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Liu R, Xing Y, Shen J. Establishment and methodological evaluation of a rapid detection method for Cryptococcus neoformans and Cryptococcus gattii species complexes based on CRISPR-Cas12a technology. J Microbiol Methods 2024; 225:107026. [PMID: 39182694 DOI: 10.1016/j.mimet.2024.107026] [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: 05/31/2024] [Revised: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
PURPOSE The opportunistic pathogens causing Cryptococcal meningitis are Cryptococcus neoformans and Cryptococcus gattii species complexes. At present, clinical detection methods for this condition include culture, ink staining, and cryptococcal antigen detection. In addition, enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and real-time quantitative PCR (qPCR) can be applied for the detection of Cryptococcus. Nevertheless, these methods cannot achieve point-of-care detection (POCT); thus, there is a pressing need to establish a fast, sensitive, and effective detection method. METHODS Recombinase polymerase amplification (RPA) and clustered regularly spaced short palindromic repeat (CRISPR) techniques are effective tools for achieving rapid POCT. In this study, RPA was combined with CRISPR-Cas12a to establish a fast, sensitive, and specific detection method for cryptococcal meningitis. RESULTS This study included RPA-Cas12a fluorescence detection and RPA-Cas12a immunochromatographic detection, which can be performed within 50 min. Moreover, the detection limit was as low as 102 copies/μL. Interestingly, the developed method demonstrated satisfactory specificity and no cross-reactivity with other fungi and bacteria. 36 clinical samples were tested, and the consistency between the test results and those obtained using the commonly used clinical culture method was 100 %. CONCLUSION In this study, a rapid detection method for Cryptococcus neoformans and Cryptococcus gattii species complexes was developed based on CRISPR-Cas12a technology, characterized by its high sensitivity and specificity, ease of use, and cost-effectiveness, making it suitable for on-site detection.
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Affiliation(s)
- Runde Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China; Department of Clinical Laboratory, Anhui Public Health Clinical Center, Hefei, People's Republic of China
| | - Yuqing Xing
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China; Department of Clinical Laboratory, Anhui Public Health Clinical Center, Hefei, People's Republic of China
| | - Jilu Shen
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China; Department of Clinical Laboratory, Anhui Public Health Clinical Center, Hefei, People's Republic of China.
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Wang X, Xu T, Ding S, Xu Y, Jin X, Guan F. Recombinase polymerase amplification combined with lateral flow dipstick assay for rapid visual detection of A.simplex (s. s.) and A.pegreffii in sea foods. Heliyon 2024; 10:e28943. [PMID: 38623257 PMCID: PMC11016599 DOI: 10.1016/j.heliyon.2024.e28943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Anisakiasis is a food-borne parasitic disease mainly caused by the third stage of Anisakis simplex (s. s.) and Anisakis pegreffii. Traditional methods for detecting of Anisakis involve morphology identification such as visual inspection, enzyme digestion, and molecular methods based on PCR, but they have certain limitations. In this study, the internal transcribed spacer 1 (ITS 1) regions of Anisakis were targeted to develop a visual screening method for detecting A. simplex (s. s.) and A. pegreffii in fish meat based on recombinase polymerase amplification (RPA) combined with lateral flow dipstick (LFD). Specific primers and probes were designed and optimized for temperature, reaction time, and detection threshold. LFD produced clear visual results that were easily identifiable after a consistent incubation of 10-20 min at 37 °C. The whole process of DNA amplification by RPA and readout by LFD did not exceed 30 min. In addition, the detection limit is up to 9.5 × 10-4 ng/μL, and the detection of the artificially contaminated samples showed that the developed assay can effectively and specifically detect A. simplex (s. s.) and A. pegreffii, which fully meet the market's requirements for fish food safety supervision.
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Affiliation(s)
- Xiaoming Wang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Zhejiang Museum of Natural History, Hangzhou 310018, China
| | - Ting Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Siling Ding
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Ye Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xingsheng Jin
- Zhejiang Museum of Natural History, Hangzhou 310018, China
| | - Feng Guan
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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Park SB, Zhang Y. Development of Multienzyme Isothermal Rapid Amplification (MIRA) Combined with Lateral-Flow Dipstick (LFD) Assay to Detect Species-Specific tlh and Pathogenic trh and tdh Genes of Vibrio parahaemolyticus. Pathogens 2024; 13:57. [PMID: 38251364 PMCID: PMC10819497 DOI: 10.3390/pathogens13010057] [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: 12/04/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Vibrio parahaemolyticus causes severe gastroenteritis in humans after consuming contaminated raw or undercooked seafood. A species-specific marker, the thermolabile hemolysin (tlh) gene, and two pathogenic markers, thermostable-related hemolysin (trh) and thermostable-direct hemolysin (tdh) genes, have been used to identify V. parahaemolyticus and determine its pathogenicity using both PCR and qPCR assays. To enable testing in field conditions with limited resources, this study aimed to develop a simple and rapid method to detect the species-specific (tlh) and pathogenic (trh and tdh) genes of V. parahaemolyticus using multienzyme isothermal rapid amplification (MIRA) combined with a lateral-flow dipstick (LFD). The amplification of the tlh, trh, and tdh genes could be completed within 20 min at temperatures ranging from 30 to 45 °C (p < 0.05). The test yielded positive results for V. parahaemolyticus but produced negative results for nine Vibrio species and eighteen foodborne pathogenic bacterial species. MIRA-LFD could detect 10 fg of DNA and 2 colony-forming units (CFU) of V. parahaemolyticus per reaction, demonstrating a sensitivity level comparable to that of qPCR, which can detect 10 fg of DNA and 2 CFU per reaction. Both MIRA-LFD and qPCR detected seven tlh-positive results from thirty-six oyster samples, whereas one positive result was obtained using the PCR assay. No positive results for the trh and tdh genes were obtained from any oyster samples using MIRA-LFD, PCR, and qPCR. This study suggests that MIRA-LFD is a simple and rapid method to detect species-specific and pathogenic genes of V. parahaemolyticus with high sensitivity.
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Affiliation(s)
- Seong Bin Park
- Experimental Seafood Processing Laboratory, Coastal Research & Extension Center, Mississippi State University, Pascagoula, MS 39567, USA
| | - Yan Zhang
- Experimental Seafood Processing Laboratory, Coastal Research & Extension Center, Mississippi State University, Pascagoula, MS 39567, USA
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Xu R, Li D, Zhao J, Zhong H, Chen H, Jia Y, Chen F, Han L. Rapid detection of Mucorales based on recombinase polymerase amplification and real-time PCR. Front Microbiol 2023; 14:1273073. [PMID: 37954252 PMCID: PMC10635347 DOI: 10.3389/fmicb.2023.1273073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Mucormycosis, an invasive fungal disease with severe consequences, poses a significant threat to immunocompromised individuals. However, the timely and accurate identification of Mucorales infection continues to present difficulties. In this study, novel detection techniques utilizing recombinase polymerase amplification (RPA) and quantitative real-time polymerase chain reaction (qPCR) were developed, specifically targeting the mitochondrial rnl gene, in order to address this challenge. The specificity of the RPA and qPCR assay was assessed by adding genomic DNAs extracted from 14 non-targeted strains, as well as human and mouse blood. No false-positive results were observed. Additionally, genomic DNAs from 13 species in five genera of order Mucorales were tested and yielded positive results in both methods. To further evaluate the sensitivity of the assays, DNAs from Rhizopus oryzae, Mucor racemosus, Absidia glauca, Rhizomucor miehei, and Cunninghamella bertholletiae were utilized, with concentrations ranging from 1 ng/μL to 1 fg/μL. The limit of detection (LoD) for the RPA assay was determined to be 1 pg., with the exception of Rhizomucor miehei which had a LoD of 1 ng. The LoD for the qPCR assay varied between 10 fg and 1 pg., depending on the specific species being tested. Sensitivity analysis conducted on simulated clinical samples revealed that the LoD for RPA and qPCR assays were capable of detecting DNA extracted from 103 and 101 colony forming units (CFU) conidia in 200 μL of blood and serum, respectively. Consequently, the real-time RPA and qPCR assays developed in this study exhibited favorable sensitivity and specificity for the diagnosis of mucormycosis.
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Affiliation(s)
- Rui Xu
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
- School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Dingchen Li
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jingya Zhao
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hanying Zhong
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
- School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Hong Chen
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
- School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Yajing Jia
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Fangyan Chen
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Li Han
- Department for Disinfection and Infection Control, Chinese PLA Center for Disease Control and Prevention, Beijing, China
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Dantas KC, de Freitas—Xavier RS, Spina Lombardi SCF, Júnior AM, da Silva MV, Criado PR, de Freitas VLT, de Almeida TMB. Comparative analysis of diagnostic methods for the detection of Cryptococcus neoformans meningitis. PLoS Negl Trop Dis 2023; 17:e0011140. [PMID: 36877731 PMCID: PMC10019727 DOI: 10.1371/journal.pntd.0011140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/16/2023] [Accepted: 02/05/2023] [Indexed: 03/07/2023] Open
Abstract
BACKGROUND Cryptococcosis is a devastating opportunistic infection in immunocompromised individuals, primarily in people living with HIV/AIDS. This study evaluated a protocol for the early diagnosis of meningitis due to C. neoformans, utilizing established molecular techniques from serum and CSF samples. METHODS The 18S and 5.8S (rDNA-ITS) sequence-specific nested PCR assays were compared with direct India ink staining and the latex agglutination test for detection of C. neoformans in serum and cerebrospinal fluid (CSF) from 49 Brazilian suspected meningitis patients. Results were validated with samples obtained from 10 patients negative for cryptococcosis and HIV, and by analysis of standard C. neoformans strains. PRINCIPAL FINDINGS The 5.8S DNA-ITS PCR was more sensitive (89-100%) and specific (100%) than the 18S rDNA PCR and conventional tests (India ink staining and latex agglutination) for identification of C. neoformans. While the 18S PCR exhibited a sensitivity (72%) similar to that of the latex agglutination assay in serum samples, it was superior to the latex agglutination assay when testing CSF, with a sensitivity of 84%. However, the latex agglutination was superior to the 18SrDNA PCR in specificity in CSF (92%). The 5.8S DNA-ITS PCR yielded the highest levels of accuracy (96-100%) of any test for detection (serological and mycological) of C. neoformans in both serum and CSF. CONCLUSION Use of the nested 5.8S PCR was superior to other techniques for the diagnosis of cryptococcosis. The possibility of using serum, a non-invasively collected material, in a targeted 5.8S PCR analysis to identify Cryptococcus spp. is recommended, especially in immunosuppressed patients. Our results indicate that nested 5.8S PCR can increase the diagnostic capability of cryptococcosis, and we suggest its use to monitor patients in the future.
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Affiliation(s)
- Katia Cristina Dantas
- Department of Pathology, Sao Paulo University Medical School, Sao Paulo, Brazil
- * E-mail:
| | | | | | - Alfredo Mendroni Júnior
- Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in OncoImmuno-Hematology (LIM-31), Department of Hematology, Hospital das Clínicas -HCFMUSP, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Marcos Vinicius da Silva
- Emilio Ribas Institute of Infectious Diseases, Consultant, Ministry of Health, Department of Medicine, Catholic University of Sao Paulo, and Professor, Program in Postgraduate Sciences and Coordination of Disease Control, Department of State Health, São Paulo, Brazil
| | | | - Vera Lúcia Teixeira de Freitas
- Laboratory of Medical Investigation in Imunology (LIM-48), Department of Infectious and Parasitic Diseases, Sao Paulo University Medical School, Sao Paulo, Brazil
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Beardsley J, Dao A, Keighley C, Garnham K, Halliday C, Chen SCA, Sorrell TC. What's New in Cryptococcus gattii: From Bench to Bedside and Beyond. J Fungi (Basel) 2022; 9:jof9010041. [PMID: 36675862 PMCID: PMC9865494 DOI: 10.3390/jof9010041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Cryptococcus species are a major cause of life-threatening infections in immunocompromised and immunocompetent hosts. While most disease is caused by Cryptococcus neoformans, Cryptococcus gattii, a genotypically and phenotypically distinct species, is responsible for 11-33% of global cases of cryptococcosis. Despite best treatment, C. gattii infections are associated with early mortality rates of 10-25%. The World Health Organization's recently released Fungal Priority Pathogen List classified C. gattii as a medium-priority pathogen due to the lack of effective therapies and robust clinical and epidemiological data. This narrative review summarizes the latest research on the taxonomy, epidemiology, pathogenesis, laboratory testing, and management of C. gattii infections.
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Affiliation(s)
- Justin Beardsley
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Correspondence:
| | - Aiken Dao
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Caitlin Keighley
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
| | - Katherine Garnham
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Sunshine Coast University Hospital, Sunshine Coast University, Birtinya, QLD 4575, Australia
| | - Catriona Halliday
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Institute of Clinical Pathology and Medical Research (ICPMR), NSW Health Pathology, Sydney, NSW 2145, Australia
| | - Sharon C.-A. Chen
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Institute of Clinical Pathology and Medical Research (ICPMR), NSW Health Pathology, Sydney, NSW 2145, Australia
| | - Tania C. Sorrell
- Sydney Infectious Disease Institute, University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, New South Wales Health, Sydney, NSW 2145, Australia
- Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
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7
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Tan M, Liao C, Liang L, Yi X, Zhou Z, Wei G. Recent advances in recombinase polymerase amplification: Principle, advantages, disadvantages and applications. Front Cell Infect Microbiol 2022; 12:1019071. [PMID: 36519130 PMCID: PMC9742450 DOI: 10.3389/fcimb.2022.1019071] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022] Open
Abstract
After the outbreak of SARS-CoV-2, nucleic acid testing quickly entered people's lives. In addition to the polymerase chain reaction (PCR) which was commonly used in nucleic acid testing, isothermal amplification methods were also important nucleic acid testing methods. Among several common isothermal amplification methods like displaced amplification, rolling circle amplification, and so on, recombinase polymerase amplification (RPA) was recently paid more attention to. It had the advantages like a simple operation, fast amplification speed, and reaction at 37-42°C, et al. So it was very suitable for field detection. However, there were still some disadvantages to RPA. Herein, our review mainly summarized the principle, advantages, and disadvantages of RPA. The specific applications of RPA in bacterial detection, fungi detection, virus detection, parasite detection, drug resistance gene detection, genetically modified food detection, and SARS-CoV-2 detection were also described. It was hoped that the latest research progress on RPA could be better delivered to the readers who were interested in RPA.
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Idrus HH, Sunarno. Evaluation of the Performance of a Multiplex Real-Time PCR Assay for the Identification of Aspergillus, Cryptococcus neoformans, and Pneumocystis jirovecii Simultaneously from Sputum in Multicenter [Letter]. Infect Drug Resist 2022; 15:6799-6800. [PMID: 36451899 PMCID: PMC9703898 DOI: 10.2147/idr.s396184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Hasta Handayani Idrus
- Center for Biomedical Research, Research Organization for Health, National Research and Innovation Agency (BRIN), Cibinong Science Center, Bogor, West Java, Indonesia,Correspondence: Hasta Handayani Idrus, Center for Biomedical Research, Research Organization for Health, National Research and Innovation Agency (BRIN), Genomic Building, Cibinong Science Center, Jl. Raya Bogor No. 490, Cibinong – Bogor Km. 46, Bogor, West Java, Indonesia, Email ;
| | - Sunarno
- Center for Biomedical Research, Research Organization for Health, National Research and Innovation Agency (BRIN), Cibinong Science Center, Bogor, West Java, Indonesia
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9
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de Olazarra AS, Cortade DL, Wang SX. From saliva to SNP: non-invasive, point-of-care genotyping for precision medicine applications using recombinase polymerase amplification and giant magnetoresistive nanosensors. LAB ON A CHIP 2022; 22:2131-2144. [PMID: 35537344 PMCID: PMC9156572 DOI: 10.1039/d2lc00233g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Genetic testing is considered a cornerstone of the precision medicine paradigm. Genotyping of single nucleotide polymorphisms (SNPs) has been shown to provide insights into several important issues, including therapy selection and drug responsiveness. However, a scarcity of widely deployable and cost-effective genotyping tools has limited the integration of precision medicine into routine clinical practice. The objective of our work was to develop a portable, cost-effective, and automated platform that performs SNP genotyping at the point-of-care (POC). Using recombinase polymerase amplification (RPA) and giant magnetoresistive (GMR) nanosensors, we present a highly automated and multiplexed point-of-care platform that utilizes direct saliva for the qualitative genotyping of four SNPs (rs4633, rs4680, rs4818, rs6269) along the catechol-O-methyltransferase gene (COMT), which is associated with the modulation of pain sensitivity and perioperative opioid use. Using this approach, we successfully amplify, detect, and genotype all four of the SNPs, demonstrating 100% accordance between the experimental results obtained using the automated RPA and GMR genotyping assay and the results obtained using a COMT PCR genotyping assay that was formerly validated using pyrosequencing. This automated, portable, and multiplexed RPA and GMR assay shows great promise as a solution for SNP genotyping at the POC and reinforces the broad applications of magnetic nanotechnology in biomedicine.
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Affiliation(s)
| | - Dana Lee Cortade
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Shan X Wang
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA.
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
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Li N, Wang L, Wang F, Chen H, Tao S, Zhu Q, Liu L, Liang W, Ma F. Rapid Detection of Klebsiella pneumoniae Carrying Virulence Gene rmpA2 by Recombinase Polymerase Amplification Combined With Lateral Flow Strips. Front Cell Infect Microbiol 2022; 12:877649. [PMID: 35663473 PMCID: PMC9160666 DOI: 10.3389/fcimb.2022.877649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022] Open
Abstract
Highly virulent Klebsiella pneumoniae often causes invasive infections with high morbidity and mortality rates, posing an immense clinical challenge. Rapid and accurate detection of pathogenic bacteria is of great significance for treatment and preventive control. Conventional detection by polymerase chain reaction (PCR) is limited by a dependence on laboratory equipment and professional staff. Recombinase polymerase amplification (RPA) combined with a lateral flow strip (LFS) can rapidly amplify and visualize target genes in a short period of time. The aim of this study was to develop an RPA-LFS technique for detection of the K. pneumoniae virulence gene rmpA2. Primers were designed against conserved sequences specific to the virulence gene, and primer probe design was optimized by introducing base substitution to obtain a specific and sensitive primer-probe combination for clinical detection. We tested 65 actual samples collected from clinics to evaluate the performance of the newly established RPA-LFS system in comparison with conventional PCR methods and qPCR methods. The RPA-LFS assay was performed at for 25 min a constant temperature of 37°C, and results could be observed without instrumentation. The system could specifically identify highly virulent K. pneumoniae carrying the virulence gene rmpA2 with a minimum detection limit of 10−1 ng/μL and 10 copies/μL. For the 65 clinical samples tested, The RPA-LFS assay results were in complete agreement with the qPCR results and PCR results. The RPA-LFS assay provides a rapid, accurate, and simple method for identification of highly virulent K. pneumoniae carrying rmpA2.
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Affiliation(s)
- Na Li
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
- Department of Medical Laboratory, Bengbu Medical College, Bengbu, China
| | - Lei Wang
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Fang Wang
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
| | - Huimin Chen
- Department of Central Laboratory, Lianyungang Second People’s Hospital affiliated to Jiangsu University, Lianyungang, China
| | - Shuan Tao
- Department of Central Laboratory, Lianyungang Second People’s Hospital affiliated to Jiangsu University, Lianyungang, China
| | - Qing Zhu
- Lianyungang Second People’s Hospital affiliated to Xuzhou Medical University, Lianyungang, China
| | - Liping Liu
- Lianyungang Second People’s Hospital affiliated to Xuzhou Medical University, Lianyungang, China
| | - Wei Liang
- Department of Laboratory Medicine, The Second People’s Hospital of Lianyungang City, Affiliated to Bengbu Medical College, Lianyungang, China
- *Correspondence: Wei Liang, ; Fang Ma,
| | - Fang Ma
- Department of Medical Laboratory, Bengbu Medical College, Bengbu, China
- *Correspondence: Wei Liang, ; Fang Ma,
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11
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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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Chen S, Yuan H, Yan X. Rapid visual detection of benzimidazole resistance in Botrytis cinerea by recombinase polymerase amplification combined with a lateral flow dipstick. PEST MANAGEMENT SCIENCE 2022; 78:821-830. [PMID: 34719103 DOI: 10.1002/ps.6697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/24/2021] [Accepted: 10/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Benzimidazole resistance in Botrytis cinerea is related to point mutations in the target β-tubulin gene (TUB2). Three mutations (E198A, E198K, E198V) at codon 198 account for most of the resistant strains. A rapid on-site diagnostic assay would be useful to detect the presence and monitor further spread of this resistance mechanism. RESULTS A recombinase polymerase amplification combined with lateral flow detection (RPA-LFD) method was established for the rapid detection of methyl benzimidazole carbamate (MBC) resistance in B. cinerea. Based on the three mutations at TUB2 codon 198, three sets of RPA-LFD primers were designed, and each of these primer sets was able to specifically amplify the DNA containing its corresponding mutation; no amplification was detected with other mutated or wild-type DNA. The assay was optimized for specificity and sensitivity and was shown to detect the presence of 2 × 102 copies μl-1 of target DNA per reaction within 10 min. DNA from eight other common fungal species of small fruit did not yield a signal. The system worked well over a wide range of temperatures from 25 to 45°C. Crude DNA obtained from boiled mycelium and conidia of symptomatic fruit could be used as templates, which simplified the assay process. CONCLUSION This study developed a novel assay based on RPA-LFD for the rapid and equipment-free detection of MBC-resistant isolates. In combination with a simple DNA extraction method, the assay could detect B. cinerea MBC-resistant isolates even without specialized equipment within 30 min. Considering its specificity, stability and simplicity, the RPA-LFD assay could be a promising tool for rapid on-site diagnosis of fungicide-resistant isolates. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Shuning Chen
- China and Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huizhu Yuan
- China and Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaojing Yan
- China and Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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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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Wang F, Wang L, Chen H, Li N, Wang Y, Li Y, Liang W. Rapid Detection of blaKPC, blaNDM, blaOXA-48-like and blaIMP Carbapenemases in Enterobacterales Using Recombinase Polymerase Amplification Combined With Lateral Flow Strip. Front Cell Infect Microbiol 2021; 11:772966. [PMID: 34926319 PMCID: PMC8674914 DOI: 10.3389/fcimb.2021.772966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/15/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of carbapenemase-producing Enterobacterales (CPE) infections is a major global public health threat. Rapid and accurate detection of pathogenic bacteria is essential to optimize treatment and timely avoid further transmission of these bacteria. Here, we aimed to develop a rapid on site visualization detection method for CPE using improved recombinase polymerase amplification (RPA) combined with lateral flow strip (LFS) method, based on four most popular carbapenemase genes: blaKPC, blaNDM, blaOXA-48-like, and blaIMP. All available allelic variants of the above carbapenemases were downloaded from the β-lactamase database, and the conserved regions were used as targets for RPA assay. Five primer sets were designed targeting to each carbapenemase gene and the RPA amplification products were analyzed by agarose gel electrophoresis. FITC-labeled specific probes were selected, combined with the best performance primer set (Biotin-labeled on the reverse primer), and detected by RPA-LFS. Mismatches were made to exclude the false positive signals interference. This assay was evaluated in 207 clinically validated carbapenem-resistant Enterobacterales (CRE) isolates and made a comparison with conventional PCR. Results showed that the established RPA-LFS assay for CPE could be realized within 30 min at a constant temperature of 37°C and visually detected amplification products without the need for special equipment. This assay could specifically differentiate the four classes of carbapenemases without cross-reactivity and shared a minimum detection limit of 100 fg/reaction (for blaKPC, blaNDM, and blaOXA-48-like) or 1000 fg/reaction (for blaIMP), which is ten times more sensitive than PCR. Furthermore, the detection of 207 pre-validated clinically CRE strains using the RPA-LFS method resulted in 134 blaKPC, 69 blaNDM, 3 blaOXA-48-like, and 1 blaIMP. The results of the RPA-LFS assay were in consistent with PCR, indicating that this method shared high sensitivity and specificity. Therefore, the RPA-LFS method for CPE may be a simple, specific, and sensitive method for the rapid diagnosis of carbapenemase Enterobacterales.
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Affiliation(s)
- Fang Wang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Lei Wang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Huimin Chen
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Na Li
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yan Wang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yan Li
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Wei Liang
- Department of Central Laboratory, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
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Wang F, Ge D, Wang L, Li N, Chen H, Zhang Z, Zhu W, Wang S, Liang W. Rapid and sensitive recombinase polymerase amplification combined with lateral flow strips for detecting Candida albicans. Anal Biochem 2021; 633:114428. [PMID: 34678249 DOI: 10.1016/j.ab.2021.114428] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 12/30/2022]
Abstract
Owing to modern lifestyles and increasing amounts of medical intervention, clinical infections caused by conditionally pathogenic fungi are becoming increasingly serious. Among these, Candida albicans is the most common. Therefore, the rapid and accurate detection of this pathogenic fungus is important to guiding the selection of clinical therapeutic agents. Recombinase polymerase amplification (RPA) combined with lateral flow strips (LFS) is a promising molecular detection method with the advantages of rapidity, simplicity of operation and high sensitivity. However, this simplicity brings with it the inherent and non-negligible risk of false-positive signals from primer-dimers. In this study, primer-dependent artifacts were eliminated by using probes in the RPA reaction, introducing specific base substitutions to the primer and probe sequences and analyzing and screening the formation of primer-probe complexes. These measures were rigorously tested for efficacy, leading to the creation of an improved RPA-LFS system. The standardized method enabled the specific detection of C. albicans within 25 min at 37 °C without interference. The system had a detection limit of 1 CFU per reaction without DNA purification or 102 fg genomic DNA/50 μL. The detection sensitivity was not affected by the presence of other fungal DNA. The RPA-LFS method can therefore be used to detect clinical samples, and the results are accurate and consistent in comparison with those obtained using quantitative PCR. This study provides a paradigm for eliminating the risk of false-positive primer dimers in isothermal amplification assays and establishes a simple and easy method for the detection of C. albicans.
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Affiliation(s)
- Fang Wang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Duobao Ge
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Lei Wang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China; School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Na Li
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Huimin Chen
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Zhexiong Zhang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Wenjun Zhu
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Siming Wang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China.
| | - Wei Liang
- Department of Central Laboratory, the Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Affiliated to Bengbu Medical College, Lianyungang, 222000, Jiangsu, China.
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Gupta Y, Ghrera AS. Recent advances in gold nanoparticle-based lateral flow immunoassay for the detection of bacterial infection. Arch Microbiol 2021; 203:3767-3784. [PMID: 34086107 DOI: 10.1007/s00203-021-02357-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/24/2021] [Accepted: 05/03/2021] [Indexed: 12/17/2022]
Abstract
Diagnosis of bacterial infections (BI) is becoming an increasingly difficult task in clinical practice due to their high prevalence and frequency, as well as the growth of antibiotic resistance worldwide. World Health Organization (WHO) reported antibiotic resistance is a major public health problem. BI becomes difficult or impossible to treat when the bacteria acquire immunity against antibiotics. Thus, there is a need for a quick and accurate technique to detect infection. Lateral flow immunoassay (LFIA) is an ideal technique for point-of-care testing of a disease or pathological changes inside the human body. In recent years, several LFIA based strips are being used for the detection of BI by targeting specific analytes which may range from the causative bacterium, whole-cell, DNA, or biomarker. Numerous nanoparticles like lipid-based nanoparticles, polymeric nanoparticles, and inorganic nanoparticles such as quantum dots, magnetic, ceramic, and metallic nanoparticles (copper, silver gold, iron) are widely being used in the advanced treatment of BI. Out of these gold nanoparticle (AuNPs), is being used for detection BI more effectively than other nanoparticles due to their surface functionalization, extraordinary chemical stability, biorecognition, and signal amplification properties and help to improve in conjugation with capture antibodies, and act as a color marker with unique optical properties on LFIA strips. Herein, a review that provides an overview of the principle of LFIA, how LFIA based strip is developed, and how it is helpful to detect a specific biomarker for bedside detection of the BI.
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Affiliation(s)
- Yachana Gupta
- Applied Science Department, The NorthCap University, Gurugram, India
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CRISPR-Cas13a-based diagnostic method for Chlamydia trachomatis from nongonococcal urethritis. Bioanalysis 2021; 13:901-912. [PMID: 33961493 DOI: 10.4155/bio-2021-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Development of a routine screening technique for Chlamydia trachomatis infection. The proposed approach involves the CRISPR RNA (crRNA). In the presence of the target sequence, the RNase activity of the Cas13a protein is activated, and it cleaves RNA fluorescent probe so that fluorescence will be emitted. Results: The sensitivity of the detection based on CRISPR-Cas13a was 10 fM. The results obtained by CRISPR-Cas13a and quantitative polymerase chain reaction were closely correlated: χ2 = 81.798 (p < 0.001). Conclusion: The method can be carried out at room temperature and yields results within 2 h. The developed technique does not require expensive instruments and, thus, can meet the needs of community hospitals and other institutions for screening.
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Brunauer A, Verboket RD, Kainz DM, von Stetten F, Früh SM. Rapid Detection of Pathogens in Wound Exudate via Nucleic Acid Lateral Flow Immunoassay. BIOSENSORS-BASEL 2021; 11:bios11030074. [PMID: 33800856 PMCID: PMC8035659 DOI: 10.3390/bios11030074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/24/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
The rapid detection of pathogens in infected wounds can significantly improve the clinical outcome. Wound exudate, which can be collected in a non-invasive way, offers an attractive sample material for the detection of pathogens at the point-of-care (POC). Here, we report the development of a nucleic acid lateral flow immunoassay for direct detection of isothermally amplified DNA combined with fast sample preparation. The streamlined protocol was evaluated using human wound exudate spiked with the opportunistic pathogen Pseudomonas aeruginosa that cause severe health issues upon wound colonization. A detection limit of 2.1 × 105 CFU per mL of wound fluid was achieved, and no cross-reaction with other pathogens was observed. Furthermore, we integrated an internal amplification control that excludes false negative results and, in combination with the flow control, ensures the validity of the test result. The paper-based approach with only three simple hands-on steps has a turn-around time of less than 30 min and covers the complete analytical process chain from sample to answer. This newly developed workflow for wound fluid diagnostics has tremendous potential for reliable pathogen POC testing and subsequent target-oriented therapy.
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Affiliation(s)
- Anna Brunauer
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - René D Verboket
- Department of Trauma-, Hand- and Reconstructive Surgery, University Hospital Frankfurt, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Daniel M Kainz
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Susanna M Früh
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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Lass-Flörl C, Samardzic E, Knoll M. Serology anno 2021-fungal infections: from invasive to chronic. Clin Microbiol Infect 2021; 27:1230-1241. [PMID: 33601011 DOI: 10.1016/j.cmi.2021.02.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/26/2021] [Accepted: 02/04/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Diagnosing invasive or chronic fungal infections is a challenge, particularly in the immunocompromised host. Microscopy and culture remain the reference standard, but are insensitive. The use of non-culture-based techniques is recommended in conjunction with conventional methods to improve the diagnostic yield. OBJECTIVES The aim was to provide an updated 2021 inventory of fungal antigen and serology tests for diagnosing invasive and chronic fungal infections, the key focus was set on Aspergillus, Candida and Cryptococcus species. SOURCES Pubmed search for publications with the key words fungal antigen tests, laboratory-based diagnosis of invasive pulmonary aspergillosis, chronic pulmonary aspergillosis, invasive candidiasis, invasive fungal infections and cryptococcal infections published from 2017 to 2020. CONTENT Antigen assays such as the galactomannan (GM) and β-d-glucan detection systems are frequently used, but these tests vary in sensitivity and specificity, depending on the patient population involved, specimens inspected, cut-offs defined, test strategy applied and inclusion or exclusion of possible fungal case definitions. Multiple different detection systems are available, with recently introduced new point-of-care tests such as the lateral flow device and the lateral flow assay. Despite a wide heterogeneity in populations evaluated, studies indicate a better diagnostic performance of bronchoalveolar lavage GM in comparison with serum GM, and a suboptimal specificity of GM bronchoalveolar lavages (cut-off ≥1) and serum β-d-glucan in non-neutropenic individuals. Point-of-care cryptococcal antigen tests show excellent performance. IMPLICATIONS There are fungal antigen detection tests available with excellent to reasonable clinical performance to diagnose invasive fungal infections. Only a few assays are useful to monitor therapeutic response. There are multiple marketed IgG antibody tests to detect Aspergillus fumigatus antibodies, the titres vary widely and the performance differs significantly. In general, diagnostic tests are vulnerable to being affected by the host, the microbe and laboratory setting.
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Affiliation(s)
- Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria.
| | - Eldina Samardzic
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria
| | - Miriam Knoll
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria
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Bushmeat Species Identification: Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow (LF) Strip for Identification of Formosan Reeves' Muntjac ( Muntiacus reevesi micrurus). Animals (Basel) 2021; 11:ani11020426. [PMID: 33562213 PMCID: PMC7914887 DOI: 10.3390/ani11020426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Illegal hunting of wild animals and the consumption of bushmeat are recognized not only as a threat to biodiversity, but also as a risk for transmitting zoonotic diseases. Illegal sales of meat products from Formosan Reeves’ muntjac (Muntiacus reevesi micrurus) is a growing issue in Taiwan, bringing forth the demand for a fast and cost-effective technique for meat species identification. In this study, a new recombinase polymerase amplification combined with a lateral flow strip to identify Formosan Reeves’ muntjac in meat products was described. This method only requires minimal sample preparation and an isothermal heating process. The result can be interpreted by the naked eye within 30 min. The system we designed efficiently detected a variety of meat products, and no cross-reactions were observed with other animal species. This simple assay provides a sensitive and specific method to identify bushmeat sources in various meat products, which holds the potential for on-field application in the future. Abstract The identification of animal species of meat in meat products is of great concern for various reasons, such as public health, religious beliefs, food allergies, legal perspectives, and bushmeat control. In this study, we developed a new technique to identify Formosan Reeves’ muntjac in meat using recombinase polymerase amplification (RPA) in combination with a lateral flow (LF) strip. The DNA extracted from a piece of Formosan Reeves’ muntjac meat was amplified by a pair of specific primers based on its mitochondrial cytochrome b gene for 10 min at a constant temperature ranging from 30 to 45 °C using RPA. Using the specific probe added to the RPA reaction system, the amplified products were visualized on the LF strip within 5 min. The total operating time from quick DNA extraction to visualizing the result was approximately 30 min. The RPA-LF system we designed was efficient when using boiled, pan-fried, roasted, stir-fried, or stewed samples. The advantages of simple operation, speediness, and cost-effectiveness make our RPA-LF method a promising molecular detection tool for meat species identification of either raw or variously cooked Formosan Reeves’ muntjac meat. It is also possible to apply this method to identify the meat of other wildlife sources.
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Fang W, Cai Y, Zhu L, Wang H, Lu Y. Rapid and Highly Sensitive Detection of Toxigenic Vibrio cholerae Based on Recombinase-Aided Amplification Combining with Lateral Flow Assay. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01909-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Afzal A, Kaplan H, Motazedi T, Qureshi T, Woc-Colburn L. Diagnostics: The Role of the Laboratory. HIGHLY INFECTIOUS DISEASES IN CRITICAL CARE 2020:37-68. [DOI: 10.1007/978-3-030-33803-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Kumar S, Nehra M, Mehta J, Dilbaghi N, Marrazza G, Kaushik A. Point-of-Care Strategies for Detection of Waterborne Pathogens. SENSORS (BASEL, SWITZERLAND) 2019; 19:E4476. [PMID: 31623064 PMCID: PMC6833035 DOI: 10.3390/s19204476] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/11/2019] [Accepted: 10/13/2019] [Indexed: 12/31/2022]
Abstract
Waterborne diseases that originated due to pathogen microorganisms are emerging as a serious global health concern. Therefore, rapid, accurate, and specific detection of these microorganisms (i.e., bacteria, viruses, protozoa, and parasitic pathogens) in water resources has become a requirement of water quality assessment. Significant research has been conducted to develop rapid, efficient, scalable, and affordable sensing techniques to detect biological contaminants. State-of-the-art technology-assisted smart sensors have improved features (high sensitivity and very low detection limit) and can perform in a real-time manner. However, there is still a need to promote this area of research, keeping global aspects and demand in mind. Keeping this view, this article was designed carefully and critically to explore sensing technologies developed for the detection of biological contaminants. Advancements using paper-based assays, microfluidic platforms, and lateral flow devices are discussed in this report. The emerging recent trends, mainly point-of-care (POC) technologies, of water safety analysis are also discussed here, along with challenges and future prospective applications of these smart sensing technologies for water health diagnostics.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Jyotsana Mehta
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Giovanna Marrazza
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
| | - Ajeet Kaushik
- Department of Natural Sciences, Florida Polytechnic University, Lakeland, FL 33805-8531, USA.
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