DOI QR코드

DOI QR Code

A new cell-direct quantitative PCR based method to monitor viable genetically modified Escherichia coli

  • Yang Qin (Environmental Science & Biotechnology, Jeonju University) ;
  • Bo Qu (Environmental Science & Biotechnology, Jeonju University) ;
  • Bumkyu Lee (Environmental Science & Biotechnology, Jeonju University)
  • Received : 2022.09.21
  • Accepted : 2022.11.03
  • Published : 2022.12.01

Abstract

The development and commercialization of industrial genetically modified (GM) organisms is actively progressing worldwide, highlighting an increased need for improved safety management protocols. We sought to establish an environmental monitoring method, using real-time polymerase chain reaction (PCR) and propidium monoazide (PMA) treatment to develop a quantitative detection protocol for living GM microorganisms. We developed a duplex TaqMan quantitative PCR (qPCR) assay to simultaneously detect the selectable antibiotic gene, ampicillin (AmpR), and the single-copy Escherichia coli taxon-specific gene, D-1-deoxyxylulose 5-phosphate synthase (dxs), using a direct cell suspension culture. We identified viable engineered E. coli cells by performing qPCR on PMA-treated cells. The theoretical cell density (true copy numbers) calculated from mean quantification cycle (Cq) values of PMA-qPCR showed a bias of 7.71% from the colony-forming unit (CFU), which was within ±25% of the acceptance criteria of the European Network of GMO Laboratories (ENGL). PMA-qPCR to detect AmpR and dxs was highly sensitive and was able to detect target genes from a 10,000-fold (10-4) diluted cell suspension, with a limit of detection at 95% confidence (LOD95%) of 134 viable E. coli cells. Compared to DNA-based qPCR methods, the cell suspension direct PMA-qPCR analysis provides reliable results and is a quick and accurate method to monitor living GM E. coli cells that can potentially be released into the environment.

Keywords

Acknowledgement

This work was supported by the Technology Innovation Program (20014752, Development of industrial LMO monitoring technology in production and utilization facilities) funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea).

References

  1. Ali M, Hashim U, Mustafa S, Man YC, Dhahi TS, Kashif M, Uddin MK, Hamid SA. 2012. Analysis of pork adulteration in commercial meatballs targeting porcine-specific mitochondrial cytochrome b gene by TaqMan probe real-time polymerase chain reaction. Meat Science 91:454-459. https://doi.org/10.1016/j.meatsci.2012.02.031
  2. Ben-Amar A, Oueslati S, Mliki A. 2017. Universal direct PCR amplification system: A time- and cost-effective tool for high-throughput applications. 3 Biotechnology 7:246.
  3. Chen Y, Bi C, Tong S, Gong Z, Hou H. 2019. An improved and reliable method for microalgae direct PCR. Journal of Applied Phycology 31:2411-2421.
  4. Choi SW. 2020. Market trends and promising technology development and corporate status by bio-industry sector. pp. 9-12. Korea Industrial Marketing Research, Suwon, Korea. [in Korean]
  5. Choo YJ, Kim SJ. 2006. Detection of human adenoviruses and enteroviruses in Korean oysters using cell culture, integrated cell culture-PCR, and direct PCR. Journal of Microbiology 44:162-170.
  6. da Cunha ET, Pedrolo AM, Paludo F, Scariot MC, Arisi ACM. 2020. Azospirillum brasilense viable cells enumeration using propidium monoazide-quantitative PCR. Archives of Microbiology 2027:1653-1662.
  7. Dreo T, Pirc M, Ramsak Z, Pavsic J, Milavec M, Zel J, Gruden K. 2014. Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria: A case study of fire blight and potato brown rot. Analytical and Bioanalytical Chemistry 406:6513-6528. https://doi.org/10.1007/s00216-014-8084-1
  8. ENGL (European Network of GMO Laboratories). 2015. Definition of minimum performance requirements for analytical methods for GMO testing. 2015. Accessed in http://gmo-crl.jrc.ec.europa.eu/doc/MPR%20Report%20Application%2020_10_2015.pdf on 20 October 2015.
  9. Fittipaldi M, Nocker A, Codony F. 2012. Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification. Journal of Microbiological Methods 912:276-289. https://doi.org/10.1016/j.mimet.2012.08.007
  10. Fraiture MA, Deckers M, Papazova N, Roosens NHC. 2020. Are antimicrobial resistance genes key targets to detect genetically modified microorganisms in fermentation products? International Journal of Food Microbiology 331:108749.
  11. Grohmann L, Broll H, Dagand E, Hildebrandt S, Hubert P, Kiesecker H, Lieske K, Made D, Mankertz J, Reiting R, et al. 2016. Guidelines for the validation of qualitative real-time PCR methods by means of a collaborative study. Technical Report BVL 1.
  12. Han SM, Kim DY, Hwang KS, Lee B, Kim CG, Park KW. 2014. Appearance/instance of genetically modified maize at grain receiving harbors and along transportation routes in Korea. Weed&Turfgrass Science 30:221-224.
  13. Han SM, Lee B, Won OJ, Hwang KS, Suh SJ, Kim CG, Park KW. 2015. Gene flow from herbicide resistant genetically modified rice to conventional rice (Oryza sativa L.) cultivars. Journal of Ecology and Environment 38:397-403. https://doi.org/10.5141/ecoenv.2015.042
  14. Heijnen L, Medema G. 2006. Quantitative detection of E. coli, E. coli O157 and other shiga toxin producing E. coli in water samples using a culture method combined with real-time PCR. Journal of Water & Health 44:487-498. https://doi.org/10.2166/wh.2006.0032
  15. ISAAA (International Service for the Acquisition of Agri-biotech Applications). 2019. Global status of commercialized biotech/GM brops in 2019: Biotech crops drive socioeconomic development and sustainable environment in the new frontier. ISAAA Brief No. 55, Ithaca, NY, USA.
  16. Joo S, Park P, Park S. 2019. Applicability of propidium monoazide (PMA) for discrimination between living and dead phytoplankton cells. PLOS ONE 146:e0218924.
  17. KBCH (Korean Biosafety Clearing House). 2022a. LMO status: Approval report status. Accessed in https://www.biosafety.or.kr/portal/page/f_03 on 2 August 2022. [in Korean]
  18. KBCH (Korean Biosafety Clearing House). 2022b. Industrial LMO information system. Accessed in https://www.biosafety.or.kr/portal/page/f_03 on 2 August 2022. [in Korean]
  19. Kim JH, Yoon JS, Lee DY, Kim D, Oh SW. 2016. Detection and quantitation of Bacillus cereus, Staphylococcus aureus, Salmonella typhimurium and Escherichia coli O157:H7 by droplet digital PCR. Korean Journal of Food Science and Technology 48:454-460. [in Korean] https://doi.org/10.9721/KJFST.2016.48.5.454
  20. KSBB (The Korean Society for Biotechnology and Bioengineering). 2020. A study on the advancement of industrial LMO safety management. pp. 17-21. KSBB, Seoul, Korea. [in Korean]
  21. Lee B. 2020. A study on the environmental monitoring and safety management of genetically modified canola (Brassica napus L.). Weed & Turfgrass Science 9:209-218. [in Korean]
  22. Lee B, Kim CG, Park JY, Park KW, Kim HJ, Yi H, Jung SC, Yoon WK, Kim HM. 2009a. Monitoring the occurrence of genetically modified soybean and maize in cultivated fields and along the transportation routes of the Incheon Port in South Korea. Food Control 20:250-254. https://doi.org/10.1016/j.foodcont.2008.05.006
  23. Lee B, Kim CG, Park JY, Yi H, Park KW, Jeong SC, Yoon WK, An JH, Cho KH, Kim HM. 2007. Survey of herbicide resistant oilseed rapes around the basin of rivers in Incheon Harbor area. Korean Journal of Weed Science 27:29-35. [in Korean]
  24. Lee B, Park KW, Kim CG, Kang HG, Sun HJ, Kwon YI, Song IJ, Ryu TH, Lee HY. 2014. Environmental monitoring of herbicide tolerant genetically modified zoysiagrass (Zoysia japonica) around confined field trials. Weed&Turfgrass Science 3:305-311. [in Korean]
  25. Lee B, Suh SC. 2011. A study on the trends and biosafety assessment of genetically modified crops. Korean Environmental Law 33:1-25. [in Korean]
  26. Lee C, Kim J, Shin SG, Hwang S. 2006. Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli. Journal of Biotechnology 123:273-280. https://doi.org/10.1016/j.jbiotec.2005.11.014
  27. Lee YJ, Kang MH, Noh TH, Lee DK, Lee GH, Kim SJ. 2009b. Direct PCR detection of the causal agents, soybean bacterial pustule, Xanthomonas axonopodis pv. glycines in Soybean Seeds. Research in Plant Disease 15:83-87. [in Korean] https://doi.org/10.5423/RPD.2009.15.2.083
  28. Lin CH, Chen YC, Pan TM. 2011. Quantification bias caused by plasmid DNA conformation in quantitative real-time PCR assay. PLOS ONE 612:e29101.
  29. Nocker A, Cheung CY, Camper AK. 2006. 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 67:310-320. https://doi.org/10.1016/j.mimet.2006.04.015
  30. Park MJ, Lee H, Ryoo R, Jang Y, Ka KH. 2021. A rapid and universal direct PCR method for macrofungi. The Korean Journal of Mycology 49:455-467.
  31. Piskata Z, Servusova E, Babak V, Nesvadbova M, Borilova G. 2019. The quality of DNA isolated from processed food and feed via different extraction procedures. Molecules 246:1188.
  32. Rasmussen R. 2001. Quantification on the light cycler. In Rapid cycle real-time PCR edited by Meuer S, Wittwer C, Nakagawara K. pp. 21-34. Springer-Verlag, Berlin, Germany.
  33. Rudi K, Moen B, Dromtorp SM, Holck AL. 2005. Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples. Applied and Environmental Microbiology 71:1018-1024. https://doi.org/10.1128/AEM.71.2.1018-1024.2005
  34. Sung J, Hawkins JR. 2020. A highly sensitive internally-controlled real-time PCR assay for mycoplasma detection in cell cultures. Biologicals 64:58-72. https://doi.org/10.1016/j.biologicals.2019.12.007
  35. Walch G, Knapp M, Rainer G, Peintner U. 2016. Colony-PCR is a rapid method for DNA amplification of hyphomycetes. Journal of Fungi 2:12.
  36. Whelan JA, Russell NB, Whelan MA. 2003. A method for the absolute quantification of cDNA using real-time PCR. Journal of Immunological Methods 278:261-269. https://doi.org/10.1016/S0022-1759(03)00223-0
  37. Zhang T, Fang HH. 2006. Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Applied Microbiology and Biotechnology 70:281-289. https://doi.org/10.1007/s00253-006-0333-6
  38. Zhao X, Wang J, Forghani F, Park JH, Park MS, Seo KH, Oh DH. 2013. Rapid detection of viable Escherichia coli O157 by coupling propidium monoazide with loop-mediated isothermal amplification. Journal of Microbiology and Biotechnology 23:1708-1716. https://doi.org/10.4014/jmb.1306.06003