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Aninagyei E, Boakye AA, Tettey CO, Ntiri KA, Ofori SO, Tetteh CD, Aphour TT, Rufai T. Utilization of 18s ribosomal RNA LAMP for detecting Plasmodium falciparum in microscopy and rapid diagnostic test negative patients. PLoS One 2022; 17:e0275052. [PMID: 36201568 PMCID: PMC9536604 DOI: 10.1371/journal.pone.0275052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022] Open
Abstract
In this study, Plasmodium falciparum was detected in patients that were declared negative for malaria microscopy and rapid diagnostic test kit (mRDT), using Plasmodium 18s rRNA loop-mediated isothermal amplification (LAMP) technique. The main aim of this study was to assess the usefulness of LAMP assay for detecting pre-clinical malaria, when microscopy and mRDT were less sensitive. DNA was obtained from 100 μL of whole blood using the boil and spin method. Subsequently, the Plasmodium 18s rRNA LAMP assay was performed to amplify the specific Plasmodium 18s rRNA gene. Microscopy and mRDT negative samples [697/2223 (31.2%)] were used for this study. Compared to frequencies obtained for the other demographic variables, most of the patients were < 6 years (37.7%), females (59.0%), peri-urban dwellers (39.0%) and patients that sought outpatient department services (39.3%). Overall, the prevalence of Plasmodium 18s rRNA was 17.5%. when stratified by study variables, Plasmodium 18s rRNA LAMP positivity was higher in patients over 30 years [58/122 (54.2%)], males [69/122 (56.5%)], rural dwellers [69/122 (56.5%)] and patients that sought OPD services [68/122 (55.7%)]. The risk of being infected with Plasmodium when routine tests were negative was higher in 15-30-year group (OR = 3.03, 95% CI: 1.6-5.8, p = 0.0007), patients > 30 years (OR = 15.2, 95% CI: 8.3-27.7, p<0.001), males (OR = 2.1, 95% CI: 1.4-3.2, p = 0.0002) and rural dwellers (OR = 2.2, 95% CI:1.4-3.6, p = 0.0009). However, risk was lower in post-natal children (OR = 0.3, 95% CI: 0.18-0.51, p<0.001). Majority (81.5%) of the infected patients presented with headache, herpes labialis, diarrhea and vomiting. We demonstrated the lack of sensitivities of microscopy and mRDT for one-time diagnosis of malaria. Therefore, it is essential to utilize a sensitive technique such as Plasmodium 18s rRNA LAMP to increase the detection rate of Plasmodium infection.
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Affiliation(s)
- Enoch Aninagyei
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
- * E-mail:
| | - Adjoa Agyemang Boakye
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
| | - Clement Okraku Tettey
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
| | - Kofi Adjei Ntiri
- Ghana Health Service, Greater Accra Region, Mayera-Faase Health Centre, Mayera-Faase, Ghana
| | | | - Comfort Dede Tetteh
- Ghana Health Service, Municipal Health Directorate, Ga West Municipal, Amasaman, Ghana
| | - Thelma Teley Aphour
- Ghana Health Service, Greater Accra Region, Ablekuma North Health Directorate, Accra, Ghana
| | - Tanko Rufai
- Ghana Health Service, Eastern Region, New Juaben South Municipal Health Directorate, Koforidua, Ghana
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States of America
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Ryoo S, Kang T, Lee DG, Jung J. The utility of a real-time polymerase chain reaction kit for differentiating between Mycobacterium tuberculosis and the Beijing familythe utility of a real-time polymerase chain reaction kit for differentiating between Mycobacterium tuberculosis and the Beijing family. Int J Mycobacteriol 2022; 11:268-272. [DOI: 10.4103/ijmy.ijmy_99_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Reliability of direct varicella zoster virus loop-mediated isothermal amplification method for rapid diagnosis of breakthrough varicella. J Clin Virol 2019; 119:53-58. [PMID: 31491710 DOI: 10.1016/j.jcv.2019.07.009] [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] [Received: 04/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Since patients with breakthrough varicella (BV) have mild symptoms, clinical diagnosis is difficult. In high vaccine coverage area, as BV occurs sporadically, point of care test is required for controlling varicella outbreak. In this study, the reliability of varicella zoster virus (VZV)-loop mediated isothermal amplification (LAMP) was evaluated for the rapid diagnosis of BV. STUDY DESIGN A total of 328 swab samples collected from patients with suspected varicella were analyzed. For the laboratory diagnosis of varicella, VZV real-time PCR was carried out using DNA extracted from swab samples. Swab samples without DNA extraction were used for VZV-LAMP(direct-LAMP). RESULTS VZV infection was diagnosed by real-time PCR in 285 cases, including 105 natural varicella cases and 180 BV cases. VZV DNA was detected in 250 (87.8%) of the 285 cases by direct-LAMP. The presence and duration of fever, number of skin eruptions, and VZV DNA load were significantly lower in BV than natural varicella. The sensitivity of direct-LAMP for the diagnosis of varicella and BV was 93.3% and 84.4%, respectively. CONCLUSIONS Direct LAMP was considered to be useful for rapid diagnosis of BV as it has several advantages such as low cost, ease and rapidity, as compared to real time PCR.
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Filipenko ML, Oscorbin IP, Khrapov EA, Shamovskaya DA, Cherednichenko AG, Shvartz Y. Detection of Ser450Leu mutation in rpoB gene of Mycobacterium tuberculosis by allele-specific loop-mediated isothermal DNA amplification method. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To identify genetic mutations a rather time-consuming and expensive method of polymerase chain reaction (PCR) is widely used. The aim of the present work was to evaluate the possibility of using the two schemes of the method of allele-specific isothermal loop amplification (LAMP) to detect the TCG/TTG (S450L) mutation in the rpoB gene of Mycobacterium tuberculosis. 48 clinical isolates of M. tuberculosis and 11 samples of sputum were used, randomized and obtained in the microbiological laboratory of the city of Novosibirsk from incident patients. It is shown that the use of an analysis scheme using the allele-specific primer FIP compared to F3 has the best resolution: the difference between the amplification time of the mutation and the wild type allele was 22 ± 2,4 versus 13 ± 4,1 minutes (p = 0,0011). When using 100 DNA genomic equivalents a true positive signal (amplification of the rpoB gene with a mutation using the corresponding allele-specific primer) was detected after 29,4 ± 3,4 minutes. A positive signal was visualized after adding SYBR Green I to the reaction, both when illuminated with daylight and when using a UV transilluminator. Using the developed method the DNA sample of 20 RIFR isolates from M. tuberculosis was analyzed containing the Ser450Leu mutation in the rpoB gene, 10 RIFR isolates containing other mutations in the rpoB gene and 18 RIFs isolates without any mutations; the presence of mutations in the samples was determined using classical Sanger sequencing. The sensitivity and specificity of LAMP for detecting a Ser450Leu mutation in the rpoB gene was 100%. This approach allows the use of crude lysates of mycobacteria as DNA, which reduces the total analysis time to 1,5 hour.
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Affiliation(s)
- ML Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - IP Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - EA Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - DA Shamovskaya
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - YaSh Shvartz
- Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia
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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: 344] [Impact Index Per Article: 57.3] [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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Zhang Y, Yao Y, Du W, Wu K, Xu W, Lin M, Tan H, Li J. Development of loop-mediated isothermal amplification with Plasmodium falciparum unique genes for molecular diagnosis of human malaria. Pathog Glob Health 2017; 111:247-255. [PMID: 28683669 PMCID: PMC5560202 DOI: 10.1080/20477724.2017.1347379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In order to achieve better outcomes for treatment and in the prophylaxis of malaria, it is imperative to develop a sensitive, specific, and accurate assay for early diagnosis of Plasmodium falciparum infection, which is the major cause of malaria. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay with P. falciparum unique genes for sensitive, specific, and accurate detection of P. falciparum infection. The unique genes of P. falciparum were randomly selected from PlasmoDB. The LAMP primers of the unique genes were designed using PrimerExplorer V4. LAMP assays with primers from unique genes of P. falciparum and conserved 18S rRNA gene were developed and their sensitivity was assessed. The specificity of the most sensitive LAMP assay was further examined using genomic DNA from Plasmodium vivax, Plasmodium yoelii and Toxoplasma gondii. Finally, the unique gene-based LAMP assay was validated using clinical samples of P. falciparum infection cases. A total of 31 sets of top-scored LAMP primers from nine unique genes were selected from the pools of designed primers. The LAMP assay with PF3D7_1253300-5 was the most sensitive with the detection limit 5 parasites/μl, and it displayed negative LAMP assay with the genomic DNA samples of P. vivax, P. yoelii, and T. gondii. The LAMP assay with PF3D7_0112300 (18S rRNA) was less sensitive with the detection limit 50 parasites/μl, and it displayed negative LAMP assay with the genomic DNA samples of P. yoelii and T. gondii, but displayed positive LAMP detection with P. vivax. The positive detection rate of the LAMP assay with PF3D7_1253300-5 was 90% (27/30), higher than that (80%, 24/30) of the positive rate of PF3D7_0112300 (18S rRNA) in examining clinical samples of P. falciparum infection cases. The LAMP assay with the primer set PF3D7_1253300-5 was more sensitive, specific, and accurate than those with PF3D7_0112300 (18S rRNA) in examining P. falciparum infection, and therefore it is a promising tool for diagnosis of P. falciparum infection.
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Affiliation(s)
- Yijing Zhang
- Department of Human Parasitology, College of Basic Medicine; Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, People’s Republic of China
| | - Yi Yao
- Department of Human Parasitology, College of Basic Medicine; Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, People’s Republic of China
| | - Weixing Du
- Department of Human Parasitology, College of Basic Medicine; Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, People’s Republic of China
| | - Kai Wu
- Department of Schistosomiasis and Endemic Diseases, Wuhan City Center for Disease Prevention and Control, Wuhan, People’s Republic of China
| | - Wenyue Xu
- The Department of Pathogenic Biology, Third Military Medical University, Chongqing, People’s Republic of China
| | - Min Lin
- Department of Histology and Embryology, Shantou University Medical College, Shantou, People’s Republic of China
| | - Huabing Tan
- Department of Human Parasitology, College of Basic Medicine; Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, People’s Republic of China
| | - Jian Li
- Department of Human Parasitology, College of Basic Medicine; Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, People’s Republic of China
- Corresponding author.
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