1
|
Zhang Y, Wang Z, Wang W, Yu H, Jin M. Applications of polymerase chain reaction‑based methods for the diagnosis of plague (Review). Exp Ther Med 2022; 24:511. [DOI: 10.3892/etm.2022.11438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yanan Zhang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Wenrui Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, Inner Mongolia 010031, P.R. China
| | - Hui Yu
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Min Jin
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| |
Collapse
|
2
|
A Multiplex PCR/LDR Assay for Viral Agents of Diarrhea with the Capacity to Genotype Rotavirus. Sci Rep 2018; 8:13215. [PMID: 30181651 PMCID: PMC6123451 DOI: 10.1038/s41598-018-30301-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Rotavirus and noroviruses are major causes of diarrhea. Variable rotavirus vaccination efficacy in Africa and Asia is multifactorial, including the diversity of circulating strains and viral co-infection. We describe a multiplexed assay that detects and genotypes viruses from stool specimens. It includes a one-step reverse transcriptase PCR reaction, a ligase detection reaction (LDR), then hybridization of fluorescent products to micro-beads. In clinical samples it detects rotavirus, caliciviruses (sapovirus and norovirus), mixed infections, and genotypes or genogroups of rotaviruses and noroviruses, respectively. The assay also has the capacity to detect hepatitis A. The assay was validated on reference isolates and 296 stool specimens from the US and Ghana. The assay was 97% sensitive and 100% specific. The genogroup was concordant in 100% of norovirus, and the genotype in 91% and 89% of rotavirus G- and P-types, respectively. Two rare rotavirus strains, G6P[6] and G6P[8], were detected in stool specimens from Ghana. The high-throughput assay is sensitive, specific, and may be of utility in the epidemiological surveillance for rare and emerging viral strains post-rotavirus vaccine implementation.
Collapse
|
3
|
Affiliation(s)
- Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
4
|
Gibriel AA, Adel O. Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:66-90. [PMID: 28927538 PMCID: PMC7108312 DOI: 10.1016/j.mrrev.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
Collapse
Affiliation(s)
- Abdullah A Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt.
| | - Ola Adel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
| |
Collapse
|
5
|
Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System. J Clin Microbiol 2016; 55:291-301. [PMID: 27847371 DOI: 10.1128/jcm.01126-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a potential bioterrorism agent that is highly infectious at very low doses. Diagnosis of tularemia by blood culture and nucleic acid-based diagnostic tests is insufficiently sensitive. Here, we demonstrate a highly sensitive F. tularensis assay that incorporates sample processing and detection into a single cartridge suitable for point-of-care detection. The assay limit of detection (LOD) and dynamic range were determined in a filter-based cartridge run on the GeneXpert system. F. tularensis DNA in buffer or CFU of F. tularensis was spiked into human or macaque blood. To simulate detection in human disease, the assay was tested on blood drawn from macaques infected with F. tularensis Schu S4 at daily intervals. Assay detection was compared to that with a conventional quantitative PCR (qPCR) assay and blood culture. The assay LOD was 0.1 genome equivalents (GE) per reaction and 10 CFU/ml F. tularensis in both human and macaque blood. In infected macaques, the assay detected F. tularensis on days 1 to 4 postinfection in 21%, 17%, 60%, and 83% of macaques, respectively, compared to conventional qPCR positivity rates of 0%, 0%, 30%, and 100% and CFU detection of blood culture at 0%, 0%, 0%, and 10% positive, respectively. Assay specificity was 100%. The new cartridge-based assay can rapidly detect F. tularensis in bloodstream infections directly in whole blood at the early stages of infection with a sensitivity that is superior to that of other methods. The simplicity of the automated testing procedures may make this test suitable for rapid point-of-care detection.
Collapse
|
6
|
Molecular and Mass Spectrometry Detection and Identification of Causative Agents of Bloodstream Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
7
|
Das S, Rundell MS, Mirza AH, Pingle MR, Shigyo K, Garrison AR, Paragas J, Smith SK, Olson VA, Larone DH, Spitzer ED, Barany F, Golightly LM. A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus. PLoS One 2015; 10:e0138484. [PMID: 26381398 PMCID: PMC4575071 DOI: 10.1371/journal.pone.0138484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 08/30/2015] [Indexed: 02/04/2023] Open
Abstract
CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus).
Collapse
Affiliation(s)
- Sanchita Das
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Mark S. Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aashiq H. Mirza
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Maneesh R. Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Kristi Shigyo
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason Paragas
- Integrated Research Facility, Division of Clinical Research, NIAID, NIH, Fort Detrick, Maryland, United States of America
| | - Scott K. Smith
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Davise H. Larone
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, United States of America
| | - Eric D. Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York, United States of America
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Linnie M. Golightly
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
8
|
Lohman GJS, Bauer RJ, Nichols NM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Evans TC. A high-throughput assay for the comprehensive profiling of DNA ligase fidelity. Nucleic Acids Res 2015; 44:e14. [PMID: 26365241 PMCID: PMC4737175 DOI: 10.1093/nar/gkv898] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/28/2015] [Indexed: 11/24/2022] Open
Abstract
DNA ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. Ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. In order to achieve a high sensitivity and low background, the ligase must efficiently join correctly base-paired substrates, while discriminating against the ligation of substrates containing even one mismatched base pair. In the current study, we report the use of capillary electrophoresis to rapidly generate mismatch fidelity profiles that interrogate all 256 possible base-pair combinations at a ligation junction in a single experiment. Rapid screening of ligase fidelity in a 96-well plate format has allowed the study of ligase fidelity in unprecedented depth. As an example of this new method, herein we report the ligation fidelity of Thermus thermophilus DNA ligase at a range of temperatures, buffer pH and monovalent cation strength. This screen allows the selection of reaction conditions that maximize fidelity without sacrificing activity, while generating a profile of specific mismatches that ligate detectably under each set of conditions.
Collapse
Affiliation(s)
| | | | | | | | - Joanna Bybee
- New England BioLabs, Inc., Ipswich, MA 01938-2723, USA
| | | | | | | |
Collapse
|
9
|
Hamada M, Shimase K, Tsukagoshi K, Hashimoto M. Discriminative detection of low-abundance point mutations using a PCR/ligase detection reaction/capillary gel electrophoresis method and fluorescence dual-channel monitoring. Electrophoresis 2014; 35:1204-10. [PMID: 24510795 DOI: 10.1002/elps.201300584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/18/2014] [Accepted: 01/19/2014] [Indexed: 12/27/2022]
Abstract
We applied a facile LIF dual-channel monitoring system recently developed and reported by our group to the polymerase chain reaction/ligase detection reaction/CGE method for detecting low-abundance point mutations present in a wild-type sequence-dominated population. Mutation discrimination limits and signaling fidelity of the analytical system were evaluated using three mutant variations in codon 12 of the K-ras oncogene that have high diagnostic value for colorectal cancer. We demonstrated the high sensitivity of the present method by detecting rare mutations present among an excess of wild-type alleles (one mutation among ~100 normal sequences). This method also simultaneously interrogated the allelic compositions of the test samples with high specificity through spectral discrimination of the dye-tagged ligase detection reaction products using the dual-channel monitoring system.
Collapse
Affiliation(s)
- Mariko Hamada
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
| | | | | | | |
Collapse
|
10
|
Rundell MS, Pingle M, Das S, Hussain A, Ocheretina O, Charles M, Larone DH, Spitzer ED, Golightly L, Barany F. A multiplex PCR/LDR assay for simultaneous detection and identification of the NIAID category B bacterial food and water-borne pathogens. Diagn Microbiol Infect Dis 2014; 79:135-40. [PMID: 24709368 DOI: 10.1016/j.diagmicrobio.2014.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/17/2014] [Accepted: 02/26/2014] [Indexed: 01/06/2023]
Abstract
Enteric pathogens that cause gastroenteritis remain a major global health concern. The goal of this study was to develop a multiplex PCR/ligation detection reaction (LDR) assay for the detection of all NIAID category B bacterial food and water-borne pathogens directly from stool specimens. To validate the PCR/LDR assay, clinical isolates of Campylobacter spp., Vibrio spp., Shigella spp., Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and diarrheagenic Escherichia coli were tested. The sensitivity and specificity of the assay were assessed using a large number of seeded culture-negative stool specimens and a smaller set of clinical specimens from Haiti. The overall sensitivity ranged from 91% to 100% (median 100%) depending on the species. For the majority of organisms, the sensitivity was 100%. The overall specificity based on initial testing ranged from 98% to 100% depending on the species. After additional testing of discordant samples, the lowest specificity was 99.4%. PCR/LDR detected additional category B agents (particularly diarrheagenic E. coli) in 11/40 specimens from Haiti that were culture-positive for V. cholerae and in approximately 1% of routine culture-negative stool specimens from a hospital in New York. This study demonstrated the ability of the PCR/LDR assay to detect a large comprehensive panel of category B enteric bacterial pathogens as well as mixed infections. This type of assay has the potential to provide earlier warnings of possible public health threats and more accurate surveillance of food and water-borne pathogens.
Collapse
Affiliation(s)
- Mark S Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Sanchita Das
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Aashiq Hussain
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Oksana Ocheretina
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021; Groupe Haitien d'Étude du Sarcome de Kaposi et des Infections Opportunistes, Port-Au-Prince, Haiti
| | - Macarthur Charles
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021; Groupe Haitien d'Étude du Sarcome de Kaposi et des Infections Opportunistes, Port-Au-Prince, Haiti
| | - Davise H Larone
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Eric D Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, NY 11794
| | - Linnie Golightly
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021.
| |
Collapse
|
11
|
Watanabe S, Hagihara K, Tsukagoshi K, Hashimoto M. Microbead-Based Ligase Detection Reaction Assay Using a Molecular Beacon Probe for the Detection of Low-Abundance Point Mutations. Anal Chem 2013; 86:900-6. [DOI: 10.1021/ac403531x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sho Watanabe
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Kenta Hagihara
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Kazuhiko Tsukagoshi
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Masahiko Hashimoto
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| |
Collapse
|
12
|
Shin GW, Chung B, Jung GY, Jung GY. Multiplex ligase-based genotyping methods combined with CE. Electrophoresis 2013; 35:1004-16. [PMID: 24123070 DOI: 10.1002/elps.201300361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 12/30/2022]
Abstract
In this genomic era, the ability to assay multiple genomic hot spots that have strong clinical implications is greatly desired. Conventional PCR-based methods suffer from frequent false-positive detections, particularly when a multiplex analysis is desirable. As an alternative to the error-prone conventional methods, multiplex ligase-based genotyping methods combined with CE have a strong potential. In this review, both previously developed methods and emerging methods are described to reveal the specificity, sensitivity, and simplicity of the ligase-based methods. For each step (ligation, amplification, and separation), the principles of several alternative methods are discussed along with their applications to explore the future development of ligase-based diagnostic methods.
Collapse
Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Sciences and Technology, Pohang, Gyeongbuk, Korea
| | | | | | | |
Collapse
|
13
|
Development of a ligase detection reaction/CGE method using a LIF dual-channel detection system for direct identification of allelic composition of mutated DNA in a mixed population of excess wild-type DNA. Electrophoresis 2013; 34:1415-22. [DOI: 10.1002/elps.201200671] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 02/09/2013] [Accepted: 02/16/2013] [Indexed: 11/07/2022]
|
14
|
Hartmann M, Betz P, Sun Y, Gorb SN, Lindhorst TK, Krueger A. Saccharide-Modified Nanodiamond Conjugates for the Efficient Detection and Removal of Pathogenic Bacteria. Chemistry 2012; 18:6485-92. [DOI: 10.1002/chem.201104069] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Indexed: 11/11/2022]
|
15
|
Cheng Y, Du Q, Wang L, Jia H, Li Z. Fluorescently Cationic Conjugated Polymer as an Indicator of Ligase Chain Reaction for Sensitive and Homogeneous Detection of Single Nucleotide Polymorphism. Anal Chem 2012; 84:3739-44. [DOI: 10.1021/ac300314c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Qing Du
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Liyong Wang
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Hailian Jia
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Zhengping Li
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| |
Collapse
|
16
|
Hashimoto M, Morimoto C, Hagihara K, Tsukagoshi K. Rapid and Convenient Sample Preparation in a Single Tube Using Magnetic Beads for Fluorescence Detection of Single Nucleotide Variation Based on Oligonucleotide Ligation. CHEM LETT 2012. [DOI: 10.1246/cl.2012.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Chika Morimoto
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Kenta Hagihara
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Kazuhiko Tsukagoshi
- Department of Chemical Engineering and Materials Science, Doshisha University
| |
Collapse
|
17
|
Frickmann H, Essig A, Hagen RM, Riecker M, Jerke K, Ellison D, Poppert S. Rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH) from colony and blood culture material. Eur J Microbiol Immunol (Bp) 2011; 1:289-96. [PMID: 24516735 DOI: 10.1556/eujmi.1.2011.4.4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 08/23/2011] [Indexed: 11/19/2022] Open
Abstract
Multi-drug-resistant strains of the Acinetobacter baumannii complex cause nosocomial infections. Rapid identification of Acinetobacter spp. is desirable in order to facilitate therapeutic or hygiene decisions. We evaluated a newly designed DNA probe that can be used under standard conditions in both a microwave oven and a slide chamber for the rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH). Using FISH, the new probe correctly identified 81/81 Acinetobacter spp. isolates and excluded 109/109 tested non-target organisms from agar culture. Furthermore, the new probe correctly identified 7/7 Acinetobacter spp. in 214 blood cultures determined to contain Gram-negative bacteria by Gram staining. Using either the microwave oven or slide chamber technique, the new probe was able to identify Acinetobacter spp. in 100% of the samples tested. FISH used in conjunction with our newly designed probe provides an easy, cheap, precise, and rapid method for the preliminary identification of Acinetobacter spp., especially in laboratories where more sophisticated methods like matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) are not available.
Collapse
|
18
|
Species-specific probes and real-time PCR as a tool for fast detection and differentiation of 15 bacteria relevant in intensive care medicine. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
19
|
Molecular Detection of Group B
Streptococcus. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
20
|
Update on the Detection and Characterization of Bacterial Pathogens by Nucleic Acid Amplification. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
21
|
Peng Z, Soper SA, Pingle MR, Barany F, Davis LM. Ligase detection reaction generation of reverse molecular beacons for near real-time analysis of bacterial pathogens using single-pair fluorescence resonance energy transfer and a cyclic olefin copolymer microfluidic chip. Anal Chem 2010; 82:9727-35. [PMID: 21047095 PMCID: PMC4382962 DOI: 10.1021/ac101843n] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detection of pathogenic bacteria and viruses require strategies that can signal the presence of these targets in near real-time due to the potential threats created by rapid dissemination into water and/or food supplies. In this paper, we report an innovative strategy that can rapidly detect bacterial pathogens using reporter sequences found in their genome without requiring polymerase chain reaction (PCR). A pair of strain-specific primers was designed based on the 16S rRNA gene and were end-labeled with a donor (Cy5) or acceptor (Cy5.5) dye. In the presence of the target bacterium, the primers were joined using a ligase detection reaction (LDR) only when the primers were completely complementary to the target sequence to form a reverse molecular beacon (rMB), thus bringing Cy5 (donor) and Cy5.5 (acceptor) into close proximity to allow fluorescence resonance energy transfer (FRET) to occur. These rMBs were subsequently analyzed using single-molecule detection of the FRET pairs (single-pair FRET; spFRET). The LDR was performed using a continuous flow thermal cycling process configured in a cyclic olefin copolymer (COC) microfluidic device using either 2 or 20 thermal cycles. Single-molecule photon bursts from the resulting rMBs were detected on-chip and registered using a simple laser-induced fluorescence (LIF) instrument. The spFRET signatures from the target pathogens were reported in as little as 2.6 min using spFRET.
Collapse
Affiliation(s)
- Zhiyong Peng
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, United States
| | - Steven A. Soper
- Departments of Chemistry and Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, United States, and Nano-BioTechnology and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Maneesh R. Pingle
- Department of Microbiology, Weill Medical College of Cornell University, New York, New York, United States
| | - Francis Barany
- Department of Microbiology, Weill Medical College of Cornell University, New York, New York, United States
| | - Lloyd M. Davis
- Center for Laser Applications, University of Tennessee Space Institute, Tullahoma, Tennessee, United States
| |
Collapse
|
22
|
|
23
|
Shin GW, Hwang HS, Chung B, Jung GY. Recent developments in CE-based detection methods for food-borne pathogens. Electrophoresis 2010; 31:2137-53. [DOI: 10.1002/elps.200900682] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
24
|
Yi P, Chen Z, Yu L, Zheng Y, Liu G, Xie H, Zhou Y, Zheng X, Han J, Li L. Development of a PCR/LDR/capillary electrophoresis assay with potential for the detection of a beta-thalassemia fetal mutation in maternal plasma. J Matern Fetal Neonatal Med 2010; 23:920-7. [DOI: 10.3109/14767050903387060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
25
|
Pingle M, Rundell M, Das S, Golightly LM, Barany F. PCR/LDR/universal array platforms for the diagnosis of infectious disease. Methods Mol Biol 2010; 632:141-57. [PMID: 20217576 DOI: 10.1007/978-1-60761-663-4_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections.
Collapse
Affiliation(s)
- Maneesh Pingle
- Department of Microbiology, Weill Medical College, Cornell University, New York, NY, USA.
| | | | | | | | | |
Collapse
|
26
|
Shin GW, Cho YS, Hwang HS, Oh MH, Nam HG, Park JH, Jung GY. A new single-step quantitative pathogen detection system: template-tagging followed by multiplex asymmetric PCR using common primers and CE-SSCP. Electrophoresis 2009; 30:2728-36. [PMID: 19621380 DOI: 10.1002/elps.200900074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid diagnosis of bacterial infection is important for patient management and appropriate therapy during the early phase of bacteria-induced disease. Among the existing techniques for identifying microbial, CE-SSCP combined with 16S ribosomal RNA gene-specific PCR has the benefits of excellent sensitivity, resolution, and reproducibility. However, even though CE-SSCP can separate PCR products with high-resolution, multiplex detection and quantification are complicated by primer-dimer formation and non-specific amplification. Here, we describe a novel technique for multiplex detection and quantification of pathogens by template-tagging followed by multiplex asymmetric PCR and subsequent CE-SSCP. More specifically, we reverse transcribed 16S ribosomal RNAs from seven septicemia-inducing pathogens, tagged the templates with common end sequences, and amplified them using common primers. The resulting amplicons could be successfully separated by CE-SSCP and quantified by comparison to an internal standard. This method yielded results that illustrate the potential of this system for diagnosing infectious disease.
Collapse
Affiliation(s)
- Gi Won Shin
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
| | | | | | | | | | | | | |
Collapse
|
27
|
Multiplex PCR-ligation detection reaction assay for simultaneous detection of drug resistance and toxin genes from Staphylococcus aureus, Enterococcus faecalis, and Enterococcus faecium. J Clin Microbiol 2009; 48:277-80. [PMID: 19864481 DOI: 10.1128/jcm.01411-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex PCR-ligation detection reaction (PCR-LDR) assay was developed for rapid detection of methicillin, tetracycline, and vancomycin resistance, as well as toxic shock toxin and Panton-Valentine leukocidin. The assay was tested on 470 positive blood culture bottles containing Staphylococcus aureus or enterococci. PCR-LDR exhibited a sensitivity and specificity of > or = 98% for all components except tetracycline resistance, which had a sensitivity of 94.7%. Rapid and sensitive detection of antimicrobial resistance and virulence genes could help guide therapy and appropriate infection control measures.
Collapse
|
28
|
Severgnini M, Cremonesi P, Consolandi C, Caredda G, De Bellis G, Castiglioni B. ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design. Nucleic Acids Res 2009; 37:e109. [PMID: 19531738 PMCID: PMC2760787 DOI: 10.1093/nar/gkp499] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 04/30/2009] [Accepted: 05/24/2009] [Indexed: 11/24/2022] Open
Abstract
16S rRNA gene is one of the preferred targets for resolving species phylogenesis issues in microbiological-related contexts. However, the identification of single-nucleotide variations capable of distinguishing a sequence among a set of homologous ones can be problematic. Here we present ORMA (Oligonucleotide Retrieving for Molecular Applications), a set of scripts for discriminating positions search and for performing the selection of high-quality oligonucleotide probes to be used in molecular applications. Two assays based on Ligase Detection Reaction (LDR) are presented. First, a new set of probe pairs on cyanobacteria 16S rRNA sequences of 18 different species was compared to that of a previous study. Then, a set of LDR probe pairs for the discrimination of 13 pathogens contaminating bovine milk was evaluated. The software determined more than 100 candidate probe pairs per dataset, from more than 300 16S rRNA sequences, in less than 5 min. Results demonstrated how ORMA improved the performance of the LDR assay on cyanobacteria, correctly identifying 12 out of 14 samples, and allowed the perfect discrimination among the 13 milk pathogenic-related species. ORMA represents a significant improvement from other contexts where enzyme-based techniques have been employed on already known mutations of a single base or on entire subsequences.
Collapse
Affiliation(s)
- Marco Severgnini
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Italy.
| | | | | | | | | | | |
Collapse
|
29
|
Boyle B, Dallaire N, MacKay J. Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR. BMC Biotechnol 2009; 9:75. [PMID: 19715565 PMCID: PMC2741440 DOI: 10.1186/1472-6750-9-75] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 08/28/2009] [Indexed: 11/25/2022] Open
Abstract
Background Robust designs of PCR-based molecular diagnostic assays rely on the discrimination potential of sequence variants affecting primer-to-template annealing. However, for accurate quantitative PCR (qPCR) assessment of gene expression in populations with gene polymorphisms, the effects of sequence variants within primer binding sites must be minimized. This dichotomy in PCR applications prompted us to design experiments to specifically address the quantitative nature of PCR amplifications with oligonucleotides containing mismatches. Results We performed qPCR reactions with several primer-target combinations and calculated ratios of molecules obtained with mismatch oligonucleotides to the average obtained with perfect match primer pairs. Amplifications were performed with genomic DNA and complementary DNA samples from different genotypes to validate the findings obtained with plasmid DNA. Our results demonstrate that PCR amplifications are driven by probabilities of oligonucleotides annealing to target sequences. Empiric probabilities can be measured for any primer pair. Alternatively, for primers containing mismatches, probabilities can be measured for individual primers and calculated for primer pairs. Conclusion The ability to evaluate priming (and mispriming) rates and to predict their impacts provided a precise and quantitative description of assay performance. Priming probabilities were also found to be a good measure of analytical specificity.
Collapse
Affiliation(s)
- Brian Boyle
- Centre d'Etude de la Forêt, Institut de biologie intégrative et des systèmes, Pav, CE Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada.
| | | | | |
Collapse
|
30
|
Testing and validation of high density resequencing microarray for broad range biothreat agents detection. PLoS One 2009; 4:e6569. [PMID: 19668365 PMCID: PMC2719057 DOI: 10.1371/journal.pone.0006569] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 06/06/2009] [Indexed: 11/19/2022] Open
Abstract
Rapid and effective detection and identification of emerging microbiological threats and potential biowarfare agents is very challenging when using traditional culture-based methods. Contemporary molecular techniques, relying upon reverse transcription and/or polymerase chain reaction (RT-PCR/PCR) provide a rapid and effective alternative, however, such assays are generally designed and optimized to detect only a limited number of targets, and seldom are capable of differentiation among variants of detected targets. To meet these challenges, we have designed a broad-range resequencing pathogen microarray (RPM) for detection of tropical and emerging infectious agents (TEI) including biothreat agents: RPM-TEI v 1.0 (RPM-TEI). The scope of the RPM-TEI assay enables detection and differential identification of 84 types of pathogens and 13 toxin genes, including most of the class A, B and C select agents as defined by the Centers for Disease Control and Prevention (CDC, Atlanta, GA). Due to the high risks associated with handling these particular target pathogens, the sensitivity validation of the RPM-TEI has been performed using an innovative approach, in which synthetic DNA fragments are used as templates for testing the assay's limit of detection (LOD). Assay specificity and sensitivity was subsequently confirmed by testing with full-length genomic nucleic acids of selected agents. The LOD for a majority of the agents detected by RPM-TEI was determined to be at least 104 copies per test. Our results also show that the RPM-TEI assay not only detects and identifies agents, but is also able to differentiate near neighbors of the same agent types, such as closely related strains of filoviruses of the Ebola Zaire group, or the Machupo and Lassa arenaviruses. Furthermore, each RPM-TEI assay results in specimen-specific agent gene sequence information that can be used to assess pathogenicity, mutations, and virulence markers, results that are not generally available from multiplexed RT-PCR/PCR-based detection assays.
Collapse
|
31
|
Cremonesi P, Pisoni G, Severgnini M, Consolandi C, Moroni P, Raschetti M, Castiglioni B. Pathogen detection in milk samples by ligation detection reaction-mediated universal array method. J Dairy Sci 2009; 92:3027-39. [DOI: 10.3168/jds.2008-1773] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
32
|
Yi P, Chen Z, Zhao Y, Guo J, Fu H, Zhou Y, Yu L, Li L. PCR/LDR/capillary electrophoresis for detection of single-nucleotide differences between fetal and maternal DNA in maternal plasma. Prenat Diagn 2009; 29:217-22. [PMID: 19177453 DOI: 10.1002/pd.2072] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND The discovery of fetal DNA in maternal plasma has opened up an approach for noninvasive diagnosis. We have now assessed the possibility of detecting single-nucleotide differences between fetal and maternal DNA in maternal plasma by polymerase chain reaction (PCR)/ligase detection reaction((LDR)/capillary electrophoresis. METHODS PCR/LDR/capillary electrophoresis was applied to detect the genotype of c.454-397T>gene (ESR1) from experimental DNA models of maternal plasma at different sensitivity levels and 13 maternal plasma samples.alphaC in estrogen receptor. RESULTS (1) Our results demonstrated that the technique could discriminate low abundance single-nucleotide mutation with a mutant/normal allele ratio up to 1:10 000. (2) Examination of ESR1 c.454-397T>C genotypes by using the method of restriction fragment length analysis was performed in 25 pregnant women, of whom 13 pregnant women had homozygous genotypes. The c.454-397T>C genotypes of paternally inherited fetal DNA in maternal plasma of these 13 women were detected by PCR/LDR/capillary electrophoresis, which were accordant with the results of umbilical cord blood. CONCLUSIONS PCR/LDR/capillary electrophoresis has very high sensitivity to distinguish low abundance single nucleotide differences and can discriminate point mutations and single-nucleotide polymorphisms(SNPs) of paternally inherited fetal DNA in maternal plasma.
Collapse
Affiliation(s)
- Ping Yi
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Lauri A, Mariani PO. Potentials and limitations of molecular diagnostic methods in food safety. GENES AND NUTRITION 2008; 4:1-12. [PMID: 19067016 DOI: 10.1007/s12263-008-0106-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 11/19/2008] [Indexed: 11/26/2022]
Abstract
Molecular methods allow the detection of pathogen nucleic acids (DNA and RNA) and, therefore, the detection of contamination in food is carried out with high selectivity and rapidity. In the last 2 decades molecular methods have accompanied traditional diagnostic methods in routine pathogen detection, and might replace them in the upcoming future. In this review the implementation in diagnostics of four of the most used molecular techniques (PCR, NASBA, microarray, LDR) are described and compared, highlighting advantages and limitations of each of them. Drawbacks of molecular methods with regard to traditional ones and the difficulties encountered in pathogen detection from food or clinical specimen are also discussed. Moreover, criteria for the choice of the target sequence for a secure detection and classification of pathogens and possible developments in molecular diagnostics are also proposed.
Collapse
|
34
|
Terefework Z, Pham CL, Prosperi AC, Entius MM, Errami A, van Spanning RJM, Zaura E, Ten Cate JM, Crielaard W. MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms. J Microbiol Methods 2008; 75:558-65. [PMID: 18824042 DOI: 10.1016/j.mimet.2008.08.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 08/01/2008] [Accepted: 08/29/2008] [Indexed: 11/27/2022]
Abstract
A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts.
Collapse
Affiliation(s)
- Zewdu Terefework
- Department of Cariology, Endodontology, Pedodontology, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, The Netherlands.
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Detection and serotyping of dengue virus in serum samples by multiplex reverse transcriptase PCR-ligase detection reaction assay. J Clin Microbiol 2008; 46:3276-84. [PMID: 18685000 DOI: 10.1128/jcm.00163-08] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The detection and successful typing of dengue virus (DENV) from patients with suspected dengue fever is important both for the diagnosis of the disease and for the implementation of epidemiologic control measures. A technique for the multiplex detection and typing of DENV serotypes 1 to 4 (DENV-1 to DENV-4) from clinical samples by PCR-ligase detection reaction (LDR) has been developed. A serotype-specific PCR amplifies the regions of genes C and E simultaneously. The two amplicons are targeted in a multiplex LDR, and the resultant fluorescently labeled ligation products are detected on a universal array. The assay was optimized using 38 DENV strains and was evaluated with 350 archived acute-phase serum samples. The sensitivity of the assay was 98.7%, and its specificity was 98.4%, relative to the results of real-time PCR. The detection threshold was 0.017 PFU for DENV-1, 0.004 PFU for DENV-2, 0.8 PFU for DENV-3, and 0.7 PFU for DENV-4. The assay is specific; it does not cross-react with the other flaviviruses tested (West Nile virus, St. Louis encephalitis virus, Japanese encephalitis virus, Kunjin virus, Murray Valley virus, Powassan virus, and yellow fever virus). All but 1 of 26 genotypic variants of DENV serotypes in a global DENV panel from different geographic regions were successfully identified. The PCR-LDR assay is a rapid, sensitive, specific, and high-throughput technique for the simultaneous detection of all four serotypes of DENV.
Collapse
|
36
|
Lantz AW, Brehm‐Stecher BF, Armstrong DW. Combined capillary electrophoresis and DNA‐fluorescence in situ hybridization for rapid molecular identification of Salmonella Typhimurium in mixed culture. Electrophoresis 2008; 29:2477-84. [DOI: 10.1002/elps.200700835] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
37
|
Development of multiplex PCR-ligase detection reaction assay for detection of West Nile virus. J Clin Microbiol 2008; 46:2269-79. [PMID: 18495862 DOI: 10.1128/jcm.02335-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We have developed a novel multiplex reverse transcription-PCR ligase detection reaction (RT-PCR/LDR) assay for the detection of West Nile virus (WNV) in both clinical and mosquito pool samples. The method relies on the amplification of three different genomic regions, one in the coding sequence of nonstructural protein NS2a and two in nonstructural protein NS5, to minimize the risk of detection failure due to genetic variation. The sensitivity of the PCR is complemented by the high specificity of the LDR step, and the detection of the LDR products can be achieved with capillary electrophoresis (CE) or a universal DNA microarray. We evaluated the limit of detection by both one-step and two-step multiplex RT-PCR/LDR/CE approaches, which reached, respectively, 0.005 and 0.017 PFU. The assay demonstrated 99% sensitivity when mosquito pool samples were tested and 100% sensitivity with clinical samples when the one-step approach was used. The broad strain coverage was confirmed by testing 34 WNV isolates belonging to lineages 1 and 2, and the high specificity of the assay was determined by testing other flaviviruses, as well as negative mosquito pool and clinical samples. In summary, the multiplex RT-PCR/LDR assay could represent a valuable complement to WNV serological diagnosis, especially in early symptomatic patients. In addition, the multiplexing capacity of the technique, which can be coupled to universal DNA microarray detection, makes it an amenable tool to develop a more comprehensive assay for viral pathogens.
Collapse
|
38
|
Song JH, Myung SC, Choi SH, Jeon EJ, Kang HG, Lee HM, Cho SK, Choi JC, Shin JW, Park IW, Choi BW, Kim JY. Multiplex PCR of Endotracheal Aspirate for the Detection of Pathogens in Ventilator Associated Pneumonia. Tuberc Respir Dis (Seoul) 2008. [DOI: 10.4046/trd.2008.64.3.194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Ju Han Song
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Soon Chul Myung
- Department of Urology, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Song Ho Choi
- Department of Cell Genomics, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Eun Ju Jeon
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Hyung Gu Kang
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Hye Min Lee
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Sung Keun Cho
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Jae Chol Choi
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Jong Wook Shin
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - In Won Park
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Byoung Whui Choi
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Jae Yeol Kim
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| |
Collapse
|