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Sharma K, Verma R, Advani J, Chatterjee O, Solanki HS, Sharma A, Varma S, Modi M, Ray P, Mukherjee KK, Sharma M, Dhillion MS, Suar M, Chatterjee A, Pandey A, Prasad TSK, Gowda H. Whole Genome Sequencing of Mycobacterium tuberculosis Isolates From Extrapulmonary Sites. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:413-425. [PMID: 28692415 DOI: 10.1089/omi.2017.0070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide. Extrapulmonary tuberculosis (EPTB) constitutes around 15-20% of TB cases in immunocompetent individuals. Extrapulmonary sites that are affected by TB include bones, lymph nodes, meningitis, pleura, and genitourinary tract. Whole genome sequencing has emerged as a powerful tool to map genetic diversity among Mycobacterium tuberculosis (MTB) isolates and identify the genomic signatures associated with drug resistance, pathogenesis, and disease transmission. Several pulmonary isolates of MTB have been sequenced over the years. However, availability of whole genome sequences of MTB isolates from extrapulmonary sites is limited. Some studies suggest that genetic variations in MTB might contribute to disease presentation in extrapulmonary sites. This can be addressed if whole genome sequence data from large number of extrapulmonary isolates becomes available. In this study, we have performed whole genome sequencing of five MTB clinical isolates derived from EPTB sites using next-generation sequencing platform. We identified 1434 nonsynonymous single nucleotide variations (SNVs), 143 insertions and 105 deletions. This includes 279 SNVs that were not reported before in publicly available datasets. We found several mutations that are known to confer resistance to drugs. All the five isolates belonged to East-African-Indian lineage (lineage 3). We identified 9 putative prophage DNA integrations and 14 predicted clustered regularly interspaced short palindromic repeats (CRISPR) in MTB genome. Our analysis indicates that more work is needed to map the genetic diversity of MTB. Whole genome sequencing in conjunction with comprehensive drug susceptibility testing can reveal clinically relevant mutations associated with drug resistance.
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Affiliation(s)
- Kusum Sharma
- 1 Department of Medical Microbiology, PGIMER , Chandigarh, India
| | - Renu Verma
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,3 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Jayshree Advani
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 Manipal University , Manipal, India
| | - Oishi Chatterjee
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,5 School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Hitendra S Solanki
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,3 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Aman Sharma
- 6 Department of Internal Medicine, PGIMER, Chandigarh, India
| | - Subhash Varma
- 6 Department of Internal Medicine, PGIMER, Chandigarh, India
| | - Manish Modi
- 7 Department of Neurology, PGIMER, Chandigarh, India
| | - Pallab Ray
- 1 Department of Medical Microbiology, PGIMER , Chandigarh, India
| | | | - Megha Sharma
- 1 Department of Medical Microbiology, PGIMER , Chandigarh, India
| | | | - Mrutyunjay Suar
- 3 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Aditi Chatterjee
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,10 YU-IOB Center for Systems Biology and Molecular Medicine , Mangalore, India
| | - Akhilesh Pandey
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,11 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland.,12 Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland.,13 Department of Pathology, Johns Hopkins University School of Medicine , Baltimore, Maryland.,14 Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Thottethodi Subrahmanya Keshava Prasad
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,10 YU-IOB Center for Systems Biology and Molecular Medicine , Mangalore, India .,15 NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India
| | - Harsha Gowda
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,10 YU-IOB Center for Systems Biology and Molecular Medicine , Mangalore, India
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2
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Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clin Infect Dis 2018; 64:1494-1501. [PMID: 28498943 PMCID: PMC5434337 DOI: 10.1093/cid/cix169] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/30/2017] [Indexed: 11/12/2022] Open
Abstract
Background. India is home to 25% of all tuberculosis cases and the second highest number of multidrug resistant cases worldwide. However, little is known about the genetic diversity and resistance determinants of Indian Mycobacterium tuberculosis, particularly for the primary lineages found in India, lineages 1 and 3. Methods. We whole genome sequenced 223 randomly selected M. tuberculosis strains from 196 patients within the Tiruvallur and Madurai districts of Tamil Nadu in Southern India. Using comparative genomics, we examined genetic diversity, transmission patterns, and evolution of resistance. Results. Genomic analyses revealed (11) prevalence of strains from lineages 1 and 3, (11) recent transmission of strains among patients from the same treatment centers, (11) emergence of drug resistance within patients over time, (11) resistance gained in an order typical of strains from different lineages and geographies, (11) underperformance of known resistance-conferring mutations to explain phenotypic resistance in Indian strains relative to studies focused on other geographies, and (11) the possibility that resistance arose through mutations not previously implicated in resistance, or through infections with multiple strains that confound genotype-based prediction of resistance. Conclusions. In addition to substantially expanding the genomic perspectives of lineages 1 and 3, sequencing and analysis of M. tuberculosis whole genomes from Southern India highlight challenges of infection control and rapid diagnosis of resistant tuberculosis using current technologies. Further studies are needed to fully explore the complement of diversity and resistance determinants within endemic M. tuberculosis populations.
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Affiliation(s)
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | - James E Galagan
- Department of Biomedical Engineering, and.,National Emerging Infectious Diseases Laboratory, Boston University, Massachusetts
| | | | - Alex Salazar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | - Thies Gehrmann
- Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | | | | | | | | | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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Roychowdhury T, Singh VK, Bhattacharya A. Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences. Genomics 2018; 111:205-211. [PMID: 29432978 DOI: 10.1016/j.ygeno.2018.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 02/04/2018] [Accepted: 02/08/2018] [Indexed: 11/16/2022]
Abstract
In a context specific manner, Intra-species genomic variation plays an important role in phenotypic diversity observed among pathogenic microbes. Efficient classification of these pathogens is important for diagnosis and treatment of several infectious diseases. NGS technologies have provided access to wealth of data that can be utilized to discover important markers for pathogen classification. In this paper, we described three different approaches (Jensen-Shannon divergence, random forest and Shewhart control chart) for identification of a minimal set of SNPs that can be used for classification of organisms. These methods are generic and can be implemented for analysis of any organism. We have shown usefulness of these approaches for analysis of Mycobacterium tuberculosis and Escherichia coli isolates. We were able to identify a minimal set of 18 SNPs that can be used as molecular markers for phylogroup based classification and 8 SNPs for pathogroup based classification of E. coli.
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Affiliation(s)
- Tanmoy Roychowdhury
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vinod Kumar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India; School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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Xu B, Hu J, Chen A, Hao Y, Liu G, Wang C, Wang X. Risk Factors Related with Retroperitoneal Laparoscopic Converted to Open Nephrectomy for Nonfunctioning Renal Tuberculosis. J Endourol 2017; 31:588-592. [PMID: 28358254 DOI: 10.1089/end.2017.0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE The present study was designed to investigate the risk factors affecting the conversion to open surgery in retroperitoneal laparoscopic nephrectomy of nonfunctioning renal tuberculosis (TB). PATIENTS AND METHODS The records of 144 patients who underwent a retroperitoneal laparoscopic nephrectomy procedure by a single surgeon were retrospectively reviewed. The following factors, including age, sex, body mass index (BMI), diabetes status, hypertension status, side of kidney, size of kidney, degree of calcification, mild perirenal extravasation, contralateral hydronephrosis, the time of anti-TB, and surgeon experience were analyzed. Univariate and multivariate logistic regression analyses were used for statistical assessment. RESULTS Twenty-three patients were converted to open surgery and the conversion rate was 15.97%. In univariate analysis, BMI ≥35 kg/m2 (p = 0.023), hypertension (p = 0.011), diabetes (p = 0.003), and kidney size (p = 0.032) were the main factors of conversion to open surgery. Sex, age, side, anti-TB time, calcification, mild extravasation, and surgeon experience were not significantly related. In multivariate regression analysis, BMI ≥35 kg/m2, hypertension, diabetes, and enlargement of kidney were the most important factors for conversion to open surgery. CONCLUSIONS Depending on the results achieved by a single surgeon, BMI ≥30 kg/m2, diabetes, hypertension, and enlargement of kidney significantly increased the conversion risk in retroperitoneal laparoscopic nephrectomy for nonfunctioning renal TB.
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Affiliation(s)
- Bo Xu
- 1 Department of Urology, The First Hospital of Jilin University , Changchun, P. R. China
| | - Jinghai Hu
- 1 Department of Urology, The First Hospital of Jilin University , Changchun, P. R. China
| | - Anxiang Chen
- 2 Department of Urology, Ji'an Hospital , Tonghua, P. R. China
| | - Yuanyuan Hao
- 1 Department of Urology, The First Hospital of Jilin University , Changchun, P. R. China
| | - GuoHui Liu
- 3 Department of Cardiology, China-Japan Union Hospital of Jilin University , Changchun, P. R. China
| | - Chunxi Wang
- 1 Department of Urology, The First Hospital of Jilin University , Changchun, P. R. China
| | - Xiaoqing Wang
- 1 Department of Urology, The First Hospital of Jilin University , Changchun, P. R. China
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Berger JR, Wilson MR. Next-generation sequencing of tissue: A logical extension. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2016; 3:e261. [PMID: 27458600 PMCID: PMC4946770 DOI: 10.1212/nxi.0000000000000261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Joseph R Berger
- Department of Neurology (J.R.B.), Perelman School of Medicine, University of Pennsylvania, Philadelphia; and the Department of Neurology (M.R.W.), University of California San Francisco
| | - Michael R Wilson
- Department of Neurology (J.R.B.), Perelman School of Medicine, University of Pennsylvania, Philadelphia; and the Department of Neurology (M.R.W.), University of California San Francisco
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Ye Y, Hu X, Shi Y, Zhou J, Zhou Y, Song X, Xie Y, Lu X, Wang L, Ying B, Chen X. Clinical Features and Drug-Resistance Profile of Urinary Tuberculosis in South-Western China: A Cross-sectional Study. Medicine (Baltimore) 2016; 95:e3537. [PMID: 27175652 PMCID: PMC4902494 DOI: 10.1097/md.0000000000003537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
To investigate the epidemiology, clinical features, and drug-resistance profile of urinary tuberculosis (UTB) in south-western China to improve UTB diagnostics.After the screening of 1036 cases of suspected UTB, 193 patients with UTB were enrolled during 2009 to 2014. Urine samples were collected for routine urinalysis, smear, tuberculosis DNA (TB-DNA) detection, and drug-resistant analysis, whereas blood samples were collected for erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and renal function evaluation. Clinical features (such as symptoms and outcome) and imageology results (such as B ultrasonic, computerized tomography, intravenous pyelography, and renography) were also collected and analyzed to investigate the epidemiology, clinical features, and drug-resistance profile.The most common presenting symptoms were urinary irritation (61.1%) and lumbago (49.2%). High proportions of microscopic hematuria (63.2%) and microscopic proteinuria (45.6%) were also observed. The positive rate for TB-DNA was 66.3%. The positive rate for culture was 13.1% and for smear it was 9.8%. The abnormal outcome rates of the computerized tomography, ultrasonography, intravenous pyelography, and the nephrogram were 76.9%, 70.1%, 29.8%, and 37.0%, respectively. The total rate of drug-resistant TB (resistant to at least 1 drug) was 39.7%, of which 20.7% was multidrug-resistance TB. The most prevalent mutation sites were katG S315T1, rpoB S531L, and gyrA D94G.We observed a serious epidemic of drug-resistant UTB and a substantial number of new UTB cases with multidrug resistance TB. Molecular diagnostics is crucial in the definite diagnosis of UTB, and our finding is a supplement and further confirmation of polymerase chain reaction usage for TB diagnosis. We recommend real-time polymerase chain reaction for TB-DNA identification instead of culture, and GenoType tests (MTBDRplus and MTBDRsl assay) for drug resistance as routine assays for patients with suspected UTB.
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MESH Headings
- Adult
- Antitubercular Agents/pharmacology
- Blood Sedimentation
- C-Reactive Protein/analysis
- China
- Cross-Sectional Studies
- DNA, Bacterial/urine
- Drug Resistance, Multiple, Bacterial
- Female
- Hematuria/microbiology
- Humans
- Kidney Function Tests
- Low Back Pain/microbiology
- Male
- Microbial Sensitivity Tests
- Middle Aged
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Proteinuria/microbiology
- Tuberculosis, Multidrug-Resistant/complications
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/metabolism
- Tuberculosis, Renal/complications
- Tuberculosis, Renal/diagnosis
- Tuberculosis, Renal/drug therapy
- Tuberculosis, Renal/metabolism
- Urinary Tract Infections/microbiology
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Affiliation(s)
- Yuanxin Ye
- From the Department of Laboratory Medicine (YY, XH, JZ, YZ, XS, YX, XL, LW, BY), West China Hospital, Sichuan University, Sichuan Province; Department of Nephrology (YS); and Department of Tuberculosis (XC), West China Hospital, Sichuan University, Chengdu, The People's Republic of China
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7
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Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis. Sci Rep 2015. [PMID: 26215170 PMCID: PMC4517164 DOI: 10.1038/srep12567] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Insertion sequence (IS) 6110 is found at multiple sites in the Mycobacterium tuberculosis genome and displays a high degree of polymorphism with respect to copy number and insertion sites. Therefore, IS6110 is considered to be a useful molecular marker for diagnosis and strain typing of M. tuberculosis. Generally IS6110 elements are identified using experimental methods, useful for analysis of a limited number of isolates. Since short read genome sequences generated using next-generation sequencing (NGS) platforms are available for a large number of isolates, a computational pipeline for identification of IS6110 elements from these datasets was developed. This study shows results from analysis of NGS data of 1377 M. tuberculosis isolates. These isolates represent all seven major global lineages of M. tuberculosis. Lineage specific copy number patterns and preferential insertion regions were observed. Intra-lineage differences were further analyzed for identifying spoligotype specific variations. Copy number distribution and preferential locations of IS6110 in different lineages imply independent evolution of IS6110, governed mainly through ancestral insertion, fitness (gene truncation, promoter activity) and recombinational loss of some copies. A phylogenetic tree based on IS6110 insertion data of different isolates was constructed in order to understand genome level variations of different markers across different lineages.
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8
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Ssengooba W, Cobelens FG, Nakiyingi L, Mboowa G, Armstrong DT, Manabe YC, Joloba ML, de Jong BC. High Genotypic Discordance of Concurrent Mycobacterium tuberculosis Isolates from Sputum and Blood of HIV-Infected Individuals. PLoS One 2015; 10:e0132581. [PMID: 26176604 PMCID: PMC4503667 DOI: 10.1371/journal.pone.0132581] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/16/2015] [Indexed: 11/19/2022] Open
Abstract
Background Among HIV-infected individuals with CD4 less than 200 cells/mm3, tuberculosis often has an atypical presentation, is more likely to be disseminated and is diagnostically challenging. We sought to understand the genotypic discordance of concurrent sputum and blood M. tuberculosis (MTB) isolates from HIV-infected individuals. Methods From a prospective diagnostic accuracy study with 182 HIV-infected culture-positive TB adults, isolates were obtained from 51 of 66 participants who were MTB culture-positive by both sputum and blood. Isolates were subjected to susceptibility testing to 1st line drugs, spoligotyping and 24 locus- MIRU-VNTR. Results The median age of the participants was 31 (IQR; 27–38) years and 51% were male. The median CD4 count was 29 (IQR; 10–84) cells/mm3 with 20% taking ART; 8.0% were previously treated for TB, and 63% were AFB smear-negative. The isolates belonged to two of the main global MTB-lineages; East-African-Indian (L3) 17 (16.7%) and Euro-American (L4) 85 (83.3%). We identified 26 (51.0%) participants with discordant MTB-genotypes between sputum and blood, including two patients with evidence of mixed infection in either compartment. Having discordant MTB-genotypes was not predicted by the MTB-lineage in either blood or sputum, CD4 cell count, or any other clinical characteristic. Conclusions There is a high genotypic discordance among M. tuberculosis concurrently isolated from sputum and blood of HIV-infected individuals. These findings suggest that infection with more than one strain of M. tuberculosis occurs in at least half of patients with advanced HIV infection.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Unit of Mycobacteriology Institute of Tropical Medicine, Antwerp, Belgium
| | - Frank G. Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Lydia Nakiyingi
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Derek T. Armstrong
- Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Yukari C. Manabe
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
- Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Moses L. Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
| | - Bouke C. de Jong
- Unit of Mycobacteriology Institute of Tropical Medicine, Antwerp, Belgium
- Division of Infectious Diseases, New York University, New York, NY, United States of America
- * E-mail:
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Desikan S, Narayanan S. Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis. Indian J Med Res 2015; 141:761-74. [PMID: 26205019 PMCID: PMC4525401 DOI: 10.4103/0971-5916.160695] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 11/26/2022] Open
Abstract
Molecular epidemiology (ME) is one of the main areas in tuberculosis research which is widely used to study the transmission epidemics and outbreaks of tubercle bacilli. It exploits the presence of various polymorphisms in the genome of the bacteria that can be widely used as genetic markers. Many DNA typing methods apply these genetic markers to differentiate various strains and to study the evolutionary relationships between them. The three widely used genotyping tools to differentiate Mycobacterium tuberculosis strains are IS6110 restriction fragment length polymorphism (RFLP), spacer oligotyping (Spoligotyping), and mycobacterial interspersed repeat units - variable number of tandem repeats (MIRU-VNTR). A new prospect towards ME was introduced with the development of whole genome sequencing (WGS) and the next generation sequencing (NGS) methods, where the entire genome is sequenced that not only helps in pointing out minute differences between the various sequences but also saves time and the cost. NGS is also found to be useful in identifying single nucleotide polymorphisms (SNPs), comparative genomics and also various aspects about transmission dynamics. These techniques enable the identification of mycobacterial strains and also facilitate the study of their phylogenetic and evolutionary traits.
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Affiliation(s)
- Srinidhi Desikan
- Department of Immunology, National Institute of Research in Tuberculosis (ICMR), Chennai, India
| | - Sujatha Narayanan
- Department of Immunology, National Institute of Research in Tuberculosis (ICMR), Chennai, India
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Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M. A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens. Genome Med 2014; 6:101. [PMID: 25484920 PMCID: PMC4256898 DOI: 10.1186/s13073-014-0101-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/30/2014] [Indexed: 11/20/2022] Open
Abstract
Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little has been published on how and how many pathogen strains should be selected for studies associating phenotype and genotype. There are specific challenges when identifying genetic associations in bacteria which often comprise highly structured populations. Here we consider general methodological questions related to sampling and analysis focusing on clonal to moderately recombining pathogens. We propose that a matched sampling scheme constitutes an efficient study design, and provide a power calculator based on phylogenetic convergence. We demonstrate this approach by applying it to genomic datasets for two microbial pathogens: Mycobacterium tuberculosis and Campylobacter species.
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Affiliation(s)
- Maha R Farhat
- Department of Pulmonary and Critical Care, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA ; Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue Suite 4A, Boston, MA 02115 USA
| | - B Jesse Shapiro
- Département de sciences biologiques, Université de Montréal, Montréal, QC Canada
| | - Samuel K Sheppard
- Institute of Life Science, College of Medicine, Swansea University, Swansea, SA2 8PP UK
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, UK
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue Suite 4A, Boston, MA 02115 USA ; Department of Epidemiology, Harvard School of Public Health, Boston, MA USA
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Emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management. BIOMED RESEARCH INTERNATIONAL 2014; 2014:375681. [PMID: 25343142 PMCID: PMC4197867 DOI: 10.1155/2014/375681] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/22/2014] [Accepted: 08/28/2014] [Indexed: 12/25/2022]
Abstract
Atypical and multidrug resistance, especially ESBL and carbapenemase expressing Enterobacteriaceae, is globally spreading. Therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. Consequently, rapid antibiotic resistance testing is essential. Various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. PCR- and sequencing-based approaches are the most expensive but the most frequently applied modes of testing, suitable for the detection of resistance genes even from primary material. Next generation sequencing, based either on assessment of allelic single nucleotide polymorphisms or on the detection of nonubiquitous resistance mechanisms might allow for sequence-based bacterial resistance testing comparable to viral resistance testing on the long term. Fluorescence in situ hybridization (FISH), based on specific binding of fluorescence-labeled oligonucleotide probes, provides a less expensive molecular bridging technique. It is particularly useful for detection of resistance mechanisms based on mutations in ribosomal RNA. Approaches based on MALDI-TOF-MS, alone or in combination with molecular techniques, like PCR/electrospray ionization MS or minisequencing provide the fastest resistance results from pure colonies or even primary samples with a growing number of protocols. This review details the various approaches of rapid resistance testing, their pros and cons, and their potential use for the diagnostic laboratory.
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Cunha MV, Inácio J, Freimanis G, Fusaro A, Granberg F, Höper D, King DP, Monne I, Orton R, Rosseel T. Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods Mol Biol 2014; 1247:415-36. [PMID: 25399113 PMCID: PMC7123048 DOI: 10.1007/978-1-4939-2004-4_30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.
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Affiliation(s)
- Mónica V. Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
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Next-Generation Anchor Based Phylogeny (NexABP): constructing phylogeny from next-generation sequencing data. Sci Rep 2014; 3:2634. [PMID: 24022334 PMCID: PMC3769656 DOI: 10.1038/srep02634] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 08/23/2013] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequences are ideally suited for deriving evolutionary relationship among organisms. With the availability of Next Generation sequencing (NGS) datasets in an unprecedented scale, it will be highly desirable if phylogenetic analysis can be carried out using short read NGS data. We described here an anchor based approach NexABP for phylogenetic construction of closely related strains/isolates from NGS data. This approach can be used even in the absence of a fully assembled reference genome and works by reducing the complexity of the datasets without compromising results. NexABP was used for constructing phylogeny of different strains of some of the common pathogens, such as Mycobacterium tuberculosis, Vibrio cholera and Escherichia coli. In addition to classification into distinct lineages, NexABP could resolve inner branches and also allow statistical testing using bootstrap analysis. We believe that there are some clear advantages of using NexABP based phylogenetic analysis as compared to other methods.
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Chernyaeva EN, Shulgina MV, Rotkevich MS, Dobrynin PV, Simonov SA, Shitikov EA, Ischenko DS, Karpova IY, Kostryukova ES, Ilina EN, Govorun VM, Zhuravlev VY, Manicheva OA, Yablonsky PK, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Lapidus AL, O'Brien SJ. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics 2014; 15:308. [PMID: 24767249 PMCID: PMC4234438 DOI: 10.1186/1471-2164-15-308] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 04/15/2014] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains.
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Affiliation(s)
- Ekaterina N Chernyaeva
- St, Petersburg State University, Theodosius Dobzhansky Center for Genome Bioinformatics, 41 Sredniy prospect, St, Petersburg, Russia.
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