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Duyvejonck H, Merabishvili M, Pirnay JP, De Vos D, Verbeken G, Van Belleghem J, Gryp T, De Leenheer J, Van der Borght K, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Development of a qPCR platform for quantification of the five bacteriophages within bacteriophage cocktail 2 (BFC2). Sci Rep 2019; 9:13893. [PMID: 31554892 PMCID: PMC6761158 DOI: 10.1038/s41598-019-50461-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/05/2019] [Indexed: 11/09/2022] Open
Abstract
To determine phage titers accurately, reproducibly and in a non-laborious and cost-effective manner, we describe the development of a qPCR platform for molecular quantification of five phages present in bacteriophage cocktail 2 (BFC2). We compared the performance of this molecular approach, with regard to quantification and reproducibility, with the standard culture-based double agar overlay method (DAO). We demonstrated that quantification of each of the five phages in BFC2 was possible by means of qPCR, without prior DNA extraction, but yields were significantly higher in comparison to DAO. Although DAO is assumed to provide an indication of the number of infective phage particles, whereas qPCR only provides information on the number of phage genomes, the difference in yield (qPCR/DAO ratio) was observed to be phage-dependent and appeared rather constant for all phages when analyzing different (freshly prepared) stocks of these phages. While DAO is necessary to determine sensitivity of clinical strains against phages in clinical applications, qPCR might be a valid alternative for rapid and reproducible quantification of freshly prepared stocks, after initial establishment of a correction factor towards DAO.
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Affiliation(s)
- Hans Duyvejonck
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium. .,Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium.
| | - Maya Merabishvili
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.,Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium.,The Eliava Institute of Bacteriophages, Microbiology and Virology, Gotua 3, Tbilisi, 0160, Georgia
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology (LabMCT), Burn Wound Center, Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Jonas Van Belleghem
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Tessa Gryp
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Julie De Leenheer
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Kelly Van der Borght
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research (LBR), Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
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Agrimonti C, Bottari B, Sardaro MLS, Marmiroli N. Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products. Crit Rev Food Sci Nutr 2017; 59:423-442. [DOI: 10.1080/10408398.2017.1375893] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Caterina Agrimonti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Benedetta Bottari
- Department of Food and Drug Science, University of Parma, Parma, Italy
| | - Maria Luisa Savo Sardaro
- Department of Food and Drug Science, University of Parma, Parma, Italy; Department of Nutrition and Gastronomy, University San Raffaele Roma Srl, Rome, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Refardt D. Real-time quantitative PCR to discriminate and quantify lambdoid bacteriophages of Escherichia coli K-12. BACTERIOPHAGE 2014; 2:98-104. [PMID: 23050220 PMCID: PMC3442831 DOI: 10.4161/bact.20092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Quantification of bacteriophages by real-time quantitative PCR (qPCR) is an interesting alternative to the traditional plaque assay. Importantly, the method should in principle be able to discriminate between closely related phages that are indistinguishable by most other means. Here, a method is presented that employs qPCR to discriminate and quantify ten closely related lambdoid phages of Escherichia coli str. K-12. It is shown that (1) treatment of samples with DNase efficiently removes non-encapsidated DNA, while the titer of plaque forming units is not affected, (2) individual phage types can be accurately quantified in mixed lysates, and (3) the detection limit corresponds to that of a plaque assay. The method is used to quantify individual phage types that are released from lysogens that carry up to three different prophages.
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Affiliation(s)
- Dominik Refardt
- ETH Zürich; Department of Environmental Systems Science; Institute of Integrative Biology; Zürich, Switzerland
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Abstract
This review highlights the main strategies available to control phage infection during large-scale milk fermentation by lactic acid bacteria. The topics that are emphasized include the factors influencing bacterial activities, the sources of phage contamination, the methods available to detect and quantify phages, as well as practical solutions to limit phage dispersion through an adapted factory design, the control of air flow, the use of adequate sanitizers, the restricted used of recycled products, and the selection and growth of bacterial cultures.
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Direct Quantitative Detection and Identification of Lactococcal Bacteriophages from Milk and Whey by Real-Time PCR: Application for the Detection of Lactococcal Bacteriophages in Goat's Raw Milk Whey in France. Int J Microbiol 2011; 2011:594369. [PMID: 22013446 PMCID: PMC3195528 DOI: 10.1155/2011/594369] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 07/12/2011] [Indexed: 12/04/2022] Open
Abstract
The presence of Lactococcus bacteriophages in milk can partly or completely inhibit milk fermentation. To prevent the problems associated with the bacteriophages, the real-time PCR was developed in this study for direct detection from whey and milk of three main groups of Lactococcus bacteriophages, c2, 936, and P335. The optimization of DNA extraction protocol from complex matrices such as whey and milk was optimized allowed the amplification of PCR without any matrix and nontarget contaminant interference. The real-time PCR program was specific and with the detection limit of 102 PFU/mL. The curve slopes were −3.49, −3.69, and −3.45 with the amplification efficiency estimated at 94%, 94%, and 98% and the correlation coefficient (R2) of 0.999, 0.999, and 0.998 for c2, 936 and P335 group, respectively. This method was then used to detect the bacteriophages in whey and goat's raw milk coming from three farms located in the Rhône-Alpes region (France).
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Garneau JE, Moineau S. Bacteriophages of lactic acid bacteria and their impact on milk fermentations. Microb Cell Fact 2011; 10 Suppl 1:S20. [PMID: 21995802 PMCID: PMC3231927 DOI: 10.1186/1475-2859-10-s1-s20] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Every biotechnology process that relies on the use of bacteria to make a product or to overproduce a molecule may, at some time, struggle with the presence of virulent phages. For example, phages are the primary cause of fermentation failure in the milk transformation industry. This review focuses on the recent scientific advances in the field of lactic acid bacteria phage research. Three specific topics, namely, the sources of contamination, the detection methods and the control procedures will be discussed.
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Affiliation(s)
- Josiane E Garneau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Québec, G1V 0A6, Canada
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