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Singhal R, Hingane S, Bhalla M, Sharma A, Ferdosh S, Tiwari A, Jayaswal P, Yadav RN, Arora J, Dewan RK, Sharma S. Evaluation of AAICare®-TB sequence analysis tool for accurate diagnosis of drug-resistant tuberculosis: A comparative study with TB-Profiler and Mykrobe. Tuberculosis (Edinb) 2024; 147:102515. [PMID: 38744006 DOI: 10.1016/j.tube.2024.102515] [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: 11/10/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
A rapid and comprehensive drug susceptibility test is essential for eliminating drug resistant tuberculosis. Next generation sequencing (NGS) based susceptibility testing is being explored as a potential substitute for the conventional phenotypic and genotypic testing methods. However, the adoption of NGS based genotypic susceptibility testing depends on the availability of simple, accurate and efficient analysis tools. This preliminary study aimed to evaluate the performance of a Mycobacterium tuberculosis (Mtb) genome analysis pipeline, AAICare®-TB, for susceptibility prediction, in comparison to two widely used gDST prediction tools, TB-Profiler and Mykrobe. This study was performed in a National Reference Laboratory in India on presumptive drug-resistant tuberculosis (DR-TB) isolates. Whole genome sequences of the 120 cultured isolates were obtained through Illumina sequencing on a MiSeq platform. Raw sequences were simultaneously analysed using the three tools. Susceptibility prediction reports thus generated, were compared to estimate the total concordance and discordance. WHO mutation catalogue (1st edition, 2021) was used as the reference standard for categorizing the mutations. In this study, AAICare®-TB was able to predict drug resistance status for First Line (Streptomycin, Isoniazid, Rifampicin, Ethambutol and Pyrazinamide) and Second Line drugs (Fluoroquinolones, Second Line Injectables and Ethionamide) in 93 samples along with lineage and hetero-resistance as per the WHO guidelines.
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Affiliation(s)
- Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India.
| | - Smita Hingane
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Manpreet Bhalla
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Aniruddh Sharma
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Sehnaz Ferdosh
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Avlokita Tiwari
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Praapti Jayaswal
- AarogyaAI® Innovations Pvt. Ltd., No. 677, 1st Floor, Suite 918, 13th Cross, Sector 1, HSR Layout, Bangalore, 560102, Karnataka, India
| | - Raj Narayan Yadav
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Jyoti Arora
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Ravindra Kumar Dewan
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
| | - Sangeeta Sharma
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, 110030, India
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Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. PLoS Comput Biol 2024; 20:e1011408. [PMID: 38768228 PMCID: PMC11104602 DOI: 10.1371/journal.pcbi.1011408] [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: 08/02/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.
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Affiliation(s)
- Sanjeevani Choudhery
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Aarthi Srinivasan
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
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Xiong XS, Zhang XD, Yan JW, Huang TT, Liu ZZ, Li ZK, Wang L, Li F. Identification of Mycobacterium tuberculosis Resistance to Common Antibiotics: An Overview of Current Methods and Techniques. Infect Drug Resist 2024; 17:1491-1506. [PMID: 38628245 PMCID: PMC11020249 DOI: 10.2147/idr.s457308] [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: 01/14/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is an essential cause of tuberculosis treatment failure and death of tuberculosis patients. The rapid and reliable profiling of Mycobacterium tuberculosis (MTB) drug resistance in the early stage is a critical research area for public health. Then, most traditional approaches for detecting MTB are time-consuming and costly, leading to the inappropriate therapeutic schedule resting on the ambiguous information of MTB drug resistance, increasing patient economic burden, morbidity, and mortality. Therefore, novel diagnosis methods are frequently required to meet the emerging challenges of MTB drug resistance distinguish. Considering the difficulty in treating MDR-TB, it is urgently required for the development of rapid and accurate methods in the identification of drug resistance profiles of MTB in clinical diagnosis. This review discussed recent advances in MTB drug resistance detection, focusing on developing emerging approaches and their applications in tangled clinical situations. In particular, a brief overview of antibiotic resistance to MTB was present, referred to as intrinsic bacterial resistance, consisting of cell wall barriers and efflux pumping action and acquired resistance caused by genetic mutations. Then, different drug susceptibility test (DST) methods were described, including phenotype DST, genotype DST and novel DST methods. The phenotype DST includes nitrate reductase assay, RocheTM solid ratio method, and liquid culture method and genotype DST includes fluorescent PCR, GeneXpert, PCR reverse dot hybridization, ddPCR, next-generation sequencing and gene chips. Then, novel DST methods were described, including metabolism testing, cell-free DNA probe, CRISPR assay, and spectral analysis technique. The limitations, challenges, and perspectives of different techniques for drug resistance are also discussed. These methods significantly improve the detection sensitivity and accuracy of multidrug-resistant tuberculosis (MRT) and can effectively curb the incidence of drug-resistant tuberculosis and accelerate the process of tuberculosis eradication.
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Affiliation(s)
- Xue-Song Xiong
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Xue-Di Zhang
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Jia-Wei Yan
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Ting-Ting Huang
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Zhan-Zhong Liu
- Department of Pharmacy, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Zheng-Kang Li
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Liang Wang
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fen Li
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
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Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.03.551759. [PMID: 37577548 PMCID: PMC10418283 DOI: 10.1101/2023.08.03.551759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.
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Affiliation(s)
- Sanjeevani Choudhery
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Aarthi Srinivasan
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
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Sun H, Sheng G, Xu Y, Chu H, Cao T, Dai G, Tian N, Duan H, Sun Z. Efflux pump Rv1258c activates novel functions of the oxidative stress and via the VII secretion system ESX-3-mediated iron metabolic pathway in Mycobacterium tuberculosis. Microbes Infect 2024; 26:105239. [PMID: 37863312 DOI: 10.1016/j.micinf.2023.105239] [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: 04/27/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Oxidative stress and iron metabolism are essential for Mycobacterium tuberculosis (M.tb) survival in host cells. The efflux pump Rv1258c belongs to the major facilitator superfamily (MFS) and can actively pump drugs to promote certain drug resistance in M.tb. In this study, we compared H37RvΔRv1258c with wild-type (WT) M.tb H37Rv. The qRT-PCR results suggested that Rv1258c is potentially involved in the iron metabolic pathway by regulating the expression of ESX-3, which is required for iron uptake. Protein-Protein Affinity Predictor (PPA-Pred2) and the artificial intelligence program AlphaFold 2 were used for prediction and showed that Rv1258c has direct interactions with PPE4 and EccD3 but weak interactions with EccB3. This was further determined via protein-protein interaction analysis of the yeast two-hybrid expression system. By comparing mutant H37RvΔRv1258c strains with WT strains, we discovered that the absence of Rv1258c led to elevated intracellular H+ potential and NAD+/NADH ratios in M.tb, thereby resulting in oxidative stress. We hypothesize that the efflux pump Rv1258c not only has the function of regulating drug resistance in M.tb but also has a novel function in activating oxidative stress and regulating ESX-3-associated iron metabolism in M.tb.
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Affiliation(s)
- Hong Sun
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Gang Sheng
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Yuhui Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing 100700, China
| | - Hongqian Chu
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Tingming Cao
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Guangming Dai
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Na Tian
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Huijuan Duan
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Zhaogang Sun
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China, Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
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Zhang P, Ji L, Yan W, Chen L, Zhu X, Lu Z, Dong F. Whole-genome sequencing and transcriptome-characterized mechanism of streptomycin resistance in Vibrio parahaemolyticus O10: K4. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105540. [PMID: 38114043 DOI: 10.1016/j.meegid.2023.105540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Streptomycin resistance in V. parahaemolyticus has been widespread in both clinical and environmental isolates. Therefore, it is of great significance to characterize the mechanism of streptomycin resistance in V. parahaemolyticus. O10:K4 has emerged and becoming the new dominant serotype since 2020. In this study, we isolated a total of 36 strains of V. parahaemolyticus O10:K4 from 2020 to 2022 and found that more than half of them were resistant to streptomycin. We obtained streptomycin resistant and sensitive strains by detecting the resistance profiles. Whole-genome sequencing showed that VP_RS10735 and VP_RS05605 were the predominant mutations in streptomycin resistant O10:K4 clinical isolates. In addition, this study provided global insight into the characteristics of the transcriptome signature of streptomycin resistance, revealing that efflux transporters play a key role in streptomycin resistance. Finally, we found that streptomycin resistant strain was more virulent than sensitive strain. The results of this study should advance our understanding of the mechanisms of aminoglycoside resistance.
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Affiliation(s)
- Peng Zhang
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, China
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, China
| | - Wei Yan
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, China
| | - Xiaohua Zhu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, China
| | - Zhonghao Lu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, China
| | - Fenfen Dong
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, China.
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Mekonnen D, Munshea A, Nibret E, Adnew B, Getachew H, Kebede A, Gebrewahid A, Herrera-Leon S, Aramendia AA, Benito A, Abascal E, Jacqueline C, Aseffa A, Herrera-Leon L. Mycobacterium tuberculosis Sub-Lineage 4.2.2/SIT149 as Dominant Drug-Resistant Clade in Northwest Ethiopia 2020-2022: In-silico Whole-Genome Sequence Analysis. Infect Drug Resist 2023; 16:6859-6870. [PMID: 37908783 PMCID: PMC10614653 DOI: 10.2147/idr.s429001] [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: 07/30/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Drug resistance (DR) in Mycobacterium tuberculosis complex (MTBC) is mainly associated with certain lineages and varies across regions and countries. The Beijing genotype is the leading resistant lineage in Asia and western countries. M. tuberculosis (Mtb) (sub) lineages responsible for most drug resistance in Ethiopia are not well described. Hence, this study aimed to identify the leading drug resistance sub-lineages and characterize first-line anti-tuberculosis drug resistance-associated single nucleotide polymorphisms (SNPs). Methods A facility-based cross-sectional study was conducted in 2020-2022 among new and presumptive multidrug resistant-TB (MDR-TB) cases in Northwest Ethiopia. Whole-genome sequencing (WGS) was performed on 161 isolates using Illumina NovaSeq 6000 technology. The SNP mutations associated with drug resistance were identified using MtbSeq and TB profiler Bioinformatics softwares. Results Of the 146 Mtb isolates that were successfully genotyped, 20 (13.7%) harbored one or more resistance-associated SNPs. L4.2.2.ETH was the leading drug-resistant sub-lineage, accounting for 10/20 (50%) of the resistant Mtb. MDR-TB isolates showed extensive mutations against first-line anti-TB drugs. Ser450Leu/(tcg/tTg) for Rifampicin (RIF), Ser315Thr/(agc/aCc) for Isoniazid (INH), Met306Ile/(atg/atA(C)) for Ethambutol (EMB), and Gly69Asp for Streptomycin (STR) were the leading resistance associated mutations which accounted for 56.5%, 89.5%, 47%, and 29.4%, respectively. The presence of both clustered and non-clustered drug resistance (DR) isolates indicated that the epidemics is driven by both new DR development and acquired resistance. Conclusion The high prevalence of drug-resistant TB due to geographically restricted sub-lineages (L4.2.2.ETH) indicates the ongoing local micro epidemics. The Mtb drug resistance surveillance system must be improved. Further evolutionary analysis of L4.2.2.ETH strain is highly desirable to understand evolutionary forces that leads L4.2.2.ETH in to high level DR and transmissible sub-lineage.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Laboratory Sciences, School of Health Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshea
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Endalkachew Nibret
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | | | | | - Amiro Kebede
- Amhara Public Health Institute, Bahir Dar, Ethiopia
| | | | - Silvia Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Agustín Benito
- National Center of Tropical Medicine, Institute of Health Carlos III, Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Madrid, Spain
| | - Estefanía Abascal
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Camille Jacqueline
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- European Public Health Microbiology Training Programme, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Laura Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
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Robbins L, Balaram A, Dejneka S, McMahon M, Najibi Z, Pawlowicz P, Conrad WH. Heterologous production of the D-cycloserine intermediate O-acetyl-L-serine in a human type II pulmonary cell model. Sci Rep 2023; 13:8551. [PMID: 37237156 DOI: 10.1038/s41598-023-35632-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Tuberculosis (TB) is the second leading cause of death by a single infectious disease behind COVID-19. Despite a century of effort, the current TB vaccine does not effectively prevent pulmonary TB, promote herd immunity, or prevent transmission. Therefore, alternative approaches are needed. We seek to develop a cell therapy that produces an effective antibiotic in response to TB infection. D-cycloserine (D-CS) is a second-line antibiotic for TB that inhibits bacterial cell wall synthesis. We have determined D-CS to be the optimal candidate for anti-TB cell therapy due to its effectiveness against TB, relatively short biosynthetic pathway, and its low-resistance incidence. The first committed step towards D-CS synthesis is catalyzed by the L-serine-O-acetyltransferase (DcsE) which converts L-serine and acetyl-CoA to O-acetyl-L-serine (L-OAS). To test if the D-CS pathway could be an effective prophylaxis for TB, we endeavored to express functional DcsE in A549 cells as a human pulmonary model. We observed DcsE-FLAG-GFP expression using fluorescence microscopy. DcsE purified from A549 cells catalyzed the synthesis of L-OAS as observed by HPLC-MS. Therefore, human cells synthesize functional DcsE capable of converting L-serine and acetyl-CoA to L-OAS demonstrating the first step towards D-CS production in human cells.
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Affiliation(s)
- Laurel Robbins
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Ariane Balaram
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Stefanie Dejneka
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Matthew McMahon
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Zarina Najibi
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Peter Pawlowicz
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - William H Conrad
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA.
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Stanley S, Liu Q, Fortune SM. Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine. Front Cell Infect Microbiol 2022; 12:1007958. [PMID: 36262182 PMCID: PMC9574059 DOI: 10.3389/fcimb.2022.1007958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/14/2022] [Indexed: 01/27/2023] Open
Abstract
In the face of the unrelenting global burden of tuberculosis (TB), antibiotics remain our most effective tools to save lives and control the spread of Mycobacterium tuberculosis (Mtb). However, we confront a dual challenge in our use of antibiotics: simplifying and shortening the TB drug regimen while also limiting the emergence and propagation of antibiotic resistance. This task is now more feasible due to the increasing availability of bacterial genomic data at or near the point of care. These resources create an opportunity to envision how integration of bacterial genetic determinants of antibiotic response into treatment algorithms might transform TB care. Historically, Mtb drug resistance studies focused on mutations in genes encoding antibiotic targets and the resulting increases in the minimal inhibitory concentrations (MICs) above a breakpoint value. But recent progress in elucidating the effects of functional genetic diversity in Mtb has revealed various genetic loci that are associated with drug phenotypes such as low-level MIC increases and tolerance which predict the development of resistance and treatment failure. As a result, we are now poised to advance precision medicine approaches in TB treatment. By incorporating information regarding Mtb genetic characteristics into the development of drug regimens, clinical care which tailors antibiotic treatment to maximize the likelihood of success has come into reach.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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10
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Li H, Yuan J, Duan S, Pang Y. Resistance and tolerance of Mycobacterium tuberculosis to antimicrobial agents-How M. tuberculosis can escape antibiotics. WIREs Mech Dis 2022; 14:e1573. [PMID: 35753313 DOI: 10.1002/wsbm.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) poses a serious threat to public health worldwide since it was discovered. Until now, TB has been one of the top 10 causes of death from a single infectious disease globally. The treatment of active TB cases majorly relies on various anti-tuberculosis drugs. However, under the selection pressure by drugs, the continuous evolution of Mycobacterium tuberculosis (Mtb) facilitates the emergence of drug-resistant strains, further resulting in the accumulation of tubercle bacilli with multiple drug resistance, especially deadly multidrug-resistant TB and extensively drug-resistant TB. Researches on the mechanism of drug action and drug resistance of Mtb provide a new scheme for clinical management of TB patients, and prevention of drug resistance. In this review, we summarized the molecular mechanisms of drug resistance of existing anti-TB drugs to better understand the evolution of drug resistance of Mtb, which will provide more effective strategies against drug-resistant TB, and accelerate the achievement of the EndTB Strategy by 2035. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jinfeng Yuan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shujuan Duan
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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11
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Rana V, Singh N, Nikam C, Kambli P, Singh PK, Singh U, Jain A, Rodrigues C, Sharma C. Molecular Epidemiology and Polymorphism Analysis in Drug-Resistant Genes in M. tuberculosis Clinical Isolates from Western and Northern India. Infect Drug Resist 2022; 15:1717-1732. [PMID: 35422638 PMCID: PMC9005233 DOI: 10.2147/idr.s345855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction The mechanistic details of first line drug (FLD) resistance have been thoroughly explored but the genetic resistance mechanisms of second line injectables, which form the backbone of the combinatorial drug resistant tuberculosis therapy, are partially identified. This study aims to highlight the genetic and spoligotypic differences in the second line drug (SLD) resistant and sensitive Mycobacterium tuberculosis (Mtb) clinical isolates from Mumbai (Western India) and Lucknow (Northern India). Methods The rrs, eis, whiB7, tlyA, gyrA and gyrB target loci were screened in 126 isolates and spoligotyped. Results The novel mutations were observed in whiB7 loci (A43T, C44A, C47A, G48T, G59A and T152G in 5’-UTR; A42C, C253T and T270G in gene), tlyA (+CG200, G165A, C415G, and +G543) and gyrB (+G1359 and +A1429). Altogether, the rrs, eis, and whiB7 loci harbored mutations in ~86% and ~47% kanamycin resistant isolates from Mumbai and Lucknow, respectively. Mumbai strains displayed higher prevalence of mutations in gyrA (~85%) and gyrB loci (~13%) as compared to those from Lucknow (~69% and ~3.0%, respectively). Further, spoligotyping revealed that Beijing lineage is distributed equally amongst the drug resistant strains of Mumbai and Lucknow, but EAI-5 is existed at a higher level only in Mumbai. The lineages Manu2, CAS1-Delhi and T1 are more prevalent in Lucknow. Conclusion Besides identifying novel mutations in whiB7, tlyA and gyrB target loci, our analyses unveiled a potential polymorphic and phylogeographical demarcation among two distinct regions.
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Affiliation(s)
- Vibhuti Rana
- CSIR- Institute of Microbial Technology, Chandigarh, 160036, India
| | - Nittu Singh
- CSIR- Institute of Microbial Technology, Chandigarh, 160036, India
| | - Chaitali Nikam
- Department of Microbiology, P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, 400016, Maharashtra, India
| | - Priti Kambli
- Department of Microbiology, P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, 400016, Maharashtra, India
| | - Pravin K Singh
- Department of Microbiology, King George Medical University, Lucknow, 226003, Uttar Pradesh, India
| | - Urmila Singh
- Department of Microbiology, King George Medical University, Lucknow, 226003, Uttar Pradesh, India
| | - Amita Jain
- Department of Microbiology, King George Medical University, Lucknow, 226003, Uttar Pradesh, India
| | - Camilla Rodrigues
- Department of Microbiology, P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, 400016, Maharashtra, India
| | - Charu Sharma
- CSIR- Institute of Microbial Technology, Chandigarh, 160036, India
- Correspondence: Charu Sharma, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India, Tel +911722880309/310, Fax +911722690585, Email
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12
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Abstract
Whole-genome sequencing (WGS) has shown tremendous potential in rapid diagnosis of drug-resistant tuberculosis (TB). In the current study, we performed WGS on drug-resistant Mycobacterium tuberculosis isolates obtained from Shanghai (n = 137) and Russia (n = 78). We aimed to characterise the underlying and high-frequency novel drug-resistance-conferring mutations, and also create valuable combinations of resistance mutations with high predictive sensitivity to predict multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB) phenotype using a bootstrap method. Most strains belonged to L2.2, L4.2, L4.4, L4.5 and L4.8 lineages. We found that WGS could predict 82.07% of phenotypically drug-resistant domestic strains. The prediction sensitivity for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STR), ofloxacin (OFL), amikacin (AMK) and capreomycin (CAP) was 79.71%, 86.30%, 76.47%, 88.37%, 83.33%, 70.00% and 70.00%, respectively. The mutation combination with the highest sensitivity for MDR prediction was rpoB S450L + rpoB H445A/P + katG S315T + inhA I21T + inhA S94A, with a sensitivity of 92.17% (0.8615, 0.9646), and the mutation combination with highest sensitivity for XDR prediction was rpoB S450L + katG S315T + gyrA D94G + rrs A1401G, with a sensitivity of 92.86% (0.8158, 0.9796). The molecular information presented here will be of particular value for the rapid clinical detection of MDR- and XDR-TB isolates through laboratory diagnosis.
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13
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The Neglected Contribution of Streptomycin to the Tuberculosis Drug Resistance Problem. Genes (Basel) 2021; 12:genes12122003. [PMID: 34946952 PMCID: PMC8701281 DOI: 10.3390/genes12122003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
The airborne pathogen Mycobacterium tuberculosis is responsible for a present major public health problem worsened by the emergence of drug resistance. M. tuberculosis has acquired and developed streptomycin (STR) resistance mechanisms that have been maintained and transmitted in the population over the last decades. Indeed, STR resistant mutations are frequently identified across the main M. tuberculosis lineages that cause tuberculosis outbreaks worldwide. The spread of STR resistance is likely related to the low impact of the most frequent underlying mutations on the fitness of the bacteria. The withdrawal of STR from the first-line treatment of tuberculosis potentially lowered the importance of studying STR resistance. However, the prevalence of STR resistance remains very high, could be underestimated by current genotypic methods, and was found in outbreaks of multi-drug (MDR) and extensively drug (XDR) strains in different geographic regions. Therefore, the contribution of STR resistance to the problem of tuberculosis drug resistance should not be neglected. Here, we review the impact of STR resistance and detail well-known and novel candidate STR resistance mechanisms, genes, and mutations. In addition, we aim to provide insights into the possible role of STR resistance in the development of multi-drug resistant tuberculosis.
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14
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Florou Z, Gerogianni I, Gourgoulianis K, Petinaki E. New mutations in gidB gene associated with streptomycin resistance in Mycobacterium tuberculosis in Greece. J Glob Antimicrob Resist 2021; 27:279-281. [PMID: 34742910 DOI: 10.1016/j.jgar.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/19/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022] Open
Affiliation(s)
- Zoi Florou
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Irini Gerogianni
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - K Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Efi Petinaki
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece.
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15
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Molecular Analysis of Streptomycin Resistance Genes in Clinical Strains of Mycobacterium tuberculosis and Biocomputational Analysis of the MtGidB L101F Variant. Antibiotics (Basel) 2021; 10:antibiotics10070807. [PMID: 34356728 PMCID: PMC8300841 DOI: 10.3390/antibiotics10070807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/30/2022] Open
Abstract
Globally, tuberculosis (TB) remains a prevalent threat to public health. In 2019, TB affected 10 million people and caused 1.4 million deaths. The major challenge for controlling this infectious disease is the emergence and spread of drug-resistant Mycobacterium tuberculosis, the causative agent of TB. The antibiotic streptomycin is not a current first-line anti-TB drug. However, WHO recommends its use in patients infected with a streptomycin-sensitive strain. Several mutations in the M. tuberculosisrpsL, rrs and gidB genes have proved association with streptomycin resistance. In this study, we performed a molecular analysis of these genes in clinical isolates to determine the prevalence of known or novel mutations. Here, we describe the genetic analysis outcome. Furthermore, a biocomputational analysis of the MtGidB L101F variant, the product of a novel mutation detected in gidB during molecular analysis, is also reported as a theoretical approach to study the apparent genotype-phenotype association.
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16
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Rocha DMGC, Magalhães C, Cá B, Ramos A, Carvalho T, Comas I, Guimarães JT, Bastos HN, Saraiva M, Osório NS. Heterogeneous Streptomycin Resistance Level Among Mycobacterium tuberculosis Strains From the Same Transmission Cluster. Front Microbiol 2021; 12:659545. [PMID: 34177837 PMCID: PMC8226182 DOI: 10.3389/fmicb.2021.659545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
Widespread and frequent resistance to the second-line tuberculosis (TB) medicine streptomycin, suggests ongoing transmission of low fitness cost streptomycin resistance mutations. To investigate this hypothesis, we studied a cohort of 681 individuals from a TB epidemic in Portugal. Whole-genome sequencing (WGS) analyses were combined with phenotypic growth studies in culture media and in mouse bone marrow derived macrophages. Streptomycin resistance was the most frequent resistance in the cohort accounting for 82.7% (n = 67) of the resistant Mycobacterium tuberculosis isolates. WGS of 149 clinical isolates identified 13 transmission clusters, including three clusters containing only streptomycin resistant isolates. The biggest cluster was formed by eight streptomycin resistant isolates with a maximum of five pairwise single nucleotide polymorphisms of difference. Interestingly, despite their genetic similarity, these isolates displayed different resistance levels to streptomycin, as measured both in culture media and in infected mouse bone marrow derived macrophages. The genetic bases underlying this phenotype are a combination of mutations in gid and other genes. This study suggests that specific streptomycin resistance mutations were transmitted in the cohort, with the resistant isolates evolving at the cluster level to allow low-to-high streptomycin resistance levels without a significative fitness cost. This is relevant not only to better understand transmission of streptomycin resistance in a clinical setting dominated by Lineage 4 M. tuberculosis infections, but mainly because it opens new prospects for the investigation of selection and spread of drug resistance in general.
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Affiliation(s)
- Deisy M G C Rocha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal.,i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
| | - Baltazar Cá
- i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
| | - Angelica Ramos
- Department of Clinical Pathology, Centro Hospitalar São João, Porto, Portugal
| | - Teresa Carvalho
- Department of Clinical Pathology, Centro Hospitalar São João, Porto, Portugal
| | - Iñaki Comas
- Biomedicine Institute of Valencia IBV-CSIC, Valencia, Spain.,CIBER in Epidemiology and Public Health, Valencia, Spain
| | - João Tiago Guimarães
- Department of Clinical Pathology, Centro Hospitalar São João, Porto, Portugal.,Institute of Public Health, University of Porto, Porto, Portugal.,Department of Biochemistry, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Helder Novais Bastos
- i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal.,Serviço de Pneumologia, Centro Hospitalar Universitário de São João EPE, Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
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17
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da Silva PB, Araújo VHS, Fonseca-Santos B, Solcia MC, Ribeiro CM, da Silva IC, Alves RC, Pironi AM, Silva ACL, Victorelli FD, Fernandes MA, Ferreira PS, da Silva GH, Pavan FR, Chorilli M. Highlights Regarding the Use of Metallic Nanoparticles against Pathogens Considered a Priority by the World Health Organization. Curr Med Chem 2021; 28:1906-1956. [PMID: 32400324 DOI: 10.2174/0929867327666200513080719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/11/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022]
Abstract
The indiscriminate use of antibiotics has facilitated the growing resistance of bacteria, and this has become a serious public health problem worldwide. Several microorganisms are still resistant to multiple antibiotics and are particularly dangerous in the hospital and nursing home environment, and to patients whose care requires devices, such as ventilators and intravenous catheters. A list of twelve pathogenic genera, which especially included bacteria that were not affected by different antibiotics, was released by the World Health Organization (WHO) in 2017, and the research and development of new antibiotics against these genera has been considered a priority. The nanotechnology is a tool that offers an effective platform for altering the physicalchemical properties of different materials, thereby enabling the development of several biomedical applications. Owing to their large surface area and high reactivity, metallic particles on the nanometric scale have remarkable physical, chemical, and biological properties. Nanoparticles with sizes between 1 and 100 nm have several applications, mainly as new antimicrobial agents for the control of microorganisms. In the present review, more than 200 reports of various metallic nanoparticles, especially those containing copper, gold, platinum, silver, titanium, and zinc were analyzed with regard to their anti-bacterial activity. However, of these 200 studies, only 42 reported about trials conducted against the resistant bacteria considered a priority by the WHO. All studies are in the initial stage, and none are in the clinical phase of research.
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Affiliation(s)
- Patricia Bento da Silva
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | - Bruno Fonseca-Santos
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Mariana Cristina Solcia
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | | | - Renata Carolina Alves
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Andressa Maria Pironi
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | | | - Mariza Aires Fernandes
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Paula Scanavez Ferreira
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Gilmar Hanck da Silva
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Fernando Rogério Pavan
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Marlus Chorilli
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
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18
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Guerra Maldonado JF, Vincent AT, Chenal M, Veyrier FJ. CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution. BMC Genomics 2020; 21:832. [PMID: 33243176 PMCID: PMC7690079 DOI: 10.1186/s12864-020-07232-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. For this reason, multiple tools are available to study the evolutionary events within genomes of single species, such as gene composition alterations, or subtler mutations such as SNPs. However, these tools are generally designed to compare similar genomes and require advanced skills in bioinformatics. We present CAPRIB, a unique tool developed in Java that allows to determine the amino acid changes, at the genus level, that correlate with phenotypic differences between two groups of organisms. RESULTS CAPRIB has a user-friendly graphical interface and uses databases in SQL, making it easy to compare several genomes without the need for programming or thorough knowledge in bioinformatics. This intuitive software narrows down a list of amino acid changes that are concomitant with a given phenotypic divergence at the genus scale. Each permutation found by our software is associated with two already described statistical values that indicate its potential impact on the protein's function, helping the user decide which promising candidates to further investigate. We show that CAPRIB is able to detect already known mutations and uncovers many more, and that this tool can be used to question molecular phylogeny. Finally, we exemplify the utility of CAPRIB by pinpointing amino acid changes that coincided with the emergence of slow-growing mycobacteria from their fast-growing counterparts. The software is freely available at https://github.com/BactSymEvol/Caprib . CONCLUSIONS CAPRIB is a new bioinformatics software aiming to make genus-scale comparisons accessible to all. With its intuitive graphical interface, this tool identifies key amino acid changes concomitant with a phenotypic divergence. By comparing fast and slow-growing mycobacteria, we shed light on evolutionary hotspots, such as the cytokinin pathway, that are interesting candidates for further experimentations.
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Affiliation(s)
- Juan F Guerra Maldonado
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada
| | - Antony T Vincent
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada
| | - Martin Chenal
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada
| | - Frederic J Veyrier
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada.
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19
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Lai YP, Ioerger TR. Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes. Evol Bioinform Online 2020; 16:1176934320944932. [PMID: 32782426 PMCID: PMC7385850 DOI: 10.1177/1176934320944932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/30/2020] [Indexed: 12/23/2022] Open
Abstract
Many antibacterial drugs have multiple mechanisms of resistance, which are often represented simultaneously by a mixture of resistance mutations (some more frequent than others) in a clinical population. This presents a challenge for Genome-Wide Association Studies (GWAS) methods, making it difficult to detect less prevalent resistance mechanisms purely through (weak) statistical associations. Homoplasy, or the occurrence of multiple independent mutations at the same site, is often observed with drug resistance mutations and can be a strong indicator of positive selection. However, traditional GWAS methods, such as those based on allele counting or linear regression, are not designed to take homoplasy into account. In this article, we present a new method, called ECAT (for Evolutionary Cluster-based Association Test), that extends traditional regression-based GWAS methods with the ability to take advantage of homoplasy. This is achieved through a preprocessing step which identifies hypervariable regions in the genome exhibiting statistically significant clusters of distinct evolutionary changes, to which association testing by a linear mixed model (LMM) is applied using GEMMA (a well-established LMM-based GWAS tool). Thus, the approach can be viewed as extending GEMMA from the usual site- or gene-level analysis to focusing on clustered regions of mutations. This approach was evaluated on a large collection of more than 600 clinical isolates of multidrug-resistant (MDR) Mycobacterium tuberculosis from Lima, Peru. We show that ECAT does a better job of detecting known resistance mutations for several antitubercular drugs (including less prevalent mutations with weaker associations), compared with (site- or gene-based) GEMMA, as representative of existing GWAS methods. The power of the multiphase approach in ECAT comes from focusing association testing on the hypervariable regions of the genome, which reduces complexity in the model and increases statistical power.
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Affiliation(s)
- Yi-Pin Lai
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
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20
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Molecular analysis of streptomycin-resistance associating genes in Mycobacterium tuberculosis isolates from Nepal. Tuberculosis (Edinb) 2020; 125:101985. [PMID: 32829153 DOI: 10.1016/j.tube.2020.101985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 11/24/2022]
Abstract
Mutation in rpsL (encoding ribosomal protein S12), rrs (encoding 16S ribosomal RNA) and gidB (encoding 7-methylguanosine methyltransferase) are associated with resistance to streptomycin (STR), which is used for the treatment of multi-drug resistant tuberculosis (MDR-TB) in Nepal. The aim of our study is to analyze the correlation between mutations in the target genes and STR-resistance in 197 Mycobacterium tuberculosis (MTB) isolates from Nepal. Mutations in rpsL was harbored by 65.9% of isolates, in which the most common mutation in rpsL is caused by K43R (58.8%) and were significantly associated with Beijing genotype (P < 0.001). About 13.2% of isolates harbored mutations in two highly mutable regions of rrs, the 530 loop and the 912 region. About 13.2% of gidB mutants do not show any mutation in rpsL and rrs, which might suggest the role of gidB mutations in STR-resistance in MTB. In addition, 5.6% of isolates do not show any mutations in three genes examined, suggesting the involvement of other mechanism in STR-resistance in MTB. Our findings can be implemented for the establishment of molecular STR-susceptibility testing, in which tuberculosis can be treated with appropriate drugs and can improve control strategies for DR-TB.
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21
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Wan L, Liu H, Li M, Jiang Y, Zhao X, Liu Z, Wan K, Li G, Guan CX. Genomic Analysis Identifies Mutations Concerning Drug-Resistance and Beijing Genotype in Multidrug-Resistant Mycobacterium tuberculosis Isolated From China. Front Microbiol 2020; 11:1444. [PMID: 32760357 PMCID: PMC7373740 DOI: 10.3389/fmicb.2020.01444] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/04/2020] [Indexed: 12/02/2022] Open
Abstract
Development of modern genomics provides us an effective method to understand the molecular mechanism of drug resistance and diagnose drug-resistant Mycobacterium tuberculosis. In this study, mutations in 18 genes or intergenic regions acquired by whole-genome sequencing (WGS) of 183 clinical M. tuberculosis strains, including 137 multidrug-resistant and 46 pan-susceptible isolates from China, were identified and used to analyze their associations with resistance of isoniazid, rifampin, ethambutol, and streptomycin. Using the proportional method as the gold standard method, the accuracy values of WGS to predict resistance were calculated. The association between synonymous or lineage definition mutations with different genotypes were also analyzed. The results show that, compared to the phenotypic proportional method, the sensitivity and specificity of WGS for resistance detection were 94.2 and 100.0% for rifampicin (based on mutations in rpoB), 90.5 and 97.8% for isoniazid (katG), 83.0 and 97.8% for streptomycin (rpsL combined with rrs 530 loop and 912 loop), and 90.9 and 65.1% for ethambutol (embB), respectively. WGS data also showed that mutations in the inhA promoter increased only 2.2% sensitivity for INH based on mutations in katG. Synonymous mutation rpoB A1075A was confirmed to be associated with the Beijing genotype. This study confirmed that mutations in rpoB, katG, rrs 530 loop and 912 loop, and rpsL were excellent biomarkers for predicting rifampicin, isoniazid, and streptomycin resistance, respectively, and provided clues in clarifying the drug-resistance mechanism of M. tuberculosis isolates from China.
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Affiliation(s)
- Li Wan
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhiguang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Cha-Xiang Guan
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
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22
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Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China. Int J Infect Dis 2020; 96:48-53. [DOI: 10.1016/j.ijid.2020.04.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 11/19/2022] Open
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23
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Wang WF, Lu MYJ, Cheng TJR, Tang YC, Teng YC, Hwa TY, Chen YH, Li MY, Wu MH, Chuang PC, Jou R, Wong CH, Li WH. Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome. Genome Biol Evol 2020; 12:3890-3905. [PMID: 31971587 PMCID: PMC7058165 DOI: 10.1093/gbe/evaa009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, kills over 1 million people worldwide annually. Development of drug resistance (DR) in the pathogen is a major challenge for TB control. We conducted whole-genome analysis of seven Taiwan M. tuberculosis isolates: One drug susceptible (DS) and five DR Beijing lineage isolates and one DR Euro-American lineage isolate. Developing a new method for DR mutation identification and applying it to the next-generation sequencing (NGS) data from the 6 Beijing lineage isolates, we identified 13 known and 6 candidate DR mutations and provided experimental support for 4 of them. We assembled the genomes of one DS and two DR Beijing lineage isolates and the Euro-American lineage isolate using NGS data. Moreover, using both PacBio and NGS sequencing data, we obtained a high-quality assembly of an extensive DR Beijing lineage isolate. Comparative analysis of these five newly assembled genomes and two published complete genomes revealed a large number of genetic changes, including gene gains and losses, indels and translocations, suggesting rapid evolution of M. tuberculosis. We found the MazEF toxin–antitoxin system in all the seven isolates studied and several interesting mutations in MazEF proteins. Finally, we used the four assembled Beijing lineage genomes to construct a high-quality Beijing lineage reference genome that is DS and contains all the genes in the four genomes. It contains 212 genes not found in the standard reference H37Rv, which is Euro-American. It is therefore a better reference than H37Rv for the Beijing lineage, the predominant lineage in Asia.
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Affiliation(s)
- Woei-Fuh Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Ching Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Chuan Teng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Teh-Yang Hwa
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Hua Wu
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Pei-Chun Chuang
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Chi-Huey Wong
- Genome Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago, Illinois
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24
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Resistance Sniffer: An online tool for prediction of drug resistance patterns of Mycobacterium tuberculosis isolates using next generation sequencing data. Int J Med Microbiol 2020; 310:151399. [PMID: 31980371 DOI: 10.1016/j.ijmm.2020.151399] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/13/2019] [Accepted: 12/29/2019] [Indexed: 11/21/2022] Open
Abstract
The effective control of multidrug resistant tuberculosis (MDR-TB) relies upon the timely diagnosis and correct treatment of all tuberculosis cases. Whole genome sequencing (WGS) has great potential as a method for the rapid diagnosis of drug resistant Mycobacterium tuberculosis (Mtb) isolates. This method overcomes most of the problems that are associated with current phenotypic drug susceptibility testing. However, the application of WGS in the clinical setting has been deterred by data complexities and skill requirements for implementing the technologies as well as clinical interpretation of the next generation sequencing (NGS) data. The proposed diagnostic application was drawn upon recent discoveries of patterns of Mtb clade-specific genetic polymorphisms associated with antibiotic resistance. A catalogue of genetic determinants of resistance to thirteen anti-TB drugs for each phylogenetic clade was created. A computational algorithm for the identification of states of diagnostic polymorphisms was implemented as an online software tool, Resistance Sniffer (http://resistance-sniffer.bi.up.ac.za/), and as a stand-alone software tool to predict drug resistance in Mtb isolates using complete or partial genome datasets in different file formats including raw Illumina fastq read files. The program was validated on sequenced Mtb isolates with data on antibiotic resistance trials available from GMTV database and from the TB Platform of South African Medical Research Council (SAMRC), Pretoria. The program proved to be suitable for probabilistic prediction of drug resistance profiles of individual strains and large sequence data sets.
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25
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2020; 113:336-351. [PMID: 31903874 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- M I Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - J G Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - M I Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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26
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Al-Mutairi NM, Ahmad S, Mokaddas EM. Molecular characterization of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates identifies local transmission of infection in Kuwait, a country with a low incidence of TB and MDR-TB. Eur J Med Res 2019; 24:38. [PMID: 31806020 PMCID: PMC6894303 DOI: 10.1186/s40001-019-0397-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background Increasing incidence of multidrug-resistant Mycobacterium tuberculosis infections is hampering global tuberculosis control efforts. Kuwait is a low-tuberculosis-incidence country, and ~ 1% of M. tuberculosis strains are resistant to rifampicin and isoniazid (MDR-TB). This study detected mutations in seven genes predicting resistance to rifampicin, isoniazid, pyrazinamide, ethambutol and streptomycin in MDR-TB strains. Sequence data were combined with spoligotypes for detecting local transmission of MDR-TB in Kuwait. Methods Ninety-three MDR-TB strains isolated from 12 Kuwaiti and 81 expatriate patients and 50 pansusceptible strains were used. Phenotypic drug susceptibility was determined by MGIT 460 TB/960 system. Mutations conferring resistance to rifampicin, isoniazid, pyrazinamide, ethambutol and streptomycin were detected by genotype MTBDRplus assay and/or PCR sequencing of three rpoB regions, katG codon 315 (katG315) + inhA regulatory region, pncA, three embB regions and rpsL + rrs-500–900 regions. Spoligotyping kit was used, spoligotypes were identified by SITVIT2, and phylogenetic tree was constructed by using MIRU-VNTRplus software. Phylogenetic tree was also constructed from concatenated sequences by MEGA7 software. Additional PCR sequencing of gidB and rpsA was performed for cluster isolates. Results Pansusceptible isolates contained wild-type sequences. Mutations in rpoB and katG and/or inhA were detected in 93/93 and 92/93 MDR-TB strains, respectively. Mutations were also detected for pyrazinamide resistance, ethambutol resistance and streptomycin resistance in MDR-TB isolates in pncA, embB and rpsL + rrs, respectively. Spoligotyping identified 35 patterns with 18 isolates exhibiting unique patterns while 75 isolates grouped in 17 patterns. Beijing genotype was most common (32/93), and 11 isolates showed nine orphan patterns. Phylogenetic analysis of concatenated sequences showed unique patterns for 51 isolates while 42 isolates grouped in 16 clusters. Interestingly, 22 isolates in eight clusters by both methods were isolated from TB patients typically within a span of 2 years. Five of eight clusters were confirmed by additional gidB and rpsA sequence data. Conclusions Our study provides the first insight into molecular epidemiology of MDR-TB in Kuwait and identified several potential clusters of local transmission of MDR-TB involving 2–6 subjects which had escaped detection by routine surveillance studies. Prospective detection of resistance-conferring mutations can identify possible cases of local transmission of MDR-TB in low MDR-TB settings.
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Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman M Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
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27
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Wang Y, Li Q, Gao H, Zhang Z, Liu Y, Lu J, Dai E. The roles of rpsL, rrs, and gidB mutations in predicting streptomycin-resistant drugs used on clinical Mycobacterium tuberculosis isolates from Hebei Province, China. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:2713-2721. [PMID: 31934102 PMCID: PMC6949554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/23/2019] [Indexed: 06/10/2023]
Abstract
Streptomycin (STR) is a component of first-line drugs used to treat multidrug-resistant tuberculosis. The purpose of this study was to investigate the proportion and type of mutations in Mycobacterium tuberculosis isolates resistant to STR and their relationship with the STR-resistant phenotype and with the epidemiological molecular model of the isolates. A total of 302 clinical isolates, including 215 STR-resistant and 87 STR-susceptible isolates, were characterized using the proportion method with Lowenstein-Jensen medium. The genes rpsL, rrs and gidB were screened for mutations using DNA sequencing methodology. All strains were genotyped using the spoligotyping technique. Mutations in rpsL and in rrs were observed in 63.3% and 15.8% of the STR-resistance isolates, respectively. The most prevalent mutations were the Lys43Arg substitution in the rpsL gene and the A514C change in the rrs gene. Ten novel mutations were identified in gidB. These novel mutations might be new potential markers for predicting STR-resistance in clinical Mycobacterium tuberculosis isolates. Mutations in rpsL, rrs, and gidB had a sensitivity of 84.2% and a specificity of 77.0% for the detection of STR-resistance isolates. The Beijing lineage strains were associated with the rpsL mutation Lys43Arg (P = 0.051), as well as the dual gidB mutations Glu92Asp and Ala205Ala (P < 0.001). Our study suggested that rpsL and rrs can act as useful genetic markers for predicting STR-resistance, and gidB polymorphisms play an important role in STR-resistant clinical Mycobacterium tuberculosis isolates from Hebei, China.
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Affiliation(s)
- Yuling Wang
- Department of Tuberculosis, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and TechnologyShijiazhuang 050021, Hebei, China
| | - Qianlin Li
- Department of Epidemiology and Statistics, North China University of Science and TechnologyTangshan 063210, Hebei, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and TechnologyShijiazhuang 050021, Hebei, China
| | - Zhi Zhang
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and TechnologyShijiazhuang 050021, Hebei, China
| | - Yuzhen Liu
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and TechnologyShijiazhuang 050021, Hebei, China
| | - Jianhua Lu
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and TechnologyShijiazhuang 050021, Hebei, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and TechnologyShijiazhuang 050021, Hebei, China
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28
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Advani J, Verma R, Chatterjee O, Pachouri PK, Upadhyay P, Singh R, Yadav J, Naaz F, Ravikumar R, Buggi S, Suar M, Gupta UD, Pandey A, Chauhan DS, Tripathy SP, Gowda H, Prasad TSK. Whole Genome Sequencing of Mycobacterium tuberculosis Clinical Isolates From India Reveals Genetic Heterogeneity and Region-Specific Variations That Might Affect Drug Susceptibility. Front Microbiol 2019; 10:309. [PMID: 30863380 PMCID: PMC6399466 DOI: 10.3389/fmicb.2019.00309] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/05/2019] [Indexed: 11/15/2022] Open
Abstract
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been constructive in understanding its evolution, genetic diversity and the mechanisms involved in drug resistance. A large number of sequencing efforts from across the globe have revealed genetic diversity among clinical isolates and the genetic determinants for their resistance to anti-tubercular drugs. Considering the high TB burden in India, the availability of WGS studies is limited. Here we present, WGS results of 200 clinical isolates of M. tuberculosis from North India which are categorized as sensitive to first-line drugs, mono-resistant, multi-drug resistant and pre-extensively drug resistant isolates. WGS revealed that 20% of the isolates were co-infected with M. tuberculosis and non-tuberculous mycobacteria species. We identified 12,802 novel genetic variations in M. tuberculosis isolates including 343 novel SNVs in 38 genes which are known to be associated with drug resistance and are not currently used in the diagnostic kits for detection of drug resistant TB. We also identified M. tuberculosis lineage 3 to be predominant in the northern region of India. Additionally, several novel SNVs, which may potentially confer drug resistance were found to be enriched in the drug resistant isolates sampled. This study highlights the significance of employing WGS in diagnosis and for monitoring further development of MDR-TB strains.
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Affiliation(s)
- Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bengaluru, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Praveen Kumar Pachouri
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Prashant Upadhyay
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Rajesh Singh
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Jitendra Yadav
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Farah Naaz
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Raju Ravikumar
- Department of Neuromicrobiology, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Shashidhar Buggi
- Intermediate Reference Laboratory, State Tuberculosis Training and Demonstration Centre, Someshwaranagar, SDSTRC and RGICD Campus, Bengaluru, India.,Department of Cardio Thoracic Surgery, Super Specialty State Referral Hospital for Chest Diseases, Someshwaranagar First Main Road, Dharmaram College Post, Bengaluru, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Umesh D Gupta
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Manipal Academy of Higher Education, Manipal, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Devendra S Chauhan
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Srikanth Prasad Tripathy
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Manipal Academy of Higher Education, Manipal, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
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30
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Zeng X, Kwok JSL, Yang KY, Leung KSS, Shi M, Yang Z, Yam WC, Tsui SKW. Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance. BMC Genomics 2018; 19:365. [PMID: 29769016 PMCID: PMC5956929 DOI: 10.1186/s12864-018-4734-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has focused on the relationship between insertions / deletions (indels) and drug resistance. Results Here, we retrieved whole genome sequencing data of 743 drug-resistant MTB strains and 367 pan-susceptible strains from TB patients from the public domain to identify novel genomic markers of drug resistance. A total of 20 region markers containing genes and intergenic regions (IGRs) with significant statistical correlation with antibiotic resistance were revealed, four of which have been previously reported to be associated with drug resistance. In addition, 83 point markers containing frameshift (FS) mutations and IGR indels were also identified independently based on differences in their incidence rates between drug-sensitive and -resistant strains. Among the 83 point markers, eight indels were detected in known drug-associated genes or IGRs. Furthermore, the overlap between 20 region markers and 83 point markers further indicated their associations with drug resistance. The markers identified were involved in essential bacterial metabolic functions, including cell wall and transmembrane transporter functions. A strong correlation between FS mutations and mutations in DNA repair genes including I21V in alkA, R48G in mutT4 and P2R in nth was also found. Conclusions This study identified a set of novel genetic markers with FS mutations and IGR indels associated with MTB drug resistance, which greatly broadens the pool of mutations related to MTB drug resistance. This insight may be important in identifying novel mechanisms of drug resistance in MTB. Electronic supplementary material The online version of this article (10.1186/s12864-018-4734-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi Zeng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jamie Sui-Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhiyuan Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong SAR, China.
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31
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Pandey B, Grover S, Goyal S, Jamal S, Singh A, Kaur J, Grover A. Novel missense mutations in gidB gene associated with streptomycin resistance in Mycobacterium tuberculosis: insights from molecular dynamics. J Biomol Struct Dyn 2018; 37:20-35. [DOI: 10.1080/07391102.2017.1417913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bharati Pandey
- Department of Biotechnology, Panjab University , Chandigarh 160014, India
| | - Sonam Grover
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi , New Delhi 110016, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University , Tonk 304022, Rajasthan, India
| | - Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University , Tonk 304022, Rajasthan, India
| | - Aditi Singh
- Department of Biotechnology, TERI University , Vasant Kunj, New Delhi 110070, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University , Chandigarh 160014, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University , New Delhi 110067, India
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32
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Mortimer TD, Weber AM, Pepperell CS. Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis. mSystems 2018; 3:e00108-17. [PMID: 29404424 PMCID: PMC5790871 DOI: 10.1128/msystems.00108-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis. Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis, we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution. We found resistant subpopulations to be less diverse than susceptible subpopulations, consistent with ongoing transmission of resistant M. tuberculosis. A subset of resistance genes ("sloppy targets") were characterized by high diversity and multiple rare variants; we posit that a large genetic target for resistance and relaxation of purifying selection contribute to high diversity at these loci. For "tight targets" of selection, the path to resistance appeared narrower, evidenced by single favored mutations that arose numerous times in the phylogeny and segregated at markedly different frequencies in resistant and susceptible subpopulations. These results suggest that diverse genetic architectures underlie drug resistance in M. tuberculosis and that combined approaches are needed to identify causal mutations. Extrapolating from patterns observed for well-characterized genes, we identified novel candidate variants involved in resistance. The approach outlined here can be extended to identify resistance variants for new drugs, to investigate the genetic architecture of resistance, and when phenotypic data are available, to find candidate genetic loci underlying other positively selected traits in clonal bacteria. IMPORTANCEMycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in M. tuberculosis is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of M. tuberculosis isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant M. tuberculosis to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in M. tuberculosis and other clonal pathogens.
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Affiliation(s)
- Tatum D. Mortimer
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Alexandra M. Weber
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Caitlin S. Pepperell
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Rezaei F, Haeili M, Fooladi AI, Feizabadi MM. High Resolution Melting Curve Analysis for Rapid Detection of Streptomycin and Ethambutol Resistance in Mycobacterium tuberculosis. MAEDICA 2017; 12:246-257. [PMID: 29610587 PMCID: PMC5879581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OBJECTIVES Development of molecular techniques for rapid detection of drug resistant tuberculosis allows for the prompt initiation of appropriate anti-TB treatment. We aimed to assess high-resolution melting (HRM) analysis for the detection of rpsL, rrs and embB mutations to identify streptomycin and ethambutol resistance in Mycobacterium tuberculosis. MATERIAL AND METHODS A total of 76 clinical isolates of M. tuberculosis including 25 SM-R, 21 EB-R and 30 drug susceptible - determined by the proportion method of drug susceptibility testing (DST) - were analyzed by HRM analysis, and the results were confirmed using DNA sequencing. RESULTS The sensitivity and specificity of the HRMA compared to phenotypic DST were 88% and 100.0%, respectively for the detection of streptomycin resistance (SM-R), and 90.4% and 96.6%, respectively for ethambutol resistance (EB-R). Three SM-R and two EB-R isolates had no mutations in the studied regions of rpsL, rrs and embB genes determined by DNA sequencing and therefore were not identified as resistant by HRM assay. Interestingly, one phenotypic EM-S isolate was found by sequencing to have a mutation at codon 423 (Met->Ilu) of embB gene and was clustered as resistant by HRM as well. CONCLUSIONS The sensitivity and specificity of HRM curve assay was consistent with DNA sequencing, which is the gold standard method for genotypic DST. This assay can be utilized as a screening method for detection of drug-resistant tuberculosis, offering the advantages of a high throughput, single step, cost effectiveness, and rapid work flow method.
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Affiliation(s)
- Faranak Rezaei
- Department of Microbiology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mehri Haeili
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Abbasali Imani Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Karimi S, Mirhendi H, Zaniani FR, Manesh SE, Salehi M, Esfahani BN. Rapid Detection of Streptomycin-Resistant Mycobacterium tuberculosis by rpsL-Restriction Fragment Length Polymorphism. Adv Biomed Res 2017; 6:126. [PMID: 29142889 PMCID: PMC5672647 DOI: 10.4103/abr.abr_240_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background: Molecular methods for the detection of drug-resistant tuberculosis (DR-TB) are potentially more rapid than conventional culture-based drug susceptibility testing, facilitating the commencement of appropriate treatment for patients with DR-TB. The aim of this study was to evaluate and develop polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assays for the detection of mutations within rpsL, and for the determination of streptomycin (STR) resistance in Mycobacterium tuberculosis. Materials and Methods: Clinical specimens were collected from individuals with suspected TB referred to the TB Center of Isfahan, from which 205 M. tuberclosis were isolated and identified by conventional phenotypic methods. The minimum inhibitory concentration of STR for all isolates was determined using the proportion method and 10 isolates were recognized as STR resistant M. tuberculosis. The effect of genetic alterations in the rpsL gene for these resistant isolates were investigated by PCR-RFLP method. Results: Three (30%) isolates showed point mutation at codon 43 by RLFP analysis. Conclusion: Our results suggest that RFLP analysis of the rpsL gene is useful for the rapid prediction of STR resistant strains of M. tuberculosis.
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Affiliation(s)
- Sediqe Karimi
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemh Riyahi Zaniani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Soroor Erfani Manesh
- Department of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshd Salehi
- Mollahadi Sabzevari Tuberculosis Center, Isfahan, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Clinical implication of novel drug resistance-conferring mutations in resistant tuberculosis. Eur J Clin Microbiol Infect Dis 2017; 36:2021-2028. [PMID: 28593375 DOI: 10.1007/s10096-017-3027-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
Evolving novel and/or unfamiliar mutations are revolutionizing the pathways of antibiotic resistance of clinical tuberculosis. The accumulation and interaction of these poorly characterized mutations augment the complexity of resistant pathogenic strains and raise public health concerns. This article reviews our current understanding of the genetic changes that characterize drug resistance in tuberculosis and highlights the imperative for further investigations focusing on the effects of an individual mutation and interacting mutations with detailed strain epidemiology, particularly as these pertain to technology-limited countries with high tuberculosis incidence rates. Concomitantly, there is a need for the development, testing, and uptake of new tools for studying the effects of these mutations in drug resistance and fitness cost of the pathogen. Such genetic data are critical for effective localized and global tuberculosis control interventions and for accurate epidemiological predictions.
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Hlaing YM, Tongtawe P, Tapchaisri P, Thanongsaksrikul J, Thawornwan U, Archanachan B, Srimanote P. Mutations in Streptomycin Resistance Genes and Their Relationship to Streptomycin Resistance and Lineage of Mycobacterium tuberculosis Thai Isolates. Tuberc Respir Dis (Seoul) 2017; 80:159-168. [PMID: 28416956 PMCID: PMC5392487 DOI: 10.4046/trd.2017.80.2.159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/21/2017] [Accepted: 02/15/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Streptomycin (SM) is recommended by the World Health Organization (WHO) as a part of standard regimens for retreating multidrug-resistant tuberculosis (MDR-TB) cases. The incidence of MDR-TB in retreatment cases was 19% in Thailand. To date, information on SM resistance (SMR) gene mutations correlated to the SMR of Mycobacterium tuberculosis Thai isolates is limited. In this study, the mutations in rpsL, rrs, gidB, and whiB7 were investigated and their association to SMR and the lineage of M. tuberculosis were explored. METHODS The lineages of 287 M. tuberculosis collected from 2007 to 2011 were identified by spoligotyping. Drug susceptibility profiles were evaluated by the absolute concentration method. Mutations in SMR genes of 46 SM-resistant and 55 SM-susceptible isolates were examined by DNA sequencing. RESULTS Three rpsL (Lys43Arg, Lys88Arg, and Lys88Thr) and two gidB (Trp45Ter and Gly69Asp) mutations were present exclusively in the SM resistant M. tuberculosis. Lys43Arg rpsL was the most predominant SMR mutations (69.6%) and prevailed among Beijing isolates (p<0.001). No SMR-related mutation in was found rrs. The combination of rpsL and gidB mutations provided 76.1% sensitivity for detecting SMR in M. tuberculosis Thai isolates. whiB7 was not responsible for SMR in SM resistant isolates lacking rpsL and rrs mutations. The significance of the three gidB mutations, 276A>C, 615A>G, and 330G>T, as lineage signatures for Beijing and EAI were underscored. This study identified 423G>A gidB as a novel sub-lineage marker for EAI6-BGD1. CONCLUSION Our study suggested that the majority of SMR in M. tuberculosis Thai isolates were responsible by rpsL and gidB polymorphisms constantly providing the novel lineage specific makers.
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Affiliation(s)
- Yin Moe Hlaing
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Pongsri Tongtawe
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Pramuan Tapchaisri
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Jeeraphong Thanongsaksrikul
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | | | - Buppa Archanachan
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Potjanee Srimanote
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
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Borrell S, Trauner A. Strain Diversity and the Evolution of Antibiotic Resistance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:263-279. [PMID: 29116640 DOI: 10.1007/978-3-319-64371-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Drug resistance is best thought of as an ongoing biological process. Resistant bacteria must emerge, become established and ultimately transmit in order to be relevant to human health. In this context, genetic diversity can influence the rate and likelihood of resistance emerging; it can also modulate the net physiological impact of resistance and the propensity of an organism to improve any defects that arise from it. Combined, these effects can have an impact on a larger scale, with highly transmissible drug-resistant bacterial strains posing a formidable threat to global health. These considerations are pertinent to the future of tuberculosis control as well. In this chapter, we review our current understanding of the impact of genetic diversity in the broadest sense on the evolution of drug-resistant members of the Mycobacterium tuberculosis complex.
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Affiliation(s)
- Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland
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Islam MM, Hameed HMA, Mugweru J, Chhotaray C, Wang C, Tan Y, Liu J, Li X, Tan S, Ojima I, Yew WW, Nuermberger E, Lamichhane G, Zhang T. Drug resistance mechanisms and novel drug targets for tuberculosis therapy. J Genet Genomics 2016; 44:21-37. [PMID: 28117224 DOI: 10.1016/j.jgg.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Rezaei F, Haeili M, Imani Fooladi A, Azari Garmjan GA, Feizabadi MM. Screening for streptomycin resistance conferring mutations in Mycobacterium tuberculosis isolates from Iran. J Chemother 2016; 29:14-18. [PMID: 27380108 DOI: 10.1080/1120009x.2016.1169619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Point mutations in the rpsL and rrs genes can lead to development of streptomycin (STR) resistance in Mycobacterium tuberculosis. The aims of this study were to determine the frequency of mutations in STR resistant M. tuberculosis isolates in Iran and to analyze the possible relationship between bacterial genotype and STR resistance. Twenty-three M. tuberculosis samples comprising 9 multidrug-resistant (MDR) and 14 non-MDR isolates, recovered from TB patients in four regions: Tehran (n = 14), Isfahan (n = 2), Zahedan (n = 2), and Khorasan (n = 5), were analysed. Mutational profiling was performed by sequencing of the rrs and rpsL genes and spoligotyping method was used for genotyping. Nineteen isolates were resistant to STR, among them 7 exhibited mutations in the rpsL gene and 7 had mutations in the rrs gene. The remaining 5 STR resistant as well as all susceptible isolates lacked any mutation in both genes. Beijing genotype was associated with both MDR and STR resistance in which all mutations occurred at codon 43 of the rpsL gene. There was an association between mutations in the rpsL and rrs genes and STR resistance. We also found a correlation between Beijing genotype and STR resistance.
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Affiliation(s)
- Faranak Rezaei
- a Department of Microbiology, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Mehri Haeili
- b Department of Biology, Faculty of Natural Sciences , University of Tabriz , Tabriz , Iran
| | - Abbasali Imani Fooladi
- c Applied Microbiology Research Center , Baqiyatallah University of Medical Sciences , Tehran , Iran
| | - Gholam Ali Azari Garmjan
- d Department of Microbiology and Virology , Mashhad University of Medical Science , Mashhad , Iran
| | - Mohammad Mehdi Feizabadi
- a Department of Microbiology, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran
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Ahmad S, Mokaddas E, Al-Mutairi N, Eldeen HS, Mohammadi S. Discordance across Phenotypic and Molecular Methods for Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates in a Low TB Incidence Country. PLoS One 2016; 11:e0153563. [PMID: 27096759 PMCID: PMC4838278 DOI: 10.1371/journal.pone.0153563] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/31/2016] [Indexed: 11/18/2022] Open
Abstract
With increasing incidence of multidrug-resistant tuberculosis (MDR-TB), accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis to first-line drugs has become crucial for proper patient management. We evaluated concordance of DST results for 70 M. tuberculosis isolates across two phenotypic and two molecular methods: BACTEC 460TB, MGIT 960 system, GenoType MTBDRplus and DNA sequencing of gene segments most commonly implicated in conferring resistance to anti-TB drugs. Most (84%) M. tuberculosis isolates were multidrug-resistant. Twenty-four isolates yielded discrepant DST results. For rifampicin, isoniazid and streptomycin, 96%, 97% and 93% of isolates, respectively, were susceptible or resistant by all four methods, whereas for ethambutol, this agreement was observed for only 76% of isolates (P<0.05 for rifampicin or isoniazid or streptomycin versus ethambutol). Occurrence of rare mutations in three isolates that confer low-level resistance caused lower agreement for rifampicin among the four methods (kappa coefficient (κ) range, 0.84 to 0.95). For isoniazid, there was perfect agreement among phenotypic methods and molecular methods (κ, 1.00) but lower agreement between phenotypic and molecular methods. Three isolates were detected as polydrug-resistant by MGIT 960 system but as multidrug-resistant by DNA sequence-based method. The agreement was higher for streptomycin among the two phenotypic methods (κ, 0.97) while targeted sequencing yielded lower agreement (κ range, 0.86 to 0.89). The discrepancy for ethambutol resulted largely due to lower concordance of MGIT 960 results (κ range, 0.53 to 0.64). The MGIT 960 system is an accurate method for DST of M. tuberculosis against isoniazid and streptomycin while the results of rifampicin susceptibility should be complemented with DNA sequencing-based method when the suspicion for resistance is high. The possibility of false susceptibility to ethambutol with MGIT 960 system suggests that molecular or other phenotypic methods may be more useful when accurate ethambutol susceptibility results are warranted.
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Affiliation(s)
- Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- * E-mail:
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Kuwait National TB Reference Laboratory, Shuwaikh, Kuwait
| | - Noura Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | | | - Shirin Mohammadi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
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Mutations in rrs , rpsL and gidB in streptomycin-resistant Mycobacterium tuberculosis isolates from Thailand. J Glob Antimicrob Resist 2016; 4:5-10. [DOI: 10.1016/j.jgar.2015.11.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/03/2015] [Accepted: 11/24/2015] [Indexed: 11/22/2022] Open
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Ssengooba W, Meehan CJ, Lukoye D, Kasule GW, Musisi K, Joloba ML, Cobelens FG, de Jong BC. Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda. INFECTION GENETICS AND EVOLUTION 2016; 40:8-16. [PMID: 26917365 PMCID: PMC4856735 DOI: 10.1016/j.meegid.2016.02.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 01/20/2016] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Understanding the circulating Mycobacterium tuberculosis resistance mutations is vital for better TB control strategies, especially to inform a new MDR-TB treatment programme. We complemented the phenotypic drug susceptibility testing (DST) based drug resistance surveys (DRSs) conducted in Uganda between 2008 and 2011 with Whole Genome Sequencing (WGS) of 90 Mycobacterium tuberculosis isolates phenotypically resistant to rifampicin and/or isoniazid to better understand the extent of drug resistance. A total of 31 (34.4 %) patients had MDR-TB, 5 (5.6 %) mono-rifampicin resistance and 54 (60.0 %) mono-isoniazid resistance by phenotypic DST. Pyrazinamide resistance mutations were identified in 32.3% of the MDR-TB patients. Resistance to injectable agents was detected in 4/90 (4.4%), and none to fluoroquinolones or novel drugs. Compensatory mutations in rpoC were identified in two patients. The sensitivity and specificity of drug resistance mutations compared to phenotypic DST were for rpoB 88.6% and 98.1%, katG 60.0% and 100%, fabG1 16.5% and 100%, katG and/or fabG1 71.8% and 100%, embCAB 63.0% and 82.5%, rrs 11.4% and 100%, rpsL 20.5% and 95.7% and rrs and/or rpsL 31.8% and 95.7%. Phylogenetic analysis showed dispersed MDR-TB isolate, with only one cluster of three Beijing family from South West Uganda. Among tuberculosis patients in Uganda, resistance beyond first-line drugs as well as compensatory mutations remain low, and MDR-TB isolates did not arise from a dominant clone. Our findings show the potential use of sequencing for complementing DRSs or surveillance in this setting, with good specificity compared to phenotypic DST. The reported high confidence mutations can be included in molecular assays, and population-based studies can track transmission of MDR-TB including the Beijing family strains in the South West of the country.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Deus Lukoye
- National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | | | - Kenneth Musisi
- National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Frank G Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Division of Infectious Diseases, New York University, New York, NY, USA
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Fonseca JD, Knight GM, McHugh TD. The complex evolution of antibiotic resistance in Mycobacterium tuberculosis. Int J Infect Dis 2016; 32:94-100. [PMID: 25809763 DOI: 10.1016/j.ijid.2015.01.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/12/2015] [Accepted: 01/14/2015] [Indexed: 12/23/2022] Open
Abstract
Multidrug-resistant and extensively drug-resistant tuberculosis (TB) represent a major threat to the control of the disease worldwide. The mechanisms and pathways that result in the emergence and subsequent fixation of resistant strains of Mycobacterium tuberculosis are not fully understood and recent studies suggest that they are much more complex than initially thought. In this review, we highlight the exciting new areas of research within TB resistance that are beginning to fill these gaps in our understanding, whilst also raising new questions and providing future directions.
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Affiliation(s)
- J D Fonseca
- Centre for Clinical Microbiology, University College London, London, NW3 2PF, UK.
| | - G M Knight
- TB Modelling Group, TB Centre, Centre for the Mathematical Modelling of Infectious Diseases, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - T D McHugh
- Centre for Clinical Microbiology, University College London, London, NW3 2PF, UK
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Sun H, Zhang C, Xiang L, Pi R, Guo Z, Zheng C, Li S, Zhao Y, Tang K, Luo M, Rastogi N, Li Y, Sun Q. Characterization of mutations in streptomycin-resistant Mycobacterium tuberculosis isolates in Sichuan, China and the association between Beijing-lineage and dual-mutation in gidB. Tuberculosis (Edinb) 2015; 96:102-6. [PMID: 26786661 DOI: 10.1016/j.tube.2015.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 09/05/2015] [Accepted: 09/10/2015] [Indexed: 02/05/2023]
Abstract
Mutations in rpsL, rrs, and gidB are well linked to streptomycin (STR) resistance, some of which are suggested to be potentially associated with Mycobacterium tuberculosis genotypic lineages in certain geographic regions. In this study, we aimed to investigate the mutation characteristics of streptomycin resistance and the relationship between the polymorphism of drug-resistant genes and the lineage of M. tuberculosis isolates in Sichuan, China. A total of 227 M. tuberculosis clinical isolates, including 180 STR-resistant and 47 pan-susceptible isolates, were analyzed for presence of mutations in the rpsL, rrs and gidB loci. Mutation K43R in rpsL was strongly associated with high-level streptomycin resistance (P < 0.01), while mutations in rrs and gidB potentially contributed to low-level resistance (P < 0.05). No general association was exhibited between STR resistance and Beijing genotype, however, in STR-resistant strains, Beijing genotype was significantly correlated with high-level STR resistance, as well as the rpsL mutation K43R (P < 0.01), indicating that Beijing genotype has an evolutionary advantage under streptomycin pressure. Notably, in all isolates of Beijing genotype, a dual mutation E92D (a276c) and A205A (a615g) in gidB was detected, suggesting a highly significant association between this dual mutation and Beijing genotype.
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Affiliation(s)
- Honghu Sun
- Key Laboratory of Bio-resources and Eco-environment of The Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Congcong Zhang
- Chengdu Center for Food and Drug Control, Chengdu, Sichuan 610000, PR China
| | - Ling Xiang
- Key Laboratory of Bio-resources and Eco-environment of The Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Rui Pi
- Key Laboratory of Bio-resources and Eco-environment of The Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Zhen Guo
- Key Laboratory of Bio-resources and Eco-environment of The Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Chao Zheng
- Key Laboratory of Bio-resources and Eco-environment of The Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Song Li
- Key Laboratory of Bio-resources and Eco-environment of The Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Yuding Zhao
- Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, Hainan 571101, PR China
| | - Ke Tang
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan 610500, PR China
| | - Mei Luo
- Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610000, PR China
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes 97183, Guadeloupe, France
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Qun Sun
- Key Laboratory of Bio-resources and Eco-environment of The Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, PR China.
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Shippy DC, Fadl AA. RNA modification enzymes encoded by the gid operon: Implications in biology and virulence of bacteria. Microb Pathog 2015; 89:100-7. [PMID: 26427881 DOI: 10.1016/j.micpath.2015.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/23/2015] [Indexed: 01/10/2023]
Abstract
Ribonucleic acid (RNA) molecules consist of numerous chemically modified nucleosides that are highly conserved in eukarya, archeae, and bacteria, while others are unique to each domain of life. In bacteria, hundreds of RNA modification enzymes have been identified and implicated in biological pathways associated with many cell processes. The glucose-inhibited division (gid) operon encodes genes for two RNA modification enzymes named GidA and GidB. Studies have shown GidA is essential for the proper biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) of bacterial transfer RNA (tRNA) with GidB responsible for the methylation of the 16S ribosomal RNA (rRNA). Furthermore, deletion of gidA and gidB has shown to alter numerous bacterial properties like virulence, stress response, morphology, growth, antibiotic susceptibility, and others. In this review, we discuss the present knowledge of the RNA modification enzymes GidA and GidB, and their potential role in the biology and virulence of bacteria.
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Affiliation(s)
- Daniel C Shippy
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amin A Fadl
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Zhao LL, Liu HC, Sun Q, Xiao TY, Zhao XQ, Li GL, Zeng CY, Wan KL. Identification of mutations conferring streptomycin resistance in multidrug-resistant tuberculosis of China. Diagn Microbiol Infect Dis 2015; 83:150-3. [PMID: 26254141 DOI: 10.1016/j.diagmicrobio.2015.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/01/2015] [Accepted: 06/28/2015] [Indexed: 11/25/2022]
Abstract
We investigated the spectrum and frequency of mutations in rpsL, rrs, and gidB among 140 multidrug-resistant tuberculosis (MDR-TB) clinical isolates from China. The association between mutations and different genotypes was also analyzed. Our data revealed that 65.7% of MDR-TB were resistant to streptomycin (STR), and 90.2% of STR-resistant isolates were Beijing strains. STR resistance was correlated with Beijing family (P=0.00). Compared with phenotypic data, detection of mutations for the combination of these 3 genes exhibited 94.6% sensitivity, 91.7% specificity, and 93.6% accuracy. The most common mutations in STR-resistant isolates were rpsL128, 262, and rrs514, of which rpsL128 showed association with Beijing lineage (P=0.00). A combination of these 3 mutations can serve as the reliable predictors for STR resistance, showing the sensitivity, specificity, and accuracy of 85.9%, 97.9%, and 90.0%, respectively. Furthermore, gidBA276C, not A615G, was Beijing lineage specific. These findings are useful to develop rapid molecular diagnostic methods for STR resistance in China.
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Affiliation(s)
- Li-Li Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, Changping, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Hai-Can Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, Changping, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Qing Sun
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, Changping, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; Pathogenic Biology Institute, University of South China, Hengyang 421001, Hunan Province, China
| | - Tong-Yang Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, Changping, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Xiu-Qin Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, Changping, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Gui-Lian Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, Changping, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Chun-Yan Zeng
- Hulunbeier People's Hospital, Hulunbeier 021000, China
| | - Kang-Lin Wan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, Changping, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
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Kuan CS, Chan CL, Yew SM, Toh YF, Khoo JS, Chong J, Lee KW, Tan YC, Yee WY, Ngeow YF, Ng KP. Genome Analysis of the First Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance. PLoS One 2015; 10:e0131694. [PMID: 26110649 PMCID: PMC4481353 DOI: 10.1371/journal.pone.0131694] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/04/2015] [Indexed: 11/21/2022] Open
Abstract
The outbreak of extensively drug-resistant tuberculosis (XDR-TB) has become an increasing problem in many TB-burdened countries. The underlying drug resistance mechanisms, including the genetic variation favored by selective pressure in the resistant population, are partially understood. Recently, the first case of XDR-TB was reported in Malaysia. However, the detailed genotype family and mechanisms of the formation of multiple drugs resistance are unknown. We sequenced the whole genome of the UM 1072388579 strain with a 2-kb insert-size library and combined with that from previously sequenced 500-bp-insert paired-end reads to produce an improved sequence with maximal sequencing coverage across the genome. In silico spoligotyping and phylogenetic analyses demonstrated that UM 1072388579 strain belongs to an ancestral-like, non-Beijing clade of East Asia lineage. This is supported by the presence of a number of lineage-specific markers, including fadD28, embA, nuoD and pks7. Polymorphism analysis showed that the drug-susceptibility profile is correlated with the pattern of resistance mutations. Mutations in drug-efflux pumps and the cell wall biogenesis pathway such as mmpL, pks and fadD genes may play an important role in survival and adaptation of this strain to its surrounding environment. In this work, fifty-seven putative promoter SNPs were identified. Among them, we identified a novel SNP located at -4 T allele of TetR/acrR promoter as an informative marker to recognize strains of East Asian lineage. Our work indicates that the UM 1072388579 harbors both classical and uncommon SNPs that allow it to escape from inhibition by many antibiotics. This study provides a strong foundation to dissect the biology and underlying resistance mechanisms of the first reported XDR M. tuberculosis in Malaysia.
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Affiliation(s)
- Chee Sian Kuan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chai Ling Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yue Fen Toh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jia-Shiun Khoo
- Codon Genomics SB, Seri Kembangan, Selangor Darul Ehsan, Malaysia
| | - Jennifer Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Wei Lee
- Codon Genomics SB, Seri Kembangan, Selangor Darul Ehsan, Malaysia
| | - Yung-Chie Tan
- Codon Genomics SB, Seri Kembangan, Selangor Darul Ehsan, Malaysia
| | - Wai-Yan Yee
- Codon Genomics SB, Seri Kembangan, Selangor Darul Ehsan, Malaysia
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Regmi SM, Coker OO, Kulawonganunchai S, Tongsima S, Prammananan T, Viratyosin W, Thaipisuttikul I, Chaiprasert A. Polymorphisms in drug-resistant-related genes shared among drug-resistant and pan-susceptible strains of sequence type 10, Beijing family of Mycobacterium tuberculosis. Int J Mycobacteriol 2015; 4:67-72. [DOI: 10.1016/j.ijmyco.2014.11.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 11/02/2014] [Indexed: 10/24/2022] Open
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Molecular epidemiology of tuberculosis in Kaohsiung City located at southern Taiwan, 2000-2008. PLoS One 2015; 10:e0117061. [PMID: 25629610 PMCID: PMC4309396 DOI: 10.1371/journal.pone.0117061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 12/17/2014] [Indexed: 01/03/2023] Open
Abstract
Background We present the first comprehensive analysis of Mycobacterium tuberculosis (MTB) isolates circulating in southern Taiwan. In this 9-year population-based study, the TB situation in the Kaohsiung region was characterized by genotypic analysis of 421 MTB isolates. Methods All 421 isolates of MTB were analyzed by spoligotyping and MIRU-VNTR typing. Drug-resistance patterns were also analyzed. Results The percentage of EAI (East African-Indian) strains increased across sampling years (2000–2008) in southern Taiwan, whereas the proportion of Beijing lineages remained unchanged. Clustering was more frequent with EAI genotype infections (odds ratio = 3.6, p<0.0001) when compared to Beijing genotypes. Notably, MTB resistance to streptomycin (STR) had significantly increased over time, but resistance to other antibiotics, including multidrug resistance, had not. Three major genes (gidB, rpsL and rrs) implicated in STR resistance were sequenced and specific mutations identified. Conclusions This study revealed that EAI strains were highly transmissible and that STR resistance has increased between 2000 and 2008 in Kaohsiung, Taiwan.
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Minias AE, Brzostek AM, Minias P, Dziadek J. The deletion of rnhB in Mycobacterium smegmatis does not affect the level of RNase HII substrates or influence genome stability. PLoS One 2015; 10:e0115521. [PMID: 25603150 PMCID: PMC4300193 DOI: 10.1371/journal.pone.0115521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/25/2014] [Indexed: 11/24/2022] Open
Abstract
RNase HII removes RNA from RNA/DNA hybrids, such as single ribonucleotides and RNA primers generated during DNA synthesis. Both, RNase HII substrates and RNase HII deficiency have been associated with genome instability in several organisms, and genome instability is a major force leading to the acquisition of drug resistance in bacteria. Understanding the mechanisms that underlie this phenomenon is one of the challenges in identifying efficient methods to combat bacterial pathogens. The aim of the present study was set to investigate the role of rnhB, presumably encoding RNase HII, in maintaining genome stability in the M. tuberculosis model organism Mycobacterium smegmatis. We performed gene replacement through homologous recombination to obtain mutant strains of Mycobacterium smegmatis lacking the rnhB gene. The mutants did not present an altered phenotype, according to the growth rate in liquid culture or susceptibility to hydroxyurea, and did not show an increase in the spontaneous mutation rate, determined using the Luria-Delbrück fluctuation test for streptomycin resistance in bacteria. The mutants also did not present an increase in the level of RNase HII substrates, measured as the level of alkaline degradation of chromosomal DNA or determined through immunodetection. We conclude that proteins other than RnhB proteins efficiently remove RNase HII substrates in M. smegmatis. These results highlight differences in the basic biology between Mycobacteria and eukaryotes and between different species of bacteria.
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Affiliation(s)
- Alina E. Minias
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Department of Microbiology, Biotechnology and Immunology, University of Lodz, Lodz, Poland
- * E-mail: (AM); (JD)
| | - Anna M. Brzostek
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Piotr Minias
- Department of Teacher Training and Biodiversity Studies, University of Lodz, Lodz, Poland
| | - Jaroslaw Dziadek
- Department of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- * E-mail: (AM); (JD)
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