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Flütsch S, Wiestner F, Butticaz L, Moor D, Stölting KN. Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp. BMC Genomics 2023; 24:375. [PMID: 37403035 DOI: 10.1186/s12864-023-09429-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR). RESULTS We developed six DNA standards, called Vibrio-Sequins, together with optimized TaqMan assays for their quantification in individually sequenced DNA libraries via dPCR. To enable Vibrio-Sequin quantification, we validated three duplex dPCR methods to quantify the six targets. LOQs were ranging from 20 to 120 cp/µl for the six standards, whereas the limit of detection (LOD) was ~ 10 cp/µl for all six assays. Subsequently, a quantitative genomics approach was applied to quantify Vibrio-DNA in a pooled DNA mixture derived from several Vibrio species in a proof-of-concept study, demonstrating the increased power of our quantitative genomic pipeline through the coupling of NGS and dPCR. CONCLUSIONS We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.
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Affiliation(s)
- Sabrina Flütsch
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
| | - Fabian Wiestner
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Lisa Butticaz
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Dominik Moor
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Kai N Stölting
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
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Eischeid AC. Optimised multiplex droplet digital PCR is more precise, but not more sensitive, than real-time PCR for the detection of allergenic peanut. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2022; 39:1797-1805. [PMID: 36179324 DOI: 10.1080/19440049.2022.2126530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The United States requires labelling of food products containing major allergens, such as peanut, through the Food Allergen Labeling and Consumer Protection Act. Accurate labelling requires sensitive, specific and robust detection methods, and PCR-based techniques have proven highly effective. This article describes the transition of a previously developed multiplex real-time PCR assay for allergenic peanut to a droplet digital PCR format. The triplex droplet digital PCR assay was developed in a probe mixing format and directly compared to the established real-time PCR assay. Data are provided for thorough optimisation in the digital format, including the effects of primer and probe concentration, cycle number and annealing/extension time. Optimisation parameters influenced relative location and separation of droplet clusters but not final copy number. The droplet digital PCR assay was linear over five orders of magnitude; its lower limit of detection was 0.05 pg DNA per reaction, more sensitive than published digital PCR allergen assays. It was more precise, but not more sensitive, than the previously established real-time PCR assay.
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Affiliation(s)
- Anne C Eischeid
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
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Ramos‐Cabrer AM, Fernández‐Canto N, Almeida‐García F, Gorostidi A, Lombardero‐Fernández M, Romero‐Rodríguez MÁ, Pereira‐Lorenzo S. Traceability of the local cultivar ‘Caaveiro’ in flour mixtures used to produce Galician bread by simple sequence repeats and droplet digital polymerase chain reaction technology. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.16048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ana María Ramos‐Cabrer
- Dept. of Crop Production and Engineering Projects, Universidade de Santiago de Compostela Campus de Lugo 27002 Lugo Spain
| | - Nerea Fernández‐Canto
- Dept. of Crop Production and Engineering Projects, Universidade de Santiago de Compostela Campus de Lugo 27002 Lugo Spain
- Dept. of Anatomy, Animal Production and Clinical Veterinary Sciences, Universidade de Santiago de Compostela Campus de Lugo 27002 Lugo Spain
- Area of Food Technology, Department of Analytical Chemistry and Food Science, Faculty of Science University of Santiago de Compostela Campus de Lugo 27002 Lugo Spain
| | | | - Ana Gorostidi
- Biodonostia Health Research Institute Genomic Platform 20014 San Sebastian Spain
| | - Matilde Lombardero‐Fernández
- Dept. of Anatomy, Animal Production and Clinical Veterinary Sciences, Universidade de Santiago de Compostela Campus de Lugo 27002 Lugo Spain
| | - María Ángeles Romero‐Rodríguez
- Area of Food Technology, Department of Analytical Chemistry and Food Science, Faculty of Science University of Santiago de Compostela Campus de Lugo 27002 Lugo Spain
| | - Santiago Pereira‐Lorenzo
- Dept. of Crop Production and Engineering Projects, Universidade de Santiago de Compostela Campus de Lugo 27002 Lugo Spain
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