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Li M, Zhang Y, Wu Z, Jiang Y, Sun R, Yang J, Li J, Lin H, Zhang R, Jiang Q, Wang L, Wu X, Yu F, Yuan J, Yang C, Shen X. Transmission of fluoroquinolones resistance among multidrug-resistant tuberculosis in Shanghai, China: a retrospective population-based genomic epidemiology study. Emerg Microbes Infect 2024; 13:2302837. [PMID: 38205528 PMCID: PMC10810664 DOI: 10.1080/22221751.2024.2302837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Fluoroquinolones (FQ) are essential for the treatment of multidrug-resistant tuberculosis (MDR-TB). The FQ resistance (FQ-R) rate in MDR-TB in China and its risk factors remain poorly understood. We conducted a retrospective, population-based genomic epidemiology study of MDR-TB patients in Shanghai, China, from 2009 to 2018. A genomic cluster was defined as strains with genetic distances ≤ 12 single nucleotide polymorphisms. The transmitted FQ-R was defined as the same FQ resistance-conferring mutations shared by ≥ 2 strains in a genomic cluster. We used multivariable logistic regression analysis to identify the risk factors for drug resistance. Among the total 850 MDR-TB patients included in the study, 72.8% (619/850) were male, the median age was 39 (interquartile range 28, 55) years, 52.7% (448/850) were migrants, and 34.5% (293/850) were previously treated patients. Most of the MDR-TB strains belong to the Beijing lineage (91.7%, 779/850). Overall, the genotypic resistance rate of FQ was 34.7% (295/850), and 47.1% (139/295) FQ-R patients were in genomic clusters, of which 98 (33.2%, 98/295) were presumed as transmitted FQ-R. Patients with treatment-naïve (aOR = 1.84; 95% CI: 1.09, 3.16), diagnosed in a district-level hospital (aOR = 2.69; 95% CI: 1.56, 4.75), and streptomycin resistance (aOR = 3.69; 95% CI: 1.65, 9.42) were significantly associated with the transmission of FQ-R. In summary, the prevalence of FQ-R among MDR-TB patients was high in Shanghai, and at least one-third were transmitted. Enforced interventions including surveillance of FQ drug susceptibility testing and screening among MDR-TB before initiation of treatment were urgently needed.
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Affiliation(s)
- Minjuan Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Guangdong, People’s Republic of China
| | - Yangyi Zhang
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, People’s Republic of China
| | - Zheyuan Wu
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
| | - Yuan Jiang
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
| | - Ruoyao Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Guangdong, People’s Republic of China
| | - Jinghui Yang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Jing Li
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
| | - Honghua Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Guangdong, People’s Republic of China
| | - Rui Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Guangdong, People’s Republic of China
| | - Qi Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, People’s Republic of China
| | - Lili Wang
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
| | - Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Jianhui Yuan
- Nanshan District Center for Disease Control and Prevention, Shenzhen, People’s Republic of China
| | - Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Guangdong, People’s Republic of China
- Nanshan District Center for Disease Control and Prevention, Shenzhen, People’s Republic of China
| | - Xin Shen
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
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Feng L, He W, Song Z, Zhao B, Teng C, Liu E, Zhu H, Pei S, Liu L, Song Y, Zheng Y, Liu X, Zhao Y, Ou X. Drug-Resistant Profiles and Genetic Diversity of Mycobacterium Tuberculosis Revealed by Whole-Genome Sequencing in Hinggan League of Inner Mongolia, China. Infect Drug Resist 2024; 17:3089-3100. [PMID: 39050828 PMCID: PMC11268717 DOI: 10.2147/idr.s466197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
Background Tuberculosis remains a major public health concern in China, with varying prevalence and drug resistance profiles across regions. This study explores the genetic diversity and drug-resistant profiles of MTB strains in Hinggan League, a high TB burden in Inner Mongolia, China. Methods This population-based retrospective study, encompassing all culture-positive TB cases from Jun. 2021 to Jun. 2023 in Hinggan League. Drug resistant profiles and genetic diversity of MTB strains were assessed using phenotypic drug susceptibility testing and whole-genome sequencing. Risk factors associated with drug resistance were analyzed using univariate and multivariate logistic regression models. Results A total of 211 MTB strains were recovered successfully and included into final analysis. Lineage 2.2.1 (88.6%, 187/211) was the dominant sub-lineage, followed by lineage 4.5 (7.1%, 15/211) and lineage 4.4 (4.3%, 9/211). MTB strains exhibited the highest resistance rates to isoniazid (16.1%, 34/211), followed by rifampicin (10.0, 21/211). In addition, the MTB strains also showed relatively high rates of resistance against new and repurposed anti-TB drugs, with resistant rates of 2.4% (5/211) to delamanid and 1.9% (4/211) to bedaquiline. Overall, 25.6% (54/211) of MTB strains were DR-TB, and 14 MTB strains met the definition of MDR-TB, including 7 strains of simple-MDR-TB, 5 of pre-XDR-TB, and 2 of XDR-TB. Genetic analysis revealed that the dominant mutations of isoniazid-, rifampin-, ethambutol-, levofloxacin-/moxifloxacin-, and ethionamide- resistance were katG_Ser315Thr(46.4%), rpoB_Ser450Leu (47.4%), embB_Met306Val (25.0%), gyrA_Asp94Ala (40.0%), and fabG1_c15t (42.9%), respectively. Previously treated patients (AOR = 2.015, 95% CI: 1.052-4.210) and male patients (AOR = 3.858, 95% CI: 1.416-10.511) were identified as independent risk factors associated with DR-TB. Conclusion Our study offers crucial insights into the genetic diversity and drug-resistant profiles of TB strains circulating in Hinggan League. These findings are valuable for DR-TB surveillance and for guiding treatment regimens and public health interventions in the region.
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Affiliation(s)
- Liping Feng
- Department of Microbiology, Hinggan League Center for Disease Control and Prevention, Ulanhot, 137499, People’s Republic of China
| | - Wencong He
- Department of Clinical Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, 100176, People’s Republic of China
| | - Zexuan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Bing Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Chong Teng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Eryong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Hanfang Zhu
- Department of Microbiology, Hinggan League Center for Disease Control and Prevention, Ulanhot, 137499, People’s Republic of China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, 100191, People’s Republic of China
| | - Lina Liu
- Blood Transfusion Department, Hinggan League People’s Hospital, Ulanhot, 137400, People’s Republic of China
| | - Yuanyuan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Yang Zheng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiangyi Liu
- Department of Clinical Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, 100176, People’s Republic of China
| | - Yanlin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xichao Ou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
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Dziri S, Marin J, Quagliaro P, Genestet C, Dumitrescu O, Carbonnelle E, Billard-Pomares T. Optimization of Mycobacterium tuberculosis DNA processing prior to whole genome sequencing. Tuberculosis (Edinb) 2024; 148:102543. [PMID: 39008943 DOI: 10.1016/j.tube.2024.102543] [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: 09/11/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
The process of whole genome sequencing of the Mycobacterium tuberculosis complex is dependent on complete the inactivation of the strain and subsequent DNA extraction. The objective of this study was to optimise the two steps. Firstly, the efficacy of Triton X-100 as a solvent for the inactivation step was evaluated. This solvent has been demonstrated to be effective in killing bacteria and is less toxic than the previously employed chloroform. For the extraction step, two lysis methods were evaluated: enzymatic (B1 protocol) and mechanical (B2 protocol). For whole genome sequencing, the Nextera XT DNA library preparation protocol was performed for both the B1 and B2 protocols. Subsequently, each library was subjected to whole-genome sequencing. The results demonstrated that heat lysis inactivation with Triton was effective, with no bacteria remaining viable following this treatment. The enzymatic and mechanical extraction protocols yielded comparable results in terms of DNA quantity and quality. The sequencing results showed that there was no significant difference in read depths between the two protocols. In conclusion, for MTBC strains, we recommend the use of our Triton inactivation method, which meets biosafety expectations.
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Affiliation(s)
- Samira Dziri
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie Clinique, F-93009, Bobigny, France.
| | - Julie Marin
- Université Sorbonne Paris Nord and Université Paris Cité, Inserm, IAME, F-93000, Bobigny, France
| | - Pauline Quagliaro
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie Clinique, F-93009, Bobigny, France
| | - Charlotte Genestet
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111 - CNRS UMR5308, 69007, Lyon, France; Institut des Agents Infectieux, Hôpital de La Croix Rousse, Hospices Civils de Lyon, 69004, Lyon, France
| | - Oana Dumitrescu
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111 - CNRS UMR5308, 69007, Lyon, France; Institut des Agents Infectieux, Hôpital de La Croix Rousse, Hospices Civils de Lyon, 69004, Lyon, France
| | - Etienne Carbonnelle
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie Clinique, F-93009, Bobigny, France; Université Sorbonne Paris Nord and Université Paris Cité, Inserm, IAME, F-93000, Bobigny, France
| | - Typhaine Billard-Pomares
- APHP, HUPSSD, Hôpital Avicenne, Service de Microbiologie Clinique, F-93009, Bobigny, France; Université Sorbonne Paris Nord and Université Paris Cité, Inserm, IAME, F-93000, Bobigny, France
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Serajian M, Marini S, Alanko JN, Noyes NR, Prosperi M, Boucher C. Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis. Bioinformatics 2024; 40:i39-i47. [PMID: 38940175 PMCID: PMC11211809 DOI: 10.1093/bioinformatics/btae243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome increasing trend yearly. The disease is caused by Mycobacterium tuberculosis (MTB) through airborne transmission. Treatment of TB is estimated to be 85% successful, however, this drops to 57% if MTB exhibits multiple antimicrobial resistance (AMR), for which fewer treatment options are available. RESULTS We develop a robust machine-learning classifier using both linear and nonlinear models (i.e. LASSO logistic regression (LR) and random forests (RF)) to predict the phenotypic resistance of Mycobacterium tuberculosis (MTB) for a broad range of antibiotic drugs. We use data from the CRyPTIC consortium to train our classifier, which consists of whole genome sequencing and antibiotic susceptibility testing (AST) phenotypic data for 13 different antibiotics. To train our model, we assemble the sequence data into genomic contigs, identify all unique 31-mers in the set of contigs, and build a feature matrix M, where M[i, j] is equal to the number of times the ith 31-mer occurs in the jth genome. Due to the size of this feature matrix (over 350 million unique 31-mers), we build and use a sparse matrix representation. Our method, which we refer to as MTB++, leverages compact data structures and iterative methods to allow for the screening of all the 31-mers in the development of both LASSO LR and RF. MTB++ is able to achieve high discrimination (F-1 >80%) for the first-line antibiotics. Moreover, MTB++ had the highest F-1 score in all but three classes and was the most comprehensive since it had an F-1 score >75% in all but four (rare) antibiotic drugs. We use our feature selection to contextualize the 31-mers that are used for the prediction of phenotypic resistance, leading to some insights about sequence similarity to genes in MEGARes. Lastly, we give an estimate of the amount of data that is needed in order to provide accurate predictions. AVAILABILITY The models and source code are publicly available on Github at https://github.com/M-Serajian/MTB-Pipeline.
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Affiliation(s)
- Mohammadali Serajian
- Department of Computer and Information Science and Engineering, University of Florida, 1889 Museum Road, Gainesville, Florida 32611, United States
| | - Simone Marini
- Department of Epidemiology, University of Florida, PO Box 100231, Gainesville, Florida 32601, United States
| | - Jarno N Alanko
- Department of Computer Science, University of Helsinki, P.O. Box 4, Helsinki 00014, Finland
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Mattia Prosperi
- Department of Epidemiology, University of Florida, PO Box 100231, Gainesville, Florida 32601, United States
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, 1889 Museum Road, Gainesville, Florida 32611, United States
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Wulandari DA, Hartati YW, Ibrahim AU, Pitaloka DAE, Irkham. Multidrug-resistant tuberculosis. Clin Chim Acta 2024; 559:119701. [PMID: 38697459 DOI: 10.1016/j.cca.2024.119701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
One of predominant contributors to global mortality is tuberculosis (TB), an infection caused by Mycobacterium tuberculosis (MTB). Inappropriate and ineffectual treatment can lead to the development of drug-resistant TB. One of the most common forms of drug-resistant TB is multidrug-resistant tuberculosis (MDR-TB), caused by mutations in the rpoB and katG genes that lead to resistance to anti-TB drugs, rifampicin (RIF) and isoniazid (INH), respectively. Although culturing remains the gold standard, it is not rapid thereby delaying potential treatment and potentially increasing the incidence of MDR-TB. In contrast, molecular techniques provide a highly sensitive and specific alternative. This review discusses the classification of biomarkers used to detect MDR-TB, some of the commonly used anti-TB drugs, and DNA mutations in MTB that lead to anti-TB resistance. The objective of this review is to increase awareness of the need for rapid and precise detection of MDR-TB cases to decrease morbidity and mortality of this infectious disease worldwide.
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Affiliation(s)
- Dika Apriliana Wulandari
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia
| | - Yeni Wahyuni Hartati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia
| | - Abdullahi Umar Ibrahim
- Department of Biomedical Engineering, Near East University, Mersin 10, Nicosia 99010, Turkey; Research Center for Science, Technology and Engineering (BILTEM), Near East University, 99138 Nicosia, TRNC, Mersin 10, Turkey
| | - Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, Indonesia
| | - Irkham
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia.
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Zhao J, Qian C, Jiang Y, He W, Wu W. Drug-Resistant Characteristics, Genetic Diversity, and Transmission Dynamics of Multidrug-Resistant Mycobacterium tuberculosis in Jiangxi, China. Infect Drug Resist 2024; 17:2213-2223. [PMID: 38840971 PMCID: PMC11152055 DOI: 10.2147/idr.s460267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
Purpose In this study, we aimed to determine the transmission pattern of multidrug-resistant tuberculosis (MDR-TB) isolates circulating in Jiangxi Province with whole-genome sequencing (WGS). In addition, we also sought to describe mutational resistome of MDR-TB isolates. Patients and Methods A total of 115 MDR-TB isolates determined by the phenotypic proportion method of drug susceptibility testing between January 2018 and December 2022 from provincial drug surveillance (DRS) in Jiangxi were included in our analysis. The demographic data and treatment history were extracted from the National TB Registry System. WGS was used to analyze the genotypic characteristics of drug resistance and transmissions. Results About 62.6% of MDR-TB strains were isolated from cases that received previous anti-tuberculosis treatment. According to the WGS results, 96.5% were genotypic MDR-TB, and more than half of MDR-TB isolates tested were also resistant to streptomycin (59.1%), ethambutol (56.5%), and fluroquinolones (53.0%), while resistance to cycloserine and linezolid was lowest, only in two (1.7%) and one (0.9%) isolate, respectively. Ser450Leu in rpoB (57.9%), Ser315Thr in katG (74.1%), Met306Val in embB (40.0%), Lys43Arg in rpsL (75.0%), Ala90Val in gyrA (32.8%) were predominant mutant types among the rifampin-, isoniazid-, ethambutol-, streptomycin-, fluoroquinolones-resistant isolates, respectively. Lineage 2 (East Asian genotype) occurred at the highest frequency with 97 cases (84.3%), followed by lineage 4 (Euro-American genotype) with 18 cases (15.7%). Additionally, 5 clusters consisting of 10 isolates were identified in the present study, demonstrating a clustering rate of 8.7%. Conclusion MDR/Rifampicin-Resistant (RR)-TB epidemic in this region is driven by lineage 2 clade that also show higher resistance to other anti-tuberculosis drugs. Lower cluster rates compared with a relatively higher proportion of new MDR-TB cases indicate that a considerable number of MDR-TB cases remain undiagnosed.
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Affiliation(s)
- Jingnan Zhao
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
| | - Chengyu Qian
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Youqiao Jiang
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
- Young Scientific Research and Innovation Team, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, Jiangxi, 330029, People’s Republic of China
| | - Wangrui He
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
| | - Wenhua Wu
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
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Tamrakar VK, Parihar NS, Bhat J, Rajasubramaniam S. Strengthening the Diagnosis of Drug-Resistant Tuberculosis Using NGS-Based Approaches and Bioinformatics Pipelines for Data Analysis in India. Indian J Microbiol 2024; 64:758-761. [PMID: 39011006 PMCID: PMC11246398 DOI: 10.1007/s12088-023-01134-0] [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: 04/27/2023] [Accepted: 11/02/2023] [Indexed: 07/17/2024] Open
Abstract
In India, drug-resistant tuberculosis (DR-TB) is a major public health issue and a significant challenge to stop TB program. An estimated 27% of new TB cases and 44% of previously treated TB cases are resistant to at least one anti-TB drug. The conventional methods for DR-TB diagnosis are time-consuming and have limitations, leading to delays in treatment initiation and the spread of the disease. Next-generation sequencing (NGS) based approaches have emerged as a promising tool for diagnosing DR-TB, simultaneously offering rapid and accurate detection of resistance mutations in multiple genes. NGS-based approaches generate a large amount of data, which requires efficient and reliable bioinformatics pipelines for data analysis. TBProfiler and Mykrobe are the bioinformatics pipelines that have been created to analyze NGS data for the diagnosis of DR-TB. These pipelines use reference-based and machine-learning approaches to detect resistance mutations and predict drug susceptibility, enabling clinicians to make informed treatment decisions. Implementing NGS-based approaches and bioinformatics pipelines for DR-TB diagnosis can potentially improve patient outcomes by facilitating early detection of drug resistance and guiding personalized treatment regimens. However, the widespread adoption of these approaches in India faces several challenges, including high costs, limited infrastructure, and a lack of trained personnel. Addressing these challenges requires concerted effort to ensure equitable access to and effective implementation of these innovative technologies.
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Affiliation(s)
- Vaibhav Kumar Tamrakar
- ICMR - National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh India
- Madhya Pradesh Medical Science University, Jabalpur, Madhya Pradesh India
| | - Nitish Singh Parihar
- ICMR - National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh India
- Madhya Pradesh Medical Science University, Jabalpur, Madhya Pradesh India
| | - Jyothi Bhat
- ICMR - National Institute of Traditional Medicine, Belagavi, NH-4, Nehru Nagar, Belagavi, Karnataka 590010 India
| | - S. Rajasubramaniam
- ICMR - National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh India
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Sanchini A, Lanni A, Giannoni F, Mustazzolu A. Exploring diagnostic methods for drug-resistant tuberculosis: A comprehensive overview. Tuberculosis (Edinb) 2024; 148:102522. [PMID: 38850839 DOI: 10.1016/j.tube.2024.102522] [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: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Despite available global efforts and funding, Tuberculosis (TB) continues to affect a considerable number of patients worldwide. Policy makers and stakeholders set clear goals to reduce TB incidence and mortality, but the emergence of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) complicate the reach of these goals. Drug-resistance TB needs to be diagnosed rapidly and accurately to effectively treat patients, prevent the transmission of MDR-TB, minimise mortality, reduce treatment costs and avoid unnecessary hospitalisations. In this narrative review, we provide a comprehensive overview of laboratory methods for detecting drug resistance in MTB, focusing on phenotypic, molecular and other drug susceptibility testing (DST) techniques. We found a large variety of methods used, with the BACTEC MGIT 960 being the most common phenotypic DST and the Xpert MTB/RIF being the most common molecular DST. We emphasise the importance of integrating phenotypic and molecular DST to address issues like resistance to new drugs, heteroresistance, mixed infections and low-level resistance mutations. Notably, most of the analysed studies adhered to the outdated definition of XDR-TB and did not consider the pre-XDR definition, thus posing challenges in aligning diagnostic methods with the current landscape of TB resistance.
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Affiliation(s)
| | - Alessio Lanni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Federico Giannoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
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Billows N, Phelan J, Xia D, Peng Y, Clark TG, Chang YM. Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance. Sci Rep 2024; 14:12312. [PMID: 38811658 PMCID: PMC11137121 DOI: 10.1038/s41598-024-62946-8] [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: 02/20/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, has a significant impact on global health worldwide. The development of multi-drug resistant strains that are resistant to the first-line drugs isoniazid and rifampicin threatens public health security. Rifampicin and isoniazid resistance are largely underpinned by mutations in rpoB and katG respectively and are associated with fitness costs. Compensatory mutations are considered to alleviate these fitness costs and have been observed in rpoC/rpoA (rifampicin) and oxyR'-ahpC (isoniazid). We developed a framework (CompMut-TB) to detect compensatory mutations from whole genome sequences from a large dataset comprised of 18,396 M. tuberculosis samples. We performed association analysis (Fisher's exact tests) to identify pairs of mutations that are associated with drug-resistance, followed by mediation analysis to identify complementary or full mediators of drug-resistance. The analyses revealed several potential mutations in rpoC (N = 47), rpoA (N = 4), and oxyR'-ahpC (N = 7) that were considered either 'highly likely' or 'likely' to confer compensatory effects on drug-resistance, including mutations that have previously been reported and validated. Overall, we have developed the CompMut-TB framework which can assist with identifying compensatory mutations which is important for more precise genome-based profiling of drug-resistant TB strains and to further understanding of the evolutionary mechanisms that underpin drug-resistance.
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Affiliation(s)
- Nina Billows
- Royal Veterinary College, University of London, London, UK.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Dong Xia
- Royal Veterinary College, University of London, London, UK
| | | | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Yu-Mei Chang
- Royal Veterinary College, University of London, London, UK
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10
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Esteves LS, Gomes LL, Brites D, Fandinho FCO, Bhering M, Pereira MADS, Conceição EC, Salvato R, da Costa BP, Medeiros RFDM, Caldas PCDS, Redner P, Dalcolmo MP, Eldholm V, Gagneux S, Rossetti ML, Kritski AL, Suffys PN. Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing. Antibiotics (Basel) 2024; 13:496. [PMID: 38927163 PMCID: PMC11200758 DOI: 10.3390/antibiotics13060496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.
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Affiliation(s)
- Leonardo Souza Esteves
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Lia Lima Gomes
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Daniela Brites
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Fátima Cristina Onofre Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Marcela Bhering
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Márcia Aparecida da Silva Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
| | - Richard Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
| | - Bianca Porphirio da Costa
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Reginalda Ferreira de Melo Medeiros
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Redner
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Margareth Pretti Dalcolmo
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Vegard Eldholm
- Norwegian Institute of Public Health, 0213 Oslo, Norway;
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Maria Lucia Rossetti
- Laboratório de Biologia Molecular, Universidade Luterana do Brasil (ULBRA), Canoas 92425-020, RS, Brazil;
| | - Afrânio Lineu Kritski
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
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11
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Hasan Z, Razzak SA, Kanji A, Shakoor S, Hasan R. Efflux pump gene single-nucleotide variants associated with resistance in Mycobacterium tuberculosis isolates with discrepant drug genotypes. J Glob Antimicrob Resist 2024; 38:128-139. [PMID: 38789081 DOI: 10.1016/j.jgar.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/19/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
INTRODUCTION Single-nucleotide variants (SNVs) in Mycobacterium tuberculosis (M. tuberculosis) genomes can predict multidrug resistance (MDR) but not all phenotype-genotype correlations can be explained. We investigated SNVs in efflux pumps (EPs) in the context of M. tuberculosis drug resistance. METHODS We analysed 2221 M. tuberculosis genomes from 1432 susceptible and 200 MDR, 172 pre-extensively drug resistant (XDR) and 417 XDR isolates. Analysis of 47 EP genes was conducted using MTB-VCF, an in-house bioinformatics pipeline. SNVs were categorized according to their SIFT/Polyphen scores. Resistance genotypes were also called using the TB-Profiler tool. RESULTS Genome comparisons between susceptible and drug resistant (DR) isolates identified 418 unique SNVs in EP of which; 53.5% were in MDR, 68.9% in pre-XDR and 61.3% in XDR isolates. Twenty EPs had unique SNVs with a high SIFT/PolyPhen score, comprising 38 unique SNVs. Sixteen SNVs across 12 EP genes were significantly associated with drug resistance and enriched in pre-XDR and XDR strains. These comprised 12 previously reported SNVs (in Rv0191, Rv0507, Rv0676, Rv1217, Rv1218, Rv1273, Rv1458, Rv1819, and Rv2688) and 4 novel SNVs (in Rv1877 and Rv2333). We investigated their presence in genomes of 52 MDR isolates with phenotype-genotype discrepancies to rifampicin (RIF), isoniazid (INH), or fluoroquinolones. SNVs associated with RIF and INH (Rv1217_1218, Rv1819, Rv0450, Rv1458, Rv3827, Rv0507, Rv0676, Rv1273, and Rv2333), and with fluoroquinolone (Rv2688) resistance were present in these discrepant strains. CONCLUSIONS Considering SNVs in EPs as part of M. tuberculosis genome-based resistance interpretation may add value, especially in evaluation of XDR resistance in strains with phenotype-genotype discrepancies.
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Affiliation(s)
- Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan.
| | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
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12
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Tagami Y, Horita N, Kaneko M, Muraoka S, Fukuda N, Izawa A, Kaneko A, Somekawa K, Kamimaki C, Matsumoto H, Tanaka K, Murohashi K, Aoki A, Fujii H, Watanabe K, Hara Y, Kobayashi N, Kaneko T. Whole-Genome Sequencing Predicting Phenotypic Antitubercular Drug Resistance: Meta-analysis. J Infect Dis 2024; 229:1481-1492. [PMID: 37946558 DOI: 10.1093/infdis/jiad480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND For simultaneous prediction of phenotypic drug susceptibility test (pDST) for multiple antituberculosis drugs, the whole genome sequencing (WGS) data can be analyzed using either a catalog-based approach, wherein 1 causative mutation suggests resistance, (eg, World Health Organization catalog) or noncatalog-based approach using complicated algorithm (eg, TB-profiler, machine learning). The aim was to estimate the predictive ability of WGS-based tests with pDST as the reference, and to compare the 2 approaches. METHODS Following a systematic literature search, the diagnostic test accuracies for 14 drugs were pooled using a random-effect bivariate model. RESULTS Of 779 articles, 44 with 16 821 specimens for meta-analysis and 13 not for meta-analysis were included. The areas under summary receiver operating characteristic curve suggested test accuracy was excellent (0.97-1.00) for 2 drugs (isoniazid 0.975, rifampicin 0.975), very good (0.93-0.97) for 8 drugs (pyrazinamide 0.946, streptomycin 0.952, amikacin 0.968, kanamycin 0.963, capreomycin 0.965, para-aminosalicylic acid 0.959, levofloxacin 0.960, ofloxacin 0.958), and good (0.75-0.93) for 4 drugs (ethambutol 0.926, moxifloxacin 0.896, ethionamide 0.878, prothionamide 0.908). The noncatalog-based and catalog-based approaches had similar ability for all drugs. CONCLUSIONS WGS accurately identifies isoniazid and rifampicin resistance. For most drugs, positive WGS results reliably predict pDST positive. The 2 approaches had similar ability. CLINICAL TRIALS REGISTRATION UMIN-ID UMIN000049276.
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Affiliation(s)
- Yoichi Tagami
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuyuki Horita
- Chemotherapy Center, Yokohama City University Hospital, Yokohama, Japan
| | - Megumi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Suguru Muraoka
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuhiko Fukuda
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ami Izawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ayami Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Somekawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Chisato Kamimaki
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Matsumoto
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Katsushi Tanaka
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kota Murohashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ayako Aoki
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroaki Fujii
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Keisuke Watanabe
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yu Hara
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuaki Kobayashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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13
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Paterson RL, La Manna MP, Arena De Souza V, Walker A, Gibbs-Howe D, Kulkarni R, Fergusson JR, Mulakkal NC, Monteiro M, Bunjobpol W, Dembek M, Martin-Urdiroz M, Grant T, Barber C, Garay-Baquero DJ, Tezera LB, Lowne D, Britton-Rivet C, Pengelly R, Chepisiuk N, Singh PK, Woon AP, Powlesland AS, McCully ML, Caccamo N, Salio M, Badami GD, Dorrell L, Knox A, Robinson R, Elkington P, Dieli F, Lepore M, Leonard S, Godinho LF. An HLA-E-targeted TCR bispecific molecule redirects T cell immunity against Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2024; 121:e2318003121. [PMID: 38691588 PMCID: PMC11087797 DOI: 10.1073/pnas.2318003121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/08/2024] [Indexed: 05/03/2024] Open
Abstract
Peptides presented by HLA-E, a molecule with very limited polymorphism, represent attractive targets for T cell receptor (TCR)-based immunotherapies to circumvent the limitations imposed by the high polymorphism of classical HLA genes in the human population. Here, we describe a TCR-based bispecific molecule that potently and selectively binds HLA-E in complex with a peptide encoded by the inhA gene of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis in humans. We reveal the biophysical and structural bases underpinning the potency and specificity of this molecule and demonstrate its ability to redirect polyclonal T cells to target HLA-E-expressing cells transduced with mycobacterial inhA as well as primary cells infected with virulent Mtb. Additionally, we demonstrate elimination of Mtb-infected cells and reduction of intracellular Mtb growth. Our study suggests an approach to enhance host T cell immunity against Mtb and provides proof of principle for an innovative TCR-based therapeutic strategy overcoming HLA polymorphism and therefore applicable to a broader patient population.
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Affiliation(s)
| | - Marco P. La Manna
- Department of Biomedicine, Neurosciences and Advanced Diagnostic, University of Palermo, Palermo90127, Italy
- Central Laboratory of Advanced Diagnosis and Biomedical Research, Azienda Ospedaliera Universitaria Policlinico Paolo Giaccone, University of Palermo, Palermo90127, Italy
| | | | - Andrew Walker
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Dawn Gibbs-Howe
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Rakesh Kulkarni
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | | | | | - Mauro Monteiro
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | | | - Marcin Dembek
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | | | - Tressan Grant
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Claire Barber
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Diana J. Garay-Baquero
- National Institute for Health and Care Research, Biomedical Research Centre and Institute for Life Sciences, Faculty of Medicine, University of Southampton, SouthamptonSO16 6YD, United Kingdom
| | - Liku Bekele Tezera
- Department of Biomedicine, Neurosciences and Advanced Diagnostic, University of Palermo, Palermo90127, Italy
| | - David Lowne
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | | | - Robert Pengelly
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | | | | | - Amanda P. Woon
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | | | | | - Nadia Caccamo
- Department of Biomedicine, Neurosciences and Advanced Diagnostic, University of Palermo, Palermo90127, Italy
- Central Laboratory of Advanced Diagnosis and Biomedical Research, Azienda Ospedaliera Universitaria Policlinico Paolo Giaccone, University of Palermo, Palermo90127, Italy
| | - Mariolina Salio
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Giusto Davide Badami
- Department of Biomedicine, Neurosciences and Advanced Diagnostic, University of Palermo, Palermo90127, Italy
- Central Laboratory of Advanced Diagnosis and Biomedical Research, Azienda Ospedaliera Universitaria Policlinico Paolo Giaccone, University of Palermo, Palermo90127, Italy
| | - Lucy Dorrell
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Andrew Knox
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Ross Robinson
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Paul Elkington
- National Institute for Health and Care Research, Biomedical Research Centre and Institute for Life Sciences, Faculty of Medicine, University of Southampton, SouthamptonSO16 6YD, United Kingdom
| | - Francesco Dieli
- Department of Biomedicine, Neurosciences and Advanced Diagnostic, University of Palermo, Palermo90127, Italy
- Central Laboratory of Advanced Diagnosis and Biomedical Research, Azienda Ospedaliera Universitaria Policlinico Paolo Giaccone, University of Palermo, Palermo90127, Italy
| | - Marco Lepore
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Sarah Leonard
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
| | - Luis F. Godinho
- Immunocore Ltd., Abingdon, OxfordshireOX14 4RY, United Kingdom
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14
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Hu K, Meyer F, Deng ZL, Asgari E, Kuo TH, Münch PC, McHardy AC. Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes. Brief Bioinform 2024; 25:bbae206. [PMID: 38706320 PMCID: PMC11070729 DOI: 10.1093/bib/bbae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored for this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno and Aytan-Aktug), an ML baseline and the rule-based ResFinder by training and testing each of them across 78 species-antibiotic datasets, using a rigorous benchmarking workflow that integrates three evaluation approaches, each paired with three distinct sample splitting methods. Our analysis revealed considerable variation in the performance across techniques and datasets. Whereas ML methods generally excelled for closely related strains, ResFinder excelled for handling divergent genomes. Overall, Kover most frequently ranked top among the ML approaches, followed by PhenotypeSeeker and Seq2Geno2Pheno. AMR phenotypes for antibiotic classes such as macrolides and sulfonamides were predicted with the highest accuracies. The quality of predictions varied substantially across species-antibiotic combinations, particularly for beta-lactams; across species, resistance phenotyping of the beta-lactams compound, aztreonam, amoxicillin/clavulanic acid, cefoxitin, ceftazidime and piperacillin/tazobactam, alongside tetracyclines demonstrated more variable performance than the other benchmarked antibiotics. By organism, Campylobacter jejuni and Enterococcus faecium phenotypes were more robustly predicted than those of Escherichia coli, Staphylococcus aureus, Salmonella enterica, Neisseria gonorrhoeae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Streptococcus pneumoniae and Mycobacterium tuberculosis. In addition, our study provides software recommendations for each species-antibiotic combination. It furthermore highlights the need for optimization for robust clinical applications, particularly for strains that diverge substantially from those used for training.
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Affiliation(s)
- Kaixin Hu
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Ehsaneddin Asgari
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering and Mechanical Engineering, University of California, Berkeley, USA
| | - Tzu-Hao Kuo
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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15
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Umpeleva T, Chetverikova E, Belyaev D, Eremeeva N, Boteva T, Golubeva L, Vakhrusheva D, Vasilieva I. Identification of genetic determinants of bedaquiline resistance in Mycobacterium tuberculosis in Ural region, Russia. Microbiol Spectr 2024; 12:e0374923. [PMID: 38345388 PMCID: PMC10913728 DOI: 10.1128/spectrum.03749-23] [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: 11/01/2023] [Accepted: 01/24/2024] [Indexed: 03/06/2024] Open
Abstract
Collecting data on rare Mycobacterium tuberculosis (Mtb) clinical isolates with resistance to the new anti-tuberculosis drug bedaquiline is an important task for improving antimicrobial susceptibility testing methods. Nanopore whole genome sequencing, the proportion method on Middlebrook 7H11 medium, and BACTEC MGIT 960 assays were used to analyze genotypic and phenotypic resistance to bedaquiline. We found four mutations: atpE I66M, atpE А63Р, Rv0678 А36Т, and Rv0678 S53P in five isolates with different levels of phenotypic bedaquiline resistance. IMPORTANCE Bedaquiline (BDQ) is a new anti-tuberculosis drug. The phenotypic and genotypic data describing the mechanism of drug resistance are critical for the design of rapid and accurate diagnostic tests. We consider that our work, which describes genotypic and phenotypic resistance to BDQ, can contribute to the standardization of drug susceptibility testing.
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Affiliation(s)
- Tatiana Umpeleva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Elena Chetverikova
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Danila Belyaev
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
- Laboratory of Medical Chemistry, Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Natalya Eremeeva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Tatiana Boteva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Ludmila Golubeva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Diana Vakhrusheva
- Department of Microbiology and Preclinical Research, National Medical Research Center of Phthisiopulmonology and Infection Disease, Yekaterinburg, Russia
| | - Irina Vasilieva
- Administration, National Medical Research Center of Phthisiopulmonology and Infection Disease, Moscow, Russia
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Saini A, Dadwal R, Yadav R, Kanaujia R, Aggarwal AN, Arora A, Sethi S. Whole genome sequencing for the prediction of resistant tuberculosis strains from northern India. Indian J Med Microbiol 2024; 48:100537. [PMID: 38350525 DOI: 10.1016/j.ijmmb.2024.100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/07/2023] [Accepted: 02/09/2024] [Indexed: 02/15/2024]
Abstract
PURPOSE Tuberculosis is an important public health problem among infectious diseases. The problem becomes more concerning with the emergence of MDR-TB and pre-XDR-TB. Whole genome sequencing (WGS) detection of resistance has recently gained popularity as it has advantages over other commercial techniques. METHODS We performed in-house WGS followed by detailed analysis by an in-house pipeline to identify the resistance markers. This was accompanied by Phenotypic DST, and Sanger sequencing on all the 12 XDR, 06 pre-XDR, and 06 susceptible M. tb isolates. These results were collated with online M. tb WGS pipelines (TB profiler, PhyResSE, Mykrobe predictor) for comparative analysis. RESULTS Following our in-house analysis, we observed 64 non-synonymous SNPs, fifteen synonymous SNPs, and five INDELs in 25 drug resistance-associated genes/intergenic regions (IGRs) in M. tb isolates. Sensitivity for detecting XDR is 33%, 58%, 83%, and 83%, respectively, using Mykrobe predictor, PhyResSE, TB-profiler, and in-house pipeline for WGS analysis, respectively. TB-profiler detected a rare mutation H70R in the gyrA gene in one pre-XDR isolate. Lineage 2.2.1 East-Asian (Beijing sublineage type) predominated (60%) in WGS data analysis of the XDR isolates. CONCLUSIONS Our findings suggest that in-house analysis of WGS data and TB-profiler sensitivity was better for the detection of second-line resistance as compared to other automated tested tools. Frequent upgradation of newer mutations associated with resistance needs to be updated, as it potentiates tailored treatment for patients.
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Affiliation(s)
| | | | | | | | | | - Amit Arora
- Dept. of Medical Microbiology, PGIMER, India.
| | - Sunil Sethi
- Dept. of Medical Microbiology, PGIMER, India.
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17
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Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [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: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
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Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
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18
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Song Z, He W, Cao X, Ma A, He P, Zhao B, Wang S, Liu C, Zhao Y. The Recent Transmission and Associated Risk Factor of Mycobacterium tuberculosis in Golmud City, China. Infect Drug Resist 2024; 17:417-425. [PMID: 38318210 PMCID: PMC10840525 DOI: 10.2147/idr.s437026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/05/2023] [Indexed: 02/07/2024] Open
Abstract
Background Tuberculosis (TB) remains a severe public health problem globally, and it is essential to comprehend the transmission pattern to control tuberculosis. Herein, we evaluated the drug-resistant characteristics, recent transmission, and associated risk factors of TB in Golmud, Qinghai, China. Methods In this study, we performed a population-based study of patients diagnosed with TB in Golmud from 2013 to 2018. Drug-susceptibility testing and whole-genome sequencing were performed on 133 Mycobacterium tuberculosis strains. The genomic clustering rate was calculated to evaluate the level of recent transmission. Risk factors were identified by logistic regression analysis. Results Our results showed that 46.97% (62/132) of strains were phylogenetically clustered and formed into 23 transmission clusters, suggesting a high recent transmission of TB in the area. 12.78% (17/133) strains were multidrug-resistant/rifampicin tuberculosis (MDR/RR-TB), with a high drug-resistant burden. Based on drug resistance gene analysis, we found 23 strains belonging to genotype MDR/RR-TB, where some strains may have borderline mutations. Among these strains, 65.2% (15/23) were found within putative transmission clusters. Additionally, risk factor analysis showed that recent transmission of TB happened more in patients with Tibetan nationality or older age. Conclusion Overall our study indicates that the recent transmissions of MTB strains, especially genotypic MDR/RR strains, drive the tuberculosis epidemic in Golmud, which could contribute to developing effective TB prevention and control strategies.
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Affiliation(s)
- Zexuan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Wencong He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Xiaolong Cao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Aijing Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Ping He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Bing Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Shengfen Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
| | - Chunfa Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
- Animal Science and Technology College, Beijing University of Agriculture, Huilongguan, Changping, Beijing, 102206, People’s Republic of China
| | - Yanlin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, People’s Republic of China
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Wang TT, Hu YL, Li YF, Kong XL, Li YM, Sun PY, Wang DX, Li YY, Zhang YZ, Han QL, Zhu XH, An QQ, Liu LL, Liu Y, Li HC. Polyketide synthases mutation in tuberculosis transmission revealed by whole genomic sequence, China, 2011-2019. Front Genet 2024; 14:1217255. [PMID: 38259610 PMCID: PMC10800454 DOI: 10.3389/fgene.2023.1217255] [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: 05/20/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Tuberculosis (TB) is an infectious disease caused by a bacterium called Mycobacterium tuberculosis (Mtb). Previous studies have primarily focused on the transmissibility of multidrug-resistant (MDR) or extensively drug-resistant (XDR) Mtb. However, variations in virulence across Mtb lineages may also account for differences in transmissibility. In Mtb, polyketide synthase (PKS) genes encode large multifunctional proteins which have been shown to be major mycobacterial virulence factors. Therefore, this study aimed to identify the role of PKS mutations in TB transmission and assess its risk and characteristics. Methods: Whole genome sequences (WGSs) data from 3,204 Mtb isolates was collected from 2011 to 2019 in China. Whole genome single nucleotide polymorphism (SNP) profiles were used for phylogenetic tree analysis. Putative transmission clusters (≤10 SNPs) were identified. To identify the role of PKS mutations in TB transmission, we compared SNPs in the PKS gene region between "clustered isolates" and "non-clustered isolates" in different lineages. Results: Cluster-associated mutations in ppsA, pks12, and pks13 were identified among different lineage isolates. They were statistically significant among clustered strains, indicating that they may enhance the transmissibility of Mtb. Conclusion: Overall, this study provides new insights into the function of PKS and its localization in M. tuberculosis. The study found that ppsA, pks12, and pks13 may contribute to disease progression and higher transmission of certain strains. We also discussed the prospective use of mutant ppsA, pks12, and pks13 genes as drug targets.
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Affiliation(s)
- Ting-Ting Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuan-Long Hu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yi-Fan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
| | - Xiang-Long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ya-Meng Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | | | - Da-Xing Wang
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Ying-Ying Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yu-Zhen Zhang
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Lin Han
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xue-Han Zhu
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Qi An
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Li-Li Liu
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huai-Chen Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Walter KS, Cohen T, Mathema B, Colijn C, Sobkowiak B, Comas I, Goig GA, Croda J, Andrews JR. Signatures of transmission in within-host M. tuberculosis variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.28.23300451. [PMID: 38234741 PMCID: PMC10793532 DOI: 10.1101/2023.12.28.23300451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Because M. tuberculosis evolves slowly, transmission clusters often contain multiple individuals with identical consensus genomes, making it difficult to reconstruct transmission chains. Finding additional sources of shared M. tuberculosis variation could help overcome this problem. Previous studies have reported M. tuberculosis diversity within infected individuals; however, whether within-host variation improves transmission inferences remains unclear. Methods To evaluate the transmission information present in within-host M. tuberculosis variation, we re-analyzed publicly available sequence data from three household transmission studies, using household membership as a proxy for transmission linkage between donor-recipient pairs. Findings We found moderate levels of minority variation present in M. tuberculosis sequence data from cultured isolates that varied significantly across studies (mean: 6, 7, and 170 minority variants above a 1% minor allele frequency threshold, outside of PE/PPE genes). Isolates from household members shared more minority variants than did isolates from unlinked individuals in the three studies (mean 98 shared minority variants vs. 10; 0.8 vs. 0.2, and 0.7 vs. 0.2, respectively). Shared within-host variation was significantly associated with household membership (OR: 1.51 [1.30,1.71], for one standard deviation increase in shared minority variants). Models that included shared within-host variation improved the accuracy of predicting household membership in all three studies as compared to models without within-host variation (AUC: 0.95 versus 0.92, 0.99 versus 0.95, and 0.93 versus 0.91). Interpretation Within-host M. tuberculosis variation persists through culture and could enhance the resolution of transmission inferences. The substantial differences in minority variation recovered across studies highlights the need to optimize approaches to recover and incorporate within-host variation into automated phylogenetic and transmission inference. Funding NIAID: 5K01AI173385.
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Affiliation(s)
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health; New York, United States
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University; Burnaby, Canada
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (CSIC), Valencia, Spain
| | - Galo A Goig
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Federal University of Mato Grosso do Sul - UFMS, Campo Grande, MS, Brazil
- Oswaldo Cruz Foundation Mato Grosso do Sul, Mato Grosso do Sul, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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21
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Yurtseven A, Buyanova S, Agrawal AA, Bochkareva OO, Kalinina OV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiol 2023; 23:404. [PMID: 38124060 PMCID: PMC10731705 DOI: 10.1186/s12866-023-03147-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. RESULTS In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models' performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. CONCLUSIONS Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.
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Affiliation(s)
- Alper Yurtseven
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany.
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany.
| | - Sofia Buyanova
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
| | - Amay Ajaykumar Agrawal
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
| | - Olga O Bochkareva
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Djerassiplatz 1 A, Wien, 1030, Austria
| | - Olga V Kalinina
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
- Faculty of Medicine, Saarland University, Homburg, 66421, Saarland, Germany
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22
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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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23
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Tong E, Zhou Y, Liu Z, Zhu Y, Zhang M, Wu K, Pan J, Jiang J. Bedaquiline Resistance and Molecular Characterization of Rifampicin-Resistant Mycobacterium Tuberculosis Isolates in Zhejiang, China. Infect Drug Resist 2023; 16:6951-6963. [PMID: 37928607 PMCID: PMC10625375 DOI: 10.2147/idr.s429003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Purpose This study aimed to determine the prevalence and molecular characterization of bedaquiline (BDQ) resistance among rifampicin-resistant tuberculosis (RR-TB) isolates collected from Zhejiang, China. Patients and Methods A total of 245 RR-TB isolates were collected from 19 municipal TB hospitals in Zhejiang province, China between January and December 2021. Microplate assays were used to determine the minimum inhibitory concentrations (MIC) of BDQ. Whole-genome sequencing (WGS) was performed on isolates with MIC values for BDQ ≥ 0.25 μg/mL. Results Five (2.04%) BDQ-resistant strains were isolated from 245 tuberculosis patients. The resistance rate of BDQ was not correlated to the sex, age, treatment history, or occupation of patients. Four BDQ-resistant isolates and three BDQ-sensitive isolates were found to carry Rv0678 mutations, and one BDQ-resistant strain carried both Rv0678 and pepQ mutations. No mutations within the atpE and Rv1979c genes were observed. Conclusion BDQ demonstrated strong in vitro antibacterial activity against RR-TB isolates, and the Rv0678 gene was identified as the primary mechanism contributing to BDQ resistance among RR-TB isolates from Zhejiang, China. Furthermore, in addition to the four currently known resistance-associated genes (atpE, Rv0678, Rv1979c, and pepQ), other mechanisms of resistance to BDQ may exist that need further study.
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Affiliation(s)
- Enyu Tong
- School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China
| | - Ying Zhou
- School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China
| | - Zhengwei Liu
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Yelei Zhu
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Mingwu Zhang
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Kunyang Wu
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Junhang Pan
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Jianmin Jiang
- School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Hangzhou, 310051, People’s Republic of China
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Mejía-Ponce PM, Ramos-González EJ, Ramos-García AA, Lara-Ramírez EE, Soriano-Herrera AR, Medellín-Luna MF, Valdez-Salazar F, Castro-Garay CY, Núñez-Contreras JJ, De Donato-Capote M, Sharma A, Castañeda-Delgado JE, Zenteno-Cuevas R, Enciso-Moreno JA, Licona-Cassani C. Genomic epidemiology analysis of drug-resistant Mycobacterium tuberculosis distributed in Mexico. PLoS One 2023; 18:e0292965. [PMID: 37831695 PMCID: PMC10575498 DOI: 10.1371/journal.pone.0292965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Genomics has significantly revolutionized pathogen surveillance, particularly in epidemiological studies, the detection of drug-resistant strains, and disease control. Despite its potential, the representation of Latin American countries in the genomic catalogues of Mycobacterium tuberculosis (Mtb), the bacteria responsible for Tuberculosis (TB), remains limited. In this study, we present a whole genome sequencing (WGS)-based analysis of 85 Mtb clinical strains from 17 Mexican states, providing insights into local adaptations and drug resistance signatures in the region. Our results reveal that the Euro-American lineage (L4) accounts for 94% of our dataset, showing 4.1.2.1 (Haarlem, n = 32), and 4.1.1.3 (X-type, n = 34) sublineages as the most prevalent. We report the presence of the 4.1.1.3 sublineage, which is endemic to Mexico, in six additional locations beyond previous reports. Phenotypic drug resistance tests showed that 34 out of 85 Mtb samples were resistant, exhibiting a variety of resistance profiles to the first-line antibiotics tested. We observed high levels of discrepancy between phenotype and genotype associated with drug resistance in our dataset, including pyrazinamide-monoresistant Mtb strains lacking canonical variants of drug resistance. Expanding the Latin American Mtb genome databases will enhance our understanding of TB epidemiology and potentially provide new avenues for controlling the disease in the region.
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Affiliation(s)
- Paulina M. Mejía-Ponce
- Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, México
| | - Elsy J. Ramos-González
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Axel A. Ramos-García
- Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, México
| | - Edgar E. Lara-Ramírez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Alma R. Soriano-Herrera
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Mitzy F. Medellín-Luna
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Posgrado en Ciencias Farmacobiológicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Fernando Valdez-Salazar
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Claudia Y. Castro-Garay
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - José J. Núñez-Contreras
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | | | - Ashutosh Sharma
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Querétaro, México
| | - Julio E. Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Consejo Nacional de Ciencia y Tecnología, CONACYT, Ciudad de México, México
| | - Roberto Zenteno-Cuevas
- Instituto de Salud Pública, Universidad Veracruzana, Veracruz, México
- Red Multidisciplinaria de Investigación en Tuberculosis, Ciudad de México, México
| | - Jose Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, México
| | - Cuauhtémoc Licona-Cassani
- Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, México
- Red Multidisciplinaria de Investigación en Tuberculosis, Ciudad de México, México
- Division of Integrative Biology, The Institute for Obesity Research, Tecnológico de Monterrey, Nuevo León, México
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25
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Shaw B, von Bredow B, Tsan A, Garner O, Yang S. Clinical Whole-Genome Sequencing Assay for Rapid Mycobacterium tuberculosis Complex First-Line Drug Susceptibility Testing and Phylogenetic Relatedness Analysis. Microorganisms 2023; 11:2538. [PMID: 37894195 PMCID: PMC10609454 DOI: 10.3390/microorganisms11102538] [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: 07/26/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The global rise of drug resistant tuberculosis has highlighted the need for improved diagnostic technologies that provide rapid and reliable drug resistance results. Here, we develop and validate a whole genome sequencing (WGS)-based test for identification of mycobacterium tuberculosis complex (MTB) drug resistance to rifampin, isoniazid, pyrazinamide, ethambutol, and streptomycin. Through comparative analysis of drug resistance results from WGS-based testing and phenotypic drug susceptibility testing (DST) of 38 clinical MTB isolates from patients receiving care in Los Angeles, CA, we found an overall concordance between methods of 97.4% with equivalent performance across culture media. Critically, prospective analysis of 11 isolates showed that WGS-based testing provides results an average of 36 days faster than phenotypic culture-based methods. We showcase the additional benefits of WGS data by investigating a suspected laboratory contamination event and using phylogenetic analysis to search for cryptic local transmission, finding no evidence of community spread amongst our patient population in the past six years. WGS-based testing for MTB drug resistance has the potential to greatly improve diagnosis of drug resistant MTB by accelerating turnaround time while maintaining accuracy and providing additional benefits for infection control, lab safety, and public health applications.
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Affiliation(s)
- Bennett Shaw
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA; (B.S.); (B.v.B.); (A.T.); (O.G.)
| | - Benjamin von Bredow
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA; (B.S.); (B.v.B.); (A.T.); (O.G.)
- Department of Pathology, Oakland University William Beaumont School of Medicine, Rochester, MI 48309, USA
| | - Allison Tsan
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA; (B.S.); (B.v.B.); (A.T.); (O.G.)
| | - Omai Garner
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA; (B.S.); (B.v.B.); (A.T.); (O.G.)
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA; (B.S.); (B.v.B.); (A.T.); (O.G.)
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26
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Auganova D, Atavliyeva S, Amirgazin A, Akisheva A, Tsepke A, Tarlykov P. Genomic Characterization of Drug-Resistant Mycobacterium tuberculosis L2/Beijing Isolates from Astana, Kazakhstan. Antibiotics (Basel) 2023; 12:1523. [PMID: 37887224 PMCID: PMC10604462 DOI: 10.3390/antibiotics12101523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
Kazakhstan ranks among the countries with the highest number of MDR-TB patients per 100,000 population worldwide. The successful transmission of local MDR strains of Mycobacterium tuberculosis (Mtb) poses a significant threat to disease control. In this study, we employed whole-genome sequencing to examine drug resistance, compensatory mutations, population structure, and transmission patterns in a sample of 24 clinical isolates of L2/Beijing Mtb collected in Astana, Kazakhstan between 2021 and 2022. The genotypic prediction of Mtb susceptibility to anti-TB agents was consistent with the phenotypic susceptibility, except for bedaquiline. An analysis of resistance-associated genes characterized most of the isolates as pre-extensively drug-resistant tuberculosis (pre-XDR-TB) (n = 15; 62.5%). The phylogenetic analysis grouped the isolates into four transmission clusters; the dominant cluster was assigned to the "aggressive" Central Asia outbreak (CAO) clade of L2/Beijing (n = 15; 62.5%). Thirteen mutations with putative compensatory effects were observed exclusively in Mtb isolates containing the rpoB S450L mutation. The putative compensatory mutations had a stabilizing effect on RpoABC protein stability and dynamics. The high prevalence of the CAO clade in the population structure of Mtb may explain the rapid spread of MDR-TB in Kazakhstan.
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Affiliation(s)
- Dana Auganova
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
| | | | | | - Akmaral Akisheva
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Anna Tsepke
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
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Shitol SA, Saha A, Barua M, Towhid KMS, Islam A, Sarker M. A qualitative exploration of challenges in childhood TB patients identification and diagnosis in Bangladesh. Heliyon 2023; 9:e20569. [PMID: 37818012 PMCID: PMC10560773 DOI: 10.1016/j.heliyon.2023.e20569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
Background As childhood tuberculosis is difficult to identify and diagnose, the experiences of the caregivers and healthcare providers of childhood tuberculosis patients remain a potential area of study. This study aims to illustrate the challenges caregivers and healthcare providers encounter in identifying and diagnosing childhood tuberculosis in two sub-districts of Bangladesh. Methods We conducted semi-structured in-depth interviews with eight caregivers of childhood tuberculosis patients and key informant interviews with 36 healthcare providers from September 2020 to December 2020 from different levels of the tuberculosis control program in Keraniganj (with high childhood tuberculosis cases notification), Faridpur Sadar (with low childhood tuberculosis cases notification), and Dhaka city. Results There is a dearth of understanding among caregivers about childhood tuberculosis. Passive case finding process and focus on cough during community mobilisation contribute to the delay in childhood tuberculosis identification. The stigmatisation that caregivers anticipate and experience has an impact on their mental health and implies that there are misunderstandings about tuberculosis in the community. Furthermore, diagnostic dilemma among healthcare providers accounts for diagnosis delays. Some, but not all, institutions in different geographical locations provide free diagnostic tests and have GeneXpert devices. Conclusions Various factors, including caregivers' knowledge and experience, the process of case finding and community mobilization, healthcare providers' way of service provision and diagnosis, and the unavailability of required logistics at facilities challenge the identification and diagnosis of childhood tuberculosis that need to be minimized for childhood tuberculosis's early identification, diagnosis, treatment initiation, and successful completion of treatment. Awareness should also be raised in the community of childhood tuberculosis.
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Affiliation(s)
- Sharmin Akter Shitol
- James P. Grant School of Public Health, BRAC University, Medona Tower, 28 Mohakhali Commercial Area, Bir Uttom A K Khandakar Road, Dhaka-1213, Bangladesh
| | - Avijit Saha
- James P. Grant School of Public Health, BRAC University, Medona Tower, 28 Mohakhali Commercial Area, Bir Uttom A K Khandakar Road, Dhaka-1213, Bangladesh
| | - Mrittika Barua
- James P. Grant School of Public Health, BRAC University, Medona Tower, 28 Mohakhali Commercial Area, Bir Uttom A K Khandakar Road, Dhaka-1213, Bangladesh
| | | | - Akramul Islam
- Communicable Diseases, Water, Sanitation, and Hygiene (WASH), Integrated Development, And Humanitarian Crisis Management, BRAC, 75 Mohakhali, Dhaka 1212, Bangladesh
| | - Malabika Sarker
- James P. Grant School of Public Health, BRAC University, Medona Tower, 28 Mohakhali Commercial Area, Bir Uttom A K Khandakar Road, Dhaka-1213, Bangladesh
- Institute of Public Health, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
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28
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Rao M, Wollenberg K, Harris M, Kulavalli S, Thomas L, Chawla K, Shenoy VP, Varma M, Saravu K, Hande HM, Shanthigrama Vasudeva CS, Jeffrey B, Gabrielian A, Rosenthal A. Lineage classification and antitubercular drug resistance surveillance of Mycobacterium tuberculosis by whole-genome sequencing in Southern India. Microbiol Spectr 2023; 11:e0453122. [PMID: 37671895 PMCID: PMC10580826 DOI: 10.1128/spectrum.04531-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 07/03/2023] [Indexed: 09/07/2023] Open
Abstract
Whole-genome sequencing has created a revolution in tuberculosis management by providing a comprehensive picture of the various genetic polymorphisms with unprecedented accuracy. Studies mapping genomic heterogeneity in clinical isolates of Mycobacterium tuberculosis using a whole-genome sequencing approach from high tuberculosis burden countries are underrepresented. We report whole-genome sequencing results of 242 clinical isolates of culture-confirmed M. tuberculosis isolates from tuberculosis patients referred to a tertiary care hospital in Southern India. Phylogenetic analysis revealed that the isolates in our study belonged to five different lineages, with Indo-Oceanic (lineage 1, n = 122) and East-African Indian (lineage 3, n = 80) being the most prevalent. We report several mutations in genes conferring resistance to first and second line antitubercular drugs including the genes rpoB, katG, ahpC, inhA, fabG1, embB, pncA, rpsL, rrs, and gyrA. The majority of these mutations were identified in relatively high proportions in lineage 1. Our study highlights the utility of whole-genome sequencing as a potential supplemental tool to the existing genotypic and phenotypic methods, in providing expedited comprehensive surveillance of mutations that may be associated with antitubercular drug resistance as well as lineage characterization of M. tuberculosis isolates. Further larger-scale whole-genome datasets with linked minimum inhibition concentration testing are imperative for resolving the discrepancies between whole-genome sequencing and phenotypic drug sensitivity testing results and quantifying the level of the resistance associated with the mutations for optimization of antitubercular drug and precise dose selection in clinics. IMPORTANCE Studies mapping genetic heterogeneity of clinical isolates of M. tuberculosis for determining their strain lineage and drug resistance by whole-genome sequencing are limited in high tuberculosis burden settings. We carried out whole-genome sequencing of 242 M. tuberculosis isolates from drug-sensitive and drug-resistant tuberculosis patients, identified and collected as part of the TB Portals Program, to have a comprehensive insight into the genetic diversity of M. tuberculosis in Southern India. We report several genetic variations in M. tuberculosis that may confer resistance to antitubercular drugs. Further wide-scale efforts are required to fully characterize M. tuberculosis genetic diversity at a population level in high tuberculosis burden settings for providing precise tuberculosis treatment.
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Affiliation(s)
- Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kurt Wollenberg
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Harris
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shrivathsa Kulavalli
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Vishnu Prasad Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavitha Saravu
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - H. Manjunatha Hande
- Department of Medicine, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Brendan Jeffrey
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrei Gabrielian
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alex Rosenthal
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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29
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Wang J, Yu C, Xu Y, Chen Z, Qiu W, Chen S, Pei H, Zhong Y. Analysis of Drug-Resistance Characteristics and Genetic Diversity of Multidrug-Resistant Tuberculosis Based on Whole-Genome Sequencing on the Hainan Island, China. Infect Drug Resist 2023; 16:5783-5798. [PMID: 37692467 PMCID: PMC10487742 DOI: 10.2147/idr.s423955] [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: 06/22/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose Given the high burden of Tuberculosis (TB) in China, the prevalence of multidrug-resistant tuberculosis (MDR-TB) is significant. Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) enables the identification of lineages, drug-resistant mutations, and transmission patterns, offering valuable insights for TB control, clinical diagnosis, and treatment. Methods We collected 202 MDR-MTB strains from 3519 suspected pulmonary TB patients treated at The Second Affiliated Hospital of Hainan Medical University between July 2019 and June 2021. Proportional drug-susceptibility testing was performed using 8 common anti-tuberculosis drugs. Subsequently, the genotypic drug resistance and genetic characteristics were analyzed by the WGS. Results Lineages are identified by TB-profiler revealed 202 MDR-MTB strains, showcasing three predominant lineages, with lineage 2 being the most prevalent. Close genomic relatedness analysis and evidence of MTB transmission led to the formation of 15 clusters comprising 42 isolates, resulting in a clustering rate of 20.8%. Novelty, lineage 2.1 (non-Beijing) accounted for 27.2% of the MDR-MTB strains, which is rare in China and Neighboring countries. Regarding first-line anti-TB drugs, genes associated with rifampicin resistance, primarily the rpoB gene, were detected in 200 strains (99.0%). Genes conferring resistance to isoniazid, ethambutol, and streptomycin were identified in 191 (94.5%), 125 (61.9%), and 100 (49.5%) strains, respectively. Among the second-line drugs, 97 (48.0%) strains exhibited genes encoding resistance to fluoroquinolones. Comparing the results to phenotypic drug susceptibility-based testing, the sensitivity of WGS for detecting resistance to each of the six drugs (rifampicin, isoniazid, ethambutol, ofloxacin, kanamycin, capreomycin) was 90% or higher. With the exception of ethambutol, the specificity of WGS prediction for the remaining drugs exceeded 88%. Conclusion Our study provides crucial insights into genetic mutation types, genetic diversity, and transmission of MDR-MTB on Hainan Island, serving as a significant reference for MDR-MTB surveillance and clinical decision-making.
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Affiliation(s)
- Jieying Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Chunchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yuni Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Zhuolin Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Wenhua Qiu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Shaowen Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yeteng Zhong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
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30
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Maladan Y, Safari D, Parikesit AA. Structural dynamics insights into the M306L, M306V, and D1024N mutations in Mycobacterium tuberculosis inducing resistance to ethambutol. Genomics Inform 2023; 21:e32. [PMID: 37813628 PMCID: PMC10584647 DOI: 10.5808/gi.23019] [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: 03/27/2023] [Revised: 05/18/2023] [Accepted: 08/07/2023] [Indexed: 10/11/2023] Open
Abstract
Resistance to anti-tuberculosis drugs, especially ethambutol (EMB), has been widely reported worldwide. EMB resistance is caused by mutations in the embB gene, which encodes the arabinosyl transferase enzyme. This study aimed to detect mutations in the embB gene of Mycobacterium tuberculosis from Papua and to evaluate their impact on the effectiveness of EMB. We analyzed 20 samples of M. tuberculosis culture that had undergone whole-genome sequencing, of which 19 samples were of sufficient quality for further bioinformatics analysis. Mutation analysis was performed using TBProfiler, which identified M306L, M306V, D1024N, and E378A mutations. In sample TB035, the M306L mutation was present along with E378A. The binding affinity of EMB to arabinosyl transferase was calculated using AutoDock Vina. The molecular docking results revealed that all mutants demonstrated an increased binding affinity to EMB compared to the native protein (-0.948 kcal/mol). The presence of the M306L mutation, when coexisting with E378A, resulted in a slight increase in binding affinity compared to the M306L mutation alone. The molecular dynamics simulation results indicated that the M306L, M306L + E378A, M306V, and E378A mutants decreased protein stability. Conversely, the D1024N mutant exhibited stability comparable to the native protein. In conclusion, this study suggests that the M306L, M306L + E378A, M306V, and E378A mutations may contribute to EMB resistance, while the D1024N mutation may be consistent with continued susceptibility to EMB.
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Affiliation(s)
- Yustinus Maladan
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia
| | - Dodi Safari
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong, Bogor 16911, Indonesia
| | - Arli Aditya Parikesit
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences (I3L), Jakarta 13210, Indonesia
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31
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Lempens P, Van Deun A, Aung KJM, Hossain MA, Behruznia M, Decroo T, Rigouts L, de Jong BC, Meehan CJ. Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh. Microb Genom 2023; 9:001109. [PMID: 37750750 PMCID: PMC10569737 DOI: 10.1099/mgen.0.001109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
The spread of multidrug-resistant tuberculosis (MDR-TB) is a growing problem in many countries worldwide. Resistance to one of the primary first-line drugs, rifampicin, is caused by mutations in the Mycobacterium tuberculosis rpoB gene. So-called borderline rpoB mutations confer low-level resistance, in contrast to more common rpoB mutations which confer high-level resistance. While some borderline mutations show lower fitness in vitro than common mutations, their in vivo fitness is currently unknown. We used a dataset of 394 whole genome sequenced MDR-TB isolates from Bangladesh, representing around 44 % of notified MDR-TB cases over 6 years, to look at differences in transmission clustering between isolates with borderline rpoB mutations and those with common rpoB mutations. We found a relatively low percentage of transmission clustering in the dataset (34.8 %) but no difference in clustering between different types of rpoB mutations. Compensatory mutations in rpoA, rpoB, and rpoC were associated with higher levels of transmission clustering as were lineages two, three, and four relative to lineage one. Young people as well as patients with high sputum smear positive TB were more likely to be in a transmission cluster. Our findings show that although borderline rpoB mutations have lower in vitro growth potential this does not translate into lower transmission potential or in vivo fitness. Proper detection of these mutations is crucial to ensure they do not go unnoticed and spread MDR-TB within communities.
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Affiliation(s)
- Pauline Lempens
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | | | | | | | - Tom Decroo
- Unit of HIV and TB, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Bouke C. de Jong
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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32
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Shibabaw A, Gelaw B, Ghanem M, Legall N, Schooley AM, Soehnlen MK, Salvador LCM, Gebreyes W, Wang SH, Tessema B. Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia. BMC Genomics 2023; 24:400. [PMID: 37460951 DOI: 10.1186/s12864-023-09502-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA.
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
| | - Baye Gelaw
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Angie M Schooley
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Marty K Soehnlen
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and life sciences, University of Arizona, Tucson, AZ, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Belay Tessema
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Dokrungkoon T, Tulyaprawat O, Suwannakarn K, Ngamskulrungroj P. In vitro modeling of isoniazid resistance mechanisms in Mycobacterium tuberculosis H37Rv. Front Microbiol 2023; 14:1171861. [PMID: 37492259 PMCID: PMC10364472 DOI: 10.3389/fmicb.2023.1171861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis, has been a global threat to human beings for several decades. Treating tuberculosis has become more difficult as the prevalence of drug-resistant tuberculosis has increased globally. Evidence suggests that the comprehensive landscape of resistance mechanisms in MTB is ambiguous. More importantly, little is known regarding the series of events connected to resistance mechanisms in MTB before exposure to anti-TB drugs, during exposure to the drugs, and finally, when the MTB becomes resistant after exposure, upon analyses of its genome. Methods We used the wild-type strain of MTB (H37Rv) in an in vitro model for generating induced resistance using a sub-inhibitory concentration of isoniazid, and the generated resistance-associated variants (RAVs) were identified using the whole genome sequencing method. Results The detection of an inhA promoter mutation (fabG1-15C>T), which results in increased production of InhA protein, was found to be a major mechanism for developing resistance to isoniazid in the first place. We observed adaptation of MTB resistance mechanisms in high isoniazid stress by alteration and abolishment of KatG due to the detection of katG S315N, the common region of mutation that confers isoniazid resistance, along with katG K414N, katG N138S, and katG A162E. Furthermore, we detected the ahpC-72C>T and ahpC 21C>A mutations, but further investigation is needed to determine their role in compensating for the loss of KatG activity. Discussion This suggests that increased InhA production is the main mechanism where there are low levels of isoniazid, whereas the alteration of KatG was found to be utilized in mycobacterium with a high concentration of isoniazid. Our work demonstrates that this in vitro approach of generating induced resistance could provide clinically relevant information after the fabG1-15C>T mutation, which is the common mutation found in clinical isolates. Moreover, other mutations detected in this work can also be found in clinical isolates. These findings may shed light on the impact of isoniazid in generating RAV and the resistance mechanism scenario that mycobacterium used under various isoniazid-pressuring conditions. More research is needed to understand better the role of RAV and mechanical resistance events within the mycobacterium genome in promoting a promising drug prediction platform that could lead to the right treatment for patients with MDR-TB and XDR-TB.
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Ismail N, Dippenaar A, Warren RM, Peters RPH, Omar SV. Emergence of Canonical and Noncanonical Genomic Variants following In Vitro Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine. Antimicrob Agents Chemother 2023; 67:e0136822. [PMID: 36892309 PMCID: PMC10112258 DOI: 10.1128/aac.01368-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/09/2023] [Indexed: 03/10/2023] Open
Abstract
In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible (fbiD: del555GCT) or rifampicin mono-resistant (fbiA: 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678, glpK, nuoG, and uvrD1. Genes with variants in the bedaquiline resistant mutants included atpE, fadE28, truA, mmpL5, glnH, and pks8, while clofazimine-resistant mutants displayed ppsD, fbiA, fbiD, mutT3, fadE18, Rv0988, and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.
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Affiliation(s)
- N. Ismail
- SAMRC Centre for Tuberculosis Research/DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Prinshof, Gauteng, South Africa
| | - A. Dippenaar
- Global Health Institute, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - R. M. Warren
- SAMRC Centre for Tuberculosis Research/DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - R. P. H. Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Prinshof, Gauteng, South Africa
- Department of Medical Microbiology, School CAPHRI (Care and Public Health Research Institute), Maastricht University, Maastricht, The Netherlands
| | - S. V. Omar
- Department of Medical Microbiology, School CAPHRI (Care and Public Health Research Institute), Maastricht University, Maastricht, The Netherlands
- National Institute for Communicable Diseases/National Health Laboratory Service, Centre for Tuberculosis, National TB Reference Laboratory & WHO Supranational TB Reference Laboratory, Johannesburg, Gauteng, South Africa
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Chopra H, Mohanta YK, Rauta PR, Ahmed R, Mahanta S, Mishra PK, Panda P, Rabaan AA, Alshehri AA, Othman B, Alshahrani MA, Alqahtani AS, AL Basha BA, Dhama K. An Insight into Advances in Developing Nanotechnology Based Therapeutics, Drug Delivery, Diagnostics and Vaccines: Multidimensional Applications in Tuberculosis Disease Management. Pharmaceuticals (Basel) 2023; 16:581. [PMID: 37111338 PMCID: PMC10145450 DOI: 10.3390/ph16040581] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/29/2023] Open
Abstract
Tuberculosis (TB), one of the deadliest contagious diseases, is a major concern worldwide. Long-term treatment, a high pill burden, limited compliance, and strict administration schedules are all variables that contribute to the development of MDR and XDR tuberculosis patients. The rise of multidrug-resistant strains and a scarcity of anti-TB medications pose a threat to TB control in the future. As a result, a strong and effective system is required to overcome technological limitations and improve the efficacy of therapeutic medications, which is still a huge problem for pharmacological technology. Nanotechnology offers an interesting opportunity for accurate identification of mycobacterial strains and improved medication treatment possibilities for tuberculosis. Nano medicine in tuberculosis is an emerging research field that provides the possibility of efficient medication delivery using nanoparticles and a decrease in drug dosages and adverse effects to boost patient compliance with therapy and recovery. Due to their fascinating characteristics, this strategy is useful in overcoming the abnormalities associated with traditional therapy and leads to some optimization of the therapeutic impact. It also decreases the dosing frequency and eliminates the problem of low compliance. To develop modern diagnosis techniques, upgraded treatment, and possible prevention of tuberculosis, the nanoparticle-based tests have demonstrated considerable advances. The literature search was conducted using Scopus, PubMed, Google Scholar, and Elsevier databases only. This article examines the possibility of employing nanotechnology for TB diagnosis, nanotechnology-based medicine delivery systems, and prevention for the successful elimination of TB illnesses.
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Affiliation(s)
- Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Yugal Kishore Mohanta
- Nanobiotechnology and Translational Knowledge Laboratory, Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), Techno City, 9th Mile, Ri-Bhoi, Baridua 793101, Meghalaya, India
| | | | - Ramzan Ahmed
- Nanobiotechnology and Translational Knowledge Laboratory, Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), Techno City, 9th Mile, Ri-Bhoi, Baridua 793101, Meghalaya, India
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati Centre, Guwahati 781008, Assam, India
| | | | - Paramjot Panda
- School of Biological Sciences, AIPH University, Bhubaneswar 754001, Odisha, India
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Basim Othman
- Department of Public Health, Faculty of Applied Medical Sciences, Albaha University, Albaha 65779, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ali S. Alqahtani
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, Abha 61481, Saudi Arabia
| | - Baneen Ali AL Basha
- Laboratory Department, King Fahad Specialist Hospital, Dammam 32253, Saudi Arabia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
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Hasan Z, Razzak SA, Kanji A, Shakoor S, Hasan R. Whole-genome sequencing reveals genotypic resistance in phenotypically susceptible Mycobacterium tuberculosis clinical isolates. Int J Mycobacteriol 2023; 12:179-183. [PMID: 37338481 DOI: 10.4103/ijmy.ijmy_101_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Background Whole-genome sequencing (WGS) data of Mycobacterium tuberculosis (MTB) complex strains have revealed insights about genetic variants associated with drug resistance (DR). Rapid genome-based diagnostics are being sought for specific and sensitive identification of DR; however, correct prediction of resistance genotypes requires both informatics tools and understanding of available evidence. We analyzed WGS datasets from phenotypically susceptible MTB strains using MTB resistance identification software. Methods WGS data for 1526 MTB isolates classified as phenotypically drug susceptible were downloaded from the ReSeqTB database. The TB-Profiler software was used to call Single Nucleotide Variants (SNV) associated with resistance to rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide, fluoroquinolone (FLQ), streptomycin (STR), and aminoglycosides. The SNV were further matched against the 2021 World Health Organization (WHO) catalogue of resistance mutations. Results Genome analysis of 1526 MTB strains susceptible to first-line drugs revealed 39 SNV associated with DR to be present in across 14 genes in 5.9% (n = 90) isolates. Further interpretation of SNV based on the WHO catalog of mutations revealed resistance that 21 (1.4%) MTB isolates were resistant to first-line (4 to RIF, 14 to INH, 3 to EMB) drugs. While, 36 (2.6%) isolates were resistant to second-line (19 to STR, 14 to FLQ, and three to capreomycin) agents. The most frequent predictive SNV were; rpoB Ser450 Leu for RIF; katG Ser315Thr, inhA Ser94Ala, fabG1-15C >T (for INH); gyrA Asp94Gly for FLQ; embB Met306 Leu for EMB; rpsL Lys43Arg for STR; and tlyA Asn236 Lys for Capreomycin. Conclusions Our study highlights the value of WGS-based sequence data for identifying resistance in MTB. It also shows how MTB strains may be misclassified simply on phenotypic drug susceptibility testing, and that correct genome interpretation is key for correct interpretation of resistance genotypes that can be used to guide clinical treatment.
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Affiliation(s)
- Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
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Huang YQ, Sun P, Chen Y, Liu HX, Hao GF, Song BA. Bioinformatics toolbox for exploring target mutation-induced drug resistance. Brief Bioinform 2023; 24:7026012. [PMID: 36738254 DOI: 10.1093/bib/bbad033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/25/2022] [Accepted: 01/14/2023] [Indexed: 02/05/2023] Open
Abstract
Drug resistance is increasingly among the main issues affecting human health and threatening agriculture and food security. In particular, developing approaches to overcome target mutation-induced drug resistance has long been an essential part of biological research. During the past decade, many bioinformatics tools have been developed to explore this type of drug resistance, and they have become popular for elucidating drug resistance mechanisms in a low cost, fast and effective way. However, these resources are scattered and underutilized, and their strengths and limitations have not been systematically analyzed and compared. Here, we systematically surveyed 59 freely available bioinformatics tools for exploring target mutation-induced drug resistance. We analyzed and summarized these resources based on their functionality, data volume, data source, operating principle, performance, etc. And we concisely discussed the strengths, limitations and application examples of these tools. Specifically, we tested some predictive tools and offered some thoughts from the clinician's perspective. Hopefully, this work will provide a useful toolbox for researchers working in the biomedical, pesticide, bioinformatics and pharmaceutical engineering fields, and a good platform for non-specialists to quickly understand drug resistance prediction.
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Affiliation(s)
- Yuan-Qin Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Ping Sun
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Yi Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Huan-Xiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078, SAR, China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Bao-An Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
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Sarmah DT, Parveen R, Kundu J, Chatterjee S. Latent tuberculosis and computational biology: A less-talked affair. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 178:17-31. [PMID: 36781150 DOI: 10.1016/j.pbiomolbio.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
Tuberculosis (TB) is a pervasive and devastating air-borne disease caused by the organisms belonging to the Mycobacterium tuberculosis (Mtb) complex. Currently, it is the global leader in infectious disease-related death in adults. The proclivity of TB to enter the latent state has become a significant impediment to the global effort to eradicate TB. Despite decades of research, latent tuberculosis (LTB) mechanisms remain poorly understood, making it difficult to develop efficient treatment methods. In this review, we seek to shed light on the current understanding of the mechanism of LTB, with an accentuation on the insights gained through computational biology. We have outlined various well-established computational biology components, such as omics, network-based techniques, mathematical modelling, artificial intelligence, and molecular docking, to disclose the crucial facets of LTB. Additionally, we highlighted important tools and software that may be used to conduct a variety of systems biology assessments. Finally, we conclude the article by addressing the possible future directions in this field, which might help a better understanding of LTB progression.
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Affiliation(s)
- Dipanka Tanu Sarmah
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Rubi Parveen
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Jayendrajyoti Kundu
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Samrat Chatterjee
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India.
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Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains. Tuberculosis (Edinb) 2023; 139:102324. [PMID: 36848710 DOI: 10.1016/j.tube.2023.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 02/15/2023]
Abstract
Whole-genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a rapidly growing tool to obtain results regarding the resistance and phylogeny of the strains. We evaluated the performances of two bioinformatics tools for the analysis of whole-genome sequences of MTBC strains. Two hundred and twenty-seven MTBC strains were isolated and whole-genome sequenced at the laboratory of Avicenne Hospital between 2015 and 2021. We investigated the resistance and susceptibility status of strains using two online tools, Mykrobe and PhyResSE. We compared the genotypic and phenotypic resistance results obtained by drug susceptibility testing. Unlike with the Mykrobe tool, sequencing quality data were obtained using PhyResSE: average coverage of 98% and average depth of 119X. We found a similar concordance between phenotypic and genotypic results when determining susceptibility to first-line anti-tuberculosis drugs (95%) with both tools. The sensitivity and specificity of each tool compared to the phenotypic method were respectively 72% [52-87] and 98% [96-99] for Mykrobe and 76% [57-90] and 97% [94-99] for PhyResSE. Mykrobe and PhyResSE were easy to use and efficient. These platforms are accessible to people not trained in bioinformatics and constitute a complementary approach to phenotypic methods for the study of MTBC strains.
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Macedo R, Isidro J, Ferreira R, Pinto M, Borges V, Duarte S, Vieira L, Gomes JP. Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. Int J Mol Sci 2023; 24:ijms24032912. [PMID: 36769230 PMCID: PMC9918089 DOI: 10.3390/ijms24032912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The application of whole genome sequencing of Mycobacterium tuberculosis directly on clinical samples has been investigated as a means to avoid the time-consuming need for culture isolation that can lead to a potential prolonged suboptimal antibiotic treatment. We aimed to provide a proof-of-concept regarding the application of the molecular capture of M. tuberculosis genomes directly from positive sputum samples as an approach for epidemiological and drug susceptibility predictions. Smear-positive sputum samples (n = 100) were subjected to the SureSelectXT HS Target Enrichment protocol (Agilent Technologies, Santa Clara, CA, USA) and whole-genome sequencing analysis. A higher number of reads on target were obtained for higher smear grades samples (i.e., 3+ followed by 2+). Moreover, 37 out of 100 samples showed ≥90% of the reference genome covered with at least 10-fold depth of coverage (27, 9, and 1 samples were 3+, 2+, and 1+, respectively). Regarding drug-resistance/susceptibility prediction, for 42 samples, ≥90% of the >9000 hits that are surveyed by TB-profiler were detected. Our results demonstrated that M. tuberculosis genome capture and sequencing directly from clinical samples constitute a potential valid backup approach for phylogenetic inferences and resistance prediction, essentially in settings when culture is not routinely performed or for samples that fail to grow.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
- Correspondence:
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Muacevic A, Adler JR. Multidrug-Resistant TB (MDR-TB) and Extensively Drug-Resistant TB (XDR-TB) Among Children: Where We Stand Now. Cureus 2023; 15:e35154. [PMID: 36819973 PMCID: PMC9938784 DOI: 10.7759/cureus.35154] [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] [Accepted: 02/18/2023] [Indexed: 02/20/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) has continued to be a global health cataclysm. It is an arduous condition to tackle but is curable with the proper choice of drug and adherence to the drug therapy. WHO has introduced newer drugs with all-oral shorter regimens, but the COVID-19 pandemic has disrupted the achievements and raised the severity. The COVID-19 controlling mechanism is based on social distancing, using face masks, personal protective equipment, medical glove, head shoe cover, face shield, goggles, hand hygiene, and many more. Around the globe, national and international health authorities impose lockdown and movement control orders to ensure social distancing and prevent transmission of COVID-19 infection. Therefore, WHO proposed a TB control program impaired during a pandemic. Children, the most vulnerable group, suffer more from the drug-resistant form and act as the storehouse of future fatal cases. It has dire effects on physical health and hampers their mental health and academic career. Treatment of drug-resistant cases has more success stories in children than adults, but enrollment for treatment has been persistently low in this age group. Despite that, drug-resistant childhood tuberculosis has been neglected, and proper surveillance has not yet been achieved. Insufficient reporting, lack of appropriate screening tools for children, less accessibility to the treatment facility, inadequate awareness, and reduced funding for TB have worsened the situation. All these have resulted in jeopardizing our dream to terminate this deadly condition. So, it is high time to focus on this issue to achieve our Sustainable Development Goals (SDGs), the goal of ending TB by 2030, as planned by WHO. This review explores childhood TB's current position and areas to improve. This review utilized electronic-based data searched through PubMed, Google Scholar, Google Search Engine, Science Direct, and Embase.
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Tanwar AS, Shruptha P, Paul B, Murali TS, Brand A, Satyamoorthy K. How Can Omics Inform Diabetic Foot Ulcer Clinical Management? A Whole Genome Comparison of Four Clinical Strains of Staphylococcus aureus. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:51-61. [PMID: 36753700 DOI: 10.1089/omi.2022.0184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Foot ulcers and associated infections significantly contribute to morbidity and mortality in diabetes. While diverse pathogens are found in the diabetes-related infected ulcers, Staphylococcus aureus remains one of the most virulent and widely prevalent pathogens. The high prevalence of S. aureus in chronic wound infections, especially in clinical settings, is attributed to its ability to evolve and acquire resistance against common antibiotics and to elicit an array of virulence factors. In this study, whole genome comparison of four strains of S. aureus (MUF168, MUF256, MUM270, and MUM475) isolated from diabetic foot ulcer (DFU) infections showing varying resistance patterns was carried out to study the genomic similarity, antibiotic resistance profiling, associated virulence factors, and sequence variations in drug targets. The comparative genome analysis showed strains MUM475 and MUM270 to be highly resistant, MUF256 with moderate levels of resistance, and MUF168 to be the least resistant. Strain MUF256 and MUM475 harbored more virulence factors compared with other two strains. Deleterious sequence variants were observed suggesting potential role in altering drug targets and drug efficacy. This comparative whole genome study offers new molecular insights that may potentially inform evidence-based diagnosis and treatment of DFUs in the clinic.
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Affiliation(s)
- Ankit Singh Tanwar
- Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.,United Nations University-Maastricht Economic and Social Research Institute on Innovation and Technology (UNU-MERIT), Maastricht, The Netherlands
| | - Padival Shruptha
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Bobby Paul
- Department of Bioinformatics, and Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Thokur Sreepathy Murali
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Angela Brand
- Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.,United Nations University-Maastricht Economic and Social Research Institute on Innovation and Technology (UNU-MERIT), Maastricht, The Netherlands.,Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
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Valdemar-Aguilar CM, Manisekaran R, Acosta-Torres LS, López-Marín LM. Spotlight on mycobacterial lipid exploitation using nanotechnology for diagnosis, vaccines, and treatments. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 48:102653. [PMID: 36646193 PMCID: PMC9839462 DOI: 10.1016/j.nano.2023.102653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/24/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
Tuberculosis (TB), historically the most significant cause of human morbidity and mortality, has returned as the top infectious disease worldwide, under circumstances worsened by the COVID-19 pandemic's devastating effects on public health. Although Mycobacterium tuberculosis, the causal agent, has been known of for more than a century, the development of tools to control it has been largely neglected. With the advancement of nanotechnology, the possibility of engineering tools at the nanoscale creates unique opportunities to exploit any molecular type. However, little attention has been paid to one of the major attributes of the pathogen, represented by the atypical coat and its abundant lipids. In this review, an overview of the lipids encountered in M. tuberculosis and interest in exploiting them for the development of TB control tools are presented. Then, the amalgamation of nanotechnology with mycobacterial lipids from both reported and future works are discussed.
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Affiliation(s)
- Carlos M. Valdemar-Aguilar
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, 76230 Querétaro, Mexico,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico
| | - Ravichandran Manisekaran
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37689 León, Mexico.
| | - Laura S. Acosta-Torres
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37689 León, Mexico
| | - Luz M. López-Marín
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, 76230 Querétaro, Mexico,Corresponding authors
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Phelan J, Gomez-Gonzalez PJ, Andreu N, Omae Y, Toyo-Oka L, Yanai H, Miyahara R, Nedsuwan S, de Sessions PF, Campino S, Sallah N, Parkhill J, Smittipat N, Palittapongarnpim P, Mushiroda T, Kubo M, Tokunaga K, Mahasirimongkol S, Hibberd ML, Clark TG. Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease. Nat Commun 2023; 14:549. [PMID: 36725857 PMCID: PMC9892022 DOI: 10.1038/s41467-023-36282-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
The genetics underlying tuberculosis (TB) pathophysiology are poorly understood. Human genome-wide association studies have failed so far to reveal reproducible susceptibility loci, attributed in part to the influence of the underlying Mycobacterium tuberculosis (Mtb) bacterial genotype on the outcome of the infection. Several studies have found associations of human genetic polymorphisms with Mtb phylo-lineages, but studies analysing genome-genome interactions are needed. By implementing a phylogenetic tree-based Mtb-to-human analysis for 714 TB patients from Thailand, we identify eight putative genetic interaction points (P < 5 × 10-8) including human loci DAP and RIMS3, both linked to the IFNγ cytokine and host immune system, as well as FSTL5, previously associated with susceptibility to TB. Many of the corresponding Mtb markers are lineage specific. The genome-to-genome analysis reveals a complex interactome picture, supports host-pathogen adaptation and co-evolution in TB, and has potential applications to large-scale studies across many TB endemic populations matched for host-pathogen genomic diversity.
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Affiliation(s)
- Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Nuria Andreu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Licht Toyo-Oka
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Yanai
- Fukujuji Hospital and Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Reiko Miyahara
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neneh Sallah
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nat Smittipat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Prasit Palittapongarnpim
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom.
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Sanabria GE, Sequera G, Aguirre S, Méndez J, Dos Santos PCP, Gustafson NW, Godoy M, Ortiz A, Cespedes C, Martínez G, García-Basteiro AL, Andrews JR, Croda J, Walter KS. Phylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay. Nat Commun 2023; 14:303. [PMID: 36658111 PMCID: PMC9849832 DOI: 10.1038/s41467-023-35813-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Recent rises in incident tuberculosis (TB) cases in Paraguay and the increasing concentration of TB within prisons highlight the urgency of targeting strategies to interrupt transmission and prevent new infections. However, whether specific cities or carceral institutions play a disproportionate role in transmission remains unknown. We conducted prospective genomic surveillance, sequencing 471 Mycobacterium tuberculosis complex genomes, from inside and outside prisons in Paraguay's two largest urban areas, Asunción and Ciudad del Este, from 2016 to 2021. We found genomic evidence of frequent recent transmission within prisons and transmission linkages spanning prisons and surrounding populations. We identified a signal of frequent M. tuberculosis spread between urban areas and marked recent population size expansion of the three largest genomic transmission clusters. Together, our findings highlight the urgency of strengthening TB control programs to reduce transmission risk within prisons in Paraguay, where incidence was 70 times that outside prisons in 2021.
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Affiliation(s)
| | - Guillermo Sequera
- Instituto de Salud Global de Barcelona (ISGLOBAL), Barcelona, Spain
- Programa Nacional de Control de la Tuberculosis, Ministerio de Salud Pública y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Sarita Aguirre
- Programa Nacional de Control de la Tuberculosis, Ministerio de Salud Pública y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Julieta Méndez
- Instituto Regional de Investigación en Salud, Caaguazú, Paraguay
| | - Paulo César Pereira Dos Santos
- Postgraduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Mato Grosso do Sul, Brazil
| | - Natalie Weiler Gustafson
- Laboratorio Central de Salud Pública (LCSP), Ministerio de Salud Publica y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Margarita Godoy
- Laboratorio Central de Salud Pública (LCSP), Ministerio de Salud Publica y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Analía Ortiz
- Instituto Regional de Investigación en Salud, Caaguazú, Paraguay
| | - Cynthia Cespedes
- Programa Nacional de Control de la Tuberculosis, Ministerio de Salud Pública y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Gloria Martínez
- Instituto Regional de Investigación en Salud, Caaguazú, Paraguay
| | - Alberto L García-Basteiro
- Instituto de Salud Global de Barcelona (ISGLOBAL), Barcelona, Spain
- Centro de Investigação em Saude de Manhiça (CISM), Maputo, Mozambique
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julio Croda
- Federal University of Mato Grosso do Sul - UFMS, Campo Grande, MS, Brazil
- Oswaldo Cruz Foundation Mato Grosso do Sul, Mato Grosso do Sul, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
| | - Katharine S Walter
- Division of Epidemiology, University of Utah, Salt Lake City, UT, 84105, USA.
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Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multi-drug resistant tuberculosis. Sci Rep 2023; 13:623. [PMID: 36635309 PMCID: PMC9837068 DOI: 10.1038/s41598-023-27516-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
Resistance to isoniazid (INH) and rifampicin (RIF) first-line drugs in Mycobacterium tuberculosis (Mtb), together called multi-drug resistance, threatens tuberculosis control. Resistance mutations in katG (for INH) and rpoB (RIF) genes often come with fitness costs. To overcome these costs, Mtb compensatory mutations have arisen in rpoC/rpoA (RIF) and ahpC (INH) loci. By leveraging the presence of known compensatory mutations, we aimed to detect novel resistance mutations occurring in INH and RIF target genes. Across ~ 32 k Mtb isolates with whole genome sequencing (WGS) data, there were 6262 (35.7%) with INH and 5435 (30.7%) with RIF phenotypic resistance. Known mutations in katG and rpoB explained ~ 99% of resistance. However, 188 (0.6%) isolates had ahpC compensatory mutations with no known resistance mutations in katG, leading to the identification of 31 putative resistance mutations in katG, each observed in at least 3 isolates. These putative katG mutations can co-occur with other INH variants (e.g., katG-Ser315Thr, fabG1 mutations). For RIF, there were no isolates with rpoC/rpoA compensatory mutations and unknown resistance mutations. Overall, using WGS data we identified putative resistance markers for INH that could be used for genotypic drug-resistance profiling. Establishing the complete repertoire of Mtb resistance mutations will assist the clinical management of tuberculosis.
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Morey-León G, Andrade-Molina D, Fernández-Cadena JC, Berná L. Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador. BMC Genomics 2022; 23:844. [PMID: 36544084 PMCID: PMC9769008 DOI: 10.1186/s12864-022-09042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador. RESULTS Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected. CONCLUSION This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance. In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.
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Affiliation(s)
- Gabriel Morey-León
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.442157.10000 0001 1183 0630Universidad de Guayaquil, Guayaquil, Ecuador ,grid.442156.00000 0000 9557 7590Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Derly Andrade-Molina
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Juan Carlos Fernández-Cadena
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Luisa Berná
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.11630.350000000121657640Facultad de Ciencias, Unidad de Genómica Evolutiva, Universidad de La República, Montevideo, Uruguay
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Yee R, Simner PJ. Next-Generation Sequencing Approaches to Predicting Antimicrobial Susceptibility Testing Results. Clin Lab Med 2022; 42:557-572. [PMID: 36368782 DOI: 10.1016/j.cll.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rebecca Yee
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
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Kim N, Seok KH, Shin S, Kim B, Park H, Roh EY, Yoon JH, Shin S. Evaluation of Five User-Friendly Whole Genome Sequencing Software for Mycobacterium tuberculosis in Clinical Application. J Korean Med Sci 2022; 37:e328. [PMID: 36631026 PMCID: PMC9705210 DOI: 10.3346/jkms.2022.37.e328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/15/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) is an increasingly useful tool for tuberculosis (TB) diagnosis and disease management. In this study, we evaluated the utility of user-friendly WGS tools in reporting resistance profiles and identifying lineages of clinical TB isolates from South Korea. METHODS Forty clinical samples from TB patients showing discrepancies between their rapid molecular and conventional drug susceptibility tests were used in this study. Among these clinical isolates, 37 strains were successfully evaluated via WGS software, using the GenTB, TB Profiler, PhyResSE, CASTB, and Mykrobe. RESULTS More accurate and faster susceptibility results could be obtained with isoniazid than with rifampin. Using the phenotypic test as the gold standard, the isoniazid concordance rate between phenotypic drug susceptibility test (DST) and WGS (GenTB: 45.9%, TB profiler: 40.5%, PhyResSE: 40.5%, CASTB: 48.6%, and Mykrobe: 43.2%) was much higher than between phenotypic DST and rapid molecular genotypic DST (18.9%) among the 37 strains. In contrast, the rifampin concordance rate between phenotypic DST and WGS and that between phenotypic DST and rapid molecular genotypic DST was similar (81.1-89.2%). We also found novel mutations associated with INH in katG and ahpC gene region, not covered by the line probe assay. In addition, lineage analysis identified 81.1% of these samples as L2 East Asian lineage strains, and 18.9% as L4 Euro-American lineage strains. CONCLUSION WGS may play a pivotal role in TB diagnosis and the detection of drug resistance, genetic diversity, and transmission dynamics in the near future because of its accuracy, speed, and extensibility.
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Affiliation(s)
- Namhee Kim
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kwang Hyuk Seok
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Cheongju, Korea
| | - Soyoun Shin
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Cheongju, Korea
- Seegene Medical Foundation, Daejeon, Korea
| | - Boram Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.
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Khanna A, Saha R, Ahmad N. National TB elimination programme - What has changed. Indian J Med Microbiol 2022; 42:103-107. [PMID: 36402676 PMCID: PMC9672688 DOI: 10.1016/j.ijmmb.2022.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Before the start of Coronavirus (COVID-19) pandemic, TB was the leading cause of death due to a single infectious agent, ranking well above HIV/AIDS. Almost one-fourth of the world's population is infected with M. tuberculosis. TB is curable and preventable. About 85% of people who develop TB can be successfully treated with drug regimens of 6 months. Universal health coverage (UHC) is necessary to ensure that all those with the disease can access these treatments. Research breakthroughs (e.g., newer rapid diagnostic techniques, drugs, newer vaccine) are needed to rapidly reduce the number of new cases each year (TB incidence) worldwide. OBJECTIVE Changes in the National TB Elimination Programme since its inception. CONTENT The Government of India launched the "National TB Programme" in 1962 as District TB Centre model involved with BCG vaccination and TB treatment to fight tuberculosis, a major public health problem. The tuberculosis control programme has come a long way since then and has undergone major changes over the past few years The Ministry of Health and Family Welfare has developed the "National Strategic Plan" for Tuberculosis Elimination (2017-25) which encapsulates the bold and innovative steps required to eliminate TB in India by 2025, five years ahead of the global targets. By 2020 it was clear that the NSP- 2017-25 will not be able to meet these objectives, so another new NSP India 2025 had been launched in 2020. India has been actively involved in TB control activities for more than 50 years now. TB still continues to be a severe health problem in India. The country is now better prepared to tackle TB than before. It now has advanced and effective interventions and technologies for diagnosis, treatment and care of TB cases.
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Affiliation(s)
| | - Rumpa Saha
- Department of Microbiology, University College of Medical Sciences & GTB Hospital, Dilshad Garden, Delhi, 95, India.
| | - Nadeem Ahmad
- Department of Microbiology, University College of Medical Sciences & GTB Hospital, Dilshad Garden, Delhi, 95, India.
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