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Gao P, Fan Y, Kong X, Zhang R, Chen L, Jiang Y, Liu Y, Zhao M, Deng G, Cao Y, Ma L. A novel assay based on DNA melting temperature for multiplexed identification of SARS-CoV-2 and influenza A/B viruses. Front Microbiol 2023; 14:1249085. [PMID: 38173675 PMCID: PMC10762780 DOI: 10.3389/fmicb.2023.1249085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses can cause respiratory illnesses with similar clinical symptoms, making their differential diagnoses challenging. Additionally, in critically ill SARS-CoV-2-infected patients, co-infections with other respiratory pathogens can lead to severe cytokine storm and serious complications. Therefore, a method for simultaneous detection of SARS-CoV-2 and influenza A and B viruses will be clinically beneficial. Methods We designed an assay to detect five gene targets simultaneously via asymmetric PCR-mediated melting curve analysis in a single tube. We used specific probes that hybridize to corresponding single-stranded amplicons at low temperature and dissociate at high temperature, creating different detection peaks representing the targets. The entire reaction was conducted in a closed tube, which minimizes the risk of contamination. The limit of detection, specificity, precision, and accuracy were determined. Results The assay exhibited a limit of detection of <20 copies/μL for SARS-CoV-2 and influenza A and <30 copies/μL for influenza B, with high reliability as demonstrated by a coefficient of variation for melting temperature of <1.16% across three virus concentrations. The performance of our developed assay and the pre-determined assay showed excellent agreement for clinical samples, with kappa coefficients ranging from 0.98 (for influenza A) to 1.00 (for SARS-CoV-2 and influenza B). No false-positive, and no cross-reactivity was observed with six common non-influenza respiratory viruses. Conclusion The newly developed assay offers a straightforward, cost-effective and nucleic acid contamination-free approach for simultaneous detection of the SARS-CoV-2, influenza A, and influenza B viruses. The method offers high analytical sensitivity, reliability, specificity, and accuracy. Its use will streamline testing for co-infections, increase testing throughput, and improve laboratory efficacy.
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Affiliation(s)
- Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Lida Chen
- Department of Blood Transfusion, China-Japan Friendship Hospital, Beijing, China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
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2
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Guo J, You W, Lin K, Li Q, Guo X, Wang S, Bian Y, Ren W, Zhang R, Wang Y, Li B. An extraction-free method for rapid detection of CYP2C19 * 2/3/17 polymorphisms in one tube using melting curve analysis. Biotechnol J 2023; 18:e2300207. [PMID: 37551831 DOI: 10.1002/biot.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
Drug-metabolizing enzymes play an important role in the metabolism of drugs in vivo. Their activity is an important factor affecting the rate of drug metabolism, which directly determines the intensity and persistence of drug action. Patients taking medication can be divided into different metabolic types through detection of CYP2C19 drug-metabolizing enzyme gene polymorphisms, which can then be used for medication guidance for clopidogrel. Here, we describe a detection method based on real-time polymerase chain reaction (PCR). This method uses multicolor melting curve analysis to accurately identify different mutation sites and genotypes of CYP2C19 * 2, CYP2C19 * 3, and CYP2C19 * 17. The detection limit of plasmid samples was 1 copies μL-1 ; that of genomic samples was 0.1 ng μL-1 . The system can detect nine types of CYP2C19 * 2/3/17 at three sites in one tube, quickly achieving detection within 1 h. Combined with the sample release agent, sample extraction was completed in 5 s, achieving rapid diagnosis without extraction for timely diagnosis and treatment. Furthermore, the system is not limited to blood samples and can also be applied to oropharyngeal and saliva samples, increasing sampling diversity and convenience. When using clinical blood samples (n = 93), the detection system we established was able to quickly and accurately identify different genotypes, and the accuracy and effectiveness of the detection were confirmed by Sanger sequencing. Due to its accuracy, rapidity, simple operation, and low cost, detection technology based on real-time polymerase amplification combined with melting curve analysis is expected to become a powerful tool for detecting and guiding clopidogrel use in countries with limited resources.
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Affiliation(s)
- Jianguang Guo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Weixin You
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Kangfeng Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qinghan Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiangju Guo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shuai Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ya Bian
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wenjing Ren
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Rui Zhang
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen, University, School of Medicine, Xiamen University, Xiamen, China
| | - Yanping Wang
- Emergency Department, HuBei ProvinciaI HospitaI Of TCM, Wuhan, China
| | - Boan Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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Tokamani M, Figgou E, Papamichail L, Sakka E, Toros A, Bouchorikou A, Giannakakis A, Matthaiou EI, Sandaltzopoulos R. A Multiplex PCR Melting-Curve-Analysis-Based Detection Method for the Discrimination of Five Aspergillus Species. J Fungi (Basel) 2023; 9:842. [PMID: 37623613 PMCID: PMC10455196 DOI: 10.3390/jof9080842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Aspergillus mold is a ubiquitously found, airborne pathogen that can cause a variety of diseases from mild to life-threatening in severity. Limitations in diagnostic methods combined with anti-fungal resistance render Aspergillus a global emerging pathogen. In industry, Aspergilli produce toxins, such as aflatoxins, which can cause food spoilage and pose public health risk issues. Here, we report a multiplex qPCR method for the detection and identification of the five most common pathogenic Aspergillus species, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, and Aspergillus nidulans. Our approach exploits species-specific nucleotide polymorphisms within their ITS genomic regions. This novel assay combines multiplex single-color real time qPCR and melting curve analysis and provides a straight-forward, rapid, and cost-effective detection method that can identify five Aspergillus species simultaneously in a single reaction using only six unlabeled primers. Due to their unique fragment lengths, the resulting amplicons are directly linked to certain Aspergillus species like fingerprints, following either electrophoresis or melting curve analysis. Our method is characterized by high analytical sensitivity and specificity, so it may serve as a useful and inexpensive tool for Aspergillus diagnostic applications both in health care and the food industry.
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Affiliation(s)
- Maria Tokamani
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleftheria Figgou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Lito Papamichail
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleni Sakka
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Athanasios Toros
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Anastasia Bouchorikou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Efthymia Iliana Matthaiou
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA;
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
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Pandey M, Sachdev J, Yadav RK, Sharad N, Kanodia A, Biswas J, Janani RS, Gupta S, Singh G, Ekka M, Rana B, Gourav S, Thakar A, Biswas A, Sikka K, Mathur P, Pushker N, Jyotsna VP, Kumar R, Soneja M, Wig N, Srivastava MVP, Xess I. Utility of in-house and commercial PCR assay in diagnosis of Covid-19 associated mucormycoss in an emergency setting in a tertiary care center. J Med Microbiol 2023; 72. [PMID: 37624041 DOI: 10.1099/jmm.0.001745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023] Open
Abstract
Introduction. Invasive mucormycosis (IM) is a potentially fatal infection caused by fungi of the order Mucorales. Histopathology, culture, and radiology are the mainstays of diagnosis, but they are not sufficiently sensitive, resulting in delayed diagnosis and intervention. Recent studies have shown that PCR-based techniques can be a promising way to diagnose IM.Hypothesis/Gap Statement. Early diagnosis of fungal infections using molecular diagnostic techniques can improve patient outcomes, especially in invasive mucormycosis.Aim. The aim of this study was to evaluate the utility of our in-house mould-specific real time PCR assay (qPCR) in comparison with the commercially available real time PCR (MucorGenius PCR), for the early diagnosis of mucormycosis in tissue samples from patients with suspicion of invasive mucormycosis (IM). This in-house assay can detect and distinguish three clinically relevant mould species, e.g. Aspergillus spp., Mucorales and Fusarium spp. in a single reaction with only one pair of primers, without the need for sequencing.Methodology. We enrolled 313 tissue samples from 193 patients with suspected IM in this prospective study. All cases were classified using EORTC/MSGERC guidelines. All samples were tested using traditional methods, in-house qPCR, and MucorGenius PCR.Results. Using direct microscopy as a gold standard, the overall sensitivity and specificity of in-house qPCR for detection of IM was 92.46% and 80% respectively, while that of the MucorGenius PCR was 66.67% and 90% respectively. However, co-infection of IM and IA adversely affected the performance of MucorGenius PCR in detection of IM.The in-house PCR detected Aspergillus spp. in 14 cases and Fusarium spp. in 4 cases which showed clinical and radiological features of fungal sinusitis. The in-house qPCR also performed better in detecting possible cases of IM. This aids early diagnosis and appropriate treatment to improve patient outcomes.Conclusion. Because the in-house PCR is not only sensitive and specific, but also entirely based on SYBR Green for detection of targets, it is less expensive than probe-based assays and can be used on a regular basis for the diagnosis of IM in resource-constrained settings. It can be used to distinguish between mucormycosis and fungal sinusitis caused by Aspergillus and Fusarium in high-risk patients, as well as to accurately detect Mucorales in fungal co-infection cases.
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Affiliation(s)
- Mragnayani Pandey
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Janya Sachdev
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Renu Kumari Yadav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Neha Sharad
- Department of Lab medicine JPNATC, All India Institute of Medical Sciences, New Delhi, India
| | - Anupam Kanodia
- Department of ENT, All India Institute of Medical Sciences, New Delhi, India
| | - Jaya Biswas
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - R Sruti Janani
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sonakshi Gupta
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Gagandeep Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Meera Ekka
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Bhaskar Rana
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sudesh Gourav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Alok Thakar
- Department of ENT, All India Institute of Medical Sciences, New Delhi, India
| | - Ashutosh Biswas
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Kapil Sikka
- Department of ENT, All India Institute of Medical Sciences, New Delhi, India
| | - Purva Mathur
- Department of Lab medicine JPNATC, All India Institute of Medical Sciences, New Delhi, India
| | - Neelam Pushker
- Department of Ophthalmology, All India Institute of Medical Sciences, New Delhi, India
| | - Viveka P Jyotsna
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Department of ENT, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Soneja
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - M V Padma Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Immaculata Xess
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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Montrasio C, Cheli S, Clementi E. Pharmacogenetic Practice of Anticancer Drugs: Multiple Approaches for an Accurate and Comprehensive Genotyping. Pharmgenomics Pers Med 2023; 16:739-746. [PMID: 37534027 PMCID: PMC10390719 DOI: 10.2147/pgpm.s412430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
The application of pharmacogenetics in oncology is part of the routine clinical practice. In particular, genotyping of dihydropyrimidine dehydrogenase (DPYD) and UDP-glucuronosyltransferase (UGT1A1) is crucial to manage the treatment of patients taking fluoropyrimidines and irinotecan. The unique approach of our laboratory to the pharmacogenetic diagnostic service in oncology is to combine two real-time PCR methods, LightSNiP assay (TIB MOLBIOL), and more recently FRET (Fluorescent Resonance Energy Transfer) probes technology (Nuclear Laser Medicine), plus TaqMan assay (Thermo Fisher) for the confirmation of the presence of variant alleles on DNA from a second extraction. We found that both the FRET and LightSNiP assays, where detection occurs by melting curve analysis, offer an advantage over the competing TaqMan technology. Whereas unexpected genetic variants may be missed using a mutation-specific TaqMan assay, the information thus obtained can be useful to adjust the therapy in case of unexpected post-treatment toxicity. The combination of TaqMan and FRET assays helped us to achieve more accurate genotyping and a correct result for the patient. The added value of the DPYD FRET assay is the possibility of detecting, with the same amplification profile of the polymorphisms detailed in the guidelines, also the c.2194G>A (*6 rs1801160), cited in the recommendations as a variant to be investigated in case of severe toxicity. Regarding the UGT1A1 (TA)n promoter polymorphism (rs3064744), the distinctive and positive feature of the FRET assay is to allow clearly identifying all those potential variant alleles, including the (TA)5 and (TA)8 alleles, that are frequent in African Americans. Our clinical practice emphasizes the importance of not only rapid and easy-to-use assays, such as the new FRET ones, but also of accurate and comprehensive genotyping for good pharmacogenetic diagnostic activity.
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Affiliation(s)
- Cristina Montrasio
- Unit of Clinical Pharmacology, ASST Fatebenefratelli Sacco, L. Sacco University Hospital, Milan, Italy
| | - Stefania Cheli
- Unit of Clinical Pharmacology, ASST Fatebenefratelli Sacco, L. Sacco University Hospital, Milan, Italy
| | - Emilio Clementi
- Clinical Pharmacology Unit, Department of Biomedical and Clinical Sciences, L. Sacco University Hospital, Università degli Studi di Milano, Milan, Italy
- Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
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Li R, Li Y, Chen X, Jia L, Yu H, Huang Y, Wu Q, Xiao M, Ge S, Zhang Y, Feng Z, Li Q, Xu Y, Shi W, Sun F, Zhang W. Ability of the MeltPro MTB/PZA Assay to Detect Susceptibility to Pyrazinamide in Rifampin-Resistant Tuberculosis Patients. Microbiol Spectr 2023; 11:e0483622. [PMID: 37162355 PMCID: PMC10269598 DOI: 10.1128/spectrum.04836-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023] Open
Abstract
Prediction of susceptibility to pyrazinamide (PZA) directly from sputum has been challenging. The MeltPro MTB/PZA assay, based on melting curve analysis, can simultaneously detect Mycobacterium tuberculosis and the resistance to PZA from sputum. We aimed to evaluate the MeltPro MTB/PZA assay to predict PZA resistance among rifampin-resistant tuberculosis (RR-TB) patients. We prospectively enrolled RR-TB patients in the registered trials, and their baseline sputum samples were obtained to perform the assay and culture. DNA sequencing of culture isolates was analyzed and used as the reference standard. Sanger sequencing was performed for samples with discrepant results between next-generation sequencing (NGS) and the investigational assay. The main analysis was conducted in the population of patients with interpretable results by both NGS and the assay. A total of 239 patients with RR-TB were screened, and 220 underwent the MeltPro MTB/PZA assay. The assay provided no information for 25 of 220 patients (11.4%). Among the remaining 195 patients, 13 had negative culture or insufficient raw NGS sequencing data, and 15 had indeterminate assay results. A total of 167 patients were included in the main analysis. Against DNA sequencing, the sensitivity, specificity, and negative predictive value of the assay for detecting resistance to PZA were 91.4% (95% confidence interval [CI], 87.1% to 95.6%), 89.9% (95% CI, 85.3% to 94.5%), and 95.2% (95% CI, 91.9% to 98.4%), respectively. In conclusion, the MeltPro MTB/PZA assay is a fast semiautomatic molecular platform to rapidly predict resistance to PZA from sputum and holds promise as a screening tool with satisfactory sensitivity. IMPORTANCE This study evaluated the accuracy of the MeltPro MTB/PZA assay at detecting the presence of PZA resistance through registered clinical trials. Compared to DNA sequencing, the assay had high sensitivity and negative predictive value, suggesting its potential utility as a screening tool in clinical practice. The assay could serve as an ideal primary screening tool in low PZA-resistant M. tuberculosis prevalence settings and could be used as an additional test to identify PZA resistance rapidly and initially in the RR-TB population.
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Affiliation(s)
- Rong Li
- Department of Infectious Diseases, Jing’an District Central Hospital, Fudan University, Shanghai, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yang Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinchang Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Lina Jia
- Department of Tuberculosis, Guiyang Public Health Clinical Center, Guiyang, China
| | - Hongying Yu
- Center for Infectious Diseases, The First People’s Hospital of Huaihua, Huaihua, Hunan, China
| | - Ya Huang
- Department of Tuberculosis, Ge Jiu Infectious Disease Hospital, Gejiu, China
| | - Qianhong Wu
- Department of Tuberculosis, Shaanxi Provincial Tuberculosis Prevention and Control Hospital, Xi’an, Shannxi, China
| | - Mingying Xiao
- Department of Tuberculosis, Baoshan People’s Hospital, Baoshan, China
| | - Shijia Ge
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yilin Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhen Feng
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Wenzhi Shi
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Feng Sun
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Jing’an District Central Hospital, Fudan University, Shanghai, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China
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Ramos-Gómez S, Busto MD, Ortega N. Detection of Hazelnut and Almond Adulteration in Olive Oil: An Approach by qPCR. Molecules 2023; 28:molecules28104248. [PMID: 37241987 DOI: 10.3390/molecules28104248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 05/28/2023] Open
Abstract
Virgin olive oil (VOO), characterized by its unique aroma, flavor, and health benefits, is subject to adulteration with the addition of oils obtained from other edible species. The consumption of adulterated olive oil with nut species, such as hazelnut or almond, leads to health and safety issues for consumers, due to their high allergenic potential. To detect almond and hazelnut in olive oil, several amplification systems have been analyzed by qPCR assay with a SYBR Green post-PCR melting curve analysis. The systems selected were Cora1F2/R2 and Madl, targeting the genes coding the allergenic protein Cor a 1 (hazelnut) and Pru av 1 (almond), respectively. These primers revealed adequate specificity for each of the targeted species. In addition, the result obtained demonstrated that this methodology can be used to detect olive oil adulteration with up to 5% of hazelnut or almond oil by a single qPCR assay, and with a level as low as 2.5% by a nested-qPCR assay. Thus, the present research has shown that the SYBR-based qPCR assay can be a rapid, precise, and accurate method to detect adulteration in olive oil.
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Affiliation(s)
- Sonia Ramos-Gómez
- Department of Biotechnology and Food Science, Area of Biochemistry and Molecular Biology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - María D Busto
- Department of Biotechnology and Food Science, Area of Biochemistry and Molecular Biology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natividad Ortega
- Department of Biotechnology and Food Science, Area of Biochemistry and Molecular Biology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
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Chauhan K, Kim DM, Cho E, Kim DE. Facilitation of Dye-Based Quantitative Real-Time Polymerase Chain Reaction with Poly(ethylene glycol)-Engrafted Graphene Oxide. Nanomaterials (Basel) 2023; 13:1348. [PMID: 37110934 PMCID: PMC10144433 DOI: 10.3390/nano13081348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is an important and extensively utilized technique in medical and biotechnological applications. qPCR enables the real-time detection of nucleic acid during amplification, thus surpassing the necessity of post-amplification gel electrophoresis for amplicon detection. Despite being widely employed in molecular diagnostics, qPCR exhibits limitations attributed to nonspecific DNA amplification that compromises the efficiency and fidelity of qPCR. Herein, we demonstrate that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly improve the efficiency and specificity of qPCR by adsorbing single-stranded DNA (ssDNA) without affecting the fluorescence of double-stranded DNA binding dye during DNA amplification. PEG-nGO adsorbs surplus ssDNA primers in the initial phase of PCR, having lower concentrations of DNA amplicons and thus minimizing the nonspecific annealing of ssDNA and false amplification due to primer dimerization and erroneous priming. As compared to conventional qPCR, the addition of PEG-nGO and the DNA binding dye, EvaGreen, in the qPCR setup (dubbed as PENGO-qPCR) significantly enhances the specificity and sensitivity of DNA amplification by preferential adsorption of ssDNA without inhibiting DNA polymerase activity. The PENGO-qPCR system for detection of influenza viral RNA exhibited a 67-fold higher sensitivity than the conventional qPCR setup. Thus, the performance of a qPCR can be greatly enhanced by adding PEG-nGO as a PCR enhancer as well as EvaGreen as a DNA binding dye to the qPCR mixture, which exhibits a significantly improved sensitivity of the qPCR.
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Ferreira JDJG, Costa SCB, Addas-Carvalho M, Pereira MB, França ADO, de Lima RG, Andrade PD, Wanderley JDS, Martins LC, de Almeida EA, Marcon GEB. Evaluation of Molecular Methods to Identify Chagas Disease and Leishmaniasis in Blood Donation Candidates in Two Brazilian Centers. Pathogens 2023; 12:pathogens12040508. [PMID: 37111394 PMCID: PMC10141534 DOI: 10.3390/pathogens12040508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 04/29/2023] Open
Abstract
In Brazil, blood donation is regulated by the Brazilian Ministry of Health, and all States follow the same protocol for clinical and laboratory screening. Brazil is an endemic country for Chagas disease (CD), caused by Trypanosoma cruzi, and for leishmaniasis, caused by a species of Leishmania spp. Screening for leishmaniosis is not routinely performed by blood banks. Given the antigenic similarity between T. cruzi and Leishmania spp., cross-reactions in serological tests can occur, and inconclusive results for CD have been found. The objective of this study was to apply molecular techniques, e.g., nPCR, PCR, and qPCR, to clarify cases of blood donation candidates with non-negative serology for CD and to analyze the difference between the melting temperature during real-time PCR using SYBR Green. Thirty-seven cases that showed non-negative results for CD using chemiluminescent microparticle immunoassay (CMIA) tests from blood banks in Campo Grande, MS, and Campinas, SP, were analyzed. In the serum samples, 35 samples were evaluated by ELISA, and 24.3% (9/35) showed positive results for CD. nPCR was able to detect 12 positive results in 35 samples (34.28%). qPCR for T. cruzi was quantifiable in the samples that showed a value ≥0.002 par eq/mL (parasite equivalents per milliliter), and in 35 samples, 11 (31.42%) were positive. Of all evaluated samples using the described tests (CMIA, ELISA, nPCR, and qPCR), 18 (48.6%) were positive for CD. For MCA by qPCR, the melting temperature was 82.06 °C ± 0.46 for T. cruzi and 81.9 °C ± 0.24 for Leishmania infantum. The Mann-Whitney test showed a significant value of p < 0.0001. However, the differentiation between T. cruzi and L. infantum could not be considered due to temperature overlap. For leishmaniasis, of the 35 samples with non-negative serology for CD tested by the indirect fluorescent antibody test (IFAT), only one sample (2.85%) was positive (1:80). The PCR for Leishmania spp. was performed on 36 blood samples from donation candidates, and all were negative. qPCR for L. infantum showed 37 negative results for the 37 analyzed samples. The data presented here show the importance of performing two different tests in CD screening at blood banks. Molecular tests should be used for confirmation, thereby improving the blood donation system.
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Affiliation(s)
- Juliana de Jesus Guimarães Ferreira
- Laboratório de Diagnóstico de Doenças Infecciosas por Técnicas de Biologia Molecular, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Sandra Cecília Botelho Costa
- Laboratório de Diagnóstico de Doenças Infecciosas por Técnicas de Biologia Molecular, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Marcelo Addas-Carvalho
- Centro de Hematologia e Hemoterapia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Mariane Barroso Pereira
- Laboratório de Diagnóstico de Doenças Infecciosas por Técnicas de Biologia Molecular, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Adriana de Oliveira França
- Laboratório de Doenças Infecciosas e Parasitárias (LabDIP), Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Universidade Federal de Mato Grosso do Sul, Cidade Universitária s/n, Campo Grande 79090-900, MS, Brazil
| | - Rodrigo Gonçalves de Lima
- Laboratório de Diagnóstico de Doenças Infecciosas por Técnicas de Biologia Molecular, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Paula Durante Andrade
- Laboratório de Diagnóstico de Doenças Infecciosas por Técnicas de Biologia Molecular, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Jamiro da Silva Wanderley
- Grupo de Estudos em Doença de Chagas (GEDoCh), Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Luiz Cláudio Martins
- Grupo de Estudos em Doença de Chagas (GEDoCh), Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Eros Antonio de Almeida
- Grupo de Estudos em Doença de Chagas (GEDoCh), Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
| | - Gláucia Elisete Barbosa Marcon
- Laboratório de Diagnóstico de Doenças Infecciosas por Técnicas de Biologia Molecular, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-887, SP, Brazil
- Fundação Oswaldo Cruz Mato Grosso do Sul (FIOCRUZ MS), Rua Gabriel Abrão, 92, Jardim das Nações, Campo Grande 79081-746, MS, Brazil
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Aoki A, Jinno H, Ogawa K, Nakagawa T, Inagaki T, Wajima T, Okamoto Y, Uchiya KI. A Rapid Screening Assay for Clarithromycin-Resistant Mycobacterium avium Complex Using Melting Curve Analysis with Nonfluorescent Labeled Probes. Microbiol Spectr 2023; 11:e0432622. [PMID: 36622171 PMCID: PMC9927575 DOI: 10.1128/spectrum.04326-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
Mycobacterium avium complex (MAC) thrives in various environments and mainly causes lung disease in humans. Because macrolide antibiotics such as clarithromycin or azithromycin are key drugs for MAC lung disease, the emergence of macrolide-resistant strains prevents the treatment of MAC. More than 95% of macrolide-resistant MAC strains are reported to have a point mutation in 23S rRNA domain V. This study successfully developed a melting curve assay using nonfluorescent labeled probes to detect the MAC mutation at positions 2058 to 2059 of the 23S rRNA gene (AA genotype, clarithromycin susceptible; TA, GA, AG, CA, AC, and AT genotypes, clarithromycin resistant). In the AA-specific probe assay, the melting peak of the DNA fragment of the AA genotype was higher than that of DNA fragments of other genotypes. Melting temperature (Tm) values of the AA genotype and the other genotypes were about 80°C and 77°C, respectively. DNA fragments of each genotype were identified correctly in six other genotype-specific probes (TA, GA, AG, CA, AC, and AT) assays. Using genomic DNA from six genotype strains of M. avium and four genotype strains of M. intracellulare, we confirmed that all genomic DNAs could be correctly identified as individual genotypes according to the highest Tm values among the same probe assays. These results indicate that this melting curve-based assay is able to determine MAC genotypes at positions 2058 to 2059 of the 23S rRNA gene. This simple method could contribute to the rapid detection of clarithromycin-resistant MAC strains and help to provide accurate drug therapy for MAC lung disease. IMPORTANCE Since macrolide antibiotics such as clarithromycin or azithromycin are key drugs in multidrug therapy for Mycobacterium avium complex (MAC) lung diseases, the rapid detection of macrolide-resistant MAC strains has important implications for the treatment of MAC. Previous studies have reported a correlation between drug susceptibility testing and the mutation of macrolide resistance genes. In this study, we developed a novel melting curve-based assay using nonfluorescent labeled probes to identify both clarithromycin-resistant M. avium and M. intracellulare with mutations in the 23S rRNA gene, which is the clarithromycin or azithromycin resistance gene. This assay contributed to not only the detection of MAC mutations but also the determination of all genotypes at positions 2058 to 2059 of the 23S rRNA gene. Furthermore, because nonfluorescent labeled probes are used, this assay is more easily and more immediately available than other methods.
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Affiliation(s)
- Akira Aoki
- Department of Hygienic Chemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Hideto Jinno
- Department of Hygienic Chemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Kenji Ogawa
- Department of Respiratory Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
| | - Taku Nakagawa
- Department of Respiratory Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya, Japan
| | - Takayuki Inagaki
- Division of Pharmaceutical Sciences I, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Takeaki Wajima
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Yoshinori Okamoto
- Department of Hygienic Chemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Kei-ichi Uchiya
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
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Yuasa S, Nakajima J, Takatsuki Y, Takahashi Y, Tani‐Sassa C, Iwasaki Y, Nagano K, Sonobe K, Yoshimoto T, Nukui Y, Takeuchi H, Tanimoto K, Tanaka Y, Kimura A, Ichimura N, Tohda S. Viral load of SARS-CoV-2 Omicron is not high despite its high infectivity. J Med Virol 2022; 94:5543-5546. [PMID: 35790476 PMCID: PMC9349670 DOI: 10.1002/jmv.27974] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 12/15/2022]
Abstract
Patients infected with the Omicron variant of severe acute respiratory syndrome coronavirus 2 has increased worldwide since the beginning of 2022 and the variant has spread more rapidly than the Delta variant, which spread in the summer of 2021. It is important to clarify the cause of the strong transmissibility of the Omicron variant to control its spread. In 694 patients with coronavirus disease 2019, the copy numbers of virus in nasopharyngeal swab-soaked samples and the viral genotypes were examined using quantitative polymerase chain reaction (PCR) and PCR-based melting curve analysis, respectively. Whole-genome sequencing was also performed to verify the viral genotyping data. There was no significant difference (p = 0.052) in the copy numbers between the Delta variant cases (median 1.5 × 105 copies/μl, n = 174) and Omicron variant cases (median 1.2 × 105 copies/μl, n = 328). During this study, Omicron BA.1 cases (median 1.1 ×105 copies/μl, n = 275) began to be replaced by BA.2 cases (median 2.3 × 105 copies/μl, n = 53), and there was no significant difference between the two groups (p = 0.33). Our results suggest that increased infectivity of the Omicron variant and its derivative BA.2 is not caused by higher viral loads but by other factors, such as increased affinity to cell receptors or immune escape.
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Affiliation(s)
- Sonoka Yuasa
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Jun Nakajima
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yuna Takatsuki
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yuta Takahashi
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Chihiro Tani‐Sassa
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yumi Iwasaki
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Katsutoshi Nagano
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Kazunari Sonobe
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Tomoyo Yoshimoto
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Yoko Nukui
- Infection Control and PreventionTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Hiroaki Takeuchi
- Department of Molecular VirologyTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Kousuke Tanimoto
- Genome Laboratory, Medical Research InstituteTokyo Medical and Dental University (TMDU)TokyoJapan,Research Core, Institute of ResearchTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Yukie Tanaka
- Department of Molecular MicrobiologyTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Akinori Kimura
- Institute of ResearchTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Naoya Ichimura
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
| | - Shuji Tohda
- Clinical LaboratoryTokyo Medical and Dental University (TMDU) HospitalTokyoJapan
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12
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Li H, Mulati G, Shang Y, Yao C, Wang Y, Ren W, Xue Z, Li S, Pang Y. Rapid Detection of Clarithromycin and Amikacin Resistance in Mycobacterium abscessus Complex by High-Resolution Melting Curve Analysis. Microbiol Spectr 2022; 10:e0057422. [PMID: 35638787 DOI: 10.1128/spectrum.00574-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The emergence of Mycobacterium abscessus complex (MABC) infection is the most noteworthy health care problem. Clarithromycin (CLA) and amikacin (AMK) constitute the cornerstone of treatment for patients infected with MABC; thus, early detection of resistance to these two drugs is essential for formulating effective therapeutic regimens. In the present study, we aimed to validate the use of MeltPro MAB assay, a melting curve analysis with dually labeled probes, on a set of clinical isolates to detect CLA and AMK resistance. A total of 103 clinical MABC strains were collected in our analysis, including 76 strains of M. abscessussubsp. Abscessus (MAA) and 27 strains of M. abscessussubsp. Massiliense (MAM). In vitro susceptibility testing revealed that two isolates exhibited intrinsic CLA resistance by harboring A2270T mutation in rrl, and inducible resistance was noted in 42 isolates. Additionally, two MAA isolates with erm(41)T28 genotype were susceptible to CLA. Notably, we found three out of 44 isolates had two melting curve peaks, representing the simultaneous presence of mutant and the wild type in these specimens. In contrast, no known mutations were identified in six AMK-resistant isolates. Further analysis revealed that MeltPro yielded 100% and 96.67% sensitivity and specificity for detecting CLA resistance. In summary, this study firstly demonstrates that MeltPro is a promising diagnostic for early detection of CLA resistance for MABC isolates, which significantly improves the turnaround time within 2 h. Approximate two fifths of MABC isolates are resistant to CLA by 23S rRNA mutation or its methylation, emphasizing the urgent need for early detection of CLA resistance prior to empirical treatment of MABC infections. IMPORTANCEMycobacterium abscessus complex (MABC) has attracted increasing attention due to the numerous cases of infection. This pathogen is notorious for its intrinsic drug resistance, which complicates clinical management of patients with MABC infections. Clarithromycin (CLA) and amikacin (AMK) are the cornerstone of treatment regimens for MABC. Herein, our data firstly demonstrates that MeltPro is a promising diagnostic for early detection of CLA resistance for MABC isolates. The high frequency of CLA-resistant MABC isolates in China emphasizes the urgent need for early detection of CLA resistance prior to empirical treatment of MABC infections.
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13
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Kong X, Xu Y, Gao P, Liu Y, Wang X, Zhao M, Jiang Y, Yang H, Cao Y, Ma L. Rapid detection of the irinotecan-related UGT1A1*28 polymorphism by asymmetric PCR melting curve analysis using one fluorescent probe. J Clin Lab Anal 2022; 36:e24578. [PMID: 35766440 PMCID: PMC9396174 DOI: 10.1002/jcla.24578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 06/09/2022] [Accepted: 06/18/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Determination of UGT1A1 (TA)n polymorphism prior to irinotecan therapy is necessary to avoid severe adverse drug effects. Thus, accurate and reliable genotyping methods for (TA)n polymorphism are highly desired. Here, we present a new method for polymerase chain reaction (PCR) melting curve analysis using one fluorescent probe to discriminate the UGT1A1*1 [(TA)6 ] and *28 [(TA)7 ] genotypes. METHODS After protocol optimization, this technique was applied for genotyping of 64 patients (including 23 with UGT1A1*1/*1, 22 with *1/*28, and 19 with *28/*28) recruited between 2016 and 2021 in China-Japan Friendship Hospital. The accuracy of the method was evaluated by comparing the results with those of direct sequencing and fragment analysis. The intra- and inter-run precision of the melting temperatures (Tm s) were calculated to assess the reliability, and the limit of detection was examined to assess the sensitivity. RESULTS All genotypes were correctly identified with the new method, and its accuracy was higher than that of fragment analysis. The intra- and inter-run coefficients of variation for the Tm s were both ≤0.27%, with standard deviations ≤0.14°C. The limit of detection was 0.2 ng of input genomic DNA. CONCLUSION The developed PCR melting curve analysis using one fluorescent probe can provide accurate, reliable, rapid, simple, and low-cost detection of UGT1A1 (TA)n polymorphism, and its use can be easily generalized in clinical laboratories with a fluorescent PCR platform.
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Affiliation(s)
- Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Xuran Wang
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Hui Yang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
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14
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Rajan-Babu IS, Lian M, Chong SS. Triplet-Primed PCR Assays for Accurate Screening of FMR1 CGG Repeat Expansion and Genotype Verification. Curr Protoc 2022; 2:e427. [PMID: 35609145 DOI: 10.1002/cpz1.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fragile X syndrome and other fragile X-associated disorders are caused by the full-mutation (>200 copies) and premutation (55 to 200 copies) expansion, respectively, of the CGG short tandem repeat in the fragile X messenger ribonucleoprotein 1 (FMR1) gene. Clinical diagnostic laboratories use Southern blot analysis and polymerase chain reaction (PCR)-based tests to detect and/or size the FMR1 CGG repeats. The development of sensitive and high-throughput triplet-primed PCR (TP-PCR) assays has diminished the need to subject all samples to Southern blot analysis, which is both labor- and time-intensive. In this article, we describe two direct TP-PCR (dTP-PCR) assays for the detection of FMR1 CGG repeat expansions. We outline a protocol that is based on melting curve analysis of dTP-PCR amplicons for a rapid and cost-effective first-tier screening and identification of individuals with premutation and full-mutation expansions. We also describe a protocol that employs capillary electrophoresis to resolve the dTP-PCR amplicon fragments and to estimate the repeat sizes of normal (5 to 44 copies), intermediate (45 to 54 copies), and premutation alleles, as well as to detect full mutations and determine the structure of the FMR1 alleles. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for melting curve analysis Basic Protocol 2: Melting curve analysis of direct triplet-primed PCR amplicons on the Rotor-Gene Q MD × 5plex high-resolution melt platform Alternate Protocol: Melting curve analysis of direct triplet-primed PCR amplicons on the LightCycler 480 system Basic Protocol 3: Generation of direct triplet-primed PCR melting curve analysis profiles Basic Protocol 4: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for capillary electrophoresis Basic Protocol 5: Generation of control FMR1 plasmids for direct triplet-primed PCR melting curve analysis Basic Protocol 6: Sanger sequencing assay to verify FMR1 CGG repeat size and structure of plasmid DNA controls.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Children's & Women's Hospital, Vancouver, British Columbia, Canada
| | - Mulias Lian
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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15
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Huang Q, Chen D, Du C, Liu Q, Lin S, Liang L, Xu Y, Liao Y, Li Q. Highly multiplex PCR assays by coupling the 5'-flap endonuclease activity of Taq DNA polymerase and molecular beacon reporters. Proc Natl Acad Sci U S A 2022; 119:e2110672119. [PMID: 35197282 DOI: 10.1073/pnas.2110672119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 01/23/2023] Open
Abstract
We describe a highly multiplex PCR approach that can identify 10-fold more targets in current real-time PCR assays without additional enzymes or separate reactions. This single-step, single-tube, homogeneous detection approach, termed MeltArray, is achieved by coupling the 5′-flap endonuclease activity of the Taq DNA polymerase and multiple annealing sites of the molecular beacon reporters. The 5′-flap endonuclease cleaves a probe specifically into a “mediator” primer, and one molecular beacon reporter allows for the extension of multiple “mediator” primers to produce a series of fluorescent hybrids with different melting temperatures unique to each target. The overall number of targets detectable per reaction is equal to the number of the reporters multiplied by the number of mediator primers per reporter. Real-time PCR is the most utilized nucleic acid testing tool in clinical settings. However, the number of targets detectable per reaction are restricted by current modes. Here, we describe a single-step, multiplex approach capable of detecting dozens of targets per reaction in a real-time PCR thermal cycler. The approach, termed MeltArray, utilizes the 5′-flap endonuclease activity of Taq DNA polymerase to cleave a mediator probe into a mediator primer that can bind to a molecular beacon reporter, which allows for the extension of multiple mediator primers to produce a series of fluorescent hybrids of different melting temperatures unique to each target. Using multiple molecular beacon reporters labeled with different fluorophores, the overall number of targets is equal to the number of the reporters multiplied by that of mediator primers per reporter. The use of MeltArray was explored in various scenarios, including in a 20-plex assay that detects human Y chromosome microdeletions, a 62-plex assay that determines Escherichia coli serovars, a 24-plex assay that simultaneously identifies and quantitates respiratory pathogens, and a minisequencing assay that identifies KRAS mutations, and all of these different assays were validated with clinical samples. MeltArray approach should find widespread use in clinical settings owing to its combined merits of multiplicity, versatility, simplicity, and accessibility.
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Pandey M, Xess I, Sachdev J, Yadav U, Singh G, Pradhan D, Xess AB, Rana B, Dar L, Bakhshi S, Seth R, Mahapatra M, Jyotsna VP, Jain AK, Kumar R, Agarwal R, Mani P. Development of a Sensitive and Specific Novel qPCR Assay for Simultaneous Detection and Differentiation of Mucormycosis and Aspergillosis by Melting Curve Analysis. Front Fungal Biol 2022; 2:800898. [PMID: 37744098 PMCID: PMC10512281 DOI: 10.3389/ffunb.2021.800898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 09/26/2023]
Abstract
Molecular diagnostic assays can expedite the diagnosis of fungal infections, and subsequently help in early interventions and appropriate management of patients. The aim of this study was to develop a single set of primers for a real-time quantitative polymerase chain reaction (qPCR) assay to detect and identify commonly reported, clinically relevant molds i.e., Aspergillus spp, Mucorales and Fusarium spp., up to genus level by melting curve analysis. This assay was evaluated in whole blood from patients with suspected invasive aspergillosis (IA), and in tissue biopsy, bronchoalveolar lavage (BAL) fluid and other site-specific samples from patients with suspected invasive mucormycosis (IM). The limit of detection (LoD) was determined as 10 copies/μl for all three molds. The mean coefficient of variation (CV) across all sets of intra- and inter-assay data was 0.63% (ranging from 0.42 to 1.56%), showing high reproducibility of the assay. Sensitivity and specificity of the assay were 93.3 and 97.1% respectively for diagnosis of IA, and 99.29 and 83.84% respectively for diagnosis of IM. Fusarium was not detected in any of the clinical samples included and the few laboratory confirmed cases of fusariosis did not meet the inclusion criteria of the study. Hence no ROC curve or cutoff value could be generated for the same. This newly developed qPCR assay therefore appears to be a promising tool in detection of IA and IM.
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Affiliation(s)
- Mragnayani Pandey
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Immaculata Xess
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Janya Sachdev
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Usha Yadav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Gagandeep Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Dibyabhaba Pradhan
- ICMR Computational Genomics Centre Informatics, Systems & Research Management Division Indian Council of Medical Research, All India Institute of Medical Sciences, New Delhi, India
| | - Ashit Bhushan Xess
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bhaskar Rana
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rachna Seth
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Manoranjan Mahapatra
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Viveka P. Jyotsna
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - Arun Kumar Jain
- Departments of Environmental Toxicology and Bioinformatics, ICMR-National Institute of Pathology Sri Ramachari Bhawan, Safdarjang Hospital Campus, New Delhi, India
| | - Rakesh Kumar
- Department of Otorhinolaryngology, All India Institute of Medical Sciences, New Delhi, India
| | - Reshu Agarwal
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Prashant Mani
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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17
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Soejima M, Koda Y. Rapid genotyping of 508G>A (rs3745635) and 1067T>A (rs3894326) of FUT3 by a duplex Eprobe-mediated melting curve analysis. Vox Sang 2022; 117:741-745. [PMID: 35020216 DOI: 10.1111/vox.13251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND OBJECTIVES Lewis histo-blood group phenotypes are regulated by the action of FUT3-encoded α(1,3/1,4)fucosyltransferase and FUT2-encoded α(1,2)fucosyltransferase. Since Lewis phenotypes are suggested to be associated with various clinical conditions, a method for large-scale FUT3 genotyping is desirable. In worldwide populations, 508G>A and 1067T>A of FUT3 are two of three common causal single nucleotide polymorphisms for Lewis-negative alleles. MATERIALS AND METHODS We developed a duplex Eprobe-mediated melting curve analysis for genotyping 508G>A and 1067T>A simultaneously and applied this method to 106 Ghanaian and 140 Japanese subjects. RESULTS The results of both 508G>A and 1067T>A genotyping by duplex Eprobe-mediated melting curve analysis were completely in agreement with the results of a DNA sequence analysis in 106 Ghanaians and polymerase chain reaction-restriction fragment length polymorphism analysis in 140 Japanese subjects. CONCLUSION The present duplex Eprobe-mediated melting curve analysis is valid and credible for large-scale estimation of Lewis-negative alleles.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan
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18
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Tani-Sassa C, Iwasaki Y, Ichimura N, Nagano K, Takatsuki Y, Yuasa S, Takahashi Y, Nakajima J, Sonobe K, Nukui Y, Takeuchi H, Tanimoto K, Tanaka Y, Kimura A, Tohda S. Viral loads and profile of the patients infected with SARS-CoV-2 Delta, Alpha, or R.1 variants in Tokyo. J Med Virol 2021; 94:1707-1710. [PMID: 34825717 PMCID: PMC9015476 DOI: 10.1002/jmv.27479] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 01/07/2023]
Abstract
The rapid spread of the Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) became a serious concern worldwide in summer 2021. We examined the copy number and variant types of all SARS‐CoV‐2‐positive patients who visited our hospital from February to August 2021 using polymerase chain reaction (PCR) tests. Whole genome sequencing was performed for some samples. The R.1 variant (B.1.1.316) was responsible for most infections in March, replacing the previous variant (B.1.1.214); the Alpha (B.1.1.7) variant caused most infections in April and May; and the Delta variant (B.1.617.2) was the most prevalent in July and August. There was no significant difference in the copy numbers among the previous variant cases (n = 29, median 3.0 × 104 copies/µl), R.1 variant cases (n = 28, 2.1 × 105 copies/µl), Alpha variant cases (n = 125, 4.1 × 105 copies/µl), and Delta variant cases (n = 106, 2.4 × 105 copies/µl). Patients with Delta variant infection were significantly younger than those infected with R.1 and the previous variants, possibly because many elderly individuals in Tokyo were vaccinated between May and August. There was no significant difference in mortality among the four groups. Our results suggest that the increased infectivity of Delta variant may be caused by factors other than the higher viral loads. Clarifying these factors is important to control the spread of Delta variant infection. There was no significant difference in copy numbers among the previous variant cases, R.1 variant cases, Alpha variant cases, and Delta variant cases. This suggests that the increased infectivity of Delta variant may be caused by factors other than the higher viral loads.
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Affiliation(s)
- Chihiro Tani-Sassa
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yumi Iwasaki
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Naoya Ichimura
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Katsutoshi Nagano
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yuna Takatsuki
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Sonoka Yuasa
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yuta Takahashi
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Jun Nakajima
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Kazunari Sonobe
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yoko Nukui
- Infection Control and Prevention, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, Japan
| | - Kousuke Tanimoto
- Genome Laboratory, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, Japan.,Research Core, Institute of Research, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, Japan
| | - Yukie Tanaka
- Research Core, Institute of Research, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, Japan
| | - Shuji Tohda
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Bunkyo-ku, Tokyo, Japan
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19
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Nagano K, Tani-Sassa C, Iwasaki Y, Takatsuki Y, Yuasa S, Takahashi Y, Nakajima J, Sonobe K, Ichimura N, Nukui Y, Takeuchi H, Tanimoto K, Tanaka Y, Kimura A, Tohda S. SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. J Med Virol 2021; 93:6833-6836. [PMID: 34314050 PMCID: PMC8426954 DOI: 10.1002/jmv.27240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/24/2021] [Indexed: 11/16/2022]
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants, such as B.1.1.7 and B.1.351, has become a crucial issue worldwide. Therefore, we began testing all patients with COVID‐19 for the N501Y and E484K mutations by using polymerase chain reaction (PCR)‐based methods. Nasopharyngeal swab samples from 108 patients who visited our hospital between February and April 2021 were analyzed. The samples were analyzed using reverse transcription‐PCR with melting curve analysis to detect the N501Y and E484K mutations. A part of the samples was also subjected to whole‐genome sequencing (WGS). Clinical parameters such as mortality and admission to the intensive care unit were analyzed to examine the association between increased disease severity and the E484K mutation. The ratio of cases showing the 501N + 484K mutation rapidly increased from 8% in February to 46% in March. WGS revealed that the viruses with 501N + 484K mutation are R.1 lineage variants. Evidence of increased disease severity related to the R.1 variants was not found. We found that the R.1 lineage variants rapidly prevailed in Tokyo in March 2021, which suggests the increased transmissibility of R.1 variants, while they showed no increased severity.
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Affiliation(s)
- Katsutoshi Nagano
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Chihiro Tani-Sassa
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Yumi Iwasaki
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Yuna Takatsuki
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Sonoka Yuasa
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Yuta Takahashi
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Jun Nakajima
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Kazunari Sonobe
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Naoya Ichimura
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Yoko Nukui
- Infection Control and Prevention, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kousuke Tanimoto
- Genome Laboratory, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Research Core, Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yukie Tanaka
- Research Core, Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shuji Tohda
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
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20
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Camp JV, Buchta C, Jovanovic J, Puchhammer-Stöckl E, Benka B, Griesmacher A, Aberle SW, Goerzer I. RT-PCR based SARS-CoV-2 variant screening assays require careful quality control. J Clin Virol 2021; 141:104905. [PMID: 34273859 PMCID: PMC8262392 DOI: 10.1016/j.jcv.2021.104905] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/31/2022]
Abstract
Background Distinctive genotypes of SARS-CoV-2 have emerged that are or may be associated with increased transmission, pathogenicity, and/or antibody escape. In many countries, clinical and diagnostic laboratories are under mandate to identify and report these so-called variants of concern (VOC). Objectives We used an external quality assessment scheme to determine the scope, accuracy, and reliability of laboratories using various molecular diagnostic assays to identify current VOC (03 March 2021). Study design Participant laboratories were sent the same five patient-derived samples and were asked to provide their variant detection methods, variant detection results and interpretation of results. Results Twenty-five laboratories reported a range of RT-qPCR-based assays to identify specific variations in the SARS-CoV-2 spike protein that are characteristic of three VOC lineages. Laboratories that detected VOC-associated nucleotide mutations at four specific sites had the highest ratio of correct classification. Low template copy number and additional variation in target regions resulted in loss of confidence and accuracy in sample classification. Conclusions Melting-curve-based assays to identify genomic variants are less time-consuming and require less bioinformatic analysis compared to partial or whole genome sequencing. However, our results suggest that correct classification of a given genotype/lineage (e.g., a VOC) relies on the ability to detect more than one variant site, adequate template in the sample (i.e., relatively high viral load/copy number) and results may be unclear in certain samples with additional genetic variations. These initial results suggest that some diagnostic laboratories may require additional training to interpret and report complex genetic information about a dynamic emerging virus.
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Affiliation(s)
- Jeremy V Camp
- Center for Virology, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Christoph Buchta
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Hörlgasse 18/5, 1090 Vienna, Austria
| | - Jovana Jovanovic
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Hörlgasse 18/5, 1090 Vienna, Austria
| | | | - Bernhard Benka
- Federal Ministry of Social Affairs, Health, Care and Consumer Protection, Stubenring 1, 1010, Vienna, Austria
| | - Andrea Griesmacher
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Hörlgasse 18/5, 1090 Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Irene Goerzer
- Center for Virology, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria.
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21
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Oscorbin IP, Shevelev GY, Pronyaeva KA, Stepanov AA, Shamovskaya DV, Mishukova OV, Pyshnyi DV, Filipenko ML. Detection of SARS-CoV-2 RNA by a Multiplex Reverse-Transcription Loop-Mediated Isothermal Amplification Coupled with Melting Curves Analysis. Int J Mol Sci 2021; 22:5743. [PMID: 34072209 DOI: 10.3390/ijms22115743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a method of nucleic acid amplification that is more stable and resistant to DNA amplification inhibitors than conventional PCR. LAMP multiplexing with reverse transcription allows for the single-tube amplification of several RNA fragments, including an internal control sample, which provides the option of controlling all analytical steps. We developed a method of SARS-CoV-2 viral RNA detection based on multiplex reverse-transcription LAMP, with single-tube qualitative analysis of SARS-CoV-2 RNA and MS2 phage used as a control RNA. The multiplexing is based on the differences in characteristic melting peaks generated during the amplification process. The developed technique detects at least 20 copies of SARS-CoV-2 RNA per reaction on a background of 12,000 MS2 RNA copies. The total time of analysis does not exceed 40 min. The method validation, performed on 125 clinical samples of patients' nasal swabs, showed a 97.6% concordance rate with the results of real-time (RT)-PCR assays. The developed multiplexed LAMP can be employed as an alternative to PCR in diagnostic practice to save personnel and equipment time.
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22
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Orrù G, Scano A, Fais S, Loddo M, Carta MG, Steri GC, Santus S, Cappai R, Ferrando ML, Coghe F. Evaluation of " Caterina assay": An Alternative Tool to the Commercialized Kits Used for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Identification. Pathogens 2021; 10:325. [PMID: 33802049 PMCID: PMC7998653 DOI: 10.3390/pathogens10030325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Here we describe the first molecular test developed in the early stage of the pandemic to diagnose the first cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Sardinian patients in February-March 2020, when diagnostic certified methodology had not yet been adopted by clinical microbiology laboratories. The "Caterina assay" is a SYBR®Green real-time reverse-transcription polymerase chain reaction (rRT-PCR), designed to detect the nucleocapsid phosphoprotein (N) gene that exhibits high discriminative variation RNA sequence among bat and human coronaviruses. The molecular method was applied to detect SARS-CoV-2 in nasal swabs collected from 2110 suspected cases. The study article describes the first molecular test developed in the early stage of the declared pandemic to identify the coronavirus disease 2019 (COVID-19) in Sardinian patients in February-March 2020, when a diagnostic certified methodology had not yet been adopted by clinical microbiology laboratories. The assay presented high specificity and sensitivity (with a detection limit ≥50 viral genomes/μL). No false-positives were detected, as confirmed by the comparison with two certified commercial kits. Although other validated molecular methods are currently in use, the Caterina assay still represents a valid and low-cost detection procedure that could be applied in countries with limited economic resources.
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Affiliation(s)
- Germano Orrù
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Alessandra Scano
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Sara Fais
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
| | - Miriam Loddo
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Mauro Giovanni Carta
- Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy;
| | - Giorgio Carlo Steri
- Azienda per la Tutela della Salute (ATS), Aree Socio-Sanitarie Locali (ASSL) of Cagliari, 09131 Cagliari, Italy; (G.C.S.); (S.S.)
| | - Simonetta Santus
- Azienda per la Tutela della Salute (ATS), Aree Socio-Sanitarie Locali (ASSL) of Cagliari, 09131 Cagliari, Italy; (G.C.S.); (S.S.)
| | - Riccardo Cappai
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Maria Laura Ferrando
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
| | - Ferdinando Coghe
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
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23
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Wen X, Chen Q, Yin H, Wu S, Wang X. Rapid identification of clinical common invasive fungi via a multi-channel real-time fluorescent polymerase chain reaction melting curve analysis. Medicine (Baltimore) 2020; 99:e19194. [PMID: 32049856 PMCID: PMC7035122 DOI: 10.1097/md.0000000000019194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/31/2019] [Accepted: 01/15/2020] [Indexed: 01/25/2023] Open
Abstract
The incidence of invasive fungal infections (IFIs) has recently increased, and early and accurate diagnosis of IFIs is important for the rational selection of antifungal drugs with high efficacy. We developed a method for rapid and accurate clinical diagnosis of IFIs and provide a reference for personalized drug treatment.We designed and screened fungal internal transcribed spacer regions with universal primers and designed 8 TaqMan detection probes to establish a multi-channel real-time fluorescent polymerase chain reaction (PCR) melting curve analysis (MCA) method. The sensitivity, specificity, and reproducibility of this method were investigated using standard fungal strains and clinical isolates. Candidemia was detected using the MCA method.The limit of detection and assay cut-off (melting temperature [Tm]) for Candida albicans were 0.05 pg/μL and 66.50 °C; Candida glabrata were 0.1 pg/μL and 66.25 °C; Candida tropicalis were 0.1 pg/μL and 60.15 °C; Candida krusei were 0.1 pg/μL and 72.15 °C; Candida parapsilosis were 0.2 pg/μL and 63.10 °C; Candida guilliermondii were 0.1 pg/μL and 61.84 °C; Cryptococcus neoformans were 0.1 pg/μL and 65.50 °C; Aspergillus flavus were 0.05 pg/μL and 71.50 °C; Aspergillus terreus, Aspergillus fumigatus, and Aspergillus niger were 0.05 pg/μL and 76.80 °C. Analytical specificity was evaluated using 13 clinical pathogens including Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae, etc. No false-positive results were obtained for any of these samples. The MCA method can detect and identify different candidemia simulations. The limit detection concentration of C albicans was 44 cfu/mL, C glabrata was 73 cfu/mL, C tropicalis was 29 cfu/mL, C parapsilosis was 21 cfu/mL, C krusei was 71 cfu/mL, and C guilliermondii was 53 cfu/mL.The multi-channel real-time fluorescence PCR melting curve analysis displayed high sensitivity and specificity in detecting various clinically invasive fungi. Furthermore, it simultaneously detected the genera Candida, Cryptococcus, and Aspergillus and identified Candida at the species level. Our method can facilitate early and accurate clinical diagnosis and personalized medication regimens.
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Affiliation(s)
- Xiaozi Wen
- Department of The Fourth Clinical Medical College affiliated to Zhejiang Chinese Medical University
| | - Qiong Chen
- Department of Clinical Laboratory, Hangzhou First People's Hospital affiliated to Zhejiang Chinese Medical University
| | - Huali Yin
- Department of Research and Development, Hangzhou Qianji Biological Technology Co., Ltd., Hangzhou, China
| | - Shenghai Wu
- Department of Clinical Laboratory, Hangzhou First People's Hospital affiliated to Zhejiang Chinese Medical University
| | - Xianjun Wang
- Department of Clinical Laboratory, Hangzhou First People's Hospital affiliated to Zhejiang Chinese Medical University
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Kim YT, Moon J, Hong IS. Simultaneous Detection of Multiple Pathogenic Targets with Stem-Tagged Primer Sets. Chembiochem 2020; 21:1116-1120. [PMID: 31705704 DOI: 10.1002/cbic.201900668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 11/07/2022]
Abstract
Simultaneous multiple gene detection is indispensable for the detection of various genes in a small sample obtained by an invasive method. A typical detection method is probe-based fluorescence melting curve analysis by means of real-time PCR. It is very limited because, for each target, a probe sequence with at least a different Tm must be designed. To overcome this limitation, we developed a simultaneous multiple gene detection method based on a giant amplicon molecular beacon. PCR was performed by attaching stem sequences with different Tm values to each primer set, and the melting Tm was measured by hybridizing the stem sequences at both ends of the amplified amplicon; this generated well-separated Tm signals. The important point here is that the stem sequence that produces the Tm signal is an arbitrarily selectable sequence unrelated to the target gene. Because it is arbitrarily selectable, the desired Tm can be freely adjusted. As a result, we succeeded in the simultaneous detection of four samples with the use of only one fluorophore. Theoretically, a combination of five fluorophores could detect more than 20 multiple genes simultaneously.
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Affiliation(s)
- Yong-Tae Kim
- Department of Chemistry, College of Natural Science, Kongju National University, 56, Gongjudaehak-ro, Gongju-si, Chungnam, 32588, Republic of Korea
| | - Junhye Moon
- Research Institute, Sejong Medical Co. Ltd., 11, Sinchon 2-ro, Paju-si, Gyeonggi-do, 10880, Republic of Korea
| | - In Seok Hong
- Department of Chemistry, College of Natural Science, Kongju National University, 56, Gongjudaehak-ro, Gongju-si, Chungnam, 32588, Republic of Korea
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25
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Lyozin GT, Brunelli L. Live-cell PCR and one-step purification streamline DNA engineering. FASEB J 2020; 34:3448-3460. [PMID: 31944382 DOI: 10.1096/fj.201902261r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/21/2019] [Accepted: 12/16/2019] [Indexed: 01/12/2023]
Abstract
In vivo DNA engineering such as recombineering (recombination-mediated genetic engineering) and DNA gap repair typically involve growing Escherichia coli (E coli) containing plasmids, followed by plasmid DNA extraction and purification prior to downstream PCR-mediated DNA modifications and DNA sequencing. We previously demonstrated that crude cell lysates could be used for some limited downstream DNA applications. Here, we show how live E coli cell PCR and one-step LiCl-isopropanol purification can streamline DNA engineering. In DNA gap repair, live-cell PCR allowed the convenient elimination of clones containing background plasmids prior to DNA sequencing. Live-cell PCR also enabled the generation of specific DNA sequences for DNA engineering up to 11 kilo base pairs in length and with up to 80 base pair terminal non-homology. Using gel electrophoresis and DNA melting curve analysis, we showed that LiCl-isopropanol DNA precipitation removed primers and small, nonspecific PCR products from live-cell PCR products in only ~10-minutes. DNA sequencing of purified products yielded Phred quality scores values of ~55%. These data indicate that live-cell PCR and LiCl-isopropanol DNA precipitation are ideal to prepare DNA for sequencing and other downstream DNA applications, and might therefore accelerate high-throughput DNA engineering pipelines.
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Affiliation(s)
- George T Lyozin
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Luca Brunelli
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
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Kisoi M, Moritsugu M, Imai M, Fukumoto K, Sakaguchi Y, Murata S, Kawai S, Ichikawa A, Kinoshita K. Rapid and Cost-Effective Genotyping Protocol for Angiotensin-Converting Enzyme Insertion/Deletion (Ins/Del) Polymorphism from Saliva. Biol Pharm Bull 2019; 42:1345-1349. [PMID: 31366869 DOI: 10.1248/bpb.b19-00110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA extraction and purification have been generally considered to be required for PCR assay. We demonstrated a new protocol using biological specimens directly as templates for real-time PCR with melting curve analysis. We confirmed the melting curve analysis was particularly suitable for the identification of the insertion/deletion (Ins/Del) polymorphism of the angiotensin-converting enzyme (ACE) gene. The new protocol we developed can be set up using simple and complete PCR analysis including data interpretation in under four hours with additional advantages of application for large-scale clinical research, diagnostics, and epidemiological studies at low cost.
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Affiliation(s)
- Madoka Kisoi
- School of Pharmaceutical Sciences, Mukogawa Women's University
| | | | - Miho Imai
- School of Pharmaceutical Sciences, Mukogawa Women's University
| | - Kae Fukumoto
- School of Pharmaceutical Sciences, Mukogawa Women's University
| | - Yui Sakaguchi
- School of Pharmaceutical Sciences, Mukogawa Women's University
| | - Shigenori Murata
- School of Pharmaceutical Sciences, Mukogawa Women's University.,Institute of Biosciences, Mukogawa Women's University
| | - Sayuri Kawai
- Institute of Biosciences, Mukogawa Women's University
| | | | - Kenji Kinoshita
- School of Pharmaceutical Sciences, Mukogawa Women's University.,Institute of Biosciences, Mukogawa Women's University
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Xu Y, Liang B, Du C, Tian X, Cai X, Hou Y, Li H, Zheng R, Li J, Liu Y, Wang K, Ammar Athar M, Tan Y, Li Q. Rapid Identification of Clinically Relevant Mycobacterium Species by Multicolor Melting Curve Analysis. J Clin Microbiol 2019; 57:e01096-18. [PMID: 30333128 DOI: 10.1128/JCM.01096-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/07/2018] [Indexed: 11/20/2022] Open
Abstract
The sustained increase in the incidence of nontuberculous mycobacterial (NTM) infection and the difficulty in distinguishing these infections from tuberculosis constitute an urgent need for NTM species-level identification. The MeltPro Myco assay is the first diagnostic system that identifies 19 clinically relevant mycobacteria in a single reaction based on multicolor melting curve analysis run on a real-time PCR platform. The assay was comprehensively evaluated regarding its analytical and clinical performances. The MeltPro Myco assay accurately identified 51 reference mycobacterial strains to the species/genus level and showed no cross-reactivity with 16 nonmycobacterial strains. The limit of detection was 300 bacilli/ml, and 1% of the minor species was detected in the case of mixed infections. Clinical studies using 1,163 isolates collected from five geographically distinct health care units showed that the MeltPro Myco assay correctly identified 1,159 (99.7%) samples. Further testing with 94 smear-positive sputum samples showed that all samples were correctly identified. Additionally, the entire assay can be performed within 3 h. The results of this study confirmed the efficacy of this assay in the reliable identification of mycobacteria, suggesting that it might potentially be used as a screening tool in regions endemic for tuberculosis.
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Arastehfar A, Fang W, Daneshnia F, Al-Hatmi AM, Liao W, Pan W, Khan Z, Ahmad S, Rosam K, Lackner M, Lass-Flörl C, Hagen F, Boekhout T. Novel multiplex real-time quantitative PCR detecting system approach for direct detection of Candida auris and its relatives in spiked serum samples. Future Microbiol 2018; 14:33-45. [PMID: 30539665 DOI: 10.2217/fmb-2018-0227] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The multidrug-resistant opportunistic yeast species of Candida auris, Candida haemulonii, Candida duobushaemulonii and Candida pseudohaemulonii continue to endanger the healthcare settings around the globe. Due to the lack of a specific qPCR assay for detection of these species from clinical samples, we developed a multiplex qPCR assay. Analytical specificity and sensitivity showed 100% specificity and the sensitivity of up to ten genomes of target species with a high value of reproducibility (R2 >0.99). Subsequently, from spiked serum samples, our qPCR specifically could detect up to ten genomes of C. auris and one genome of C. haemulonii, C. duobushaemulonii and C. pseudohaemulonii (R2 >0.98). Lack of cross reaction with the human DNA, a high degree of specificity and sensitivity, showed the potential of our multiplex PCR for direct detection of C. auris and closely related species from serum samples of suspected patients. Future studies are warranted to assure its applicability in clinical settings.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands
| | - Wenjie Fang
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands.,Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands
| | - Abdullah Ms Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands.,Center of Expertise in Mycology Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen 6500HB, The Netherlands.,Ministry of Health, Directorate General of Health Services, PO Box 393, 100 Muscat, Oman
| | - Wanqing Liao
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Weihua Pan
- Department of Dermatology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China
| | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Katharina Rosam
- Division of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michaela Lackner
- Division of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584, The Netherlands.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, PR China.,Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam 1012 WX, The Netherlands
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Zeng X, Xu Y, Zhou Y, Li H, Zheng R, Tan Y, Sun B, Zhao Y, Li Q. McSpoligotyping, a One-Step Melting Curve Analysis-Based Protocol for Spoligotyping of Mycobacterium tuberculosis. J Clin Microbiol 2018; 56:e00539-18. [PMID: 29875194 DOI: 10.1128/JCM.00539-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/31/2018] [Indexed: 11/20/2022] Open
Abstract
The direct repeat (DR) region in the Mycobacterium tuberculosis (MTB) genome is composed of highly polymorphic direct variant repeats, which are the basis of spacer oligonucleotide typing (spoligotyping) to study the population structure and epidemiology of M. tuberculosis However, the membrane hybridization-based detection format requires various post-PCR manipulations and is prone to carryover contamination, restricting its wide use in high-TB-burden and resource-limited countries. We developed a one-step spoligotyping protocol, termed McSpoligotyping, based on real-time PCR. The typing results can be generated within 3 h by a single step of DNA addition. When evaluated with a collection of 1,968 isolates of MTB, McSpoligotyping agreed 97.71% (1,923/1,968) by sample and 99.93% (84,568/84,624) by spacer with traditional spoligotyping. Sequencing results showed that McSpoligotyping was even more accurate than spoligotyping (99.34% versus 98.37%). Further exploration of the false results of McSpoligotyping revealed the presence of single-nucleotide polymorphisms in the DR region. We concluded that McSpoligotyping could be used in epidemiology studies of tuberculosis by taking advantage of the shortened procedure, ease of use, and compatibility of results with standard spoligotyping.
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Postina P, Skladny J, Boch T, Cornely OA, Hamprecht A, Rath PM, Steinmann J, Bader O, Miethke T, Dietz A, Merker N, Hofmann WK, Buchheidt D, Spiess B. Comparison of Two Molecular Assays for Detection and Characterization of Aspergillus fumigatus Triazole Resistance and Cyp51A Mutations in Clinical Isolates and Primary Clinical Samples of Immunocompromised Patients. Front Microbiol 2018; 9:555. [PMID: 29662479 PMCID: PMC5890139 DOI: 10.3389/fmicb.2018.00555] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/12/2018] [Indexed: 11/23/2022] Open
Abstract
In hematological patients, the incidence of invasive aspergillosis (IA) caused by azole resistant Aspergillus fumigatus (ARAf) is rising. As the diagnosis of IA is rarely based on positive culture in this group of patients, molecular detection of resistance mutations directly from clinical samples is crucial. In addition to the in-house azole resistance ARAf polymerase chain reaction (PCR) assays detecting the frequent mutation combinations TR34/L98H, TR46/Y121F/T289A, and M220 in the Aspergillus fumigatus (A. fumigatus) Cyp51A gene by subsequent DNA sequence analysis, we investigated in parallel the commercially available AsperGenius® real time PCR system in detecting the Cyp51A alterations TR34/L98H and Y121F/T289A directly from 52 clinical samples (15 biopsies, 22 bronchoalveolar lavage (BAL), 15 cerebrospinal fluid (CSF) samples) and ARAf isolates (n = 3) of immunocompromised patients. We analyzed DNA aliquots and compared both methods concerning amplification and detection of Aspergillus DNA and Cyp51A alterations. As positive control for the feasibility of our novel Y121F and T289A PCR assays, we used two A. fumigatus isolates with the TR46/Y121F/T289A mutation combination isolated from hematological patients with known Cyp51A alterations and a lung biopsy sample of a patient with acute myeloid leukemia (AML). The rate of positive ARAf PCR results plus successful sequencing using the ARAf PCR assays was 61% in biopsies, 29% in CSF, 67% in BAL samples and 100% in isolates. In comparison the amount of positive PCRs using the AsperGenius® assays was 47% in biopsies, 42% in CSF, 59% in BAL samples and 100% in isolates. Altogether 17 Cyp51A alterations were detected using our ARAf PCRs plus DNA sequencing and therefrom 10 alterations also by the AsperGenius® system. The comparative evaluation of our data revealed that our conventional PCR assays are more sensitive in detecting ARAf in BAL and biopsy samples, whereby differences were not significant. The advantage of the AsperGenius® system is the time saving aspect. We consider non-culture based molecular detection of Aspergillus triazole resistance to be of high epidemiological and clinical relevance in patients with hematological malignancies.
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Affiliation(s)
- Patricia Postina
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Julian Skladny
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Tobias Boch
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Oliver A Cornely
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,Clinical Trials Centre Cologne, ZKS Köln and Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Axel Hamprecht
- Institute of Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, Essen, Germany
| | - Jörg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Miethke
- Institute of Medical Microbiology and Hygiene, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Anne Dietz
- Institute of Medical Microbiology and Hygiene, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Natalia Merker
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Dieter Buchheidt
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Birgit Spiess
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
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Liang B, Tan Y, Li Z, Tian X, Du C, Li H, Li G, Yao X, Wang Z, Xu Y, Li Q. Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium tuberculosis by DeepMelt Assay. J Clin Microbiol 2018; 56:e01239-17. [PMID: 29118176 DOI: 10.1128/JCM.01239-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022] Open
Abstract
Detection of heteroresistance of Mycobacterium tuberculosis remains challenging using current genotypic drug susceptibility testing methods. Here, we described a melting curve analysis-based approach, termed DeepMelt, that can detect less-abundant mutants through selective clamping of the wild type in mixed populations. The singleplex DeepMelt assay detected 0.01% katG S315T in 105M. tuberculosis genomes/μl. The multiplex DeepMelt TB/INH detected 1% of mutant species in the four loci associated with isoniazid resistance in 104M. tuberculosis genomes/μl. The DeepMelt TB/INH assay was tested on a panel of DNA extracted from 602 precharacterized clinical isolates. Using the 1% proportion method as the gold standard, the sensitivity was found to be increased from 93.6% (176/188, 95% confidence interval [CI] = 89.2 to 96.3%) to 95.7% (180/188, 95% CI = 91.8 to 97.8%) compared to the MeltPro TB/INH assay. Further evaluation of 109 smear-positive sputum specimens increased the sensitivity from 83.3% (20/24, 95% CI = 64.2 to 93.3%) to 91.7% (22/24, 95% CI = 74.2 to 97.7%). In both cases, the specificity remained nearly unchanged. All heteroresistant samples newly identified by the DeepMelt TB/INH assay were confirmed by DNA sequencing and even partially by digital PCR. The DeepMelt assay may fill the gap between current genotypic and phenotypic drug susceptibility testing for detecting drug-resistant tuberculosis patients.
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Basyoni MMA, Elghobary HAF. Genotypic Identification of Cystoisospora in Immunocompromised Patients Using Tm-Variation Analysis. Korean J Parasitol 2018; 55:601-606. [PMID: 29320814 PMCID: PMC5776892 DOI: 10.3347/kjp.2017.55.6.601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/04/2017] [Accepted: 11/24/2017] [Indexed: 01/05/2023]
Abstract
Cystoisospora is responsible for morbidity in immunocompromised patients. PCR is sensitive for diagnosing Cystoisospora; however, it needs reevaluation for differential molecular diagnosis of cystoisosporiasis. We aimed at evaluating melting curve analysis (MCA) after real-time PCR (qPCR) in diagnosis and genotyping of Cystoisospora as an alternative to conventional PCR. We included 293 diarrheic stool samples of patients attending the Department of Clinical Oncology and Nuclear Medicine of Cairo University Hospitals, Egypt. Samples were subjected to microscopy, nested PCR (nPCR), and qPCR targeting the internal transcribed spacer 2 region (ITS2) of the ribosomal RNA (r RNA) gene followed by melting temperatures (Tms) analysis and comparing the results to PCR-RFLP banding patterns. Using microscopy and ITS2-nPCR, 3.1% and 5.8% of cases were Cystoisospora positive, respectively, while 10.9% were positive using qPCR. Genotyping of Cystoisospora by qPCR-MCA revealed 2 genotypes. These genotypes matched with 2 distinct melting peaks with specified Tms at 85.8°C and 88.6°C, which indicated genetic variation among Cystoisospora isolates in Egypt. Genotype II proved to be more prevalent (65.6%). HIV-related Kaposi sarcoma and leukemic patients harbored both genotypes with a tendency to genotype II. Genotype I was more prevalent in lymphomas and mammary gland tumors while colorectal and hepatocellular tumors harbored genotype II suggesting that this genotype might be responsible for the development of cystoisosporiasis in immunocompromised patients. Direct reliable identification and differentiation of Cystoisospora species could be established using qPCR-Tms analysis which is useful for rapid detection and screening of Cystoisospora genotypes principally in high risk groups.
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Affiliation(s)
- Maha M A Basyoni
- Parasitology Department, Faculty of Medicine, Cairo University, Egypt
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Balog JA, Fehér LZ, Puskás LG. Decoding DNA labels by melting curve analysis using real-time PCR. Biotechniques 2017; 63:261-6. [PMID: 29235972 DOI: 10.2144/000114618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/31/2017] [Indexed: 11/23/2022] Open
Abstract
Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.
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Kim WJ, Yang S, Choi G, Moon BC. Peptide Nucleic Acid Based Molecular Authentication for Identification of Four Medicinal Paeonia Species Using Melting Array Analysis of the Internal Transcribed Spacer 2 Region. Molecules 2017; 22:E1922. [PMID: 29112146 PMCID: PMC6150393 DOI: 10.3390/molecules22111922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/03/2017] [Accepted: 11/03/2017] [Indexed: 11/16/2022] Open
Abstract
Accurate taxonomic identification of plant materials in herbal medicines is important for product quality control. The genus Paeonia (Saxifragales) is the source of the herbal preparations Paeoniae Radix (Paeoniae Radix Alba and Paeoniae Radix Rubra) and Moutan Radicis Cotex. However, confusion has arisen regarding their contents due to linguistic and taxonomic ambiguities, similar morphologies and different definitions of Paeoniae Radix in the Korean and Chinese national pharmacopoeias, leading to the distribution of adulterated products. To develop a method for identifying the four Paeonia species used in these medicines, three fluorescently-labeled peptide nucleic acid (PNA) probes were designed against ITS2 sequences containing single nucleotide polymorphisms (SNPs) and used in a real-time PCR melting curve assay. Each of the four Paeonia species was accurately identified using this analysis. The accuracy and analytical stability of the PNA melting curve assay was confirmed using commercially available samples of the four Paeonia species. This assay is a reliable genetic tool to distinguish between different Paeonia-derived herbal medicines and identify the botanical origins of Paeoniae Radix and Moutan Radicis Cortex. This technique may also contribute to quality control and standardization of herbal medicines by providing a reliable authentication tool and preventing the distribution of inauthentic adulterants.
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Affiliation(s)
- Wook Jin Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
| | - Sungyu Yang
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
| | - Goya Choi
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
| | - Byeong Cheol Moon
- K-herb Research Center, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon 305-811, Korea.
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Rajan-Babu IS, Chong SS. Molecular Correlates and Recent Advancements in the Diagnosis and Screening of FMR1-Related Disorders. Genes (Basel) 2016; 7:E87. [PMID: 27754417 DOI: 10.3390/genes7100087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 12/12/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common monogenic cause of intellectual disability and autism. Molecular diagnostic testing of FXS and related disorders (fragile X-associated primary ovarian insufficiency (FXPOI) and fragile X-associated tremor/ataxia syndrome (FXTAS)) relies on a combination of polymerase chain reaction (PCR) and Southern blot (SB) for the fragile X mental retardation 1 (FMR1) CGG-repeat expansion and methylation analyses. Recent advancements in PCR-based technologies have enabled the characterization of the complete spectrum of CGG-repeat mutation, with or without methylation assessment, and, as a result, have reduced our reliance on the labor- and time-intensive SB, which is the gold standard FXS diagnostic test. The newer and more robust triplet-primed PCR or TP-PCR assays allow the mapping of AGG interruptions and enable the predictive analysis of the risks of unstable CGG expansion during mother-to-child transmission. In this review, we have summarized the correlation between several molecular elements, including CGG-repeat size, methylation, mosaicism and skewed X-chromosome inactivation, and the extent of clinical involvement in patients with FMR1-related disorders, and reviewed key developments in PCR-based methodologies for the molecular diagnosis of FXS, FXTAS and FXPOI, and large-scale (CGG)n expansion screening in newborns, women of reproductive age and high-risk populations.
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Kawaguchi-Ihara N, Itoh M, Murohashi I, Tohda S. Establishment of a quenching probe method for detection of NPM1 mutations in acute myeloid leukemia cells. Oncol Lett 2016; 11:2429-2432. [PMID: 27073492 DOI: 10.3892/ol.2016.4225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/26/2016] [Indexed: 12/31/2022] Open
Abstract
Nucleophosmin (NPM1) mutations, generally consisting of a four base-pair insertion, are present in ~60% of all cytogenetically normal acute myeloid leukemia (AML) cases. The mutation is clinically significant as an important prognostic factor. Direct sequencing is the current standard method of mutation detection, however, it is quite costly and time consuming. The present study aimed to establish a highly sensitive quenching probe (QP) method to detect NPM1 mutations efficiently. Melting curve analysis was performed using a QP, following polymerase chain reaction for amplification of the involved region of the gene. The curve derived from the fluorescent intensity with respect to the temperature of OCI/AML3, a heterozygous NPM1 mutant AML cell line, was W-shaped with melting peaks at 61°C and 68°C. That of M-07e, the homozygous wild type cell line, was V-shaped with a melting peak at 68°C. Thus, the curve derived from the mutant allele was easily discriminated from that of the wild-type allele. The mutant allele was detected in concentrations as low as 3% as determined by a subsequent sensitivity study. With a short testing time and a high sensitivity, this assay was applicable for NPM1-mutated AML patient samples and is appropriate for screening NPM1 mutations. It does require further examination as to whether it would be useful as a detection method for other mutant alleles since NPM1 mutations may consist of 61 known types of mutant sequences. To the best of our knowledge, this is the first report describing the QP method for the detection of NPM1 mutations.
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Affiliation(s)
- Noriko Kawaguchi-Ihara
- Department of Laboratory Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8519, Japan; Department of Health Sciences, Saitama Prefectural University, Koshigaya, Saitama 343-8540, Japan
| | - Mai Itoh
- Department of Laboratory Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Ikuo Murohashi
- Department of Health Sciences, Saitama Prefectural University, Koshigaya, Saitama 343-8540, Japan
| | - Shuji Tohda
- Department of Laboratory Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8519, Japan
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Abstract
Antelope horn is a valuable Chinese traditional medicine and widely used in clinic. However, with the deterioration of antelope's living environment and a lot of killing, the saiga population begins falling and in some places plummet. Since the increasing demand of this expensive and good bioactive medicine, the horn of artiodactyla animals is often used as the antelope horn. The adulterated or impostor not only cause damage to clinical medicine but also affect the antelope resources protection and sustainable development. Here, in order to establish a melting curve analysis (MCA) method to distinguish the antelope horn from other animal horns and identify the decoction pieces and Chinese patent medicine in a fast and easy way, animal horns and its decoction pieces, Chinese patent medicines were collected from the market and the DNA of all the collected samples were extracted. The melting curve of two universal fragments (COI and Cyt b) was scanned and Cyt b was selected as feasibility fragment for identifying authentic antelope horn from eight adulterant animal horns. After optimizing the condition for MCA, inspecting the precision and the replication of the method, a reference melting curve modern was established and we performed MCA on the antelope horns, fakes, and adulterants on a 1:1 mix, decoction pieces, and Chinese patent medicine. Thus, this study provides fast and easy methods so that MCA can detect the truth, fakes, and adulterations of antelope horns.
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Affiliation(s)
- Yuru Tong
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and.,b School of Traditional Chinese Medicine , Capital Medical University , Beijing , PR China
| | - Chao Jiang
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Yuan Yuan
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Yan Jin
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Zhan-Hu Cui
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Luqi Huang
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and.,b School of Traditional Chinese Medicine , Capital Medical University , Beijing , PR China
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Chaudhary AG, Hussein IR, Abuzenadah A, Gari M, Bassiouni R, Sogaty S, Lary S, Al-Quaiti M, Al Balwi M, Al Qahtani M. Molecular diagnosis of fragile X syndrome using methylation sensitive techniques in a cohort of patients with intellectual disability. Pediatr Neurol 2014; 50:368-76. [PMID: 24630283 DOI: 10.1016/j.pediatrneurol.2013.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/04/2013] [Accepted: 11/23/2013] [Indexed: 11/26/2022]
Abstract
BACKGROUND Fragile X syndrome, the most common form of inherited intellectual disability, is caused by expansion of CGG trinucleotide repeat at the 5' untranslated region of the FMR1 gene at Xq27. In affected individuals, the CGG repeat expansion leads to hypermethylation and the gene is transcriptionally inactive. Our aim was to identify fragile X syndrome among children with intellectual disability in Saudi Arabia. PATIENTS AND METHODS The study included 63 patients (53 males, 10 females) presented with intellectual disability, 29 normal subjects, and 23 other family members. DNA samples from six patients previously diagnosed with fragile X syndrome by Southern blot technique were used as positive controls. The method was based on bisulfite treatment of DNA followed by two different techniques. The first technique applied polymerase chain reaction amplification using one set of primers specific for amplifying methylated CpG dinucleotide region; another set designed to amplify the unmethylated CGG repeats. The second technique used the methylation-specific melting curve analysis for detection of methylation status of the FMR1 promoter region. RESULTS Molecular testing using methylation sensitive polymerase chain reaction had shown amplified products in all normal subjects using unmethylated but not methylated primers indicating normal alleles, whereas amplified products were obtained using methylated polymerase chain reaction primers in fragile X syndrome-positive samples and in 9 of 53 males, indicating affected individuals. Molecular testing using melting curve analysis has shown a single low melting peak in all normal males and in (44/53) patients indicating unmethylated FMR1 gene, whereas high melting peak indicating methylated gene was observed in the fragile X syndrome-positive samples and in 9 of 53 patients. We found 100% concordance between results of both techniques and the results of Southern blot analysis. Three samples have shown both methylated and unmethylated alleles, indicating possible mosaicism. No female patients or carriers could be detected by both techniques. CONCLUSION The technique can be applied for the rapid screening for fragile X syndrome among patients with intellectual disability. The impact of mosaicism on clinical severity needs further investigation.
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Affiliation(s)
- Adeel G Chaudhary
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ibtessam R Hussein
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Adel Abuzenadah
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mamdouh Gari
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Randa Bassiouni
- Pediatric Hospital, Ministry of Health, Al Taif, Kingdom of Saudi Arabia
| | | | - Sahira Lary
- Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Maha Al-Quaiti
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammed Al Balwi
- King Abdulaziz Medical City for National Guard Health Affairs, and King Saud bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Al Qahtani
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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Kaya AD, Oztürk CE, Akcan Y, Behçet M, Karakoç AE, Yücel M, Mısırlıoglu M, Tuncer S. Prevalence of Helicobacter pylori in symptomatic patients and detection of clarithromycin resistance using melting curve analysis. Curr Ther Res Clin Exp 2014; 68:151-60. [PMID: 24683206 DOI: 10.1016/j.curtheres.2007.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2007] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Abstract. BACKGROUND Clarithromycin is often a component of combination therapies for Helicobacter pylori eradication; however, increases in resistance rates have decreased the success of the treatment. OBJECTIVE This study was designed to determine the prevalence of H pylori infection in symptomatic patients and to detect clarithromycin resistance rates using melting curve analysis. METHODS Patients scheduled for upper endoscopy at the Endoscopy Unit of the Department of Gastroenterology, Duzce University, Medical Faculty Hospital, Konuralp/Duzce, Turkey, were assessed for enrollment in the study. Two pairs of gastric biopsy specimens (antrum and corpus) were obtained from each study patient. Histopathologic examination, rapid urease test, culture, and polymerase chain reaction (PCR) of the specimens were used to identify H pylori infection. Clarithromycin resistance was detected using melting curve analysis. RESULTS Seventy-five patients (41 women, 34 men; mean [SD]age, 42.6 [14.5] years [range, 17-70 years]) were included in the study. Using histopathology and rapid urease test, H pylori was detected in 40 (53.3%) of the 75 specimens. H pylori was detected using PCR in 40 (53.3%) specimens and by culture in 10 (13.3%) specimens. The specificity and sensitivity of PCR and culture were interpreted by comparing them with the results of histopathologic examination and urease tests. The specificity and sensitivity of PCR were 68.6% and 72.5%, respectively, and the specificity and sensitivity of culture were 97.1% and 22.5%, respectively. Of the 40 isolates, 21 (52.5%) were susceptible to clarithromycin, 12 (30.0%) were resistant, and a mixed susceptibility pattern was detected in 7 (17.5%) specimens. H pylori isolates from 19 (79.2%) of the 24 patients who had formerly used clarithromycin showed clarithromycin resistance. CONCLUSIONS The prevalence of H pylori infection was 53.3% for the symptomatic patients in this study, and 47.5% of the isolates showed clarithromycin resistance using melting curve analysis. The PCR-based system used in this study was accurate for the detection of H pylori infection as well as clarithromycin susceptibility testing directly in biopsy specimens.
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Affiliation(s)
- Ayse Demet Kaya
- Department of Microbiology, Duzce University, Medical Faculty Hospital, Konuralp/Duzce, Turkey
| | - C Elif Oztürk
- Department of Microbiology, Duzce University, Medical Faculty Hospital, Konuralp/Duzce, Turkey
| | - Yusuf Akcan
- Department of Gastroenterology, Duzce University, Medical Faculty Hospital, Konuralp/Duzce, Turkey
| | - Mustafa Behçet
- Department of Microbiology, Duzce University, Medical Faculty Hospital, Konuralp/Duzce, Turkey
| | - A Esra Karakoç
- Department of Microbiology, Ministry of Health, Ankara Training and Research Hospital, Ankara, Turkey
| | - Mihriban Yücel
- Department of Microbiology, Ministry of Health, Ankara Training and Research Hospital, Ankara, Turkey
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Wilkening S, Bader A. Quantitative real-time polymerase chain reaction: methodical analysis and mathematical model. J Biomol Tech 2004; 15:107-11. [PMID: 15190083 PMCID: PMC2291683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Real-time polymerase chain reaction was established for 16 genes using the LightCycler system to evaluate gene expression in human hepatocytes. During the experiments a large set of data has been obtained. These data have now been evaluated with respect to template stability, accuracy of melting curve analysis, and reproducibility. In addition, the statistical evaluation of the efficiencies of all 16 polymerase chain reactions led to a new mathematical model. To examine template stability, the degradation of mRNA and cDNA was determined at different temperatures. Surprisingly, cDNA, which was obtained by first-strand synthesis, appeared to degrade significantly faster than the respective mRNA. Melting curve analysis is a fast and sensitive method to check for polymerase chain reaction specificity. However, we show that two transcription variants of the glutathione S-transferase 1 gene, with over 100 bp length difference, could not be distinguished by this method. Furthermore, an equation was set up describing the correlation between polymerase chain reaction efficiency and crossing point. This equation can be used to estimate the number of template molecules without having a standard of known concentration. Finally, experimental reproducibility of the real-time polymerase chain reaction was defined.
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Affiliation(s)
- Stefan Wilkening
- German Research Centre for Biotechnology, Braunschweig, Germany.
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