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Oscorbin IP, Novikova LM, Khrapov EA, Filipenko ML. PI primers increase the efficacy of LAMP and RT-LAMP for SARS-CoV-2 and MS2 phage detection. Diagn Microbiol Infect Dis 2024; 110:116449. [PMID: 39133998 DOI: 10.1016/j.diagmicrobio.2024.116449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 06/15/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024]
Abstract
LAMP (Loop-mediated isothermal amplification) is a popular method for the molecular diagnostics of numerous pathogens, specifically useful for point-of-care testing. However, the efficacy and sensitivity of LAMP still need to be maximised for the best performance in clinical settings. Adding a novel fourth primer pair is a promising way to accelerate the LAMP speed. Here, we report PI primers that are part of inner primers and can be used in LAMP without a specific design. PI primers were tested in quantitative LAMP detecting SARS-CoV-2 and MS2. The new primers have increased the speed and sensitivity of quantitative LAMP, RT-LAMP, and duplex LAMP with artificial templates and RNA samples from nasal swabs. Adding PI primers could become a valuable option for LAMP optimisation, especially when a desirable LAMP target is a highly variable DNA sequence with a few conservative sites for primers.
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Affiliation(s)
- Igor P Oscorbin
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia.
| | - Lidiya M Novikova
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia
| | - Evgeniy A Khrapov
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia
| | - Maxim L Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia
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2
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Saifuddin SA, Rashid R, Nor Azmi NJ, Mohamad S. Colorimetric strategies applicable for loop-mediated isothermal amplification. J Microbiol Methods 2024; 223:106981. [PMID: 38945305 DOI: 10.1016/j.mimet.2024.106981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
In recent years, loop-mediated isothermal amplification (LAMP) has gained popularity for detecting various pathogen-specific genes due to its superior sensitivity and specificity compared to conventional polymerase chain reaction (PCR). The simplicity and flexibility of naked-eye detection of the amplicon make LAMP an ideal rapid and straightforward diagnostic tool, especially in resource-limited laboratories. Colorimetric detection is one of the simplest and most straightforward among all detection methods. This review will explore various colorimetric dyes used in LAMP techniques, examining their reaction mechanisms, advantages, limitations and latest applications.
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Affiliation(s)
- Syaidatul Akmal Saifuddin
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Roslina Rashid
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nurin Jazlina Nor Azmi
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Suharni Mohamad
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.
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Cano I, Wood G, Stone D, Noyer M, Canier L, Arzul I. Loop-Mediated Isothermal Amplification for the Fast Detection of Bonamia ostreae and Bonamia exitiosa in Flat Oysters. Pathogens 2024; 13:132. [PMID: 38392870 PMCID: PMC10893247 DOI: 10.3390/pathogens13020132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
The haplosporidian parasites Bonamia ostreae (BO) and B. exitiosa (BE) are serious oyster pathogens. Two independent laboratories evaluated fluorescence real-time loop-mediated isothermal amplification (LAMP) assays for rapidly detecting these parasites. Specific LAMP assays were designed on the BO actin-1 and BE actin genes. A further generic assay was conceived on a conserved region of the 18S gene to detect both Bonamia species. The optimal reaction temperature varied from 65 to 67 °C depending on the test and instrument. Melting temperatures were 89.8-90.2 °C, 87.0-87.6 °C, and 86.2-86.6 °C for each of the BO, BE, and generic assays. The analytical sensitivity of these assays was 50 copies/µL in a 30 min run. The BO and BE test sensitivity was ~1 log lower than a real-time PCR, while the generic test sensitivity was similar to the real-time PCR. Both the BO and BE assays were shown to be specific; however, the generic assay potentially cross-reacts with Haplosporidium costale. The performance of the LAMP assays evaluated on samples of known status detected positives within 7-20 min with a test accuracy of 100% for the BO and generic tests and a 95.8% accuracy for BE. The ease of use, rapidity and affordability of these tests allow for field deployment.
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Affiliation(s)
- Irene Cano
- The International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK (D.S.)
| | - Gareth Wood
- The International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK (D.S.)
| | - David Stone
- The International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK (D.S.)
| | - Mathilde Noyer
- The Institut Français de Recherche pour l’Exploitation de la Mer Ifremer, RBE-SG2M-ASIM, Station de La Tremblade, Avenue de Mus de Loup, La Tremblade, 17390 Brest, France; (M.N.); (L.C.); (I.A.)
| | - Lydie Canier
- The Institut Français de Recherche pour l’Exploitation de la Mer Ifremer, RBE-SG2M-ASIM, Station de La Tremblade, Avenue de Mus de Loup, La Tremblade, 17390 Brest, France; (M.N.); (L.C.); (I.A.)
| | - Isabelle Arzul
- The Institut Français de Recherche pour l’Exploitation de la Mer Ifremer, RBE-SG2M-ASIM, Station de La Tremblade, Avenue de Mus de Loup, La Tremblade, 17390 Brest, France; (M.N.); (L.C.); (I.A.)
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Abusheraida NSA, AlBaker AAH, Aljabri ASA, Abdelrahman HA, Al-Mana H, Wilson GJ, Anan KA, Eltai NO. Rapid Visual Detection of Methicillin-Resistant Staphylococcus aureus in Human Clinical Samples via Closed LAMP Assay Targeting mecA and spa Genes. Microorganisms 2024; 12:157. [PMID: 38257983 PMCID: PMC10819026 DOI: 10.3390/microorganisms12010157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
The emergence of antimicrobial resistance (AMR), particularly methicillin-resistant Staphylococcus aureus (MRSA), poses a significant global health threat as these bacteria increasingly become resistant to the most available therapeutic options. Thus, developing an efficient approach to rapidly screen MRSA directly from clinical specimens has become vital. In this study, we establish a closed-tube loop-mediated isothermal amplification (LAMP) method incorporating hydroxy-naphthol blue (HNB) colorimetric dye assay to directly detect MRSA from clinical samples based on the presence of mecA and spa genes. In total, 125 preidentified S. aureus isolates and 93 clinical samples containing S. aureus were sourced from the microbiology laboratory at Hamad General Hospital (HGH). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were computed based on conventional PCR. The assay demonstrated 100% specificity, 91.23% sensitivity, 0.90 Cohen Kappa (CK), 100% PPV, and 87.8% NPV for the clinical samples, while clinical isolates exhibited 100% specificity, 97% sensitivity, 0.926 CK, 100% PPV, and 88.89% NPV. Compared to cefoxitin disk diffusion, LAMP provided 100% specificity and sensitivity, 1.00 CK, and 100% for PPV and NPV. The study revealed that the closed-tube LAMP incorporating (HNB) dye is a rapid technique with a turnaround time of less than 1 h and high specificity and sensitivity.
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Affiliation(s)
- Noora S. A. Abusheraida
- College of Health Science, Qatar University, Doha P.O. Box 2713, Qatar; (N.S.A.A.); (A.A.H.A.); (A.S.A.A.)
| | - Asraa A. H. AlBaker
- College of Health Science, Qatar University, Doha P.O. Box 2713, Qatar; (N.S.A.A.); (A.A.H.A.); (A.S.A.A.)
| | - Asmaa S. A. Aljabri
- College of Health Science, Qatar University, Doha P.O. Box 2713, Qatar; (N.S.A.A.); (A.A.H.A.); (A.S.A.A.)
| | - Hana A. Abdelrahman
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.A.); (H.A.-M.)
| | - Hassan Al-Mana
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.A.); (H.A.-M.)
| | - Godwin J. Wilson
- Laboratory Medicine and Pathology, Hamad General Hospital, Doha P.O. Box 3050, Qatar;
| | | | - Nahla O. Eltai
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.A.); (H.A.-M.)
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Logeshwari R, Gopalakrishnan C, Kamalakannan A, Ramalingam J, Saraswathi R. A colorimetric hydroxy naphthol blue based loop-mediated isothermal amplification detection assay targeting the β-tubulin locus of Sarocladium oryzae infecting rice seed. FRONTIERS IN PLANT SCIENCE 2022; 13:1077328. [PMID: 36479512 PMCID: PMC9720317 DOI: 10.3389/fpls.2022.1077328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Sarocladium oryzae is a widely prevalent seed-borne pathogen of rice. The development of a rapid and on-site detection method for S. oryzae is therefore important to ensure the health of rice seeds. Loop-mediated isothermal amplification (LAMP) is ideal for field-level diagnosis since it offers quick, high-specific amplification of target template sequences at a single temperature. We designed primers based on the β-tubulin region of S. oryzae. The LAMP technique devised was extremely sensitive, detecting the presence of the S. oryzae template at concentrations as low as 10 fg in 30 minutes at 65°C. The assay specificity was confirmed by performing the experiment with genomic DNA isolated from 22 different phytopathogens. Through the addition of hydroxy naphthol blue in the reaction process prior to amplification, a colour shift from violet to deep sky blue was seen in the vicinity of the target pathogen only. Finally, the LAMP assay was validated using live infected tissues, weeds and different varieties of seeds collected from different locations in Tamil Nadu, India. If developed into a detection kit, the LAMP assay developed in this study has potential applications in seed health laboratories, plant quarantine stations, and on-site diagnosis of S. oryzae in seeds and plants.
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Affiliation(s)
- R. Logeshwari
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, India
| | - C. Gopalakrishnan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, India
| | - A. Kamalakannan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, India
| | - J. Ramalingam
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - R. Saraswathi
- Department of Plant Genetic Resources, Tamil Nadu Agricultural University, Coimbatore, India
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6
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Zhao L, Huang X, Zhang T, Zhang X, Jiang M, Lu H, Sui G, Zhao Y, Zhao W, Liu X. A point-of-care test device for MRSA rapid detection. J Pharm Biomed Anal 2021; 209:114464. [PMID: 34915322 DOI: 10.1016/j.jpba.2021.114464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
Staphylococcus aureus (SA) is one of the most common pathogenic bacteria, and methicillin-resistant SA (MRSA) is an equally common drug-resistant bacteria. MRSA detection is of great significance for clinical diagnosis, medication guidance, and prevention of antibiotic abuse. Traditional MRSA detection using the culture method is time-consuming, laborious, and difficult to conduct rapid on-site detection. In this research, we developed a device for rapid MRSA detection, which can detect the nuc gene in SA and mecA gene in MRSA simultaneously for 30-40 min. After simple sample processing, the mixture can be directly loaded onto the chip device. The detection results can be directly determined by a color change, with a limitation of approximately 102 copies. This isothermal amplification chip device can be widely applied in many fields, with simple operation and low contamination.
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Affiliation(s)
- Linlin Zhao
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China
| | - Xiaochun Huang
- Department of Laboratory, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China
| | - Tong Zhang
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Xinlian Zhang
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Mengni Jiang
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China
| | - Huijun Lu
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Guodong Sui
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Yue Zhao
- Liaocheng Center for Disease Control and Prevention, 2 East Hunan Road, Liaocheng 252000, Shandong, PR China
| | - Wang Zhao
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China.
| | - Xiao Liu
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China.
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7
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Natoli ME, Kundrod KA, Chang MM, Smith CA, Paul S, Coole JB, Butlin NG, Tanner NA, Baker E, Schmeler KM, Richards-Kortum R. Improving Performance of a SARS-CoV-2 RT-LAMP Assay for Use With a Portable Isothermal Fluorimeter: Towards a Point-of-Care Molecular Testing Strategy. J Biomol Tech 2021; 32:180-185. [PMID: 35027875 DOI: 10.7171/jbt.21-3203-013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Frequent and accessible testing is a critical tool to contain the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To develop low-cost rapid tests, many researchers have used reverse transcription loop-mediated isothermal amplification (RT-LAMP) with fluorescent readout. Fluorescent LAMP-based assays can be performed using cost-effective, portable, isothermal instruments that are simpler to use and more rugged than polymerase chain reaction (PCR) instruments. However, false-positive results due to nonspecific priming and amplification have been reported for a number of LAMP-based assays. In this report, we implemented a RT-LAMP assay for SARS-CoV-2 on a portable isothermal fluorimeter and a traditional thermocycler; nonspecific amplification was not observed using the thermocycler but did occur frequently with the isothermal fluorimeter. We explored 4 strategies to optimize the SARS-CoV-2 RT-LAMP assay for use with an isothermal fluorimeter and found that overlaying the reaction with mineral oil and including the enzyme Tte UvrD helicase in the reaction eliminated the problem. We anticipate these results and strategies will be relevant for use with a wide range of portable isothermal instruments.
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Affiliation(s)
- Mary E Natoli
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | | | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | - Chelsey A Smith
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | - Sai Paul
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | - Jackson B Coole
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | | | | | - Ellen Baker
- Department of Gynecologic Oncology and Reproductive Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, MD Anderson Cancer Center, Houston, Texas, USA
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Sensitivity Validation of EWOD Devices for Diagnosis of Early Mortality Syndrome (EMS) in Shrimp Using Colorimetric LAMP-XO Technique. SENSORS 2021; 21:s21093126. [PMID: 33946302 PMCID: PMC8124682 DOI: 10.3390/s21093126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/17/2022]
Abstract
Electrowetting-on-dielectric (EWOD) is a microfluidic technology used for manipulating liquid droplets at microliter to nanoliter scale. EWOD has the ability to facilitate the accurate manipulation of liquid droplets, i.e., transporting, dispensing, splitting, and mixing. In this work, EWOD fabrication with suitable and affordable materials is proposed for creating EWOD lab-on-a-chip platforms. The EWOD platforms are applied for the diagnosis of early mortality syndrome (EMS) in shrimp by utilizing the colorimetric loop-mediated isothermal amplification method with pH-sensitive xylenol orange (LAMP-XO) diagnosis technique. The qualitative sensitivity is observed by comparing the limit of detection (LOD) while performing the LAMP-XO diagnosis test on the proposed lab-on-a-chip EWOD platform, alongside standard LAMP laboratory tests. The comparison results confirm the reliability of EMS diagnosis on the EWOD platform with qualitative sensitivity for detecting the EMS DNA plasmid concentration at 102 copies in a similar manner to the common LAMP diagnosis tests.
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