis recurrence. Among patients developing a second tuberculosis episode, WGS was performed to distinguish relapse or reinfection through a distance threshold of 6-single-nucleotide polymorphisms (SNP). We analyzed risk factors for recurrence and epidemiological characteristics of different types of recurrent patients. RESULTS Of 1,897 successful treated tuberculosis patients, 7.4% (141/1879) developed recurrent tuberculosis. Compared with non-recurrent tuberculosis, patients were at higher risk of recurrence in older age (Adjusted Odds Ratio [AOR], 1.02 for each additional year; 95% CI, 1.01-1.03, P=0.003), patients previously treated for tuberculosis (AOR=2.22; 95% CI, 1.52-3.26, P<0.001), or with bilateral cavities (AOR, 1.56; 95% CI, 1.05-2.32, P=0.029). Among 27.0% (38/141) recurrent tuberculosis patients with successfully sequenced pairs, relapse was substantially more common than reinfection (71.1% versus 28.9%, P=0.014). CONCLUSIONS Endogenous relapse was significantly more common than exogenous reinfection in the first two years after treatment in eastern China. Prioritization of high-risk groups for recurrence, such as the elderly, with a previous tuberculosis diagnosis, or with bilateral cavities, may provide opportunities to reduce post-tuberculosis morbidity.
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Affiliation(s)
- Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Guoli Li
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Tingting Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, PR China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, Massachusetts, United States
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Xuhua Mao
- Department of Clinical Laboratory, Affiliated Yixing People's Hospital, Jiangsu University, Wuxi, China.
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China.
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Chen Y, Liu Q, Takiff HE, Gao Q. Comprehensive genomic analysis of Mycobacterium tuberculosis reveals limited impact of high-fitness genotypes on MDR-TB transmission. J Infect 2022; 85:49-56. [PMID: 35588941 DOI: 10.1016/j.jinf.2022.05.012] [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: 01/17/2022] [Revised: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Environmental and host-related factors that contribute to the transmission of multidrug-resistant tuberculosis (MDR-TB) have become an increasing concern, but the impact of bacterial genetic factors associated with bacterial fitness on MDR-TB transmission is poorly understood. Here, we present a global view of the correlation between common fitness-related genotypes and MDR-TB transmission by analyzing a representative number of MDR-TB isolates. METHODS We assembled a global whole genome sequencing (WGS) dataset of MDR-TB strains collected through retrospective cohorts or population-based approaches using public databases and literature curation. WGS-based clusters were defined as groups of strains with genomic difference of ≤ 5 SNPs. RESULTS We curated high-quality WGS data of 4696 MDR-TB isolates from 17 countries with a mean clustering rate of 48% (range 0-100%). Correlational analysis showed that increased risk of MDR-TB strain clustering was not associated with compensatory mutations (OR 1.07, 95% CI 0.72-1.59), low-fitness cost drug-resistant mutations (katG S315T: OR 1.42, 95% CI 0.82-2.47; rpoB S450L: OR 1.26, 95% CI 0.87-1.83) or Lineage 2 (OR 1.50, 95% CI 0.95-2.39). CONCLUSIONS The factors most commonly thought to increase bacterial fitness were not significantly associated with increased MDR-TB transmission, and thus do not appear to be major contributors to the current epidemic of MDR-TB.
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Affiliation(s)
- Yiwang Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; National Clinical Research Center for Infectious Diseases, Shenzhen, Guangdong, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Howard E Takiff
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Centre for Chronic Disease Control, Shenzhen, China; Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; National Clinical Research Center for Infectious Diseases, Shenzhen, Guangdong, China.
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Whole-genome sequencing of Mycobacterium tuberculosis from Cambodia. Sci Rep 2022; 12:7693. [PMID: 35562174 PMCID: PMC9095694 DOI: 10.1038/s41598-022-10964-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 04/04/2022] [Indexed: 01/07/2023] Open
Abstract
Cambodia has one of the highest tuberculosis (TB) incidence rates in the WHO Western Pacific region. Remarkably though, the prevalence of multidrug-resistant TB (MDR-TB) remains low. We explored the genetic diversity of Mycobacterium tuberculosis (MTB) circulating in this unique setting using whole-genome sequencing (WGS). From October 2017 until January 2018, we collected one hundred sputum specimens from consenting adults older than 21 years of age, newly diagnosed with bacteriologically confirmed TB in 3 districts of Phnom Penh and Takeo provinces of Cambodia before they commence on their TB treatment, where eighty MTB isolates were successfully cultured and sequenced. Majority of the isolates belonged to Lineage 1 (Indo-Oceanic) (69/80, 86.25%), followed by Lineage 2 (East Asian) (10/80, 12.5%) and Lineage 4 (Euro-American) (1/80, 1.25%). Phenotypic resistance to both streptomycin and isoniazid was found in 3 isolates (3/80, 3.75%), while mono-resistance to streptomycin and isoniazid was identical at 2.5% (N = 2 each). None of the isolates tested was resistant to either rifampicin or ethambutol. The specificities of genotypic prediction for resistance to all drugs tested were 100%, while the sensitivities of genotypic resistance predictions to isoniazid and streptomycin were lower at 40% (2/5) and 80% (4/5) respectively. We identified 8 clusters each comprising of two to five individuals all residing in the Takeo province, making up half (28/56, 50%) of all individuals sampled in the province, indicating the presence of multiple ongoing transmission events. All clustered isolates were of Lineage 1 and none are resistant to any of the drugs tested. This study while demonstrating the relevance and utility of WGS in predicting drug resistance and inference of disease transmission, highlights the need to increase the representation of genotype-phenotype TB data from low and middle income countries in Asia and Africa to improve the accuracies for prediction of drug resistance.
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30
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Fernández-Morales EA, Bermudez G, Montero H, Luzania-Valerio M, Zenteno-Cuevas R. Whole genome characterization, and geographical distribution of M. tuberculosis in central region of Veracruz, Mexico. Braz J Infect Dis 2022; 26:102357. [PMID: 35533727 PMCID: PMC9387445 DOI: 10.1016/j.bjid.2022.102357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 11/17/2022] Open
Abstract
The purpose of this work was to perform by Whole Genomic Sequencing (WGS) a characterization of tuberculosis isolates circulating in the central region of Veracruz, Mexico, and to determine its geographical distribution. The genome of 25 clinical isolates of tuberculosis patients, recovered from central zone of Veracruz, Mexico, were sequenced and the information obtained was used to characterize lineage, prediction of drug resistance, identification of clonal complexes, and finally correlated with the geolocalization data. Isolates analyzed were included into seven L4 sublineages, most frequent was X3; X1 (4.1.1.3) in 35%. rpoBSer450Leu polymorphism was the most frequently found variant. Sublineage Haarlem (4.1.2) had the widest distribution, found in five municipalities. Of the of two clonal complexes found, the most abundant included eight isolates, with X3/X1 lineage, placed in two municipalities. Combination of WGS and geographic information system was very useful for the identification of sublineages, clonal complexes, and their geographical dispersion with important implications in the epidemiological surveillance and clinical control of TB.
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Affiliation(s)
- Esdras Antonio Fernández-Morales
- University of Veracruz, Health Sciences Institute, Health Sciences Master Program, Mexico; University of Veracruz, Public Health Institute, Mexico
| | - Gustavo Bermudez
- University of Veracruz, Health Sciences Institute, Health Sciences Doctoral Program, Mexico
| | - Hilda Montero
- University of Veracruz, Public Health Institute, Mexico
| | | | - Roberto Zenteno-Cuevas
- University of Veracruz, Public Health Institute, Mexico; Multidisciplinary Network of Tuberculosis Research, Mexico.
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31
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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: 2.7] [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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32
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Hong JM, Lee H, Menon NV, Lim CT, Lee LP, Ong CWM. Point-of-care diagnostic tests for tuberculosis disease. Sci Transl Med 2022; 14:eabj4124. [PMID: 35385338 DOI: 10.1126/scitranslmed.abj4124] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid diagnosis is one key pillar to end tuberculosis (TB). Point-of-care tests (POCTs) facilitate early detection, immediate treatment, and reduced transmission of TB disease. This Review evaluates current diagnostic assays endorsed by the World Health Organization and identifies the gaps between existing conventional tests and the ideal POCT. We discuss the commercial development of new rapid tests and research studies on nonsputum-based diagnostic biomarkers from both pathogen and host. Last, we highlight advances in integrated microfluidics technology that may aid the development of new POCTs.
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Affiliation(s)
- Jia Mei Hong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Hyeyoung Lee
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Nishanth V Menon
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore.,Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Luke P Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720-1764, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.,Harvard Medical School, Brigham and Women's Hospital, Harvard Institute of Medicine, Harvard University, Boston, MA 02115, USA.,Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Korea
| | - Catherine W M Ong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
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Wang Z, Sun R, Mu C, Wang C, Zhao H, Jiang L, Ju H, Dai W, Zhang F. Characterization of Fluoroquinolone-Resistant and Multidrug-Resistant Mycobacterium tuberculosis Isolates Using Whole-Genome Sequencing in Tianjin, China. Infect Drug Resist 2022; 15:1793-1803. [PMID: 35444430 PMCID: PMC9013706 DOI: 10.2147/idr.s361635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/02/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Methods Results Conclusion
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Affiliation(s)
- Zhirui Wang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Rui Sun
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Cheng Mu
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Chunhua Wang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Hui Zhao
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Lina Jiang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Hanfang Ju
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Wenxi Dai
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Fan Zhang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
- Correspondence: Fan Zhang, Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, No. 124, Chifeng Road, Heping District, Tianjin, 300041, People’s Republic of China, Tel +86-22-27124491, Fax +86-22-27117595, Email
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34
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Innovations in Molecular Identification of Mycobacterium tuberculosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant public health concern on a global scale. Quick and precise identification of Mycobacterium tuberculosis (MTB) in symptomatic patients is pivotal for worldwide TB eradication initiatives. As an infectious disorder induced by MTB, it remains a critical threat to public health, particularly in poor countries, due to an inadequate diagnostic research laboratory. There is a need for a persistent incentive to reduce response time for effective diagnosis and control of TB infection, which is a benefit that molecular techniques provide over traditional methods. Although there is a tremendous overall prevalence of TB and a relatively poor probability of case identification worldwide. Common screening techniques have focused on tests that have many fundamental shortcomings. Due to the development of antibiotic-resistant Mycobacterium strains, TB is one of the leading contributors to fatalities. It is now possible to examine TB using molecular detection techniques, which are faster and more cost-effective than previous methods, such as standard culture procedures to test and verify antibiotic resistance in patients with TB. Whole genome sequencing (WGS), faster nucleic acid amplification tests, has made it easier to diagnose and treat TB more quickly. This article addresses the genetic approaches for detecting Mycobacterium tuberculosis complex (MTBC) in clinical specimens as well as antibiotic resistance in mycobacterium and discusses the practical limitations of using these methods.
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Abstract
Whole-genome sequencing (WGS) has shown tremendous potential in rapid diagnosis of drug-resistant tuberculosis (TB). In the current study, we performed WGS on drug-resistant Mycobacterium tuberculosis isolates obtained from Shanghai (n = 137) and Russia (n = 78). We aimed to characterise the underlying and high-frequency novel drug-resistance-conferring mutations, and also create valuable combinations of resistance mutations with high predictive sensitivity to predict multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB) phenotype using a bootstrap method. Most strains belonged to L2.2, L4.2, L4.4, L4.5 and L4.8 lineages. We found that WGS could predict 82.07% of phenotypically drug-resistant domestic strains. The prediction sensitivity for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STR), ofloxacin (OFL), amikacin (AMK) and capreomycin (CAP) was 79.71%, 86.30%, 76.47%, 88.37%, 83.33%, 70.00% and 70.00%, respectively. The mutation combination with the highest sensitivity for MDR prediction was rpoB S450L + rpoB H445A/P + katG S315T + inhA I21T + inhA S94A, with a sensitivity of 92.17% (0.8615, 0.9646), and the mutation combination with highest sensitivity for XDR prediction was rpoB S450L + katG S315T + gyrA D94G + rrs A1401G, with a sensitivity of 92.86% (0.8158, 0.9796). The molecular information presented here will be of particular value for the rapid clinical detection of MDR- and XDR-TB isolates through laboratory diagnosis.
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Investigation on the cause of recurrent tuberculosis in a rural area in China using whole-genome sequencing: A retrospective cohort study. Tuberculosis (Edinb) 2022; 133:102174. [DOI: 10.1016/j.tube.2022.102174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/17/2022]
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Sodja E, Koren S, Toplak N, Truden S, Žolnir-Dovč M. Next-generation sequencing to characterize pyrazinamide resistance in Mycobacterium tuberculosis isolates from two Balkan countries. J Glob Antimicrob Resist 2021; 29:507-512. [PMID: 34818592 DOI: 10.1016/j.jgar.2021.09.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES Next-generation sequencing (NGS) provide a comprehensive analysis of the genetic alterations that are most commonly linked with pyrazinamide (PZA) resistance. There are no studies reporting molecular background of PZA resistance in TB isolates from Balkan Peninsula. We aimed to examine the feasibility of full-length analysis of a gene linked with PZA resistance, pncA, using Ion Torrent technology in comparison to phenotypic BACTEC MGIT 960 DST in clinical TB isolates from two countries of the Balkan Peninsula. METHODS Between 1996 and 2017, we retrospectively selected 61 TB isolates. To identify gene variants related to drug resistance in genomic DNA extracted from TB isolates, AmpliSeq libraries were generated automatically using the AmpliSeq™ Kit for Chef DL8 and the Ion AmpliSeq TB Research Panel. RESULTS Of all 61 TB isolates included, 56 TB were phenotypically resistant to any antibiotic. Among them, 38/56 (67.9%) TB isolates were phenotypically resistant to pyrazinamide and pncA mutations were detected in 33/38 cases (86.8%). A mutation in the pncA promoter region was the most prevalent genetic alteration, detected in eight TB isolates. Comparison of NGS to conventional BACTEC MGIT 960 DST revealed very strong agreement (90.2%) between the two methods in identifying PZA resistance, with high sensitivity (89.5%) and specificity (95.7%) for NGS. CONCLUSIONS Detection of PZA resistance using NGS seems to be a valuable tool for surveillance of TB drug resistance also in the Balkan Peninsula, with great potential to provide useful information at least one weak earlier than is possible with phenotypic DST.
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Affiliation(s)
- Eva Sodja
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia.
| | | | | | - Sara Truden
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Manca Žolnir-Dovč
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
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38
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Realegeno S, Adeyiga O, Winston DJ, Beaird OE, Garner OB, Yang S. Utilization of whole genome sequencing for resolution of discrepant Mycobacterium tuberculosis drug susceptibility results: A case report. IDCases 2021; 26:e01308. [PMID: 34745885 PMCID: PMC8551521 DOI: 10.1016/j.idcr.2021.e01308] [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: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 11/26/2022] Open
Abstract
A 44-year-old woman undergoing therapy for acute promyelocytic leukemia (APL) developed disseminated tuberculosis. Mycobacterium tuberculosis (TB) was isolated from the blood and sputum. Initial drug susceptibility testing (DST) of the blood isolate revealed resistance to isoniazid and ethambutol but the sputum isolate showed no resistance. Due to drug resistance concerns, the patient was treated with multiple second and third-line drugs, and suffered from drug side effects. To further investigate the DST discrepancies, whole genome sequencing (WGS) was performed on both isolates. No known resistance mutations to first line or second line drugs were identified in either isolate, which was confirmed by additional susceptibility testing performed by a different reference laboratory and the California Department of Public Health (CDPH) laboratory. Treatment was reduced to a simpler and less toxic regimen due to these investigations. WGS is shown to be a valuable tool for resolving discordant phenotypic DST results of TB isolates and has the potential to provide accurate and timely results guiding appropriate therapy in the clinical setting.
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Affiliation(s)
- Susan Realegeno
- UCLA Clinical Microbiology Laboratory, Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oladunni Adeyiga
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Drew J Winston
- Division of Hematology and Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Omer E Beaird
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Omai B Garner
- UCLA Clinical Microbiology Laboratory, Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shangxin Yang
- UCLA Clinical Microbiology Laboratory, Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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39
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Zhang Y, Zhao R, Zhang Z, Liu Q, Zhang A, Ren Q, Li S, Long X, Xu H. Analysis of Factors Influencing Multidrug-Resistant Tuberculosis and Validation of Whole-Genome Sequencing in Children with Drug-Resistant Tuberculosis. Infect Drug Resist 2021; 14:4375-4393. [PMID: 34729015 PMCID: PMC8554314 DOI: 10.2147/idr.s331890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 11/29/2022] Open
Abstract
Objective Pediatric tuberculosis (TB) is one of the top ten causes of death in children. Our study was to analyze influencing factors of multidrug-resistant tuberculosis (MDR-TB) and validation of whole-genome sequencing (WGS) used in children with drug-resistant TB (DR-TB). Methods All Mycobacterium tuberculosis (Mtb) strains were isolated from patients aged below 18 years old of Children’s Hospital of Chongqing Medical University, China. A total of 208 Mtb isolates were tested for eight anti-TB drugs with phenotypic drug susceptibility test (DST) and for genetic prediction of the susceptible profile with WGS. The patients corresponding to each strain were grouped according to drug resistance and genotype. Influencing factors of MDR-TB and DR-TB were analyzed. Results According to the phenotypic DST and WGS, 82.2% of Mtb strains were susceptible to all eight drugs, and 6.3% were MDR-TB. Using the phenotypic DSTs as the gold standard, the kappa value of WGS to predict isoniazid, rifampin, ethambutol, rifapentine, prothionamide, levofloxacin, moxifloxacin and amikacin was 0.84, 0.89, 0.59, 0.86, 0.89, 0.82, 0.88 and 1.00, respectively. There was significant difference in the distribution of severe TB, diagnosis, treatment and outcome between MDR and drug-susceptible group (P<0.05). The distribution of severe TB and treatment between DR and drug-susceptible group was statistically different (P<0.05). The results of binary logistic regression showed that Calmette–Guérin bacillus (BCG) vaccine is the protective factor for MDR-TB (OR=0.19), and MDR-TB is the risk factor for PTB and EPTB (OR=17.98). Conclusion The BCG vaccine is a protective factor for MDR-TB, and MDR-TB might not be confined to pulmonary infection, spreading to extrapulmonary organs in children. MDR-TB had more severe cases and a lower recovery rate than drug-susceptible TB. WGS could provide an accurate prediction of drug susceptibility test results for anti-TB drugs, which are needed for the diagnosis and precise treatment of TB in children.
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Affiliation(s)
- Ying Zhang
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Ruiqiu Zhao
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zhenzhen Zhang
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Quanbo Liu
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Aihua Zhang
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Qiaoli Ren
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Siyuan Li
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaoru Long
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hongmei Xu
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Campelo TA, Cardoso de Sousa PR, Nogueira LDL, Frota CC, Zuquim Antas PR. Revisiting the methods for detecting Mycobacterium tuberculosis: what has the new millennium brought thus far? Access Microbiol 2021; 3:000245. [PMID: 34595396 PMCID: PMC8479963 DOI: 10.1099/acmi.0.000245] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/17/2021] [Indexed: 01/07/2023] Open
Abstract
Tuberculosis (TB) affects around 10 million people worldwide in 2019. Approximately 3.4 % of new TB cases are multidrug-resistant. The gold standard method for detecting Mycobacterium tuberculosis, which is the aetiological agent of TB, is still based on microbiological culture procedures, followed by species identification and drug sensitivity testing. Sputum is the most commonly obtained clinical specimen from patients with pulmonary TB. Although smear microscopy is a low-cost and widely used method, its sensitivity is 50-60 %. Thus, owing to the need to improve the performance of current microbiological tests to provide prompt treatment, different methods with varied sensitivity and specificity for TB diagnosis have been developed. Here we discuss the existing methods developed over the past 20 years, including their strengths and weaknesses. In-house and commercial methods have been shown to be promising to achieve rapid diagnosis. Combining methods for mycobacterial detection systems demonstrates a correlation of 100 %. Other assays are useful for the simultaneous detection of M. tuberculosis species and drug-related mutations. Novel approaches have also been employed to rapidly identify and quantify total mycobacteria RNA, including assessments of global gene expression measured in whole blood to identify the risk of TB. Spoligotyping, mass spectrometry and next-generation sequencing are also promising technologies; however, their cost needs to be reduced so that low- and middle-income countries can access them. Because of the large impact of M. tuberculosis infection on public health, the development of new methods in the context of well-designed and -controlled clinical trials might contribute to the improvement of TB infection control.
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Affiliation(s)
- Thales Alves Campelo
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | | | - Lucas de Lima Nogueira
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Cristiane Cunha Frota
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Paulo Renato Zuquim Antas
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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41
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Anwaierjiang A, Wang Q, Liu H, Yin C, Xu M, Li M, Liu M, Liu Y, Zhao X, Liu J, Li G, Mijiti X, Wan K. Prevalence and Molecular Characteristics Based on Whole Genome Sequencing of Mycobacterium tuberculosis Resistant to Four Anti-Tuberculosis Drugs from Southern Xinjiang, China. Infect Drug Resist 2021; 14:3379-3391. [PMID: 34466004 PMCID: PMC8402983 DOI: 10.2147/idr.s320024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/07/2021] [Indexed: 12/25/2022] Open
Abstract
Objective Drug-resistant tuberculosis is a major public health problem, especially in the southern region of Xinjiang, China; however, there is little information regarding drug resistance profiles and mechanism of Mycobacterium tuberculosis in this area. The aim of this study was to determine the prevalence and molecular characteristics of M. tuberculosis resistant to four anti-tuberculosis drugs from this area. Methods Three hundred and forty-six isolates from the southern region of Xinjiang, China were included and used to perform phenotypic drug susceptibility testing and whole genome sequencing (WGS). Mutations in seven loci associated with drug resistance, including rpoB for rifampicin (RMP), katG, inhA promoter and oxyR-ahpC for isoniazid (INH), rrs 530 and 912 loops and rpsL for streptomycin (STR), and embB for ethambutol (EMB), were characterized. Results Among 346 isolates, 106, 60, 70 and 29 were resistant to INH, RMP, STR and EMB, respectively; 132 were resistant to at least one of the four anti-tuberculosis drugs and 51 were multi-drug resistant (MDR). Beijing genotype and retreated patients showed a significantly increased risk for developing MDR tuberculosis. Compared with the phenotypic data, the sensitivity and specificity for WGS to predict resistance were 96.7% and 98.6% for RMP, 75.5% and 97.1% for INH, 68.6% and 99.6% for STR, 93.1% and 93.7% for EMB, respectively. The most common mutations conferring RMP, INH, STR and EMB resistance were Ser450Leu (51.7%) in rpoB, Ser315Thr (44.3%) in katG, Lys43Arg (35.7%) in rpsL and Met306Val (24.1%) in embB. Conclusion This study provides the first information on the prevalence and molecular characters of drug resistant M. tuberculosis in the southern region of Xinjiang, China, which will be helpful for choosing early detection methods for drug resistance (ig, molecular methods) and subsequently initiation of proper therapy of tuberculosis in this area.
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Affiliation(s)
- Aiketaguli Anwaierjiang
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, 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
| | - Chunjie Yin
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, 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
| | - Mengwen Liu
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Yan Liu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, 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
| | - Jinbao Liu
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, 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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42
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Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
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Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
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43
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Kontsevaya I, Lange C, Comella-Del-Barrio P, Coarfa C, DiNardo AR, Gillespie SH, Hauptmann M, Leschczyk C, Mandalakas AM, Martinecz A, Merker M, Niemann S, Reimann M, Rzhepishevska O, Schaible UE, Scheu KM, Schurr E, Abel Zur Wiesch P, Heyckendorf J. Perspectives for systems biology in the management of tuberculosis. Eur Respir Rev 2021; 30:30/160/200377. [PMID: 34039674 DOI: 10.1183/16000617.0377-2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/28/2021] [Indexed: 12/18/2022] Open
Abstract
Standardised management of tuberculosis may soon be replaced by individualised, precision medicine-guided therapies informed with knowledge provided by the field of systems biology. Systems biology is a rapidly expanding field of computational and mathematical analysis and modelling of complex biological systems that can provide insights into mechanisms underlying tuberculosis, identify novel biomarkers, and help to optimise prevention, diagnosis and treatment of disease. These advances are critically important in the context of the evolving epidemic of drug-resistant tuberculosis. Here, we review the available evidence on the role of systems biology approaches - human and mycobacterial genomics and transcriptomics, proteomics, lipidomics/metabolomics, immunophenotyping, systems pharmacology and gut microbiomes - in the management of tuberculosis including prediction of risk for disease progression, severity of mycobacterial virulence and drug resistance, adverse events, comorbidities, response to therapy and treatment outcomes. Application of the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach demonstrated that at present most of the studies provide "very low" certainty of evidence for answering clinically relevant questions. Further studies in large prospective cohorts of patients, including randomised clinical trials, are necessary to assess the applicability of the findings in tuberculosis prevention and more efficient clinical management of patients.
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Affiliation(s)
- Irina Kontsevaya
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Christoph Lange
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Patricia Comella-Del-Barrio
- Research Institute Germans Trias i Pujol, CIBER Respiratory Diseases, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Molecular and Cellular Biology, Center for Precision Environmental health, Baylor College of Medicine, Houston, TX, USA
| | - Andrew R DiNardo
- The Global Tuberculosis Program, Texas Children's Hospital, Dept of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Matthias Hauptmann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Christoph Leschczyk
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Anna M Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Dept of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Antal Martinecz
- Dept of Biology, Pennsylvania State University, University Park, PA, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.,Dept of Pharmacy, Faculty of Health Sciences, UiT, Arctic University of Norway, Tromsø, Norway
| | - Matthias Merker
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Stefan Niemann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Maja Reimann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Olena Rzhepishevska
- Dept of Chemistry, Umeå University, Umeå, Sweden.,Dept of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Ulrich E Schaible
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Pia Abel Zur Wiesch
- Dept of Biology, Pennsylvania State University, University Park, PA, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Jan Heyckendorf
- Research Center Borstel, Borstel, Germany .,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
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Sharma A, De Rosa M, Singla N, Singh G, Barnwal RP, Pandey A. Tuberculosis: An Overview of the Immunogenic Response, Disease Progression, and Medicinal Chemistry Efforts in the Last Decade toward the Development of Potential Drugs for Extensively Drug-Resistant Tuberculosis Strains. J Med Chem 2021; 64:4359-4395. [PMID: 33826327 DOI: 10.1021/acs.jmedchem.0c01833] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis (TB) is a slow growing, potentially debilitating disease that has plagued humanity for centuries and has claimed numerous lives across the globe. Concerted efforts by researchers have culminated in the development of various strategies to combat this malady. This review aims to raise awareness of the rapidly increasing incidences of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis, highlighting the significant modifications that were introduced in the TB treatment regimen over the past decade. A description of the role of pathogen-host immune mechanisms together with strategies for prevention of the disease is discussed. The struggle to develop novel drug therapies has continued in an effort to reduce the treatment duration, improve patient compliance and outcomes, and circumvent TB resistance mechanisms. Herein, we give an overview of the extensive medicinal chemistry efforts made during the past decade toward the discovery of new chemotypes, which are potentially active against TB-resistant strains.
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Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India.,UIPS, Panjab University, Chandigarh 160014, India
| | - Maria De Rosa
- Drug Discovery Unit, Ri.MED Foundation, Palermo 90133, Italy
| | - Neha Singla
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- UIPS, Panjab University, Chandigarh 160014, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
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45
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A population-based genomic epidemiological study of the source of tuberculosis infections in an emerging city: Shenzhen, China. LANCET REGIONAL HEALTH-WESTERN PACIFIC 2021; 8:100106. [PMID: 34327429 PMCID: PMC8315418 DOI: 10.1016/j.lanwpc.2021.100106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/13/2021] [Accepted: 01/27/2021] [Indexed: 11/28/2022]
Abstract
Background Tuberculosis (TB) in emerging cities is often a disease of recent immigrants, and understanding this epidemiology is crucial for designing effective control and prevention strategies. Methods We conducted a retrospective population-based genomic epidemiological study of culture-positive pulmonary TB patients diagnosed between June 2014 and November 2017 in the Bao'an District of Shenzhen, a Chinese city with dramatic recent growth. After whole genome sequencing, transmission clusters were defined as strains differing by no more than 12 SNPs. Findings Of 1696 culture-positive TB patients, 93•8% (1591/1696) were migrants, with 51•6% (821/1591) employed in housekeeping or unemployed. Of the 1460 migrants with known residence time, 47•7% (697/1460) developed TB within two years after arriving in Bao'an. Only 12•2% (207/1696) of Bao'an isolates were in genomic clusters, indicating that recent transmission was not the primary cause of TB in Bao'an. The isolates’ median terminal branch length was 56 SNPs, more than could have accumulated since the arrival of the migrants in Bao'an. The migrants’ isolates had genotypic distributions similar to those in their home provinces. One strain isolated in Bao'an belonged to a clade circulating in the patient's home province, providing further evidence that the strains were brought to Bao'an with the migrants. Interpretation TB in the Bao'an District is principally caused by reactivation of infections acquired by migrants in their home provinces. Nearly half developed TB within two years after arriving in Bao'an, suggesting a need for increased TB screening of migrants, especially housekeeping workers and the unemployed. Funding Sanming Project of Medicine in Shenzhen; National Science and Technology Major Project of China; Natural Science Foundation of China.
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Malenfant JH, Brewer TF. Rifampicin Mono-Resistant Tuberculosis-A Review of an Uncommon But Growing Challenge for Global Tuberculosis Control. Open Forum Infect Dis 2021; 8:ofab018. [PMID: 33623803 PMCID: PMC7888568 DOI: 10.1093/ofid/ofab018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/26/2021] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) remains the leading cause of death by an infectious pathogen worldwide, and drug-resistant TB is a critical and rising obstacle to global control efforts. Most scientific studies and global TB efforts have focused on multidrug-resistant TB (MDR-TB), meaning isolates resistant to both isoniazid (INH) and rifampicin (RIF). Newer diagnostic tests are resulting in an increasing awareness of RIF-resistant TB in addition to MDR disease. To date, RIF resistance has been assumed to be synonymous with MDR-TB, but this approach may expose TB patients with RIF mono-resistance disease to unnecessarily long and toxic treatment regimens. We review what is currently known about RIF mono-resistant TB, its history and epidemiology, mechanisms of RIF resistance, available diagnostic techniques, treatment outcomes reported globally, and future directions for combatting this disease.
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Affiliation(s)
- Jason H Malenfant
- Public Health & Preventive Medicine Program, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Timothy F Brewer
- Division of Infectious Diseases, University of California, Los Angeles, Los Angeles, California, USA.,Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, USA
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Chen X, Hu TY. Strategies for advanced personalized tuberculosis diagnosis: Current technologies and clinical approaches. PRECISION CLINICAL MEDICINE 2021; 4:35-44. [PMID: 33842836 PMCID: PMC8023014 DOI: 10.1093/pcmedi/pbaa041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 02/05/2023] Open
Abstract
Diagnosis of tuberculosis can be difficult as advances in molecular diagnosis approaches (especially nanoparticles combined with high-throughput mass spectrometry for detecting mycobacteria peptide) and personalized medicine result in many changes to the diagnostic framework. This review will address issues concerning novel technologies from bench to bed and new strategies for personalized tuberculosis diagnosis.
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Affiliation(s)
- Xuerong Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, School of Medicine, Tulane University, New Orleans, LA 70112, USA
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Laniado-Laborín R. Clinical Interpretation of Drug Susceptibility Tests in Tuberculosis. CURRENT RESPIRATORY MEDICINE REVIEWS 2021. [DOI: 10.2174/1573398x16999201007164411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Prompt and accurate diagnosis of drug resistance is essential for optimal treatment of
drug-resistant tuberculosis. However, only 20% of the more than half a million patients eligible for
the treatment of MDR-TB/RR-TB receive an appropriate drug regimen. Drug-resistant TB regimens
must include a sufficient number of effective medications, a significant challenge for clinicians
worldwide, as most are forced to make therapeutic decisions without any, or very little information
on drug susceptibility testing. Although phenotypic DST is still commonly regarded as the
gold standard for determining M. tuberculosis susceptibility to antituberculosis drugs, it has several
limitations, mainly its prolonged turnaround time. Molecular methods based on M. tuberculosis genomic
DNA sequencing have been developed during the past two decades, to identify the most
common mutations involved in drug resistance. The Xpert
®
MTB/RIF is a real-time polymerase
chain reaction that offers results in less than two hours and has an overall sensitivity for rifampin resistance
of 96% and 98% specificity. Line probe assays (LPAs) are commercial DNA strip-based
tests for detecting the most frequent mutations responsible for resistance to rifampin, isoniazid, fluoroquinolones,
and second-line injectable drugs.
:
Discrepancies between phenotypic and genotyping methods are a problem that the clinician will
face in everyday practice. However, any resistance result (with any type of test) in a person with
risk factors for harboring resistant microorganisms should be considered appropriate while the results
of complementary tests are available.
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Affiliation(s)
- Rafael Laniado-Laborín
- Clinica y Laboratorio de Tuberculosis, Hospital General Tijuana, ISESALUD, Mexicali, Mexico
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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: 0.4] [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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Wang H, Song S, Peng F, Yang F, Chen T, Li X, Cheng X, He Y, Huang Y, Su Z. Whole-genome and enzymatic analyses of an androstenedione-producing Mycobacterium strain with residual phytosterol-degrading pathways. Microb Cell Fact 2020; 19:187. [PMID: 33008397 PMCID: PMC7532642 DOI: 10.1186/s12934-020-01442-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 09/25/2020] [Indexed: 01/29/2023] Open
Abstract
Mycobacterium neoaurum strains can transform phytosterols to 4-androstene-3,17-dione (4-AD), a key intermediate for the synthesis of advanced steroidal medicines. In this work, we presented the complete genome sequence of the M. neoaurum strain HGMS2, which transforms β-sitosterol to 4-AD. Through genome annotation, a phytosterol-degrading pathway in HGMS2 was predicted and further shown to form a 9,10-secosteroid intermediate by five groups of enzymes. These five groups of enzymes included three cholesterol oxidases (ChoM; group 1: ChoM1, ChoM2 and Hsd), two monooxygenases (Mon; group 2: Mon164 and Mon197), a set of enzymes for side-chain degradation (group 3), one 3-ketosteroid-1,2-dehydrogenase (KstD; group 4: KstD211) and three 3-ketosteroid-9a-hydroxylases (Ksh; group 5: KshA226, KshA395 and KshB122). A gene cluster encoding Mon164, KstD211, KshA226, KshB122 and fatty acid β-oxidoreductases constituted one integrated metabolic pathway, while genes encoding other key enzymes were sporadically distributed. All key enzymes except those from group 3 were prepared as recombinant proteins and their activities were evaluated, and the proteins exhibited distinct activities compared with enzymes identified from other bacterial species. Importantly, we found that the KstD211 and KshA395 enzymes in the HGMS2 strain retained weak activities and caused the occurrence of two major impurities, i.e., 1,4-androstene-3,17-dione (ADD) and 9-hydroxyl-4-androstene-3,17-dione (9OH-AD) during β-sitosterol fermentation. The concurrence of these two 4-AD analogs not only lowered 4-AD production yield but also hampered 4-AD purification. HGMS2 has the least number of genes encoding KstD and Ksh enzymes compared with current industrial strains. Therefore, HGMS2 could be a potent strain by which the 4-AD production yield could be enhanced by disabling the KstD211 and KshA395 enzymes. Our work also provides new insight into the engineering of the HGMS2 strain to produce ADD and 9OH-AD for industrial application.
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Affiliation(s)
- Hongwei Wang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Shikui Song
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Fei Peng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Fei Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Tian Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Xin Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China.,Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan, 430075, Hubei, China
| | - Yijun He
- Hubei Goto Biotech Inc., No. 1 Baiguoshu Road, Shuidu Industrial Park, Danjiangkou, 442700, Hubei, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China. .,Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan, 430075, Hubei, China.
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