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Liu W, Lu G, Wang Y, Chen Z, Gao Y, Yin Z, Wu Y, Lv X, Guo P, Zhao Y. A novel loop-mediated isothermal amplification-lateral flow dipstick method for Helicobacter pylori detection. Front Microbiol 2023; 14:1094600. [PMID: 37032891 PMCID: PMC10076779 DOI: 10.3389/fmicb.2023.1094600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction To eradicate Helicobacter pylori (H. pylori) and reduce the risk of gastric cancer, a sensitive, specific, convenient, and simple detection method is needed. This study aimed to establish a novel loop-mediated isothermal amplification-lateral flow dipstick (LAMP-LFD) method for H. pylori detection. Methods LAMP primer design software was used to design primers for the conserved sites of the H. pylori ureB gene. UreB-FIP-labeled biotin was used for LAMP amplification, and FAM-labeled probes were specifically hybridized with LAMP amplification products, which were then detected by LFD. In addition, a clinical study was conducted to assess LAMP-LFD in 20 fecal samples. Results The results of the optimization indicated that H. pylori could be specifically detected by LFD without cross-reaction with other non-H. pylori bacteria when the LAMP was performed at 65°C for 60 min. The lower limit of the detection method was 102 copies/μL, which was 100 times the sensitivity of polymerase chain reaction (PCR). H. pylori-positive fecal samples were detected by LAMP-LFD in 13/20 patients. Discussion In conclusion, a new LAMP-LFD assay has been fully established and confirmed for H. pylori detection. The entire process can be completed in approximately 1.5 h, with the advantages of strong specificity, high sensitivity, and simple operation. This study provides a novel potential method for the detection of H. pylori in the clinical settings of primary hospitals and low-resource countries.
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Affiliation(s)
- Wenwen Liu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Gang Lu
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Department of Clinical Microbiology Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yu Wang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Department of Clinical Microbiology Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhenghong Chen
- Key Laboratory of Medical Microbiology and Parasitology, Department of Microbiology, Guizhou Medical University, Guiyang, China
| | - Yunyun Gao
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Zhipeng Yin
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yi Wu
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xiaoqian Lv
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Pengbo Guo
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Department of Clinical Microbiology Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- *Correspondence: Pengbo Guo
| | - Yinghui Zhao
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Department of Clinical Microbiology Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Yinghui Zhao
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Avila HG, Risso MG, Cabrera M, Ruybal P, Repetto SA, Butti MJ, Trangoni MD, Santillán G, Pérez VM, Periago MV. Development of a New LAMP Assay for the Detection of Ancylostoma caninum DNA (Copro-LAMPAc) in Dog Fecal Samples. Front Vet Sci 2021; 8:770508. [PMID: 34869740 PMCID: PMC8633310 DOI: 10.3389/fvets.2021.770508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/13/2021] [Indexed: 01/17/2023] Open
Abstract
Ancylostoma caninum is a zoonotic nematode which is able to affect animals and humans. Diagnosis in the definitive host and environmental detection are key to prevent its dissemination and achieve control. Herein, a new coprological LAMP method for the detection of A. caninum (Copro-LAMPAc) DNA was developed. DNA extraction was performed using a low-cost method and a fragment of the cox-1 gene was used for primer design. The analytical sensitivity, evaluated with serial dilutions of genomic DNA from A. caninum adult worms, was 100 fg. A specificity of 100% was obtained using genomic DNA from the host and other pathogens. The Copro-LAMPAc was evaluated using environmental canine fecal samples. When compared with gold standard optical microscopy in epidemiological studies, it proved to be more sensitive. This new LAMP assay can provide an alternative protocol for screening and identification of A. caninum for epidemiological studies in endemic areas.
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Affiliation(s)
- Héctor Gabriel Avila
- Laboratorio Provincial de Zoonosis de San Juan, Facultad de Ciencias Veterinarias, Facultad de Ciencias Químicas y Tecnológicas, Universidad Católica de Cuyo, San Juan, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Marikena Guadalupe Risso
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marta Cabrera
- Departamento de Parasitología, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Paula Ruybal
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvia Analía Repetto
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Microbiología y Parasitología Médica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Buenos Aires, Argentina.,División Infectología, Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcos Javier Butti
- Laboratorio de Parasitosis Humanas y Zoonosis Parasitarias, Cátedra de Parasitología Comparada, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Marcos David Trangoni
- Laboratorio de Brucella, Campylobacter y Microbiota del rumen, Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular, Unidades Ejecutoras de Doble Dependencia (UEDD) INTA-CONICET, Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Centro Nacional de Investigaciones Agropecuarias (CNIA), INTA Castelar, Buenos Aires, Argentina
| | - Graciela Santillán
- Departamento de Parasitología, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Verónica Mirtha Pérez
- Laboratorio Provincial de Zoonosis de San Juan, Facultad de Ciencias Veterinarias, Facultad de Ciencias Químicas y Tecnológicas, Universidad Católica de Cuyo, San Juan, Argentina.,Sección de Rabia y Zoonosis, Dirección de Epidemiología, Ministerio de Salud Pública de San Juan, San Juan, Argentina
| | - María Victoria Periago
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Fundación Mundo Sano, Buenos Aires, Argentina
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Efficacy of Loop-Mediated Isothermal Amplification for H. pylori Detection as Point-of-Care Testing by Noninvasive Sampling. Diagnostics (Basel) 2021; 11:diagnostics11091538. [PMID: 34573879 PMCID: PMC8467764 DOI: 10.3390/diagnostics11091538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 11/23/2022] Open
Abstract
For targeted eradication of Helicobacterpylori (H. pylori) to reduce gastric cancer burden, a convenient approach is definitely needed. The purpose of this study was to evaluate the LAMP assay for H. pylori detection using samples collected by noninvasive and self-sampling methods. The available LAMP assay for H. pylori detection was appraised and verified using reference and clinically isolated H. pylori strains. In addition, a clinical study was conducted to assess the LAMP assay on 51 patients, from whom saliva, oral brushing samples, feces, corpus, and antrum specimens were available. Clarithromycin resistance was also analysed through detection of A2143G mutation using the LAMP-RFLP method. The validation and verification analysis demonstrated that the LAMP assay had an acceptable result in terms of specificity, sensitivity, reproducibility, and accuracy for clinical settings. The LAMP assay showed a detection limit for H. pylori down to 0.25 fg/µL of genomic DNA. An acceptable consensus was observed using saliva samples (sensitivity 58.1%, specificity 84.2%, PPV 85.7%, NPV 55.2%, accuracy 68%) in comparison to biopsy sampling as the gold standard. The performance testing of different combinations of noninvasive sampling methods demonstrated that a combination of saliva and oral brushing could achieve a sensitivity of 74.2% and a specificity of 57.9%. A2143G mutation detection by LAMP-RFLP showed perfect consensus with Sanger sequencing results. It appears that the LAMP assay in combination with noninvasive and self-sampling as a point-of-care testing (POCT) approach has potential usefulness to detect H.pylori infection in clinic settings and screening programs.
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Avila HG, Risso MG, Ruybal P, Repetto SA, Butti MJ, Trangoni MD, Grune Löffler S, Pérez VM, Periago MV. Development of a low-cost copro-LAMP assay for simultaneous copro-detection of Toxocara canis and Toxocara cati. Parasitology 2021; 148:819-826. [PMID: 33593468 PMCID: PMC11010131 DOI: 10.1017/s0031182021000342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/02/2021] [Accepted: 02/13/2021] [Indexed: 11/06/2022]
Abstract
Toxocariasis is a zoonotic disease caused mainly by Toxocara canis and Toxocara cati and diagnosis in dogs and cats is an important tool for its control. For this reason, a new coprological loop-mediated isothermal amplification (LAMP) assay was developed for the simultaneous detection of these species. The primer set was designed on a region of the mitochondrial cox-1 gene. Amplification conditions were evaluated using a temperature gradient (52°C to 68°C), different incubation times (15–120 min), and different concentrations of malachite green dye (0.004–0.4% w/v). The analytical sensitivity was evaluated with serial dilutions of genomic DNA from T. canis and T. cati adult worms, and with serial dilutions of DNA extracted from feces using a low-cost in-house method. The specificity was evaluated using genomic DNA from Canis lupus familiaris, Felis catus, Escherichia coli, Toxascaris leonina, Ancylostoma caninum, Echinococcus granulosus sensu stricto and Taenia hydatigena. The LAMP assay applied to environmental fecal samples from an endemic area showed an analytical sensitivity of 10–100 fg of genomic DNA and 10−5 serial dilutions of DNA extracted from feces using the low-cost in-house method; with a specificity of 100%. Additionally, the total development of the assay was carried out in a basic laboratory and per-reaction reagent cost decreased by ~80%. This new, low-cost tool can help identify the most common agents of toxocariasis in endemic areas in order to manage prevention strategies without having to rely on a laboratory with sophisticated equipment.
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Affiliation(s)
- Héctor Gabriel Avila
- Laboratorio Provincial de Zoonosis de San Juan, Facultad de Ciencias Veterinarias, Facultad de Ciencias Químicas y Tecnológicas, Universidad Católica de Cuyo, San Luis, San Juan, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina
| | - Marikena Guadalupe Risso
- Instituto de Investigaciones en Microbiología y Parasitología Médica, IMPAM-UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, CABA, Argentina
| | - Paula Ruybal
- Instituto de Investigaciones en Microbiología y Parasitología Médica, IMPAM-UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, CABA, Argentina
| | - Silvia Analía Repetto
- Instituto de Investigaciones en Microbiología y Parasitología Médica, IMPAM-UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, CABA, Argentina
| | - Marcos Javier Butti
- Laboratorio de Parasitosis Humanas y Zoonosis Parasitarias, Cátedra de Parasitología Comparada, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Marcos David Trangoni
- Laboratorio de Brucella, Campylobacter y Microbiota del rumen, Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (IB/IABIMO), UEDD INTA-CONICET, CICVyA, CNIA, INTA Castelar, Hurlingham, Buenos Aires, Argentina
| | - Sylvia Grune Löffler
- Laboratorio de Leptospirosis, Instituto de Patobiología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria Castelar, Buenos Aires, Argentina
| | - Verónica Mirtha Pérez
- Sección de Rabia y Zoonosis, Dirección de Epidemiología, Ministerio de Salud Pública de San Juan, San Juan, Argentina
| | - María Victoria Periago
- Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina
- Fundación Mundo Sano, Buenos Aires, Argentina
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Bangpanwimon K, Mittraparp-arthorn P, Srinitiwarawong K, Tansila N. Non-Invasive Colorimetric Magneto Loop-Mediated Isothermal Amplification (CM-LAMP) Method for Helicobacter pylori Detection. J Microbiol Biotechnol 2021; 31:501-509. [PMID: 33746187 PMCID: PMC9705857 DOI: 10.4014/jmb.2101.01008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/02/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
More than half the world's population is thought to be infected with Helicobacter pylori. Although the majority of infected people are asymptomatic, H. pylori infection may cause gastric ulcers and deadly gastric cancer. Owing to the difficulty and invasiveness of current routine culture and diagnostic methods, a highly sensitive and specific noninvasive assay for H. pylori is of interest. This study highlighted the design and performance of a colorimetric magneto loop-mediated isothermal amplification (CM-LAMP) assay to detect H. pylori in spiked saliva samples. LF primers were coated on magnetic nanoparticles by carbodiimide-induced immobilization and functionally used for solidphase amplification. During the LAMP reaction at 66°C, biotin-tagged FIPs were incorporated into LAMP amplicons. The colorimetric signal developed after the addition of NeutrAvidin horseradish peroxidase conjugate (NA-HRP) and ABTS. None of the tested microorganisms, including closely related bacteria, was shown positive by the CM-LAMP assay except H. pylori isolates. This novel platform was highly specific and 100-fold more sensitive (40 CFU/ml or 0.2 CFU per reaction) than the PCR and conventional LAMP assays for the detection of H. pylori in spiked saliva. Our results demonstrated the feasibility of using this noninvasive molecular diagnostic test to detect H. pylori in saliva samples.
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Affiliation(s)
- Khotchawan Bangpanwimon
- Department of Microbiology, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90110, Thailand
| | - Pimonsri Mittraparp-arthorn
- Department of Microbiology, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90110, Thailand,Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90110, Thailand
| | - Kanchana Srinitiwarawong
- Department of Microbiology, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90110, Thailand
| | - Natta Tansila
- Faculty of Medical Technology, Prince of Songkla University, Hat-Yai, Songkhla 90110, Thailand,Corresponding author Phone: +66-74-289106 Fax: +66-74-289101 E-mail:
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Diagnostic Values of Multiplex Loop-Mediated Isothermal Amplification and Multiplex Polymerase Chain Reaction for Detection of Methicillin-Resistant Staphylococcus aureus. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.96682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background: Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a significant pathogen in community and hospital environments and is associated with high mortality and morbidity. Both polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) methods are sensitive and acceptable molecular methods for the diagnosis of infectious diseases. Objectives: This study aimed to develop detection assays for Staphylococcal mecA and spa using multiplex PCR and LAMP. Methods: Both methods were standardized, and detection limits were determined using serial dilutions of S. aureus DNA samples. Fifty-three clinical isolates of S. aureus were confirmed to the species level using biochemical tests and multiplex PCR and multiplex LAMP for the spa gene, while disk diffusion, minimum inhibitory concentration, and detection of mecA genes were used for the assessment of methicillin resistance. Results: The PCR could detect the mecA and spa genes at 1 fg/mL and 10 fg/mL of bacterial DNA, which were equal to 35 and 350 gene copy numbers, respectively. Similarly, multiplex LAMP detected the spa and mecA genes at 0.1 fg/mL and 1 fg/mL of bacterial DNA, which were equal to 3.5 and 35 genome copy numbers, respectively. According to MIC and disk diffusion methods, four (7.54%) cases were oxacillin-sensitive methicillin-resistant S. aureus, 16 isolates were methicillin-sensitive, and 37 isolates were methicillin-resistant. According to multiplex PCR, 47.75% of the isolates were mecA-positive while in multiplex LAMP, 41 (35.77%) isolates were mecA-positive. Conclusions: The sensitivity and specificity of the multiplex LAMP were higher than those of multiplex PCR and biochemical methods. Thus, we can apply the LAMP for the routine detection of MRSA.
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Liao W, Long D, Huang Q, Wei D, Liu X, Wan L, Feng Y, Zhang W, Liu Y. Rapid Detection to Differentiate Hypervirulent Klebsiella pneumoniae (hvKp) From Classical K. pneumoniae by Identifying peg-344 With Loop-Mediated Isothermal Amplication (LAMP). Front Microbiol 2020; 11:1189. [PMID: 32655515 PMCID: PMC7325879 DOI: 10.3389/fmicb.2020.01189] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
Objectives To establish a rapid molecular diagnostics of hvKp using the peg-344 loop-mediated isothermal amplification technique (LAMP). Methods In all, 28 K. pneumoniae strains isolated from the blood of patients were used for the peg-344 LAMP. K. pneumoniae NTUH-K2044 and K. pneumoniae ATCC700603 were used as positive control and negative control, respectively. For comparison, all the results were detected in a polymerase chain reaction (PCR), which was considered the gold standard for the detection of the gene. Mouse lethality assay, and Serum killing assay were also used to determine the virulence phenotype of K. pneumoniae. Results We determined the specificity and sensitivity of the primers for peg-344 detection in the LAMP reactions. This LAMP assay was able to specifically differentiate hvKp from classical K. pneumoniae (cKp) at 65°C, which was 100-fold more sensitive than a PCR assay for peg-344 detection. The virulence phenotype of K. pneumoniae detected by LAMP was as precise as by Mouse lethality assay and Serum killing assay. Conclusion The LAMP assay is easy to perform and rapid. Therefore, it can be routinely applied to differentiate hvKp from cKp in the clinical laboratory.
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Affiliation(s)
- Wenjian Liao
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dan Long
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qisen Huang
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dandan Wei
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaobing Liu
- Department of Endocrinology Medicine, The Third Hospital of Nanchang, Nanchang, China
| | - Lagen Wan
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuling Feng
- Medicine College, Nanchang University, Nanchang, China
| | - Wei Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yang Liu
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Avila HG, Mozzoni C, Trangoni MD, Cravero SLP, Pérez VM, Valenzuela F, Gertiser ML, Butti MJ, Kamenetzky L, Jensen O, Rosenzvit MC. Development of a copro-LAMP assay for detection of several species of Echinococcus granulosus sensu lato complex. Vet Parasitol 2019; 277:109017. [PMID: 31901535 DOI: 10.1016/j.vetpar.2019.109017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 11/18/2022]
Abstract
Cystic echinococcosis represents a significant problem in human and animal health and constitutes one of the most severe Neglected Tropical Diseases prioritized by the World Health Organization. The etiological agent is the complex Echinococcus granulosus sensu lato (s. l.), composed of several species/genotypes. Diagnosis in the definitive host and molecular epidemiology studies are important points for cystic echinococcosis control. Here we developed a new copro-LAMP assay, LAMP EGSL, for diagnosis in the definitive host for simultaneous detection of Echinococcus granulosus sensu stricto (s. s.), Echinococcus ortleppi, and Echinococcus canadensis species. Also, the analytical sensitivity, specificity and plausibility of performance in a rural context of a previously reported species-specific LAMP reaction, was evaluated. Both reactions showed high analytical sensitivity values (10 fg-100 fg DNA) and did not show cross reaction with DNA from host or other helminthic parasites. LAMP EGSL was performed with samples from an endemic area. In addition, the alkaline hydrolysis of one E. granulosus s. s. adult parasite followed by specific LAMP to E. granulosus s. s. was performed in a laboratory with low resources from another cystic echinococcosis endemic area. The results obtained suggest that LAMP EGSL represents a potential tool for canine diagnosis that could be useful for cystic echinococcosis control programs. In addition, we showed that LAMP reaction for E. granulous s. s., E. ortleppi and E. canadensis specific detection, could be useful for molecular epidemiology studies applicable to the definitive host. Both reactions were performed in endemic, rural areas without sophisticated equipment.
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Affiliation(s)
- Héctor Gabriel Avila
- Instituto de Investigaciones en Microbiología y Parasitología Médica, IMPAM-UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina; Centro de Investigaciones en Zoonosis, Sarmiento, Chubut, Argentina
| | - Cecilia Mozzoni
- Hospital Zonal Caleta Olivia, Ministerio de Salud y Ambiente, Santa Cruz, Argentina
| | - Marcos David Trangoni
- Laboratorio de Brucella, Campylobacter & Microbiota, INTA, Hulingham, Buenos Aires, Argentina
| | | | | | | | | | - Marcos Javier Butti
- Laboratorio de Parasitosis Humanas y Zoonosis Parasitarias, Cátedra de Parasitología Comparada, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica, IMPAM-UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Oscar Jensen
- Centro de Investigaciones en Zoonosis, Sarmiento, Chubut, Argentina
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médica, IMPAM-UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina.
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Horiuchi S, Nakano R, Nakano A, Hishiya N, Uno K, Suzuki Y, Tanouchi A, Kakuta N, Masui T, Jojima N, Yano H. Development of a loop-mediated isothermal amplification assay for rapid Helicobacter pylori detection. J Microbiol Methods 2019; 163:105653. [PMID: 31199937 DOI: 10.1016/j.mimet.2019.105653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/10/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023]
Abstract
Infection with cagA-positive Helicobacter pylori is associated with gastric cancer. Molecular techniques are vital for accurate H. pylori diagnosis. We developed a loop-mediated isothermal amplification (LAMP) for detecting the H. pylori cagA gene and evaluated its use for clinical diagnosis. A LAMP primer set was designed to recognize the homologous regions of cagA gene sequences of 6 H. pylori strains. LAMP sensitivity was evaluated with serial dilutions of H. pylori ATCC 43504 and fecal specimens; specificity was evaluated with H. pylori ATCC 49396 and CIP 104086. The LAMP sensitivity for H. pylori specimens was 10-1 cfu/tube (reaction time, 37 min), which was 10-fold more sensitive than polymerase chain reaction. LAMP was also highly sensitive and rapid for fecal specimens. It detected cagA gene from ATCC 49396 and CIP 104086. The findings suggest LAMP can be used for diagnosing and screening of H. pylori infections to decrease gastric cancer incidence.
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Affiliation(s)
- Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan; Department of Public Health Nursing, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan.
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
| | - Naokuni Hishiya
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan; Department of Infectious Diseases, Minami-Nara General Medical Center, 8-1 Fukugami, Yoshino-gun, Oyodo, Nara 638-8551, Japan
| | - Kenji Uno
- Department of Infectious Diseases, Minami-Nara General Medical Center, 8-1 Fukugami, Yoshino-gun, Oyodo, Nara 638-8551, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
| | - Ayako Tanouchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
| | - Naoki Kakuta
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
| | - Takashi Masui
- Department of otolaryngology - Head and Neck Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
| | - Noriko Jojima
- Department of Public Health Nursing, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara 634-8521, Japan
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10
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Bakhtiari S, Hasanvand B, Pajavand H, Alvandi A, Abiri R. Rapid and accurate detection of Helicobacter pylori from biopsy specimens using loop-mediated isothermal amplification. APMIS 2019; 127:510-514. [PMID: 31009119 DOI: 10.1111/apm.12953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 04/03/2019] [Indexed: 01/08/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a promising nucleic acid-based assay for quick, accurate and cost-effective diagnosis of many infectious agents. The purpose of this study was to assess the diagnostic value of LAMP for rapid and accurate detection of Helicobacter pylori in biopsy specimens. Patients suffering from one or several gastroduodenal disorders were enrolled in the study. Specificity, sensitivity, and the positive and negative predictive values of LAMP were compared with the gold standard result, which was the assembled result of culture, rapid urease test and polymerase chain reaction. Sensitivity, specificity, and the positive and negative predictive values of LAMP in comparison with the gold standard result were 100%, 30.76%, and 87.67% and 100% respectively [%95 CI]. As the diagnostic value of LAMP is favourable, the method is an optimum technique for diagnosis the presence of H. pylori in different clinical and environmental samples.
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Affiliation(s)
- Somaye Bakhtiari
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Banafsheh Hasanvand
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamid Pajavand
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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11
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Anupama KP, Chakraborty A, Karunasagar I, Karunasagar I, Maiti B. Loop-mediated isothermal amplification assay as a point-of-care diagnostic tool for Vibrio parahaemolyticus: recent developments and improvements. Expert Rev Mol Diagn 2019; 19:229-239. [PMID: 30657706 DOI: 10.1080/14737159.2019.1571913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION A number of DNA-based diagnostic tools have been developed for the detection of Vibrio parahaemolyticus in seafood. However, the loop-mediated isothermal amplification (LAMP) has distinct advantages with regards to its simplicity, speed and the ease of performing without any need for sophisticated equipment. Over the last decade, LAMP has emerged as a potential tool for the detection of V. parahaemolyticus. Area covered: The literature search was restricted to LAMP assay and its variants for the detection of V. parahaemolyticus. The focus in this review is to enlist the various techniques that have been developed using the principle of the LAMP towards improved simplicity, sensitivity and specificity of the assay. Expert commentary: LAMP assay and its variants are significantly faster and require minimum accessories compared to other DNA based molecular techniques such as PCR and their types. Despite the availability of several versions, LAMP-based diagnostics is not the first choice for the detection of V. parahaemolyticus in the seafood sector. Our recommendation would be to explore the possibilities of developing cost-effective LAMP kits and implementing these kits as point-of-care diagnostic tools for rapid and sensitive detection of pathogenic V. parahaemolyticus.
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Affiliation(s)
- Karanth Padyana Anupama
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India
| | - Anirban Chakraborty
- b Division of Molecular Genetics and Cancer , Nitte University Centre for Science Education and Research , Mangaluru , India
| | - Iddya Karunasagar
- c NITTE (Deemed to be University), University Enclave , Mangaluru, Medical Sciences Complex , India
| | - Indrani Karunasagar
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India.,c NITTE (Deemed to be University), University Enclave , Mangaluru, Medical Sciences Complex , India
| | - Biswajit Maiti
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India
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12
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Keikha M. LAMP Method as One of the Best Candidates for Replacing with PCR Method. Malays J Med Sci 2018; 25:121-123. [PMID: 29599643 DOI: 10.21315/mjms2018.25.1.15] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/01/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Masoud Keikha
- Department of Microbiology, School of Medicine, Isfahan Medical University, Isfahan, Iran
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13
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Wong YP, Othman S, Lau YL, Radu S, Chee HY. Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms. J Appl Microbiol 2018; 124:626-643. [PMID: 29165905 PMCID: PMC7167136 DOI: 10.1111/jam.13647] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022]
Abstract
Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (2000Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro‐organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro‐organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real‐time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro‐organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.
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Affiliation(s)
- Y-P Wong
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - S Othman
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Y-L Lau
- Department of Parasitology, Faculty of Medicine, Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
| | - S Radu
- Centre of Excellence for Food Safety Research (FOSREC), Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - H-Y Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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14
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Moreira MG, Barreto LM, Dos Santos VL, Monteiro AS, Nobre V, Dos Santos SG. Rapid detection of the New Delhi metallo-b-lactamase 1 (NDM-1) gene by loop-mediated isothermal amplification (LAMP). J Clin Lab Anal 2017; 32:e22323. [PMID: 28960568 DOI: 10.1002/jcla.22323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND New Delhi Metallo-b-lactamase (NDM-1) is an enzyme emerging around the world conferring resistance to a wide range of β-lactams agents and whose early detection is extremely important. We proposed to standardize the detection of the blaNDM-1 gene using the LOOP-mediated isothermal amplification technique (LAMP). METHODS In all, 14 Gram-negative bacterial strains isolated from patients presenting pneumonia associated with mechanical ventilation were used for the blaNDM-1 standardization by LAMP. Klebsiella pneumoniae ATCC BAA-2473 and two clinical strains were used as a positive control. All results were compared to the reaction in polymerase chain reaction (PCR), considered gold standard for this detection. RESULTS There was an excellent correlation between the two techniques employed, since all measured clinical strains were negative in both employed tests and two clinical, and a reference strains were positive. CONCLUSIONS The lamp technique seems to be an excellent option for the rapid detection of blaNDM-1. The amplification time is much shorter than other molecular techniques, the PCR machine is not necessary, it is easy of implementation and costs is low.
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Affiliation(s)
- Mirna Giselle Moreira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | | | - Vera Lúcia Dos Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Andrea Souza Monteiro
- Departamento de Parasitologia e Biologia, Centro Universitário do Maranhão, São Luís, Brasil
| | - Vandack Nobre
- Programa de Pós Graduação em Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas, Belo Horizonte, Brasil
| | - Simone Gonçalves Dos Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
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15
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Detection of Helicobacter pylori in Drinking Water by Loop-Mediated Isothermal Amplification. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.41895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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