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MOL-PCR and xMAP technology – a novel approach to the detection of African swine fever virus DNA. ACTA VET BRNO 2022. [DOI: 10.2754/avb202291020141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
African swine fever (ASF) is highly contagious haemorrhagic viral disease of domestic pigs and wild boars. The causative agent can be transmitted by direct contact with infected animals or via a contaminated environment, fomites, feed, meat and products thereof. Soft ticks (genus Ornithodoros) are known reservoirs and transmission vectors of the virus. As the disease causes serious problems in many countries, rapid detection of the agent and early diagnosis could help in prevention of its spread. Therefore, a multiple-analyte profile (xMAP) technology based on multiple oligonucleotide ligation followed by polymerase chain reaction (MOL-PCR) was introduced and verified. A system targeting two independent loci of the virus genome was designed to increase the likelihood of different strains detection and an internal control was employed to verify the correct course of the analysis. The sensitivity was experimentally determined as 10 genomic copies of the virus in one µl of isolated DNA. The system was verified on samples originating from a recent ASF outbreak in the Czech Republic (six spleen) and the Czech market (eight liver and heart tissues) with real-time polymerase chain reaction used as a reference method. The results of both methods were in agreement, even in samples with a low concentration of the virus genome (9.45 × 101 genomic copies/µl of DNA). The system introduced represents an open method allowing the detection and semi-quantification of up to 50 targets/agents in one reaction. It can, therefore, be used for rapid one-step screening and as an effective tool for risk management.
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2
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Hrdy J, Vasickova P, Nesvadbova M, Novotny J, Mati T, Kralik P. MOL-PCR and xMAP Technology: A Multiplex System for Fast Detection of Food- and Waterborne Viruses. J Mol Diagn 2021; 23:765-776. [PMID: 33864939 DOI: 10.1016/j.jmoldx.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses are common causes of food- and waterborne diseases worldwide. Conventional identification of these agents is based on cultivation, antigen detection, electron microscopy, or real-time PCR. Because recent technological advancements in detection methods are focused on fast and robust analysis, a rapid multiplexing technology, which can detect a broad spectrum of pathogenic viruses connected to food or water contamination, was utilized. A new semiquantitative magnetic bead-based multiplex system has been designed for simultaneous detection of several targets in one reaction. The system includes adenoviruses 40/41 (AdV), rotavirus A (RVA), norovirus (NoV), hepatitis E virus (HEV), hepatitis A virus (HAV), and a target for external control of the system. To evaluate the detection system, interlaboratory ring tests were performed in four independent laboratories. Analytical specificity of the tool was tested on a cohort of pathogenic agents and biological samples with quantitative PCR as a reference method. Limit of detection (analytical sensitivity) of 5 × 100 (AdV, HEV, and RVA) and 5 × 101 (HAV and NoV) genome equivalents per reaction was reached. This robust, senstivie, and rapid multiplexing technology may be used to routinely monitor and manage viruses in food and water to prevent food and waterborne diseases.
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Affiliation(s)
- Jakub Hrdy
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Petra Vasickova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic
| | - Michaela Nesvadbova
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jiri Novotny
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Tomas Mati
- Military Veterinary Institute, Hlucin, Czech Republic
| | - Petr Kralik
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
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Development of a Multiplex PCR and Magnetic DNA Capture Assay for Detecting Six Species Pathogens of the Genera Anaplasma and Ehrlichia in Canine, Bovine, Caprine and Ovine Blood Samples from Grenada, West Indies. Pathogens 2021; 10:pathogens10020192. [PMID: 33578784 PMCID: PMC7916465 DOI: 10.3390/pathogens10020192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/03/2021] [Accepted: 02/07/2021] [Indexed: 02/08/2023] Open
Abstract
Infections with tick-borne pathogens belonging to Anaplasma/Ehrlichia in various vertebrate hosts are a persistent problem resulting in nonspecific clinical signs during early infection. Diagnosis of single and multi-infections with these pathogens, causing diseases in companion/agricultural animals and people, remains a challenge. Traditional methods of diagnosis, such as microscopy and serology, have low sensitivity and specificity. Polymerase chain reaction (PCR) assays are widely used to detect early-phase infections, since these have high sensitivity and specificity. We report the development and validation of an assay involving PCR followed by magnetic capture method using species-specific oligonucleotides to detect six Anaplasma/Ehrlichia species pathogens in canine, bovine, caprine, and ovine blood samples. Overall, the assay application to 455 samples detected 30.1% (137/455) positives for one or more out of six screened pathogens. Single-pathogen infections were observed in 94.9% (130/137) of the positive samples, while co-infections were detected in 5.1% (7/137). Anaplasma marginale infection in cattle had the highest detection rate (34.4%), followed by canines positive for Anaplasma platys (16.4%) and Ehrlichia canis (13.9%). The assay aided in documenting the first molecular evidence for A. marginale in cattle and small ruminants and Ehrlichia chaffeensis and Ehrlichia ewingii in dogs in the Caribbean island of Grenada.
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Jelinkova P, Hrdy J, Markova J, Dresler J, Pajer P, Pavlis O, Branich P, Borilova G, Reichelova M, Babak V, Reslova N, Kralik P. Development and Inter-Laboratory Validation of Diagnostics Panel for Detection of Biothreat Bacteria Based on MOL-PCR Assay. Microorganisms 2020; 9:microorganisms9010038. [PMID: 33374468 PMCID: PMC7823616 DOI: 10.3390/microorganisms9010038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Early detection of biohazardous bacteria that can be misused as biological weapons is one of the most important measures to prevent the spread and outbreak of biological warfare. For this reason, many instrument platforms need to be introduced into operation in the field of biological warfare detection. Therefore the purpose of this study is to establish a new detection panel for biothreat bacteria (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella spp.) and confirm it by collaborative validation by using a multiplex oligonucleotide ligation followed by polymerase chain reaction and hybridization to microspheres by MagPix detection platform (MOL-PCR). Appropriate specific sequences in bacterial DNA were selected and tested to assemble the detection panel, and MOLigo probes (short specific oligonucleotides) were designed to show no cross-reactivity when tested between bacteria and to decrease the background signal measurement on the MagPix platform. During testing, sensitivity was assessed for all target bacteria using serially diluted DNA and was determined to be at least 0.5 ng/µL. For use as a diagnostic kit and easier handling, the storage stability of ligation premixes (MOLigo probe mixes) was tested. This highly multiplex method can be used for rapid screening to prevent outbreaks arising from the use of bacterial strains for bioterrorism, because time of analysis take under 4 h.
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Affiliation(s)
- Pavlina Jelinkova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
- Correspondence:
| | - Jakub Hrdy
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jirina Markova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
| | - Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic; (J.D.); (P.P.); (O.P.)
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic; (J.D.); (P.P.); (O.P.)
| | - Oto Pavlis
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic; (J.D.); (P.P.); (O.P.)
| | - Pavel Branich
- Military Veterinary Institute, Opavska 29, 748 01 Hlucin, Czech Republic;
| | - Gabriela Borilova
- Department of Meat Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; (G.B.); (P.K.)
| | - Marketa Reichelova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
- Collection of Animal Pathogenic Microorganisms, Department of Bacteriology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - Vladimir Babak
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic; (J.H.); (J.M.); (M.R.); (V.B.)
| | - Nikol Reslova
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic;
| | - Petr Kralik
- Department of Meat Hygiene and Technology, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; (G.B.); (P.K.)
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Reslova N, Huvarova V, Hrdy J, Kasny M, Kralik P. A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay. Sci Rep 2019; 9:2719. [PMID: 30804418 PMCID: PMC6389906 DOI: 10.1038/s41598-019-40035-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/06/2019] [Indexed: 12/28/2022] Open
Abstract
Multiplex oligonucleotide ligation-PCR (MOL-PCR) is a rapid method for simultaneous detection of multiple molecular markers within a single reaction. MOL-PCR is increasingly employed in microbial detection assays, where its ability to facilitate identification and further characterization via simple analysis is of great benefit and significantly simplifies routine diagnostics. When adapted to microsphere suspension arrays on a MAGPIX reader, MOL-PCR has the potential to outperform standard nucleic acid-based diagnostic assays. This study represents the guideline towards in-house MOL-PCR assay optimization using the example of foodborne pathogens (bacteria and parasites) with an emphasis on the appropriate choice of crucial parameters. The optimized protocol focused on specific sequence detection utilizes the fluorescent reporter BODIPY-TMRX and self-coupled magnetic microspheres and allows for a smooth and brisk workflow which should serve as a guide for the development of MOL-PCR assays intended for pathogen detection.
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Affiliation(s)
- Nikol Reslova
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic. .,Faculty of Science, Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Veronika Huvarova
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic.,Faculty of Science, Department of Experimental Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jakub Hrdy
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic.,Faculty of Science, Department of Experimental Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Martin Kasny
- Faculty of Science, Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Petr Kralik
- Veterinary Research Institute, Department of Food and Feed Safety, Hudcova 296/70, 621 00, Brno, Czech Republic
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6
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Performance Characterization of Two-Dimensional Paper Chromatography-based Biosensors for Biodefense, Exemplified by Detection of Bacillus anthracis Spores. BIOCHIP JOURNAL 2018. [DOI: 10.1007/s13206-017-2108-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Molecular Subtyping of Salmonella Typhimurium with Multiplex Oligonucleotide Ligation-PCR (MOL-PCR). Methods Mol Biol 2018; 1616:39-69. [PMID: 28600761 DOI: 10.1007/978-1-4939-7037-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
A multiplex oligonucleotide ligation-PCR (MOL-PCR) assay is a valuable high-throughput technique for the detection of bacteria and viruses, for characterization of pathogens and for diagnosis of genetic diseases, as it allows one to combine different types of molecular markers in a high-throughput multiplex assay. A MOL-PCR assay starts with a multiplex oligonucleotide ligation reaction for detection of the molecular marker, followed by a singleplex PCR for signal amplification and analysis of the MOL-PCR products on a Luminex platform. This last step occurs through a liquid bead suspension array in which the MOL-PCR products are hybridized to MagPlex-TAG beads.In this chapter, we describe the complete procedure for a MOL-PCR assay for subtyping of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant S. 1,4[5],12:i:- from DNA isolation through heat lysis up to data interpretation through a Gödel Prime Product. The subtyping assay consists of 50 discriminative molecular markers and two internal positive control markers divided over three MOL-PCR assays.
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8
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Wang X, Ying S, Wei X, Yuan J. Development of a gold nanoparticle-based universal oligonucleotide microarray for multiplex and low-cost detection of foodborne pathogens. Int J Food Microbiol 2017; 253:66-74. [PMID: 28505584 DOI: 10.1016/j.ijfoodmicro.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 01/16/2023]
Abstract
Bacterial foodborne diseases remain major threats to food safety and public health, especially in developing countries. In this study a novel assay, combining gold nanoparticle (GNP)-based multiplex oligonucleotide ligation-PCR and universal oligonucleotide microarray technology, was developed for inexpensive, specific, sensitive, and multiplex detection of eight common foodborne pathogens, including Shigella spp., Campylobacter jejuni, Bacillus cereus, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, and Vibrio parahaemolyticus. The target fragments of the eight pathogens were enriched by multiplex PCR and subjected to multiplex ligase detection reaction. Ligation products were enriched and labeled with GNPs by universal asymmetric PCR, using excess GNP-conjugated primers. The labeled single-stranded amplicons containing complementary tag sequences were captured by the corresponding tag sequences immobilized on microarrays, followed by silver staining for signal enhancement. Black images of microarray spots were visualized by naked eyes or scanned on a simple flatbed scanner, and quantified. The results indicated that this assay could unambiguously discriminate all eight pathogens in single and multiple infections, with detection sensitivity of 3.3-85CFU/mL for pure cultures. Microarray results of ninety-five artificially contaminated and retail food samples were consistent with traditional culture, biochemical and real-time PCR findings. Therefore, the novel assay has the potential to be used for routine detection due to rapidity, low cost, and high specificity and sensitivity.
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Affiliation(s)
- Xiaoqiang Wang
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an 710054, China.
| | - Sisi Ying
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an 710054, China
| | - Xiaoguang Wei
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an 710054, China
| | - Jun Yuan
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an 710054, China
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9
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Reslova N, Michna V, Kasny M, Mikel P, Kralik P. xMAP Technology: Applications in Detection of Pathogens. Front Microbiol 2017; 8:55. [PMID: 28179899 PMCID: PMC5263158 DOI: 10.3389/fmicb.2017.00055] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022] Open
Abstract
xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
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Affiliation(s)
- Nikol Reslova
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Veronika Michna
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Martin Kasny
- Department of Botany and Zoology, Faculty of Science, Masaryk University Brno, Czechia
| | - Pavel Mikel
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute Brno, Czechia
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Wuyts V, Roosens NHC, Bertrand S, Marchal K, De Keersmaecker SCJ. Optimized MOL-PCR for Characterization of Microbial Pathogens. ACTA ACUST UNITED AC 2016; 75:13.15.1-13.15.15. [PMID: 26742655 DOI: 10.1002/0471142956.cy1315s75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Characterization of microbial pathogens is necessary for surveillance, outbreak detection, and tracing of outbreak sources. This unit describes a multiplex oligonucleotide ligation-PCR (MOL-PCR) optimized for characterization of microbial pathogens. With MOL-PCR, different types of markers, like unique sequences, single-nucleotide polymorphisms (SNPs) and indels, can be simultaneously analyzed in one assay. This assay consists of a multiplex ligation for detection of the markers, a singleplex PCR for signal amplification, and hybridization to MagPlex-TAG beads for readout on a Luminex platform after fluorescent staining. The current protocol describes the MOL-PCR, as well as methods for DNA isolation, probe design, and data interpretation and it is based on an optimized MOL-PCR assay for subtyping of Salmonella Typhimurium.
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Affiliation(s)
- Véronique Wuyts
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Nancy H C Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Sophie Bertrand
- National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, Ghent University, IMinds, Ghent, Belgium
| | - Sigrid C J De Keersmaecker
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
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Wuyts V, Mattheus W, Roosens NHC, Marchal K, Bertrand S, De Keersmaecker SCJ. A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium. Appl Microbiol Biotechnol 2015. [PMID: 26205523 PMCID: PMC4561068 DOI: 10.1007/s00253-015-6831-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Subtyping below the serovar level is essential for surveillance and outbreak detection and investigation of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant 1,4,[5],12:i:- (S. 1,4,[5],12:i:-), frequent causes of foodborne infections. In an attempt to overcome the intrinsic shortcomings of currently used subtyping techniques, a multiplex oligonucleotide ligation-PCR (MOL-PCR) assay was developed which combines different types of molecular markers in a high-throughput microsphere suspension array. The 52 molecular markers include prophage genes, amplified fragment length polymorphism (AFLP) elements, Salmonella genomic island 1 (SGI1), allantoinase gene allB, MLVA locus STTR10, antibiotic resistance genes, single nucleotide polymorphisms (SNPs) and phase 2 flagellar gene fljB. The in vitro stability of these markers was confirmed in a serial passage experiment. The validation of the MOL-PCR assay for subtyping of S. Typhimurium and S. 1,4,[5],12:i:- on 519 isolates shows that the method is rapid, reproducible, flexible, accessible, easy to use and relatively inexpensive. Additionally, a 100 % typeability and a discriminatory power equivalent to that of phage typing were observed, and epidemiological concordance was assessed on isolates of 2 different outbreaks. Furthermore, a data analysis method is provided so that the MOL-PCR assay allows for objective, computerised data analysis and data interpretation of which the results can be easily exchanged between different laboratories in an international surveillance network.
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Affiliation(s)
- Véronique Wuyts
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 bus 2460, 3001, Leuven, Belgium
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12
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Miller S, Karaoz U, Brodie E, Dunbar S. Solid and Suspension Microarrays for Microbial Diagnostics. METHODS IN MICROBIOLOGY 2015; 42:395-431. [PMID: 38620236 PMCID: PMC7172482 DOI: 10.1016/bs.mim.2015.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.
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Affiliation(s)
- Steve Miller
- Clinical Microbiology Laboratory, University of California, San Francisco, California, USA
| | - Ulas Karaoz
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Eoin Brodie
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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13
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Klupp F, Diers J, Kahlert C, Neumann L, Halama N, Franz C, Schmidt T, Lasitschka F, Warth A, Weitz J, Koch M, Schneider M, Ulrich A. Expressional STAT3/STAT5 Ratio is an Independent Prognostic Marker in Colon Carcinoma. Ann Surg Oncol 2015; 22 Suppl 3:S1548-55. [PMID: 25773877 DOI: 10.1245/s10434-015-4485-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND Signal transducer and activator of transcription proteins (STATs) are crucial regulators of cell growth and differentiation; however, their specific prognostic impact in human colon cancer has only been studied to limited extent. We aimed to assess the prognostic significance of specific STAT expression patterns in colon carcinoma. METHODS Protein expression patterns of activated STAT1, STAT3, STAT4, and STAT5 in human colon carcinoma tissue and corresponding healthy mucosa (n = 104) were assessed using multiplex bead-based immunoassay technologies. Expression patterns were correlated with clinical and survival data. Immunohistochemistry was performed to assess spatial expression of STAT3 and STAT5. RESULTS STAT3 was underexpressed whereas STAT4 and STAT5 were overexpressed in colon carcinoma tissue. Primary tumors from patients with distant metastases (M1) displayed significantly increased expression of STAT1 and STAT3 but decreased expression of STAT4 and STAT5. Increased tumor expression of STAT1 or STAT3 was associated with impaired patient survival, whereas increased expression of STAT4 or STAT5 correlated with improved survival. Multivariate analysis identified an increased STAT3/STAT5 expressional ratio as an adverse prognostic marker in colon cancer patients. CONCLUSIONS The tumor progression-associated transcription factors STAT3, STAT4, and STAT5 are differently expressed in colon carcinoma tissue and colon mucosa. Moreover, the STAT3/STAT5 expression ratio is an independent prognostic marker in colon cancer patients.
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Affiliation(s)
- Fee Klupp
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Johannes Diers
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Christoph Kahlert
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Lena Neumann
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Niels Halama
- National Center for Tumor Diseases, Medical Oncology, and Internal Medicine VI, Tissue Imaging and Analysis Center, Bioquant, University of Heidelberg, Heidelberg, Germany
| | - Clemens Franz
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thomas Schmidt
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Tissue Bank of the National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Juergen Weitz
- Department of Visceral, Thoracic, and Vascular Surgery, University of Dresden, Dresden, Germany
| | - Moritz Koch
- Department of Visceral, Thoracic, and Vascular Surgery, University of Dresden, Dresden, Germany
| | - Martin Schneider
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany.
| | - Alexis Ulrich
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
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14
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Guidelines for optimisation of a multiplex oligonucleotide ligation-PCR for characterisation of microbial pathogens in a microsphere suspension array. BIOMED RESEARCH INTERNATIONAL 2015; 2015:790170. [PMID: 25705689 PMCID: PMC4332752 DOI: 10.1155/2015/790170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 01/05/2015] [Accepted: 01/12/2015] [Indexed: 12/27/2022]
Abstract
With multiplex oligonucleotide ligation-PCR (MOL-PCR) different molecular markers can be simultaneously analysed in a single assay and high levels of multiplexing can be achieved in high-throughput format. As such, MOL-PCR is a convenient solution for microbial detection and identification assays where many markers should be analysed, including for routine further characterisation of an identified microbial pathogenic isolate. For an assay aimed at routine use, optimisation in terms of differentiation between positive and negative results and of cost and effort is indispensable. As MOL-PCR includes a multiplex ligation step, followed by a singleplex PCR and analysis with microspheres on a Luminex device, several parameters are accessible for optimisation. Although MOL-PCR performance may be influenced by the markers used in the assay and the targeted bacterial species, evaluation of the method of DNA isolation, the probe concentration, the amount of microspheres, and the concentration of reporter dye is advisable in the development of any MOL-PCR assay. Therefore, we here describe our observations made during the optimisation of a 20-plex MOL-PCR assay for subtyping of Salmonella Typhimurium with the aim to provide a possible workflow as guidance for the development and optimisation of a MOL-PCR assay for the characterisation of other microbial pathogens.
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Rödiger S, Liebsch C, Schmidt C, Lehmann W, Resch-Genger U, Schedler U, Schierack P. Nucleic acid detection based on the use of microbeads: a review. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1243-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Development of a Luminex-based multiplex assay for detection of mutations conferring resistance to Echinocandins in Candida glabrata. J Clin Microbiol 2013; 52:790-5. [PMID: 24353003 DOI: 10.1128/jcm.03378-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Echinocandins are the recommended treatment for invasive candidiasis due to Candida glabrata. Resistance to echinocandins is known to be caused by nonsynonymous mutations in the hot spot-1 (HS1) regions of the FKS1 and FKS2 genes, which encode a subunit of the β-1,3-glucan synthase, the target of echinocandins. Here, we describe the development of a microsphere-based assay using Luminex MagPix technology to identify mutations in the FKS1 HS1 and FKS2 HS1 domains, which confer in vitro echinocandin resistance in C. glabrata isolates. The assay is rapid and can be performed with high throughput. The assay was validated using 102 isolates that had FKS1 HS1 and FKS2 HS1 domains previously characterized by DNA sequencing. The assay was 100% concordant with DNA sequencing results. The assay was then used for high-throughput screening of 1,032 C. glabrata surveillance isolates. Sixteen new isolates with mutations, including a mutation that was new to our collection (del659F), were identified. This assay provides a rapid and cost-effective way to screen C. glabrata isolates for echinocandin resistance.
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