1
|
Mohsina K, Kaur M, Bowman JP, Powell S, Tamplin ML. qPCR quantification of Carnobacterium maltaromaticum, Brochothrix thermosphacta, and Serratia liquefaciens growth kinetics in mixed culture. J Microbiol Methods 2020; 175:105961. [PMID: 32479869 DOI: 10.1016/j.mimet.2020.105961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 10/24/2022]
Abstract
Quantifying growth kinetics of specific spoilage microorganisms in mixed culture is required to describe the evolution of food microbiomes. A qPCR method was developed to selectively amplify individual meat spoilage bacteria, Carnobacterium maltaromaticum, Brochothrix thermosphacta and Serratia liquefaciens, within a broth medium designed to simulate the composition of beef. An optimized method of DNA extraction was produced for standard curve construction. Method specificity was determined by individual single peaks in melt curves. Reaction efficiency for standard curves of C. maltaromaticum, B. thermosphacta and S. liquefaciens was high (R2 = 0.98-0.99), and linear quantification was achieved over a 5 log CFU/ml range. Coefficient of variation was calculated considering both threshold cycle (Ct) and bacterial concentration; the value did not exceed 14% for inter- or intra-runs for either method. Comparison of growth kinetic parameters derived from plate count and qPCR showed no significant variation (P > .05) for growth rate (GR) and maximum population density (MPD); lag phase duration (LPD) was not included in this comparison due to high innate variability. Log quantification of each isolate was validated in a mixed-culture experiment for all three species with qPCR and plate count differing less than 0.3 log CFU/ml (average 0.10 log CFU/ml, R2 = 0.98).
Collapse
Affiliation(s)
- Kaniz Mohsina
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - Mandeep Kaur
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - Shane Powell
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| | - Mark L Tamplin
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
| |
Collapse
|
2
|
Cui Z, Ojaghian M, Tao Z, Kakar K, Zeng J, Zhao W, Duan Y, Vera Cruz C, Li B, Zhu B, Xie G. Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J Appl Microbiol 2016; 120:1357-67. [DOI: 10.1111/jam.13094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Z. Cui
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - M.R. Ojaghian
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - Z. Tao
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - K.U. Kakar
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - J. Zeng
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - W. Zhao
- Chinese Academy of Inspection and Quarantine; Beijing China
| | - Y. Duan
- USDA-ARS-USHRL; Fort Pierce FL USA
| | - C.M. Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division; International Rice Research Institute; Metro Manila Philippines
| | - B. Li
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - B. Zhu
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation; College of Life Science; Zhejiang Sci-Tech University; Hangzhou China
| | - G. Xie
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| |
Collapse
|
3
|
Samson MC, Gullí M, Marmiroli N. Multiplex real-time PCR assays for simultaneous detection of maize MON810 and GA21 in food samples. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
4
|
García-Cañas V, Mondello M, Cifuentes A. Simultaneous detection of genetically modified organisms by multiplex ligation-dependent genome amplification and capillary gel electrophoresis with laser-induced fluorescence. Electrophoresis 2010; 31:2249-59. [PMID: 20593401 DOI: 10.1002/elps.201000078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this work, an innovative method useful to simultaneously analyze multiple genetically modified organisms is described. The developed method consists in the combination of multiplex ligation-dependent genome dependent amplification (MLGA) with CGE and LIF detection using bare-fused silica capillaries. The MLGA process is based on oligonucleotide constructs, formed by a universal sequence (vector) and long specific oligonucleotides (selectors) that facilitate the circularization of specific DNA target regions. Subsequently, the circularized target sequences are simultaneously amplified with the same couple of primers and analyzed by CGE-LIF using a bare-fused silica capillary and a run electrolyte containing 2-hydroxyethyl cellulose acting as both sieving matrix and dynamic capillary coating. CGE-LIF is shown to be very useful and informative for optimizing MLGA parameters such as annealing temperature, number of ligation cycles, and selector probes concentration. We demonstrate the specificity of the method in detecting the presence of transgenic DNA in certified reference and raw commercial samples. The method developed is sensitive and allows the simultaneous detection in a single run of percentages of transgenic maize as low as 1% of GA21, 1% of MON863, and 1% of MON810 in maize samples with signal-to-noise ratios for the corresponding DNA peaks of 15, 12, and 26, respectively. These results demonstrate, to our knowledge for the first time, the great possibilities of MLGA techniques for genetically modified organisms analysis.
Collapse
Affiliation(s)
- Virginia García-Cañas
- Department of Food Analysis, Institute of Industrial Fermentations (CSIC), Madrid, Spain
| | | | | |
Collapse
|
5
|
Muthaiyan A, Ricke SC. Current perspectives on detection of microbial contamination in bioethanol fermentors. BIORESOURCE TECHNOLOGY 2010; 101:5033-5042. [PMID: 19951838 DOI: 10.1016/j.biortech.2009.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 10/31/2009] [Accepted: 11/02/2009] [Indexed: 05/28/2023]
Abstract
In recent years bioethanol has encompassed worldwide interest as a non-conventional bioenergy source. This fact has driven several bioethanol industries to produce more ethanol on a large scale via cost effective methods. However in the process of scaling up ethanol production bacterial contamination is becoming one of the more challenging problems facing the bioethanol industry. There are several traditional microbiological methods available to detect and subsequently limit these bacterial contaminants. These methods are time consuming, laborious and can be less sensitive. Consequently, it is necessary to find novel sensitive and economic detection methods to eradicate the contaminants long before they disrupt ethanol production. Molecular methods that can detect the contaminants even at very low numbers at any given stage would help in the design of more cost effective eradication strategies and better targeted antimicrobial treatments. Application of rapid molecular detection approaches have the potential to provide much more sensitive and rapid means to not only detect but quantitate microbial contaminants long before they become problematic to overall bioethanol formation.
Collapse
Affiliation(s)
- Arunachalam Muthaiyan
- Center for Food Safety, IFSE and Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
| | | |
Collapse
|
6
|
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]
|
7
|
Kim H, Park K, Oh S, Chang I. Rapid detection of lactobacillus and yeast concentrations using a particle size distribution analyser. J Appl Microbiol 2009; 107:1499-504. [DOI: 10.1111/j.1365-2672.2009.04331.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
8
|
Rapid identification of Lactobacillus nantensis, Lactobacillus spicheri and Lactobacillus hammesii species using species-specific primers. Int J Food Microbiol 2008; 123:269-76. [PMID: 18378031 DOI: 10.1016/j.ijfoodmicro.2008.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 01/09/2008] [Accepted: 02/14/2008] [Indexed: 11/22/2022]
Abstract
Based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR), an identification tool for rapid differentiation of Lactobacillus nantensis, Lactobacillus spicheri and Lactobacillus hammesii, species isolated recently from French sourdough was developed. The DNA fragments containing ISRs were amplified with primers pairs 16S/p2 and 23S/p7. Clone libraries of the PCR-amplified rDNA with these primers were constructed using a pCR2.1 TA cloning kit and sequenced. The DNA sequences obtained were analyzed and species-specific primers were designed from these sequences. Two PCR amplicons, which were designated small ISR (S-ISR) and large ISR (L-ISR), were obtained for all Lactobacillus species studied. The L-ISR sequence reveale2d the presence of two tRNA genes, tRNAAla and tRNAIle. Species-specific primers designed allowed rapid identification of these species. The specificity of these primers was positively demonstrated as no response was obtained for more than 200 other species tested.
Collapse
|
9
|
García-Cañas V, Cifuentes A. Detection of microbial food contaminants and their products by capillary electromigration techniques. Electrophoresis 2007; 28:4013-30. [DOI: 10.1002/elps.200700253] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
10
|
Detection of Clostridium botulinum neurotoxin coding genes: analysis of PCR products by real time versus capillary gel electrophoresis methods. Eur Food Res Technol 2007. [DOI: 10.1007/s00217-007-0746-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Settanni L, Corsetti A. The use of multiplex PCR to detect and differentiate food- and beverage-associated microorganisms: a review. J Microbiol Methods 2006; 69:1-22. [PMID: 17280731 DOI: 10.1016/j.mimet.2006.12.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 11/17/2006] [Accepted: 12/08/2006] [Indexed: 10/23/2022]
Abstract
Regarding food safety, rapid detection of microbial species is crucial to develop effective preventive and/or adjustment measures. Classical methods for determining the presence of certain species are time-consuming and labor-intensive, hence, molecular methods, which offer speed, sensitivity and specificity, have been developed to address this problem. Multiplex PCR (MPCR) is widely applied in the various fields of microbiology for the rapid differentiation of microbial species without compromising accuracy. This paper describes the method and reports on the state-of-the-art application of this technique to the identification of microorganisms vehiculated with foods and beverages. The identification of both pathogens and probiotics and the species important for food fermentation or deterioration will be discussed. Applications of MPCR in combination with other techniques are also reviewed. Potentials, pitfalls, limitations and future prospects are summarised.
Collapse
Affiliation(s)
- L Settanni
- Dipartimento di Scienze degli Alimenti, Sezione di Microbiologia Agro-Alimentare ed Ambientale, Università degli Studi di Teramo, V. C.R. Lerici 1, 64023 Mosciano Sant' Angelo, Teramo, Italy
| | | |
Collapse
|
12
|
Cifuentes A. Recent advances in the application of capillary electromigration methods for food analysis. Electrophoresis 2006; 27:283-303. [PMID: 16307427 DOI: 10.1002/elps.200500474] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This article reviews the latest developments in the application of capillary electromigration methods for the analysis of foods and food components. Nowadays, methods based on CE techniques are becoming widely used in food analytical and research laboratories. This review covers the application of CE to analyze amino acids, biogenic amines, peptides, proteins, DNAs, carbohydrates, phenols, polyphenols, pigments, toxins, pesticides, vitamins, additives, small organic and inorganic ions, chiral compounds, and other compounds in foods, as well as to investigate food interactions and food processing. The use of microchips as well as other foreseen trends in CE analysis of foods is discussed. Papers that were published during the period June 2002-June 2005 are included following the previous review by Frazier and Papadopoulou (Electrophoresis 2003, 24, 4095-4105).
Collapse
Affiliation(s)
- Alejandro Cifuentes
- Department of Food Analysis, Institute of Industrial Fermentations (CSIC), Madrid, Spain.
| |
Collapse
|
13
|
Cailliez-Grimal C, Miguindou-Mabiala R, Leseine M, Revol-Junelles AM, Millière JB. Quantitative polymerase chain reaction used for the rapid detection of Carnobacterium species from French soft cheeses. FEMS Microbiol Lett 2005; 250:163-9. [PMID: 16009510 DOI: 10.1016/j.femsle.2005.05.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 05/09/2005] [Accepted: 05/19/2005] [Indexed: 11/20/2022] Open
Abstract
An identification method by PCR, specific to the Carnobacterium genus, was optimised by testing it on 28 bacterial strains. Primers from the literature were tested to differentiate Carnobacterium strains present among various bacterial species. The DNA of Carnobacterium species (C. alterfunditum, C. divergens, C. funditum, C. gallinarum, C. inhibens, C. maltaromaticum, C. mobile, C. viridans), specifically amplified by the Cb1-Cb2R primer couple at a hybridization temperature of 69 degrees C, gave only one band of 340 bp. The validation of this technique was carried out on a French soft cheese made with pasteurised milk inoculated with C. maltaromaticum LMA 28. Using classical PCR, detection was not possible for decimal dilutions of the cheese above 1 g L(-1). With Sybr Green I real time PCR, the specificity of the reaction was confirmed by the T(m) value. The standard curve constructed using the main threshold cycle and various concentrations of C. maltaromaticum LMA 28 (ranging from 10(0) to 10(8) cfu mL(-1)) showed good linearity and a sensitivity limit of > or = 10(4) cfu g(-1) of cheese. This technique was applied on commercially available cheeses made from raw cow's milk. The Sybr Green I real time PCR method constitutes an effective and easy-to-perform method to quantify Carnobacterium sp. in cheese.
Collapse
Affiliation(s)
- Catherine Cailliez-Grimal
- Laboratoire de Science et Génie Alimentaires, Ecole Nationale Supérieure d'Agronomie et des Industries, Alimentaires-Institut National Polytechnique de Lorraine, F-54505 Vandoeuvre-lès-Nancy, Cedex, France.
| | | | | | | | | |
Collapse
|