Abstract
In recent years, rapid detection methods such as polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR) have been continuously developed to improve the detection of food-borne pathogens in food samples. The recent developments of PCR and qPCR in the detection and identification of these food-borne pathogens are described and elaborated throughout this review. Specifically, further developments and improvements of qPCR are discussed in detecting Salmonella and norovirus. Promising advances in these molecular detection methods have been widely used to prevent human food-borne illnesses and death caused by the food-borne pathogens. In addition, this review presents the limitations and challenges of the detection methods which include conventional culture method and conventional PCR method in detecting Salmonella and norovirus. Furthermore, several advances of qPCR such as viability PCR (vPCR) and digital PCR (dPCR) have been discussed in the detection of Salmonella and norovirus. Good practice of analysis of the food-borne pathogens and other contaminants in the food industry as well as the advancement of molecular detection methods will help improve and ensure food safety and food quality.
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Abbreviations
- ATP:
-
Adenosine triphosphate
- PCR:
-
Polymerisation chain reaction
- qPCR:
-
Quantitative real-time polymerisation chain reaction
- vPCR:
-
Viability polymerisation chain reaction
- dPCR:
-
Digital polymerisation chain reaction
- NoV:
-
Norovirus
- rt-PCR:
-
Real-time polymerisation chain reaction
- ssRNA:
-
Single-stranded ribonucleic acid
- VPg:
-
Viral protein genome-linked
- ORF:
-
Open reading frame
- BPW:
-
Buffered peptone water
- LB:
-
Lactose broth
- EIA:
-
Enzyme immunoassay
- dsDNA:
-
Double-stranded deoxynucleic acid
- ssDNA:
-
Single-stranded ribonucleic acid
- dNTP:
-
Deoxynucleoside triphosphate
- RT-PCR:
-
Reverse transcriptase polymerisation
- cDNA:
-
Complementary deoxyribonucleic acid
- LOD:
-
Limit of detection
- Tm:
-
Melting temperature
- FRET:
-
Fluorescence resonance energy transfer
- IMS:
-
Immunomagnetic separation
- PMA:
-
Propidium monoazide
- EMA:
-
Ethidium monoazide bromide
- HBGA:
-
Histo-blood group antigens
References
Adams G (2020) A Beginner’s Guide to RT-PCR, qPCR and RT-qPCR. Biochem 42(3):48–53. https://doi.org/10.1042/BIO20200034
Ali AA, Altemimi AB, Alhelfi N, Ibrahim SA (2020) Application of biosensors for detection of pathogenic food bacteria: a review. Biosensors 10(58). https://doi.org/10.3390/bios10060058
Andrews WH, Hammack TS (2020) Bacteriological analytical manual, 8th Edition, Revision A. Chapter 5 (Old version 1998, Chapter 4). https://www.fda.gov/food/laboratory-methods-food/bam-chapter-1-foodsamplingpreparation-sample-homogenate
Baert L, Mattison K, Loisy-Hamon F, Harlow J, Martyres A, Lebeau B, Stals A, Van Coillie E, Herman L, Uyttendaele M (2011) Review: Norovirus prevalence in Belgian, Canadian and French fresh produce: a threat to human health? Int J Food Microbiol 151(3):261–269. https://doi.org/10.1016/j.ijfoodmicro.2011.09.013
Bell RL, Jarvis KG, Ottesen AR, Mcfarland MA, Brown EW (2016) Recent and emerging innovations in Salmonella detection: a food and environmental perspective. Microb Biotechnol 9(3):279–292. https://doi.org/10.1111/1751-7915.12359
Biotium (2010) Product Information: EvaGreen™ Dye, 20x in water
Bonnet M, Lagier JC, Raoult D, Khelaifia S (2020) Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology. New Microbes New Infect. https://doi.org/10.1016/j.nmni.2019.100622
Bosch A, Bidawid S, Le Guyader FS, Lees DN, Jaykus L-A (2011) Norovirus and Hepatitis A virus in shellfish, soft fruits and water. Rapid Detect Identif Quantif Foodborne Pathog 44:466
Chen SY, Feng Y, Chao HC, Lai MW, Huang WL, Lin CY, Tsai CN, Chen CL, Chiu CH (2015) Emergence in Taiwan of novel norovirus GII.4 variants causing acute gastroenteritis and intestinal haemorrhage in children. J Med Microbiol 64:544–550. https://doi.org/10.1099/jmm.0.000046
Cotten M, Petrova V, Phan MVT, Rabaa MA, Watson SJ, Ong SH, Kellam P, Baker S (2014) Deep sequencing of Norovirus genomes defines evolutionary patterns in an urban tropical setting. J Virol 88(19):11056–11069. https://doi.org/10.1128/jvi.01333-14
Defrancesco L (2003) Real-time PCR takes center stage. Anal Chem 75(7):175–179
Donaldson EF, Lindesmith LC, Lobue AD, Baric RS (2010) Viral shape-shifting: norovirus evasion of the human immune system. Nat Rev Microbiol 8(3):231–241. https://doi.org/10.1038/nrmicro2296
Eed HR, Abdel-Kader NS, El Tahan MH, Dai T, Amin R (2016) Bioluminescence-sensing assay for microbial growth recognition. J Sens 2016. https://doi.org/10.1155/2016/1492467
Elizaquível P, Aznar R, Sánchez G (2014) Recent developments in the use of viability dyes and quantitative PCR in the food microbiology field. J Appl Microbiol 116(1):1–13. https://doi.org/10.1111/jam.12365
Eyigor A, Carli KT, Unal CB (2002) Implementation of real-time PCR to tetrathionate broth enrichment step of Salmonella detection in poultry. Lett Appl Microbiol 34(1):37–41. https://doi.org/10.1046/j.1472-765X.2002.01036.x
Fittipaldi M, Codony F, Adrados B, Camper AK, Morató J (2011) Viable real-time pcr in environmentalsamples: can all data be interpreted directly?. Microb Ecol 61:7–12. https://doi.org/10.1007/s00248-010-9719-1
Giannella RA (1996) Salmonella. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston. Available from: https://www.ncbi.nlm.nih.gov/books/NBK8435/
Gunstream S, Hellemans J, Menezes A, Owens B, Rose S, Sander R, Vandesompele J (2012) qPCR Application Guide: Experimental Overview, Protocol, Troubleshooting
Gupta N (2019) DNA extraction and polymerase chain reaction. J Cytol 36(2):116–117. https://doi.org/10.4103/JOC.JOC_110_18
Gwida MM, Al-Ashmawy MAM (2014) Culture versus PCR for salmonella species identification in some dairy products and dairy handlers with special concern to its zoonotic importance. Vet Med Int. https://doi.org/10.1155/2014/502370
Ahmed OB, Asghar AH, El-Rahim IHA, AI H (2014) Detection of salmonella in food samples by culture and polymerase chain reaction methods. J Bacteriol Parasitol 05(03):5–7. https://doi.org/10.4172/2155-9597.1000187
Hsu CY, Hsu BM, Chang TY, Hsu TK, Shen SM, Chiu YC, Wang HJ, Ji WT, Fan CW, Chen JL (2014) Evaluation of immunomagnetic separation for the detection of Salmonella in surface waters by polymerase chain reaction. Int J Environ Res Public Health 11(9):9811–9821. https://doi.org/10.3390/ijerph110909811
Hu J, Huang R, Wang Y, Wei X, Wang Z, Geng Y, Jing J, Gao H, Sun X, Dong C, Jiang C (2018) Development of duplex PCR-ELISA for simultaneous detection of Salmonella spp. and Escherichia coli O157: H7 in food. J Microbiol Methods 154(136):127–133
Jayan H, Pu H, Sun DW (2020) Recent development in rapid detection techniques for microorganismactivities in food matrices using bio-recognition: a review. Trends Food Sci Technol 95:233–246. https://doi.org/10.1016/j.tifs.2019.11.007
Johnson G, Nolan T, Bustin SA (2013) Real-time quantitative PCR, pathogen detection and MIQE. Methods Mol Biol 943:1–16. https://doi.org/10.1007/978-1-60327-353-4_1
Jones MK, Grau KR, Costantini V, Kolawole AO, De Graaf M, Freiden P, Graves CL, Koopmans M, Wallet SM, Tibbetts SA, Schultz-Cherry S, Wobus CE, Vinjé J, Karst SM (2015) Human norovirus culture in B cells. Nat Protoc 10(12):1939–1947. https://doi.org/10.1038/nprot.2015.121
Kim SY, Ko G (2012) Using propidium monoazide to distinguish between viable and nonviable bacteria, MS2 and murine norovirus. Lett Appl Microb 55(3):182–188. https://doi.org/10.1111/j.1472-765X.2012.03276.x
Kim K, Katayama H, Kitajima M, Tohya Y, Ohgaki S (2011) Development of a real-time RT-PCR assay combined with ethidium monoazide treatment for RNA viruses and its application to detect viral RNA after heat exposure. Water Sci Technol 63(3):502–507. https://doi.org/10.2166/wst.2011.249
Koopmans M, Duizer E (2004) Foodborne viruses: an emerging problem. Int J Food Microbiol 90(1):23–41. https://doi.org/10.1016/S0168-1605(03)00169-7
Kumar R, Surendran PK, Thampuran N (2008) Evaluation of culture, ELISA and PCR assays for the detection of Salmonella in seafood. Lett Appl Microbiol 46(2):221–226. https://doi.org/10.1111/j.1472-765X.2007.02286.x
Lee K, Park K, Seo DJ, Lee MH, Jung JY, Park GJ, Yoon D, Park KH, Choi C (2014) Enhanced immunomagnetic separation for the detection of norovirus using the polyclonal antibody produced with human norovirus GI.I4-like particles. Food Sci Biotechnol 23(5):1569–1576. https://doi.org/10.1007/s10068-014-0213-2
Lee KM, Runyon M, Herrman TJ, Phillips R, Hsieh J (2015) Review of Salmonella detection and identification methods: aspects of rapid emergency response and food safety. Food Control 47:264–276. https://doi.org/10.1016/j.foodcont.2014.07.011
Liu P, Kim M, Schlesinger D, Kranz C, Ha S, Ha J, Slauch J, Baek S, Moe C (2015) Immunomagnetic separation combined with RT-qPCR for determining the efficacy of disinfectants against human noroviruses. J Infect Public Health 8(2):145–154. https://doi.org/10.1016/j.jiph.2014.08.007
Louten J (2016) Detection and diagnosis of viral infections. In: Essential Human Virology, pp 111–132
Málková K, Rauch P, Wyatt GM, Morgan MRA (1998) Combined immunomagnetic separation and detection of Salmonella enteritidis in food samples. Food Hydrocoll 10(3):271–280. https://doi.org/10.1080/09540109809354990
Matthews JE, Dickey BW, Miller RD, Felzer JR, Dawson BP, Lee AS, Rocks JJ, Kiel J, Montes JS, Moe CL, Eisenberg JNS, Leon JS (2012) The epidemiology of published norovirus outbreaks: a systematic review of risk factors associated with attack rate and genogroup. Epidemiol Infect 140(7):1161–1172. https://doi.org/10.1017/S0950268812000234
Mead PS, Slutsker L, Dietz V, McCaig LF, Bresee JS, Shapiro C, Griffin PM, Tauxe RV (1999) Food-related illness and death in the United States. Emerg Infect Dis 5(5):607–625. https://doi.org/10.3201/eid0505.990502
Merino L, Procura F, Trejo FM, Bueno DJ, Golowczyc MA (2017) Biofilm formation by Salmonella sp. in the poultry industry: detection, control and eradication strategies. Food Res Int. https://doi.org/10.1016/j.foodres.2017.11.024
Nogva HK, Drømtorp SM, Nissen H, Rudi K (2003) Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5′-nuclease PCR. Biotechniques 34(4):804–813. https://doi.org/10.2144/03344rr02
Nyaruaba R, Mwaliko C, Kering KK, Wei H (2019) Droplet digital PCR applications in the tuberculosis world. Tuberculosis 117:85–92. https://doi.org/10.1016/j.tube.2019.07.001
Parker AM, Mohler VL, Gunn AA, House JK (2020) Development of a qPCR for the detection and quantification of Salmonella spp. in sheep feces and tissues. J Vet Diagn Investig. https://doi.org/10.1177/1040638720952359
Postollec F, Falentin H, Pavan S, Combrisson J, Sohier D (2011) Recent advances in quantitative PCR (qPCR) applications in food microbiology. Food Microbiol 28(5):848–861. https://doi.org/10.1016/j.fm.2011.02.008
Robilotti E, Deresinski S, Pinsky BA (2015) Norovirus. Clin Microbiol Rev 28(1):134–164. https://doi.org/10.1128/CMR.00075-14
Rodríguez-Lázaro D, Hernández M (2013) Real-time PCR in food science: introduction. Current Issues Mol Biol 15(2):25–38. https://doi.org/10.21775/cimb.015.025
Rooney BL, Pettipas J, Grudeski E, Mykytczuk O, Pang XL, Booth TF, Hatchette TF, Leblanc JJ (2014) Detection of circulating norovirus genotypes: hitting a moving target. Virol J 11(1):20–25. https://doi.org/10.1186/1743-422X-11-129
Rostron P, Pennance T, Bakar F, Rollinson D, Knopp S, Allan F, Kabole F, Ali SM, Ame SM, Webster BL (2019) Development of a recombinase polymerase amplification (RPA) fluorescence assay for thedetection of Schistosoma haematobium. Parasites Vectors 1–7. https://doi.org/10.1186/s13071-019-3755-6
Salihah NT, Hossain MM, Lubis H, Ahmed MU (2016) Trends and advances in food analysis by realtimepolymerase chain reaction. J Food Sci Technol 53(5):2196–2209. https://doi.org/10.1007/s13197-016-2205-0
Sánchez G, Elizaquível P, Aznar R (2012) A single method for recovery and concentration of enteric viruses and bacteria from fresh-cut vegetables. Int J Food Microbiol 152(1–2):9–13. https://doi.org/10.1016/j.ijfoodmicro.2011.10.002
Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM (2011) Foodborne illness acquired in the United States-Major pathogens. Emerg Infect Dis 17(1):7–15. https://doi.org/10.3201/eid1701.P11101
Schmid M, Oehme R, Schalasta G, Brockmann S, Kimmig P, Enders G (2004) Fast detection of Noroviruses using a real-time PCR assay and automated sample preparation. BMC Infect Dis 4:1–8. https://doi.org/10.1186/1471-2334-4-15
Shaheen MNF, Elmahdy EM, Chawla-Sarkar M (2019) Quantitative PCR-based identification of enteric viruses contaminating fresh produce and surface water used for irrigation in Egypt. Environ Sci Pollut Res 26(21):21619–21628. https://doi.org/10.1007/s11356-019-05435-0
Shen Z, Qu W, Wang W, Lu Y, Wu Y, Li Z, Hang X, Wang X, Zhao D, Zhang C (2010) MPprimer: a program for reliable multiplex PCR primer design. BMC Bioinf 11. https://doi.org/10.1186/1471-2105-11-143
Shen J, Zhou T, Huang R (2019) Recent advances in Electrochemiluminescence sensors for pathogenicbacteria detection. Micromachines 10(8). https://doi.org/10.3390/mi10080532
Siala M, Barbana A, Smaoui S, Hachicha S, Marouane C, Kammoun S, Gdoura R, Messadi-Akrout F (2017) Screening and detecting Salmonella in different food matrices in Southern Tunisia using a combined enrichment/real-time PCR method: correlation with conventional culture method. Front Microbiol. https://doi.org/10.3389/fmicb.2017.02416
Smith CJ, Osborn AM (2009) Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol Ecol 67(1):6–20. https://doi.org/10.1111/j.1574-6941.2008.00629.x
Stals A, Mathijs E, Baert L, Botteldoorn N, Denayer S, Mauroy A, Scipioni A, Daube G, Dierick K, Herman L, van Coillie E, Thiry E, Uyttendaele M (2012) Molecular detection and genotyping of Noroviruses. Food Environ Virol 4(4):153–167. https://doi.org/10.1007/s12560-012-9092-y
Steingroewer J, Knaus H, Bley T, Boschke E (2005) A rapid method for the pre-enrichment and detection of Salmonella typhimurium by immunomagnetic separation and subsequent fluorescence microscopical techniques. Eng Life Sci 5(3):267–272. https://doi.org/10.1002/elsc.200420072
Sue MJ, Yeap SK, Omar AR, Tan SW (2014) Application of PCR-ELISA in molecular diagnosis. BioMed Res Int 2014. https://doi.org/10.1155/2014/653014
Taylor SC, Laperriere G, Germain H (2017) Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep 7(1):1–8. https://doi.org/10.1038/s41598-017-02217-x
Topping JR, Schnerr H, Haines J, Scott M, Carter MJ, Willcocks MM, Bellamy K, Brown DW, Gray JJ, Gallimore CI, Knight AI (2009) Temperature inactivation of Feline calicivirus vaccine strain FCV F-9 in comparison with human noroviruses using an RNA exposure assay and reverse transcribed quantitative real-time polymerase chain reaction-A novel method for predicting virus infectivity. J Virol Methods 156(1–2):89–95. https://doi.org/10.1016/j.jviromet.2008.10.024
Vinayaka AC, Ngo TA, Kant K, Engelsmann P, Dave VP, Shahbazi MA, Wolff A, Bang DD (2019) Rapid detection of Salmonella enterica in food samples by a novel approach with combination of sample concentration and direct PCR. Biosens Bioelectron. https://doi.org/10.1016/j.bios.2018.09.078
Vinjé J (2015) Advances in laboratory methods for detection and typing of norovirus. J Clin Microbiol 53(2):373–381. https://doi.org/10.1128/JCM.01535-14
Wang M, Yang J, Gai Z, Huo S, Zhu J, Li J, Wang R, Xing S, Shi G, Shi F, Zhang L (2018) Comparison between digital PCR and real-time PCR in detection of Salmonella typhimurium in milk. Int J Food Microbiol 266:251–256. https://doi.org/10.1016/j.ijfoodmicro.2017.12.011
World Health Organisation (WHO) (2020) Food Safety. https://www.int/news-room/factsheets/detail/food-safety. Accessed 20 Mar 2021
Yao L, Wu Q, Wang D, Kou X, Zhang J (2009) Development of monoclonal antibody-coated immunomagnetic beads for separation and detection of norovirus (genogroup II) in faecal extract samples. Lett Appl Microbiol 49(2):173–178. https://doi.org/10.1111/j.1472-765X.2009.02638.x
Yoo JE, Lee C, Park SJ, Ko G (2017) Evaluation of various real-time reverse transcription quantitative pcr assays for norovirus detection. J Microbiol Biotechnol 27(4):816–824. https://doi.org/10.4014/jmb.1612.12026
Zou Y, Mason MG, Botella JR (2020) Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics. PLoS ONE 15(6):1–19. https://doi.org/10.1371/journal.pone.0235216
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The author is grateful to Universiti Brunei Darussalam and the Ministry of Education for supporting and funding this research.
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This research was funded by the Ministry of Education under Brunei Darussalam Government Scholarship.
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Chin, N.A., Salihah, N.T., Shivanand, P. et al. Recent trends and developments of PCR-based methods for the detection of food-borne Salmonella bacteria and Norovirus. J Food Sci Technol 59, 4570–4582 (2022). https://doi.org/10.1007/s13197-021-05280-5
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DOI: https://doi.org/10.1007/s13197-021-05280-5