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Sutipatanasomboon A, Wongsantichon J, Sakdee S, Naksith P, Watthanadirek A, Anuracpreeda P, Blacksell SD, Saisawang C. RPA-CRISPR/Cas12a assay for the diagnosis of bovine Anaplasma marginale infection. Sci Rep 2024; 14:7820. [PMID: 38570576 PMCID: PMC10991388 DOI: 10.1038/s41598-024-58169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Anaplasma marginale infection is one of the most common tick-borne diseases, causing a substantial loss in the beef and dairy production industries. Once infected, the pathogen remains in the cattle for life, allowing the parasites to spread to healthy animals. Since clinical manifestations of anaplasmosis occur late in the disease, a sensitive, accurate, and affordable pathogen identification is crucial in preventing and controlling the infection. To this end, we developed an RPA-CRISPR/Cas12a assay specific to A. marginale infection in bovines targeting the msp4 gene. Our assay is performed at one moderately high temperature, producing fluorescent signals or positive readout of a lateral flow dipstick, which is as sensitive as conventional PCR-based DNA amplification. This RPA-CRISPR/Cas12a assay can detect as few as 4 copies/μl of Anaplasma using msp4 marker without cross-reactivity to other common bovine pathogens. Lyophilized components of the assay can be stored at room temperature for an extended period, indicating its potential for field diagnosis and low-resource settings of anaplasmosis in bovines.
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Affiliation(s)
- Arpaporn Sutipatanasomboon
- Molecular Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Salaya, Thailand
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Somsri Sakdee
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, 25/25 Phuttamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Piyaporn Naksith
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, 25/25 Phuttamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Amaya Watthanadirek
- Molecular Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Salaya, Thailand
| | - Panat Anuracpreeda
- Molecular Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Salaya, Thailand
| | - Stuart D Blacksell
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Chonticha Saisawang
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, 25/25 Phuttamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand.
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Li J, Shang MY, Deng SL, Li M, Su N, Ren XD, Sun XG, Li WM, Li YW, Li RX, Huang Q, Lu WP. Development of a novel integrated isothermal amplification system for detection of bacteria-spiked blood samples. AMB Express 2023; 13:135. [PMID: 38019349 PMCID: PMC10686969 DOI: 10.1186/s13568-023-01643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/19/2023] [Indexed: 11/30/2023] Open
Abstract
Bloodstream infection (BSI) caused by bacteria is highly pathogenic and lethal, and easily develops whole-body inflammatory state. Immediate identification of disease-causing bacteria can improve patient prognosis. Traditional testing methods are not only time-consuming, but such tests are limited to laboratories. Recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) holds great promise for rapid nucleic acid detection, but the uncapping operation after amplification easily contaminates laboratories. Therefore, the establishment of a more effective integrated isothermal amplification system has become an urgent problem to be solved. In this study, we designed and fabricated a hermetically sealed integrated isothermal amplification system. Combining with this system, a set of RPA-LFD assays for detecting S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI were established and evaluated. The whole process could be completed in less than 15 min and the results can be visualized by the naked eye. The developed RPA-LFD assays displayed a good sensitivity, and no cross-reactivity was observed in seven similar bacterial genera. The results obtained with 60 clinical samples indicated that the developed RPA-LFD assays had high specifcity and sensitivity for identifying S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI. In conclusion, our results showed that the developed RPA-LFD assay is an alternative to existing PCR-based methods for detection of S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI in primary hospitals.
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Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Shao-Li Deng
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Min Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Xian-Ge Sun
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Wen-Man Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Yu-Wei Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Ruo-Xu Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China.
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China.
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3
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Wang F, Wang H, Zhang L, Ji T, Gao Y, Wang Y, Dong S, Gao X. An improved recombinase polymerase amplification assay for the visual detection of Staphylococcus epidermidis with lateral flow strips. Clin Chim Acta 2023; 548:117455. [PMID: 37394163 DOI: 10.1016/j.cca.2023.117455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Staphylococcus epidermidis is an opportunistic pathogenic microorganism that is an important cause of cross-infection in hospitals. The development of rapid and effective detection techniques is important for its control. The application of traditional identification and PCR-based methods is limited by their requirements for both laboratory instrumentation and trained personnel. To overcome this issue, we developed a fast detection approach for S. epidermidis that was based on recombinase polymerase amplification (RPA) and lateral flow strips (LFS). First, five pairs of primers were designed for molecular diagnosis using the sesB gene as the target, and were screened for their amplification performance and the formation of primer dimers. Specific probes were then designed based on the best primer pairs screened, which were susceptible to primer-dependent artifacts and generated false-positive signals when used for LFS detection. This weakness of the LFS assay was overcome by modifying the sequences of the primers and probes. The efficacy of these measures was rigorously tested, and improved the RPA-LFS system. Standardized systems completed the amplification process within 25 min at a constant temperature of 37 °C, followed by visualization of the LFS within 3 min. The approach was very sensitive (with a detection limit of 8.91 CFU/μL), with very good interspecies specificity. In the analysis of clinical samples, the approach produced results consistent with PCR and 97.78% consistent with the culture-biochemical method, with a kappa index of 0.938. Our method was rapid, accurate, and less dependent on equipment and trained personnel than traditional methods, and provided information for the timely development of rational antimicrobial treatment plans. It has high potential utility in clinical settings, particularly in resource-constrained locations.
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Affiliation(s)
- Fang Wang
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222023, China
| | - Hui Wang
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China
| | - Linhai Zhang
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China
| | - Tuo Ji
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222023, China
| | - Yuzhi Gao
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222023, China
| | - Yan Wang
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China
| | - Shude Dong
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China.
| | - Xuzhu Gao
- Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Lianyungang Second People's Hospital Affiliated to Kangda College of Nanjing Medical University), Lianyungang 222023, China; Institute of Clinical Oncology, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang 222023, China.
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4
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Ge D, Wang F, Hu Y, Wang B, Gao X, Chen Z. Fast, Simple, and Highly Specific Molecular Detection of Porphyromonas gingivalis Using Isothermal Amplification and Lateral Flow Strip Methods. Front Cell Infect Microbiol 2022; 12:895261. [PMID: 35694545 PMCID: PMC9174636 DOI: 10.3389/fcimb.2022.895261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/27/2022] [Indexed: 12/16/2022] Open
Abstract
Porphyromonas gingivalis is an important oral pathogen that causes periodontal disease and is difficult to culture under conventional conditions. Therefore, a reliable technique for detecting this pathogenic bacterium is required. Here, isothermal recombinase polymerase amplification (RPA), a new nucleic acid amplification method, was combined with a visualization method based on nanoparticle-based lateral flow strips (LFS) for the rapid detection of P. gingivalis. The species-specific 16S rRNA sequence of P. gingivalis was used as the target for RPA, and a set of specific primer–probe combinations were designed and screened to amplify the target sequences. As a thermostatic amplification method, the RPA reaction, under optimized conditions, takes only 30 min to complete at a constant temperature (37°C). The amplification reaction products can be detected visually by LFS without any need for special equipment. The RPA-LFS method established for the detection of P. gingivalis was shown to be highly specific in distinguishing P. gingivalis from other pathogenic organisms by using 20 clinical isolates of P. gingivalis and 23 common pathogenic microorganisms. Susceptibility measurements and probit regression analysis were performed with gradient dilutions of P. gingivalis genomic DNA. The method was obtained to be highly sensitive, with a detection limit of 9.27 CFU per reaction at 95% probability. By analyzing the gingival sulcus fluid specimens from 130 patients with chronic periodontitis, the results showed that the RPA-LFS method detected 118 positive cases and 12 negative cases of P. gingivalis, and the results obtained were consistent with those of a conventional PCR assay. The RPA–LFS method is an efficient, rapid, and convenient diagnostic method that simplifies the tedious process of detecting P. gingivalis.
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Affiliation(s)
| | | | | | | | - Xuzhu Gao
- *Correspondence: Zhenxing Chen, ; Xuzhu Gao,
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5
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Wang L, Wang Y, Wang F, Zhao M, Gao X, Chen H, Li N, Zhu Q, Liu L, Zhu W, Liu X, Chen Y, Zhou P, Lu Y, Wang K, Zhao W, Liang W. Development and Application of Rapid Clinical Visualization Molecular Diagnostic Technology for Cryptococcus neoformans/ C. gattii Based on Recombinase Polymerase Amplification Combined With a Lateral Flow Strip. Front Cell Infect Microbiol 2022; 11:803798. [PMID: 35096653 PMCID: PMC8790172 DOI: 10.3389/fcimb.2021.803798] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Cryptococcus neoformans (C. neoformans)/C. gattii can easily invade the human central nervous system and cause cryptococcal meningitis (CM). The clinical fatality rate of these fungi is extremely high and causes more than 180,000 deaths worldwide every year. At present, the common clinical identification methods of these fungi are traditional culture methods and Indian ink staining. In addition, enzyme-linked immunosorbent assay (ELISAs), polymerase chain reaction (PCR), real-time quantitative PCR detecting system (qPCR), mass spectrometry, and metagenomic next-generation sequencing (mNGS) have also been applied to detect these fungus. Due to the rapid progress of meningitis caused by C. neoformans/C. gattii infection, there is a desperate need for fast, sensitive, and on-site detection methods to meet the clinical diagnosis. Recombinase polymerase amplification (RPA) is a promising isothermal amplification technique that can compensate for the shortcomings of the above techniques, featuring short reaction time, high specificity, and high sensitivity, thus meeting the demand for in-field detection of C.neoformans/C. gattii. In our study, RPA- lateral flow strip (LFS) was used to amplify the capsule-associated gene, CAP64, of C. neoformans/C. gattii, and the primer-probe design was optimized by introducing base mismatches to obtain a specific and sensitive primer-probe combination for clinical testing, and specificity of the detection system was determined for 26 common clinical pathogens. This system was developed to obtain results in 20 min at an isothermal temperature of 37°C with a lower limit of detection as low as 10 CFU/μL or 1 fg/μL. A total of 487 clinical samples collected from multicenter multiplexes were tested to evaluate the detection performance of the RPA-LFS system, which revealed that the system could specifically detect C. neoformans/C. gattii, meeting the need for rapid, specific, and sensitive detection.
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Affiliation(s)
- Lei Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China.,School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yan Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Fang Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Mengdi Zhao
- Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Xuzhu Gao
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Huimin Chen
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Na Li
- Lianyungang Second People's Hospital Affiliated to Bengbu Medical College, Lianyungang, China
| | - Qing Zhu
- Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China
| | - Lipin Liu
- Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China
| | - Wenjun Zhu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Xia Liu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Yujiao Chen
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Ping Zhou
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Yingzhi Lu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Kun Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Weiguo Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Wei Liang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
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6
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Li J, Zhong Q, Shang MY, Li M, Jiang YS, Zou JJ, Ma SS, Huang Q, Lu WP. Preliminary Evaluation of Rapid Visual Identification of Burkholderia pseudomallei Using a Newly Developed Lateral Flow Strip-Based Recombinase Polymerase Amplification (LF-RPA) System. Front Cell Infect Microbiol 2022; 11:804737. [PMID: 35118011 PMCID: PMC8804217 DOI: 10.3389/fcimb.2021.804737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/20/2021] [Indexed: 12/23/2022] Open
Abstract
Burkholderia pseudomallei is an important infectious disease pathogen that can cause melioidosis. Melioidosis is mainly prevalent in Thailand, northern Australia and southern China and has become a global public health problem. Early identification of B. pseudomallei is of great significance for the diagnosis and prognosis of melioidosis. In this study, a simple and visual device combined with lateral flow strip-based recombinase polymerase amplification (LF-RPA) was developed, and the utility of the LF-RPA assay for identifying B. pseudomallei was evaluated. In order to screen out the optimal primer probe, a total of 16 pairs of specific primers targeting the orf2 gene of B. pseudomallei type III secretion system (T3SS) cluster genes were designed for screening, and F1/R3 was selected as an optimal set of primers for the identification of B. pseudomallei, and parameters for LF-RPA were optimized. The LF-RPA can be amplified at 30-45°C and complete the entire reaction in 5-30 min. This reaction does not cross-amplify the DNA of other non-B. pseudomallei species. The limit of detection (LOD) of this assay for B. pseudomallei genomic DNA was as low as 30 femtograms (fg), which was comparable to the results of real-time PCR. Moreover, 21 clinical B. pseudomallei isolates identified by 16S rRNA gene sequencing were retrospectively confirmed by the newly developed LF-RPA system. Our results showed that the newly developed LF-RPA system has a simple and short time of operation and has good application prospect in the identification of B. pseudomallei.
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Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Laboratory Medicine, Ministry of Education (M.O.E.) Key Laboratory of Laboratory Medicine Diagnostics, Chongqing Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Min Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yuan-Su Jiang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jia-Jun Zou
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shan-Shan Ma
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
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7
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Yang H, Wang Y, Yang Q, Fan H, Wang L, Zhang T, Li Z, Liu G, Zhao P, Wu H, Dong J, Liang W. A Rapid and Sensitive Detection Method for Pseudomonas aeruginosa Using Visualized Recombinase Polymerase Amplification and Lateral Flow Strip Technology. Front Cell Infect Microbiol 2021; 11:698929. [PMID: 34595129 PMCID: PMC8478171 DOI: 10.3389/fcimb.2021.698929] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Pseudomonas aeruginosa is a common opportunistic pathogen that causes acute nosocomial necrotizing pneumonia and is the predominant source of chronic lung infections in patients with the genetic disorder cystic fibrosis. Early diagnosis in infected patients and monitoring P. aeruginosa contamination is therefore of great importance in controlling disease spread and development with timely drugs intervention treatment and cut off infection source. Traditional culture-biochemical methods are time consuming and highly dependent on technicians and expensive instruments. To address these challenges, the present study aimed to develop a rapid, sensitive, and specific, on-site detection method for P. aeruginosa based on recombinase polymerase amplification (RPA) combined with lateral flow strip (LFS) technology. The experimental process included screening and modification of primer and probe sets targeting the unique virulence gene elastase B (lasB); specificity detection in 29 strains of P. aeruginosa and 23 closely-related pathogenic bacteria; sensitivity measurements with gradient-diluted P. aeruginosa genomic DNA and probit regression analysis; and clinical application evaluation using 574 patients samples and calculating coincidence rate and kappa index value in comparison with the culture-biochemical method. The P. aeruginosa RPA-LFS assay could complete the amplification process at 37°C constant temperature within 30 min and results could be visualized by the naked eye within 10 min on LFS. The assay displayed high sensitivity with a limit of detection of 3.05 CFU/reaction. It also demonstrated high specificity by showing no cross reaction with other pathogenic bacteria, and rapidness by being completed in less than an hour. Furthermore, when used with clinical samples, the assay had a coincidence rate of 98.26% with the culture-biochemical method and a kappa index value of 0.9433. These data indicate that the RPA-LFS assay represents a major improvement for P. aeruginosa detection, especially in resource-limited areas.
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Affiliation(s)
- Haitao Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Yan Wang
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungangg City, Lianyungangg, China
| | - Qiankun Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Hui Fan
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Lei Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China.,Department of Laboratory Medicine, The Second People's Hospital of Lianyungangg City, Lianyungangg, China
| | - Tianmeng Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Zhixing Li
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Gang Liu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Panpan Zhao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China.,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Huahua Wu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungangg, China
| | - Wei Liang
- Laboratory Department of Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, China
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8
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Recombinase polymerase amplification (RPA) with lateral flow detection for three Anaplasma species of importance to livestock health. Sci Rep 2021; 11:15962. [PMID: 34354122 PMCID: PMC8342517 DOI: 10.1038/s41598-021-95402-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Anaplasma marginale, A. ovis, and A. phagocytophilum are the causative agents of bovine anaplasmosis, ovine anaplasmosis, and granulocytic anaplasmosis, respectively. The gold standard for diagnosis of post-acute and long-term persistent infections is the serological cELISA, which does not discriminate between Anaplasma species and requires highly equipped laboratories and trained personnel. This study addresses the development of a rapid, isothermal, sensitive, species-specific RPA assays to detect three Anaplasma species in blood and cELISA A. marginale-positive serum samples. Three RPA primer and probe sets were designed targeting msp4 genes of each Anaplasma species and the internal control (GAPDH gene) for each assay. The limit of detection of gel-based or RPA-basic assays is 8.99 × 104 copies/µl = A. marginale, 5.04 × 106 copies/µl = A. ovis, and 4.58 × 103 copies/µl = A. phagocytophilum, and for each multiplex lateral flow or RPA-nfo assays is 8.99 × 103 copies/µl of A. marginale, 5.04 × 103 copies/µl of A. ovis, 4.58 × 103 copies/µl of A. phagocytophilum, and 5.51 × 103 copies/µl of internal control (GAPDH). Although none of the 80 blood samples collected from Oklahoma cattle were positive, the RPA-nfo assays detected all A. marginale cattle blood samples with varying prevalence rates of infection, 83% of the 24 cELISA A. marginale-positive serum samples, and all A. phagocytophilum cell culture samples. Overall, although early detection of three Anaplasma species was not specifically addressed, the described RPA technique represents an improvement for detection of three Anaplasma in regions where access to laboratory equipment is limited.
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Yukhet P, Buddhachat K, Vilaivan T, Suparpprom C. Isothermal Detection of Canine Blood Parasite ( Ehrlichia canis) Utilizing Recombinase Polymerase Amplification Coupled with Graphene Oxide Quenching-Based Pyrrolidinyl Peptide Nucleic Acid. Bioconjug Chem 2021; 32:523-532. [PMID: 33651604 DOI: 10.1021/acs.bioconjchem.0c00639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Canine monocytic ehrlichiosis (CME), caused by transmitted Ehrlichia canis infection, is a major disease in dogs with worldwide distribution. Herein, a nucleic acid assay was established for the identification of E. canis infection employing a fluorescently labeled conformationally constrained pyrrolidinyl PNA probe (Flu-acpcPNA) designed to sequence-specifically target the 16S rRNA gene. The sensing principle is based on the excellent quenching ability of graphene oxide (GO) of the free PNA probe, that was diminished upon binding to the DNA target. The addition of DNase I improved the performance of the detection system by eliminating the nonspecific quenching capability of long-chain dsDNA and thus enhancing the fluorescence signaling. The assay was coupled with a recombinase polymerase amplification (RPA) technique, which could be performed under isothermal conditions (37 °C) without DNA denaturation and purification steps. The established method is simple to set up and execute, proving a rapid, specific, and sensitive detection of 16S rRNA gene of E. canis with a limit of detection at least 11.1 pM. This technique shows good potential for the visual detection of double-stranded DNA targets without the need for PCR or complicated instruments, which shows great promise for practical usage in resource limited areas.
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Affiliation(s)
- Phanomsak Yukhet
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand.,Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand
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Pumford EA, Lu J, Spaczai I, Prasetyo ME, Zheng EM, Zhang H, Kamei DT. Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics. Biosens Bioelectron 2020; 170:112674. [PMID: 33035900 PMCID: PMC7529604 DOI: 10.1016/j.bios.2020.112674] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 01/03/2023]
Abstract
Early disease detection through point-of-care (POC) testing is vital for quickly treating patients and preventing the spread of harmful pathogens. Disease diagnosis is generally accomplished using quantitative polymerase chain reaction (qPCR) to amplify nucleic acids in patient samples, permitting detection even at low target concentrations. However, qPCR requires expensive equipment, trained personnel, and significant time. These resources are not available in POC settings, driving researchers to instead utilize isothermal amplification, conducted at a single temperature, as an alternative. Common isothermal amplification methods include loop-mediated isothermal amplification, recombinase polymerase amplification, rolling circle amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. There has been a growing interest in combining such amplification methods with POC detection methods to enable the development of diagnostic tests that are well suited for resource-limited settings as well as developed countries performing mass screenings. Exciting developments have been made in the integration of these two research areas due to the significant impact that such approaches can have on healthcare. This review will primarily focus on advances made by North American research groups between 2015 and June 2020, and will emphasize integrated approaches that reduce user steps, reliance on expensive equipment, and the system's time-to-result.
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Affiliation(s)
- Elizabeth A Pumford
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Jiakun Lu
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Iza Spaczai
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Matthew E Prasetyo
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Elaine M Zheng
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Hanxu Zhang
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Daniel T Kamei
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA.
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