Abstract
Foodborne pathogenic bacteria are one of the main factors causing food safety issues. The rapid and accurate detection of pathogenic bacteria using molecular techniques is an effective and powerful strategy for preventing and controlling outbreaks of foodborne diseases, thereby ensuring food safety. This article summarizes the rapid and efficient molecular diagnostic techniques for detecting pathogenic bacteria, including polymerase chain reaction and its derivatives, isothermal amplification, DNA hybridization, genomic sequencing, and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated (CRISPR/Cas)-based detection technique. Through a comparative analysis of the technical principles, advantages, and potential limitations of these diagnostic methods, as well as an outlook on the future development directions for molecular biological detection technology, which will provide a valuable reference for developing more accurate, convenient, and sensitive methods for foodborne pathogens detection, and will help better address the challenges posed by foodborne diseases, thereby ensuring public health and safety.
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References
Abdelshafy AM, Younis HA, Osman AI, Hussein SM, El-Ela ASA, Mahmoud EA, Elsherbiny O, Rashwan AK (2025) Recent advances in detection and control strategies for foodborne bacteria in Raw and ready‐to‐eat fruits and vegetables. Food Front 6:605–629. https://doi.org/10.1002/fft2.541
Abdolahzadeh A, Dolgosheina EV, Unrau PJ (2019) RNA detection with high specificity and sensitivity using nested fluorogenic Mango NASBA. RNA 25(12), 1806–1813. http://www.rnajournal.org/cgi/doi/https://doi.org/10.1261/rna.072629.119
Ahmed MO, Vinueza-Burgos C, Medina-Santana J, Ishida M, Sauders B, Deiulio G, Dickey A, Endara P, Terán R (2025) Salmonella isolated from street foods and environment of an urban park: A whole genome sequencing approach. PLoS ONE 20:e0320735. https://doi.org/10.1371/journal.pone.0320735
Aladhadh M (2023) A review of modern methods for the detection of foodborne pathogens. Microorganisms 11:1111. https://doi.org/10.3390/microorganisms11051111
Aworh MK, Sunmonu GT, Adzitey F, Odih EE, Tibile BA, Ekli R, Aduah M, Oaikhena AO, Akinlabi OC, Abia ALK, Amoako DG, Okeke IN (2025) Genomic characterization of foodborne Salmonella enterica and Escherichia coli isolates from Saboba district and Bolgatanga municipality Ghana. PLoS ONE 20:e0315583. https://doi.org/10.1371/journal.pone.0315583
Babu US, Harrison LM, Mammel MK, Bigley EC III, Hiett KL, Balan KV (2020) A loop-mediated isothermal amplification (LAMP) assay for the consensus detection of human pathogenic Campylobacter species. J Microbiol Methods 176:106009. https://doi.org/10.1016/j.mimet.2020.106009
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712. https://doi.org/10.1126/science.1138140
Bonfiglio S, Sutton L-A, Ljungström V, Capasso A, Pandzic T, Weström S, Foroughi-Asl H, Skaftason A, Gellerbring A, Lyander A (2023) BTK and PLCG2 remain unmutated in one-third of patients with CLL relapsing on ibrutinib. Blood Adv 7:2794–2806. https://doi.org/10.1182/bloodadvances.2022008821
Boukharouba A (2022) Isolation and identification of foodborne pathogens of special interest in food safety. Degree-Granting, Universitat Politècnica de València
Bumunang EW, Zaheer R, Niu D, Narvaez-Bravo C, Alexander T, McAllister TA, Stanford K (2023) Bacteriophages for the targeted control of foodborne pathogens. Foods 12:2734. https://doi.org/10.3390/foods12142734
Bundidamorn D, Supawasit W, Trevanich S (2021) Taqman® probe based multiplex RT-PCR for simultaneous detection of Listeria monocytogenes, Salmonella spp. And Shiga toxin-producing Escherichia coli in foods. LWT 147:111696. https://doi.org/10.3390/foods11111557
Busch A, Becker A, Schotte U, Plötz M, Abdulmawjood A (2022) Mpl-gene-based loop-mediated isothermal amplification assay for specific and rapid detection of listeria monocytogenes in various food samples. Foodborne Pathog Dis 19:463–472. https://doi.org/10.1089/fpd.2021.0080
Buytaers FE, Verhaegen B, Van Nieuwenhuysen T, Roosens NH, Vanneste K, Marchal K, De Keersmaecker SC (2024) Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling. Front Microbiol 15:1330814. https://doi.org/10.3389/fmicb.2024.1330814
Cao X, Li P, Feng X, Liu D, Wang X, Wang L (2024) Detection of 13 foodborne pathogens in aquatic products using visual chromogenic chips based on asymmetric multiplex polymerase chain reaction and nucleic acid hybridization. Food Control 155:110100. https://doi.org/10.1016/j.foodcont.2023.110100
Chen M, Lan X, Zhu L, Ru P, Liu H, Xu W (2023) Nucleic acid-aided molecular amplification techniques for food microorganism detection. TrAC Trend Anal Chem 165:117116. https://doi.org/10.1016/j.trac.2023.117116
Chen J, Su H, Kim JH, Liu L, Liu R (2024) Recent advances in the CRISPR/Cas system-based visual detection method. Anal Methods 16:6599–6614. https://doi.org/10.1039/D4AY01147C
Deng R, Xu L, Zhang Y, Zhang X, Yuan Z, Chen J, Xia X (2024) CRISPR-based nucleic acid assays for food authentication. Trends Food Sci Technol 145:104351. https://doi.org/10.1016/j.tifs.2024.104351
Dhital R, Mustapha A (2023) DNA concentration by solid phase reversible immobilization improves its yield and purity, and detection time of E. coli O157: H7 in foods by high resolution melt curve qPCR. Food Control 145:109456. https://doi.org/10.1016/j.foodcont.2022.109456
Dong X, Huang A, He L, Cai C, You T (2024) Recent advances in foodborne pathogen detection using photoelectrochemical biosensors: from photoactive material to sensing strategy. Front Sustain Food Syst 8:1432555. https://doi.org/10.3389/fsufs.2024.1432555
Du J, Ma B, Li J, Shuai J, Yu X, Zhang X, Zhang M (2022) Probe-based loop-mediated isothermal amplification assay for multi-target quantitative detection of three foodborne pathogens in seafood. Food Analy Methods 15:3479–3489. https://doi.org/10.1007/s12161-022-02381-5
Elbehiry A, Abalkhail A, Marzouk E, Elmanssury AE, Almuzaini AM, Alfheeaid H, Alshahrani MT, Huraysh N, Ibrahem M, Alzaben F, Alanazi F, Alzaben M, Anagreyyah SA, Bayameen AM, Draz A, Abu-Okail A (2023) An overview of the public health challenges in diagnosing and controlling human foodborne pathogens. Vaccines 11:725. https://doi.org/10.3390/vaccines11040725
Fan L, Qinghua Y, Moutong C, Xinran X, Jumei Z, Rui P, Liang X, Juan W, Qihui G, Tao L, Xianhu W, Yu D, Qingping W (2021) Cas12aFDet: A CRISPR/Cas12a-based fluorescence platform for sensitive and specific detection of Listeria monocytogenes serotype 4c. Anal Chim Acta 1151. https://doi.org/10.1016/j.aca.2021.338248
Fang W, Cai Y, Zhu L, Wang H, Lu Y (2021) Rapid and highly sensitive detection of toxigenic Vibrio cholerae based on recombinase-aided amplification combining with lateral flow assay. Food Analy Methods 14:687–696. https://doi.org/10.1007/s12161-020-01909-x
Fang GY, Mu XJ, Huang BW, Jiang YJ (2023a) Monitoring longitudinal trends and assessment of the health risk of Shigella flexneri antimicrobial resistance. Environ Sci Technol 57:4971–4983. https://doi.org/10.1021/acs.est.2c08766
Fang Z, Zhou X, Wang X, Shi X (2023b) Development of a 3-plex droplet digital PCR for identification and absolute quantification of Salmonella and its two important serovars in various food samples. Food Control 145:109465. https://doi.org/10.1016/j.foodcont.2022.109465
Feng Y, Yao H, Chen S, Sun X, Yin Y, Jiao X (2020) Rapid detection of hypervirulent serovar 4h Listeria monocytogenes by multiplex PCR. https://doi.org/10.3389/fmicb.2020.01309. Front Microbiol 11
Foddai ACG, Grant IR (2020) Methods for detection of viable foodborne pathogens: current state-of-art and future prospects. Appl Microbiol Biotechnol 104:4281–4288. https://doi.org/10.1007/s00253-020-10542-x
Gao S, Liu J, Li Z, Ma Y, Wang J (2021) Sensitive detection of foodborne pathogens based on CRISPR-Cas13a. J Food Sci 86(6):2615–2625. https://doi.org/10.1111/1750-3841.15745
Gao R, Liu X, Xiong Z, Wang G, Ai L (2024) Research progress on detection of foodborne pathogens: the more rapid and accurate answer to food safety. Food Res Int 114767. https://doi.org/10.1016/j.foodres.2024.114767
Garrido-Maestu A, Fuciños P, Azinheiro S, Carvalho C, Carvalho J, Prado M (2019) Specific detection of viable Salmonella enteritidis by phage amplification combined with qPCR (PAA-qPCR) in spiked chicken meat samples. Food Control 99:79–83. https://doi.org/10.1016/j.foodcont.2018.12.038
Geng Y, Liu G, Liu L, Deng Q, Zhao L, Sun XX, Wang J, Zhao B, Wang J (2019) Real-time recombinase polymerase amplification assay for the rapid and sensitive detection of Campylobacter jejuni in food samples. J Microbiol Methods 157:31–36. https://doi.org/10.1016/j.mimet.2018.12.017
Ghosh PK, Ghosh PK, Ghosh N (2025) Foodborne pathogens and food-related microorganisms: an overview. Funct Foods: 351–388
Głowacka K, Kromdijk J, Leonelli L, Niyogi KK, Clemente TE, Long SP (2016) An evaluation of new and established methods to determine T-DNA copy number and homozygosity in Transgenic plants. Plant Cell Environ 39:908–917. https://doi.org/10.1111/pce.12693
Goenka SD, Gorzynski JE, Shafin K, Fisk DG, Pesout T, Jensen TD, Monlong J, Chang P-C, Baid G, Bernstein JA (2022) Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nat Biotechnol 40:1035–1041. https://doi.org/10.1038/s41587-022-01221-5
Grinevich D, Harden L, Thakur S, Callahan B (2024) Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing. Msystems 9:e00757–e00723. https://doi.org/10.1128/msystems.00757-23
Hadi J, Rapp D, Dhawan S, Gupta SK, Gupta TB, Brightwell G (2023) Molecular detection and characterization of foodborne bacteria: recent progresses and remaining challenges. Compr Rev Food Sci Food Saf 22:2433–2464. https://doi.org/10.1111/1541-4337.13153
Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362:839–842. https://doi.org/10.1126/science.aav4294
Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, Hindson BJ, Vessella RL, Tewari M (2013) Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods 10:1003–1005. https://doi.org/10.1038/nmeth.2633
Hodzic E, Glavinic A, Wademan C (2023) A novel approach for simultaneous detection of the most common food-borne pathogens by multiplex qPCR. Biomol Biomed 23(4):640–648. https://doi.org/10.17305/bb.2022.8693
Hong Y-P, Chen B-H, Wang Y-W, Teng R-H, Wei H-L, Chiou C-S (2024) The usefulness of nanopore sequencing in whole-genome sequencing-based genotyping of Listeria monocytogenes and Salmonella enterica serovar enteritidis. Microbiol Spectr 12:e00509–00524. https://doi.org/10.1128/spectrum.00509-24
Hu X, Cheng X, Wang Z, Zhao J, Wang X, Yang W, Chen Y (2022) Multiplexed and DNA amplification-free detection of foodborne pathogens in egg samples: combining electrical resistance-based microsphere counting and DNA hybridization reaction. Anal Chim Acta 1228:340336. https://doi.org/10.1016/j.aca.2022.340336
Hurtado A, Ocejo M, Oporto B, Lavín JL, Rodríguez R, Marcos MÁ, Urrutikoetxea-Gutiérrez M, Alkorta M, Marimón JM (2025) A one health approach for the genomic characterization of antibiotic-resistant Campylobacter isolates using nanopore whole-genome sequencing. Front Microbiol 16:1540210. https://doi.org/10.3389/fmicb.2025.1540210
Kabiraz MP, Majumdar PR, Mahmud MMC, Bhowmik S, Ali A (2023) Conventional and advanced detection techniques of foodborne pathogens: a comprehensive review. Heliyon 9:e15482. https://doi.org/10.1016/j.heliyon.2023.e15482
Kim E, Choi CH, Yang S-M, Shin M-K, Kim H-Y (2023) Rapid identification and absolute quantitation of zero tolerance-Salmonella Enterica subsp. Enterica serovar Thompson using droplet digital polymerase chain reaction. Lwt 173:114333. https://doi.org/10.1016/j.lwt.2022.114333
Kim SM, Kim EJ, Jang EJ, Kim TY, Park HM, Woo MA, Lim MC, Lim JA (2024) Bacteriophage-assisted Lysis and eluted genomic DNA-based detection of pathogenic bacterial contamination in food. Food Control 162:110433. https://doi.org/10.1016/j.foodcont.2020.107679
Kumar Y (2021) Isothermal amplification-based methods for assessment of Microbiological safety and authenticity of meat and meat products. Food Control 121:107679. https://doi.org/10.1016/j.foodcont.2020.107679
Lei S, Gu X, Xue W, Rong Z, Wang Z, Chen S, Zhong Q (2020) A 4-plex droplet digital PCR method for simultaneous quantification and differentiation of pathogenic and non-pathogenic Vibrio parahaemolyticus based on single intact cells. Front Microbiol 11:1727. https://doi.org/10.3389/fmicb.2020.01727
Li X, Zheng T, Xie Y-N, Li F, Jiang X, Hou X, Wu P (2021) Recombinase polymerase amplification coupled with a photosensitization colorimetric assay for fast Salmonella spp. Testing. Analy Chem 93:6559–6566. https://doi.org/10.1021/acs.analchem.1c00791
Li Y, Man S, Ye S, Liu G, Ma L (2022) CRISPR-Cas‐based detection for food safety problems: current status, challenges, and opportunities. Compre Rev Food Sci F 21:3770–3798. https://doi.org/10.1111/1541-4337.13000
Liu H, Wang J, Zeng H, Liu X, Jiang W, Wang Y, Ouyang W, Tang X (2021) RPA-Cas12a-FS: A frontline nucleic acid rapid detection system for food safety based on CRISPR-Cas12a combined with recombinase polymerase amplification. Food Chem 334:127608. https://doi.org/10.1016/j.foodchem.2020.127608
Liu A, Phillips K, Jia J, Deng P, Zhang D, Chang S, Lu S-E (2023) Development of a qPCR detection approach for pathogenic Burkholderia cenocepacia associated with fresh vegetables. Food Microbiol 115:104333. https://doi.org/10.1016/j.fm.2023.104333
Lombardi EC, Ullah S, de Oliveira CAF (2024) Rapid detection and occurrence of foodborne pathogens in minimally processed vegetables: a review. Int J Food Sci Tech 59:6905–6915. https://doi.org/10.1111/ijfs.17507
Lu Y, Yang H, Bai J, He Q, Deng R (2024) CRISPR-Cas based molecular diagnostics for foodborne pathogens. Crit Rev Food Sci Nutr 64:5269–5289. https://doi.org/10.3390/foods9030278
Ma B, Li J, Chen K, Yu X, Sun C, Zhang M (2020) Multiplex recombinase polymerase amplification assay for the simultaneous detection of three foodborne pathogens in seafood. Foods 9:278. https://doi.org/10.3390/foods9030278
Mao Z, Lei H, Chen R, Ren S, Liu B, Gao Z (2023) CRISPR molecular detection techniques: advances from single to multiple detection methods. TrAC Trend Analy Chem 166:117198. https://doi.org/10.1016/j.trac.2023.117198
Mather AE, Gilmour MW, Reid SW, French NP (2024) Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nat Rev Microbiol 1–13. https://doi.org/10.1038/s41579-024-01051-z
Meng T, Ren Y, Wang Q, Lu L, Luo Y, Zhang J, Zhang Q, Dzantiev BB, Negahdary M, Wan Y (2024) CRISPR-Cas14a with competitive isothermal amplification for rapid visual pathogen diagnosis. Sens Actuat B Chem 400:134946. https://doi.org/10.1016/j.snb.2023.134946
Moppert I, Kim E, Yang S-M, Park SH (2025) Development of multiplex PCR for detection of foodborne pathogens in fresh produce. Lett Appl Microbiol 78:ovaf038. https://doi.org/10.1093/lambio/ovaf038
Mu D, Zhou D, Xie G, Liu J, Xiong Q, Feng X, Xu H (2021) The fluorescent probe-based recombinase-aided amplification for rapid detection of Escherichia coli O157: H7. Mol Cell Probes 60:101777. https://doi.org/10.1016/j.mcp.2021.101777
Nassarawa SS, Luo Z, Lu Y (2022) Conventional and emerging techniques for detection of foodborne pathogens in horticulture crops: a leap to food safety. Food Bioprocess Tech 15:1248–1267. https://doi.org/10.1007/s11947-021-02730-y
Ndraha N, Lin H-Y, Wang C-Y, Hsiao H-I, Lin H-J (2023) Rapid detection methods for foodborne pathogens based on nucleic acid amplification: recent advances, remaining challenges, and possible opportunities. Food Chem Mol Sci 7:100183. https://doi.org/10.1016/j.fochms.2023.100183
Nesterova E, Morozova P, Gladkikh M, Kazemzadeh S, Syromyatnikov M (2024) Molecular methods for detecting microorganisms in beverages. Beverages 10:46. https://doi.org/10.3390/beverages10020046
Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:e63. https://doi.org/10.1093/nar/28.12.e63
Pakbin B, Brück WM, Brück TB, Allahyari S, Ashrafi Tamai I (2022) A quantitative prevalence of Escherichia coli O157 in different food samples using real-time qPCR method. Food Sci Nutr 11:228–235. https://doi.org/10.1002/fsn3.3055
Pang L, Pi X, Yang X, Song D, Qin X, Wang L, Man C, Zhang Y, Jiang Y (2024) Nucleic acid amplification-based strategy to detect foodborne pathogens in milk: a review. Crit Rev Food Sci Nutr 64:5398–5413. https://doi.org/10.1080/10408398.2022.2154073
Panwar S, Duggirala KS, Yadav P, Debnath N, Yadav AK, Kumar A (2022) Advanced diagnostic methods for identification of bacterial foodborne pathogens: contemporary and upcoming challenges. Crit Rev Biotechnol 43:982–1000. https://doi.org/10.1080/07388551.2022.2095253
Park JY, Lim M-C, Park K, Ok G, Chang H-J, Lee N, Park TJ, Choi S-W (2020) Detection of E. coli O157: H7 in food using automated immunomagnetic separation combined with real-time PCR. Processes 8:908. https://doi.org/10.3390/pr8080908
Park D-G, Kwon J-G, Ha E-S, Kang B, Choi I, Kwak J-E, Choi J, Lee W, Kim SH, Kim SH (2023) Novel next generation sequencing panel method for the multiple detection and identification of foodborne pathogens in agricultural wastewater. Fron Microbiol 14:1179934. https://doi.org/10.3389/fmicb.2023.1179934
Parra-Flores J, Daza-Prieto B, Chavarria P, Troncoso M, Stöger A, Figueroa G, Mancilla-Rojano J, Cruz-Córdova A, Martinovic A, Ruppitsch W (2025) From traditional typing to genomic precision: whole-genome sequencing of listeria monocytogenes isolated from refrigerated foods in Chile. Foods 14:290. https://doi.org/10.3390/foods14020290
Piepenburg O, Williams CH, Stemple DL, Armes NA (2006) DNA detection using recombination proteins. PLoS Biol 4:e204. https://doi.org/10.1371/journal.pbio.0040204
Prasad M, Milton A, Menon V, Ghatak S, Srinivas K, Momin K, Vineesha S, Das S, Sen A, Latha C (2023) Saltatory rolling circle amplification assay for simple and visual detection of Listeria monocytogenes in milk and milk products. Int Dairy J 137:105498. https://doi.org/10.1016/j.idairyj.2022.105498
Qin H, Shi X, Yu L, Li K, Wang J, Chen J, Yang F, Xu H, Xu H (2020) Multiplex real-time PCR coupled with sodium dodecyl sulphate and propidium monoazide for the simultaneous detection of viable Listeria monocytogenes, Cronobacter sakazakii, Staphylococcus aureus and Salmonella spp. in milk. Int Dairy J 108: 104739. https://doi.org/10.1016/j.idairyj.2020.104739
Rahn K, De Grandis S, Clarke R, McEwen S, Galan J, Ginocchio C, Curtiss Iii R, Gyles C (1992) Amplification of an InvA gene sequence of Salmonella typhimurium by polymerase chain reaction as a specific method of detection of Salmonella. Mol Cell Probes 6:271–279. https://doi.org/10.1016/0890-8508(92)90002-f
Rathore P, Basnet A, Kilonzo-Nthenge A, Dumenyo K, Yadegari Z, Taheri A (2024) Rapid detection of pathogenic E. coli based on CRISPR Cas system. Fron Microbiol 15. https://doi.org/10.3389/fmicb.2024.1423478
Saleh EAM, Ali E, Muxamadovna GM, Kassem AF, Kaur I, Kumar A, Jabbar HS, Alwaily ER, Elawady A, Omran AA (2024) CRISPR/Cas-based colorimetric biosensors: a promising tool for the diagnosis of bacterial foodborne pathogens in food products. Analy Methods 16:3448–3463. https://doi.org/10.1039/d4ay00578c
Saravanan A, Kumar PS, Hemavathy RV, Jeevanantham S, Kamalesh R, Sneha S, Yaashikaa PR (2020) Methods of detection of food-borne pathogens: a review. Environ Chem Lett 19:189–207. https://doi.org/10.1007/s10311-020-01072-z
Sarno E, Pezzutto D, Rossi M, Liebana E, Rizzi V (2021) A review of significant European foodborne outbreaks in the last decade. J Food Prot 84:2059–2070. https://doi.org/10.3389/fmicb.2019.03089
Shen X-x, Qiu F-z, Shen L-P, Yan T-f, Zhao M-c, Qi J-J, Chen C, Zhao L, Wang L, Feng Z-s (2019) A rapid and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA extraction. BMC Infect Dis 19:1–5. https://doi.org/10.1186/s12879-019-3814-9
Sheng L, Lu Y, Deng S, Liao X, Zhang K, Ding T, Gao H, Liu D, Deng R, Li J (2019) A transcription aptasensor: amplified, label-free and culture-independent detection of foodborne pathogens via light-up RNA aptamers. Chem Comm 55:10096–10099. https://doi.org/10.1039/c9cc05036a
Shin J, Miller M, Wang YC (2022) Recent advances in CRISPR-based systems for the detection of foodborne pathogens. Compr Rev Food Sci F 21:3010–3029. https://doi.org/10.1111/1541-4337.12956
Shrivastava SR, Shrivastava PS (2020) Indispensable need to involve multiple stakeholders to ensure global food safety: world health organization. J Integr Health Sci 8:49–50. https://doi.org/10.4103/JIHS.JIHS_15_20
Soroka M, Wasowicz B, Rymaszewska A (2021) Loop-mediated isothermal amplification (LAMP): the better sibling of PCR? Cells 10: 1931. https://doi.org/10.3390/cells10081931
Sousa M, Rocha R, Araújo D, Castro J, Barbosa A, Azevedo NF, Cerqueira L, Almeida C (2024) A new peptide nucleic acid fluorescence in situ hybridization probe for the specific detection of Salmonella species in food matrices. Foodborne Pathog Dis 21:298–305. https://doi.org/10.1089/fpd.2023.0127
Srinivasa C, Shivamallu C, Prasad KS, Rajanna SKS, Ashwini P, Mahadevamurthy M (2023) Tracing foodborne pathogens using molecular-based approaches global food safety. Apple Academic, pp 159–190
Sun J, Shi Y, Du Y, Wang Z, Liu Z, Wang H, Zhao G, Ma Y, Zheng M (2020a) Rapid detection of diarrheagenic Escherichia coli by a new multiplex Real-Time quantitative PCR assay. Appl Biochem Microbiol 56:748–757. https://doi.org/10.1134/s0003683820060174
Sun X, Wang Y, Zhang L, Liu S, Zhang M, Wang J, Ning B, Peng Y, He J, Hu Y (2020b) CRISPR-Cas9 triggered two-step isothermal amplification method for E. coli O157: H7 detection based on a metal-organic framework platform. Analy Chem 92:3032–3041. https://doi.org/10.1021/acs.analchem.9b04162
Sykes P, Neoh S, Brisco M, Hughes E, Condon J, Morley A (1992) Quantitation of targets for PCR by use of limiting Dilution. Biotechniques 13:444–449
Tan M, Liao C, Liang L, Yi X, Zhou Z, Wei G (2022) Recent advances in recombinase polymerase amplification: principle, advantages, disadvantages and applications. Front Cell Infect Microbiol 12:1019071. https://doi.org/10.3389/fcimb.2022.1019071
Tao J, Liu W, Ding W, Han R, Shen Q, Xia Y, Zhang Y, Sun W (2020) A multiplex PCR assay with a common primer for the detection of eleven foodborne pathogens. J Food Sci 85:744–754. https://doi.org/10.1111/1750-3841.15033
Trinh TND, Nam NN (2024) Isothermal amplification-based microfluidic devices for detecting foodborne pathogens: a review. Analy Methods. https://doi.org/10.1039/d3ay02039h
Turanoglu B, Omeroglu MA, Baltaci MO, Adiguzel G, Adiguzel A (2024) Determination of foodborne pathogens in minced beef by real-time PCR without culture enrichment. J Microbiol Meth 219:106896. https://doi.org/10.1016/j.mimet.2024.106896
Vidovic S, Taylor R, Hedderley D, Fletcher GC, Wei N (2024) Detection of non-pathogenic and pathogenic populations of Vibrio parahaemolyticus in various samples by the conventional, quantitative and droplet digital PCRs. Sci Rep 14:4137. https://doi.org/10.1038/s41598-024-54753-y
Vidyadharani G, Vijaya Bhavadharani HK, Sathishnath P, Ramanathan S, Sariga P, Sandhya A, Subikshaa S, Sugumar S (2021) Present and pioneer methods of early detection of food borne pathogens. J Food Sci Technol 59:2087–2107. https://doi.org/10.1007/s13197-021-05130-4
Wang Y, Ke Y, Liu W, Sun Y, Ding X (2020) A one-pot toolbox based on Cas12a/crRNA enables rapid foodborne pathogen detection at attomolar level. Acs Sens 5:1427–1435. https://doi.org/10.1021/acssensors.0c00320
Wang N, Sun X, Zhang J, Chen Y, Zhang J, Huang F, Chen A (2024) An instrument-free, integrated micro-platform for rapid and multiplexed detection of dairy adulteration in resource-limited environments. Biosens Bioelectron 257:116325. https://doi.org/10.1016/j.bios.2024.116325
Wang J, Sun H, Gao Y, Bu S, Zhang Z, Wang C, Zhang H, Zhang W, Wan J (2025) A novel biosensor for detecting V. parahaemolyticus based on cascade signal amplification of CRISPR/Cas14a and exo III. Food Control 167:110788. https://doi.org/10.1016/j.foodcont.2024.110788
Wei L, Wang Z, Wu L, Chen Y (2023) CRISPR/Cas12a-based magnetic relaxation switching biosensor for nucleic acid amplification-free and ultrasensitive detection of methicillin-resistant Staphylococcus aureus. Biosens Bioelectron 222:114984. https://doi.org/10.1016/j.bios.2022.114984
Wu S, Yuan J, Xu A, Wang L, Li Y, Lin J, Yue X, Xi X (2023) A lab-on-a-tube biosensor combining recombinase-aided amplification and CRISPR-Cas12a with rotated magnetic extraction for Salmonella detection. Micromachines-basel 14:830. https://doi.org/10.3390/mi14040830
Xia J, Bu T, Jia P, He K, Wang X, Sun X, Wang L (2022) Polydopamine nanospheres-assisted direct PCR for rapid detection of Escherichia coli O157: H7. Anal Biochem 654:114797. https://doi.org/10.1016/j.ab.2022.114797
Xu X, Ma X, Wang H, Wang Z (2018) Aptamer based SERS detection of Salmonella typhimurium using DNA-assembled gold nanodimers. Microchim Acta 185:1–8. https://doi.org/10.1007/s00604-018-2852-0
Xu H, Ma X, Ye Z, Yu X, Liu G, Wang Z (2022) A droplet digital PCR based approach for identification and quantification of Porcine and chicken derivatives in beef. Foods 11:3265. https://doi.org/10.3390/foods11203265
Xue T, Lu Y, Yang H, Hu X, Zhang K, Ren Y, Wu C, Xia X, Deng R, Wang Y (2022) Isothermal RNA amplification for the detection of viable pathogenic bacteria to estimate the Salmonella virulence for causing enteritis. J Agric Food Chem 70:1670–1678. https://doi.org/10.1021/acs.jafc.1c07182
Xue Y, He S, Li M, Qiu Y (2025) Development and application of four foodborne pathogens by Taqman multiplex real-time PCR. Foodborne Pathog Dis 22:193–201. https://doi.org/10.1089/fpd.2023.0134
Yang R, Zhang H, Li X, Ye L, Gong M, Yang J, Yu J, Bai J (2018) A multiplex loop-mediated isothermal amplification assay for rapid screening of Acinetobacter baumannii and D carbapenemase OXA-23 gene. Biosci Rep 38:BSR20180425. https://doi.org/10.1042/BSR20180425
Yang J, Zhang N, Lv J, Zhu P, Pan X, Hu J, Wu W, Li S, Li H (2020) Comparing the performance of conventional PCR, RTQ-PCR, and droplet digital PCR assays in detection of Shigella. Mol Cell Probes 51:101531. https://doi.org/10.1016/j.mcp.2020.101531
Yang N, Zhang H, Han X, Liu Z, Lu Y (2024) Advancements and applications of loop-mediated isothermal amplification technology: a comprehensive overview. Front Microbiol 15:1406632. https://doi.org/10.3389/fmicb.2024.1406632
Yin J, Zou Z, Hu Z, Zhang S, Zhang F, Wang B, Lv S, Mu Y (2020) A sample-in-multiplex-digital-answer-out chip for fast detection of pathogens. Lab Chip 20:979–986. https://doi.org/10.1039/c9lc01143a
Yin L, Li Y, Zhang W, Han X, Wu Q, Xie Y, Fan J, Ma L (2023) Detection methods for foodborne viruses: current state-of-art and future perspectives. J Agric Food Chem 71:3551–3563. https://doi.org/10.1021/acs.jafc.2c06537
Young SR, Domesle KJ, McDonald RC, Lozinak KA, Laksanalamai P, Harrell E, Thakur S, Kabera C, Strain EA, McDermott PF (2022) Toward the adoption of loop-mediated isothermal amplification for Salmonella screening at the National antimicrobial resistance monitoring system’s retail meat sites. Foodborne Pathog Dis 19:758–766. https://doi.org/10.1089/fpd.2022.0047
Zeng D, Chen S, Jiang L, Ren J, Su J, Zhao Y, Jiang Y, Xue F, Tang F, Chen W (2020) A polymerase chain reaction based lateral flow test strip with Propidium monoazide for detection of viable Vibrio parahaemolyticus in codfish. Microchem J 159:105418. https://doi.org/10.1016/j.microc.2020.105418
Zhai L, Liu H, Chen Q, Lu Z, Zhang C, Lv F, Bie X (2019) Development of a real-time nucleic acid sequence–based amplification assay for the rapid detection of Salmonella spp. From food. Braz J Microbiol 50:255–261. https://doi.org/10.1007/s42770-018-0002-9
Zhai L, Liu H, Li J, Lu Z, Bie X (2022) A duplex real-time NASBA assay targeting a serotype-specific gene for rapid detection of viable Salmonella Paratyphi C in retail foods of animal origin. Can J Microbiol 68:259–268. https://doi.org/10.1139/cjm-2021-0054
Zhou J, Yin L, Dong Y, Peng L, Liu G, Man S, Ma L (2020) CRISPR-Cas13a based bacterial detection platform: sensing pathogen Staphylococcus aureus in food samples. Anal Chim Acta 1127:225–233. https://doi.org/10.1016/j.aca.2020.06.041
Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y (2022) Application of nanopore sequencing in the detection of foodborne microorganisms. Nanomaterials 12:1534. https://doi.org/10.3390/nano12091534
Zhou C, Zhao Y, Guo B, Yang M, Xu Q, Lei C, Wang H (2024) Establishment of a simple, sensitive, and specific salmonella detection method based on recombinase-aided amplification combined with dsDNA-specific nucleases. Foods 13:1380. https://doi.org/10.3390/foods13091380
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Y. X.: Conceptualization, writing original draft, and revision; L. L.: formal analysis, compilation and summary of references; Y. C. and B. L.: review and editing; Z. X.: supervision and revision. All authors have read and agreed to the published version of the manuscript.
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Ye, Y., Li, L., Chen, Y. et al. Molecular methods for rapid detection and identification of foodborne pathogenic bacteria. World J Microbiol Biotechnol 41, 175 (2025). https://doi.org/10.1007/s11274-025-04396-6
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DOI: https://doi.org/10.1007/s11274-025-04396-6