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Mousavi-Sagharchi SMA, Afrazeh E, Seyyedian-Nikjeh SF, Meskini M, Doroud D, Siadat SD. New insight in molecular detection of Mycobacterium tuberculosis. AMB Express 2024; 14:74. [PMID: 38907086 PMCID: PMC11192714 DOI: 10.1186/s13568-024-01730-3] [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: 11/29/2023] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.
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Affiliation(s)
| | - Elina Afrazeh
- Department of Marine Biology, Faculty of Marine Science, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | | | - Maryam Meskini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.
| | - Delaram Doroud
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Solanki P, Elton L, Honeyborne I, Park M, Satta G, McHugh TD. Improving the diagnosis of tuberculosis: old and new laboratory tools. Expert Rev Mol Diagn 2024; 24:487-496. [PMID: 38832527 DOI: 10.1080/14737159.2024.2362165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
INTRODUCTION Despite recent advances in diagnostic technologies and new drugs becoming available, tuberculosis (TB) remains a major global health burden. If detected early, screened for drug resistance, and fully treated, TB could be easily controlled. AREAS COVERED Here the authors discuss M. tuberculosis culture methods which are considered the definitive confirmation of M. tuberculosis infection, and limited advances made to build on these core elements of TB laboratory diagnosis. Literature searches showed that molecular techniques provide enhanced speed of turnaround, sensitivity, and richness of data. Sequencing of the whole genome, is becoming well established for identification and inference of drug resistance. PubMed® literature searches were conducted (November 2022-March 2024). EXPERT OPINION This section highlights future advances in diagnosis and infection control. Prevention of prolonged hospital admissions and rapid TAT are of the most benefit to the overall patient experience. Host transcriptional blood markers have been used in treatment monitoring studies and, with appropriate evaluation, could be rolled out in a diagnostic setting. Additionally, the MBLA is being incorporated into latest clinical trial designs. Whole genome sequencing has enhanced epidemiological evidence. Artificial intelligence, along with machine learning, have the ability to revolutionize TB diagnosis and susceptibility testing within the next decade.
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Affiliation(s)
- Priya Solanki
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Linzy Elton
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Isobella Honeyborne
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Mirae Park
- Respiratory Medicine, Imperial Healthcare NHS Trust, London, UK
| | - Giovanni Satta
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Timothy D McHugh
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
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Shabani S, Farnia P, Ghanavi J, Velayati AA, Farnia P. Pharmacogenetic Study of Drugs Affecting Mycobacterium tuberculosis. Int J Mycobacteriol 2024; 13:206-212. [PMID: 38916393 DOI: 10.4103/ijmy.ijmy_106_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/29/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Pharmacogenetic research has led to significant progress in understanding how genetic factors influence drug response in tuberculosis (TB) treatment. One ongoing challenge is the variable occurrence of adverse drug reactions in some TB patients. Previous studies have indicated that genetic variations in the N-acetyltransferase 2 (NAT2) and solute carrier organic anion transporter family member 1B1 (SLCO1B1) genes can impact the blood concentrations of the first-line anti-TB drugs isoniazid (INH) and rifampicin (RIF), respectively. This study aimed to investigate the influence of pharmacogenetic markers in the NAT2 and SLCO1B1 genes on TB treatment outcomes using whole-exome sequencing (WES) analysis. METHODS DNA samples were collected from 30 healthy Iranian adults aged 18-40 years. The allelic frequencies of single-nucleotide polymorphisms (SNPs) in the NAT2 and SLCO1B1 genes were determined through WES. RESULTS Seven frequent SNPs were identified in the NAT2 gene (rs1041983, rs1801280, rs1799929, rs1799930, rs1208, rs1799931, rs2552), along with 16 frequent SNPs in the SLCO1B1 gene (rs2306283, rs11045818, rs11045819, rs4149056, rs4149057, rs2291075, rs201722521, rs11045852, rs11045854, rs756393362, rs11045859, rs74064211, rs201556175, rs34671512, rs71581985, rs4149085). CONCLUSION Genetic variations in NAT2 and SLCO1B1 can affect the metabolism of INH and RIF, respectively. A better understanding of the pharmacogenetic profile in the study population may facilitate the design of more personalized and effective TB treatment strategies. Further research is needed to directly correlate these genetic markers with clinical outcomes in TB patients.
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Affiliation(s)
- Samira Shabani
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Wang Y, Jiang Z, Liang P, Liu Z, Cai H, Sun Q. TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations. BMC Genomics 2024; 25:167. [PMID: 38347478 PMCID: PMC10860279 DOI: 10.1186/s12864-024-10066-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
The most widely practiced strategy for constructing the deep learning (DL) prediction model for drug resistance of Mycobacterium tuberculosis (MTB) involves the adoption of ready-made and state-of-the-art architectures usually proposed for non-biological problems. However, the ultimate goal is to construct a customized model for predicting the drug resistance of MTB and eventually for the biological phenotypes based on genotypes. Here, we constructed a DL training framework to standardize and modularize each step during the training process using the latest tensorflow 2 API. A systematic and comprehensive evaluation of each module in the three currently representative models, including Convolutional Neural Network, Denoising Autoencoder, and Wide & Deep, which were adopted by CNNGWP, DeepAMR, and WDNN, respectively, was performed in this framework regarding module contributions in order to assemble a novel model with proper dedicated modules. Based on the whole-genome level mutations, a de novo learning method was developed to overcome the intrinsic limitations of previous models that rely on known drug resistance-associated loci. A customized DL model with the multilayer perceptron architecture was constructed and achieved a competitive performance (the mean sensitivity and specificity were 0.90 and 0.87, respectively) compared to previous ones. The new model developed was applied in an end-to-end user-friendly graphical tool named TB-DROP (TuBerculosis Drug Resistance Optimal Prediction: https://github.com/nottwy/TB-DROP ), in which users only provide sequencing data and TB-DROP will complete analysis within several minutes for one sample. Our study contributes to both a new strategy of model construction and clinical application of deep learning-based drug-resistance prediction methods.
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Affiliation(s)
- Yu Wang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Zhonghua Jiang
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Pengkuan Liang
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Zhuochong Liu
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Haoyang Cai
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
| | - Qun Sun
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
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Morey-León G, Mejía-Ponce PM, Granda Pardo JC, Muñoz-Mawyin K, Fernández-Cadena JC, García-Moreira E, Andrade-Molina D, Licona-Cassani C, Berná L. A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools. PLoS One 2023; 18:e0294670. [PMID: 38051742 DOI: 10.1371/journal.pone.0294670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
INTRODUCTION Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. In this study, we evaluated the performance and functionalities of web-based tools, including Mykrobe, TB-profiler, PhyResSE, KvarQ, and SAM-TB, for detecting resistance in 88 Ecuadorian isolates of Mycobacterium tuberculosis drug susceptibility tested previously. Statistical analysis was used to determine the correlation between genomic and phenotypic analysis. Our results showed that with the exception of KvarQ, all tools had the highest correlation with the conventional drug susceptibility test (DST) for global resistance detection (98% agreement and 0.941 Cohen's kappa), while SAM-TB, PhyResSE, TB-profiler and Mykrobe had better correlations with DST for first-line drug analysis individually. We also identified that in our study, only 50% of mutations characterized by the web-based tools in the rpoB, katG, embB, pncA, gyrA and rrs regions were canonical and included in the World Health Organization (WHO) catalogue. Our findings suggest that SAM-TB, PhyResSE, TB-profiler and Mykrobe were efficient in determining canonical resistance-related mutations, but more analysis is needed to improve second-line detection. Improving surveillance programs using whole-genome sequencing tools for first-line drugs, MDR-TB and XDR-TB is essential to understand the molecular epidemiology of TB in Ecuador. IMPORTANCE Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, most commonly affects the lungs and is often spread through the air when infected people cough, sneeze, or spit. However, despite the existence of effective drug treatment, patient adherence, long duration of treatment, and late diagnosis have reduced the effectiveness of therapy and increased drug resistance. The increase in resistant cases, added to the impact of the COVID-19 pandemic, has highlighted the importance of implementing efficient and timely diagnostic methodologies worldwide. The significance of our research is in evaluating and identifying a more efficient and user-friendly web-based tool to characterize resistance in Mycobacterium tuberculosis by whole-genome sequencing, which will allow more routine application to improve TB strain surveillance programs locally.
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Affiliation(s)
- Gabriel Morey-León
- Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
- Universidad de la República, Montevideo, Uruguay
- University of Guayaquil, Guayaquil, Ecuador
| | - Paulina M Mejía-Ponce
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Nuevo León, México
| | - Juan Carlos Granda Pardo
- Centro de Referencia Nacional de Micobacterias, Instituto Nacional de Investigación en Salud Pública Dr Leopoldo Izquieta Perez, INSPI-LIP, Guayaquil, Ecuador
| | - Karen Muñoz-Mawyin
- Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | | | - Derly Andrade-Molina
- Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
- Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - Luisa Berná
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Komine T, Ihara H, Inohana M, Kwok JC, Shimizu A, Terasawa T, Miyazaki A, Srivorakul S, Iwao H, Harada S, Yoshida M, Hoshino Y, Kurata O, Fukano H, Wada S. Non-tuberculous mycobacterial disease associated with Mycobacterium montefiorense in salamanders. Front Vet Sci 2023; 10:1248288. [PMID: 37954664 PMCID: PMC10637390 DOI: 10.3389/fvets.2023.1248288] [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: 06/27/2023] [Accepted: 09/22/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Mycobacterium montefiorense is one of the causes of non-tuberculous mycobacterial infections in moray eels and salamanders. Although M. montefiorense infection could be a threat to salamanders, little information is available regarding this pathogen and associated infection. This study aimed to provide fundamental information regarding M. montefiorense and its infection in salamanders. Methods Nine M. montefiorense strains isolated from three species of salamanders, namely, Japanese black salamander (Hynobius nigrescens), Hakuba salamander (H. hidamontanus), and Tohoku hynobiid salamander (H. lichenatus), between 2010 and 2018, were characterized based on phenotypic and genetic examination. We also pathologically observed salamanders infected with the M. montefiorense strains, including Hakuba salamanders and Tohoku hynobiid salamanders. Results The microbiological and chemical characteristics of the M. montefiorense salamander and an eel strain (reference strain) matched. Susceptibility testing for antimicrobials suggested that clarithromycin may be effective. Regarding disinfectants, phtharal, peracetic acid, glutaral, sodium hypochlorite, and benzalkonium chloride may be effective. Phylogenetic analyses revealed that the strains isolated from salamanders in 2014 and 2018 were genetically closely related, which could indicate an outbreak. The main gross findings in infected salamanders include skin ulcerative lesions or nodules in the enlarged liver. Microscopically, multifocal to coalescent granulomatous lesions composed of massive macrophages containing numerous acid-fast bacilli were prominently observed in the liver. Conclusion This study contributes to our understanding of the genetic diversity and phenotypic characteristics of M. montefiorense, as well as the pathology of the infection.
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Affiliation(s)
- Takeshi Komine
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Hyogo Ihara
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Mari Inohana
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Jennifer Caroline Kwok
- Retinal Disease Studies Facility, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Akane Shimizu
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Tsumugi Terasawa
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Ayaka Miyazaki
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Saralee Srivorakul
- Center of Veterinary Diagnosis and Technology Transfer, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Osamu Kurata
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Shinpei Wada
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
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Dohál M, Porvazník I, Solovič I, Mokrý J. Advancing tuberculosis management: the role of predictive, preventive, and personalized medicine. Front Microbiol 2023; 14:1225438. [PMID: 37860132 PMCID: PMC10582268 DOI: 10.3389/fmicb.2023.1225438] [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: 05/19/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Tuberculosis is a major global health issue, with approximately 10 million people falling ill and 1.4 million dying yearly. One of the most significant challenges to public health is the emergence of drug-resistant tuberculosis. For the last half-century, treating tuberculosis has adhered to a uniform management strategy in most patients. However, treatment ineffectiveness in some individuals with pulmonary tuberculosis presents a major challenge to the global tuberculosis control initiative. Unfavorable outcomes of tuberculosis treatment (including mortality, treatment failure, loss of follow-up, and unevaluated cases) may result in increased transmission of tuberculosis and the emergence of drug-resistant strains. Treatment failure may occur due to drug-resistant strains, non-adherence to medication, inadequate absorption of drugs, or low-quality healthcare. Identifying the underlying cause and adjusting the treatment accordingly to address treatment failure is important. This is where approaches such as artificial intelligence, genetic screening, and whole genome sequencing can play a critical role. In this review, we suggest a set of particular clinical applications of these approaches, which might have the potential to influence decisions regarding the clinical management of tuberculosis patients.
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Affiliation(s)
- Matúš Dohál
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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Couvin D, Stattner E, Segretier W, Cazenave D, Rastogi N. simpiTB - a pipeline designed to extract meaningful information from whole genome sequencing data of Mycobacterium tuberculosis complex, allows to combine genomic, phylogenetic and clustering analyses in existing SITVIT databases. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105466. [PMID: 37331497 DOI: 10.1016/j.meegid.2023.105466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/20/2023]
Abstract
Data obtained from new sequencing technologies are evolving rapidly, leading to the development of specific bioinformatic tools, pipelines and softwares. Several algorithms and tools are today available allowing a better identification and description of Mycobacterium tuberculosis complex (MTBC) isolates worldwide. Our approach consists in applying existing methods to analyze DNA sequencing data (from FASTA or FASTQ files), and tentatively extract meaningful information that would facilitate identification as well as a better understanding and management of MTBC isolates (taking into account whole genome sequencing and classical genotyping data). The aim of this study is to propose a pipeline analysis allowing to potentially simplify MTBC data analysis by providing different ways to interpret genomic or genotyping information based on existing tools. Furthermore, we propose a "reconciledTB" list making a link with results directly obtained from whole genome sequencing (WGS) data and results obtained from classical genotyping analysis (data inferred from SpoTyping and MIRUReader). Data visualization graphics and trees generated provide additional elements to better understand and confer associations among information overlap analyses. Additionally, comparison between data entered in an international genotyping database (SITVITEXTEND) and ensuing data obtained from the pipeline not only provide meaningful information, but further suggest that simpiTB could also be suitable for new data integration in specific TB genotyping databases.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France; Transmission, Reservoir and Diversity of Pathogens Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France.
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Damien Cazenave
- Transmission, Reservoir and Diversity of Pathogens Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe, France
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9
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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: 4] [Impact Index Per Article: 4.0] [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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Mycobacterium tuberculosis Genotypes and Drug Susceptibility Test Results from Timor-Leste: A Pilot Study. Genes (Basel) 2022; 13:genes13101733. [PMID: 36292618 PMCID: PMC9602296 DOI: 10.3390/genes13101733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) is prevalent and a major public health problem in Timor-Leste. The government of Timor-Leste is prioritising the surveillance of TB and drug-susceptibility testing (DST) to understand the burden of TB and TB drug resistance in the country. Moreover, little is known about the origin of Mycobacterium tuberculosis (MTB) in Timor-Leste. This study reports MTB DST and sequencing for Timor-Leste. A pilot study was carried out in which a convenience sample of TB isolates from mucopurulent sputum collected from presumptive TB patients in the capital Dili between July and December 2016 was tested for phenotypic and genotypic evidence of drug resistance. Standard MTB culture was performed at the Timor-Leste National Health Laboratory (NHL). The MTB isolates were sent to the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Australia for DST and sequencing. Overall, 36 MTB isolates were detected at the NHL; 20 isolates were recovered during sub-culturing at VIDRL. All 20 isolates were susceptible to rifampicin, isoniazid, pyrazinamide, and ethambutol, with no genotypic markers of resistance identified. On sequencing, lineage 4 was the most common. The results of this study provide a small snapshot of MTB diversity and resistance in an under-sampled region with very high TB incidence. Future investment in whole-genome sequencing capacity in Timor-Leste will make it possible to undertake further, more representative analyses that may be used to evaluate transmission dynamics and epidemiology of genotypic markers of resistance.
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11
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Disseminated tuberculosis with paradoxical reactions caused by a Mycobacterium tuberculosis strain belonging to the Indo-Oceanic lineage: An imported case in Japan. J Infect Chemother 2022; 28:965-970. [DOI: 10.1016/j.jiac.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/30/2021] [Accepted: 02/06/2022] [Indexed: 11/20/2022]
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12
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Grenni P. Antimicrobial Resistance in Rivers: A Review of the Genes Detected and New Challenges. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:687-714. [PMID: 35191071 DOI: 10.1002/etc.5289] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 11/11/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
River ecosystems are very important parts of the water cycle and an excellent habitat, food, and drinking water source for many organisms, including humans. Antibiotics are emerging contaminants which can enter rivers from various sources. Several antibiotics and their related antibiotic resistance genes (ARGs) have been detected in these ecosystems by various research programs and could constitute a substantial problem. The presence of antibiotics and other resistance cofactors can boost the development of ARGs in the chromosomes or mobile genetic elements of natural bacteria in rivers. The ARGs in environmental bacteria can also be transferred to clinically important pathogens. However, antibiotics and their resistance genes are both not currently monitored by national or international authorities responsible for controlling the quality of water bodies. For example, they are not included in the contaminant list in the European Water Framework Directive or in the US list of Water-Quality Benchmarks for Contaminants. Although ARGs are naturally present in the environment, very few studies have focused on non-impacted rivers to assess the background ARG levels in rivers, which could provide some useful indications for future environmental regulation and legislation. The present study reviews the antibiotics and associated ARGs most commonly measured and detected in rivers, including the primary analysis tools used for their assessment. In addition, other factors that could enhance antibiotic resistance, such as the effects of chemical mixtures, the effects of climate change, and the potential effects of the coronavirus disease 2019 pandemic, are discussed. Environ Toxicol Chem 2022;41:687-714. © 2022 SETAC.
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Affiliation(s)
- Paola Grenni
- Water Research Institute, National Research Council of Italy, via Salaria km 29.300, Monterotondo, Rome, 00015, Italy
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13
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Yang T, Gan M, Liu Q, Liang W, Tang Q, Luo G, Zuo T, Guo Y, Hong C, Li Q, Tan W, Gao Q. SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission. Brief Bioinform 2022; 23:6535677. [PMID: 35211720 PMCID: PMC8921607 DOI: 10.1093/bib/bbac030] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/28/2021] [Accepted: 01/25/2022] [Indexed: 01/28/2023] Open
Abstract
Whole genome sequencing (WGS) can provide insight into drug-resistance, transmission chains and the identification of outbreaks, but data analysis remains an obstacle to its routine clinical use. Although several drug-resistance prediction tools have appeared, until now no website integrates drug-resistance prediction with strain genetic relationships and species identification of nontuberculous mycobacteria (NTM). We have established a free, function-rich, user-friendly online platform for MTB WGS data analysis (SAM-TB, http://samtb.szmbzx.com) that integrates drug-resistance prediction for 17 antituberculosis drugs, detection of variants, analysis of genetic relationships and NTM species identification. The accuracy of SAM-TB in predicting drug-resistance was assessed using 3177 sequenced clinical isolates with results of phenotypic drug-susceptibility tests (pDST). Compared to pDST, the sensitivity of SAM-TB for detecting multidrug-resistant tuberculosis was 93.9% [95% confidence interval (CI) 92.6–95.1%] with specificity of 96.2% (95% CI 95.2–97.1%). SAM-TB also analyzes the genetic relationships between multiple strains by reconstructing phylogenetic trees and calculating pairwise single nucleotide polymorphism (SNP) distances to identify genomic clusters. The incorporated mlstverse software identifies NTM species with an accuracy of 98.2% and Kraken2 software can detect mixed MTB and NTM samples. SAM-TB also has the capacity to share both sequence data and analysis between users. SAM-TB is a multifunctional integrated website that uses WGS raw data to accurately predict antituberculosis drug-resistance profiles, analyze genetic relationships between multiple strains and identify NTM species and mixed samples containing both NTM and MTB. SAM-TB is a useful tool for guiding both treatment and epidemiological investigation.
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Affiliation(s)
- Tingting Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | | | | | | | | | - Geyang Luo
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Tianyu Zuo
- Fudan University, Shanghai, China. Presently, he is a data analyst in patsnap, Shanghai, China
| | - Yongchao Guo
- Shenzhen Uni-medica Technology Co., Ltd, Shenzhen, China
| | - Chuangyue Hong
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | | | - Weiguo Tan
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - 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 and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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14
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Gomes LC, Campino S, Marinho CRF, Clark TG, Phelan JE. Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes. Microb Genom 2021; 7:000724. [PMID: 34889724 PMCID: PMC8767347 DOI: 10.1099/mgen.0.000724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Drug resistance in Mycobacterium tuberculosis, the causative agent of tuberculosis disease, arises from genetic mutations in genes coding for drug-targets or drug-converting enzymes. SNPs linked to drug resistance have been extensively studied and form the basis of molecular diagnostics and sequencing-based resistance profiling. However, alternative forms of functional variation such as large deletions and other loss of function (LOF) mutations have received much less attention, but if incorporated into diagnostics they are likely to improve their predictive performance. Our work aimed to characterize the contribution of LOF mutations found in 42 established drug resistance genes linked to 19 anti-tuberculous drugs across 32689 sequenced clinical isolates. The analysed LOF mutations included large deletions (n=586), frameshifts (n=4764) and premature stop codons (n=826). We found LOF mutations in genes strongly linked to pyrazinamide (pncA), isoniazid (katG), capreomycin (tlyA), streptomycin (e.g. gid) and ethionamide (ethA, mshA) (P<10-5), but also in some loci linked to drugs where relatively less phenotypic data is available [e.g. cycloserine, delaminid, bedaquiline, para-aminosalicylic acid (PAS), and clofazimine]. This study reports that large deletions (median size 1115 bp) account for a significant portion of resistance variants found for PAS (+7.1% of phenotypic resistance percentage explained), pyrazinamide (+3.5%) and streptomycin (+2.6%) drugs, and can be used to improve the prediction of cryptic resistance. Overall, our work highlights the importance of including LOF mutations (e.g. large deletions) in predicting genotypic drug resistance, thereby informing tuberculosis infection control and clinical decision-making.
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Affiliation(s)
- Laura C. Gomes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Cláudio R. F. Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK,*Correspondence: Taane G. Clark,
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK,*Correspondence: Jody E. Phelan,
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15
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Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Yerezhepov D, Chingissova L, Bismilda V, Toksanbayeva B, Rakisheva A, Akilzhanova A, Kozhamkulov U, Kairov U. Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan. Front Genet 2021; 12:683515. [PMID: 34858467 PMCID: PMC8630622 DOI: 10.3389/fgene.2021.683515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence of antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) of TB is increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known and novel potential genetic variants that are associated with drug resistance in Mycobacterium tuberculosis (Mtb). There are limited reports and data related to whole-genome characteristics of drug-resistant Mtb strains circulating in Kazakhstan. Here, we report whole-genome sequencing and analysis results of eight multidrug-resistant strains collected from TB patients in Kazakhstan. Genotyping and validation of all strains by MIRU-VNTR and spoligotyping methodologies revealed that these strains belong to the Beijing family. The spectrum of specific and potentially novel genomic variants (single-nucleotide polymorphisms, insertions, and deletions) related to drug resistance was identified and annotated. ResFinder, CARD, and CASTB antibiotic resistance databases were used for the characterization of genetic variants in genes associated with drug resistance. Our results provide reference data and genomic profiles of multidrug-resistant isolates for further comparative studies and investigations of genetic patterns in drug-resistant Mtb strains.
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Affiliation(s)
- Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Bekzat Toksanbayeva
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Anar Rakisheva
- Department of Phthisiopulmonology, School of General Medicine, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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16
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Meumann EM, Horan K, Ralph AP, Farmer B, Globan M, Stephenson E, Popple T, Boyd R, Kaestli M, Seemann T, Vandelannoote K, Lowbridge C, Baird RW, Stinear TP, Williamson DA, Currie BJ, Krause VL. Tuberculosis in Australia's tropical north: a population-based genomic epidemiological study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2021; 15:100229. [PMID: 34528010 PMCID: PMC8350059 DOI: 10.1016/j.lanwpc.2021.100229] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/03/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND The Northern Territory (NT) has the highest tuberculosis (TB) rate of all Australian jurisdictions. We combined TB public health surveillance data with genomic sequencing of Mycobacterium tuberculosis isolates in the tropical 'Top End' of the NT to investigate trends in TB incidence and transmission. METHODS This retrospective observational study included all 741 culture-confirmed cases of TB in the Top End over three decades from 1989-2020. All 497 available M. tuberculosis isolates were sequenced. We used contact tracing data to define a threshold pairwise SNP distance for hierarchical single linkage clustering, and examined putative transmission clusters in the context of epidemiologic information. FINDINGS There were 359 (48%) cases born overseas, 329 (44%) cases among Australian First Nations peoples, and 52 (7%) cases were Australian-born and non-Indigenous. The annual incidence in First Nations peoples from 1989-2019 fell from average 50.4 to 11.0 per 100,000 (P<0·001). First Nations cases were more likely to die from TB (41/329, 12·5%) than overseas-born cases (11/359, 3·1%; P<0·001). Using a threshold of ≤12 SNPs, 28 clusters of between 2-64 individuals were identified, totalling 250 cases; 214 (86%) were First Nations cases and 189 (76%) were from a remote region. The time between cases and past epidemiologically- and genomically-linked contacts ranged from 4·5 months to 24 years. INTERPRETATION Our findings support prioritisation of timely case detection, contact tracing augmented by genomic sequencing, and latent TB treatment to break transmission chains in Top End remote hotspot regions.
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Affiliation(s)
- Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
- Territory Pathology, Royal Darwin Hospital, Darwin, Australia
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna P Ralph
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Belinda Farmer
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Maria Globan
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Elizabeth Stephenson
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Tracy Popple
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Rowena Boyd
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Koen Vandelannoote
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Christopher Lowbridge
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Robert W. Baird
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
- Territory Pathology, Royal Darwin Hospital, Darwin, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Deborah A. Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
| | - Vicki L. Krause
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
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17
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Gröschel MI, Owens M, Freschi L, Vargas R, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR. GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. Genome Med 2021; 13:138. [PMID: 34461978 PMCID: PMC8407037 DOI: 10.1186/s13073-021-00953-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/12/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drug-susceptibility testing. User-friendly and accurate resistance prediction tools are needed to enable public health and clinical practitioners to rapidly diagnose resistance and inform treatment regimens. RESULTS We present Translational Genomics platform for Tuberculosis (GenTB), a free and open web-based application to predict antibiotic resistance from next-generation sequence data. The user can choose between two potential predictors, a Random Forest (RF) classifier and a Wide and Deep Neural Network (WDNN) to predict phenotypic resistance to 13 and 10 anti-tuberculosis drugs, respectively. We benchmark GenTB's predictive performance along with leading TB resistance prediction tools (Mykrobe and TB-Profiler) using a ground truth dataset of 20,408 isolates with laboratory-based drug susceptibility data. All four tools reliably predicted resistance to first-line tuberculosis drugs but had varying performance for second-line drugs. The mean sensitivities for GenTB-RF and GenTB-WDNN across the nine shared drugs were 77.6% (95% CI 76.6-78.5%) and 75.4% (95% CI 74.5-76.4%), respectively, and marginally higher than the sensitivities of TB-Profiler at 74.4% (95% CI 73.4-75.3%) and Mykrobe at 71.9% (95% CI 70.9-72.9%). The higher sensitivities were at an expense of ≤ 1.5% lower specificity: Mykrobe 97.6% (95% CI 97.5-97.7%), TB-Profiler 96.9% (95% CI 96.7 to 97.0%), GenTB-WDNN 96.2% (95% CI 96.0 to 96.4%), and GenTB-RF 96.1% (95% CI 96.0 to 96.3%). Averaged across the four tools, genotypic resistance sensitivity was 11% and 9% lower for isoniazid and rifampicin respectively, on isolates sequenced at low depth (< 10× across 95% of the genome) emphasizing the need to quality control input sequence data before prediction. We discuss differences between tools in reporting results to the user including variants underlying the resistance calls and any novel or indeterminate variants CONCLUSIONS: GenTB is an easy-to-use online tool to rapidly and accurately predict resistance to anti-tuberculosis drugs. GenTB can be accessed online at https://gentb.hms.harvard.edu , and the source code is available at https://github.com/farhat-lab/gentb-site .
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Affiliation(s)
- Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Martin Owens
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Maximilian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Zamin Iqbal
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 ISD, UK
| | - Avika Dixit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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18
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Yoshida S, Iwamoto T, Arikawa K, Sekizuka T, Kuroda M, Inoue Y, Mitarai S, Tsuji T, Tsuyuguchi K, Suzuki K. Bacterial population kinetics in heteroresistant Mycobacterium tuberculosis harbouring rare resistance-conferring mutations in gyrA and rpoB imply an epistatic interaction of mutations in a pre-XDR-TB patient. J Antimicrob Chemother 2021; 75:1722-1725. [PMID: 32303065 DOI: 10.1093/jac/dkaa109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Bacterial population kinetics of strains harbouring drug resistance-conferring mutations within a patient often show cryptic resistance in clinical practice. We report a case that showed emergence and dominance of Mycobacterium tuberculosis with uncommon rpoB and gyrA mutations, followed by an rpoC compensatory mutation, during treatment. METHODS A pre-XDR-TB patient showed heteroresistance to rifampicin and levofloxacin during treatment as a result of intermittent self-cessation. WGS was applied to investigate intra-host strain composition using five pairs of isolates from sputum samples. RESULTS The subclone in this study possessed rare mutations conferring resistance to rifampicin (rpoB V170F) and levofloxacin (gyrA S91P) and it rapidly outcompeted other subclones during treatment that included levofloxacin but not rifampicin (<7 days). The high-probability compensatory mutation rpoC V483A also emerged and became dominant subsequent to the rpoB V170F mutation. CONCLUSIONS To the best of our knowledge, this is the first case showing the emergence of such a rare variant that dominated the population within a patient during treatment of TB.
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Affiliation(s)
- Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshikazu Inoue
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Taisuke Tsuji
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Kazunari Tsuyuguchi
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Katsuhiro Suzuki
- Department of Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
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19
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Characterization of genetic diversity and clonal complexes by whole genome sequencing of Mycobacterium tuberculosis isolates from Jalisco, Mexico. Tuberculosis (Edinb) 2021; 129:102106. [PMID: 34218194 DOI: 10.1016/j.tube.2021.102106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/14/2021] [Accepted: 06/20/2021] [Indexed: 11/24/2022]
Abstract
Whole genome sequencing (WGS) analysis in tuberculosis allows the prediction of drug-resistant phenotypes, identification of lineages, and to better understanding of the epidemiology and transmission chains. Nevertheless the procedure has been scarcely assessed in Mexico, in this work we analyze by WGS isolates of Mycobacterium tuberculosis circulating in Jalisco, Mexico. Lineage and phylogenetic characterization, drug resistant prediction, "in silico" spoligotyping determination, were provided by WGS in 32 M. tuberculosis clinical isolates. Lineage 4 (L4), with 28 isolates (87%) and eleven sublineages was dominant. Forty SNPs and INDELs were found in genes related to first-, and second-line drugs. Eleven isolates were sensitive, seven (22%) were predicted to be resistant to isoniazid, two resistant to rifampicin (6%) and two (6%) were multidrug-resistant tuberuclosis. Spoligotyping shows that SIT 53 (19%) and SIT 119 (16%) were dominant. Four clonal transmission complexes were found. This is the first molecular epidemiological description of TB isolates circulating in western Mexico, achieved through WGS. L4 was dominant and included a high diversity of sublineages. It was possible to track the transmission route of two clonal complexes. The WGS demonstrated to be of great utility and with further implications for clinical and epidemiological study of TB in the region.
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20
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Eldholm V, Rønning JO, Mengshoel AT, Arnesen T. Import and transmission of Mycobacterium orygis and Mycobacterium africanum, Norway. BMC Infect Dis 2021; 21:562. [PMID: 34118874 PMCID: PMC8199368 DOI: 10.1186/s12879-021-06269-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Background The aim of the current study was to improve our understanding of the origins and transmission of Mycobacterium africanum (MAF) in Norway. Methods Whole-genome sequences (WGS) were generated for all (n = 29) available clinical isolates received at the Norwegian National Reference Laboratory for Mycobacteria (NRL) and identified as MAF in Norway, in the period 2010–2020. Phylogenetic analyses were performed. Results The analyses indicated several imports of MAF lineage 6 from both East and West African countries, whereas MAF lineage 5 was restricted to patients with West African connections. We also find evidence for transmission of MAF in Norway. Finally, our analyses revealed that a group of isolates from patients originating in South Asia, identified as MAF by means of a commercial line-probe assay, in fact belonged to Mycobacterium orygis. Conclusions Most MAF cases in Norway are the result of import, but transmission is occurring within Norway.
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Affiliation(s)
- Vegard Eldholm
- National Reference Laboratory for Mycobacteria, Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.
| | - Janne O Rønning
- National Reference Laboratory for Mycobacteria, Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Anne Torunn Mengshoel
- National Reference Laboratory for Mycobacteria, Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Trude Arnesen
- National Reference Laboratory for Mycobacteria, Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
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21
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Fernandez Do Porto DA, Monteserin J, Campos J, Sosa EJ, Matteo M, Serral F, Yokobori N, Benevento AF, Poklepovich T, Pardo A, Wainmayer I, Simboli N, Castello F, Paul R, Martí M, López B, Turjanski A, Ritacco V. Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment. BMC Infect Dis 2021; 21:394. [PMID: 33926375 PMCID: PMC8082761 DOI: 10.1186/s12879-021-06069-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution -the genetic variability of M. tuberculosis at short time scales- of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. CASE PRESENTATION In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5' untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. CONCLUSIONS This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.
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Affiliation(s)
- Darío A Fernandez Do Porto
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Mario Matteo
- Instituto de Tisioneumonología Raúl F. Vaccarezza, Hospital de Infecciosas Dr. F. J. Muñiz, Buenos Aires, Argentina
| | - Federico Serral
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Noemí Yokobori
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés Fernández Benevento
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Tomás Poklepovich
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Agustín Pardo
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Ingrid Wainmayer
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Florencia Castello
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roxana Paul
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Marcelo Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Beatriz López
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, IQUIBICEN, CONICET, Buenos Aires, Argentina.
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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22
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Khan MT, Ali S, Khan AS, Ali A, Khan A, Kaushik AC, Irfan M, Chinnasamy S, Zhang S, Zhang YJ, Cui Z, Wei AJ, Wang Y, Zhao M, Liu K, Wang H, Zeb MT, Wei DQ. Insight into the drug resistance whole genome of Mycobacterium tuberculosis isolates from Khyber Pakhtunkhwa, Pakistan. INFECTION GENETICS AND EVOLUTION 2021; 92:104861. [PMID: 33862292 DOI: 10.1016/j.meegid.2021.104861] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022]
Abstract
Whole genome sequencing (WGS) is one of the most reliable methods for detection of drug resistance, genetic diversity in other virulence factor and also evolutionary dynamics of Mycobacterium tuberculosis complex (MTBC). First-line anti-tuberculosis drugs are the major weapons against Mycobacterium tuberculosis (MTB). However, the emergence of drug resistance remained a major obstacle towards global tuberculosis (TB) control program 2030, especially in high burden countries including Pakistan. To overcome the resistance and design potent drugs, genomic variations in drugs targets as well as in the virulence and evolutionary factors might be useful for better understanding and designing potential inhibitors. Here we aimed to find genomic variations in the first-line drugs targets, along with other virulence and evolutionary factors among the circulating isolates in Khyber Pakhtunkhwa, Pakistan. Samples were collected and drug susceptibility testing (DST) was performed as per WHO standard. The resistance samples were subjected to WGS. Among the five whole genome sequences, three samples (NCBI BioProject Accession: PRJNA629298, PRJNA629388) harbored 1997, 1162, and 2053 mutations. Some novel mutations have been detected in drugs targets. Similarly, numerous novel variants have also been detected in virulency and evolutionary factors, PE, PPE, and secretory system of MTB isolates. Exploring the genomic variations among the circulating isolates in geographical specific locations might be useful for future drug designing. To the best of our knowledge, this is the first study that provides useful data regarding the insight genomic variations in virulency, evolutionary factors including ESX and PE/PPE as well as drug targets, for better understanding and management of TB in a WHO declared high burden country.
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Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology and Provincial Tuberculosis Reference Laboratory, Peshawar, Pakistan.
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | | | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Shulin Zhang
- Department of Immunology and Microbiology, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing, China.
| | - Zhilei Cui
- Zhilei Cui, Department of Respiratory Medicine, XinHua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Amie Jinghua Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Yanjie Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Mingzhu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Kejia Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Heng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Muhammad Tariq Zeb
- Khyber Medical University and Senior Research Officer, In-charge Genomic Laboratory, Veterinary Research Institute, Peshawar 25000, Pakistan
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
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23
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Couvin D, Segretier W, Stattner E, Rastogi N. Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families. Database (Oxford) 2020; 2020:baaa108. [PMID: 33320180 PMCID: PMC7737520 DOI: 10.1093/database/baaa108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 11/18/2022]
Abstract
Bioinformatic tools are currently being developed to better understand the Mycobacterium tuberculosis complex (MTBC). Several approaches already exist for the identification of MTBC lineages using classical genotyping methods such as mycobacterial interspersed repetitive units-variable number of tandem DNA repeats and spoligotyping-based families. In the recently released SITVIT2 proprietary database of the Institut Pasteur de la Guadeloupe, a large number of spoligotype families were assigned by either manual curation/expertise or using an in-house algorithm. In this study, we present two complementary data-driven approaches allowing fast and precise family prediction from spoligotyping patterns. The first one is based on data transformation and the use of decision tree classifiers. In contrast, the second one searches for a set of simple rules using binary masks through a specifically designed evolutionary algorithm. The comparison with the three main approaches in the field highlighted the good performances of our contributions and the significant runtime gain. Finally, we propose the 'SpolLineages' software tool (https://github.com/dcouvin/SpolLineages), which implements these approaches for MTBC spoligotype families' identification.
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, F-97183, Abymes, Guadeloupe, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, F-97154, Pointe-à-Pitre, Guadeloupe, France
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, F-97154, Pointe-à-Pitre, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, F-97183, Abymes, Guadeloupe, France
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24
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Genetic Variation Putatively Associated with Mycobacterium tuberculosis Resistance to Perchlozone, a New Thiosemicarbazone: Clues from Whole Genome Sequencing and Implications for Treatment of Multidrug-Resistant Tuberculosis. Antibiotics (Basel) 2020; 9:antibiotics9100669. [PMID: 33022959 PMCID: PMC7601826 DOI: 10.3390/antibiotics9100669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 11/16/2022] Open
Abstract
Perchlozone ([PCZ] 4-thioureido-iminomethylpyridinium perchlorate) is a new thiosemicarbazone approved for the treatment of multidrug-resistant tuberculosis (MDR-TB) in Russia and some other countries. The ethA and hadABC mutations may confer PCZ resistance. At the same time, ethA mutations are known to mediate resistance to ethionamide (ETH) and prothionamide (PTH). We aimed to study the genetic variation underlying Mycobacterium tuberculosis resistance to PCZ through whole genome sequencing (WGS) of consecutive isolates recovered during long-term treatment. This prospective study included patients admitted in 2018–2019 to the regional tuberculosis dispensary, Kaliningrad, Russia, whose treatment regimen included PCZ. Multiple M. tuberculosis isolates were recovered during PCZ treatment, and the bacterial DNA was subjected to WGS followed by bioinformatics analysis. We identified mutations in the genes putatively associated with PCZ resistance, ethA, and hadA. The most frequent one was a frameshift ethA 106 GA > G (seven of nine patients) and most of the other mutations were also likely present before PCZ treatment. In one patient, a frameshift mutation ethA 702 CT > C emerged after six months of PCZ treatment. A frequent presence of cross-resistance mutations to PCZ and ETH/PTH should be taken into consideration when PCZ is included in the treatment regimen of MDR-TB patients.
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25
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Tarlykov P, Atavliyeva S, Alenova A, Ramankulov Y. Genomic analysis of Latin American-Mediterranean family of Mycobacterium tuberculosis clinical strains from Kazakhstan. Mem Inst Oswaldo Cruz 2020; 115:e200215. [PMID: 32965331 PMCID: PMC7508292 DOI: 10.1590/0074-02760200215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/20/2020] [Indexed: 11/22/2022] Open
Abstract
The human-adapted strains of the Mycobacterium tuberculosis complex (MTBC) comprise seven phylogenetic lineages originally associated with their geographical distribution. Here, we report the genomes of three drug-resistant clinical isolates of the Latin American-Mediterranean (LAM) family collected in Kazakhstan. We utilised whole-genome sequencing to study the distribution and drug resistance of these isolates. Phylogenetic analysis grouped the genomes described in this study with the sequences from Russia, Uzbekistan, and Kazakhstan belonging to the LAM family. One isolate has acquired extensive drug resistance to seven antituberculosis drugs. Our results suggest at least two multi-drug resistant (MDR)/extensively drug-resistant (XDR)-associated genotypes of the LAM family circulate in Kazakhstan.
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Affiliation(s)
- Pavel Tarlykov
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | | | - Arike Alenova
- National Scientific Center for Phthisiopulmonology, Almaty, Kazakhstan
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26
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He Y, Gong Z, Zhao X, Zhang D, Zhang Z. Comprehensive Determination of Mycobacterium tuberculosis and Nontuberculous Mycobacteria From Targeted Capture Sequencing. Front Cell Infect Microbiol 2020; 10:449. [PMID: 32984073 PMCID: PMC7491257 DOI: 10.3389/fcimb.2020.00449] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/21/2020] [Indexed: 12/27/2022] Open
Abstract
Infection of Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) challenges effective pulmonary infectious disease control. Current phenotypic and molecular assays could not comprehensively and accurately diagnose MTB, NTM, and drug resistance. Next-generation sequencing allows an “all-in-one” approach providing results on expected drug susceptibility testing (DST) and the genotype of NTM strains. In this study, targeted capture sequencing was used to analyze the genetic backgrounds of 4 MTB strains and 32 NTM pathogenic strains in 30 clinical samples, including 14 sputum specimens and 16 bronchoalveolar lavage fluid samples. Through comparing with other TB diagnostic tests, we proved that targeted capture sequencing could be used as a highly sensitive (91.3%) and accurate (83.3%) method to diagnose TB, as well as MGIT 960. Also, we identified 7 NTM strains in 11 patients; among them, seven patients were MTB/NTM co-affected, which indicated that it was a meaningful tool for the diagnosis and treatment of NTM infection diseases in clinic. However, based on a drug-resistant mutation library (1,325 drug resistance loci), only 9 drug resistance strains and 22 drug resistance loci were discovered, having considerable discordance with the drug-resistant results of MGIT 960. Our finding indicated that targeted capture sequencing approach was applicable for the comprehensive and accurate diagnosis of MTB and NTM. However, from data presented here, the DST results identified by next-generation sequencing (NGS) showed a relatively low consistency with MGIT 960, especially in sputum samples. Further work should be done to explore the reasons for low drug-resistance detection rate of NGS.
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Affiliation(s)
- Ya He
- Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ziying Gong
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China
| | - Xiaokai Zhao
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China
| | - Daoyun Zhang
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, China
| | - Zhongshun Zhang
- Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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27
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Yoshiyama T, Mitarai S, Takaki A, Aono A, Okumura M, Ohta K, Kato S. Multi-drug resistant tuberculosis with simultaneously acquired-drug resistance to bedaquiline and delamanid. Clin Infect Dis 2020; 73:2329-2331. [PMID: 32730621 DOI: 10.1093/cid/ciaa1064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/25/2020] [Indexed: 11/13/2022] Open
Abstract
This study is the first to report a clinical case of simultaneously acquired resistance to bedaquiline (BDQ) and delamanid (DLM). Whole genome sequencing revealed two nucleotide insertions (Rv0678 and fbiC) in the Mycobacterium tuberculosis isolate. The minimum inhibitory concentrations for BDQ and DLM were 0.25 µg/ml and >2.0 µg/ml, respectively.
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Affiliation(s)
- Takashi Yoshiyama
- Research institute of tuberculosis and Fukujuji hospital, Tokyo Japan
| | - Satoshi Mitarai
- Department of mycobacterial reference and research, Research institute of tuberculosis, Tokyo, Japan
| | - Akiko Takaki
- Department of mycobacterial reference and research, Research institute of tuberculosis, Tokyo, Japan
| | - Akio Aono
- Department of mycobacterial reference and research, Research institute of tuberculosis, Tokyo, Japan
| | - Masao Okumura
- Respiratory diseases center, Fukujuji hospital, Tokyo, Japan
| | | | - Seiya Kato
- Research institute of tuberculosis, Tokyo, Japan
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28
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Farhat MR, Sixsmith J, Calderon R, Hicks ND, Fortune SM, Murray M. Rifampicin and rifabutin resistance in 1003 Mycobacterium tuberculosis clinical isolates. J Antimicrob Chemother 2020; 74:1477-1483. [PMID: 30793747 DOI: 10.1093/jac/dkz048] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVES Drug-resistant TB remains a public health challenge. Rifamycins are among the most potent anti-TB drugs. They are known to target the RpoB subunit of RNA polymerase; however, our understanding of how rifamycin resistance is genetically encoded remains incomplete. Here we investigated rpoB genetic diversity and cross-resistance between the two rifamycin drugs rifampicin and rifabutin. METHODS We performed WGS of 1003 Mycobacterium tuberculosis clinical isolates and determined MICs of both rifamycin agents on 7H10 agar using the indirect proportion method. We generated rpoB mutants in a laboratory strain and measured their antibiotic susceptibility using the alamarBlue reduction assay. RESULTS Of the 1003 isolates, 766 were rifampicin resistant and 210 (27%) of these were rifabutin susceptible; 102/210 isolates had the rpoB mutation D435V (Escherichia coli D516V). Isolates with discordant resistance were 17.2 times more likely to harbour a D435V mutation than those resistant to both agents (OR 17.2, 95% CI 10.5-27.9, P value <10-40). Compared with WT, the D435V in vitro mutant had an increased IC50 of both rifamycins; however, in both cases to a lesser degree than the S450L (E. coli S531L) mutation. CONCLUSIONS The observation that the rpoB D435V mutation produces an increase in the IC50 of both drugs contrasts with findings from previous smaller studies that suggested that isolates with the D435V mutation remain rifabutin susceptible despite being rifampicin resistant. Our finding thus suggests that the recommended critical testing concentration for rifabutin should be revised.
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Affiliation(s)
- Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA, USA.,Division of Pulmonary and Critical Care, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, USA
| | - Jaimie Sixsmith
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | | | - Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA, USA.,Division of Global Health Equity, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA
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29
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Dohál M, Porvazník I, Pršo K, Rasmussen EM, Solovič I, Mokrý J. Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis. Tuberculosis (Edinb) 2020; 123:101946. [PMID: 32741530 DOI: 10.1016/j.tube.2020.101946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
Abstract
The numbers of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine resistance more quickly and precisely, than it is with the currently used phenotypic and genotypic methods. In recent years, technological advances have been made and the whole-genome sequencing (WGS) method has been introduced as a part of routine diagnostics in clinical laboratories. Comparing a wide range of mycobacterial genomic variations with a reference genome leads to a consistent evaluation of molecular-epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a wide range of anti-TB drugs. The quality of the obtained sequencing data is closely related to the type of sample and the method used for DNA extraction and sequencing library preparation. Moreover, the correct interpretation of results is also influenced by a bioinformatic data processing. A large number of bioinformatics pipelines are currently available, the sensitivity of which varies due to the different sizes of databases containing relevant mutations. This review focuses on the individual steps included in the sequencing workflow and factors that may affect the interpretation of final results.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia.
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia; Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Kristián Pršo
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
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Mokrousov I, Sinkov V, Vyazovaya A, Pasechnik O, Solovieva N, Khromova P, Zhuravlev V, Ogarkov O. Genomic signatures of drug resistance in highly resistant Mycobacterium tuberculosis strains of the early ancient sublineage of Beijing genotype in Russia. Int J Antimicrob Agents 2020; 56:106036. [PMID: 32485278 DOI: 10.1016/j.ijantimicag.2020.106036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 01/09/2023]
Abstract
The Mycobacterium tuberculosis Beijing genotype is a clinically and epidemiologically important lineage that is subdivided into ancient/ancestral and modern strains. In our previous study in western Siberia, we identified variable number of tandem repeats (VNTR)-based clusters within the early ancient sublineage of the Beijing genotype characterized by an unexpectedly high rate of extensive drug resistance (XDR). In the current study, next generation sequencing data were analysed to gain insight into genomic signatures underlying drug resistance of these strains. A total of 184 genomes of the Beijing early ancient sublineage from Russia (16), China (15), Japan (36), Korea (25), Vietnam (18), Thailand (73), and the USA (1) were used for phylogenetic analysis. The drug-resistant profile was deduced genotypically. The Russian isolates were distributed into two clusters and were all drug resistant, mainly pre-XDR and XDR. The largest of these clusters included only Russian isolates from remote locations in both Asian and European parts of the country. All its isolates had a quadruple drug resistance (to isoniazid, rifampin, ethambutol and streptomycin) due to the 6-mutation signature (KatG Ser315Thr, KatG Ile335Val, RpoB Ser450Leu, RpoC Asp485Asn, EmbB Gln497Arg, and RpsL Lys43Arg). In most samples, it was complemented with additional and different pncA, gyrA and rrs mutations leading to the pre-XDR/XDR genotype. Phylogenomic analysis indicates a distant origin of this Russian resistant cluster in the early 1970s but location and circumstances are yet to be clarified.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia.
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia
| | - Oksana Pasechnik
- Department of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
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Garzon-Chavez D, Garcia-Bereguiain MA, Mora-Pinargote C, Granda-Pardo JC, Leon-Benitez M, Franco-Sotomayor G, Trueba G, de Waard JH. Population structure and genetic diversity of Mycobacterium tuberculosis in Ecuador. Sci Rep 2020; 10:6237. [PMID: 32277077 PMCID: PMC7148308 DOI: 10.1038/s41598-020-62824-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis (TB) is a significant public health problem in Ecuador with an incidence of 43 per 100,000 inhabitants and an estimated multidrug-resistant-TB prevalence in all TB cases of 9%. Genotyping of Mycobacterium tuberculosis (MTBC) is important to understand regional transmission dynamics. This study aims to describe the main MTBC lineages and sublineages circulating in the country. A representative sample of 373 MTBC strains from 22 provinces of Ecuador, with data comprising geographic origin and drug susceptibility, were genotyped using 24 loci-MIRU-VNTR. For strains with an ambiguous sublineage designation, the lineage was confirmed by Regions of Difference analysis or by Whole Genome Sequencing. We show that lineage 4 is predominant in Ecuador (98.3% of the strains). Only 4 strains belong to lineages 2-sublineage Beijing and two strains to lineage 3-sublineage Delhi. Lineage 4 strains included sublineages LAM (45.7%), Haarlem (31.8%), S (13.1%), X (4.6%), Ghana (0.6%) and NEW (0.3%). The LAM sublineage showed the strongest association with antibiotic resistance. The X and S sublineages were found predominantly in the Coastal and the Andean regions respectively and the reason for the high prevalence of these strains in Ecuador should be addressed in future studies. Our database constitutes a tool for MIRU-VNTR pattern comparison of M. tuberculosis isolates for national and international epidemiologic studies and phylogenetic purposes.
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Affiliation(s)
- Daniel Garzon-Chavez
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- Instituto Nacional de Salud Pública e Investigación Leopoldo Izquieta Pérez, Guayaquil, Ecuador
| | - Miguel Angel Garcia-Bereguiain
- One Health Research Group. Universidad de las Américas, Quito, Ecuador.
- Laboratorio para Investigaciones Biomédicas. Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador.
| | - Carlos Mora-Pinargote
- Laboratorio para Investigaciones Biomédicas. Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | | | - Margarita Leon-Benitez
- Instituto Nacional de Salud Pública e Investigación Leopoldo Izquieta Pérez, Guayaquil, Ecuador
| | - Greta Franco-Sotomayor
- Instituto Nacional de Salud Pública e Investigación Leopoldo Izquieta Pérez, Guayaquil, Ecuador
- Facultad de Ciencias Médicas. Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Jacobus H de Waard
- One Health Research Group. Universidad de las Américas, Quito, Ecuador.
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Caracas, Venezuela.
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Acharya B, Acharya A, Gautam S, Ghimire SP, Mishra G, Parajuli N, Sapkota B. Advances in diagnosis of Tuberculosis: an update into molecular diagnosis of Mycobacterium tuberculosis. Mol Biol Rep 2020; 47:4065-4075. [DOI: 10.1007/s11033-020-05413-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/28/2020] [Indexed: 01/02/2023]
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Draft Genome Sequence of an Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis from Nepal. Microbiol Resour Announc 2020; 9:9/4/e01404-19. [PMID: 31974155 PMCID: PMC6979304 DOI: 10.1128/mra.01404-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Extensively drug-resistant (XDR) Mycobacterium tuberculosis has become a challenge to the treatment of tuberculosis (TB) in several countries, including Nepal. Here, we report for the first time the draft genome sequence of an isolate of XDR-TB collected in Nepal and describe single-nucleotide variations associated with its extensively drug-resistant phenotype. Extensively drug-resistant (XDR) Mycobacterium tuberculosis has become a challenge to the treatment of tuberculosis (TB) in several countries, including Nepal. Here, we report for the first time the draft genome sequence of an isolate of XDR-TB collected in Nepal and describe single-nucleotide variations associated with its extensively drug-resistant phenotype.
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Takii T, Seki K, Wakabayashi Y, Morishige Y, Sekizuka T, Yamashita A, Kato K, Uchimura K, Ohkado A, Keicho N, Mitarai S, Kuroda M, Kato S. Whole-genome sequencing-based epidemiological analysis of anti-tuberculosis drug resistance genes in Japan in 2007: Application of the Genome Research for Asian Tuberculosis (GReAT) database. Sci Rep 2019; 9:12823. [PMID: 31492902 PMCID: PMC6731343 DOI: 10.1038/s41598-019-49219-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/21/2019] [Indexed: 11/10/2022] Open
Abstract
We investigated the lineages of Mycobacterium tuberculosis (Mtb) isolates from the RYOKEN study in Japan in 2007 and the usefulness of genotypic drug susceptibility testing (DST) using the Genome Research for Asian Tuberculosis (GReAT) database. In total, 667 isolates were classified into lineage 1 (4.6%), lineage 2 (0.8%), lineage 2/Beijing (72.1%), lineage 3 (0.5%), and lineage 4 (22.0%). The nationality, gender, and age groups associated with the isolates assigned to lineage 1 were significantly different from those associated with other lineages. In particular, isolates of lineage 1.2.1 (EAI2) formed sub-clusters and included a 2,316-bp deletion in the genome. The proportion of the isolates resistant to at least one anti-tuberculosis (TB) drug was 10.8%, as determined by either the genotypic or phenotypic method of DST. However, the sensitivities to isoniazid, streptomycin, and ethambutol determined by the genotypic method were low. Thus, unidentified mutations in the genome responsible for drug resistance were explored, revealing previously unreported mutations in the katG, gid, and embB genes. This is the first nationwide report of whole-genome analysis of TB in Japan.
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Affiliation(s)
- Takemasa Takii
- Department of Mycobacteriology, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan.
| | - Kouhei Seki
- Department of Mycobacteriology, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
| | - Yasutaka Wakabayashi
- Department of Mycobacteriology, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
| | - Yuta Morishige
- Department of Mycobacteriology, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Kengo Kato
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Kazuhiro Uchimura
- Department of Epidemiology and Clinical Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
| | - Akihiro Ohkado
- Department of Epidemiology and Clinical Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
| | - Naoto Keicho
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
| | - Satoshi Mitarai
- Department of Mycobacteriology, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Seiya Kato
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo, 204-8533, Japan
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Kuroda M, Sekizuka T, Matsui H, Ohsuga J, Ohshima T, Hanaki H. IS 256-Mediated Overexpression of the WalKR Two-Component System Regulon Contributes to Reduced Vancomycin Susceptibility in a Staphylococcus aureus Clinical Isolate. Front Microbiol 2019; 10:1882. [PMID: 31474962 PMCID: PMC6702299 DOI: 10.3389/fmicb.2019.01882] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/30/2019] [Indexed: 11/13/2022] Open
Abstract
Vancomycin (VAN)-intermediate-resistant Staphylococcus aureus (VISA) is continually isolated globally, with a systematic review suggesting a prevalence of 2% in all blood culture samples. Most VISA strains exhibit common characteristics, such as a thickened cell wall, reduced autolysis, and attenuated virulence. Here, based on multi-omics approaches, we have characterized clinical VISA isolates obtained through prolonged antimicrobial treatment in a single patient. All VISA isolates were isogenic, based on multi-locus sequence typing (MLST) ST5, SCCmec type II (2A), and spa type t17639. Core-genome single nucleotide variations (SNVs) found among thirteen isolates during the patient's hospitalization, indicated clonality, but not notable genetic features of the VISA phenotype. We determined the complete genome sequence of VAN-susceptible strain KG-03 (minimum inhibitory concentration [MIC] 0.5 μg/mL) and two VISA strains, KG-18 and KG-22 (MIC 8.0 and 4.0 μg/mL, respectively). Comparative genome analysis showed remarkable strain-specific IS256 insertions. RNA-Seq transcriptome analysis revealed IS256-mediated overexpression of the walKR two-component system in VISA KG-18, possibly leading to modulation of cell wall integrity (lytM and sceD) and surface charge (mprF and dltABCD). In addition, secretome analysis indicated that cell wall-anchored proteins (Protein A, SasG, and SdrD) were significantly decreased. KG-18 and KG-22 exhibit thickened cell wall, and are relatively resistant to lysostaphin, which cleaves a staphylococcus-unique pentaglycine chain in the peptidoglycan. We conclude that KG-18 achieved reduced susceptibility to VAN by IS256-mediated WalKR overexpression, leading to a markedly thickened cell wall for trapping free VAN molecules with redundant D-Ala-D-Ala targets. In addition, a positively charged surface with lysyl-phosphatidylglycerol and depolarization of wall teichoic acid could contribute to inhibiting cationic daptomycin and VAN antimicrobial activity. Comparative omics approaches in this study strongly suggest that fully complete and annotated genome sequences will be indispensable for characterizing overall VISA phenotype.
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Affiliation(s)
- Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku, Japan
| | - Hidehito Matsui
- Infection Control Research Center, Kitasato University, Minato-ku, Japan
| | - Jun Ohsuga
- Department of Clinical Laboratory, Tokai University Oiso Hospital, Kanagawa, Japan
| | - Toshio Ohshima
- Department of Medical Risk and Crisis Management, Chiba Institute of Science, Chiba, Japan
| | - Hideaki Hanaki
- Infection Control Research Center, Kitasato University, Minato-ku, Japan
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Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
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GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nat Commun 2019; 10:2128. [PMID: 31086182 PMCID: PMC6513847 DOI: 10.1038/s41467-019-10110-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/18/2019] [Indexed: 01/28/2023] Open
Abstract
Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole-genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We evaluate genome-wide associations between mutations in MTB genes or non-coding regions and resistance, followed by validation in an independent data set of 792 patient isolates. We confirm associations at 13 non-canonical loci, with two involving non-coding regions. Promoter mutations are measured to have smaller average effects on resistance than gene body mutations. We estimate the heritability of the resistance phenotype to 11 anti-TB drugs and identify a lower than expected contribution from known resistance genes. This study highlights the complexity of the genomic mechanisms associated with the MTB resistance phenotype, including the relatively large number of potentially causal loci, and emphasizes the contribution of the non-coding portion of the genome.
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Prasanna A, Niranjan V. Classification of Mycobacterium tuberculosis DR, MDR,XDR Isolates and Identification of Signature MutationPattern of Drug Resistance. Bioinformation 2019; 15:261-268. [PMID: 31285643 PMCID: PMC6599436 DOI: 10.6026/97320630015261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/15/2019] [Accepted: 04/15/2019] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis - a global threat, the recent breakout in MDR-TB and XDR-TB has challenged researchers in diagnosis to provide effective treatment. The main objective to combat drug resistance is to provide rapid, reliable and sensitive diagnostic methods in health care centres. This study focuses on development of an effective pipeline to identify drug resistance mutations in whole genome data of Mycobacterium tuberculosis utilizing the Next Generation Sequencing approach and classification of drug resistance strains based on genetic markers obtained from TGS-TB, tbvar and TBDReamDB. 74 isolates are characterized into 20 DR-TB, 16 MDR-TB, 16 XDR-TB and 6 nonresistant strains based on known drug resistance genetic markers. Results provide mutation pattern for each of the classified strains and profiling of drug resistance to the group of anti-TB drugs. The presence of specific mutation causing resistance to a drug will help set the dosage levels which play an important role in the treatment. Findings on amino acid changes and its respective codon positions in candidate genes will provide insights in drug sensitivity and a way for discovery of potent drugs. The implementation of these approaches in clinical setting provides rapid and sensitive diagnostics to combat the emerging drug resistance.
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Affiliation(s)
- Akshatha Prasanna
- Department of Biotechnology, Rashtreeya Vidyalaya College of Engineering,Mysuru road,Bangaluru,India
| | - Vidya Niranjan
- Department of Biotechnology, Rashtreeya Vidyalaya College of Engineering,Mysuru road,Bangaluru,India
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Gautam SS, Kc R, Leong KW, Mac Aogáin M, O'Toole RF. A step-by-step beginner's protocol for whole genome sequencing of human bacterial pathogens. J Biol Methods 2019; 6:e110. [PMID: 31453259 PMCID: PMC6706130 DOI: 10.14440/jbm.2019.276] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/13/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023] Open
Abstract
Bacterial whole genome sequencing (WGS) is becoming a widely-used technique in research, clinical diagnostic, and public health laboratories. It enables high resolution characterization of bacterial pathogens in terms of properties that include antibiotic resistance, molecular epidemiology, and virulence. The introduction of next-generation sequencing instrumentation has made WGS attainable in terms of costs. However, the lack of a beginner’s protocol for WGS still represents a barrier to its adoption in some settings. Here, we present detailed step-by-step methods for obtaining WGS data from a range of different bacteria (Gram-positive, Gram-negative, and acid-fast) using the Illumina platform. Modifications have been performed with respect to DNA extraction and library normalization to maximize the output from the laboratory consumables invested. The protocol represents a simplified and reproducible method for producing high quality sequencing data. The key advantages of this protocol include: simplicity of the protocol for users with no prior genome sequencing experience and reproducibility of the protocol across a wide range of bacteria.
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Affiliation(s)
- Sanjay S Gautam
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7001, Australia
| | - Rajendra Kc
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7001, Australia
| | - Kelvin Wc Leong
- School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Victoria 3690, Australia
| | - Micheál Mac Aogáin
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland
| | - Ronan F O'Toole
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS 7001, Australia.,Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland.,School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Victoria 3690, Australia
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40
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Bouzouita I, Cabibbe AM, Trovato A, Daroui H, Ghariani A, Midouni B, Essalah L, Mehiri E, Cirillo DM, Saidi LS. Whole-Genome Sequencing of Drug-Resistant Mycobacterium tuberculosis Strains, Tunisia, 2012-2016. Emerg Infect Dis 2019; 25:538-546. [PMID: 30789128 PMCID: PMC6390741 DOI: 10.3201/eid2503.181370] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To investigate transmission of drug-resistant strains of Mycobacterium tuberculosis in Tunisia, we performed whole-genome sequencing on 46 multidrug-resistant strains isolated during 2012-2016. Core-genome multilocus sequence typing grouped 30 strains (65.2%) into 3 clusters, indicating extensive recent transmission and Haarlem clone predominance. Whole-genome sequencing might help public health services undertake appropriate control actions.
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Iwamoto T, Murase Y, Yoshida S, Aono A, Kuroda M, Sekizuka T, Yamashita A, Kato K, Takii T, Arikawa K, Kato S, Mitarai S. Overcoming the pitfalls of automatic interpretation of whole genome sequencing data by online tools for the prediction of pyrazinamide resistance in Mycobacterium tuberculosis. PLoS One 2019; 14:e0212798. [PMID: 30817803 PMCID: PMC6394917 DOI: 10.1371/journal.pone.0212798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/09/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Automated online software tools that analyse whole genome sequencing (WGS) data without the need for bioinformatics expertise can motivate the implementation of WGS-based molecular drug susceptibility testing (DST) in routine diagnostic settings for tuberculosis (TB). Pyrazinamide (PZA) is a key drug for current and future TB treatment regimens; however, it was reported that predictive power for PZA resistance by the available tools is low. Therefore, this low predictive power may make users hesitant to use the tools. This study aimed to elucidate why and to uncover the real performance of the tools when taking into account their variation calling lists (manual inspection), not just their automated reporting system (default setting) that was evaluated by previous studies. METHODS WGS data from 191 datasets comprising 108 PZA-resistant and 83 susceptible strains were used to evaluate the potential performance of the available online tools (TB Profiler, TGS-TB, PhyResSE, and CASTB) for predicting phenotypic PZA resistance. RESULTS When taking into consideration the variation calling lists, 73 variants in total (47 non-synonymous mutations and 26 indels) in pncA were detected by TGS-TB and PhyResSE, covering all mutations for the 108 PZA-resistant strains. The 73 variants were confirmed by Sanger sequencing. TB Profiler also detected all but three complete loss, two large deletion at the 3'-end, and one relatively large insertion of pncA. On the other hand, many of the 73 variants were lacking in the automated reporting systems except by TGS-TB; of these variants, CASTB detected only 20. By applying the 'non-wild type sequence' approach for predicting PZA resistance, accuracy of the results significantly improved compared with that of the automated results obtained by each tool. CONCLUSION Users can obtain more accurate predictions for PZA resistance than previously reported by manually checking the results and applying the 'non-wild type sequence' approach.
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Affiliation(s)
- Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe City, Japan
- * E-mail: (TI); (SM)
| | - Yoshiro Murase
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Akio Aono
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kengo Kato
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Takemasa Takii
- Molecular Epidemiology Division, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe City, Japan
| | - Seiya Kato
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Satoshi Mitarai
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
- Basic Mycobacteriosis, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki City, Nagasaki, Japan
- * E-mail: (TI); (SM)
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Min J, Kim K, Choi H, Kang ES, Shin YM, An JY, Choe KH, Lee KM. Investigation of false-positive Mycobacterium tuberculosis culture tests using whole genome sequencing. Ann Thorac Med 2019; 14:90-93. [PMID: 30745941 PMCID: PMC6341868 DOI: 10.4103/atm.atm_184_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Although accurate identification of Mycobacterium tuberculosis is the gold standard for tuberculosis (TB) diagnosis, there have been several reports of false-positive results. After identifying a sudden increase in extensively drug-resistant TB, false-positive mycobacterial culture tests were suspected, and we contacted the supranational reference center for molecular typing. In silico genotyping tests showed that isolates from all five patients had an identical genotype pattern, and all harbored the same Beijing strain based on sequence-based phylogenic analysis and drug-resistant single nucleotide polymorphisms (SNPs) analysis. We also used whole genome sequencing (WGS) to compare the SNPs of all isolates with a reference genome, and all were identical. We adapted WGS to efficiently detect false-positive MTB culture tests.
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Affiliation(s)
- Jinsoo Min
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Republic of Korea
| | - Kyungjong Kim
- Department of Research and Development, Korean Institute of Tuberculosis, Osong, Cheongju, Republic of Korea
| | - Hongjo Choi
- Department of Research and Development, Korean Institute of Tuberculosis, Osong, Cheongju, Republic of Korea
| | - Eun Seok Kang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Yoon Mi Shin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Jin Young An
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea.,Department of Internal Medicine, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Kang Hyeon Choe
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea.,Department of Internal Medicine, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Ki Man Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea.,Department of Internal Medicine, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
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Panossian B, Salloum T, Araj GF, Khazen G, Tokajian S. First insights on the genetic diversity of MDR Mycobacterium tuberculosis in Lebanon. BMC Infect Dis 2018; 18:710. [PMID: 30594126 PMCID: PMC6311033 DOI: 10.1186/s12879-018-3626-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/17/2018] [Indexed: 11/24/2022] Open
Abstract
Background Lebanon hosts a heterogeneous population coming from underdeveloped and developing countries, resulting in increasing incidences of tuberculosis over the past years. The genetic heterogeneity and lineages associated with tuberculosis, along with their resistance determinants have not been studied at the genomic level previously in the region. Methods Isolates were recovered from the American University of Beirut Medical Center (AUBMC). Antimicrobial susceptibility profiles were determined using the MGIT automated system for the first-line drugs at AUBMC, while second-line drug susceptibility was tested at Mayo Clinic Laboratories. Whole Genome Sequencing (WGS) was performed to classify mycobacterial lineages and highlight single nucleotide mutations causing resistance to both 1st line and 2nd line antimicrobials. wgSNP analysis provided insights on the phylogeny of the isolates along with spoligotyping and core genomic SNVs, IS6110 insertion sites, and variable number tandem repeats (VNTR). Results The analyzed isolates carry distinct resistance determinants to isoniazid, rifampicin, ethambutol, quinolones, and streptomycin. The isolates belonged to different lineages including the Euro/American lineage (Lineage 4) (53.8%), M. bovis (15.4%) and Delhi/Central Asia (Lineage 1) (15.4%), Beijing/East Asia (Lineage 2) (7.7%), and East Africa/Indian Ocean lineage (Lineage 3) (7.7%) showing great phylogenetic differences at the genomic level. Conclusions The population diversity in Lebanon holds an equally diverse and uncharacterized population of drug resistant mycobacteria. To achieve the WHO “END-TB” milestones of 2025 and 2035, Lebanon must decrease TB incidences by 95% in the next decade. This can only be done through WGS-based patient centered diagnosis with higher throughput and genomic resolution to improve treatment outcomes and to monitor transmission patterns. Electronic supplementary material The online version of this article (10.1186/s12879-018-3626-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Balig Panossian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, P.O. Box 36, Byblos, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, P.O. Box 36, Byblos, Lebanon
| | - George F Araj
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Georges Khazen
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, P.O. Box 36, Byblos, Lebanon.
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Ezewudo M, Borens A, Chiner-Oms Á, Miotto P, Chindelevitch L, Starks AM, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl TA, Warren RM, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo DM, Schito M, Rodwell TC, Posey J. Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Sci Rep 2018; 8:15382. [PMID: 30337678 PMCID: PMC6194142 DOI: 10.1038/s41598-018-33731-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022] Open
Abstract
Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.
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Affiliation(s)
- Matthew Ezewudo
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Amanda Borens
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Álvaro Chiner-Oms
- Joint unit Infection and Public Health FISABIO-CSISP/University of Valencia, Institute of integrative Systems Biology, Valencia, Spain
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Leonid Chindelevitch
- School of Computing Science, Simon Fraser University, 8888 University Ave, Burnaby, BC, V5A 1S6, Canada
| | - Angela M Starks
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA
| | - Debra Hanna
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Richard Liwski
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Matteo Zignol
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Christopher Gilpin
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Borstel, Borstel, Germany
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Priority area Infections, Research Center Borstel, Borstel, Germany
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Derrick Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | | | - Sven Hoffner
- Department of Public Health Sciences, Karolinska institute, Stockholm, Sweden
| | | | - Iñaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia (IBV-CSIC), Street Jaime Roig 11. P.O., 4010, Valencia, Spain
| | - David M Engelthaler
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste 106, Flagstaff, AZ, 86005, USA
| | - David Alland
- Center for Emerging Pathogens, Rutgers-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, USA
| | - Leen Rigouts
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christoph Lange
- Division of Clinical Infectious Diseases and German Center for Infection Research Tuberculosis Unit, Research Center Borstel, Borstel, Germany
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Ruth McNerney
- Department of Medicine, Division of Pulmonology, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Marco Schito
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, CA, USA.,The Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA.
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Shi J, Zheng D, Zhu Y, Ma X, Wang S, Li H, Xing J. Role of MIRU-VNTR and spoligotyping in assessing the genetic diversity of Mycobacterium tuberculosis in Henan Province, China. BMC Infect Dis 2018; 18:447. [PMID: 30176820 PMCID: PMC6122615 DOI: 10.1186/s12879-018-3351-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 08/21/2018] [Indexed: 01/31/2023] Open
Abstract
Background Tuberculosis remains a serious threat to human health as an infectious disease in China. Henan, a most populated province in China, has a high incidence of tuberculosis (TB). Though the genetic diversity of Mycobacterium tuberculosis (MTB) has been investigated in many regions, there have been only a few studies on the molecular characteristics and drug resistance phenotypes in Henan. This is the first study on the genetic profile of MTB from Henan. Methods A total of 668 MTB isolates from various areas were genotyped with spoligotyping and 26-locus MIRU-VNTR (classical 24-locus MIRU-VNTR and 2 other loci). The association between TB spoligotype signatures and drug-resistant profiles was analysed. Results Our data revealed that MTB isolates circulating in Henan had a high degree of genetic variation. The Beijing family was the most predominant genotype (83.53%,n = 558), and the typical Beijing type(ST1) was the major sublineage (81.73%,n = 546). In total,668 isolates were divided into 567 different types, forming 38 clusters (2–15 isolates per cluster), and 529 unique types by 26-locus MIRU-VNTR analysis. There was no correlation between the Beijing family and gender, age at diagnosis or treatment history, whereas the Beijing family was significantly associated with all four first-line drug resistance and multidrug-resistant phenotypes. For these samples, 15 of 26 MIRU-VNTR loci had high or moderate discriminatory power according to the Hunter-Gaston discriminatory index. A combination of the 10 most polymorphic loci had similar discriminatory power as the 26-locus set. Conclusion The Beijing genotype is the most prevalent family. Ten-locus MIRU-VNTR in combination with spoligotyping can efficiently classify the molecular type of MTB in Henan Province. Electronic supplementary material The online version of this article (10.1186/s12879-018-3351-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Shi
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China.
| | - Danwei Zheng
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Yankun Zhu
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Xiaoguang Ma
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Shaohua Wang
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Hui Li
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China.
| | - Jin Xing
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
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Roa MB, Tablizo FA, Morado EKD, Cunanan LF, Uy IDC, Ng KCS, Manalastas-Cantos KG, Reyes JM, Ganchua SKC, Ang CF, Kato-Maeda M, Cattamanchi A, Karaoz U, Destura RV, Lluisma AO. Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines. J Glob Antimicrob Resist 2018; 15:239-245. [PMID: 30130640 DOI: 10.1016/j.jgar.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/06/2018] [Accepted: 08/11/2018] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES Thousands of cases of multidrug-resistant tuberculosis (TB) have been observed in the Philippines, but studies on the Mycobacterium tuberculosis (MTB) genotypes that underlie the observed drug resistance profiles are lacking. This study aimed to analyse the whole genomes of clinical MTB isolates representing various resistance profiles to identify single nucleotide polymorphisms (SNPs) in resistance-associated genes. METHODS The genomes of ten MTB isolates cultured from banked sputum sources were sequenced. Bioinformatics analysis consisted of assembly, annotation and SNP identification in genes reported to be associated with resistance to isoniazid (INH), rifampicin (RIF), ethambutol (ETH), streptomycin, pyrazinamide (PZA) and fluoroquinolones (FQs). RESULTS The draft assemblies covered an average of 97.08% of the expected genome size. Seven of the ten isolates belonged to the Indo-Oceanic lineage/EA12-Manila clade. Two isolates were classified into the Euro-American lineage, whilst the pre-XDR (pre-extensively drug-resistant) isolate was classified under the East Asian/Beijing clade. The SNPs katG Ser315Thr, rpoB Ser450Leu and embB Met306Val were found in INH- (4/7), RIF- (3/6) and ETH-resistant (2/6) isolates, respectively, but not in susceptible isolates. Mutations in the inhA promoter and in the pncA and gyrA genes known to be involved in resistance to INH, PZA and FQs, respectively, were also identified. CONCLUSIONS This study represents the first effort to investigate the whole genomes of Philippine clinical strains of MTB exhibiting various multidrug resistance profiles. Whole-genome data can provide valuable insights to the mechanistic and epidemiological qualities of TB in a high-burden setting such as the Philippines.
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Affiliation(s)
- Marylette B Roa
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Francis A Tablizo
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - El King D Morado
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Lovette F Cunanan
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Iris Diana C Uy
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Kamela Charmaine S Ng
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | | | - Joeriggo M Reyes
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Sharie Keanne C Ganchua
- Institute of Molecular Biology and Biochemistry, National Institutes of Health, University of the Philippines-Manila, Ermita, Manila 1000, Philippines
| | - Concepcion F Ang
- Section of Infectious Diseases, Philippine General Hospital, University of the Philippines-Manila, Ermita, Manila 1000, Philippines
| | - Midori Kato-Maeda
- University of California, San Francisco, San Francisco General Hospital, Division of Pulmonary and Critical Care Medicine, 1001 Potrero Avenue, Mail Box 0841, San Francisco, CA 94110, USA
| | - Adithya Cattamanchi
- University of California, San Francisco, San Francisco General Hospital, Division of Pulmonary and Critical Care Medicine, 1001 Potrero Avenue, Mail Box 0841, San Francisco, CA 94110, USA
| | - Ulas Karaoz
- Climate and Ecosystems Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Raul V Destura
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines; Institute of Molecular Biology and Biochemistry, National Institutes of Health, University of the Philippines-Manila, Ermita, Manila 1000, Philippines.
| | - Arturo O Lluisma
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines; Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines.
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Rajwani R, Shehzad S, Siu GKH. MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis. PeerJ 2018; 6:e5090. [PMID: 30018852 PMCID: PMC6045920 DOI: 10.7717/peerj.5090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022] Open
Abstract
Background Tuberculosis (TB) resulted in an estimated 1.7 million deaths in the year 2016. The disease is caused by the members of Mycobacterium tuberculosis complex, which includes Mycobacterium tuberculosis, Mycobacterium bovis and other closely related TB causing organisms. In order to understand the epidemiological dynamics of TB, national TB control programs often conduct standardized genotyping at 24 Mycobacterial-Interspersed-Repetitive-Units (MIRU)-Variable-Number-of-Tandem-Repeats (VNTR) loci. With the advent of next generation sequencing technology, whole-genome sequencing (WGS) has been widely used for studying TB transmission. However, an open-source software that can connect WGS and MIRU-VNTR typing is currently unavailable, which hinders interlaboratory communication. In this manuscript, we introduce the MIRU-profiler program which could be used for prediction of MIRU-VNTR profile from WGS of M. tuberculosis. Implementation The MIRU-profiler is implemented in shell scripting language and depends on EMBOSS software. The in-silico workflow of MIRU-profiler is similar to those described in the laboratory manuals for genotyping M. tuberculosis. Given an input genome sequence, the MIRU-profiler computes alleles at the standard 24-loci based on in-silico PCR amplicon lengths. The final output is a tab-delimited text file detailing the 24-loci MIRU-VNTR pattern of the input sequence. Validation The MIRU-profiler was validated on four datasets: complete genomes from NCBI-GenBank (n = 11), complete genomes for locally isolated strains sequenced using PacBio (n = 4), complete genomes for BCG vaccine strains (n = 2) and draft genomes based on 250 bp paired-end Illumina reads (n = 106). Results The digital MIRU-VNTR results were identical to the experimental genotyping results for complete genomes of locally isolated strains, BCG vaccine strains and five out of 11 genomes from the NCBI-GenBank. For draft genomes based on short Illumina reads, 21 out of 24 loci were inferred with a high accuracy, while a number of inaccuracies were recorded for three specific loci (ETRA, QUB11b and QUB26). One of the unique features of the MIRU-profiler was its ability to process multiple genomes in a batch. This feature was tested on all complete M. tuberculosis genome (n = 157), for which results were successfully obtained in approximately 14 min. Conclusion The MIRU-profiler is a rapid tool for inference of digital MIRU-VNTR profile from the assembled genome sequences. The tool can accurately infer repeat numbers at the standard 24 or 21/24 MIRU-VNTR loci from the complete or draft genomes respectively. Thus, the tool is expected to bridge the communication gap between the laboratories using WGS and those using the conventional MIRU-VNTR typing.
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Affiliation(s)
- Rahim Rajwani
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China
| | - Sheeba Shehzad
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China
| | - Gilman Kit Hang Siu
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China
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Morimoto K, Aono A, Murase Y, Sekizuka T, Kurashima A, Takaki A, Sasaki Y, Igarashi Y, Chikamatsu K, Goto H, Yamada H, Kuroda M, Mitarai S. Prevention of aerosol isolation of nontuberculous mycobacterium from the patient's bathroom. ERJ Open Res 2018; 4:00150-2017. [PMID: 29977902 PMCID: PMC6028744 DOI: 10.1183/23120541.00150-2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/29/2018] [Indexed: 12/04/2022] Open
Abstract
Recent clinical studies have revealed that reappearance of the same nontuberculous mycobacterium (NTM) infection is common after successful standard treatment [1, 2]. Using pulsed-field gel electrophoresis analysis, Wallaceet al. [1] found that ∼75% of Mycobacterium avium-intracellulare complex (MAC) isolates identified after successful treatment are the result of reinfection. According to a recent study conducted by Kohet al. [2] using repetitive sequence-based PCR analysis, all re-identified M. abscessus subsp. abscessus isolates had a unique genotype. Therefore, patients with NTM are exposed to large amounts of microbes in their daily lives, particularly in cases of reinfection. Reinfection of nontuberculous mycobacterium pulmonary disease may be caused by identical and not different genotypeshttp://ow.ly/62cH30krdpa
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Affiliation(s)
- Kozo Morimoto
- Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan.,Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan.,Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan.,Both authors contributed equally
| | - Akio Aono
- Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan.,Both authors contributed equally
| | - Yoshiro Murase
- Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Atsuyuki Kurashima
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Akiko Takaki
- Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yuka Sasaki
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yuriko Igarashi
- Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Kinuyo Chikamatsu
- Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Hajime Goto
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Hiroyuki Yamada
- Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoshi Mitarai
- Dept of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
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49
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A molecular epidemiological analysis of tuberculosis trends in South Korea. Tuberculosis (Edinb) 2018; 111:127-134. [PMID: 30029897 DOI: 10.1016/j.tube.2018.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/25/2018] [Accepted: 06/05/2018] [Indexed: 11/24/2022]
Abstract
Molecular epidemiological data are needed to assess tuberculosis (TB)-management policy outcomes in South Korea. IS6110 restriction fragment-length polymorphism (IS6110-RFLP) and mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) analyses are major molecular epidemiological tools for investigating the transmission or reactivation of active TB. Here, we determined trends in the clustering rate (i.e., the prevalence of Mycobacterium tuberculosis isolates with identical genotype patterns) of active TB and related differences between the 1990s and 2000s in Korea. M. tuberculosis isolates (1,007) of nationwide origins were analyzed by IS6110-RFLP and 24-locus standardized MIRU-VNTR genotyping. The clustering rate was measured by IS6110-RFLP, 24-locus MIRU-VNTR, and both analytical methods in combination. IS6110-RFLP, 24-locus MIRU-VNTR typing, and the combined method revealed 882, 754, and 983 distinct profiles; 809, 651, and 961 unique isolates; and 198, 356, and 46 clustered isolates grouped into 73, 103, and 22 clusters, respectively. In addition, we confirmed that the clustering rates in the 2000s decreased by 11.2%, 2.1%, and 3.1% relative to that in the 1990s using the three methods, respectively. Furthermore, in multivariate analysis, the younger-age group (<30) clustered more frequently than the older-age group (>50), based on all the three methods. Our study is the first report to provide nationwide molecular epidemiological information on TB in Korea.
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50
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Kimura M, Araoka H, Baba H, Okada C, Murase Y, Takaki A, Mitarai S, Yoneyama A. First case of sexually transmitted asymptomatic female genital tuberculosis from spousal epididymal tuberculosis diagnosed by active screening. Int J Infect Dis 2018; 73:60-62. [PMID: 29879525 DOI: 10.1016/j.ijid.2018.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis screening was performed for a healthy asymptomatic woman to determine whether she had been infected with active genital tuberculosis via sexual intercourse with her husband who had epididymal tuberculosis. Vaginal swab culture yielded Mycobacterium tuberculosis. Furthermore, whole genome sequencing revealed that the two causative isolates were genetically identical. This appears to be the first report on the sexual transmission of genital tuberculosis from a man to an asymptomatic woman, detected by active screening for genital tuberculosis and molecular analysis, including whole genome sequencing. Active screening for genital tuberculosis in the female partner should be considered soon after diagnosis of male genital tuberculosis, even when the female partner is asymptomatic.
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Affiliation(s)
- Muneyoshi Kimura
- Department of Infectious Diseases, Toranomon Hospital, Tokyo, Japan.
| | - Hideki Araoka
- Department of Infectious Diseases, Toranomon Hospital, Tokyo, Japan; Okinaka Memorial Institute for Medical Research, Tokyo, Japan
| | - Hiromi Baba
- Department of Infectious Diseases, Toranomon Hospital, Tokyo, Japan
| | - Chikako Okada
- Department of Infectious Diseases, Toranomon Hospital, Tokyo, Japan
| | - Yoshiro Murase
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Akiko Takaki
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Akiko Yoneyama
- Department of Infectious Diseases, Toranomon Hospital, Tokyo, Japan
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