Establishment of a Real-Time Recombinase Polymerase Amplification for Rapid Detection of Pathogenic Yersinia enterocolitica
Abstract
1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Culture Condition
2.2. Extraction of Genomic DNA
2.3. RPA Primer and Probe Designs
2.4. Real-Time RPA Assay
2.5. Analytical Sensitivity and Specificity
2.6. Repeatability Testing
2.7. Validation with Artificially Contaminated Samples
2.8. Data Analysis
3. Results
3.1. Optimal Combination Primers and Probes for Real-Time RPA Assay
3.2. Analytical Sensitivity and Specificity of the Real-Time RPA Assay
3.3. Analytical Repeatability of the Real-Time RPA Assay
3.4. Validation of the Real-Time RPA Assay on Artificially Contaminated Samples
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Bottone, E.J. Yersinia enterocolitica: Revisitation of an Enduring Human Pathogen. Clin. Microbiol. Newsl. 2015, 37, 1–8. [Google Scholar] [CrossRef]
- Rusak, L.A.; Pereira, R.D.C.L.; Freitag, I.G.; Hofer, C.B.; Hofer, E.; Asensi, M.D.; Vallim, D.C. Rapid detection of Yersinia enterocolitica serotype O:3 using a duplex PCR assay. J. Microbiol. Methods 2018, 154, 107–111. [Google Scholar] [CrossRef]
- Galindo, C.L.; Rosenzweig, J.A.; Kirtley, M.L.; Chopra, A.K. Pathogenesis of Y. enterocolitica and Y. pseudotuberculosis in Human Yersiniosis. J. Pathog. 2011, 2011, 182051. [Google Scholar]
- Stachelska, M. Detection of Yersinia Enterocolitica Species in Pig Tonsils and Raw Pork Meat by the Real-Time Pcr and Culture Methods. Pol. J. Veter. Sci. 2017, 20, 477–484. [Google Scholar] [CrossRef]
- Gupta, V.; Gulati, P.; Bhagat, N.; Dhar, M.S.; Virdi, J.S. Detection of Yersinia enterocolitica in food: An overview. Eur. J. Clin. Microbiol. 2015, 34, 641. [Google Scholar] [CrossRef]
- Platt-Samoraj, A.; Syczyło, K.; Szczerba-Turek, A.; Bancerz-Kisiel, A.; Jabłoński, A.; Łabuć, S.; Pajdak, J.; Oshakbaeva, N.; Szweda, W. Presence of ail and ystB genes in Yersinia enterocolitica biotype 1A isolates from game animals in Poland. Veter. J. 2017, 221, 11–13. [Google Scholar] [CrossRef]
- Kraushaar, B.; Dieckmann, R.; Wittwer, M.; Knabner, D.; Konietzny, A.; Mäde, D.; Strauch, E. Characterization of a Yersinia enterocolitica biotype 1A strain harbouring an ail gene. J. Appl. Microbiol. 2011, 111, 997–1005. [Google Scholar] [CrossRef]
- Bui, T.H.; Ikeuchi, S.; O’Brien, Y.S.; Niwa, T.; Hara-Kudo, Y.; Taniguchi, T.; Hayashidani, H. Multiplex PCR method for differentiating highly pathogenic Yersinia enterocolitica and low pathogenic Yersinia enterocolitica, and Yersinia pseudotuberculosis. J. Veter. Med. Sci. 2021, 83, 1982–1987. [Google Scholar] [CrossRef]
- Rohde, A.; Hammerl, J.A.; Appel, B.; Dieckmann, R.; Al Dahouk, S. Differential detection of pathogenic Yersinia spp. by fluorescence in situ hybridization. Food Microbiol. 2017, 62, 39–45. [Google Scholar] [CrossRef]
- Tack, D.M.; Marder, E.; Griffin, P.; Cieslak, P.; Dunn, J.; Hurd, S.; Scallan, E.; Lathrop, S.; Muse, A.; Ryan, P.; et al. Preliminary Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food-Foodborne Diseases Active Surveillance Network, 10 US Sites, 2015–2018. Mmwr-Morb. Mortal. Wkly. Rep. 2019, 68, 369–373. [Google Scholar] [CrossRef]
- Wang, J.; Liu, M.; Wang, H.; Wu, Q.; Ding, Y.; Xu, T.; Ma, G.; Zhong, Y.; Zhang, J.; Chen, M.; et al. Occurrence, molecular characterization, and antimicrobial susceptibility of Yersinia enterocolitica isolated from retail food samples in China. LWT 2021, 150, 111876. [Google Scholar] [CrossRef]
- Aldová, E.; Švandová, E.; Votýpka, J.; Šourek, J. Comparative Study of Culture Methods to Detect Yersinia enterocolitica Serogroup O3 on Swine Tongues. Zent. Bakteriol. Int. J. Med. Microbiol. 1990, 272, 306–312. [Google Scholar] [CrossRef] [PubMed]
- Kwaga, J.; Iversen, J.O.; Misra, V. Detection of pathogenic Yersinia enterocolitica by polymerase chain reaction and digoxigenin-labeled polynucleotide probes. J. Clin. Microbiol. 1992, 30, 2668–2673. [Google Scholar] [CrossRef] [PubMed]
- Lambertz, S.T.; Nilsson, C.; Hallanvuo, S.; Lindblad, M. Real-Time PCR Method for Detection of Pathogenic Yersinia enterocolitica in Food. Appl. Environ. Microbiol. 2008, 74, 6060–6067. [Google Scholar] [CrossRef]
- Ranjbar, R.; Afshar, D. Development of a loop-mediated isothermal amplification assay for rapid detection of Yersinia enterocolitica via targeting a conserved locus. Iran. J. Microbiol. 2015, 7, 185–190. [Google Scholar] [PubMed]
- Luciani, M.; Schirone, M.; Portanti, O.; Visciano, P.; Armillotta, G.; Tofalo, R.; Suzzi, G.; Sonsini, L.; Di Febo, T. Development of a rapid method for the detection of Yersinia enterocolitica serotype O:8 from food. Food Microbiol. 2018, 73, 85–92. [Google Scholar] [CrossRef]
- Mullis, K.; Faloona, F.; Scharf, S.; Saiki, R.; Horn, G.; Erlich, H. Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 1986, 51 Pt 1, 263–273. [Google Scholar] [CrossRef]
- Gao, B.; Ma, J.; Li, X.; Wang, R.; Chen, S. A real-time recombinase polymerase amplification assay for fast and accurate detection of Ditylenchus destructor. Mol. Cell. Probes 2021, 61, 101788. [Google Scholar] [CrossRef]
- Moore, M.D.; Jaykus, L.-A. Development of a Recombinase Polymerase Amplification Assay for Detection of Epidemic Human Noroviruses. Sci. Rep. 2017, 7, 40244. [Google Scholar] [CrossRef]
- Prescott, M.A.; Reed, A.N.; Jin, L.; Pastey, M.K. Rapid Detection of Cyprinid Herpesvirus 3 in Latently Infected Koi by Recombinase Polymerase Amplification. J. Aquat. Anim. Health 2016, 28, 173–180. [Google Scholar] [CrossRef]
- Lobato, I.M.; O’Sullivan, C.K. Recombinase polymerase amplification: Basics, applications and recent advances. TrAC Trends Anal. Chem. 2017, 98, 19–35. [Google Scholar] [CrossRef]
- Frimpong, M.; Kyei-Tuffuor, L.; Fondjo, L.A.; Ahor, H.S.; Adjei-Kusi, P.; Maiga-Ascofare, O.; Phillips, R.O. Evaluation of a real-time recombinase polymerase amplification assay for rapid detection of Schistosoma haematobium infection in resource-limited setting. Acta Trop. 2021, 216, 105847. [Google Scholar] [CrossRef]
- Wang, H.; Hou, P.; Zhao, G.; Yu, L.; Gao, Y.-W.; He, H. Development and evaluation of serotype-specific recombinase polymerase amplification combined with lateral flow dipstick assays for the diagnosis of foot-and-mouth disease virus serotype A, O and Asia1. BMC Veter. Res. 2018, 14, 359. [Google Scholar] [CrossRef]
- Zhao, G.; Hou, P.; Huan, Y.; He, C.; Wang, H.; He, H. Development of a recombinase polymerase amplification combined with a lateral flow dipstick assay for rapid detection of the Mycoplasma bovis. BMC Veter. Res. 2018, 14, 412. [Google Scholar] [CrossRef]
- Geng, Y.; Liu, G.; Liu, L.; Deng, Q.; Zhao, L.; Sun, X.X.; Wang, J.; Zhao, B.; Wang, J. Real-time recombinase polymerase amplification assay for the rapid and sensitive detection of Campylobacter jejuni in food samples. J. Microbiol. Methods 2018, 157, 31–36. [Google Scholar] [CrossRef] [PubMed]
- Yang, X.; Zhang, X.; Wang, Y.; Shen, H.; Jiang, G.; Dong, J.; Zhao, P.; Gao, S. A Real-Time Recombinase Polymerase Amplification Method for Rapid Detection of Vibrio vulnificus in Seafood. Front. Microbiol. 2020, 11, 586981. [Google Scholar] [CrossRef] [PubMed]
- Ma, L.; Shi, H.; Zhang, M.; Song, Y.; Zhang, K.; Cong, F. Establishment of a Real-Time Recombinase Polymerase Amplification Assay for the Detection of Avian Reovirus. Front. Veter. Sci. 2020, 7, 551350. [Google Scholar] [CrossRef]
- Laporte, J.; Savin, C.; Lamourette, P.; Devilliers, K.; Volland, H.; Carniel, E.; Créminon, C.; Simon, S. Fast and Sensitive Detection of Enteropathogenic Yersinia by Immunoassays. J. Clin. Microbiol. 2015, 53, 146–159. [Google Scholar] [CrossRef]
- Van Noyen, R.; Vandepitte, J.; Wauters, G. Nonvalue of cold enrichment of stools for isolation of Yersinia enterocolitica serotypes 3 and 9 from patients. J. Clin. Microbiol. 1980, 11, 127–131. [Google Scholar] [CrossRef]
- Blom, M.; Meyer, A.; Gerner-Smidt, P.; Gaarslev, K.; Espersen, F. Evaluation of Statens Serum Institut enteric medium for detection of enteric pathogens. J. Clin. Microbiol. 1999, 37, 2312–2316. [Google Scholar] [CrossRef]
- Petsios, S.; Fredriksson-Ahomaa, M.; Sakkas, H.; Papadopoulou, C. Conventional and molecular methods used in the detection and subtyping of Yersinia enterocolitica in food. Int. J. Food Microbiol. 2016, 237, 55–72. [Google Scholar] [CrossRef] [PubMed]
- Zheng, Y.; Hu, P.; Ren, H.; Wang, H.; Cao, Q.; Zhao, Q.; Li, H.; Zhang, H.; Liu, Z.; Li, Y.; et al. RPA-SYBR Green I based instrument-free visual detection for pathogenic Yersinia enterocolitica in meat. Anal. Biochem. 2021, 621, 114157. [Google Scholar] [CrossRef] [PubMed]
Strain | Species | Source | ail Gene |
---|---|---|---|
ZDN 6 | Y. enterocolitica | isolated from Yak | + |
ATCC 23715 | Y. enterocolitica | CIVDC | + |
08-01 | Y. enterocolitica | isolated from Landrace | + |
GN 22 | Y. enterocolitica | isolated from Yak | + |
ZDN 22 | Y. enterocolitica | isolated from Yak | + |
GLN 1 | Y. enterocolitica | isolated from Yak | − |
HNN 18 | Y. enterocolitica | isolated from Yak | − |
HNN 47 | Y. enterocolitica | isolated from Yak | − |
ZDN 37 | Y. enterocolitica | isolated from Yak | − |
HNN 63 | Y. enterocolitica | isolated from Yak | − |
06-01-03 | Shigella Castellani | isolated from Yak | − |
06-03-01 | Salmonella | isolated from Feedstuff | − |
03-03 | Escherichia coli | isolated from Feedstuff | − |
AH 1302 | Aeromonas hydrophila | isolated from Gymnocypris przewalskii | − |
06-05-02 | Bacillus cereus | isolated from Feedstuff | − |
P0810 | Pasteurella | isolated from Yak | − |
04-011 | Staphylococcus aureus | isolated from Yak | − |
Name | Sequence (5′-3′) |
---|---|
RPA-F-1 | TCATGGAAAGGTTAAGGCATCTGTATTTGA |
RPA-F-2 | ATAGGTTCGTTTGCTTATACTCATCAGGGA |
RPA-F-3 | AAAGGTTTTAACCTGAAGTACCGTTATGAA |
RPA-R-1 | TTTTATGCTATCGAGTTTGGAGTATTCATA |
RPA-R-2 | AGTAATCCATAAAGGCTAACATATTCGTTG |
RPA-R-3 | TAATCCATAAAGGCTAACATATTCGTTGAT |
RPA-Probe-5 | AGGTTCGTTTGCTTATACTCATCAGGGATA(FAM-dT) (THF)A(BHQ1-dT) TTCTTCTATGGCAGTA(3′-block) |
RPA-Probe-6 | GAATAGTAATCAACATCACCATGACCAAACT(FAM-dT) (THF) (BHQ1-dT) TACTGCCATAGAAGA(3′-block) |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Zhang, H.; Zhao, M.; Hu, S.; Ma, K.; Li, J.; Zhao, J.; Wei, X.; Tong, L.; Li, S. Establishment of a Real-Time Recombinase Polymerase Amplification for Rapid Detection of Pathogenic Yersinia enterocolitica. Pathogens 2023, 12, 226. https://doi.org/10.3390/pathogens12020226
Zhang H, Zhao M, Hu S, Ma K, Li J, Zhao J, Wei X, Tong L, Li S. Establishment of a Real-Time Recombinase Polymerase Amplification for Rapid Detection of Pathogenic Yersinia enterocolitica. Pathogens. 2023; 12(2):226. https://doi.org/10.3390/pathogens12020226
Chicago/Turabian StyleZhang, Hongjian, Meng Zhao, Siyun Hu, Kairu Ma, Jixu Li, Jing Zhao, Xin Wei, Lina Tong, and Shengqiang Li. 2023. "Establishment of a Real-Time Recombinase Polymerase Amplification for Rapid Detection of Pathogenic Yersinia enterocolitica" Pathogens 12, no. 2: 226. https://doi.org/10.3390/pathogens12020226
APA StyleZhang, H., Zhao, M., Hu, S., Ma, K., Li, J., Zhao, J., Wei, X., Tong, L., & Li, S. (2023). Establishment of a Real-Time Recombinase Polymerase Amplification for Rapid Detection of Pathogenic Yersinia enterocolitica. Pathogens, 12(2), 226. https://doi.org/10.3390/pathogens12020226