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Ezewudo M, Borens A, Chiner-Oms Á, Miotto P, Chindelevitch L, Starks AM, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl TA, Warren RM, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo DM, Schito M, Rodwell TC, Posey J. Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Sci Rep 2018; 8:15382. [PMID: 30337678 PMCID: PMC6194142 DOI: 10.1038/s41598-018-33731-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022] Open
Abstract
Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.
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Affiliation(s)
- Matthew Ezewudo
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Amanda Borens
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Álvaro Chiner-Oms
- Joint unit Infection and Public Health FISABIO-CSISP/University of Valencia, Institute of integrative Systems Biology, Valencia, Spain
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Leonid Chindelevitch
- School of Computing Science, Simon Fraser University, 8888 University Ave, Burnaby, BC, V5A 1S6, Canada
| | - Angela M Starks
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA
| | - Debra Hanna
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Richard Liwski
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Matteo Zignol
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Christopher Gilpin
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Borstel, Borstel, Germany
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Priority area Infections, Research Center Borstel, Borstel, Germany
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Derrick Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | | | - Sven Hoffner
- Department of Public Health Sciences, Karolinska institute, Stockholm, Sweden
| | | | - Iñaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia (IBV-CSIC), Street Jaime Roig 11. P.O., 4010, Valencia, Spain
| | - David M Engelthaler
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste 106, Flagstaff, AZ, 86005, USA
| | - David Alland
- Center for Emerging Pathogens, Rutgers-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, USA
| | - Leen Rigouts
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christoph Lange
- Division of Clinical Infectious Diseases and German Center for Infection Research Tuberculosis Unit, Research Center Borstel, Borstel, Germany
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Ruth McNerney
- Department of Medicine, Division of Pulmonology, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Marco Schito
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, CA, USA.,The Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA.
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Mbugi EV, Katale BZ, Siame KK, Keyyu JD, Kendall SL, Dockrell HM, Streicher EM, Michel AL, Rweyemamu MM, Warren RM, Matee MI, van Helden PD. Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania. Tuberculosis (Edinb) 2014; 95:170-8. [PMID: 25522841 PMCID: PMC4364622 DOI: 10.1016/j.tube.2014.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 11/05/2022]
Abstract
This study was part of a larger cross-sectional survey that was evaluating tuberculosis (TB) infection in humans, livestock and wildlife in the Serengeti ecosystem in Tanzania. The study aimed at evaluating the genetic diversity of Mycobacterium tuberculosis isolates from TB patients attending health facilities in the Serengeti ecosystem. DNA was extracted from 214 sputum cultures obtained from consecutively enrolled newly diagnosed untreated TB patients aged ≥18 years. Spacer oligonucleotide typing (spoligotyping) and Mycobacterium Interspersed Repetitive Units and Variable Number Tandem Repeat (MIRU-VNTR) were used to genotype M. tuberculosis to establish the circulating lineages. Of the214 M. tuberculosis isolates genotyped, 55 (25.7%) belonged to the Central Asian (CAS) family, 52 (24.3%) were T family (an ill-defined family), 38 (17.8%) belonged to the Latin American Mediterranean (LAM) family, 25 (11.7%) to the East-African Indian (EAI) family, 25 (11.7%) comprised of different unassigned (‘Serengeti’) strain families, while 8 (3.7%) belonged to the Beijing family. A minority group that included Haarlem, X, U and S altogether accounted for 11 (5.2%) of all genotypes. MIRU-VNTR typing produced diverse patterns within and between families indicative of unlinked transmission chains. We conclude that, in the Serengeti ecosystem only a few successful families predominate namely CAS, T, LAM and EAI families. Other types found in lower prevalence are Beijing, Haarlem, X, S and MANU. The Haarlem, EAI_Somalia, LAM3 and S/convergent and X2 subfamilies found in this study were not reported in previous studies in Tanzania.
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Affiliation(s)
- Erasto V Mbugi
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, P. O. Box 65001 Dar es Salaam, Tanzania; Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania.
| | - Bugwesa Z Katale
- Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania; Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania.
| | - Keith K Siame
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania.
| | - Sharon L Kendall
- The Royal Veterinary College, Royal College Street, London, NW1 0TU, United Kingdom.
| | - Hazel M Dockrell
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
| | - Elizabeth M Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
| | - Anita L Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa.
| | - Mark M Rweyemamu
- Southern African Centre for Infectious Disease Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania.
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
| | - Mecky I Matee
- Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania.
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa.
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Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG. PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb) 2014; 94:346-54. [PMID: 24637013 PMCID: PMC4066953 DOI: 10.1016/j.tube.2014.02.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/08/2014] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from an infectious disease worldwide. Recent advances in DNA sequencing are leading to the ability to generate whole genome information in clinical isolates of M. tuberculosis complex (MTBC). The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies. Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies. Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800). We have developed the PolyTB web-based tool (http://pathogenseq.lshtm.ac.uk/polytb) to visualise the resulting variation and important meta-data (e.g. in silico inferred strain-types, location) within geographical map and phylogenetic views. This resource will allow researchers to identify polymorphisms within candidate genes of interest, as well as examine the genomic diversity and distribution of strains. PolyTB source code is freely available to researchers wishing to develop similar tools for their pathogen of interest.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.
| | - Mark Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - José Afonso Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Grant Hill-Cawthorn
- Pathogen Genomics Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney, NSW 2006, Australia
| | - David Harris
- Pathogen Genomics Faculty, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - João Perdigão
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Francis Drobniewski
- Centre for Immunology and Infectious Disease, Queen Mary University of London, E1 2AT London, UK
| | | | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Julian Parkhill
- Pathogen Genomics Faculty, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Nigel Martin
- School of Computer Science and Information Systems, Birkbeck College, WC1E 7HX London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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4
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Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria. BIOMED RESEARCH INTERNATIONAL 2014; 2014:645802. [PMID: 24527454 PMCID: PMC3914561 DOI: 10.1155/2014/645802] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022]
Abstract
In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.
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Wang TK, Wong CF, Au WK, Cheng VC, Wong SS. Mycobacterium tuberculosis sternal wound infection after open heart surgery: a case report and review of the literature. Diagn Microbiol Infect Dis 2007; 58:245-9. [PMID: 17300911 DOI: 10.1016/j.diagmicrobio.2006.11.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 11/28/2006] [Accepted: 11/28/2006] [Indexed: 11/29/2022]
Abstract
Tuberculous osteomyelitis of sternum after open heart surgery is a rare disease entity. We report a case of wound infection with osteomyelitis caused by Mycobacterium tuberculosis in a patient with diabetic nephropathy, requiring peritoneal dialysis after coronary artery bypass grafting, who was successfully treated with antituberculous agents and surgical debridement. In addition, we provide a literature review on reported cases of tuberculous sternal osteomyelitis and mediastinitis after open heart surgery, and discuss about the risk factors, clinical features, and treatment of this infection.
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Affiliation(s)
- Teresa K Wang
- Department of Microbiology, Research Centre of Infection and Immunology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
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Kanduma E, McHugh TD, Gillespie SH. Molecular methods for Mycobacterium tuberculosis strain typing: a users guide. J Appl Microbiol 2003; 94:781-91. [PMID: 12694442 DOI: 10.1046/j.1365-2672.2003.01918.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
There are now a wide range of techniques available to type Mycobacterium tuberculosis, the problem is to choose the correct technique. For large scale epidemiological studies the portability and standardization of IS6110 restriction fragment length polymorphism (RFLP) means that this remains the gold standard technique. In the next few years the internationally standard mycobacterial interspersed repetitive unit (MIRU) may come to challenge this primacy. Low copy number stains remain a problem and these can be typed by either polymorphic Guanine cytosine-rich repetitive sequence (PGRS) or MIRU-variable numbers of tandem repeat (VNTR). To confirm whether strains are part of a true cluster PGRS remains the method of choice. For local outbreaks and investigations of laboratory cross contamination where speed is of greatest importance suspect strains should be initially investigated using a PCR-based method. The superior reproducibility and discrimination of MIRU-VNTR means that these methods should be favoured. If matches are found, then further confirmation of identity can be achieved using IS6110 RFLP or PGRS if the strains prove to have a low IS6110 copy number.
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Affiliation(s)
- E Kanduma
- Clinical Laboratory, Kilimanjaro Christian Medical College, PO Box 3010, Moshi, Tanzania
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Yates MD, Drobniewski FA, Wilson SM. Evaluation of a rapid PCR-based epidemiological typing method for routine studies of Mycobacterium tuberculosis. J Clin Microbiol 2002; 40:712-4. [PMID: 11826004 PMCID: PMC153374 DOI: 10.1128/jcm.40.2.712-714.2002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Restriction fragment length polymorphism (RFLP) based on the insertion sequence IS6110 is used to investigate episodes of suspected transmission of infection of tuberculosis but usually takes a number of weeks from receipt of request to obtain a result. Often investigations would benefit from a more rapid method, possibly one containing an amplification step. The method employed uses a simple DNA extraction followed by a PCR step involving a single primer. Restriction enzyme analysis was performed when the patterns obtained from the PCR products were indistinguishable, especially when only single similar-size bands were obtained. The isolates used were strains of Mycobacterium tuberculosis submitted for epidemiological investigations as part of (i) possible contact-outbreak (22 episodes involving between 2 and 20 patients), (ii) possible incidents of laboratory cross-contamination (21 episodes), and (iii) possible change in drug resistance pattern or a case of reinfection (1 patient). The PCR products giving similar patterns were then subjected to restriction enzyme analysis. In conclusion it has been shown that this method is rapid, with results within 1 to 2 days of the request being received; is reproducible; and gives the same results as does RFLP. The restriction enzyme analysis stage has improved the efficiency of the technique.
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Affiliation(s)
- Malcolm D Yates
- PHLS Mycobacterium Reference Unit, Public Health Laboratory, Dulwich Hospital, East Dulwich Grove, London SE22 8QF, United Kingdom.
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8
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Waléria-Aleixo A, Kroon EG, Campos MA, Margutti-Pinto ME, Bonjardim CA, Ferreira PC. Heteroduplex mobility assay for rapid, sensitive and specific detection of mycobacteria. Diagn Microbiol Infect Dis 2000; 36:225-35. [PMID: 10764964 DOI: 10.1016/s0732-8893(00)00112-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report an improved method for the detection and identification of mycobacteria using PCR and the heteroduplex mobility shift assay (HMA). The HMA for detection of mycobacteria was based on the microheterogeneity within the DNA coding sequences for 16S rRNA. A remarkable shift between single-stranded, heteroduplex and homoduplex bands in PAGE was observed among the Mycobacterium spp. tested. The Mycobacteria HMA (MHMA) of amplified PCR products from mycobacteria DNA coding for 16S rDNA derived from culture showed a specific heteroduplexes formed among different Mycobacterium species. Other bacterium species were distinguished from Mycobaterium due to slow migrating heteroduplexes mobility bands observed when M. bovis (BCG), M. avium, or M. fortuitum were used as a standard. The specific heteroduplexes were detected when as little as 1 etag of DNA template was used, although better results were obtained with 5 etag and when PCR products of sample test and mycobacterium standard were mixed at a ratio of 1.8. To correctly evaluate the feasibility of using MHMA to detect and identify mycobacteria, 15 clinical sample patients were tested. All MTB-positive clinical samples were identified by MHMA as well as the negative samples. In addition, MHMA will, in principle, be applicable to the detection and classification of any microorganism showing differences within the 16S rRNA as well as to the identification of new and unrecognized bacterial species.
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Affiliation(s)
- A Waléria-Aleixo
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Wilson SM, Goss S, Drobniewski F. Evaluation of strategies for molecular fingerprinting for use in the routine work of a Mycobacterium reference unit. J Clin Microbiol 1998; 36:3385-8. [PMID: 9774602 PMCID: PMC105338 DOI: 10.1128/jcm.36.11.3385-3388.1998] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have investigated the role of two rapid PCR-based typing methods, IS6110-based PCR and spacer-oligonucleotide typing, within a national tuberculosis reference service. The validity of clusters with IS6110 restriction fragment length polymorphism fingerprints with less than 6 bands was also investigated in the context of referred isolates.
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Affiliation(s)
- S M Wilson
- Public Health Laboratory Service Mycobacterium Reference Unit, Dulwich Hospital, East Dulwich Grove, East Dulwich, London SE22 8QF, United Kingdom.
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10
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Pestel-Caron M, Arbeit RD. Characterization of IS1245 for strain typing of Mycobacterium avium. J Clin Microbiol 1998; 36:1859-63. [PMID: 9650925 PMCID: PMC104941 DOI: 10.1128/jcm.36.7.1859-1863.1998] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
IS1245 is an insertion element widely prevalent among isolates of Mycobacterium avium. We used PvuII Southern blots to analyze IS1245 polymorphisms among 159 M. avium isolates (141 clinical isolates from 40 human immunodeficiency virus-infected patients plus 18 epidemiologically related environmental isolates) that represented 40 distinct M. avium strains, as resolved by previous studies by pulsed-field gel electrophoresis (PFGE). All 40 strains carried DNA homologous to IS1245 and thus were typeable. Twenty-five (63%) strains had > or = 10 copies of the element, 6 (15%) had 4 to 9 copies, and 9 (23%) had only 1 to 3 copies. Among the last group of nine strains (each of which was distinct by PFGE analysis), IS1245 typing resolved only four patterns and thus provided poor discriminatory power. To evaluate the in vivo stability of IS1245, we analyzed 32 strains for which sets of 2 to 19 epidemiologically related isolates were available. For 19 (59%) of these sets, all isolates representing the same strain had indistinguishable IS1245 patterns. Within eight (25%) sets, one or more isolates had IS1245 patterns that differed by one or two fragments from the modal pattern for the isolates of that strain. Five (16%) sets included isolates whose patterns differed by three or more fragments; on the basis of IS1245 typing those isolates would have been designated distinct strains. IS1245 was stable during in vitro passage, suggesting that the variations observed represented natural translocations of the element. IS1245 provides a useful tool for molecular strain typing of M. avium but may have limitations for analyzing strains with low copy numbers or for resolving extended epidemiologic relationships.
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Affiliation(s)
- M Pestel-Caron
- Groupe de Recherche sur les Anti-microbiens et les Micro-organismes, Laboratoire de Bactériologie, Centre Hospitalier Universitaire Charles Nicolle, Rouen, France
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11
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Suffys PN, de Araujo ME, Degrave WM. The changing face of the epidemiology of tuberculosis due to molecular strain typing--a review. Mem Inst Oswaldo Cruz 1997; 92:297-316. [PMID: 9332592 DOI: 10.1590/s0074-02761997000300001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
About one third of the world population is infected with tubercle bacilli, causing eight million new cases of tuberculosis (TB) and three million deaths each year. After years of lack of interest in the disease, World Health Organization recently declared TB a global emergency and it is clear that there is need for more efficient national TB programs and newly defined research priorities. A more complete epidemiology of tuberculosis will lead to a better identification of index cases and to a more efficient treatment of the disease. Recently, new molecular tools became available for the identification of strains of Mycobacterium tuberculosis (M. tuberculosis), allowing a better recognition of transmission routes of defined strains. Both a standardized restriction-fragment-length-polymorphism-based methodology for epidemiological studies on a large scale and deoxyribonucleic acids (DNA) amplification-based methods that allow rapid detection of outbreaks with multidrug-resistant (MDR) strains, often characterized by high mortality rates, have been developed. This review comments on the existing methods of DNA-based recognition of M. tuberculosis strains and their peculiarities. It also summarizes literature data on the application of molecular fingerprinting for detection of outbreaks of M. tuberculosis, for identification of index cases, for study of interaction between TB and infection with the human immuno-deficiency virus, for analysis of the behavior of MDR strains, for a better understanding of risk factors for transmission of TB within communities and for population-based studies of TB transmission within and between countries.
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Affiliation(s)
- P N Suffys
- Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brasil
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