Analytical opportunities of quantitative polymerase chain reaction in dairy microbiology

International Dairy Journal

Volumn 30, Issue 1, 2013, Pages 45-52

  Boyer, Mickaël ^a   Combrisson, Jérôme ^a  

^a Danone Research Centre Daniel Carasso   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DAIRY INDUSTRY; FOOD INDUSTRIES; FOOD MICROORGANISMS; HIGH THROUGHPUT; MOLECULAR METHODS; MOLECULAR TOOLS; QUANTITATIVE PCR; QUANTITATIVE POLYMERASE CHAIN REACTION; REAL-TIME PCR; SPECIFIC PRIMERS; TECHNOLOGICAL ADVANCES; VIABLE CELLS; WORK-FLOWS;

BACTERIA; DAIRY PRODUCTS; FOOD MICROBIOLOGY; FOOD PRODUCTS; MICROBIOLOGY;

POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS);

EID: 84872670868     PISSN: 09586946     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.idairyj.2012.11.008     Document Type: Review

References (65)

1. Aparecida de Oliveira M., Abeid Ribeiro E.G., Morato Bergamini A.M., Pereira De Martinis E.C. Quantification of Listeria monocytogenes in minimally processed leafy vegetables using a combined method based on enrichment and 16S rRNA real-time PCR. Food Microbiology 2010, 27:19-23.
2. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., et al. Enterotypes of the human gut microbiome. Nature 2011, 474:666.
3. Bae S., Wuertz S. Discrimination of viable and dead fecal Bacteroidales bacteria by quantitative PCR with propidium monoazide. Applied and Environmental Microbiology 2009, 75:2940-2944.
4. Baker M. Digital PCR hits its stride. Nature Methods 2012, 9:541-544.
5. Bustin S.A. Why the need for qPCR publication guidelines? The case for MIQE. Methods 2009, 50:217-226.
6. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry 2009, 55:611-622.
7. Charteris W.P., Kelly P.M., Morelli L., Collins J.K. Selective detection, enumeration and identification of potentially probiotic Lactobacillus and Bifidobacterium species in mixed bacterial populations. International Journal of Food Microbiology 1997, 35:1-27.
8. Chen J., Zhang L., Paoli G.C., Shi C., Tu S.I., Shi X. A real-time PCR method for the detection of Salmonella enterica from food using a target sequence identified by comparative genomic analysis. International Journal of Food Microbiology 2010, 137:168-174.
9. Cummings J., Boyd G., Macpherson J.S., Wolf H., Smith G., Smyth J.F., et al. Factors influencing the cellular accumulation of SN-38 and camptothecin. Cancer Chemotherapy and Pharmacology 2002, 49:194-200.
10. Desfosses-Foucault E., Dussault-Lepage V., Le Boucher C., Savard P., Lapointe G., Roy D. Assessment of probiotic viability during Cheddar cheese manufacture and ripening using propidium monoazide-PCR quantification. Frontiers in Microbiology 2012, 3:350.
11. Elizaquivel P., Aznar R. A multiplex RTi-PCR reaction for simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Staphylococcus aureus on fresh, minimally processed vegetables. Food Microbiology 2008, 25:705-713.
12. Ellison S.L., English C.A., Burns M.J., Keer J.T. Routes to improving the reliability of low level DNA analysis using real-time PCR. BMC Biotechnology 2006, 6:33.
13. Falentin H., Postollec F., Parayre S., Henaff N., Le Bivic P., Richoux R., et al. Specific metabolic activity of ripening bacteria quantified by real-time reverse transcription PCR throughout Emmental cheese manufacture. International Journal of Food Microbiology 2010, 144:10-19.
14. FAO/WHO. (2002). Guidelines for the evaluation of probiotics in food. Joint FAO/WHO Working Group meeting, London Ontario, Canada, 30 April-1 May 2002.
15. Fittipaldi M., Nocker A., Codony F. Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification. Journal of Microbiological Methods 2012, 91:276-289.
16. Flekna G., Stefanic P., Wagner M., Smulders F.J., Mozina S.S., Hein I. Insufficient differentiation of live and dead Campylobacter jejuni and Listeria monocytogenes cells by ethidium monoazide (EMA) compromises EMA/real-time PCR. Research in Microbiology 2007, 158:405-412.
17. Fujimoto J., Tanigawa K., Kudo Y., Makino H., Watanabe K. Identification and quantification of viable Bifidobacterium breve strain Yakult in human faeces by using strain-specific primers and propidium monoazide. Journal of Applied Microbiology 2010, 110:209-217.
18. García-Cayuelaa T., Tabascoa R., Peláeza C., Requena T. Simultaneous detection and enumeration of viable lactic acid bacteria and bifidobacteria in fermented milk by using propidium monoazide and real-time PCR. International Dairy Journal 2009, 19:405-409.
19. Gendre, F., & Brignon, P. (1998). Method for detecting live microbiological contaminants in a food product sample. WO Patent 98/18958.
20. Gionchetti P., Rizzello F., Venturi A., Brigidi P., Matteuzzi D., Bazzocchi G., et al. Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial. Gastroenterology 2000, 119:305-309.
21. Gonzalez-Escalona N., Hammack T.S., Russell M., Jacobson A.P., De Jesus A.J., Brown E.W., et al. Detection of live Salmonella sp. cells in produce by a TaqMan-based quantitative reverse transcriptase real-time PCR targeting invA mRNA. Applied and Environmental Microbiology 2009, 75:3714-3720.
22. Heyman M., Menard S. Probiotic microorganisms: how they affect intestinal pathophysiology. Cellular and Molecular Life Sciences 2002, 59:1151-1165.
23. Hierro N., Esteve-Zarzoso B., Gonzalez A., Mas A., Guillamon J.M. Real-time quantitative PCR (QPCR) and reverse transcription-QPCR for detection and enumeration of total yeasts in wine. Applied and Environmental Microbiology 2006, 72:7148-7155.
24. Hierro N., Esteve-Zarzoso B., Mas A., Guillamon J.M. Monitoring of Saccharomyces and Hanseniaspora populations during alcoholic fermentation by real-time quantitative PCR. FEMS Yeast Research 2007, 7:1340-1349.
25. ISO Microbiology of food and animal feeding stuffs. Horizontal method for the enumeration of mesophilic lactic acid bacteria: Colony-count technique at 30 degrees C 1998, ISO15214:1998, International Standardisation Organisation, Geneva, Switzerland.
26. ISO Yogurt. Enumeration of characteristic microorganisms: Colony-count technique at 37 degrees C 2003, ISO7889:2003 (IDF 117: 2003), International Standardisation Organisation, Geneva, Switzerland.
27. ISO Microbiology of food and animal feeding stuffs - Protocol for the validation of alternative methods 2003, ISO16140:2003, International Standardisation Organisation, Geneva, Switzerland.
28. ISO Microbiology of food and animal feeding stuffs. Polymerase chain reaction (PCR) for the detection of food-borne pathogens: General requirements and definitions 2005, ISO22174:2005, International Standardisation Organisation, Geneva, Switzerland.
29. ISO Microbiology of food and animal feeding stuffs. Polymerase chain reaction (PCR) for the detection of food-borne pathogens: Performance testing for thermal cyclers 2005, ISO/TS20836:2005, International Standardisation Organisation, Geneva, Switzerland.
30. ISO Milk, milk products and mesophilic starter cultures. Enumeration of citrate-fermenting lactic acid bacteria: Colony-count technique at 25 degrees C 2006, ISO17792:2006 (IDF 180: 2006), International Standardisation Organisation, Geneva, Switzerland.
31. ISO Milk products. Enumeration of presumptive Lactobacillus acidophilus on a selective medium: Colony-count technique at 37 degrees C 2006, ISO20128:2006 (IDF 192: 2006), International Standardisation Organisation, Geneva, Switzerland.
32. ISO Microbiology of food and animal feeding stuffs. Polymerase chain reaction (PCR) for the detection of food-borne pathogens: Requirements for sample preparation for qualitative detection 2006, ISO20837:2006, International Standardisation Organisation, Geneva, Switzerland.
33. ISO Microbiology of food and animal feeding stuffs. Polymerase chain reaction (PCR) for the detection of food-borne pathogens: Requirements for amplification and detection for qualitative methods 2006, ISO20838:2006, International Standardisation Organisation, Geneva, Switzerland.
34. ISO Milk products. Enumeration of presumptive bifidobacteria: Colony count technique at 37 degrees C 2010, ISO29981:2010 (IDF 220: 2010), International Standardisation Organisation, Geneva, Switzerland.
35. ISO Microbiology of food and animal feeding stuffs. Real-time polymerase chain reaction (PCR) for the detection of food-borne pathogens: General requirements and definitions 2010, ISO22119:2010, International Standardisation Organisation, Geneva, Switzerland.
36. Jasson V., Jacxsens L., Luning P., Rajkovic A., Uyttendaele M. Alternative microbial methods: an overview and selection criteria. Food Microbiology 2010, 27:710-730.
37. Kalliomaki M., Salminen S., Arvilommi H., Kero P., Koskinen P., Isolauri E. Probiotics in primary prevention of atopic disease: a randomised placebo-controlled trial. Lancet 2001, 357:1076-1079.
38. Kramer M., Obermajer N., Bogovic Matijasic B., Rogelj I., Kmetec V. Quantification of live and dead probiotic bacteria in lyophilised product by real-time PCR and by flow cytometry. Applied Microbiology and Biotechnology 2009, 84:1137-1147.
39. Le Drean G., Mounier J., Vasseur V., Arzur D., Habrylo O., Barbier G. Quantification of Penicillium camemberti and P. roqueforti mycelium by real-time PCR to assess their growth dynamics during ripening cheese. International Journal of Food Microbiology 2010, 138:100-107.
40. Lefever S., Hellemans J., Pattyn F., Przybylski D.R., Taylor C., Geurts R., et al. RDML: structured language and reporting guidelines for real-time quantitative PCR data. Nucleic Acids Research 2009, 37:2065-2069.
41. Masco L., Vanhoutte T., Temmerman R., Swings J., Huys G. Evaluation of real-time PCR targeting the 16S rRNA and recA genes for the enumeration of bifidobacteria in probiotic products. International Journal of Food Microbiology 2007, 113:351-357.
42. Matsuda K., Tsuji H., Asahara T., Matsumoto K., Takada T., Nomoto K. Establishment of an analytical system for the human fecal microbiota, based on reverse transcription-quantitative PCR targeting of multicopy rRNA molecules. Applied and Environmental Microbiology 2009, 75:1961-1969.
43. Monnet C., Correia K., Sarthou A.S., Irlinger F. Quantitative detection of Corynebacterium casei in cheese by real-time PCR. Applied and Environmental Microbiology 2006, 72:6972-6979.
44. Mustapha A., Jiang T., Savaiano D.A. Improvement of lactose digestion by humans following ingestion of unfermented acidophilus milk: influence of bile sensitivity, lactose transport, and acid tolerance of Lactobacillus acidophilus. Journal of Dairy Science 1997, 80:1537-1545.
45. Nocker A., Camper A.K. Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Applied and Environmental Microbiology 2006, 72:1997-2004.
46. Nocker A., Cheung C.Y., Camper A.K. Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. Journal of Microbiological Methods 2006, 67:310-320.
47. Nocker A., Sossa-Fernandez P., Burr M.D., Camper A.K. Use of propidium monoazide for live/dead distinction in microbial ecology. Applied and Environmental Microbiology 2007, 73:5111-5117.
48. O'Grady J., Ruttledge M., Sedano-Balbas S., Smith T.J., Barry T., Maher M. Rapid detection of Listeria monocytogenes in food using culture enrichment combined with real-time PCR. Food Microbiology 2009, 26:4-7.
49. Omiccioli E., Amagliani G., Brandi G., Magnani M. A new platform for real-time PCR detection of Salmonella spp., Listeria monocytogenes and Escherichia coli O157 in milk. Food Microbiology 2009, 26:615-622.
50. Palaria A., Johnson-Kanda I., O'Sullivan D.J. Effect of a synbiotic yogurt on levels of fecal bifidobacteria, clostridia, and enterobacteria. Applied and Environmental Microbiology 2012, 78:933-940.
51. Pan Y., Breidt F. Enumeration of viable Listeria monocytogenes cells by real-time PCR with propidium monoazide and ethidium monoazide in the presence of dead cells. Applied and Environmental Microbiology 2007, 73:8028-8031.
52. Postollec F., Falentin H., Pavan S., Combrisson J., Sohier D. Recent advances in quantitative PCR (qPCR) applications in food microbiology. Food Microbiology 2011, 28:848-861.
53. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
54. Raggi C.C., Verderio P., Pazzagli M., Marubini E., Simi L., Pinzani P., et al. An Italian program of external quality control for quantitative assays based on real-time PCR with Taq-Man probes. Clinical Chemistry and Laboratory Medicine 2005, 43:542-548.
55. Reimann S., Grattepanche F., Rezzonico E., Lacroix C. Development of a real-time RT-PCR method for enumeration of viable Bifidobacterium longum cells in different morphologies. Food Microbiology 2010, 27:236-242.
56. Sheu S.J., Hwang W.Z., Chen H.C., Chiang Y.C., Tsen H.Y. Development and use of tuf gene-based primers for the multiplex PCR detection of Lactobacillus acidophilus, Lactobacillus casei group, Lactobacillus delbrueckii, and Bifidobacterium longum in commercial dairy products. Journal of Food Protection 2009, 72:93-100.
57. Sheu S.J., Hwang W.Z., Chiang Y.C., Lin W.H., Chen H.C., Tsen H.Y. Use of tuf gene-based primers for the PCR detection of probiotic Bifidobacterium species and enumeration of bifidobacteria in fermented milk by cultural and quantitative real-time PCR methods. Journal of Food Science 2010, 75:M521-M527.
58. Suo B., He Y., Tu S.I., Shi X. A multiplex real-time polymerase chain reaction for simultaneous detection of Salmonella spp., Escherichia coli O157, and Listeria monocytogenes in meat products. Foodborne Pathogens and Disease 2010, 7:619-628.
59. Takahashi H., Kimura B., Tanaka Y., Shinozaki J., Suda T., Fujii T. Real-time PCR and enrichment culture for sensitive detection and enumeration of Escherichia coli. Journal of Microbiological Methods 2009, 79:124-127.
60. Turnbaugh P.J., Quince C., Faith J.J., McHardy A.C., Yatsunenko T., Niazi F., et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:7503-7508.
61. Varma M., Field R., Stinson M., Rukovets B., Wymer L., Haugland R. Quantitative real-time PCR analysis of total and propidium monoazide-resistant fecal indicator bacteria in wastewater. Water Research 2009, 43:4790-4801.
62. Vogelstein B., Kinzler K.W. Digital PCR. Proceedings of the National Academy of Sciences of the United States of America 1999, 96:9236-9241.
63. Wagner A.O., Malin C., Knapp B.A., Illmer P. Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide. Applied and Environmental Microbiology 2008, 74:2537-2539.
64. White R.A., Blainey P.C., Fan H.C., Quake S.R. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics 2009, 10:116.
65. Wolffs P.F., Glencross K., Norling B., Griffiths M.W. Simultaneous quantification of pathogenic Campylobacter and Salmonella in chicken rinse fluid by a flotation and real-time multiplex PCR procedure. International Journal of Food Microbiology 2007, 117:50-54.