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Hirano M, Sahashi K, Ichikawa Y, Katsuno M, Natsume A. A rapid and easy-to-use spinal muscular atrophy screening tool based on primers with high specificity and amplification efficiency for SMN1 combined with single-stranded tag hybridization assay. PLoS One 2024; 19:e0308179. [PMID: 39088538 PMCID: PMC11293695 DOI: 10.1371/journal.pone.0308179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/17/2024] [Indexed: 08/03/2024] Open
Abstract
Spinal muscular atrophy (SMA) is an intractable neuromuscular disorder primarily caused by homozygous deletions in exon 7 of the SMN1 gene. Early diagnosis and prompt treatment of patients with SMA have a significant impact on prognosis, and several therapies have recently been developed. Current SMA screening tests require a significant turnaround time to identify patients with suspected SMA, due both to the interval between the birth of a newborn and the collection of blood for newborn mass screening and the difficulty in distinguishing between SMN1 and SMN2, a paralog gene that requires testing in specialized laboratories. The aim of this study was therefore to develop a novel SMA screening assay that can be rapidly performed in ordinary hospitals and clinics to overcome these issues. We designed over 100 combinations of forward and reverse primers with 3' ends targeting SMN1-specific sites around exon 7, and evaluated their specificity and amplification efficiency by quantitative PCR to identify the best primer pair. Furthermore, we performed a single-stranded tag hybridization assay after PCR. To evaluate the accuracy and practicality of the newly developed assay, we analyzed saliva specimens from five patients with SMA and two SMA carriers collected in an outpatient clinic and DNA specimens from three patients with SMA and four SMA carriers from a biobank, together with those from healthy individuals. DNA and raw saliva specimens from all patients with SMA demonstrated a biallelic loss of SMN1, whereas those from carriers and healthy individuals did not. The results of 50 independent experiments were consistent for all samples. The assay could be completed within one hour. This simple and convenient new screening tool has the potential to allow patients with SMA to receive disease-modifying therapies within a shorter timeframe.
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Affiliation(s)
- Masaki Hirano
- Division of Molecular Oncology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
- Craif Inc., Tokyo, Japan
| | - Kentaro Sahashi
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | | | - Masahisa Katsuno
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Institute of Innovation for Future Society of Nagoya University, Nagoya, Aichi, Japan
| | - Atsushi Natsume
- Institute of Innovation for Future Society of Nagoya University, Nagoya, Aichi, Japan
- Kawamura Medical Associates, Nagoya, Aichi, Japan
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2
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Mikita K, Tajima M, Haque A, Kato Y, Iwata S, Suzuki K, Hasegawa N, Yano H, Matsumoto T. Development of a Simple Method to Detect the Carbapenemase-Producing Genes blaNDM, blaOXA-48-like, blaIMP, blaKPC, and blaVIM Using a LAMP Method with Lateral Flow DNA Chromatography. Diagnostics (Basel) 2024; 14:1027. [PMID: 38786325 PMCID: PMC11119924 DOI: 10.3390/diagnostics14101027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Infections by carbapenemase-producing Enterobacterales constitute a global public health threat. The rapid and efficient diagnosis of Enterobacterales infection is critical for prompt treatment and infection control, especially in hospital settings. We developed a novel loop-mediated isothermal amplification (LAMP) method combined with DNA chromatography to identify five major groups of carbapenemase-producing genes (blaNDM, blaOXA-48-like, blaIMP, blaKPC, and blaVIM). This method uses DNA-DNA hybridization-based detection in which LAMP products can be easily visualized as colored lines. No specific technical expertise, expensive equipment, or special facilities are required for this method, allowing its broad application. Here, 73 bacteria collections including strains with carbapenemase-producing genes were tested. Compared to sequencing results, LAMP DNA chromatography for five carbapenemase-producing genes had a sensitivity and specificity of 100% and >97%, respectively. This newly developed method can be a valuable rapid diagnostic test to guide appropriate treatments and infection control measures, especially in resource-limited settings.
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Affiliation(s)
- Kei Mikita
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo 160-8582, Japan; (M.T.); (N.H.)
| | - Moe Tajima
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo 160-8582, Japan; (M.T.); (N.H.)
| | - Anwarul Haque
- Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita 286-8520, Japan; (A.H.); (Y.K.); (T.M.)
| | - Yasuyuki Kato
- Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita 286-8520, Japan; (A.H.); (Y.K.); (T.M.)
| | - Satoshi Iwata
- Department of Microbiology, Tokyo Medical University, Tokyo 160-8402, Japan;
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo 173-8606, Japan;
| | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo 160-8582, Japan; (M.T.); (N.H.)
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara 634-8522, Japan;
| | - Tetsuya Matsumoto
- Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita 286-8520, Japan; (A.H.); (Y.K.); (T.M.)
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3
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Nakanishi H, Takada A, Yoneyama K, Sakai K, Saito K. Simplified detection of the species of origin of antler velvets using single-stranded tag hybridization chromatographic printed-array strip. J Nat Med 2023; 77:998-1004. [PMID: 37574465 DOI: 10.1007/s11418-023-01734-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
In this study, we developed a convenient and easy-to-use origin identification method for antler velvets based on a simple DNA extraction technique and single-stranded tag hybridization chromatographic printed-array strip (STH-PAS). The primer sets used to detect Cervus elaphus, Rangifer tarandus, and 12S rRNA did not engage in non-specific reactions such as primer dimer formation. In both the triplex and singleplex assays, the sensitivity was < 1 ng DNA. Moreover, Cervus elaphus DNA could be detected in OTC crude drug products. Although the detection sensitivity resulting from the simplified extraction was slightly lower than that obtained with extraction by conventional methods, the amount of DNA was sufficient even from a small sample. The choice of a triplex or singleplex assay will depend on the purpose of the test. For example, if it is important to determine whether the antler velvet is derived from Cervus elaphus or Rangifer tarandus, a triplex assay is appropriate. If it is necessary to explore whether antler velvet from Cervus elaphus is included in an OTC crude drug product, a singleplex assay using the Cervus elaphus primer set is informative. If it is necessary to explore whether powdered antler velvet includes counterfeit products (from Rangifer tarandus), a singleplex assay employing the Rangifer tarandus primer is appropriate. The singleplex assay detects minor components even at a 1,000:1 ratio. Our study thus demonstrated the utility of a method combining simple DNA extraction with STH-PAS for efficient identification of the origin of antler velvets.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan.
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
- Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo, 112-0012, Japan
| | - Katsumi Yoneyama
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Kentaro Sakai
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo, 112-0012, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
- Tokyo Medical Examiner's Office, Tokyo Metropolitan Government, 4-21-18, Otsuka, Bunkyo-Ku, Tokyo, 112-0012, Japan
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4
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Okamoto M, Monden Y, Shindo A, Takeuchi T, Endo T, Shigematsu Y, Takasaki K, Fujii H, Shimada T. A target cultivar-specific identification system based on the chromatographic printed array strip method for eight prominent Japanese citrus cultivars. BREEDING SCIENCE 2023; 73:146-157. [PMID: 37404354 PMCID: PMC10316311 DOI: 10.1270/jsbbs.22065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/10/2022] [Indexed: 07/06/2023]
Abstract
Citrus is a major cultivated crop in Japan, and new cultivars are of great interest in the Japanese and global market. Recently, the infringement of breeders' rights to citrus cultivars bred in Japan has become a problem related to the agricultural product export strategy promoted by the Japanese government. Cultivar identification systems using DNA markers are an effective tool for protecting breeders' rights. Here, a novel target cultivar-specific identification system using the chromatographic printed array strip method was developed for eight prominent Japanese citrus cultivars. A polymorphic InDel fragment specific to each cultivar was explored through the screening of published citrus InDel markers and next-generation sequencing of retrotransposon libraries. The cultivar-specific DNA marker set for each cultivar comprised 1-3 polymorphic InDel fragments in combination with a PCR-positive DNA marker for the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene. The DNA markers were detected within 3 hours from DNA extraction to the detection by the C-PAS4 membrane stick following multiplex PCR. The developed system is superior as a convenient, rapid, and cost-effective DNA diagnostic method during inspection. The proposed target cultivar-specific identification system is expected to serve as an efficient tool for the injunction of suspicious registered cultivars, contributing to the protection of breeders' rights.
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Affiliation(s)
- Mitsutoshi Okamoto
- Ehime Research Institute of Citrus Fruits, Yoshida, Uwajima, Ehime 799-3742, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530, Japan
| | - Akiko Shindo
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530, Japan
| | | | - Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Yukinori Shigematsu
- Ehime Research Institute of Citrus Fruits, Yoshida, Uwajima, Ehime 799-3742, Japan
| | - Kazuto Takasaki
- FASMAC Co., Ltd., 3088 Okada, Atsugi, Kanagawa 243-0021, Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
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5
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Hayashida K, Garcia A, Moonga LC, Sugi T, Takuya K, Kawase M, Kodama F, Nagasaka A, Ishiguro N, Takada A, Kajihara M, Nao N, Shingai M, Kida H, Suzuki Y, Hall WW, Sawa H, Yamagishi J. Field-deployable multiplex detection method of SARS-CoV-2 and influenza virus using loop-mediated isothermal amplification and DNA chromatography. PLoS One 2023; 18:e0285861. [PMID: 37192155 DOI: 10.1371/journal.pone.0285861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023] Open
Abstract
A novel multiplex loop-mediated isothermal amplification (LAMP) method combined with DNA chromatography was developed for the simultaneous detection of three important respiratory disease-causing viruses: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus, and influenza B virus. Amplification was performed at a constant temperature, and a positive result was confirmed by a visible colored band. An in-house drying protocol with trehalose was used to prepare the dried format multiplex LAMP test. Using this dried multiplex LAMP test, the analytical sensitivity was determined to be 100 copies for each viral target and 100-1000 copies for the simultaneous detection of mixed targets. The multiplex LAMP system was validated using clinical COVID-19 specimens and compared with the real-time qRT-PCR method as a reference test. The determined sensitivity of the multiplex LAMP system for SARS-CoV-2 was 71% (95% CI: 0.62-0.79) for cycle threshold (Ct) ≤ 35 samples and 61% (95% CI: 0.53-0.69) for Ct ≤40 samples. The specificity was 99% (95%CI: 0.92-1.00) for Ct ≤35 samples and 100% (95%CI: 0.92-1.00) for the Ct ≤40 samples. The developed simple, rapid, low-cost, and laboratory-free multiplex LAMP system for the two major important respiratory viral diseases, COVID-19 and influenza, is a promising field-deployable diagnosis tool for the possible future 'twindemic, ' especially in resource-limited settings.
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Affiliation(s)
- Kyoko Hayashida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Alejandro Garcia
- UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Ireland
| | - Lavel Chinyama Moonga
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Tatsuki Sugi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | | | | | - Nobuhisa Ishiguro
- Division of Infection Control, Hokkaido University Hospital, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Masashi Shingai
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Ireland
- Global Virus Network, Baltimore, Maryland, United States of America
| | - Hirofumi Sawa
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
- Global Virus Network, Baltimore, Maryland, United States of America
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
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6
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Sano R, Yokobori T, Harimoto N, Saeki H, Kominato Y, Shirabe K, Yazawa S. A novel genotyping method for rapid identification of the Le gene to select patients for diagnosis with CA19-9. Clin Chim Acta 2023; 538:181-188. [PMID: 36403666 DOI: 10.1016/j.cca.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND The antigenic determinant of CA19-9 is synthesized by the α1,3/4fucosyltransferase encoded by the Le gene in the Lewis blood group system. Accordingly, a diagnosis with CA19-9 is not appropriate forLe-negative patients who possess the Le gene-mutated le alleles homozygously. METHODS A Le gene-specific PCR was undertaken to determine c59T>G by using a set of tag-sense and biotin-labeled anti-sense primers and a peptide nucleic acid-le-clamp which bound to G59 in the le alleles. Following mixing with streptavidin-coatedbluelatex beads, the PCR products were developed on a strip on which the complementary tag oligonucleotide to theLe gene-specific amplicon was immobilized. RESULTS When the PCR products were developed on the strip, a clear line was rapidly observed in Le-positive but not in Le-negative individuals. In contrast, a significant number of cancer patients with Lewis-negative phenotype were found to possess CA19-9, while they were specifically genotyped asLe/-. No contradictory results were observed in cancer patients (n = 315) with respect to their Lewis genotypes and CA19-9 levels. CONCLUSIONS c59T>G occurred commonly in the le alleles could be specifically and rapidly identified by the present method. This method appeared to be relevant forselecting cancer patientsto bediagnosed with CA19-9.
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Affiliation(s)
- Rie Sano
- Department of Legal Medicine, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Takehiko Yokobori
- Department of Innovative Cancer Immunotherapy, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Norifumi Harimoto
- Department of General Surgical Science, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Hiroshi Saeki
- Department of General Surgical Science, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Yoshihiko Kominato
- Department of Legal Medicine, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Ken Shirabe
- Department of General Surgical Science, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Shin Yazawa
- Department of General Surgical Science, Graduate School of Medicine, Gunma University, Maebashi, Japan.
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7
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Development of a Multiplex Polymerase Chain Reaction-Based DNA Lateral Flow Assay as a Point-of-Care Diagnostic for Fast and Simultaneous Detection of MRSA and Vancomycin Resistance in Bacteremia. Diagnostics (Basel) 2022; 12:diagnostics12112691. [DOI: 10.3390/diagnostics12112691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
To reduce high mortality and morbidity rates, timely and proper treatment of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection is required. A multiplex polymerase reaction (mPCR)-based DNA lateral flow assay (MBDLFA) was developed as a point-of-care diagnostic for simultaneous identification of S. aureus, methicillin resistance, and vancomycin resistance directly from blood or blood cultures. A mPCR was developed to detect nuc, mecA, and vanA/B; its sensitivity, specificity, and limit of detection (LOD) were determined. The developed reaction was further modified for use in MBDLFA and its sensitivity for detection of target genes from artificially inoculated blood samples was checked. The optimized mPCR successfully detected nuc, mecA, and vanA/B from genomic DNA of bacterial colonies with LODs of 107, 107, and 105 CFU/mL, respectively. The reaction was sensitive and specific. The optimized mPCR was used in MBDLFA that detected nuc, mecA, and vanA/B with LODs of 107, 108, and 104 CFU/mL, respectively, directly from artificially inoculated blood. The developed MBDLFA can be used as a rapid, cheap point-of-care diagnostic for detecting S. aureus, MRSA, and vancomycin resistance directly from blood and blood cultures in ~2 h with the naked eye. This will reduce morbidity, mortality, and treatment cost in S. aureus bacteremia.
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8
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Tahmasebi M, Bamdad T, Svendsen WE, Forouzandeh-Moghadam M. An enzymatic nucleic acid vertical flow assay. Anal Bioanal Chem 2022; 414:3605-3615. [PMID: 35352165 DOI: 10.1007/s00216-022-03988-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 11/28/2022]
Abstract
Vertical flow assays have been developed in recent years addressing limitations of the lateral flow assays, including limited multiplexing capability, quantitation, and hook effect. In the present study, the first passive paper-based vertical flow assay is developed for the detection of the nucleic acid target. Horseradish peroxidase was used as an enzymatic tracer with a high potential for signal amplification. In order to achieve the best signal-to-noise ratio, different parameters of paper-based assays were optimized. The sample is heat denatured and hybridized with a specific probe to form a dual-labeled hybridization complex. A small volume of diluted sample, 12 µl, can be analyzed within 6 min on the assay in a sandwich format. Assay specificity was evaluated by testing different unrelated samples, and also, 1.7 nM was obtained as the limit of detection (LOD) using the 0 + 3SD method, which is equivalent to 8.5 fmol of double-stranded DNA in the 12 µl sample volume. The linear range of 3-194 nM with a 0.978 correlation coefficient was obtained according to the calibration curve. The developed assay was evaluated with 45 hepatitis B virus clinical plasma samples, and the result showed 100% consistency of the assay with the real-time PCR benchmark. In the present study, we sought to develop a mere detection system for nucleic acid targets, and to investigate the possibility of using enzyme reporter in a passive vertical flow assay.
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Affiliation(s)
- Mehdi Tahmasebi
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran
| | - Taravat Bamdad
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran
| | - Winnie Edith Svendsen
- Department of Micro and Nanotechnology, Technical University of Denmark, Ørsteds Plads, 2800 Kgs, Lyngby, Denmark
| | - Mehdi Forouzandeh-Moghadam
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran.
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9
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Zamani M, Dupaty J, Baer RC, Kuzmanovic U, Fan A, Grinstaff MW, Galagan JE, Klapperich CM. Paper-Based Progesterone Sensor Using an Allosteric Transcription Factor. ACS OMEGA 2022; 7:5804-5808. [PMID: 35224340 PMCID: PMC8867790 DOI: 10.1021/acsomega.1c05737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Progesterone monitoring is an essential component of in vitro fertilization treatments and reproductive management of dairy cows. Gold-standard biosensors for progesterone monitoring rely on antibodies, which are expensive and difficult to procure. We have developed an alternative transcription factor-based sensor that is superior to conventional progesterone biosensors. Here, we incorporate this transcription factor-based progesterone sensor into an affordable, portable paperfluidic format to facilitate widespread implementation of progesterone monitoring at the point of care. Oligonucleotides labeled with a fluorescent dye are immobilized onto nitrocellulose via a biotin-streptavidin interaction. In the absence of progesterone, these oligonucleotides form a complex with a transcription factor that is fluorescently labeled with tdTomato. In the presence of progesterone, the fluorescent transcription factor unbinds from the immobilized DNA, resulting in a decrease in tdTomato fluorescence. The limit of detection of our system is 27 nm, which is a clinically relevant level of progesterone. We demonstrate that transcription factor-based sensors can be incorporated into paperfluidic devices, thereby making them accessible to a broader population due to the portability and affordability of paper-based devices.
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Affiliation(s)
| | - Josh Dupaty
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | | | - Uros Kuzmanovic
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Mark W. Grinstaff
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - James E. Galagan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Catherine M. Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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10
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Rapid Genetic Diagnosis for Okinawan Patients with Enlarged Vestibular Aqueduct Using Single-Stranded Tag Hybridization Chromatographic Printed-Array Strip. J Clin Med 2022; 11:jcm11041099. [PMID: 35207372 PMCID: PMC8880462 DOI: 10.3390/jcm11041099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Both Pendred syndrome (PS) and nonsyndromic hearing loss with an enlarged vestibular aqueduct (EVA) are autosomal recessive disorders caused by SLC26A4 pathogenic variants. The spectrum of SLC26A4 pathogenic variants varies with the ethnic background. Among the patients with EVA in Okinawa, 94% had some combination of NM_000441.2(SLC26A4):c.1707+5G>A and NM_000441.2(SLC26A4):c.2168A>G(p.His723Arg), the two SLC26A4 pathogenic variants that are the most common in this population. We identified these two pathogenic variants using a novel genotyping method that employed an allele-specific polymerase chain reaction (PCR) from a gDNA and single-stranded tag hybridization chromatographic printed-array strip (STH-PAS) in DNA samples obtained from 48 samples in Okinawa, including 34 patients with EVA and 14 carriers of c.1707+5G>A or c.2168A>G. In addition, whole blood and saliva samples were used for analysis in this genotyping method with direct PCR. The results of STH-PAS genotyping were consistent with those obtained using standard Sanger sequencing for all samples. The accuracy of the STH-PAS method is 100% under the optimized conditions. STH-PAS genotyping provided a diagnosis in 30 out of 34 patients (88%) in Okinawan patients with EVA in under 3 h. The turn-around time for STH-PAS genotyping used with direct PCR was 2 h as a result of the omission of the DNA extraction and purification steps. Using information about the ethnic distribution of pathogenic variants in the SLC26A4 gene, STH-PAS genotyping performs a rapid genetic diagnosis that is simple and has a considerably improved efficiency.
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11
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Modern on-site tool for monitoring contamination of halal meat with products from five non-halal animals using multiplex polymerase chain reaction coupled with DNA strip. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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12
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Pourshahidi AM, Achtsnicht S, Nambipareechee MM, Offenhäusser A, Krause HJ. Multiplex Detection of Magnetic Beads Using Offset Field Dependent Frequency Mixing Magnetic Detection. SENSORS 2021; 21:s21175859. [PMID: 34502749 PMCID: PMC8433651 DOI: 10.3390/s21175859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022]
Abstract
Magnetic immunoassays employing Frequency Mixing Magnetic Detection (FMMD) have recently become increasingly popular for quantitative detection of various analytes. Simultaneous analysis of a sample for two or more targets is desirable in order to reduce the sample amount, save consumables, and save time. We show that different types of magnetic beads can be distinguished according to their frequency mixing response to a two-frequency magnetic excitation at different static magnetic offset fields. We recorded the offset field dependent FMMD response of two different particle types at frequencies f1 + n⋅f2, n = 1, 2, 3, 4 with f1 = 30.8 kHz and f2 = 63 Hz. Their signals were clearly distinguishable by the locations of the extremes and zeros of their responses. Binary mixtures of the two particle types were prepared with different mixing ratios. The mixture samples were analyzed by determining the best linear combination of the two pure constituents that best resembled the measured signals of the mixtures. Using a quadratic programming algorithm, the mixing ratios could be determined with an accuracy of greater than 14%. If each particle type is functionalized with a different antibody, multiplex detection of two different analytes becomes feasible.
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Affiliation(s)
- Ali Mohammad Pourshahidi
- Institute of Biological Information Processing-Biolelectronics (IBI-3), Forschungszentrum Jülich, 52425 Jülich, Germany; (A.M.P.); (S.A.); (M.M.N.); (A.O.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Stefan Achtsnicht
- Institute of Biological Information Processing-Biolelectronics (IBI-3), Forschungszentrum Jülich, 52425 Jülich, Germany; (A.M.P.); (S.A.); (M.M.N.); (A.O.)
- Institute of Nano- and Biotechnologies (INB), FH Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Mrinal Murali Nambipareechee
- Institute of Biological Information Processing-Biolelectronics (IBI-3), Forschungszentrum Jülich, 52425 Jülich, Germany; (A.M.P.); (S.A.); (M.M.N.); (A.O.)
| | - Andreas Offenhäusser
- Institute of Biological Information Processing-Biolelectronics (IBI-3), Forschungszentrum Jülich, 52425 Jülich, Germany; (A.M.P.); (S.A.); (M.M.N.); (A.O.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Hans-Joachim Krause
- Institute of Biological Information Processing-Biolelectronics (IBI-3), Forschungszentrum Jülich, 52425 Jülich, Germany; (A.M.P.); (S.A.); (M.M.N.); (A.O.)
- Institute of Nano- and Biotechnologies (INB), FH Aachen University of Applied Sciences, 52428 Jülich, Germany
- Correspondence: h.-; Tel.: +49-2461-61-2955
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13
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Design and Evaluation of Multiplex One-Step Reverse Transcription PCR-Dipstick Chromatography Method for the Analysis of Seven Respiratory Pathogens. Curr Microbiol 2021; 78:3656-3666. [PMID: 34338833 PMCID: PMC8326646 DOI: 10.1007/s00284-021-02621-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Influenza A, influenza B, severe acute respiratory syndrome coronavirus 2, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, and Chlamydophila pneumoniae are common pathogens that can cause severe pneumonia and other symptoms, resulting in acute lower respiratory tract infections. The objective of this study was to design and evaluate a sensitive and specific multiplex one-step reverse transcription PCR (RT-PCR)–dipstick chromatography method for simultaneous rapid detection of these seven pathogens. Streptavidin-coated blue latex particles were used to read out a positive signal. Based on the DNA–DNA hybridization of oligonucleotide sequences (Tag) for forward primer with the complementary oligonucleotide sequence (cTag) on the dipstick and biotin–streptavidin interactions, PCR products were able to be illuminated visually on the dipstick. The specificity and the limit of detection (LOD) were also evaluated. Moreover, the clinical performance of this method was compared with Sanger sequencing for 896 samples. No cross reaction with other pathogens was found, confirming the high specificity of this method. The LOD was 10 copies/µL for each of the tested pathogens, and the whole procedure took less than 40 min. Using 896 samples, the sensitivity and specificity were shown to be no lower than 94.5%. The positive predictive value was higher than 82.1%, and the negative predictive value was higher than 99.5%. The kappa value between the PCR–dipstick chromatography method and Sanger sequencing ranged from 0.869 to 0.940. In summary, our one-step RT-PCR–dipstick chromatography method is a sensitive and specific tool for rapidly detecting multiplex respiratory pathogens.
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Isaka Y, Nishio SY, Hishinuma E, Hiratsuka M, Usami SI. Improvement of a Rapid and Highly Sensitive Method for the Diagnosis of the Mitochondrial m.1555A>G Mutation Based on a Single-Stranded Tag Hybridization Chromatographic Printed-Array Strip. Genet Test Mol Biomarkers 2021; 25:79-83. [PMID: 33372830 PMCID: PMC7821431 DOI: 10.1089/gtmb.2020.0105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: Pathogenic variants in mitochondrial DNA are known to be associated with sensorineural hearing loss (SNHL) and aminoglycoside-induced HL. Among them, the m.1555A>G mutation is the most common. Thus, a rapid and easy companion diagnostic method for this mutation would be desirable to prevent HL caused by aminoglycoside therapy. In this study, we report an improved protocol for the single-stranded tag hybridization chromatographic printed-array strip (STH-PAS) method for identifying the m.1555A>G mutation. Methods: To evaluate the accuracy of a novel diagnostic for the m.1555A>G mutation we analyzed 378 DNA samples with or without the m.1555A>G mutation, as determined by Invader assay, and calculated the sensitivity, specificity, and false negative and false positive ratios of this new method. Results: The newly developed protocol was robust; we, obtained the same results using multiple DNA concentrations, differing annealing temperatures, and different polymerase chain reaction thermal cyclers. The diagnostic sensitivity based on the STH-PAS method was 0.99, and the specificity was 1.00. The false negative and false positive ratios were 0 and 0.01, respectively. Conclusion: We improved the genotyping method for m.1555A>G mutations. This assays will be useful as a rapid companion diagnostic before aminoglycoside use.
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Affiliation(s)
- Yuichi Isaka
- Department of Hearing Implant Sciences and Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-ya Nishio
- Department of Hearing Implant Sciences and Shinshu University School of Medicine, Matsumoto, Japan
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Eiji Hishinuma
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine and Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine and Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shin-ichi Usami
- Department of Hearing Implant Sciences and Shinshu University School of Medicine, Matsumoto, Japan
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
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15
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Kodera T, Yamaguchi T, Fukushima Y, Kobayashi K, Takarada Y, Chizimu JY, Nakajima C, Solo ES, Lungu PS, Kawase M, Suzuki Y. Rapid and Simple Detection of Isoniazid-Resistant Mycobacterium tuberculosis Utilizing a DNA Chromatography-Based Technique. Jpn J Infect Dis 2020; 74:214-219. [PMID: 33132303 DOI: 10.7883/yoken.jjid.2020.754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Despite the availability of anti-tuberculosis drugs, the treatment of tuberculosis has been complicated by drug-resistant tuberculosis. The early detection of drug resistance makes early treatment possible. However, the available tools are mainly for rifampicin resistance detection, and the existing isoniazid resistance detection method is expensive, highly technical, and complicated, making it unsustainable for use in developing nations. This study aimed to develop a simple, rapid, and low-cost diagnostic kit for isoniazid-resistant tuberculosis using the single-stranded tag hybridization method to target an isoniazid resistance-conferring mutation. Specificity and sensitivity were assessed using DNA extracted from 49 isoniazid-resistant and 41 isoniazid-susceptible Mycobacterium tuberculosis clinical isolates cultured in mycobacterial growth indicator tubes. Positive signals were observed on mutant and wild-type lines with 100% sensitivity and specificity compared with Sanger sequencing results. In contrast, no positive signal was observed for non-tuberculosis mycobacteria. The detection limit of this method was 103 CFU or less. The STH-PAS system for isoniazid-resistant M. tuberculosis detection developed in this study offers a better alternative to conventional phenotypic isoniazid resistance determination, which will be of both clinical and epidemiological significance in resource-limited nations.
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Affiliation(s)
| | | | | | | | | | - Joseph Yamweka Chizimu
- Hokkaido University Research Center for Zoonosis Control, Japan.,Zambia National Public Health Institute, Ministry of Health, Zambia
| | - Chie Nakajima
- Hokkaido University Research Center for Zoonosis Control, Japan.,Hokkaido University, GI-CoRE Global Station for Zoonosis Control, Japan
| | - Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital Ministry of Health, Zambia
| | | | | | - Yasuhiko Suzuki
- Hokkaido University Research Center for Zoonosis Control, Japan.,Hokkaido University, GI-CoRE Global Station for Zoonosis Control, Japan
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16
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Mori C, Matsumura S. Current issues for mammalian species identification in forensic science: a review. Int J Legal Med 2020; 135:3-12. [PMID: 32562039 DOI: 10.1007/s00414-020-02341-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022]
Abstract
Mammalian species identification is one of the important issues in forensic science. Determining the origins of non-human biological material found at crime scenes can increase the possibility of identifying the true culprit by narrowing down the range of suspects. Although many techniques based on mitochondrial DNA (mtDNA) have been developed, challenges remain to cost-effectively identify species from degraded samples containing a mixture of DNA from multiple species and to standardize procedures for mammalian species identification. This review evaluates the reliability and versatility of mtDNA-based techniques to reveal obstacles to the establishment of standard analytical methods, with a particular focus on DNA mixtures. When samples contain a mixture of DNA from multiple species, the interpretation of sequencing analysis results is difficult. Although DNA metabarcoding using next-generation sequencing (NGS) technologies can overcome the DNA mixture problem, DNA metabarcoding is not suitable for the type of small-scale analysis routinely performed by local forensic laboratories, primarily because it is costly and time-consuming. By contrast, fluorescent multiplex PCR analysis enables cost-effective and simultaneous species identification from suboptimal samples, although the number of identifiable species is currently limited in comparison with sequencing techniques. The advantages and limitations of current techniques presented in this review indicate that multiplex PCR analysis will continue to be important for mammalian species identification in forensic casework analysis. Further developments in multiplex PCR analysis that enable the identification of an increased number of species will play a key step for standardization efforts among forensic laboratories.
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Affiliation(s)
- Chikahiro Mori
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Forensic Science Laboratory, Gifu Prefectural Police Headquarters, 2-1-1 Yabutaminami, Gifu, 500-8501, Japan.
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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17
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Li J, Pollak NM, Macdonald J. Multiplex Detection of Nucleic Acids Using Recombinase Polymerase Amplification and a Molecular Colorimetric 7-Segment Display. ACS OMEGA 2019; 4:11388-11396. [PMID: 31460243 PMCID: PMC6682049 DOI: 10.1021/acsomega.9b01097] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/12/2019] [Indexed: 05/06/2023]
Abstract
Nucleic acid analysis has become highly relevant for point-of-care (POC) diagnostics since the advent of isothermal amplification methods that do not require thermal cycling. In particular, recombinase polymerase amplification (RPA) combined with lateral flow detection offers a rapid and simple solution for field-amenable low-resource nucleic acid testing. Expanding POC nucleic acid tests for the detection of multiple analytes is vital to improve diagnostic efficiency because increased multiplexing capacity enables higher information density combined with reduced assay time and costs. Here, we investigate expanding RPA POC detection by identifying a generic multiplex RPA format that can be combined with a generic multiplex lateral flow device (LFD) to enable binary and molecular encoding for the compaction of diagnostic data. This new technology relies on the incorporation of molecular labels to differentiate nucleic acid species spatially on a lateral flow membrane. In particular, we identified additional five molecular labels that can be incorporated during the RPA reaction for subsequent coupling with LFD detection. Combined with two previously demonstrated successful labels, we demonstrate potential to enable hepta-plex detection of RPA reactions coupled to multiplex LFD detection. When this hepta-plex detection is combined with binary and molecular encoding, an intuitive 7-segment output display can be produced. We note that in all experiments, we used an identical DNA template, except for the 5' label on the forward primer, to eliminate any effects of nucleic acid sequence amplification bias. Our proof-of-concept technology demonstration is highly relevant for developing information-compact POC diagnostics where space and time are premium commodities.
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Affiliation(s)
- Jia Li
- Genecology
Research Centre, School of Science and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy
Downs, Queensland 4556, Australia
| | - Nina M. Pollak
- Genecology
Research Centre, School of Science and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy
Downs, Queensland 4556, Australia
- CSIRO
Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory 2601, Australia
| | - Joanne Macdonald
- Genecology
Research Centre, School of Science and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy
Downs, Queensland 4556, Australia
- Division
of Experimental Therapeutics, Columbia University, 650 W 168th Street, New York, New York 10032, United States
- E-mail: , .
Phone: +61 7 5456 5944
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18
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Maruoka H, Hinenoya A, Yasuda N, Takeda A, Inoue S, Sumi T, Koitabashi K, Yasue H, Kogou K, Yamasaki S. Evaluation of the GeneFields® EHEC/SS PCR dipstick DNA chromatography kit for the detection of enteric bacterial pathogens in stool specimens of healthy humans. J Microbiol Methods 2019; 161:111-117. [PMID: 31054865 DOI: 10.1016/j.mimet.2019.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 11/29/2022]
Abstract
We developed a new GeneFields® EHEC/SS PCR dipstick DNA chromatography kit for the simultaneously detection of invA, ipaH, and stx genes in Salmonella enterica (56 strains), Shigella spp. (44), and enterohemorrhagic Escherichia coli (EHEC) (28), respectively, and evaluated the sensitivity and specificity with other bacteria (57) by this kit. The sensitivity and specificity were 100%, respectively. The detection limit of various methods was determined using 5% (w/v) stool suspensions spiked with each bacterium. The detection limit of the GeneFields® EHEC/SS kit ranged from approximately 102-103 CFU/g. Additionally, the relative sensitivities and specificities of the GeneFields® EHEC/SS kit vs two commercially available real-time PCR kits were >85.0% and >90.0%, respectively. These results indicate that the GeneFields® EHEC/SS kit can be used for genetic screening of S. enterica, Shigella spp., and EHEC in human stool specimens with sensitivities and specificities similar to those of the commercially available real-time PCR kits.
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Affiliation(s)
- Hiroki Maruoka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan; Technical Research Laboratory, KURABO INDUSTRIES LTD., Neyagawa, Osaka, Japan
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan
| | - Noritomo Yasuda
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan
| | - Atsuyoshi Takeda
- TOHO Biological Laboratories Co., Ltd., Osaka, Naniwa-ku, Osaka, Japan
| | - Shin Inoue
- TOHO Biological Laboratories Co., Ltd., Osaka, Naniwa-ku, Osaka, Japan
| | - Tomoko Sumi
- Japan Institute of Foods Ecology, Inc., Kobe, Hyogo, Japan
| | | | - Hiroshi Yasue
- Tsukuba GeneTechnology Laboratories Inc., Tsuchiura, Ibaraki, Japan
| | - Kazuhiko Kogou
- Bio-Medical Department, Advanced Technology Division, KURABO INDUSTRIES LTD., Neyagawa, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan.
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19
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Reed AJ, Connelly RP, Williams A, Tran M, Shim BS, Choe H, Gerasimova YV. Label-Free Pathogen Detection by a Deoxyribozyme Cascade with Visual Signal Readout. SENSORS AND ACTUATORS. B, CHEMICAL 2019; 282:945-951. [PMID: 31462856 PMCID: PMC6713451 DOI: 10.1016/j.snb.2018.11.147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A colorimetric nucleic acid based test for label-free pathogen detection has been developed and used for the detection of the Zika virus. The test relies on nucleic acid sequence-based amplification (NASBA) of a viral RNA followed by interrogation of the amplicon by a cascade of deoxyribozymes constituting a visual split deoxyribozyme (vsDz) probe. The probe consists of a split phosphodiesterase deoxyribozyme, which forms its catalytic core upon binding to a specific amplicon fragment. The catalytically active complex recognizes and cleaves an inhibited peroxidase-like deoxyribozyme (PDz), thereby activating it. Active PDz catalyzes hydrogen peroxide-mediated oxidation of a colorless substrate into a colored product, thereby generating a visible signal. Viral RNA (106 copies/mL or higher) triggers intense color within 2 hr. The test selectively differentiates between Zika and closely related dengue and West Nile viruses. The reported technology combines isothermal amplification and visual detection and therefore represents a basis for the future development of a cost-efficient and instrument-free method for point-of-care nucleic acid analysis.
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Affiliation(s)
- Adam J. Reed
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Ryan P. Connelly
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Allison Williams
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Maithi Tran
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Byoung-Shik Shim
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hyeryun Choe
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yulia V. Gerasimova
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
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20
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Liles VR, Pangilinan LAS, Daroy MLG, Dimamay MTA, Reyes RS, Bulusan MK, Dimamay MPS, Luna PAS, Mercado A, Bai G, Chagan-Yasutan H, Takarada Y, Kawase M, Hattori T. Evaluation of a rapid diagnostic test for detection of dengue infection using a single-tag hybridization chromatographic-printed array strip format. Eur J Clin Microbiol Infect Dis 2019; 38:515-521. [PMID: 30680559 DOI: 10.1007/s10096-018-03453-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2018] [Indexed: 11/26/2022]
Abstract
A dipstick DNA chromatography assay, a single-tag hybridization-printed array strip (STH-PAS), was evaluated for its efficacy to detect dengue virus (DENV). Reverse-transcribed DNA was amplified by PCR, and the amplified DNA was detected using the STH-PAS system. The method was evaluated using stored RNA samples previously identified to carry all 4 serotypes of dengue, chikungunya, and influenza viruses. Clinical performance was also assessed in a prospective study using plasma from 269 febrile cases from the Emergency Department of St. Luke's Medical Center, Quezon City, Philippines, and 30 afebrile normal healthy volunteers. A Taqman real-time PCR (RT-PCR) assay and a rapid Dengue NS1 test, SD Bioline, were used for comparison. The STH-PAS system was more sensitive in detecting dengue infection compared to Taqman RT-PCR. For DENV serotypes 1, 2, and 3, the detection was 1 to 2 dilutions (10-fold) higher, and for DENV serotype 4, the detection was 2-4 dilutions higher. In clinical studies, the STH-PAS system showed 100% sensitivity with 88.9% and 86.6% specificities compared to Taqman RT-PCR and SD Dengue Duo NS1 test, respectively. The STH-PAS system was found to have a superior sensitivity than the Taqman system. Further evaluation of its performance in the field may provide important data to extend its usefulness for surveillance and epidemiological research in outbreak situations.
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Affiliation(s)
- Veni R Liles
- Research and Biotechnology Group, St. Luke's Medical Center, Quezon City, Philippines
| | | | - Maria Luisa G Daroy
- Research and Biotechnology Group, St. Luke's Medical Center, Quezon City, Philippines
| | | | - Rachel S Reyes
- Research and Biotechnology Group, St. Luke's Medical Center, Quezon City, Philippines
| | - Mick Kelvin Bulusan
- Research and Biotechnology Group, St. Luke's Medical Center, Quezon City, Philippines
| | - Mark Pierre S Dimamay
- Research and Biotechnology Group, St. Luke's Medical Center, Quezon City, Philippines
| | - Paolo Antonio S Luna
- Department of Emergency Medicine, St. Luke's Medical Center, Quezon City, Philippines
| | - Abigail Mercado
- Department of Emergency Medicine, St. Luke's Medical Center, Quezon City, Philippines
| | - Gaowa Bai
- Department of Health Science and Social Welfare, Kibi International University, Takahashi, Japan
| | - Haorile Chagan-Yasutan
- Department of Health Science and Social Welfare, Kibi International University, Takahashi, Japan
- Mongolian Psychosomatic Medicine Department, International Mongolian Medicine Hospital of Inner Mongolia, Hohhot, China
| | | | - Mitsuo Kawase
- Tohoku Bio-Array Co., Ltd., Sendai, Japan
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Toshio Hattori
- Department of Health Science and Social Welfare, Kibi International University, Takahashi, Japan.
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21
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Development and application of a rapid and sensitive genotyping method for pharmacogene variants using the single-stranded tag hybridization chromatographic printed-array strip (STH-PAS). Drug Metab Pharmacokinet 2018; 33:258-263. [PMID: 30269962 DOI: 10.1016/j.dmpk.2018.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/06/2018] [Accepted: 08/13/2018] [Indexed: 01/06/2023]
Abstract
Genetic polymorphisms contribute to inter-individual variability in the metabolism of multiple clinical drugs, including warfarin, thiopurines, primaquine, and aminoglycosides. A rapid and sensitive clinical assessment of various genome biomarkers is, therefore, required to predict the individual responsiveness of each patient to these drugs. In this study, we developed a novel genotyping method for the detection of nine pharmacogene variants that are important in the prediction of drug efficiency and toxicity. This genotyping method uses competitive allele-specific PCR and a single-stranded tag hybridization chromatographic printed-array strip (STH-PAS) that can unambiguously determine the presence or absence of the gene variant by displaying visible blue lines on the chromatographic printed-array strip. Notably, the results of our STH-PAS method were in 100% agreement with those obtained using standard Sanger sequencing and KASP assay genotyping methods for CYP4F2 gene deletion. Moreover, the results were obtained within 90 min, including the PCR amplification and signal detection processes. The sensitive and rapid nature of this novel method make it ideal for clinical genetic testing to predict drug efficacy and toxicity, and in doing so will aid in the development of individualized medicine and better patient care.
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22
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Yamamuro T, Miyamoto S, Kitamura M, Muro T, Iwata YT, Segawa H, Kuwayama K, Tsujikawa K, Kanamori T, Inoue H. Development of simple and accurate detection systems for Cannabis sativa using DNA chromatography. Forensic Sci Int 2018; 291:68-75. [PMID: 30149281 DOI: 10.1016/j.forsciint.2018.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/03/2018] [Indexed: 10/28/2022]
Abstract
In recent years, the need for analyzing cannabis DNA has increased in order to accommodate the various types of cannabis samples encountered in forensic investigation. This study was aimed to establish a simple and accurate cannabis DNA detection system using DNA chromatography. Two chromatography chip systems with different features were successfully developed. One system (the "four-line version") involves tetraplex PCR amplification, which could be used to detect cannabis DNA and distinguish between drug-type and fiber-type cannabis using the tetrahydrocannabinolic acid synthase gene sequence. The other system was the "three-line version" with triplex amplification, which was specialized to distinguish cannabis from other plants, and had a sensitivity (10fg DNA/reaction) that was 100 times greater than the four-line version. In both versions, no false positives were observed for 60 medicinal plants, and accurate detection could be performed for several simulated forensic samples such as cannabis leaves, buds, stems, roots, seeds, resin, and cannabis leaves blended 1/100 in tobacco. Detection could be performed by the naked eye and only a thermal cycler was required for operation. Thus, DNA chromatography systems for cannabis detection are expected to contribute to the analysis of cannabis DNA in forensic chemistry laboratories without extensive equipment.
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Affiliation(s)
- Tadashi Yamamuro
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Shigehiko Miyamoto
- Medical Devices Solutions Vehicle, Kaneka Corporation, 1-8 Miyamaemachi, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Masashi Kitamura
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa, Ishikawa 920-8553, Japan
| | - Tomonori Muro
- Criminal Investigation Laboratory, Shimane Prefectural Police Headquarters, 1751-15 Heisei-cho, Matsue, Shimane 690-0038, Japan
| | - Yuko T Iwata
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hiroki Segawa
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kenji Kuwayama
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kenji Tsujikawa
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tatsuyuki Kanamori
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hiroyuki Inoue
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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23
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Koiwai K, Kodera T, Thawonsuwan J, Riani S, Kawase M, Kondo H, Hirono I. Rapid diagnosis of three shrimp RNA viruses using RT-PCR-DNA chromatography. JOURNAL OF FISH DISEASES 2018; 41:1309-1312. [PMID: 29806113 DOI: 10.1111/jfd.12821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Keiichiro Koiwai
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | - Jumroensri Thawonsuwan
- Department of Fisheries, Songkhla Aquatic Animal Health Research Center, Songkhla, Thailand
| | - Septya Riani
- PT. Sure Marketing Company, Tangerang, Indonesia
| | - Mitsuo Kawase
- TBA co., Ltd., Sendai, Japan
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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24
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Koiwai K, Kodera T, Thawonsuwan J, Kawase M, Kondo H, Hirono I. A rapid method for simultaneously diagnosing four shrimp diseases using PCR-DNA chromatography method. JOURNAL OF FISH DISEASES 2018; 41:395-399. [PMID: 29064102 DOI: 10.1111/jfd.12732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 05/21/2023]
Affiliation(s)
- K Koiwai
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | - J Thawonsuwan
- Department of Fisheries, Songkhla Aquatic Animal Health Research Center, Songkhla, Thailand
| | - M Kawase
- TBA co., Ltd., Sendai, Japan
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - H Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - I Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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25
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TIAN L, SATO T, NIWA K, KAWASE M, MAYANAGI G, WASHIO J, TAKAHASHI N. PCR-dipstick DNA chromatography for profiling of a subgroup of cariesassociated bacterial species in plaque from healthy coronal surfaces and periodontal pockets . Biomed Res 2016; 37:29-36. [DOI: 10.2220/biomedres.37.29] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Lingyang TIAN
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry
- State Key Laboratory of Oral Diseases, Sichuan University
| | - Takuichi SATO
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry
| | - Kousuke NIWA
- Future Technology Management Center, Corporate R&D, NGK Insulators
| | - Mitsuo KAWASE
- Tohoku University Graduate School of Biomedical Engineering
| | - Gen MAYANAGI
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry
| | - Jumpei WASHIO
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry
| | - Nobuhiro TAKAHASHI
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry
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26
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Zheng P, Zhou W. Relation between periodontitis and helicobacter pylori infection. Int J Clin Exp Med 2015; 8:16741-16744. [PMID: 26629215 PMCID: PMC4659103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE The correlation between periodontitis and Helicobacter pylori (H. pylori) infection in the mouth was analyzed. METHOD 70 elderly patients with periodontitis treated at our hospital from January 2013 to December 2014 were recruited. Dental plaques and gargle were collected for H. pylori detection using PCR technique. Periodontal health status of the patients was recorded. 70 control cases with healthy periodontium were also included. The symptoms of H. pylori infection in the mouth were compared between the two groups, and the results were analyzed statistically. RESULTS The positive rate of urease C gene of H. pylori in the periodontitis group was 71.4%; the positive rate of cagA gene was 35.7%. The positive rate of urease C gene of H. pylori in the control group was 34.3% and that of cagA gene was 12.9%. The two groups did not show significant differences in these two indicators (P<0.05). The positive detection rate of urease C gene of H. pylori in subgingival plaques was higher than that in supragingival plaques, and the difference was of statistical significance (P<0.05). The positive detection rate of H. pylori in patients with moderate and severe periodontitis was obviously higher than that of patients with mild periodontitis (P<0.05). CONCLUSION Periodontal health status of elderly people with periodontitis correlated with H. pylori infection in the stomach.
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Affiliation(s)
- Pei Zheng
- Department of Conservative Dentistry, Affiliated Hospital of Stomatology, Medical College, Zhejiang UniversityHangzhou 310006, China
| | - Weiying Zhou
- Department of Neurology, The Second Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhou 310015, China
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27
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Ang GY, Yu CY, Chan KG, Singh KKB, Chan Yean Y. Development of a dry-reagent-based nucleic acid-sensing platform by coupling thermostabilised LATE-PCR assay to an oligonucleotide-modified lateral flow biosensor. J Microbiol Methods 2015; 118:99-105. [PMID: 26342435 DOI: 10.1016/j.mimet.2015.08.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 01/27/2023]
Abstract
In this study, we report for the first time the development of a dry-reagent-based nucleic acid-sensing platform by combining a thermostabilised linear-after-the-exponential (LATE)-PCR assay with a one-step, hybridisation-based nucleic acid lateral flow biosensor. The nucleic acid-sensing platform was designed to overcome the need for stringent temperature control during transportation or storage of reagents and reduces the dependency on skilled personnel by decreasing the overall assay complexity and hands-on time. The platform was developed using toxigenic Vibrio cholerae as the model organism due to the bacterium's propensity to cause epidemic and pandemic cholera. The biosensor generates result which can be visualised with the naked eyes and the limit of detection was found to be 1pg of pure genomic DNA and 10CFU/ml of toxigenic V. cholerae. The dry-reagent-based nucleic acid-sensing platform was challenged with 95 toxigenic V. cholerae, 7 non-toxigenic V. cholerae and 66 other bacterial strains in spiked stool sample and complete agreement was observed when the results were compared to that of monosialoganglioside (GM1)-ELISA. Heat-stability of the thermostabilised LATE-PCR reaction mixes at different storage temperatures (4-56°C) was investigated for up to 90days. The dry-reagent-based genosensing platform with ready-to-use assay components provides an alternative method for sequence-specific detection of nucleic acid without any cold chain restriction that is associated with conventional molecular amplification techniques.
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Affiliation(s)
- Geik Yong Ang
- Division of Genetics & Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
| | - Choo Yee Yu
- Division of Genetics & Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Kok Gan Chan
- Division of Genetics & Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kirnpal Kaur Banga Singh
- School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Yean Chan Yean
- School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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