A comparison of different DNA extraction methods and molecular techniques for the detection and identification of foodborne pathogens

Spyridon Andreas Papatheodorou; Panagiotis Halvatsiotis; Dimitra Houhoula; Spyridon Andreas Papatheodorou; Panagiotis Halvatsiotis; Dimitra Houhoula

doi:10.3934/microbiol.2021019

AIMS Microbiology

2021, Volume 7, Issue 3: 304-319. doi: 10.3934/microbiol.2021019

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Research article

A comparison of different DNA extraction methods and molecular techniques for the detection and identification of foodborne pathogens

1.
Department of Food Science & Technology, School of Food Sciences, University of West Attica
2.
2nd Propaedeutic Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “ATTIKON” University Hospital, Chaidari Greece

Received: 02 June 2021 Accepted: 10 August 2021 Published: 09 September 2021

Foodborne infections continue to plague Europe. Food safety monitoring is in crisis as the existing techniques for detecting pathogens do not keep up with the global rising of food production and consumption. Thus, the development of innovative techniques for detecting and identifying pathogenic bacteria has become critical. The aim of the present study was firstly to develop an innovative simple and low cost method of extracting bacterial DNA from contaminated food and water samples with Salmonella enteric(a) subsp. enteric(a) serovar Typhimurium and Listeria monocytogenes and its comparison with two commercial DNA extraction kits (Qiagen, Macherey-Nagel). Finally, pathogens' detection using two molecular techniques (PCR-electrophoresis, LAMP), in order to evaluate the best combination of DNA extraction and identification based on their sensitivity, cost, rapidity and simplicity. Considering the above criteria, among them, best was proved an in-house bacterial DNA extraction method, based on the chloroform-isoamyl alcohol protocol, with certain modifications. This technique showed statistically similar results in terms of sensitivity, compared to the commercial kits, while at the same time maintained high rapidity and much lower cost. Lastly, between the molecular techniques, LAMP was found more promising considering its simplicity, high rapidity and sensitivity. Conclusively, the in-house DNA extraction method along with the LAMP technique, was proven to be the best among the presented combinations.
- DNA extraction methods,
- Salmonella enterica serovar Typhimurium,
- Listeria monocytogenes,
- PCR,
- LAMP,
- Limit of detection
Citation: Spyridon Andreas Papatheodorou, Panagiotis Halvatsiotis, Dimitra Houhoula. A comparison of different DNA extraction methods and molecular techniques for the detection and identification of foodborne pathogens[J]. AIMS Microbiology, 2021, 7(3): 304-319. doi: 10.3934/microbiol.2021019

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Abstract

Foodborne infections continue to plague Europe. Food safety monitoring is in crisis as the existing techniques for detecting pathogens do not keep up with the global rising of food production and consumption. Thus, the development of innovative techniques for detecting and identifying pathogenic bacteria has become critical. The aim of the present study was firstly to develop an innovative simple and low cost method of extracting bacterial DNA from contaminated food and water samples with Salmonella enteric(a) subsp. enteric(a) serovar Typhimurium and Listeria monocytogenes and its comparison with two commercial DNA extraction kits (Qiagen, Macherey-Nagel). Finally, pathogens' detection using two molecular techniques (PCR-electrophoresis, LAMP), in order to evaluate the best combination of DNA extraction and identification based on their sensitivity, cost, rapidity and simplicity. Considering the above criteria, among them, best was proved an in-house bacterial DNA extraction method, based on the chloroform-isoamyl alcohol protocol, with certain modifications. This technique showed statistically similar results in terms of sensitivity, compared to the commercial kits, while at the same time maintained high rapidity and much lower cost. Lastly, between the molecular techniques, LAMP was found more promising considering its simplicity, high rapidity and sensitivity. Conclusively, the in-house DNA extraction method along with the LAMP technique, was proven to be the best among the presented combinations.

Acknowledgments

We would like to thank the Faculty of Food Science & Technology, University of West Attica, Greece and the molecular diagnosis (polydinamo) laboratory for the meritorious collaboration.

Conflicts of interest

The authors declare no conflicts of interest regarding the present manuscript.

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