|
1
|
Zhu H, Kim BJ, Spizz G, Rothrock D, Yasmin R, Arida J, Grocholl J, Montagna R, Schwartz B, Trujillo S, Almeria S. Development and Evaluation/Verification of a Fully Automated Test Platform for the Rapid Detection of Cyclospora cayetanensis in Produce Matrices. Microorganisms 2023; 11:2805. [PMID: 38004816 PMCID: PMC10673183 DOI: 10.3390/microorganisms11112805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Cyclosporiasis, caused by the coccidian parasite Cyclospora cayetanensis, has emerged as an increasing global public health concern, with the incidence of laboratory-confirmed domestically acquired cases in the US exceeding 10,000 since 2018. A recently published qPCR assay (Mit1C) based on a mitochondrial target gene showed high specificity and good sensitivity for the detection of C. cayetanensis in fresh produce. The present study shows the integration and verification of the same mitochondrial target into a fully automated and streamlined platform that performs DNA isolation, PCR, hybridization, results visualization, and reporting of results to simplify and reduce hands-on time for the detection of this parasite. By using the same primer sets for both the target of interest (i.e., Mit1C) and the internal assay control (IAC), we were able to rapidly migrate the previously developed Mit1C qPCR assay into the more streamlined and automated format Rheonix C. cayetanensisTM Assay. Once the best conditions for detection were optimized and the migration to the fully automated format was completed, we compared the performance of the automated platform against the original "bench top" Mit1C qPCR assay. The automated Rheonix C. cayetanensis Assay achieved equivalent performance characteristics as the original assay, including the same performance for both inclusion and exclusion panels, and it was able to detect as low as 5 C. cayetanensis oocysts in fresh produce while significantly reducing hands-on time. We expect that the streamlined assay can be used as a tool for outbreak and/or surveillance activities to detect the presence of C. cayetanensis in produce samples.
Collapse
Affiliation(s)
- Hui Zhu
- Rheonix, Inc., Ithaca, NY 14850, USA; (H.Z.); (B.J.K.); (G.S.); (D.R.); (R.Y.); (R.M.); (B.S.)
| | - Beum Jun Kim
- Rheonix, Inc., Ithaca, NY 14850, USA; (H.Z.); (B.J.K.); (G.S.); (D.R.); (R.Y.); (R.M.); (B.S.)
| | - Gwendolyn Spizz
- Rheonix, Inc., Ithaca, NY 14850, USA; (H.Z.); (B.J.K.); (G.S.); (D.R.); (R.Y.); (R.M.); (B.S.)
| | - Derek Rothrock
- Rheonix, Inc., Ithaca, NY 14850, USA; (H.Z.); (B.J.K.); (G.S.); (D.R.); (R.Y.); (R.M.); (B.S.)
| | - Rubina Yasmin
- Rheonix, Inc., Ithaca, NY 14850, USA; (H.Z.); (B.J.K.); (G.S.); (D.R.); (R.Y.); (R.M.); (B.S.)
| | - Joseph Arida
- Division of Virulence Assessment, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (J.A.); (J.G.); (S.T.)
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20742, USA
| | - John Grocholl
- Division of Virulence Assessment, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (J.A.); (J.G.); (S.T.)
| | - Richard Montagna
- Rheonix, Inc., Ithaca, NY 14850, USA; (H.Z.); (B.J.K.); (G.S.); (D.R.); (R.Y.); (R.M.); (B.S.)
| | - Brooke Schwartz
- Rheonix, Inc., Ithaca, NY 14850, USA; (H.Z.); (B.J.K.); (G.S.); (D.R.); (R.Y.); (R.M.); (B.S.)
| | - Socrates Trujillo
- Division of Virulence Assessment, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (J.A.); (J.G.); (S.T.)
| | - Sonia Almeria
- Division of Virulence Assessment, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (J.A.); (J.G.); (S.T.)
| |
Collapse
|
|
2
|
Nimse SB, Song KS, Warkad SD, Kim T. A Novel Method That Allows SNP Discrimination with 160:1 Ratio for Biosensors Based on DNA-DNA Hybridization. BIOSENSORS-BASEL 2021; 11:bios11080265. [PMID: 34436067 PMCID: PMC8391390 DOI: 10.3390/bios11080265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022]
Abstract
Highly sensitive (high SBR) and highly specific (high SNP discrimination ratio) DNA hybridization is essential for a biosensor with clinical application. Herein, we propose a method that allows detecting multiple pathogens on a single platform with the SNP discrimination ratios over 160:1 in the dynamic range of 101 to 104 copies per test. The newly developed SWAT method allows achieving highly sensitive and highly specific DNA hybridizations. The detection and discrimination of the MTB and NTM strain in the clinical samples with the SBR and SNP discrimination ratios higher than 160:1 indicate the high clinical applicability of the SWAT.
Collapse
Affiliation(s)
- Satish Balasaheb Nimse
- Department of Chemistry, Institute for Applied Chemistry, Hallym University, Chuncheon 200-702, Korea;
| | - Keum-Soo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea; (K.-S.S.); (S.D.W.)
| | | | - Taisun Kim
- Department of Chemistry, Institute for Applied Chemistry, Hallym University, Chuncheon 200-702, Korea;
- Correspondence:
| |
Collapse
|
|
3
|
Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
Collapse
Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| |
Collapse
|