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Johnson AL, Keesler RI, Lewis AD, Reader JR, Laing ST. Common and Not-So-Common Pathologic Findings of the Gastrointestinal Tract of Rhesus and Cynomolgus Macaques. Toxicol Pathol 2022; 50:638-659. [PMID: 35363082 DOI: 10.1177/01926233221084634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rhesus and cynomolgus macaques are the most frequently used nonhuman primate (NHP) species for biomedical research and toxicology studies of novel therapeutics. In recent years, there has been a shortage of laboratory macaques due to a variety of competing factors. This was most recently exacerbated by the surge in NHP research required to address the severe acute respiratory syndrome (SARS)-coronavirus 2 pandemic. Continued support of these important studies has required the use of more varied cohorts of macaques, including animals with different origins, increased exposure to naturally occurring pathogens, and a wider age range. Diarrhea and diseases of the gastrointestinal tract are the most frequently occurring spontaneous findings in macaques of all origins and ages. The purpose of this review is to alert pathologists and scientists involved in NHP research to these findings and their impact on animal health and study endpoints, which may otherwise confound the interpretation of data generated using macaques.
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Affiliation(s)
| | | | - Anne D Lewis
- Oregon National Primate Research Center, Beaverton, Oregon, USA
| | - J Rachel Reader
- California National Primate Research Center, Davis, California, USA
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2
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Bui TH, Ikeuchi S, O'Brien YS, Niwa T, Hara-Kudo Y, Taniguchi T, Hayashidani H. Multiplex PCR method for differentiating highly pathogenic Yersinia enterocolitica and low pathogenic Yersinia enterocolitica, and Yersinia pseudotuberculosis. J Vet Med Sci 2021; 83:1982-1987. [PMID: 34732607 PMCID: PMC8762423 DOI: 10.1292/jvms.21-0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A multiplex PCR method for rapid and sensitive diagnosis, differentiating three pathogenic Yersinia groups such as the highly pathogenic Y. enterocolitica, including serotype O8, low pathogenic Y. enterocolitica, and Y. pseudotuberculosis, was developed. Four primer pairs were chosen to detect the genes fyuA, ail, inv, and virF, responsible for the virulence in pathogenic Yersinia species. Under the multiplex PCR conditions, the unique band patterns for the highly pathogenic Y. enterocolitica, low pathogenic Y. enterocolitica, and Y. pseudotuberculosis were generated from Yersinia strains. The detection limit of this method was 101-103 CFU per reaction tube. This multiplex PCR method could detect highly pathogenic Y. enterocolitica O8 from the wild rodent fecal samples that were culture-positive. Therefore, the new multiplex PCR method developed in this study is a useful tool for rapid and sensitive diagnosis, distinguishing three pathogenic Yersinia groups.
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Affiliation(s)
- Thi Hien Bui
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Shunsuke Ikeuchi
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yukiko Sassa O'Brien
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Takeshi Niwa
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yukiko Hara-Kudo
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Takahide Taniguchi
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Hideki Hayashidani
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
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Kumari S, Kumar RR, Mendiratta SK, Kumar D, Kumar A, Jawla J, Anurag, Rana P, Kumar D. Development of loop-mediated isothermal method and comparison with conventional PCR assay for rapid on spot identification of tissue of cattle origin. Journal of Food Science and Technology 2021; 58:4608-4615. [PMID: 34629525 DOI: 10.1007/s13197-020-04948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 10/24/2020] [Accepted: 12/21/2020] [Indexed: 11/30/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a diagnostic method for meat speciation with rapid and minimal equipment requirements. In this study, we developed cattle-specific tube-based LAMP assays targeting mitochondrial Cyt b gene sequence, compared with conventional PCR assay for specificity, sensitivity, and validation of the assay was made. The LAMP reaction was carried at 64 °C for 45 min, and results were confirmed by SYBR Green I dye and agarose gel-electrophoresis. The specificity of the assays was cross-tested with DNA of buffalo, goat, sheep, and pork. The amplification was observed with samples from cattle only without cross-reactivity with other meat species. The analytical sensitivity of LAMP and PCR method for cattle DNA detection was 0.0001 ng and 1 ng, respectively. Repeatability of the assay was achieved on samples from known/blind and admixture meat with other than cattle at the relative percentage of 20%, 10%, 5%, and 1%. The study concluded that the developed assay can be easily employed for the rapid identification of tissue of cattle origin in meat and meat products in low resource areas.
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Affiliation(s)
- Sarita Kumari
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India.,Division of Livestock Products Technology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, 334001 India
| | - R R Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India
| | - S K Mendiratta
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India
| | - Dhananjay Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India
| | - Arun Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India.,Division of Livestock Products Technology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, 334001 India
| | - Jyoti Jawla
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India
| | - Anurag
- Division of Livestock Production Management, Rajasthan University of Veterinary and Animal Sciences, Bikaner, 334001 India
| | - Preeti Rana
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatngar, Bareilly, 243122 India
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Yang Q, Deng S, Xu J, Farooq U, Yang T, Chen W, Zhou L, Gao M, Wang S. Poly(indole-5-carboxylic acid)/reduced graphene oxide/gold nanoparticles/phage-based electrochemical biosensor for highly specific detection of Yersinia pseudotuberculosis. Mikrochim Acta 2021; 188:107. [PMID: 33660086 DOI: 10.1007/s00604-020-04676-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/30/2020] [Indexed: 11/24/2022]
Abstract
Yersinia pseudotuberculosis is an enteric bacterium causing yersiniosis in humans. The existing Yersinia pseudotuberculosis detection methods are time-consuming, requiring a sample pretreatment step, and are unable to discriminate live/dead cells. The current work reports a phage-based electrochemical biosensor for rapid and specific detection of Yersinia pseudotuberculosis. The conductive poly(indole-5-carboxylic acid), reduced graphene oxide, and gold nanoparticles are applied for surface modification of the electrode. They possess ultra-high redox stability and retain 97.7% of current response after performing 50 consecutive cycles of cyclic voltammetry.The specific bacteriophages vB_YepM_ZN18 we isolated from hospital sewage water were immobilized on modified electrodes by Au-NH2 bond between gold nanoparticles and phages. The biosensor fabricated with nanomaterials and phages were utilized to detect Yersinia pseudotuberculosis successfully with detection range of 5.30 × 102 to 1.05 × 107 CFU mL-1, detection limit of 3 CFU mL-1, and assay time of 35 min. Moreover, the biosensor can specifically detect live Yersinia pseudotuberculosis without responding to phage-non-host bacteria and dead Yersinia pseudotuberculosis cells. These results suggest that the proposed biosensor is a promising tool for the rapid and selective detection of Yersinia pseudotuberculosis in food, water, and clinical samples.
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Affiliation(s)
- Qiaoli Yang
- Advanced Biomaterials & Tissue Engineering Centre, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Sangsang Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Jingjing Xu
- Advanced Biomaterials & Tissue Engineering Centre, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Umer Farooq
- Advanced Biomaterials & Tissue Engineering Centre, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Taotao Yang
- Advanced Biomaterials & Tissue Engineering Centre, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Wei Chen
- Advanced Biomaterials & Tissue Engineering Centre, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Lei Zhou
- Advanced Biomaterials & Tissue Engineering Centre, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
| | - Shenqi Wang
- Advanced Biomaterials & Tissue Engineering Centre, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
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Randriantseheno LN, Rahantamalala A, Randrianierenana AL, Rajerison M, Andrianaivoarimanana V. Development and evaluation of loop-mediated isothermal amplification for detection of Yersinia pestis in plague biological samples. PLoS One 2020; 15:e0237655. [PMID: 32810167 PMCID: PMC7437451 DOI: 10.1371/journal.pone.0237655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/30/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Several tests are available for plague confirmation but bacteriological culture with Yersinia pestis strain isolation remains the gold standard according to the World Health Organization. However, this is a time consuming procedure; requiring specific devices and well-qualified staff. In addition, strain isolation is challenging if antibiotics have been administered prior to sampling. Here, we developed a loop-mediated isothermal amplification (LAMP) technique, a rapid, simple, sensitive and specific technique that would be able to detect Y. pestis in human biological samples. METHODS LAMP primers were designed to target the caf1 gene which is specific to Y. pestis. The detection limit was determined by testing 10-fold serial dilution of Y. pestis DNA. Cross-reactivity was tested using DNA extracts from 14 pathogens and 47 residual samples from patients suffering from non-plague diseases. Specificity and sensitivity of the LAMP caf1 were assessed on DNA extracts of 160 human biological samples. Then, the performance of the LAMP caf1 assay was compared to conventional PCR and bacteriological culture. RESULTS The detection limit of the developed Y. pestis LAMP assay was 3.79 pg/μl, similar to conventional PCR. The result could be read out within 45 min and as early as 35 minutes in presence of loop primer, using a simple water bath at 63°C. This is superior to culture with respect to time (requires up to 10 days) and simplicity of equipment compared to PCR. Furthermore, no cross-reactivity was found when tested on DNA extracts from other pathogens and human biological samples from patients with non-plague diseases. Compared to the gold standard, LAMP sensitivity and specificity were 97.9% (95% CI: 89.1%-99.9%) and 94.6% (95% CI: 88.6%-97.9%), respectively. CONCLUSION LAMP detected Y. pestis effectively with high sensitivity and specificity in human plague biological samples. It can potentially be used in the field during outbreaks in resource limited countries such as Madagascar.
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Affiliation(s)
- Lovasoa N. Randriantseheno
- Plague Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Department of Applied and Fundamental Biochemistry, University of Antananarivo, Antananarivo, Madagascar
| | - Anjanirina Rahantamalala
- Immunology of Infectious Diseases Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Ando L. Randrianierenana
- Department of Applied and Fundamental Biochemistry, University of Antananarivo, Antananarivo, Madagascar
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Priya GB, Agrawal RK, Prince Milton AA, Mishra M, Mendiratta S, Luke A, Inbaraj S, Singh BR, Kumar D, Kumar GR, Rajkhowa S. Rapid and visual detection of Salmonella in meat using invasin A (invA) gene-based loop-mediated isothermal amplification assay. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Yao Y, Li Y, Liu Q, Zhou K, Zhao W, Liu S, Yang J, Jiang Y, Sui G. Rapid detection of hepatocellular carcinoma metastasis using reverse transcription loop-mediated isothermal amplification. Talanta 2020; 208:120402. [PMID: 31816739 DOI: 10.1016/j.talanta.2019.120402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
The main therapies of hepatocellular carcinoma (HCC) are hepatectomy and liver transplantation, but the recurrence rate of HCC after radical resection remains high. We established a novel method based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid identification of four cancer stem cell-specific biomarkers to estimate the potential risk of HCC metastasis. After optimizing the final concentrations of Mg2+ and betaine, the sensitivity limits for detection of CK19 and EpCAM could reach 10 to 20 copies, while the sensitivity limits for the detection of CD133 and CD90 could reach 10 copies. We detected clinical specimens from 10 HCC patients and performed analysis before and after receiving hepatectomy using RT-LAMP and quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results of both were consistent, but RT-LAMP was proved to be a more rapid, more sensitive, and more economic approach. This novel method is expected to estimate the recurrence and metastasis of HCC for clinical application by combining various low-cost circulating tumor cell sorting and detection tools.
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Affiliation(s)
- Yuhan Yao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Yuancheng Li
- Institute of Biomedical Science, Fudan University, No. 138 Yixueyuan Road, Shanghai, 200032, PR China
| | - Qi Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Kaiqian Zhou
- The Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Wang Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Sixiu Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Jielin Yang
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, 200131, PR China
| | - Yuan Jiang
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, 200131, PR China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China; Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CICAEET), Nanjing University of Information Science & Technology, Nanjing, 210044, PR China.
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8
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Li C, Murugaiyan J, Thomas C, Alter T, Riedel C. Isolate Specific Cold Response of Yersinia enterocolitica in Transcriptional, Proteomic, and Membrane Physiological Changes. Front Microbiol 2020; 10:3037. [PMID: 32038527 PMCID: PMC6990146 DOI: 10.3389/fmicb.2019.03037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022] Open
Abstract
Yersinia enterocolitica, a zoonotic foodborne pathogen, is able to withstand low temperatures. This psychrotrophic ability allows it to multiply in food stored in refrigerators. However, little is known about the Y. enterocolitica cold response. In this study, isolate-specific behavior at 4°C was demonstrated and the cold response was investigated by examining changes in phenotype, gene expression, and the proteome. Altered expression of cold-responsive genes showed that the ability to survive at low temperature depends on the capacity to acclimate and adapt to cold stress. This cold acclimation at the transcriptional level involves the transient induction and effective repression of cold-shock protein (Csp) genes. Moreover, the resumption of expression of genes encoding other non-Csp is essential during prolonged adaptation. Based on proteomic analyses, the predominant functional categories of cold-responsive proteins are associated with protein synthesis, cell membrane structure, and cell motility. In addition, changes in membrane fluidity and motility were shown to be important in the cold response of Y. enterocolitica. Isolate-specific differences in the transcription of membrane fluidity- and motility-related genes provided evidence to classify strains within a spectrum of cold response. The combination of different approaches has permitted the systematic description of the Y. enterocolitica cold response and gives a better understanding of the physiological processes underlying this phenomenon.
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Affiliation(s)
- Chenyang Li
- Institute of Food Safety and Food Hygiene, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jayaseelan Murugaiyan
- Institute for Animal Hygiene and Environmental Health, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Department of Biotechnology, SRM University AP, Amaravati, India
| | - Christian Thomas
- Department of Food Science and Technology, Beuth University of Applied Sciences Berlin, Berlin, Germany
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Carolin Riedel
- Institute of Food Safety and Food Hygiene, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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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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Zhang D, Gao B, Zhao C, Liu H. Visualized Quantitation of Trace Nucleic Acids Based on the Coffee-Ring Effect on Colloid-Crystal Substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:248-253. [PMID: 30512960 DOI: 10.1021/acs.langmuir.8b03609] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We report a visualized quantitative detection method for nucleic acid amplification tests based on the coffee-ring effect on colloid-crystal substrates. The solution for loop-mediated isothermal amplification (LAMP) of DNA is drop cast on a colloid-crystal surface. After complete drying, a coffee ring containing the LAMP byproduct (i.e., magnesium pyrophosphate) is formed, and it is found that the width of the coffee ring is linearly correlated to the logarithm of the original DNA concentration before the isothermal amplification. Importantly, compared with other substrates, we found that the colloid-crystal substrate is an appropriate substrate for carrying out the assay of high sensitivity. On the basis of these findings, we develop a coffee-ring-based assay for quantitative readout of trace DNA in a sample. The assay requires 0.50 μL of the sample and is completed in 5 min in a homemade chamber with constant humidity. Semiquantitative detection of trace DNA is performed using naked eyes. With the use of a smartphone, the DNA in a sample can be quantitatively detected with a limit of detection of 20 copies.
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Affiliation(s)
- Dagan Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Bingbing Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
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Smartphone-based pathogen diagnosis in urinary sepsis patients. EBioMedicine 2018; 36:73-82. [PMID: 30245056 PMCID: PMC6197494 DOI: 10.1016/j.ebiom.2018.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/01/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022] Open
Abstract
Background There is an urgent need for rapid, sensitive, and affordable diagnostics for microbial infections at the point-of-care. Although a number of innovative systems have been reported that transform mobile phones into potential diagnostic tools, the translational challenge to clinical diagnostics remains a significant hurdle to overcome. Methods A smartphone-based real-time loop-mediated isothermal amplification (smaRT-LAMP) system was developed for pathogen ID in urinary sepsis patients. The free, custom-built mobile phone app allows the phone to serve as a stand-alone device for quantitative diagnostics, allowing the determination of genome copy-number of bacterial pathogens in real time. Findings A head-to-head comparative bacterial analysis of urine from sepsis patients revealed that the performance of smaRT-LAMP matched that of clinical diagnostics at the admitting hospital in a fraction of the time (~1 h vs. 18–28 h). Among patients with bacteremic complications of their urinary sepsis, pathogen ID from the urine matched that from the blood – potentially allowing pathogen diagnosis shortly after hospital admission. Additionally, smaRT-LAMP did not exhibit false positives in sepsis patients with clinically negative urine cultures. Interpretation The smaRT-LAMP system is effective against diverse Gram-negative and -positive pathogens and biological specimens, costs less than $100 US to fabricate (in addition to the smartphone), and is configurable for the simultaneous detection of multiple pathogens. SmaRT-LAMP thus offers the potential to deliver rapid diagnosis and treatment of urinary tract infections and urinary sepsis with a simple test that can be performed at low cost at the point-of-care. Fund National Institutes of Health, Chan-Zuckerberg Biohub, Bill and Melinda Gates Foundation.
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12
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Virulence and resistance on various pathogens mediated by mobile genetic integrons via high flux assays. Microb Pathog 2018; 114:75-79. [DOI: 10.1016/j.micpath.2017.11.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 11/24/2017] [Accepted: 11/24/2017] [Indexed: 02/08/2023]
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13
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Feng N, Zhou Y, Fan Y, Bi Y, Yang R, Zhou Y, Wang X. Yersinia pestis detection by loop-mediated isothermal amplification combined with magnetic bead capture of DNA. Braz J Microbiol 2018; 49:128-137. [PMID: 28887007 PMCID: PMC5790586 DOI: 10.1016/j.bjm.2017.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/30/2016] [Accepted: 03/17/2017] [Indexed: 12/25/2022] Open
Abstract
We developed a loop-mediated isothermal amplification (LAMP) assay for the detection of Y. pestis by targeting the 3a sequence on chromosome. All 11 species of the genus Yersinia were used to evaluate the specificity of LAMP and PCR, demonstrating that the primers had a high level of specificity. The sensitivity of LAMP or PCR was 2.3 or 23CFU for pure culture, whereas 2.3×104 or 2.3×106CFU for simulated spleen and lung samples. For simulated liver samples, the sensitivity of LAMP was 2.3×106CFU, but PCR was negative at the level of 2.3×107CFU. After simulated spleen and lung samples were treated with magnetic beads, the sensitivity of LAMP or PCR was 2.3×103 or 2.3×106CFU, whereas 2.3×105 or 2.3×107CFU for magnetic bead-treated liver samples. These results indicated that some components in the tissues could inhibit LAMP and PCR, and liver tissue samples had a stronger inhibition to LAMP and PCR than spleen and lung tissue samples. LAMP has a higher sensitivity than PCR, and magnetic bead capture of DNAs could remarkably increase the sensitivity of LAMP. LAMP is a simple, rapid and sensitive assay suitable for application in the field or poverty areas.
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Affiliation(s)
- Na Feng
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yazhou Zhou
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yanxiao Fan
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yujing Bi
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yusen Zhou
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China.
| | - Xiaoyi Wang
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China.
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14
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Hu L, Ma L, Zheng S, He X, Wang H, Brown E, Hammack T, Zhang G. Evaluation of 3M Molecular Detection System and ANSR Pathogen Detection System for rapid detection of Salmonella from egg products. Poult Sci 2017; 96:1410-1418. [DOI: 10.3382/ps/pew399] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/13/2016] [Indexed: 01/22/2023] Open
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Zang X, Tang H, Jiao X, Huang J. Can a visual loop-mediated isothermal amplification assay stand out in different detection methods when monitoring Campylobacter jejuni from diverse sources of samples? Food Control 2017. [DOI: 10.1016/j.foodcont.2016.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Detection on integron carried gene cassettes from pathogens by loop mediated isothermal amplification assays. Microb Pathog 2017; 107:304-308. [PMID: 28392412 DOI: 10.1016/j.micpath.2017.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 11/23/2022]
Abstract
In this study, a number of frequently detected gene cassettes from bacterial integrons have been detected and characterized by rapid and simple loop-mediated isothermal amplification (LAMP) assays. Six gene cassettes commonly found in class 1 integrons were studied, including dfrA12, dfrA17, aadA2, aadA5, orfF, and blaVIM2. Primers design, sensitivity, specificity, optimization of each LAMP assay, as well as application of the developed 6 individual LAMP assays on a large scale of bacteria, had been conducted. The optimal amplification was obtained with temperature as 65 °C, reaction time span as 45 min and volume as 25 μl. For application, 272 isolates with various gene cassettes yielded expectable positive amplicons and other 685 integron-negative bacteria showed negative results for the LAMP assays, totaling 100% detection rate and specificity.
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Cao C, Zhang F, Ji M, Pei F, Fan X, Shen H, Wang Q, Yang W, Wang Y. Development of a loop-mediated isothermal amplification method for rapid detection of streptococcal pyrogenic exotoxin B. Toxicon 2016; 117:53-8. [DOI: 10.1016/j.toxicon.2016.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 11/30/2022]
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Horinouchi T, Nozu K, Hamahira K, Inaguma Y, Abe J, Nakajima H, Kugo M, Iijima K. Yersinia pseudotuberculosis infection in Kawasaki disease and its clinical characteristics. BMC Pediatr 2015; 15:177. [PMID: 26561332 PMCID: PMC4642785 DOI: 10.1186/s12887-015-0497-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 10/23/2015] [Indexed: 12/02/2022] Open
Abstract
Background The etiology of Kawasaki disease (KD) is unknown. Reportedly, there is an association between KD and Yersinia pseudotuberculosis (YPT). Steroid therapy for KD patients with high risk of cardiac sequelae (CS) has been reported; however, the number of reports is limited. Methods We conducted a prospective study of 108 patients with newly diagnosed KD in one year to determine how many KD patients have positive anti-YPT antibody titers and/or positive anti-YPT-derived mitogen (YPM) antibody titers. In addition, we tried to identify clinical differences between KD patients in whom YPT infection was or not a contributing factor. We also compared clinical characteristics of patients treated with the protocol of the Randomized controlled trial to Assess Immunoglobulin plus Steroid Efficacy for Kawasaki disease (RAISE) study (RAISE group) and with the conventional Intravenous immunoglobulin (IVIG) protocol (conventional group). Results Eleven patients (10 %) were positive for anti-YPT and/or anti-YPM antibodies (positive group) and 97 (90 %) were negative (negative group). Cardiac sequelae (CS) occurred significantly more frequently in the positive than the negative group (two patients, 18 % vs one patient, 1 %, p = 0.027). Forty patients were in the RAISE group. Two of 40 (5 %) in the RAISE group and one of 68 (1.47 %) in the conventional group had CS (p = 0.55). Conclusions KD patients with YPT infection had CS significantly more frequently and treatment with RAISE protocol did not decrease the frequency of CS in our cohort, nor did YPT infection affect risk scores of no response to IVIG. However, our sample size was overly small to draw such conclusions. Further investigation in a larger cohort is necessary to confirm our findings. Additionally, further research is needed to determine whether early diagnosis of YPT can prevent KD from developing and reduce the incidence of CS.
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Affiliation(s)
- Tomoko Horinouchi
- Department of Pediatrics, Japanese Red Cross Society Himeji Hospital, Hyogo, Japan.
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Hospital, Kobe, Japan.
| | - Kiyoshi Hamahira
- Department of Pediatrics, Japanese Red Cross Society Himeji Hospital, Hyogo, Japan.
| | - Yosuke Inaguma
- Department of Pediatrics, Japanese Red Cross Society Himeji Hospital, Hyogo, Japan.
| | - Jun Abe
- Department of Allergy and Immunology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Hiroshi Nakajima
- Department of Bacteriology, Okayama Prefectural Institute for Environmental Science and Public Health, Okayama, Japan.
| | - Masaaki Kugo
- Department of Pediatrics, Japanese Red Cross Society Himeji Hospital, Hyogo, Japan.
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Hospital, Kobe, Japan.
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Abdullah J, Saffie N, Sjasri FAR, Husin A, Abdul-Rahman Z, Ismail A, Aziah I, Mohamed M. Rapid detection of Salmonella Typhi by loop-mediated isothermal amplification (LAMP) method. Braz J Microbiol 2015; 45:1385-91. [PMID: 25763045 PMCID: PMC4323314 DOI: 10.1590/s1517-83822014000400032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 04/17/2014] [Indexed: 11/21/2022] Open
Abstract
An in-house loop-mediated isothermal amplification (LAMP) reaction was established and evaluated for sensitivity and specificity in detecting the presence of Salmonella Typhi (S. Typhi) isolates from Kelantan, Malaysia. Three sets of primers consisting of two outer and 4 inner were designed based on locus STBHUCCB_38510 of chaperone PapD of S. Typhi genes. The reaction was optimised using genomic DNA of S. Typhi ATCC7251 as the template. The products were visualised directly by colour changes of the reaction. Positive results were indicated by green fluorescence and negative by orange colour. The test was further evaluated for specificity, sensitivity and application on field samples. The results were compared with those obtained by gold standard culture method and Polymerase Chain Reaction (PCR). This method was highly specific and -10 times more sensitive in detecting S. Typhi compared to the optimised conventional polymerase chain reaction (PCR) method.
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Affiliation(s)
- J Abdullah
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - N Saffie
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - F A R Sjasri
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - A Husin
- Hospital Raja Perempuan Zainab II 15586 Kota BharuKelantan Malaysia Hospital Raja Perempuan Zainab II, 15586 Kota Bharu, Kelantan, Malaysia
| | - Z Abdul-Rahman
- School of Medical Sciences Universiti Sains Malaysia Kubang Kerian Kelantan School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan
| | - A Ismail
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - I Aziah
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - M Mohamed
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
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20
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Loop-mediated isothermal amplification assays for screening of bacterial integrons. Biol Res 2014; 47:53. [PMID: 25418445 PMCID: PMC4222780 DOI: 10.1186/0717-6287-47-53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/26/2014] [Indexed: 11/11/2022] Open
Abstract
Background The occurrence and prevalence of integrons in clinical microorganisms and their role played in antimicrobial resistance have been well studied recently. As screening and detection of integrons are concerned, current diagnostic methodologies are restricted by significant drawbacks and novel methods are required for integrons detection. Results In this study, three loop-mediated isothermal amplification (LAMP) assays targeting on class 1, 2 and 3 integrons were implemented and evaluated. Optimization of these detection assays were performed, including studing on the reaction temperature, volume, time, sensitivity and specificity (both primers and targets). Application of the established LAMP assays were further verified on a total of 1082 isolates (previously identified to be 397 integron-positive and 685 integron-negative strains). According to the results, the indispensability of each primer had been confirmed and the optimal reaction temperature, volume and time were found to be 65°C, 45 min and 25 μL, respectively. As application was concerned, 361, 28 and 8 isolates carrying intI1, intI2 and intI3 yielded positive amplicons, respectively. Other 685 integron-negative bacteria were negative for the integron-screening LAMP assays, totaling the detection rate and specificity to be 100%. Conclusions The intI1-, intI2- and intI3-LAMP assays established in this study were demonstrated to be the valid and rapid detection methodologies for the screening of bacterial integrons.
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21
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Luo J, Fang X, Ye D, Li H, Chen H, Zhang S, Kong J. A real-time microfluidic multiplex electrochemical loop-mediated isothermal amplification chip for differentiating bacteria. Biosens Bioelectron 2014; 60:84-91. [DOI: 10.1016/j.bios.2014.03.073] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/27/2014] [Accepted: 03/31/2014] [Indexed: 11/16/2022]
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22
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Zhang H, Feng J, Xue R, Du XJ, Lu X, Wang S. Loop-mediated isothermal amplification assays for detecting Yersinia pseudotuberculosis in milk powders. J Food Sci 2014; 79:M967-71. [PMID: 24697660 DOI: 10.1111/1750-3841.12436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/26/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED Yersinia pseudotuberculosis is a Gram-negative foodborne pathogen that causes several diseases, such as enteritis, septicemia, and reactive arthritis. Loop-mediated isothermal amplification (LAMP) assay targeting the 16S-23S rDNA internal transcribed spacer (ITS) region was developed to detect Y. pseudotuberculosis in milk powder. The DNA amplification could be completed in 1 h, and detected by produced white precipitate visible to naked eyes. The detection limit of LAMP assay was 10(0) fg/reaction for genomic DNA, and 10(0) CFU/100 g milk powder coupled with 12 h enrichment. LAMP assay is 100 times more sensitive than conventional polymerase chain reaction method for detecting Y. pseudotuberculosis, and correctly identified 18 cases of Y. pseudotuberculosis contaminations from 236 commercial milk powder products. In conclusion, the developed LAMP assay may facilitate rapid detection of Y. pseudotuberculosis contaminations in agricultural and food products. PRACTICAL APPLICATION Rapid and accurate detection of Yersinia pseudotuberculosis in milk products.
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Affiliation(s)
- Hongwei Zhang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin Univ. of Science and Technology, Tianjin, 300457, China; Food, Nutrition, and Health Program, Faculty of Land and Food Systems, Univ. of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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23
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Zeng Y, Zhang X, Nie K, Ding X, Ring BZ, Xu L, Dai L, Li X, Ren W, Shi L, Ma X. Rapid quantitative detection of Human immunodeficiency virus type 1 by a reverse transcription-loop-mediated isothermal amplification assay. Gene 2014; 541:123-8. [PMID: 24630968 DOI: 10.1016/j.gene.2014.03.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/13/2014] [Accepted: 03/07/2014] [Indexed: 11/28/2022]
Abstract
Accurate and rapid quantitation of Human immunodeficiency virus type 1 (HIV-1) RNA levels is a critical aspect in estimating the effect of antiviral therapy and establishing therapeutic schedule. Thus, for the first time, a rapid quantitative reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was designed to quantitate HIV-1 RNA. The results showed that the dynamic range was from 2.5×10(2) to 10(7) copies with a coefficient of determination (R(2)) of 0.991, and the limit of detection of RT-LAMP by Probit analysis at the 95% detection level was 196 copies. The intra-assay coefficient of variation (CV) ranged from 0.67% to 2.08% at 10(7) copies and 7.25% to 12.97% at 250 copies. The CVs of inter-assay were 2.39% and 13.93% for the high and low copy numbers, respectively. No cross-reaction with Human immunodeficiency virus type 2 (HIV-2), Human T lymphotrophic virus type 1 (HTLV-1) and Hepatitis C virus (HCV) was observed and a good agreement between the RT-LAMP method and the real-time reverse transcription-polymerase chain reaction (qRT-PCR) test was achieved. This proposed RT-LAMP method could be useful for rapid diagnosis of high risk group and pharmacodynamic assessment of anti-HIV drug, especially in less-equipped laboratories of impoverished areas.
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Affiliation(s)
- Yalan Zeng
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Xiaoguang Zhang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kai Nie
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiong Ding
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Brian Z Ring
- Institute of Genomic and Personalized Medicine, School of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Lanying Xu
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Lei Dai
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Xiying Li
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Wei Ren
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Lei Shi
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China.
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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Su J, Liu X, Cui H, Li Y, Chen D, Li Y, Yu G. Rapid and simple detection of methicillin-resistance Staphylococcus aureus by orfX loop-mediated isothermal amplification assay. BMC Biotechnol 2014; 14:8. [PMID: 24456841 PMCID: PMC3902190 DOI: 10.1186/1472-6750-14-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/21/2014] [Indexed: 11/10/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the most prevalent pathogens responsible for nosocomial infections throughout the world. As clinical MRSA diagnosis is concerned, current diagnostic methodologies are restricted by significant drawbacks and novel methods are required for MRSA detection. This study aimed at developing a simple loop-mediated isothermal amplification (LAMP) assay targeting on orfX for the rapid detection of methicillin-resistance Staphylococcus aureus (MRSA). Results The protocol was designed by targeting orfX, a highly conserved open reading frame in S. aureus. One hundred and sixteen reference strains, including 52 Gram-positive and 64 Gram-negative isolates, were included for evaluation and optimization of the orfX-LAMP assay. This assay had been further performed on 667 Staphylococcus (566 MRSA, 25 MSSA, 53 MRCNS and 23 MSCNS) strains and were comparatively validated by PCR assay using primers F3 and B3, with rapid template DNA processing, simple equipments (water bath) and direct result determination (both naked eye and under UV light) applied. The indispensability of each primer had been confirmed, and the optimal amplification was obtained under 65°C for 45 min. The 25 μl reactant was found to be the most cost-efficient volume, and the detection limit was determined to be 10 DNA copies and 10 CFU/reaction. High specificity was observed when orfX-LAMP assay was subjected to 116 reference strains. For application, 557 (98.4%, 557/566) and 519 (91.7%, 519/566) tested strains had been detected positive by LAMP and PCR assays. The detection rate, positive predictive value (PPV) and negative predictive value (NPV) of orfX-LAMP were 98.4%, 100% and 92.7% respectively. Conclusions The established orfX-LAMP assay had been demonstrated to be a valid and rapid detection method on MRSA.
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Affiliation(s)
| | | | | | | | - Dingqiang Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical College, Guangzhou 510120, China.
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Reverse transcription loop-mediated isothermal amplification for rapid detection of the newly emerged poultry Flavivirus. Folia Microbiol (Praha) 2012; 58:277-82. [PMID: 23152303 DOI: 10.1007/s12223-012-0204-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
Abstract
Poultry Flavivirus (PF) was a recently emerged virus with high morbidity rates and mortality rates in China. It is the causative agent of egg drop syndrome at present. Development of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was the most efficient way to prevent and control the PF disease. The assay was performed at 64 °C for 45 min, using six specific primers that recognized eight targets of the PF E gene. The RT-LAMP assay, compared to conventional reverse transcription polymerase chain reaction, has 100-fold-greater sensitivity, with a detection limit of 1 × 10(-3) copies per μL RNA and no cross-reaction with poultry other viruses. The RT-LAMP assay is a valuable tool for detected PF without requiring any sophisticated equipment, and the detection has potential usefulness for clinical diagnosis in the field.
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26
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Afzal M, Shahid AA, Shehzadi A, Nadeem S, Husnain T. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis. Bioinformation 2012; 8:687-90. [PMID: 23055611 PMCID: PMC3449372 DOI: 10.6026/97320630008687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/05/2012] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. AVAILABILITY http://www.cemb.edu.pk/sw.html ABBREVIATIONS RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.
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Affiliation(s)
- Muhammad Afzal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Department of Bioinformatics and Biotechnology, GC University, Faisalabad, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abida Shehzadi
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahid Nadeem
- Department of Bioinformatics and Biotechnology, GC University, Faisalabad, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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27
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Xie G, Zhang Q, Han N, Shi C, Wang X, Liu Q, Huang J. An improved method for detection of Edwardsiella tarda by loop-mediated isothermal amplification by targeting the EsrB gene. CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY = ZHONGGUO HAI YANG HU ZHAO XUE BAO 2012; 30:595-603. [PMID: 32214585 PMCID: PMC7087700 DOI: 10.1007/s00343-012-1293-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 02/20/2012] [Indexed: 06/02/2023]
Abstract
Edwardsiella tarda is a major pathogen in aquatic environments that can cause heavy economic losses. An improved method for quick and accurate detection of E. tarda by loop-mediated isothermal amplification (LAMP) with two additional loop primers was developed by targeting the EsrB gene (EsrB - LAMP). In this method, the Mg2+ concentration, reaction temperature, and reaction time were optimized to 8 mmol/L, 61°C, and 40 min, respectively. The detection limit with the EsrB gene was as low as 10 copies, which is 100 times more sensitive than that of conventional polymerase chain reaction (PCR). The EsrB-LAMP assay was shown more sensitive and rapid than previously reported LAMP assays targeting the hemolysin gene ( hemolysin -LAMP) for detection of E. tarda. The EsrB -LAMP was also highly specific to E. tarda and had no cross-reaction with 13 other strains of bacteria. The assay can be carried out in a simple heating device and the EsrB-LAMP products can be visually detected by adding fluorescent dye to the reaction mixture. Taken together, the improved EsrB-LAMP diagnostic protocol has the potential for detection of E. tarda from indoor and outdoor samples.
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Affiliation(s)
- Guosi Xie
- Key Laboratory of Marine Fishery Resources Sustainable Utilization, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306 China
| | - Qingli Zhang
- Key Laboratory of Marine Fishery Resources Sustainable Utilization, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
| | - Nana Han
- Key Laboratory of Marine Fishery Resources Sustainable Utilization, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
| | - Chengyin Shi
- Key Laboratory of Marine Fishery Resources Sustainable Utilization, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
| | - Xiuhua Wang
- Key Laboratory of Marine Fishery Resources Sustainable Utilization, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
| | - Qinghui Liu
- Key Laboratory of Marine Fishery Resources Sustainable Utilization, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
| | - Jie Huang
- Key Laboratory of Marine Fishery Resources Sustainable Utilization, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306 China
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Xu Z, Li L, Chu J, Peters BM, Harris ML, Li B, Shi L, Shirtliff ME. Development and application of loop-mediated isothermal amplification assays on rapid detection of various types of staphylococci strains. Food Res Int 2012; 47:166-173. [PMID: 22778501 PMCID: PMC3390935 DOI: 10.1016/j.foodres.2011.04.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) method for rapid detection of various Staphylococcus strains and associated antibiotic resistance determinant had been developed and evaluated in this study. Six primers, including outer primers, inner primers and loop primers, were specially designed for recognizing eight distinct sequences on three targets: 16SrRNA, femA and mecA.. Forty-one reference strains, including various species of gram-negative and -positive isolates, were included in this study to evaluate and optimize LAMP assays. The optimal reaction condition was found to be 65 °C for 45 min, with detection limits at 100 fg DNA/tube and 10 CFU/reaction for 16S rRNA, 100 fg DNA/tube and 10 CFU/reaction for femA, 1 pg DNA/tube and 100 CFU/reaction for mecA, respectively. Application of LAMP assays were performed on 118 various types of Staphylococcus isolates, the detection rate of LAMP assays for the 16SrRNA, femA and mecA was 100% (118/118), 98.5% (64/65) and 94.3% (66/70), and the negative predictive value (NPV) was 100%, 98.1% and 92.3% respectively; with a 100% positive predictive value (PPV) for all three targets. In conclusion, LAMP assays were demonstrated to be useful and powerful tools for rapid detection of various Staphylococcus strains, and undoubtedly, the rapidness, technical simplicity, and cost-effectiveness of LAMP assays will demonstrate broad application for bacteriological detection of food-borne Methicillin-resistant Staphylococcus (MRS) isolates.
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Affiliation(s)
- Zhenbo Xu
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
| | - Lin Li
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Jin Chu
- School of Food Science and Nutrition, Faculty of Mathematics and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Brian M. Peters
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
- Graduate Program in Life Sciences, Molecular Microbiology and Immunology Program, University of Maryland, Baltimore, Maryland, USA
| | - Megan L. Harris
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
| | - Bing Li
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Lei Shi
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Mark E. Shirtliff
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
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Multiple-locus variable-number tandem-repeat analysis of pathogenic Yersinia enterocolitica in China. PLoS One 2012; 7:e37309. [PMID: 22615971 PMCID: PMC3352880 DOI: 10.1371/journal.pone.0037309] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 04/18/2012] [Indexed: 11/19/2022] Open
Abstract
The predominant bioserotypes of pathogenic Yersinia enterocolitica in China are 2/O: 9 and 3/O: 3; no pathogenic O: 8 strains have been found to date. Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA) based on seven loci was able to distinguish 104 genotypes among 218 pathogenic Y. enterocolitica isolates in China and from abroad, showing a high resolution. The major pathogenic serogroups in China, O: 3 and O: 9, were divided into two clusters based on MLVA genotyping. The different distribution of Y. enterocolitica MLVA genotypes maybe due to the recent dissemination of specific clones of 2/O: 9 and 3/O: 3 strains in China. MLVA was a helpful tool for bacterial pathogen surveillance and investigation of pathogenic Y. enterocolitica outbreaks.
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Cai SH, Wang B, Lu YS, Jian JC, Wu ZH. Development of loop-mediated isothermal amplification method for rapid detection of Streptococcus iniae, the causative agent of streptococcicosis in fish. J Basic Microbiol 2011; 52:116-22. [PMID: 21780152 DOI: 10.1002/jobm.201100082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 04/07/2011] [Indexed: 11/06/2022]
Abstract
Streptococcus iniae is a major pathogen that causes sever economic losses in tilapia aquaculture. A set of four specific primers was designed by targeting lctO gene. With Bst DNA polymerase, the target DNA can be clearly amplified for 60 min at 64 °C in a simple water bath. The sensitivity of the LAMP assay for the detection of S. iniae is about 12.4 cells per reaction in both of pure cultures and added fish tissues cultures. LAMP products could be judged with agar gel or naked eye after addition of SYBR Green I. There were no cross-reactions with other bacterial strains indicating high specificity of the LAMP. The LAMP method was also applied to detect S. iniae-infected tilapia tissues effectively. The LAMP assay reported here indicates the potential usefulness of the technique as a valuable simple, rapid alternative procedure for the detection of S. iniae during streptococcicosis monitoring of cultured fish.
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Affiliation(s)
- Shuang-Hu Cai
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
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31
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Sun X, Xu Q, Pan Y, Lan W, Zhao Y, Wu VCH. A loop-mediated isothermal amplification method for rapid detection of Vibrio parahaemolyticus in seafood. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0255-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Rapid detection of Vibrio parahaemolyticus strains and virulent factors by loop-mediated isothermal amplification assays. Food Sci Biotechnol 2010. [DOI: 10.1007/s10068-010-0170-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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33
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Suzuki R, Ihira M, Enomoto Y, Yano H, Maruyama F, Emi N, Asano Y, Yoshikawa T. Heat denaturation increases the sensitivity of the cytomegalovirus loop-mediated isothermal amplification method. Microbiol Immunol 2010; 54:466-70. [DOI: 10.1111/j.1348-0421.2010.00236.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ahn YC, Cho MH, Yoon IK, Jung DH, Lee EY, Kim JH, Jang WC. Detection of Salmonella Using the Loop Mediated Isothermal Amplification and Real-time PCR. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2010. [DOI: 10.5012/jkcs.2010.54.02.215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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35
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Pathogenic strains of Yersinia enterocolitica isolated from domestic dogs (Canis familiaris) belonging to farmers are of the same subtype as pathogenic Y. enterocolitica strains isolated from humans and may be a source of human infection in Jiangsu Province, China. J Clin Microbiol 2010; 48:1604-10. [PMID: 20181899 DOI: 10.1128/jcm.01789-09] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated 326 Yersinia enterocolitica strains from 5,919 specimens from patients with diarrhea at outpatient clinics, livestock, poultry, wild animals, insect vectors, food, and the environment in the cities of Nantong and Xuzhou in Jiangsu Province, China, from 2004 to 2008. The results showed that the 12 pathogenic strains were of the O:3 serotype. Six strains were isolated from domestic dogs (Canis familiaris) belonging to farmers and were found to be the primary carriers of pathogenic Y. enterocolitica strains, especially in Xuzhou. Pulsed-field gel electrophoresis analysis of the pathogenic strains from dogs belonging to farmers showed that they shared the same patterns as strains from diarrhea patients isolated in 1994. This indicates that the strains from domestic dogs have a close correlation with the strains causing human infections.
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Zhao X, Li Y, Wang L, You L, Xu Z, Li L, He X, Liu Y, Wang J, Yang L. Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples. Mol Biol Rep 2009; 37:2183-8. [PMID: 19685165 DOI: 10.1007/s11033-009-9700-6] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 07/29/2009] [Indexed: 11/29/2022]
Abstract
We developed and evaluated the specificity and sensitivity of a loop-mediated isothermal amplification (LAMP) method for rapid detection of the food-borne Escherichia coli O157 strains. Six primers, including outer primers, inner primers and loop primers, were specially designed for recognizing eight distinct sequences on three targets, which were rfbE, stx1 and stx2. The detection limits were found to be 100, 100 and 10 fg DNA/tube for rfbE, stx1 and stx2, respectively. Application of LAMP assays were performed on 417 food-borne E. coli strains, the sensitivity of LAMP assays for the rfbE, stx1 and stx2 was 100, 95.3 and 96.3%, and the negative predictive value was 100, 96.7 and 97.1%, respectively; with a 100% specificity and positive predictive value for all three targets.
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Affiliation(s)
- Xihong Zhao
- College of Light Industry and Food Sciences, South China University of Technology, 510640 Guangzhou, China
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37
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Ueda S, Kuwabara Y. The rapid detection of Salmonella from food samples by loop-mediated isothermal amplification (LAMP). Biocontrol Sci 2009; 14:73-6. [PMID: 19579659 DOI: 10.4265/bio.14.73] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) assay was applied to the detection of Salmonella in food and human materials. It was possible for the assay to detect Salmonella within 60 min. All of 54 serovars of Salmonella tested were amplified, but all bacteria tested other than Salmonella were not. The LAMP assay could detect 10(2) cfu/ml levels of Salmonella. The specificity was similar to that of a PCR assay, but the sensitivity of LAMP was considered to be greater. Thus, the LAMP assay was confirmed to be a rapid, specific and sensitive detection method for Salmonella.
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Affiliation(s)
- Shigeko Ueda
- Laboratory of Hygiene, Kagawa Nutrition University, 3-9-21, Chiyoda, Sakado-shi, Saitama 350-0214, Japan
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Wang X, Cui Z, Jin D, Tang L, Xia S, Wang H, Xiao Y, Qiu H, Hao Q, Kan B, Xu J, Jing H. Distribution of pathogenic Yersinia enterocolitica in China. Eur J Clin Microbiol Infect Dis 2009; 28:1237-44. [PMID: 19575249 DOI: 10.1007/s10096-009-0773-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 06/20/2009] [Indexed: 11/29/2022]
Abstract
Yersinia enterocolitica (1,295 strains) was isolated from diarrhea patients, livestock, poultry, wild animals, insect vectors, food, and the environment. They were studied for epidemiology distribution using bacterial biochemical metabolism tests, their virulence genes, and pulsed-field gel electrophoresis (PFGE) sub-typing. The data showed that 416 of the 1,295 strains were pathogenic, where the pathogenic Chinese isolates were of serotypes O:3 and O:9. These two serotypes were found in livestock and poultry, with swine serving as the major reservoir. The geographic distribution of pathogenic isolates was significantly different, where most of the strains were isolated from the cold northern areas, whereas some serotype O:3 strains were recovered from the warm southern areas. By the analysis of the data of the Ningxia Hui Autonomous Region, we find the phenomenon of 'concentric circle distribution' around animal reservoirs and human habitation. The clustering of PFGE showed that the patterns of the pathogenic strains isolated from diarrhea patients were identical compared to those from the animals in the same area, thus, suggesting that the human infection originated from the animals.
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Affiliation(s)
- X Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, P.O. Box 5, 102206, Changping, Beijing, China
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Li X, Zhang S, Zhang H, Zhang L, Tao H, Yu J, Zheng W, Liu C, Lü D, Xiang R, Liu Y. A loop-mediated isothermal amplification method targets the phoP gene for the detection of Salmonella in food samples. Int J Food Microbiol 2009; 133:252-8. [PMID: 19540609 DOI: 10.1016/j.ijfoodmicro.2009.05.027] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 05/05/2009] [Accepted: 05/25/2009] [Indexed: 11/19/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed and validated for the specific detection of Salmonella in food. The assay used specifically designed primers to target within the phoP gene and correctly identified all 66 strains of Salmonella and 73 non-Salmonella strains tested. The phoP gene regulates the expression of genes involved in virulence and the survival of Salmonella from destruction by macrophage. The probability of detection was 100% when a Salmonella cell suspension containing 10(1) CFU/ml was used as a template in the LAMP assay. Prior to the LAMP assay, a sample preparation protocol was applied that included a pre-enrichment step in buffered peptone water, followed by extraction and purification of DNA. In this way, 85 various food samples were investigated for Salmonella including minced meat of pig and raw milk. The diagnostic accuracy was shown to be 100% when compared to the traditional culture method. This combination of sample enrichment, and LAMP assay can detect 35 CFU per 250 ml of prepared food samples. The overall analysis time for the LAMP assay method was approximately 24 h. This is in contrast to 5 to 7 days of analysis time required for the traditional culture method. Consequently, the LAMP described here has the potential to become a standardized method for the rapid detection of Salmonella in diagnostic laboratories once further validated by inter-laboratory studies.
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Affiliation(s)
- Xuefei Li
- The School of Medicine, Nankai University, Tianjin, China
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40
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Ren CH, Hu CQ, Luo P, Wang QB. Sensitive and rapid identification of Vibrio vulnificus by loop-mediated isothermal amplification. Microbiol Res 2008; 164:514-21. [PMID: 18585020 DOI: 10.1016/j.micres.2008.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/28/2008] [Accepted: 05/18/2008] [Indexed: 11/24/2022]
Abstract
Vibrio vulnificus is a serious bacterial pathogen for humans and aquatic animals. We developed a rapid, sensitive and specific identification method for V. vulnificus using loop-mediated isothermal amplification (LAMP) technique. A set of primers, composed of two outer primers and two inner primers, was designed based on the cytolysin gene sequence of V. vulnificus. The LAMP reaction was processed in a heat block at 65 degrees C for 60 min. The amplification products were detected by visual inspection using SYBR Green I, as well as by electrophoresis on agarose gels. Our results showed that the LAMP reaction was highly specific to V. vulnificus. This method was 10-fold more sensitive than conventional PCR. In conclusion, the LAMP assay was extremely rapid, simple, cost-effective, sensitive and specific for the rapid identification of V. vulnificus.
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Affiliation(s)
- Chun-Hua Ren
- The Key Laboratory of Applied Marine Biology of Guangdong Province and Chinese Academy of Sciences, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, PR China
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41
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Wang L, Li L, Alam MJ, Geng Y, Li Z, Yamasaki S, Shi L. Loop-mediated isothermal amplification method for rapid detection of the toxic dinoflagellate Alexandrium, which causes algal blooms and poisoning of shellfish. FEMS Microbiol Lett 2008; 282:15-21. [PMID: 18355290 PMCID: PMC7110188 DOI: 10.1111/j.1574-6968.2008.01074.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The marine dinoflagellate genus Alexandrium includes a number of species that produce potent neurotoxins responsible for paralytic shellfish poisoning, which in humans may cause muscular paralysis, neurological symptoms and, in extreme cases, death. Because of the genetic diversity of different genera and species, molecular tools may help to detect the presence of target microorganisms in marine field samples. Here we employed a loop-mediated isothermal amplification (LAMP) method for the rapid and simple detection of toxic Alexandrium species. A set of four primers were designed based upon the conserved region of the 5.8S rRNA gene of members of the genus Alexandrium. Using this detection system, toxic Alexandrium genes were amplified and visualized as a ladder-like pattern of bands on agarose gels under isothermal condition within 60 min. The LAMP amplicons were also directly visualized by eye in the reaction tube by the addition of SYBR Green I. This LAMP assay was 10-fold more sensitive than a conventional PCR method with a detection limit of 5 cells per tube when targeting DNA from Alexandrium minutum. The LAMP assay reported here indicates the potential usefulness of the technique as a valuable simple, rapid alternative procedure for the detection of target toxic Alexandrium species during coastal water monitoring.
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Affiliation(s)
- Li Wang
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
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42
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Inácio J, Flores O, Spencer-Martins I. Efficient identification of clinically relevant Candida yeast species by use of an assay combining panfungal loop-mediated isothermal DNA amplification with hybridization to species-specific oligonucleotide probes. J Clin Microbiol 2008; 46:713-20. [PMID: 18077626 PMCID: PMC2238081 DOI: 10.1128/jcm.00514-07] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 05/29/2007] [Accepted: 12/04/2007] [Indexed: 11/20/2022] Open
Abstract
The occurrence of invasive mycoses has progressively increased in recent years. Yeasts of the genus Candida remain the leading etiologic agents of those infections. Early identification of opportunistic yeasts may contribute significantly to improved disease management and the selection of appropriate antifungal therapy. We developed a rapid and reliable molecular identification system for clinically relevant yeasts that makes use of nonspecific primers to amplify a region of the 26S rRNA gene, followed by reverse hybridization of the digoxigenin-labeled products to a panel of species-specific oligonucleotide probes arranged on a nylon membrane macroarray format. DNA amplification was achieved by the recently developed loop-mediated isothermal DNA amplification technology, a promising option for the development of improved laboratory diagnostic kits. The newly developed method was successful in distinguishing among the major clinically relevant yeasts associated with bloodstream infections by using simple, rapid, and cost-effective procedures and equipment.
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Affiliation(s)
- João Inácio
- Centro de Recursos Microbiológicos, Department of Life Sciences, Faculty of Sciences and Technology, New University of Lisbon, 2829-516 Caparica, Portugal
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43
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Ohtsuki R, Kawamoto K, Kato Y, Shah MM, Ezaki T, Makino SI. Rapid detection of Brucella spp. by the loop-mediated isothermal amplification method. J Appl Microbiol 2008; 104:1815-23. [PMID: 18248366 DOI: 10.1111/j.1365-2672.2008.03732.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AIMS To develop a rapid and sensitive method for detecting Brucella spp. METHODS AND RESULTS Two sets of six Brucella-specific primers for loop-mediated isothermal amplification (LAMP) were designed from the sequence of the Brucella abortus BCSP31 gene. The specificity and sensitivity were examined for six Brucella species (22 strains) and 18 non-Brucella species (28 strains). The LAMP assay was specific to Brucella spp. in 35 min at 63 degrees C and sensitive (detected 10 fg of genomic DNA). The assay was also applied for the detection of Brucella DNA in contaminated milk and infected mouse organs. CONCLUSIONS We developed a sensitive and specific LAMP assay for Brucella spp., with the test appearing to be useful for the detection of the pathogen from clinical and food samples. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report of the development of LAMP for the detection of Brucella spp. As the LAMP assay can be performed at a constant temperature and its reactivity is directly observed with the naked eye without electrophoresis, our assay should be useful for the diagnosis of brucellosis as well as the detection of the bacteria in environmental or food samples.
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Affiliation(s)
- R Ohtsuki
- Laboratory of Food Microbiology and Immunology, Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
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44
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Wang L, Shi L, Alam M, Geng Y, Li L. Specific and rapid detection of foodborne Salmonella by loop-mediated isothermal amplification method. Food Res Int 2008. [DOI: 10.1016/j.foodres.2007.09.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Goto M, Hayashidani H, Takatori K, Hara-Kudo Y. Rapid detection of enterotoxigenic Staphylococcus aureus harbouring genes for four classical enterotoxins, SEA, SEB, SEC and SED, by loop-mediated isothermal amplification assay. Lett Appl Microbiol 2007; 45:100-7. [PMID: 17594468 DOI: 10.1111/j.1472-765x.2007.02142.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay targeting the genes for the four classical enterotoxins, SEA, SEB, SEC and SED, in Staphylococcus aureus. METHODS AND RESULTS Specific primers were designed which target each specific sequence of the enterotoxin genes. With 30 strains of Staph. aureus, the results of the LAMP assay to each enterotoxin, SEA, SEB, SEC and SED, completely accorded with the results of polymerase chain reaction (PCR) assay. Enterotoxin production, determined by a reverse passive latex agglutination assay, strongly correlated with the presence of the corresponding genes. Amplification was not observed when 14 strains of nonenterotoxigenic Staph. aureus and 20 strains consisting of 19 bacterial species other than Staph. aureus were tested. In addition, the sensitivity of the LAMP assay was generally higher than that of conventional PCR assay and it rapidly detected enterotoxigenic Staph. aureus strains within 60 min. CONCLUSIONS The LAMP assay developed in this study is rapid, specific and sensitive for the detection of enterotoxigenic Staph. aureus. SIGNIFICANCE AND IMPACT OF THE STUDY The method is suitable for clinical diagnosis and food safety applications.
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Affiliation(s)
- M Goto
- Division of Microbiology, National Institute of Health Sciences, Setagaya, Tokyo, Japan
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46
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Minami M, Ohta M, Ohkura T, Ando T, Torii K, Hasegawa T, Goto H. Use of a combination of brushing technique and the loop-mediated isothermal amplification method as a novel, rapid, and safe system for detection of Helicobacter pylori. J Clin Microbiol 2006; 44:4032-7. [PMID: 17088368 PMCID: PMC1698373 DOI: 10.1128/jcm.00898-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gastric mucosal biopsy is widely used in the detection of Helicobacter pylori but is associated with a number of problems, including false-negative results due to sampling error and massive bleeding after biopsy. Given the extended period required to culture H. pylori, detection would be further improved by the use of rapid detection methods such as PCR. Here, we developed a rapid, safe, and convenient method for collecting H. pylori which combines endoscopic brushing with the loop-mediated isothermal amplification (LAMP) method. The specificity and sensitivity of LAMP were examined using nine urease-generating non-H. pylori bacterial species, Escherichia coli, Clostridium perfringens, Campylobacter jejuni, Helicobacter hepaticus, and 51 H. pylori strains. Results showed that H. pylori-specific LAMP primers amplified H. pylori DNA only and that the lowest detection limit of the LAMP reaction was 10(2) CFU. Brushing and biopsy samples taken from 200 patients with peptic ulcer at Nagoya University Hospital and a regional health care center were subjected to both LAMP and culturing. No adverse effects such as severe bleeding or penetration occurred during the procedure. By LAMP assay, 123 patients were confirmed as H. pylori positive when brushing technique samples were assayed, whereas only 100 were positive when biopsy samples were assayed. Culture assay detected H. pylori in 117 patients when it was combined with the brushing technique and in 96 when it was combined with biopsy. Combination of the endoscopic brushing technique with LAMP is considered a useful and safe system for identifying H. pylori infection.
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Affiliation(s)
- Masaaki Minami
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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47
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Kato H, Yokoyama T, Kato H, Arakawa Y. Rapid and simple method for detecting the toxin B gene of Clostridium difficile in stool specimens by loop-mediated isothermal amplification. J Clin Microbiol 2006; 43:6108-12. [PMID: 16333105 PMCID: PMC1317188 DOI: 10.1128/jcm.43.12.6108-6112.2005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We applied the loop-mediated isothermal amplification (LAMP) assay to the detection of the toxin B gene (tcdB) of Clostridium difficile for identification of toxin B (TcdB)-positive C. difficile strains and detection of tcdB in stool specimens. tcdB was detected in all toxin A (TcdA)-positive, TcdB-positive (A(+)B(+)) and TcdA-negative, TcdB-positive (A(-)B(+)) C. difficile strains but not from TcdA-negative, TcdB-negative strains. Of the 74 stool specimens examined, A(+)B(+) or A(-)B(+) C. difficile was recovered from 39 specimens, of which 38 specimens were LAMP positive and one was negative. Amplification was obtained in 10 specimens that were culture negative, indicating that LAMP is highly sensitive. The LAMP assay was applied to detection of tcdB in DNA extracted by a simple boiling method from 47 of those 74 specimens, which were cultured overnight in cooked-meat medium (CMM). Twenty-two of 24 culture-positive specimens were positive for LAMP on DNA from the culture in CMM. Four specimens were culture negative but positive by LAMP on DNA from CMM cultures. The LAMP assay is a reliable tool for identification of TcdB-positive C. difficile as well as for direct detection of tcdB in stool specimens with high sensitivity. Detection of tcdB by LAMP from overnight cultures in CMM could be an alternative method of diagnostic testing at clinical laboratories without special apparatus.
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Affiliation(s)
- Haru Kato
- Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, 4-7-1 Musashimurayama, Tokyo 208-0011, Japan.
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48
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Suzuki R, Yoshikawa T, Ihira M, Enomoto Y, Inagaki S, Matsumoto K, Kato K, Kudo K, Kojima S, Asano Y. Development of the loop-mediated isothermal amplification method for rapid detection of cytomegalovirus DNA. J Virol Methods 2005; 132:216-21. [PMID: 16289345 DOI: 10.1016/j.jviromet.2005.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Revised: 09/12/2005] [Accepted: 09/30/2005] [Indexed: 11/29/2022]
Abstract
Cytomegalovirus (CMV) loop-mediated isothermal amplification (LAMP) was performed on DNA extracted from CMV (AD-169)-, herpes simplex virus (HSV) 1 (KOS)-, HSV-2 (186)-, varicella-zoster virus (Oka-vaccine)-, human herpesvirus (HHV)-6 A (U1102)-, HHV-6 B (Z29)-, and HHV-7 (RK)-infected cells. Although amplified CMV demonstrated typical ladder patterns, no LAMP product was detected in reactions performed with other viral DNAs. The sensitivity of the CMV LAMP was 500 copies/tube, as determined by either agarose gel electrophoresis or turbidity assay. To determine whether CMV LAMP could be used for quantitative analysis of viral DNA, threshold times, defined as the time (in seconds) to reach the threshold level (0.1), were measured by amplification of serial dilutions of the plasmid DNA. The standard curve exhibited a correlation coefficient of 0.944, a slope of -208.1, and a y-intercept of 3261.4. Following these initial validation experiments, we analyzed 180 samples collected serially from 20 pediatric hematopoietic stem cell transplant recipients. Detection of CMV DNA in whole blood (WB) was tested by CMV LAMP and real-time polymerase chain reaction (PCR). When >500 copies/tube (>5000 copies/200 microl of WB) was defined as positive for CMV infection, the sensitivity, specificity, positive predictive value, and negative predictive values of the CMV LAMP were 80.0, 98.9, 66.7, and 99.4%, respectively.
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Affiliation(s)
- Ryota Suzuki
- Division of Pharmacy, Fujita Health University Hospital, Toyoake, Aichi, Japan
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49
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Lim DV, Simpson JM, Kearns EA, Kramer MF. Current and developing technologies for monitoring agents of bioterrorism and biowarfare. Clin Microbiol Rev 2005; 18:583-607. [PMID: 16223949 PMCID: PMC1265906 DOI: 10.1128/cmr.18.4.583-607.2005] [Citation(s) in RCA: 218] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents.
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Affiliation(s)
- Daniel V Lim
- Department of Biology, Center for Biological Defense, University of South Florida, Tampa, FL 33620-5200, USA.
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