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Kato A, Miyata I, Tanaka Y, Oishi T, Teranishi H, Akaike H, Ohno N, Nakajima H, Kouguchi Y, Ouchi K. LAMP-based assay can rectify the diagnosis of Yersinia pseudotuberculosis infections otherwise missed by serology. J Med Microbiol 2019; 68:143-147. [PMID: 30648936 DOI: 10.1099/jmm.0.000868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Despite being a well-known but seldom encountered zoonotic pathogen, diagnosis of Yersinia pseudotuberculosis is not necessarily easy. Infected patients occasionally present with various symptoms resembling Kawasaki disease; thus discriminating the two in the acute phase is challenging. In addition to bacterial culture and serology, novel detection methods based on loop-mediated isothermal amplification (LAMP) are reported in the literature. However, the clinical utility of LAMP-based methods in comparison with the other methods is scarcely documented in the literature. AIM To clarify the clinical utility of a LAMP-based method in the diagnosis of Yersinia pseudotuberculosis infection. METHODOLOGY Inpatients admitted due to suspected Yersinia pseudotuberculosis infection during April 2008 through March 2015 were enrolled. Results of the LAMP-based method as well as culture and serology were collected and compared. RESULTS Among 16 eligible cases, serology proved positive in 13 (81.3 %) cases, LAMP in eight (50 %) cases, and bacterial culture in four (25 %) cases. No significant difference among the three methods could be proved statistically. Although serology was the most sensitive method, it is known to miss cases such as young patients, whereas LAMP could complement all three cases missed by serology. Furthermore, LAMP can return the test result within a few hours from specimen receipt, whereas serology and bacterial culture requires days to weeks of time. CONCLUSION Although second to serology in sensitivity, the LAMP-based method proved its utility in making rapid diagnosis, and serving a complementary role to serology.
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Affiliation(s)
- Atsushi Kato
- 1Department of Pediatrics, Kawasaki Medical School, Japan
| | - Ippei Miyata
- 1Department of Pediatrics, Kawasaki Medical School, Japan
| | - Yuhei Tanaka
- 1Department of Pediatrics, Kawasaki Medical School, Japan
| | - Tomohiro Oishi
- 1Department of Pediatrics, Kawasaki Medical School, Japan
| | | | - Hiroto Akaike
- 1Department of Pediatrics, Kawasaki Medical School, Japan
| | - Naoki Ohno
- 1Department of Pediatrics, Kawasaki Medical School, Japan
| | - Hiroshi Nakajima
- 2Bacteriology Section, Okayama Prefectural Institute for Environmental Science and Public Health, Japan
| | - Yutaka Kouguchi
- 3Department of Clinical Laboratory, Kawasaki Medical School Hospital, Japan
| | - Kazunobu Ouchi
- 1Department of Pediatrics, Kawasaki Medical School, Japan
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Rapid detection of herpes simplex virus-1 from bronchoalveolar lavage fluids using loop-mediated isothermal amplification (LAMP). Enferm Infecc Microbiol Clin 2018; 37:353-354. [PMID: 30389265 DOI: 10.1016/j.eimc.2018.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 11/20/2022]
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Reverse transcription loop-mediated isothermal amplification to rapidly detect Rice ragged stunt virus. Saudi J Biol Sci 2016; 25:1577-1584. [PMID: 30581320 PMCID: PMC6302892 DOI: 10.1016/j.sjbs.2016.02.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
Rice ragged stunt virus (RRSV) is a very important virus that infects rice and causes serious yield losses in Asian countries and other major rice planting areas. Thus, it is urgent to establish an efficient and practical approach for identification and diagnosis in the field. Our results indicated that reverse transcription loop-mediated isothermal amplification (RT-LAMP) reactions are more efficient and sensitive than RT-PCR for RRSV detection. The optimal LAMP conditions were as follows: 0.4–1.2 μM internal primers, 0.2–0.25 μM external primers, 0.8 μM loop primers, and incubation at 62 °C or 63 °C for 30 min. Furthermore, the RT-LAMP primers specifically targeted RRSV virus and resulted in typical waterfall-like bands by gel electrophoresis and sigmoidal amplification curves. The primers could not be used to amplify other common plant viruses including Papaya ringspot virus (PRSV), Rice yellow stunt virus (RYSV), Sorghum mosaic virus (SrMV), Cactus virus X (CVX), Melon yellow spot virus (MYSV) and Southern rice black-streaked dwarf virus (SRBSDV). Ten-fold serial dilutions of RRSV cDNA indicated that RT-LAMP is much faster and at least ten times more sensitive than RT-PCR in detecting the virus. The waterfall-like product bands could be observed within one hour. In the field study, about 77% samples were identified as RRSV. RT-LAMP has many benefits over RT-PCR such as low cost and high accuracy, sensitivity, and specificity. This technology meets the requirements for rapid diagnosis of plant virus diseases in the field to best guide management practices for growers.
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Rapid and direct detection of herpes simplex virus in cerebrospinal fluid by use of a commercial real-time PCR assay. J Clin Microbiol 2014; 52:4361-2. [PMID: 25274992 DOI: 10.1128/jcm.02623-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Central nervous system infection due to herpes simplex virus (HSV) is a medical emergency and requires rapid diagnosis and initiation of therapy. In this study, we compared a routine real-time PCR assay for HSV types 1 (HSV-1) and 2 (HSV-2) to a recently FDA-approved direct PCR assay (Simplexa HSV-1/2 Direct; Focus Diagnostics, Cypress, CA) using cerebrospinal fluid samples (n = 100). The Simplexa HSV-1/2 assays demonstrated a combined sensitivity and specificity of 96.2% (50/52) and 97.9% (47/48), respectively. In addition, the Simplexa assay does not require nucleic acid extraction, and the results are available in 60 min.
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Ohara Y, Morita A. [The cutting-edge of medicine: application of molecular diagnostics for central nervous system infections]. NIHON NAIKA GAKKAI ZASSHI. THE JOURNAL OF THE JAPANESE SOCIETY OF INTERNAL MEDICINE 2014; 103:1942-1947. [PMID: 25654891 DOI: 10.2169/naika.103.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Detection of Mycoplasma pneumoniae by loop-mediated isothermal amplification (LAMP) assay and serology in pediatric community-acquired pneumonia. J Infect Chemother 2012; 18:662-7. [DOI: 10.1007/s10156-012-0388-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/06/2012] [Indexed: 10/28/2022]
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Ren W, Renault T, Cai Y, Wang C. Development of a loop-mediated isothermal amplification assay for rapid and sensitive detection of ostreid herpesvirus 1 DNA. J Virol Methods 2010; 170:30-6. [PMID: 20813133 DOI: 10.1016/j.jviromet.2010.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 08/17/2010] [Accepted: 08/23/2010] [Indexed: 10/19/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed for rapid, specific and sensitive detection of ostreid herpesvirus 1 (OsHV-1) DNA. A set of four primers was designed, based on the sequence of the ATPase subunit of the OsHV-1 DNA-packaging terminase gene. The reaction temperature and time were optimized to 64°C and 60min, respectively. LAMP products were detected by agarose gel electrophoresis or by visual inspection of a color change due to addition of fluorescent dye. The developed method was highly specific for detection of OsHV-1, and no cross-reaction was observed with other DNA viruses, such as White spot syndrome virus (WSSV), Penaeus stylirostris densovirus (PstDNV), Turbot reddish body iridovirus (TRBIV) and Lymphocystis disease virus (LCDV) found commonly in China. The lower detection limit of the LAMP assay was approximately 20 copies per reaction, and it was 100 times more sensitive than that of conventional PCR. A comparative evaluation of 10 oyster samples using LAMP and PCR assays showed overall correlation in positive and negative results for OsHV-1. These results indicate that the LAMP assay is a simple, rapid, sensitive, specific and reliable technique for the detection of OsHV-1. The LAMP technique has capacity for use for the detection of OsHV-1 both in the laboratory and on farms.
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Affiliation(s)
- Weicheng Ren
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, 106 Nanjing Road, Qingdao, Shandong, China
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Maeda J, Inoue M, Nakabayashi K, Otomo Y, Shintani Y, Ohta M, Okumura M, Matsuura N. Rapid diagnosis of lymph node metastasis in lung cancer with loop-mediated isothermal amplification assay using carcinoembryonic antigen–mRNA. Lung Cancer 2009; 65:324-7. [DOI: 10.1016/j.lungcan.2008.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Revised: 11/20/2008] [Accepted: 12/01/2008] [Indexed: 11/25/2022]
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Saijo M, Morikawa S, Kurane I. Real-time quantitative polymerase chain reaction for virus infection diagnostics. ACTA ACUST UNITED AC 2008; 2:1155-71. [DOI: 10.1517/17530059.2.10.1155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Pandey BD, Poudel A, Yoda T, Tamaru A, Oda N, Fukushima Y, Lekhak B, Risal B, Acharya B, Sapkota B, Nakajima C, Taniguchi T, Phetsuksiri B, Suzuki Y. Development of an in-house loop-mediated isothermal amplification (LAMP) assay for detection of Mycobacterium tuberculosis and evaluation in sputum samples of Nepalese patients. J Med Microbiol 2008; 57:439-443. [PMID: 18349362 DOI: 10.1099/jmm.0.47499-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A number of nucleic acid amplification assays (NAAs) have been employed to detect tubercle bacilli in clinical specimens for tuberculosis (TB) diagnosis. Among these, loop-mediated isothermal amplification (LAMP) is an NAA possessing superior isothermal reaction characteristics. In the present study, a set of six specific primers targeting the Mycobacterium tuberculosis 16S rRNA gene with high sensitivity was selected and a LAMP system (MTB-LAMP) was developed. Using this system, a total of 200 sputum samples from Nepalese patients were investigated. The sensitivity of MTB-LAMP in culture-positive samples was 100 % (96/96), and the specificity in culture-negative samples was 94.2 % (98/104, 95 % confidence interval 90.5-97.9 %). The positive and negative predictive values of MTB-LAMP were 94.1 and 100 %, respectively. These results indicate that this MTB-LAMP method may prove to be a powerful tool for the early diagnosis of TB.
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Affiliation(s)
- Basu Dev Pandey
- Everest International Clinic and Research Center, Kathmandu, Nepal.,Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal
| | - Ajay Poudel
- Department of Microbiology, Tribhuban University, Kathmandu, Nepal
| | - Tomoko Yoda
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Japan
| | - Aki Tamaru
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Japan
| | | | - Yukari Fukushima
- Research Center for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Binod Lekhak
- Department of Microbiology, Tribhuban University, Kathmandu, Nepal
| | - Basista Risal
- Department of Microbiology, Tribhuban University, Kathmandu, Nepal
| | - Bishnu Acharya
- Everest International Clinic and Research Center, Kathmandu, Nepal
| | - Bishwa Sapkota
- Department of Research and Biotechnology, Anandaban Hospital, Kathmandu, Nepal
| | - Chie Nakajima
- Research Center for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Tooru Taniguchi
- Section of Bacterial Infections, Research Collaboration Center on Emerging and Re-emerging Infections, Osaka University, Nonthaburi, Thailand
| | - Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Yasuhiko Suzuki
- Research Center for Zoonosis Control, Hokkaido University, Hokkaido, Japan
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Kuhara T, Yoshikawa T, Ihira M, Watanabe D, Tamada Y, Katano H, Asano Y, Matsumoto Y. Rapid detection of human herpesvirus 8 DNA using loop-mediated isothermal amplification. J Virol Methods 2007; 144:79-85. [PMID: 17512061 DOI: 10.1016/j.jviromet.2007.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 03/27/2007] [Accepted: 03/29/2007] [Indexed: 10/23/2022]
Abstract
The reliability of a loop-mediated isothermal amplification (LAMP) method for the detection of human herpesvirus 8 (HHV-8) DNA was evaluated. Although LAMP products were produced with the DNA sample extracted from BCP-1 cells, LAMP products were not produced with the DNAs from seven other human herpesviruses. The detection limit of the HHV-8 LAMP method was 100 copies of target sequence/tube. To determine whether the HHV-8 LAMP method could be used to quantify viral DNA, threshold times, which are defined as the time (in s) it takes to reach the threshold turbidity level (0.1), were measured for the amplification of serial dilutions of a DNA plasmid containing the target sequence. The standard curve possessed a correlation coefficient of 0.9428 with a slope of -84.079 and y-intercept value of 1936.2. Additionally, an attempt was made to detect viral DNA in 17 specimens collected from Kaposi's sarcomas and two cell lines obtained from primary effusion lymphomas. HHV-8 DNA was detected in 14 of the 17 Kaposi's sarcoma tissue samples and both of the primary effusion lymphoma cell lines. Viral DNA was not detected in HHV-8 LAMP-negative samples using the real-time PCR method.
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Affiliation(s)
- Tomoe Kuhara
- Department of Dermatology, Aichi Medical University School of Medicine, Aichi, Nagakute, Japan
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Ihira M, Akimoto S, Miyake F, Fujita A, Sugata K, Suga S, Ohashi M, Nishimura N, Ozaki T, Asano Y, Yoshikawa T. Direct detection of human herpesvirus 6 DNA in serum by the loop-mediated isothermal amplification method. J Clin Virol 2007; 39:22-6. [PMID: 17376739 DOI: 10.1016/j.jcv.2007.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 02/01/2007] [Accepted: 02/01/2007] [Indexed: 11/24/2022]
Abstract
BACKGROUND A more rapid and easier method is needed for monitoring human herpesvirus 6 (HHV-6) infections. The loop-mediated isothermal amplification method (LAMP) can detect viral DNA with high specificity, efficiency, and speed under isothermal conditions. LAMP requires only simple equipment that is available in hospital laboratories. OBJECTIVES We evaluated LAMP as a means of detecting HHV-6 DNA directly from patients' sera. RESULTS The sensitivity of the HHV-6 LAMP protocol without heat denaturation was 1000 copies/tube; with heat denaturation 10 copies/tube were detected. Three hundred serum samples from children with fever were analyzed. Using HHV-6 isolation as a definition of HHV-6 infection, the sensitivity, specificity, positive predictive value, and negative predictive value of the HHV-6 LAMP method without DNA extraction were 95.5%, 95.2%, 94.0%, and 96.4%, respectively. CONCLUSION Direct detection of HHV-6 DNA in serum with a modified HHV-6 LAMP could be used for rapid diagnosis of exanthem subitum (ES).
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Affiliation(s)
- Masaru Ihira
- Department of Medical Information Technology, Fujita Health University College, Toyoake, Aichi, Japan
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Motani H, Sakurada K, Ikegaya H, Akutsu T, Hayakawa M, Sato Y, Yajima D, Sato K, Kobayashi K, Iwase H. Detection of herpes simplex virus type 1 DNA in bilateral human trigeminal ganglia and optic nerves by polymerase chain reaction. J Med Virol 2007; 78:1584-7. [PMID: 17063515 DOI: 10.1002/jmv.20742] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Herpes simplex virus type 1 (HSV-1) DNA was extracted from human trigeminal ganglia of 121 cadavers aged between 3 months and 94 years, and its PCR amplification was performed for the RL2 HSV-1 sequence using two pairs of primers. The HSV-1 DNA was detected in 74 of 121 patients (61%); 70/74 bilaterally, 3/74 only on the left side, and 1/74 only on the right side. Although the PCR-positive rate was significantly higher in advanced age, the correlation between the PCR-positive rate and gender was unclear. Additionally, HSV-1 DNA was not detected in any of the 50 optic nerve samples.
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Affiliation(s)
- Hisako Motani
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan.
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Iwata S, Shibata Y, Kawada JI, Hara S, Nishiyama Y, Morishima T, Ihira M, Yoshikawa T, Asano Y, Kimura H. Rapid detection of Epstein-Barr virus DNA by loop-mediated isothermal amplification method. J Clin Virol 2006; 37:128-33. [PMID: 16973412 DOI: 10.1016/j.jcv.2006.07.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 06/20/2006] [Accepted: 07/26/2006] [Indexed: 11/30/2022]
Abstract
BACKGROUND The loop-mediated isothermal amplification (LAMP) method is a novel technique for the amplification of specific DNA sequences. OBJECTIVES To establish the LAMP method for amplifying Epstein-Barr virus (EBV) DNA and to examine its reliability for the detection of EBV DNA in clinical specimens. STUDY DESIGN Sera from 108 patients, who were initially suspected of primary EBV infection, were tested by the EBV LAMP method, and the results were compared with those of the real-time PCR assay. Serological examination was regarded as the standard diagnostic method. RESULTS To diagnose primary EBV infection, the sensitivity of LAMP was 86.4% and the specificity was 100%. The sensitivity of the real-time PCR assay was 84.1% and the specificity was 98.4%. Longitudinal analysis showed that the detection rate of EBV DNA in serum by the LAMP method decreased with time in accordance with the decrease of the EBV load. EBV DNA could not be detected in serum 40 days after onset of symptoms. CONCLUSIONS These results indicate that the sensitivity and specificity of the LAMP method are comparable to those of real-time PCR and that detecting EBV DNA in serum by this method is potentially useful for diagnosing primary EBV infection.
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Affiliation(s)
- Seiko Iwata
- Department of Pediatrics, Anjo Kosei Hospital, Anjo, Japan
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