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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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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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Dymova MA, Cherednichenko AG, Alkhovik OI, Khrapov EA, Petrenko TI, Filipenko ML. Characterization of extensively drug-resistant Mycobacterium tuberculosis isolates circulating in Siberia. BMC Infect Dis 2014; 14:478. [PMID: 25186134 PMCID: PMC4161839 DOI: 10.1186/1471-2334-14-478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 08/29/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis compromises effective control of tuberculosis (TB) in Siberia. Early identification of drug-resistant isolates is, therefore, crucial for effective treatment of this disease. The aim of this study was to conduct drug susceptibility testing and identify mutations in drug resistance genes in clinical isolates of M. tuberculosis from some TB patients presenting for treatment in Siberia. METHODS Thirty randomly selected clinical isolates of M. tuberculosis were obtained from the Novosibirsk Research Institute of Tuberculosis, Russia. Isolates were screened for drug resistance and characterized by variable number of tandem repeats (VNTR)-typing using 15 standard and four additional loci. Deligotyping on multiple large sequences was performed using 10 loci. RESULTS Twenty-nine of the isolates were assigned XDR status. Twenty-eight isolates belonged to the M. tuberculosis Beijing family, from which 11 isolates were considered the M11 type (39%), two the M2 type (7%), and one the M33 type (3%). Seventeen isolates (60.7%) from this family exhibited unique genetic patterns. The remaining two isolates belonged to the Latino-American Mediterranean family. Gene sequences (rpoB, katG, rrs, rpsL, tlyA, gidB, gyrA, gyrB) were analyzed to identify mutations that confer resistance to rifampicin, isoniazid, amikacin, kanamycin, capreomycin, and ofloxacin. The most common mutations among the XDR isolates were S531L in RpoB, S315T in KatG, various codon 94 mutations in gyrA, A90V in GyrA, K43R in RpsL, and 1401 A → G in rrs; these confer resistance to rifampicin, isoniazid, ofloxacin, streptomycin and kanamycin/capreomycin, respectively. There was high congruence between the two typing methods (VNTR typing and deligotyping) and RD105, RD149, RD152, RD181, and RD207 regions of difference were absent from the 28 Beijing family isolates. CONCLUSIONS Deligotyping can be used for rapid and reliable screening of M. tuberculosis isolates, followed by more in-depth genotyping. Identification of Beijing family isolates with extensive drug resistance confirms that such strains have epidemiological importance in Siberia. Rapid detection of mutations that lead to drug resistance should facilitate selection of effective drug therapies, and the development of early prevention strategies to combat this infection.
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Affiliation(s)
- Maya A Dymova
- />Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of The Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- />Novosibirsk State University (NSU), Novosibirsk, Russia
| | - Andrey G Cherednichenko
- />Ministry of Public Health and Social Development of The Russian Federation (NRIT), Novosibirsk Research Institute of Tuberculosis, Novosibirsk, Russia
| | - Olga I Alkhovik
- />Ministry of Public Health and Social Development of The Russian Federation (NRIT), Novosibirsk Research Institute of Tuberculosis, Novosibirsk, Russia
| | - Eugeny A Khrapov
- />Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of The Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Tatjana I Petrenko
- />Ministry of Public Health and Social Development of The Russian Federation (NRIT), Novosibirsk Research Institute of Tuberculosis, Novosibirsk, Russia
| | - Maxim L Filipenko
- />Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of The Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- />Novosibirsk State University (NSU), Novosibirsk, Russia
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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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Nishida N, Mawatari Y, Sageshima M, Tokunaga K. Highly parallel and short-acting amplification with locus-specific primers to detect single nucleotide polymorphisms by the DigiTag2 assay. PLoS One 2012; 7:e29967. [PMID: 22253840 PMCID: PMC3258256 DOI: 10.1371/journal.pone.0029967] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 12/09/2011] [Indexed: 11/18/2022] Open
Abstract
The DigiTag2 assay enables analysis of a set of 96 SNPs using Kapa 2GFast HotStart DNA polymerase with a new protocol that has a total running time of about 7 hours, which is 6 hours shorter than the previous protocol. Quality parameters (conversion rate, call rate, reproducibility and concordance) were at the same levels as when genotype calls were acquired using the previous protocol. Multiplex PCR with 192 pairs of locus-specific primers was available for target preparation in the DigiTag2 assay without the optimization of reaction conditions, and quality parameters had the same levels as those acquired with 96-plex PCR. The locus-specific primers were able to achieve sufficient (concentration of target amplicon ≥5 nM) and specific (concentration of unexpected amplicons <2 nM) amplification within 2 hours, were also able to achieve detectable amplifications even when working in a 96-plex or 192-plex form. The improved DigiTag2 assay will be an efficient platform for screening an intermediate number of SNPs (tens to hundreds of sites) in the replication analysis after genome-wide association study. Moreover, highly parallel and short-acting amplification with locus-specific primers may thus facilitate widespread application to other PCR-based assays.
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Affiliation(s)
- Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Multiplex PCR-based reverse line blot assay for simultaneous detection of 22 virulence genes in uropathogenic Escherichia coli. Appl Environ Microbiol 2011; 78:1198-202. [PMID: 22156422 DOI: 10.1128/aem.06921-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections and are responsible for significant morbidity and health care costs worldwide. The main bacterial cause of uncomplicated UTI is Escherichia coli, which possesses numerous virulence factors (VFs). Many studies of the pathogenesis of E. coli UTI have centered on VF genes. Hence, the development of better molecular assays to study VF genes would facilitate these studies. We developed a highly sensitive and specific multiplex PCR-based reverse line blot (mPCR/RLB) assay to simultaneously detect 22 VF genes of uropathogenic E. coli and then used it to characterize 180 isolates from nonpregnant women of child-bearing age with cystitis and 153 fecal isolates from similar-age healthy women, in regional New South Wales, Australia. The assay accurately identified all VF genes (of the 22 under study) known to be present in 30 previously characterized control strains. The detection limits were 28 ng of DNA from E. coli isolates and 50 CFU/ml in mock-infected urine specimens containing known concentrations of E. coli. Cystitis isolates (compared to the fecal isolates) showed a significantly higher prevalence of 18 individual VF genes and contained significantly more VF genes per isolate (median number, 18.5 versus 6.5 [P = 0.001]). Discordance between paired probes for a given VF gene occurred in several clinical test isolates but no reference strains and among the test isolates was associated with fecal source (10% of VF genes versus 2% for cystitis isolates [P < 0.001]). This novel mPCR/RLB method is a potentially powerful tool for investigating the prevalence and distribution of VFs in E. coli.
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Cardoso Oelemann M, Gomes HM, Willery E, Possuelo L, Batista Lima KV, Allix-Béguec C, Locht C, Goguet de la Salmonière YOL, Gutierrez MC, Suffys P, Supply P. The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country. PLoS One 2011; 6:e18256. [PMID: 21464915 PMCID: PMC3064675 DOI: 10.1371/journal.pone.0018256] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 03/01/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages. METHODOLOGY/PRINCIPAL FINDINGS We tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission. CONCLUSIONS/SIGNIFICANCE Standard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications.
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Affiliation(s)
- Maranibia Cardoso Oelemann
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Eve Willery
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Lia Possuelo
- Center of Scientific and Technological Development, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Brazil
| | | | - Caroline Allix-Béguec
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | | | - Maria Cristina Gutierrez
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- Department of Infection and Epidemiology, Institut Pasteur, Paris, France
| | - Philip Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Philip Supply
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- * E-mail:
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Zhang J, Abadia E, Refregier G, Tafaj S, Boschiroli ML, Guillard B, Andremont A, Ruimy R, Sola C. Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay. J Med Microbiol 2009; 59:285-294. [PMID: 19959631 DOI: 10.1099/jmm.0.016949-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aims of the present study were to implement a microbead-based 'spoligotyping' technique and to evaluate improvements by the addition of a panel of 25 extra spacers that we expected to provide an increased resolution on principal genetic group 1 (PGG 1) strains. We confirmed the high sensitivity and reproducibility of the classical technique using the 43 spacer panel and we obtained perfect agreement between the membrane-based and the microbead-based techniques. We further demonstrated an increase in the discriminative power of an extended 68 spacer format for differentiation of PGG 1 clinical isolates, in particular for the East African-Indian clade. Finally, we define a limited yet highly informative reduced 10 spacer panel set which could offer a more cost-effective option for implementation in resource-limited countries and that could decrease the need for additional VNTR (variable number of tandem repeats) genotyping work in molecular epidemiological studies. We also present an economic analysis comparing membrane-based and microbead-based techniques.
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Affiliation(s)
- Jian Zhang
- IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
| | - Edgar Abadia
- IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
| | - Guislaine Refregier
- IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
| | - Silva Tafaj
- National TB Reference Laboratory, University Hospital of Lung Diseases 'Shefqet Ndroqi', Tirana, Albania
| | | | | | - Antoine Andremont
- Microbiology Laboratory, Bichat-Claude Bernard Hospital, Paris, France
| | - Raymond Ruimy
- Microbiology Laboratory, Bichat-Claude Bernard Hospital, Paris, France
| | - Christophe Sola
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris, France.,IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
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Molecular Epidemiology. BACTERIAL INFECTIONS OF HUMANS 2009. [PMCID: PMC7176198 DOI: 10.1007/978-0-387-09843-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Molecular epidemiology is now an established discipline in epidemiology.(1) It is the contemporary stage in the evolution of laboratory-based epidemiology that may have begun with the discovery in the late 1800s of ways to differentiate bacterial organisms by pure culture in artificial media.(2) Molecular epidemiology uses new molecular biology tools to address questions difficult or not possible to address by old laboratory tools. Just as statistical tools have become indispensable in epidemiological investigations and interpretations of epidemiologic data, molecular biology tools today have come to elucidate epidemiologic features of diseases that cannot be easily characterized by conventional techniques. Applied to infectious diseases, molecular biology methods have also come to challenge our traditional notions about the epidemiology of these diseases and have engendered novel opportunities for their prevention and control. This chapter will (1) review definitions commonly used in molecular epidemiology, (2) present an overview of molecular biology methods used to study infectious disease epidemiology, and (3) describe examples of the types of epidemiologic problems that can be addressed by molecular biology techniques, highlighting new concepts that emerged in the process of applying this approach to study bacterial infectious diseases.
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Djelouadji Z, Arnold C, Gharbia S, Raoult D, Drancourt M. Multispacer sequence typing for Mycobacterium tuberculosis genotyping. PLoS One 2008; 3:e2433. [PMID: 18560597 PMCID: PMC2413405 DOI: 10.1371/journal.pone.0002433] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 04/16/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genotyping methods developed to survey the transmission dynamics of Mycobacterium tuberculosis currently rely on the interpretation of restriction and amplification profiles. Multispacer sequence typing (MST) genotyping is based on the sequencing of several intergenic regions selected after complete genome sequence analysis. It has been applied to various pathogens, but not to M. tuberculosis. METHODS AND FINDINGS In M. tuberculosis, the MST approach yielded eight variable intergenic spacers which included four previously described variable number tandem repeat loci, one single nucleotide polymorphism locus and three newly evaluated spacers. Spacer sequence stability was evaluated by serial subculture. The eight spacers were sequenced in a collection of 101 M. tuberculosis strains from five phylogeographical lineages, and yielded 29 genetic events including 13 tandem repeat number variations (44.82%), 11 single nucleotide mutations (37.93%) and 5 deletions (17.24%). These 29 genetic events yielded 32 spacer alleles or spacer-types (ST) with an index of discrimination of 0.95. The distribution of M. tuberculosis isolates into ST profiles correlated with their assignment into phylogeographical lineages. Blind comparison of a further 93 M. tuberculosis strains by MST and restriction fragment length polymorphism-IS6110 fingerprinting and mycobacterial interspersed repetitive units typing, yielded an index of discrimination of 0.961 and 0.992, respectively. MST yielded 41 different profiles delineating 16 related groups and proved to be more discriminatory than IS6110-based typing for isolates containing < 8 IS6110 copies (P<0.0003). MST was successfully applied to 7/10 clinical specimens exhibiting a Cts < or = 42 cycles in internal transcribed spacer-real time PCR. CONCLUSIONS These results support MST as an alternative, sequencing-based method for genotyping low IS6110 copy-number M. tuberculosis strains. The M. tuberculosis MST database is freely available (http://ifr48.timone.univ-mrs.fr/MST_MTuberculosis/mst).
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Affiliation(s)
- Zoheira Djelouadji
- Unité des Rickettsies CNRS UMR6236, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Kong F, Gilbert GL. Multiplex PCR-based reverse line blot hybridization assay (mPCR/RLB)--a practical epidemiological and diagnostic tool. Nat Protoc 2007; 1:2668-80. [PMID: 17406523 DOI: 10.1038/nprot.2006.404] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combining multiplex PCR, sequentially, with reverse line blot hybridization (mPCR/RLB) is a convenient, objective way to identify up to 43 targets in 43 individual specimens simultaneously (using a 45-lane membrane format). It is more flexible and less expensive than DNA microarray. The number of targets is adequate for epidemiological and most clinical diagnostic applications; based on the same target (43) and specimen numbers (43), it is much more practical than conventional uniplex PCR (uPCR) and mPCR. We have used the protocol to identify and subtype bacteria, viruses and fungi and identify pathogens in clinical specimens; potentially, it could be used for many other applications, such as detection of mutations in, or identification of alleles of, eukaryotic genes. Development of each assay involves (i) careful primer and probe design, based on literature and sequence database searches, which are critical to success of the assay; and (ii) bench-top evaluation, using known samples, controls and dilution series, to confirm sensitivity, specificity and reproducibility. The assay takes about one and half working days to complete; about 4 h for the mPCR and 6 h for the RLB, including a total of 4 h 'hands-on' time.
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Affiliation(s)
- Fanrong Kong
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney West Area Health Service, Westmead, New South Wales 2145, Australia
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Yokoyama E, Kishida K, Uchimura M, Ichinohe S. Improved differentiation of Mycobacterium tuberculosis strains, including many Beijing genotype strains, using a new combination of variable number of tandem repeats loci. INFECTION GENETICS AND EVOLUTION 2007; 7:499-508. [PMID: 17398165 DOI: 10.1016/j.meegid.2007.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 02/26/2007] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
Variable number of tandem repeats (VNTR) typing was done on 230 Mycobacterium tuberculosis strains, including 41 strains isolated from 17 groups of epidemiologically linked patients. By PCR amplification, 185 (80.4%) of the 230 strains were Beijing genotype strains. VNTR typing was performed using the 15 loci proposed as a standard set by Supply et al. [Supply, P., Allix, C., Lesjean, S., Cardoso-Oelemann, M., Rusch-Gerdes, S., Willery, E., Savine, E., de Haas, P., van Deutekom, H., Roring, S., Bifani, P., Kurepina, N., Kreiswirth, B., Sola, C., Rastogi, N., Vatin, V., Gutierrez, M.C., Fauville, M., Niemann, S., Skuce, R., Kremer, K., Locht, C., van Soolingen, D., 2006. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J. Clin. Microbiol. 44, 4498-4510], and cluster analyses of these data were done. By the VNTR typing with the proposed 15 loci, strains having low similarity values by restriction fragment length polymorphism (RFLP) analysis were clustered. Use of a supplemental9 loci, proposed as a high-resolution tool, with the 15 loci showed that strains with low similarity by RFLP analysis were still clustered. Twelve VNTR loci were selected based on previously reported discriminatory index (DI) values and used with the proposed 15 loci for better differentiation by VNTR typing. When eight loci with higher DI values were used with the 15 loci, there were no clusters, including strains with low RFLP similarity. The15 loci and eight additional loci decreased the numbers of clustered strains isolated from epidemiologically unlinked patients significantly compared to using only the 15 loci. Among all tested loci, obvious differences of DI values were observed for 8 loci (miru10, miru16, miru39, Mtub29, Mtub30, QUB11a, QUB26, and QUB1895) of RD105 lineage strains compared to those of other lineage strains. These results suggest that the proposed VNTR typing method cannot be used as a routine epidemiological tool in areas where Beijing genotype strains are prevalent. Several VNTR loci should be added to the proposed method based on differences in polymorphism of VNTR loci among Beijing genotype lineages.
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Affiliation(s)
- E Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba 260-8715, Japan.
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Alland D, Lacher DW, Hazbón MH, Motiwala AS, Qi W, Fleischmann RD, Whittam TS. Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis. J Clin Microbiol 2006; 45:39-46. [PMID: 17079498 PMCID: PMC1828963 DOI: 10.1128/jcm.02483-05] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis strains contain different genomic insertions or deletions called large sequence polymorphisms (LSPs). Distinguishing between LSPs that occur one time versus ones that occur repeatedly in a genomic region may provide insights into the biological roles of LSPs and identify useful phylogenetic markers. We analyzed 163 clinical M. tuberculosis isolates for 17 LSPs identified in a genomic comparison of M. tuberculosis strains H37Rv and CDC1551. LSPs were mapped onto a single-nucleotide polymorphism (SNP)-based phylogenetic tree created using nine novel SNP markers that were found to reproduce a 212-SNP-based phylogeny. Four LSPs (group A) mapped to a single SNP tree segment. Two LSPs (group B) and 11 LSPs (group C) were inferred to have arisen independently in the same genomic region either two or more than two times, respectively. None of the group A LSPs but one group B LSP and five group C LSPs were flanked by IS6110 sequences in the references strains. Genes encoding members of the proline-glutamic acid or proline-proline-glutamic acid protein families were present only in group B or C LSPs. SNP- versus LSP-based phylogenies were also compared. We classified each isolate into 58 LSP types by using a separate LSP-based phylogenetic analysis and mapped the LSP types onto the SNP tree. LSPs often assigned isolates to the correct phylogenetic lineage; however, significant mistakes occurred for 6/58 (10%) of the LSP types. In conclusion, most LSPs occur in genomic regions that are prone to repeated insertion/deletion events and were responsible for an unexpectedly high degree of genomic variation in clinical M. tuberculosis. Group B and C LSPs may represent polymorphisms that occur due to selective pressure and affect the phenotype of the organism, while group A LSPs are preferable phylogenetic markers.
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Affiliation(s)
- David Alland
- Division of Infectious Disease, Department of Medicine, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA.
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Mathema B, Kurepina NE, Bifani PJ, Kreiswirth BN. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev 2006; 19:658-85. [PMID: 17041139 PMCID: PMC1592690 DOI: 10.1128/cmr.00061-05] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.
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Affiliation(s)
- Barun Mathema
- Tuberculosis Center, Public Health Research Institute, Newark, NJ 07103, USA.
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15
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Colborn JM, Koita OA, Cissé O, Bagayoko MW, Guthrie EJ, Krogstad DJ. Identifying and quantifying genotypes in polyclonal infections due to single species. Emerg Infect Dis 2006; 12:475-82. [PMID: 16704787 PMCID: PMC3291430 DOI: 10.3201/eid1203.05057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The combination of real-time PCR and capillary electrophoresis permits the rapid identification and quantification of pathogen genotypes. Simultaneous infection with multiple pathogens of the same species occurs with HIV, hepatitis C, Epstein-Barr virus, dengue, tuberculosis, and malaria. However, available methods do not distinguish among or quantify pathogen genotypes in individual patients; they also cannot test for novel insertions and deletions in genetically modified organisms. The strategy reported here accomplishes these goals with real-time polymerase chain reaction (PCR) and capillary electrophoresis. Real-time PCR with allotype-specific primers defines the allotypes (strains) present and the intensity of infection (copy number). Capillary electrophoresis defines the number of genotypes within each allotype and the intensity of infection by genotype. This strategy can be used to study the epidemiology of emerging infectious diseases with simultaneous infection by multiple genotypes, as demonstrated here with malaria. It also permits testing for insertions or deletions in genetically modified organisms that may be used for bioterrorism.
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Affiliation(s)
- James M. Colborn
- Tulane University Health Sciences Center, New Orleans, Louisiana, USA
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16
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Horan KL, Freeman R, Weigel K, Semret M, Pfaller S, Covert TC, van Soolingen D, Leão SC, Behr MA, Cangelosi GA. Isolation of the genome sequence strain Mycobacterium avium 104 from multiple patients over a 17-year period. J Clin Microbiol 2006; 44:783-9. [PMID: 16517855 PMCID: PMC1393153 DOI: 10.1128/jcm.44.3.783-789.2006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence strain 104 of the opportunistic pathogen Mycobacterium avium was isolated from an adult AIDS patient in Southern California in 1983. Isolates of non-paratuberculosis M. avium from 207 other patients in Southern California and elsewhere were examined for genotypic identity to strain 104. This process was facilitated by the use of a novel two-step approach. In the first step, all 208 strains in the sample were subjected to a high-throughput, large sequence polymorphism (LSP)-based genotyping test, in which DNA from each strain was tested by PCR for the presence or absence of 4 hypervariable genomic regions. Nineteen isolates exhibited an LSP type that resembled that of strain 104. This subset of 19 isolates was then subjected to high-resolution repetitive sequence-based PCR typing, which identified 10 isolates within the subset that were genotypically identical to strain 104. These isolates came from 10 different patients at 5 clinical sites in the western United States, and they were isolated over a 17-year time span. Therefore, the sequenced genome of M. avium strain 104 has been associated with disease in multiple patients in the western United States. Although M. avium is known for its genetic plasticity, these observations also show that strains of the pathogen can be genotypically stable over extended time periods.
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Affiliation(s)
- Kathleen L Horan
- Seattle Biomedical Research Institute, 307 Westlake Avenue N, Suite 500, Seattle, Washington 98109, USA.
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17
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Semret M, Turenne CY, de Haas P, Collins DM, Behr MA. Differentiating host-associated variants of Mycobacterium avium by PCR for detection of large sequence polymorphisms. J Clin Microbiol 2006; 44:881-7. [PMID: 16517871 PMCID: PMC1393138 DOI: 10.1128/jcm.44.3.881-887.2006] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mycobacterium avium species consists of a group of organisms that are genetically related but phenotypically diverse, with certain variants presenting clear differences in terms of their host association and disease manifestations. The ability to distinguish between these subtypes is of relevance for accurate diagnosis and for control programs. Using a comparative genomics approach, we have uncovered large sequence polymorphisms that are, respectively, absent from bird-type M. avium isolates and from cattle types and sheep types of M. avium subsp. paratuberculosis. By evaluating the distribution of these genomic polymorphisms across a panel of strains, we were able to assign unique genomic signatures to these host-associated variants. We propose a simple PCR-based strategy based on these polymorphisms that can rapidly type M. avium isolates into these subgroups.
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Affiliation(s)
- Makeda Semret
- McGill University Health Centre, Montreal, Quebec, Canada
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18
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Anderson BD, Gilson MC, Scott AA, Biehl BS, Glasner JD, Rajashekara G, Splitter GA, Perna NT. CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data. BMC Genomics 2006; 7:91. [PMID: 16638145 PMCID: PMC1464128 DOI: 10.1186/1471-2164-7-91] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Accepted: 04/25/2006] [Indexed: 11/28/2022] Open
Abstract
Background Comparative genomic hybridization can rapidly identify chromosomal regions that vary between organisms and tissues. This technique has been applied to detecting differences between normal and cancerous tissues in eukaryotes as well as genomic variability in microbial strains and species. The density of oligonucleotide probes available on current microarray platforms is particularly well-suited for comparisons of organisms with smaller genomes like bacteria and yeast where an entire genome can be assayed on a single microarray with high resolution. Available methods for analyzing these experiments typically confine analyses to data from pre-defined annotated genome features, such as entire genes. Many of these methods are ill suited for datasets with the number of measurements typical of high-density microarrays. Results We present an algorithm for analyzing microarray hybridization data to aid identification of regions that vary between an unsequenced genome and a sequenced reference genome. The program, CGHScan, uses an iterative random walk approach integrating multi-layered significance testing to detect these regions from comparative genomic hybridization data. The algorithm tolerates a high level of noise in measurements of individual probe intensities and is relatively insensitive to the choice of method for normalizing probe intensity values and identifying probes that differ between samples. When applied to comparative genomic hybridization data from a published experiment, CGHScan identified eight of nine known deletions in a Brucella ovis strain as compared to Brucella melitensis. The same result was obtained using two different normalization methods and two different scores to classify data for individual probes as representing conserved or variable genomic regions. The undetected region is a small (58 base pair) deletion that is below the resolution of CGHScan given the array design employed in the study. Conclusion CGHScan is an effective tool for analyzing comparative genomic hybridization data from high-density microarrays. The algorithm is capable of accurately identifying known variable regions and is tolerant of high noise and varying methods of data preprocessing. Statistical analysis is used to define each variable region providing a robust and reliable method for rapid identification of genomic differences independent of annotated gene boundaries.
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Affiliation(s)
- Bradley D Anderson
- Animal H ealth and Biomedical Sciences, University of Wisconsin, Madison WI 53706, USA
| | - Michael C Gilson
- Animal H ealth and Biomedical Sciences, University of Wisconsin, Madison WI 53706, USA
| | - Abigail A Scott
- Animal H ealth and Biomedical Sciences, University of Wisconsin, Madison WI 53706, USA
| | - Bryan S Biehl
- Animal H ealth and Biomedical Sciences, University of Wisconsin, Madison WI 53706, USA
| | - Jeremy D Glasner
- Genome Center of Wisconsin, University of Wisconsin, Madison WI 53706, USA
| | - Gireesh Rajashekara
- Animal H ealth and Biomedical Sciences, University of Wisconsin, Madison WI 53706, USA
| | - Gary A Splitter
- Animal H ealth and Biomedical Sciences, University of Wisconsin, Madison WI 53706, USA
| | - Nicole T Perna
- Animal H ealth and Biomedical Sciences, University of Wisconsin, Madison WI 53706, USA
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Kong F, Ma L, Gilbert GL. Simultaneous detection and serotype identification of Streptococcus agalactiae using multiplex PCR and reverse line blot hybridization. J Med Microbiol 2006; 54:1133-1138. [PMID: 16278425 DOI: 10.1099/jmm.0.46244-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus agalactiae (group B streptococcus, GBS) is an important cause of sepsis in neonates and their mothers, and the elderly and immunocompromised patients. Ongoing surveillance to monitor GBS serotype distribution is needed to guide the development and assess the feasibility of GBS conjugate vaccines. The authors previously developed a molecular serotype identification method based on serotype-specific PCR and partial sequencing of cps genes. In this study, a novel 10-primer pair multiplex PCR and reverse line blot (mPCR/RLB) hybridization assay was developed for simultaneous detection and serotype identification of all nine GBS serotypes. For all 316 GBS isolates tested the mPCR/RLB results corresponded with those of conventional serotyping and individual serotype-specific PCR, and the method was more convenient and practical than either alternative.
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Affiliation(s)
- Fanrong Kong
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia 2Department of Dermatology, Beijing Children's Hospital, Affiliate of Capital University of Medical Sciences, Beijing, PR China
| | - Lin Ma
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia 2Department of Dermatology, Beijing Children's Hospital, Affiliate of Capital University of Medical Sciences, Beijing, PR China
| | - Gwendolyn L Gilbert
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia 2Department of Dermatology, Beijing Children's Hospital, Affiliate of Capital University of Medical Sciences, Beijing, PR China
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20
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Rao KR, Kauser F, Srinivas S, Zanetti S, Sechi LA, Ahmed N, Hasnain SE. Analysis of genomic downsizing on the basis of region-of-difference polymorphism profiling of Mycobacterium tuberculosis patient isolates reveals geographic partitioning. J Clin Microbiol 2006; 43:5978-82. [PMID: 16333085 PMCID: PMC1317167 DOI: 10.1128/jcm.43.12.5978-5982.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis, has lost many coding and noncoding regions in its genome during the course of evolution. We performed region-of-difference (RD) analysis using PCR-based genotyping of 131 M. tuberculosis clinical isolates obtained from four different countries, namely, India, Peru, Libya, and Angola. Our studies revealed that RD patterns are often distinct for strains circulating in specific geographical regions and can be used to trace the descent and spread of an isolate from its original reservoir. We describe our findings, which show that no single isolate from the four countries (n = 131) had all the 15 RDs either deleted or retained. Tuberculosis-specific deletion 1 (TbD1) was found to be conserved in 23% of the Indian isolates, indicating their possible ancient origin. RD9 was the most conserved region, RD11 was predominantly deleted, and RD6 was the most variable among the isolates in our collection irrespective of their geographic region. In contrast to earlier reports, our results demonstrate that the deletion of RD1 does not correlate with a decrease in the virulence potential of M. tuberculosis, as Indian isolates (n = 30) examined by us were from diseased individuals and yet had lost the RD1 region. Our results further illustrated that the intactness of the RD5 region may be associated with increased virulence of the organism. This study highlights that the RDs in M. tuberculosis genomes are geographically distributed and specific and may possibly be associated with virulence spectrum.
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Affiliation(s)
- K Rajender Rao
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 076, India
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21
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Freeman R, Kato-Maeda M, Hauge KA, Horan KL, Oren E, Narita M, Wallis CK, Cave D, Nolan CM, Small PM, Cangelosi GA. Use of rapid genomic deletion typing to monitor a tuberculosis outbreak within an urban homeless population. J Clin Microbiol 2005; 43:5550-4. [PMID: 16272485 PMCID: PMC1287805 DOI: 10.1128/jcm.43.11.5550-5554.2005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Beginning in mid-2002, a large tuberculosis outbreak occurred among homeless persons in King County, Washington. In order to further monitor the outbreak following its peak in 2003, Mycobacterium tuberculosis isolates from all new King County tuberculosis (TB) patients in 2004 and the first half of 2005 (n = 220) were genotyped by using a rapid comparative genomics-based (genomic deletion-typing) approach, with confirmation by mycobacterial interspersed repetitive units and repetitive-sequence-based PCR (rep-PCR). Results were compared to retrospective genotypic data from 1995 to 2003. The outbreak strain SBRI9, which was not seen among King County homeless persons prior to 2002, accounted for 16 out of 30 TB cases (53%) within this population in 2002. This trend continued with 27 out of 35 cases (77%) caused by the outbreak strain in 2003, 11 out of 13 cases (85%) caused by the outbreak strain in 2004, and 4 out of 10 cases (40%) caused by the outbreak strain in the first 5 months of 2005. Thus, the outbreak strain remained well established within this homeless population throughout the study period. At least four SBRI9 cases were in people who had previously been infected by other strains. The novel PCR-based strain-typing approach used in this investigation proved to be cost-effective and very rapid. In most cases, it was possible to analyze DNA extracted directly from primary isolation (Mycobacterium growth indicator tube) cultures submitted by clinical laboratories, a feature that markedly reduced the delay between diagnosis and strain typing results. This rapid turnaround facilitated public health efforts to prevent new outbreaks involving this strain.
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Affiliation(s)
- Robert Freeman
- Seattle Biomedical Research Institute, 307 Westlake Avenue N, Suite 500, Seattle, WA 98107-5219, USA
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22
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Kremer K, Arnold C, Cataldi A, Gutiérrez MC, Haas WH, Panaiotov S, Skuce RA, Supply P, van der Zanden AGM, van Soolingen D. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin Microbiol 2005; 43:5628-38. [PMID: 16272496 PMCID: PMC1287774 DOI: 10.1128/jcm.43.11.5628-5638.2005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 04/18/2005] [Accepted: 06/23/2005] [Indexed: 11/20/2022] Open
Abstract
In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.
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Affiliation(s)
- Kristin Kremer
- Mycobacteria Reference Unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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Fauci AS, Touchette NA, Folkers GK. Emerging infectious diseases: a 10-year perspective from the National Institute of Allergy and Infectious Diseases. Emerg Infect Dis 2005; 11:519-25. [PMID: 15829188 PMCID: PMC3320336 DOI: 10.3201/eid1104.041167] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Advances in infectious disease research over the past 10 years have allowed breakthroughs in the diagnosis, prevention, and treatment of infectious disease. Although optimists once imagined that serious infectious disease threats would by now be conquered, newly emerging (e.g., severe acute respiratory syndrome [SARS]), reemerging (e.g., West Nile virus), and even deliberately disseminated infectious diseases (e.g., anthrax bioterrorism) continue to appear throughout the world. Over the past decade, the global effort to identify and characterize infectious agents, decipher the underlying pathways by which they cause disease, and develop preventive measures and treatments for many of the world's most dangerous pathogens has resulted in considerable progress. Intramural and extramural investigators supported by the National Institute of Allergy and Infectious Diseases (NIAID) have contributed substantially to this effort. This overview highlights selected NIAID-sponsored research advances over the past decade, with a focus on progress in combating HIV/AIDS, malaria, tuberculosis, influenza, SARS, West Nile virus, and potential bioterror agents. Many basic research discoveries have been translated into novel diagnostics, antiviral and antimicrobial compounds, and vaccines, often with extraordinary speed.
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