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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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Genetic diversity of clinical Salmonella enterica serovar Typhimurium in a university hospital of south Tunisia, 2000-2013. INFECTION GENETICS AND EVOLUTION 2020; 85:104436. [PMID: 32569743 DOI: 10.1016/j.meegid.2020.104436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/28/2020] [Accepted: 06/16/2020] [Indexed: 01/06/2023]
Abstract
Typhimurium is one of the main Salmonella serovar responsible for non-typhoidal gastro-enteritis in Tunisia. Here, we aimed to assess the genetic diversity of 88 clinical Salmonella Typhimurium strains recovered during 14 years from 2000 to 2013. Phage typing, CRISPR polymorphisms (CRISPOL), pulsed-field gel electrophoresis (PFGE), multi-locus variable-number tandem repeat analysis (MLVA) and Whole genome sequencing (WGS) were used to study the relatedness and spatio-temporal evolution of Salmonella Typhimurium populations (Typhimurium (n = 81), monophasic (n = 3) and nonmotile (n = 4) variants). Seven-locus MLST from whole genome assemblies showed that all isolates, except one, belonged to ST19. The isolates were divided into 10 definitive phage (DT) types, dominated by DT104-L (39.8%), DT41 (14.8%), DT116 (11.4%) and DT120 (5.7%). Fifty-seven MLVA patterns (DI, 0.978) were obtained compared to 11 different CRISPOL types and 15 PFGE types (DI,0.845). For cgMLST analysis, 20 profiles were found. A total of 3056 SNPs were identified from the whole genome of the 88 Salmonella Typhimurium isolates. These SNPs resolved these isolates into 86 SNP haplotypes. The phylogeny result allocated most Salmonella Typhimurium isolates into four distinct clades and seven subclades. Genetic diversity between the four clades ranged in the order of 249 to 720 nucleotide changes. The prevalent phage type DT104L formed a major clade on the phylogenetic tree. Pairwise SNP differences between the strains of this clade ranged between 0 and 59. SNP-based WGS typing seems to be the most valuable molecular markers for studying the evolutionary relationships of homogeneous serovar Typhimurium isolates.
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A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium. Food Microbiol 2020; 91:103534. [PMID: 32539977 DOI: 10.1016/j.fm.2020.103534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/22/2020] [Indexed: 11/23/2022]
Abstract
Humans are mostly contaminated by Salmonella through the consumption of pork- and poultry-derived food products. Therefore, a strict monitoring of Salmonella serotypes in food-producing animals is needed to limit the transmission of the pathogen to humans. Additionally, Salmonella can lead to economic loss in the food sector. Previously, a genoserotyping method using the MOL-PCR and Luminex technology was developed for the identification of the 6 Salmonella serotypes, and their variants, subjected to an official control in the Belgian food sector. In this study, 3 additional assays using the same technology were developed for the rapid and cost-effective detection of 13 dangerous highly invasive serotypes or other serotypes frequently isolated from the Belgian poultry and pork sector, i.e. Agona, Anatum, Brandenburg, Choleraesuis, Derby, Enteritidis vaccine strains, Gallinarum var. Gallinarum/Pullorum, Livingstone, Mbandaka, Minnesota, Ohio, Rissen and Senftenberg. Moreover, the previously developed first MOL-PCR assay was improved for S. Paratyphi B and serogroup O:3 detection. Finally, a Decision Support System hosted by a web application was created for an automatic and objective interpretation of the Luminex raw data. The 3 new assays and the modifications of the first assay were validated with a 100% accuracy, using 553 Salmonella and non-Salmonella strains in total.
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4
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Gand M, Mattheus W, Roosens NHC, Dierick K, Marchal K, De Keersmaecker SCJ, Bertrand S. A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay. Food Microbiol 2019; 87:103394. [PMID: 31948635 DOI: 10.1016/j.fm.2019.103394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/21/2019] [Accepted: 11/20/2019] [Indexed: 01/14/2023]
Abstract
Salmonella is a major pathogen having a public health and economic impact in both humans and animals. Six serotypes of the Salmonella genus are mentioned in the Belgian and European regulation as to be rapidly excluded from the food chain (EU regulation N°2160/2003, Belgian royal decree 27/04/2017). The reference method for Salmonella serotyping, including slide-agglutination and biochemical tests, is time-consuming, expensive, not always objective, and therefore does not match the fast identification criteria required by the legislation. In this study, a molecular method, using genetic markers detected by Multiplex Oligonucleotide Ligation - PCR and Luminex technology, was developed for the identification of the 6 Salmonella serotypes and their variants subjected to an official control. The resulting method was validated with the analysis of 971 Salmonella isolated from different matrixes (human, animal, food or environment) and 33 non-Salmonella strains. The results were compared with the reference identifications, achieving an accuracy of 99.7%. The cost-effective high-throughput genoserotyping assay is performed in 1 day and generates objective results, thanks to the automatic interpretation of raw data using a barcode system. In conclusion, it is fully adapted to the implementation in first line laboratories and meets the requirements of the regulation.
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Affiliation(s)
- Mathieu Gand
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium; Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium.
| | - Nancy H C Roosens
- Sciensano, Transversal Activities in Applied Genomics, B-1050 Brussels, Belgium
| | - Katelijne Dierick
- Sciensano, Infectious Diseases in Humans, Food Pathogen, B-1050 Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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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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Klotoe BJ, Molina-Moya B, Gomes HM, Gomgnimbou MK, Oliveira Suzarte L, Féres Saad MH, Ali S, Dominguez J, Pimkina E, Zholdybayeva E, Sola C, Refrégier G. TB-EFI, a novel 18-Plex microbead-based method for prediction of second-line drugs and ethambutol resistance in Mycobacterium tuberculosis complex. J Microbiol Methods 2018; 152:10-17. [PMID: 29913189 DOI: 10.1016/j.mimet.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
Abstract
Several diagnostic tests are being developed to detect drug resistance in tuberculosis. In line with previous developments detecting rifampicin and isoniazid resistance using microbead-based systems (spoligoriftyping and TB-SPRINT), we present here an assay called TB-EFI detecting mutations involved in resistance to ethambutol, fluoroquinolones and the three classical injectable drugs (kanamycin, amikacin and capreomycin) in Mycobacterium tuberculosis. The proposed test includes both wild-type and mutant probes for each targeted locus. Basic analysis can be performed manually. An upgraded interpretation is made available in Excel 2016®. Using a reference set of 61 DNA extracts, we show that TB-EFI provides perfect concordance with pyrosequencing. Concordance between genotypic resistance and phenotypic DST was relatively good (72 to 98% concordance), with lower efficiency for fluoroquinolones and ethambutol due to some untargeted mutations. When compared to phenotypical resistance, performances were similar to those obtained with Hain MTBDRsl assay, possibly thanks to the use of automatized processing of data although some mutations involved in fluoroquinolone resistance could not be included. When applied on three uncharacterized sets, phenotype could be predicted for 51% to 98% depending on the setting and the drug investigated, detecting one extensively drug-resistant isolate in each of a Pakistan and a Brazilian set of 91 samples, and 9 XDR among 43 multi-resistant Kazakhstan samples. By allowing high-throughput detection of second-line drugs resistance and of resistance to ethambutol that is often combined to second-line treatments, TB-EFI is a cost-effective assay for large-scale worldwide surveillance of resistant tuberculosis and XDR-TB control.
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Affiliation(s)
- Bernice J Klotoe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Barbara Molina-Moya
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Harrison Magdinier Gomes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France; Laboratório de Biologia Molecular Aplicada à Micobactérias, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Michel K Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France; Centre Muraz, Bobo-Dioulasso, Burkina Faso; Univ. Polytech, Bobo-Dioulasso, Burkina Faso
| | - Lorenna Oliveira Suzarte
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Maria H Féres Saad
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Av. Brasil, 4365 - 20245, Rio de Janeiro, Brazil
| | - Sajid Ali
- Microbiology Department, Quaid-i-Azam University, Islamabad, Pakistan
| | - José Dominguez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Edita Pimkina
- Infectious Diseases and Tuberculosis Hospital, Affiliate of Vilnius University Hospital Santariskiu klinikos, Vilnius, Lithuania
| | - Elena Zholdybayeva
- National Center for Biotechnology, Astana, Kazakhstan; Universitat Autònoma de Barcelona. CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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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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Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ. Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:. PLoS One 2018; 13:e0192504. [PMID: 29408896 PMCID: PMC5800660 DOI: 10.1371/journal.pone.0192504] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/24/2018] [Indexed: 12/05/2022] Open
Abstract
Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp. enterica serovar Typhimurium and serovar 1,4,[5],12:i:- isolates including five isolates from a confirmed outbreak and three isolates obtained from the same patient at different time points. The analysis was carried out using the original (high-coverage) and a down-sampled (low-coverage) datasets and two different reference genomes. All three tested workflows, namely CSI Phylogeny-based workflow, CFSAN-based workflow and PHEnix-based workflow, were able to correctly group the confirmed outbreak isolates and isolates from the same patient with all combinations of reference genomes and datasets. However, the workflows differed strongly with respect to the SNP distances between isolates and sensitivity towards sequencing coverage, which could be linked to the specific data analysis strategies used therein. To demonstrate the effect of particular data analysis steps, several modifications of the existing workflows were also tested. This allowed us to propose data analysis schemes most suitable for routine SNP-based subtyping applied to S. Typhimurium and S. 1,4,[5],12:i:-. Results presented in this study illustrate the importance of using correct data analysis strategies and to define benchmark and fine-tune parameters applied within routine data analysis pipelines to obtain optimal results.
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Affiliation(s)
- Assia Saltykova
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | - Véronique Wuyts
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Wesley Mattheus
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Sophie Bertrand
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Nancy H. C. Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB, Ghent, Belgium
- University of Pretoria, Pretoria, South Africa
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9
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Ceyssens PJ, Garcia-Graells C, Fux F, Botteldoorn N, Mattheus W, Wuyts V, De Keersmaecker S, Dierick K, Bertrand S. Development of a Luminex xTAG®assay for cost-effective multiplex detection of β-lactamases in Gram-negative bacteria. J Antimicrob Chemother 2016; 71:2479-83. [DOI: 10.1093/jac/dkw201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/29/2016] [Indexed: 01/23/2023] Open
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10
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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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Chen Y, Xie M. A colorimetric and ultrasensitive immunosensor for one-step pathogen detection via the combination of nanoparticle-triggered signal amplification and magnetic separation. RSC Adv 2015. [DOI: 10.1039/c5ra21727j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Colorimetric and ultrasensitive immunosensor for one-step pathogen detection via the combination of nanoparticle-triggered signal amplification and magnetic separation.
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Affiliation(s)
- Yiping Chen
- CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety
- National Center for NanoScience and Technology
- Beijing 100190
- China
| | - Mengxia Xie
- Analytical & Testing Center of Beijing Normal University
- Beijing 100875
- China
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