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Crego-Vicente B, del Olmo MD, Muro A, Fernández-Soto P. Multiplexing LAMP Assays: A Methodological Review and Diagnostic Application. Int J Mol Sci 2024; 25:6374. [PMID: 38928080 PMCID: PMC11203869 DOI: 10.3390/ijms25126374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/27/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The loop-mediated isothermal amplification (LAMP) technique is a great alternative to PCR-based methods, as it is fast, easy to use and works with high sensitivity and specificity without the need for expensive instruments. However, one of the limitations of LAMP is difficulty in achieving the simultaneous detection of several targets in a single tube, as the methodologies that allow this rely on fluorogenic probes containing specific target sequences, complicating their adaptation and the optimization of assays. Here, we summarize different methods for the development of multiplex LAMP assays based on sequence-specific detection, illustrated with a schematic representation of the technique, and evaluate their practical application based on the real-time detection and quantification of results, the possibility to visualize the results at a glance, the prior stabilization of reaction components, promoting the point-of-care use, the maximum number of specific targets amplified, and the validation of the technique in clinical samples. The various LAMP multiplexing methodologies differ in their operating conditions and mechanism. Each methodology has its advantages and disadvantages, and the choice among them will depend on specific application interests.
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Affiliation(s)
| | | | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (M.D.d.O.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (M.D.d.O.)
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Antonopoulos A, Gilleard JS, Charlier J. Next-generation sequencing technologies for helminth diagnostics and surveillance in ruminants: shifting diagnostic barriers. Trends Parasitol 2024; 40:511-526. [PMID: 38760257 DOI: 10.1016/j.pt.2024.04.013] [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: 03/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Helminth infections in grazing ruminants are a major issue for livestock farming globally, but are unavoidable in outdoor grazing systems and must be effectively managed to avoid deleterious effects to animal health, and productivity. Next-generation sequencing (NGS) technologies are transforming our understanding of the genetic basis of anthelmintic resistance (AR) and epidemiological studies of ruminant gastrointestinal parasites. They also have the potential to not only help develop and validate molecular diagnostic tests but to be directly used in routine diagnostics integrating species-specific identification and AR into a single test. Here, we review how these developments have opened the pathway for the development of multi-AR and multispecies identification in a single test, with widespread implications for sustainable livestock farming for the future.
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Affiliation(s)
- Alistair Antonopoulos
- Kreavet, Kruibeke, Belgium; School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - John S Gilleard
- Faculty of Veterinary Medicine, Host-Parasite Interactions Program, University of Calgary, Calgary, Alberta, Canada
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Chen P, Sun Z, Wang J, Liu X, Bai Y, Chen J, Liu A, Qiao F, Chen Y, Yuan C, Sha J, Zhang J, Xu LQ, Li J. Portable nanopore-sequencing technology: Trends in development and applications. Front Microbiol 2023; 14:1043967. [PMID: 36819021 PMCID: PMC9929578 DOI: 10.3389/fmicb.2023.1043967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.
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Affiliation(s)
- Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zepeng Sun
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Jiawei Wang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Xinlong Liu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Feng Qiao
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chenyan Yuan
- Clinical Laboratory, Southeast University Zhongda Hospital, Nanjing, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, China
| | - Jinghui Zhang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Li-Qun Xu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China,*Correspondence: Li-Qun Xu, ✉
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China,Jian Li, ✉
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4
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Zhang J, Chen X, Pan M, Qin Y, Zhao H, Yang Q, Li X, Zeng W, Xiang Z, Wu Y, Duan M, Li X, Wang X, Mazier D, Zhang Y, Zhu W, Sun K, Wu Y, Cui L, Huang Y, Yang Z. Application of a low-cost, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay to detect Plasmodium falciparum imported from Africa. Mol Biochem Parasitol 2022; 252:111529. [PMID: 36374724 PMCID: PMC9890345 DOI: 10.1016/j.molbiopara.2022.111529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/12/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Chinese citizens traveling abroad bring back imported malaria cases to China. Current malaria diagnostic tests, including microscopy and antigen-detecting rapid tests, cannot reliably detect low-density infections. To complement existing diagnostic methods, we aimed to develop a new loop-mediated isothermal amplification (LAMP) assay to detect and identify Plasmodium falciparum in Chinese travelers returning from Africa. METHODS We developed a miniaturized LAMP assay to amplify the actin I gene of P. falciparum. Each reaction consumed only 25% of the reagents used in a conventional LAMP assay and the same amount of DNA templates used in nested PCR. We evaluated this LAMP assay's performance and compared it to microscopy and a nested PCR assay using 466 suspected malaria cases imported from Africa. We assessed the sensitivity of the new LAMP assay using cultured P. falciparum, clinical samples, and a plasmid construct, allowing unprecedented precision when quantifying the limit of detection. RESULTS The new LAMP assay was highly sensitive and detected two more malaria cases than nested PCR. Compared to nested PCR, the sensitivity and specificity of the novel LAMP assay were 100% [95% confidence interval (CI) 98.5-100%] and 99.1% (95% CI 96.7-99.9%), respectively. When evaluated using serial dilutions of the plasmid construct, the detection limit of the new LAMP was as low as 102 copies/μL, 10-fold lower than PCR. The LAMP assay detected 0.01 parasites/μL of blood (equal to 0.04 parasites/μL of DNA) using cultured P. falciparum and 1-7 parasites/μL of blood (4-28 parasites/μL of DNA) in clinical samples, which is as good as or better than previously reported and commercially licensed assays. CONCLUSION The novel LAMP assay based on the P. falciparum actin I gene was specific, sensitive, and cost-effective, as it consumes 1/4 of the reagents in a typical LAMP reaction.
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Affiliation(s)
- Jiaqi Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Zhejiang Provincial Center for Disease Control and Prevention, No.3399 BinSheng Road, Binjiang District, Hangzhou, Zhejiang Province, 310051, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Maohua Pan
- Shanglin County People’s Hospital, Shanglin, Guangxi, 530500, China
| | - Yucheng Qin
- Shanglin County People’s Hospital, Shanglin, Guangxi, 530500, China
| | - Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Qi Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xinxin Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming, Yunnan,China
| | - Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Dominique Mazier
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Paris, France
| | - Yanmei Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Wenya Zhu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Kemin Sun
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Yiman Wu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, MDC84, Tampa, FL 33612, USA
| | - Yaming Huang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China,Correspondence:
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Correspondence:
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Deng Q, Cao Y, Wan X, Wang B, Sun A, Wang H, Wang Y, Wang H, Gu H. Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections. Front Cell Infect Microbiol 2022; 12:943859. [PMID: 36204638 PMCID: PMC9530710 DOI: 10.3389/fcimb.2022.943859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer patients are at high risk of infections and infection-related mortality; thereby, prompt diagnosis and precise anti-infectives treatment are critical. This study aimed to evaluate the performance of nanopore amplicon sequencing in identifying microbial agents among immunocompromised cancer patients with suspected infections. This prospective study enlisted 56 immunocompromised cancer patients with suspected infections. Their body fluid samples such as sputum and blood were collected, and potential microbial agents were detected in parallel by nanopore amplicon sequencing and the conventional culture method. Among the 56 body fluid samples, 47 (83.9%) samples were identified to have at least one pathogen by nanopore amplicon sequencing, but only 25 (44.6%) samples exhibited a positive finding by culture. Among 31 culture-negative samples, nanopore amplicon sequencing successfully detected pathogens in 22 samples (71.0%). Nanopore amplicon sequencing showed a higher sensitivity in pathogen detection than that of the conventional culture method (83.9% vs. 44.6%, P<0.001), and this advantage both existed in blood samples (38.5% vs. 0%, P=0.039) and non-blood samples (97.7% vs. 58.1%, P<0.001). Compared with the culture method, nanopore amplicon sequencing illustrated more samples with bacterial infections (P<0.001), infections from fastidious pathogens (P=0.006), and co-infections (P<0.001). The mean turnaround time for nanopore amplicon sequencing was about 17.5 hours, which was shorter than that of the conventional culture assay. This study suggested nanopore amplicon sequencing as a rapid and precise method for detecting pathogens among immunocompromised cancer patients with suspected infections. The novel and high-sensitive method will improve the outcomes of immunocompromised cancer patients by facilitating the prompt diagnosis of infections and precise anti-infectives treatment.
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Affiliation(s)
- Qingmei Deng
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Yongqing Cao
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Xiaofeng Wan
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Bin Wang
- Zhejiang ShengTing Biotechnology Company, Hangzhou, China
| | - Aimin Sun
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Huanzhong Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotechnology Company, Hangzhou, China
| | - Hongzhi Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Hongzhi Wang, ; Hongcang Gu,
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, China
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Hongzhi Wang, ; Hongcang Gu,
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6
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Sun K, Liu Y, Zhou X, Yin C, Zhang P, Yang Q, Mao L, Shentu X, Yu X. Nanopore sequencing technology and its application in plant virus diagnostics. Front Microbiol 2022; 13:939666. [PMID: 35958160 PMCID: PMC9358452 DOI: 10.3389/fmicb.2022.939666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Plant viruses threaten crop yield and quality; thus, efficient and accurate pathogen diagnostics are critical for crop disease management and control. Recent advances in sequencing technology have revolutionized plant virus research. Metagenomics sequencing technology, represented by next-generation sequencing (NGS), has greatly enhanced the development of virus diagnostics research because of its high sensitivity, high throughput and non-sequence dependence. However, NGS-based virus identification protocols are limited by their high cost, labor intensiveness, and bulky equipment. In recent years, Oxford Nanopore Technologies and advances in third-generation sequencing technology have enabled direct, real-time sequencing of long DNA or RNA reads. Oxford Nanopore Technologies exhibit versatility in plant virus detection through their portable sequencers and flexible data analyses, thus are wildly used in plant virus surveillance, identification of new viruses, viral genome assembly, and evolution research. In this review, we discuss the applications of nanopore sequencing in plant virus diagnostics, as well as their limitations.
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Affiliation(s)
- Kai Sun
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Yi Liu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xin Zhou
- Ausper Biopharma, Hangzhou, China
| | - Chuanlin Yin
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Pengjun Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Qianqian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Lingfeng Mao
- Hangzhou Baiyi Technology Co., Ltd., Hangzhou, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
- *Correspondence: Xuping Shentu,
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
- Xiaoping Yu,
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Mthethwa NP, Amoah ID, Reddy P, Bux F, Kumari S. Fluorescence and colorimetric LAMP-based real-time detection of human pathogenic Cryptosporidium spp. from environmental samples. Acta Trop 2022; 235:106606. [DOI: 10.1016/j.actatropica.2022.106606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/01/2022]
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8
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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Martín-Ramírez A, Lanza-Suárez M, Muñoz-García C, Hisam SR, Perez-Ayala A, Rubio JM. Usefulness of Malachite-Green LAMP for Diagnosis of Plasmodium and Five Human Malaria Species in a Nonendemic Setting. Am J Trop Med Hyg 2022; 106:tpmd211151. [PMID: 35292597 PMCID: PMC9128691 DOI: 10.4269/ajtmh.21-1151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022] Open
Abstract
Molecular methods are necessary to detect low-density malaria infections. The purpose of this study was to assess the diagnostic performance of six malachite-green loop-mediated amplification method (MG-LAMP) assays (MG-LAMP-Pf, MG-LAMP-Pv, MG-LAMP-Po, MG-LAMP-Pm, MG-LAMP-Pk, and MG-LAMP-Pspp) for the species-specific detection of each human Plasmodium, including P. knowlesi, and the Plasmodium genus compared with the nested-multiplex malaria polymerase chain reaction (NM-PCR), using 161 malaria-positive and 274 malaria-negative samples. MG-LAMP-Pspp assay detected the five human Plasmodium species and each species-specific MG-LAMP assay detected only its corresponding species. Sensitivity, specificity, and predictive values of MG-LAMP assays, compared with NM-PCR, were > 90%, except in the case of the MG-LAMP-Pm assay, which dropped to 47%. Limit of detection for MG-LAMP-Pspp assay ranged from 0.1 parasites/µL for P. falciparum to 16.9 parasites/µL for P. malariae samples, and it was similar for the rest of MG-LAMP assays except for the MG-LAMP-Pm assay. Turnaround time was estimated to be 2 hours and 35 minutes for one MG-LAMP assay and 4 hours and 15 minutes if all species-specific MG-LAMP is set up, whereas for the NM-PCR, turnaround time was ∼6 hours and 15 minutes. Costs per determination ranged from 1 to 6 euros for MG-LAMP assays and 5 euros for NM-PCR. Therefore, MG-LAMP assays appear to have good concordance compared with the reference method, except for the MG-LAMP-Pm assay. They can detect low parasitemia and identify malaria species, with lower costs and shorter time to obtain results, and they are suitable tools to be used in endemic and non-endemic countries for malaria detection.
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Affiliation(s)
- Alexandra Martín-Ramírez
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Lanza-Suárez
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlota Muñoz-García
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Shamilah R. Hisam
- Parasitology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health Malaysia, Setia Alam, Selangor, Malaysia
| | - Ana Perez-Ayala
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - José M. Rubio
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
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Ndiaye YD, Hartl DL, McGregor D, Badiane A, Fall FB, Daniels RF, Wirth DF, Ndiaye D, Volkman SK. Genetic surveillance for monitoring the impact of drug use on Plasmodium falciparum populations. Int J Parasitol Drugs Drug Resist 2021; 17:12-22. [PMID: 34333350 PMCID: PMC8342550 DOI: 10.1016/j.ijpddr.2021.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022]
Abstract
The use of antimalarial drugs is an effective strategy in the fight against malaria. However, selection of drug resistant parasites is a constant threat to the continued use of this approach. Antimalarial drugs are used not only to treat infections but also as part of population-level strategies to reduce malaria transmission toward elimination. While there is strong evidence that the ongoing use of antimalarial drugs increases the risk of the emergence and spread of drug-resistant parasites, it is less clear how population-level use of drug-based interventions like seasonal malaria chemoprevention (SMC) or mass drug administration (MDA) may contribute to drug resistance or loss of drug efficacy. Critical to sustained use of drug-based strategies for reducing the burden of malaria is the surveillance of population-level signals related to transmission reduction and resistance selection. Here we focus on Plasmodium falciparum and discuss the genetic signatures of a parasite population that are correlated with changes in transmission and related to drug pressure and resistance as a result of drug use. We review the evidence for MDA and SMC contributing to malaria burden reduction and drug resistance selection and examine the use and impact of these interventions in Senegal. Throughout we consider best strategies for ongoing surveillance of both population and resistance signals in the context of different parasite population parameters. Finally, we propose a roadmap for ongoing surveillance during population-level drug-based interventions to reduce the global malaria burden.
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Affiliation(s)
| | | | - David McGregor
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | | | - Fatou Ba Fall
- Programme National de Lutte Contre le Paludisme, Senegal.
| | - Rachel F Daniels
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA.
| | - Dyann F Wirth
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA.
| | | | - Sarah K Volkman
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA; Simmons University, Boston, MA, USA.
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11
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Grigg MJ, Lubis IN, Tetteh KKA, Barber BE, William T, Rajahram GS, Tan AF, Sutherland CJ, Noviyanti R, Drakeley CJ, Britton S, Anstey NM. Plasmodium knowlesi detection methods for human infections-Diagnosis and surveillance. ADVANCES IN PARASITOLOGY 2021; 113:77-130. [PMID: 34620386 DOI: 10.1016/bs.apar.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Within the overlapping geographical ranges of P. knowlesi monkey hosts and vectors in Southeast Asia, an estimated 1.5 billion people are considered at risk of infection. P. knowlesi can cause severe disease and death, the latter associated with delayed treatment occurring from misdiagnosis. Although microscopy is a sufficiently sensitive first-line tool for P. knowlesi detection for most low-level symptomatic infections, misdiagnosis as other Plasmodium species is common, and the majority of asymptomatic infections remain undetected. Current point-of-care rapid diagnostic tests demonstrate insufficient sensitivity and poor specificity for differentiating P. knowlesi from other Plasmodium species. Molecular tools including nested, real-time, and single-step PCR, and loop-mediated isothermal amplification (LAMP), are sensitive for P. knowlesi detection. However, higher cost and inability to provide the timely point-of-care diagnosis needed to guide appropriate clinical management has limited their routine use in most endemic clinical settings. P. knowlesi is likely underdiagnosed across the region, and improved diagnostic and surveillance tools are required. Reference laboratory molecular testing of malaria cases for both zoonotic and non-zoonotic Plasmodium species needs to be more widely implemented by National Malaria Control Programs across Southeast Asia to accurately identify the burden of zoonotic malaria and more precisely monitor the success of human-only malaria elimination programs. The implementation of specific serological tools for P. knowlesi would assist in determining the prevalence and distribution of asymptomatic and submicroscopic infections, the absence of transmission in certain areas, and associations with underlying land use change for future spatially targeted interventions.
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Affiliation(s)
- Matthew J Grigg
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia.
| | - Inke N Lubis
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Sumatera Utara, Indonesia
| | - Kevin K A Tetteh
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bridget E Barber
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; Clinical Research Centre, Queen Elizabeth Hospital 1, Kota Kinabalu, Malaysia; Gleneagles Medical Centre, Kota Kinabalu, Malaysia
| | - Giri S Rajahram
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; Clinical Research Centre, Queen Elizabeth Hospital 1, Kota Kinabalu, Malaysia; Queen Elizabeth Hospital 2, Kota Kinabalu, Malaysia
| | - Angelica F Tan
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Chris J Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sumudu Britton
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicholas M Anstey
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
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12
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Gimenez AM, Marques RF, Regiart M, Bargieri DY. Diagnostic Methods for Non-Falciparum Malaria. Front Cell Infect Microbiol 2021; 11:681063. [PMID: 34222049 PMCID: PMC8248680 DOI: 10.3389/fcimb.2021.681063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is a serious public health problem that affects mostly the poorest countries in the world, killing more than 400,000 people per year, mainly children under 5 years old. Among the control and prevention strategies, the differential diagnosis of the Plasmodium-infecting species is an important factor for selecting a treatment and, consequently, for preventing the spread of the disease. One of the main difficulties for the detection of a specific Plasmodium sp is that most of the existing methods for malaria diagnosis focus on detecting P. falciparum. Thus, in many cases, the diagnostic methods neglect the other non-falciparum species and underestimate their prevalence and severity. Traditional methods for diagnosing malaria may present low specificity or sensitivity to non-falciparum spp. Therefore, there is high demand for new alternative methods able to differentiate Plasmodium species in a faster, cheaper and easier manner to execute. This review details the classical procedures and new perspectives of diagnostic methods for malaria non-falciparum differential detection and the possibilities of their application in different circumstances.
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Affiliation(s)
- Alba Marina Gimenez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodolfo F. Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Matías Regiart
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Daniel Youssef Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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13
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Mthethwa NP, Amoah ID, Reddy P, Bux F, Kumari S. A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives. J Microbiol Methods 2021; 187:106269. [PMID: 34129906 DOI: 10.1016/j.mimet.2021.106269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/23/2023]
Abstract
The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and large eukaryotic genome, the prevalence of small parasite populations in environmental samples compared to bacteria, difficulties in extracting DNA from (oo)cysts, and limited reference databases for parasites. This calls for further research to develop optimized methods specifically looking at protozoan parasites in the environment. This study reviews the current workflow, methods and provide recommendations for the standardization of techniques. The article identifies and summarizes the key methods, advantages, and limitations associated with metagenomic analysis, like sample pre-processing, DNA extraction, sequencing approaches, and analysis methods. The study enhances the understanding and application of standardized protocols for profiling of protozoan parasite community from highly complexe samples and further creates a resourceful comparison among datasets without any biases.
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Affiliation(s)
- N P Mthethwa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa; Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - I D Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - P Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - F Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - S Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
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14
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Nolasco O, Montoya J, Rosales Rosas AL, Barrientos S, Rosanas-Urgell A, Gamboa D. Multicopy targets for Plasmodium vivax and Plasmodium falciparum detection by colorimetric LAMP. Malar J 2021; 20:225. [PMID: 34011373 PMCID: PMC8135177 DOI: 10.1186/s12936-021-03753-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Loop-mediated isothermal amplification (LAMP) for malaria diagnosis at the point of care (POC) depends on the detection capacity of synthesized nucleic acids and the specificity of the amplification target. To improve malaria diagnosis, new colorimetric LAMP tests were developed using multicopy targets for Plasmodium vivax and Plasmodium falciparum detection. METHODS The cytochrome oxidase I (COX1) mitochondrial gene and the non-coding sequence Pvr47 for P. vivax, and the sub-telomeric sequence of erythrocyte membrane protein 1 (EMP1) and the non-coding sequence Pfr364 for P. falciparum were targeted to design new LAMP primers. The limit of detection (LOD) of each colorimetric LAMP was established and assessed with DNA extracted by mini spin column kit and the Boil & Spin method from 28 microscopy infections, 101 malaria submicroscopic infections detected by real-time PCR only, and 183 negatives infections by both microscopy and PCR. RESULTS The LODs for the colorimetric LAMPs were estimated between 2.4 to 3.7 parasites/µL of whole blood. For P. vivax detection, the colorimetric LAMP using the COX1 target showed a better performance than the Pvr47 target, whereas the Pfr364 target was the most specific for P. falciparum detection. All microscopic infections of P. vivax were detected by PvCOX1-LAMP using the mini spin column kit DNA extraction method and 81% (17/21) were detected using Boil & Spin sample preparation. Moreover, all microscopic infections of P. falciparum were detected by Pfr364-LAMP using both sample preparation methods. In total, PvCOX1-LAMP and Pfr364-LAMP detected 80.2% (81 samples) of the submicroscopic infections using the DNA extraction method by mini spin column kit, while 36.6% (37 samples) were detected using the Boil & Spin sample preparation method. CONCLUSION The colorimetric LAMPs with multicopy targets using the COX1 target for P. vivax and the Pfr364 for P. falciparum have a high potential to improve POC malaria diagnosis detecting a greater number of submicroscopic Plasmodium infections.
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Affiliation(s)
- Oscar Nolasco
- Instituto de Medicina Tropical "Alexander von Humboldt" Universidad Peruana Cayetano Heredia, Lima, Peru.
- Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Jhoel Montoya
- Unidad de Posgrado de la Facultad de Ciencias Biológicas Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ana L Rosales Rosas
- Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Scarlett Barrientos
- Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical "Alexander von Humboldt" Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares Y Moleculares, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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15
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Rei Yan SL, Wakasuqui F, Wrenger C. Point-of-care tests for malaria: speeding up the diagnostics at the bedside and challenges in malaria cases detection. Diagn Microbiol Infect Dis 2020; 98:115122. [PMID: 32711185 DOI: 10.1016/j.diagmicrobio.2020.115122] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/21/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Malaria remains as one of the major public health problems worldwide. About 228 million cases occurred in 2018 only, with Africa bearing about 93% of the cases. Asymptomatic population carrying the various forms of the parasite Plasmodium in endemic areas plays an important role in the spread of the disease. To tackle this battle, more sensitive and precise detection kits for malaria are crucial to better control the number of new malaria cases. In this review, we not only discuss some of the available approaches to rapidly detect new malaria cases in endemic areas but also shed light on parallel problems that may affect the detection of individuals infected with the parasite, covering kelch 13 mutation, glucose 6-phosphate dehydrogenase deficiency, and hemoglobin disorders. Available approaches for malaria detection covered in this review are focused on point-of-care tests, including portable polymerase chain reaction and aptamers.
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Affiliation(s)
- Sun L Rei Yan
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Felipe Wakasuqui
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
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16
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Comparison of High-Throughput Sequencing for Phage Display Peptide Screening on Two Commercially Available Platforms. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09858-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Mongan AE, Tuda JSB, Runtuwene LR. Portable sequencer in the fight against infectious disease. J Hum Genet 2020; 65:35-40. [PMID: 31582773 PMCID: PMC6892364 DOI: 10.1038/s10038-019-0675-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022]
Abstract
Infectious disease is still a major threat in the world today. Five decades ago, it was considered soon to be eradicated, but the adaptation of pathogens to environmental pressure, such as antimicrobials, encouraged the emergence and reemergence of infectious disease. The fight with infectious disease starts with prevention, diagnosis, and treatment. Diagnosis can be upheld by observing the cause of disease under the microscope or detecting the presence of nucleic acid and proteins of the pathogens. The molecular techniques span from classical polymerase chain reaction (PCR) to sequencing the nucleic acid composition. Here, we are reviewing the works have been undertaken to utilize a portable sequencer, MinION, in various aspects of infectious disease management.
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18
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Cheaveau J, Mogollon DC, Mohon MAN, Golassa L, Yewhalaw D, Pillai DR. Asymptomatic malaria in the clinical and public health context. Expert Rev Anti Infect Ther 2019; 17:997-1010. [PMID: 31718324 DOI: 10.1080/14787210.2019.1693259] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Introduction: Historically, the global community has focused on the control of symptomatic malaria. However, interest in asymptomatic malaria has been growing, particularly in the context of malaria elimination.Areas covered: We undertook a comprehensive PubMed literature review on asymptomatic malaria as it relates to detection and elimination with emphasis between 2014 and 2019. Diagnostic tools with a low limit of detection (LOD) have allowed us to develop a more detailed understanding of asymptomatic malaria and its impact. These highly sensitive diagnostics have demonstrated that the prevalence of asymptomatic malaria is greater than previously thought. In addition, it is now possible to detect the malaria reservoir in the community, something that was previously not feasible. Asymptomatic malaria has previously not been treated, but research has begun to examine whether treating individuals with asymptomatic malaria may lead to health benefits. Finally, we have begun to understand the importance of asymptomatic malaria in ongoing transmission.Expert opinion: Therefore, with malaria elimination back on the agenda, asymptomatic malaria can no longer be ignored, especially in light of new ultra-sensitive diagnostic tools.
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Affiliation(s)
- James Cheaveau
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Daniel Castaneda Mogollon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Md Abu Naser Mohon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Dylan R Pillai
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
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19
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Kono N, Arakawa K. Nanopore sequencing: Review of potential applications in functional genomics. Dev Growth Differ 2019; 61:316-326. [DOI: 10.1111/dgd.12608] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
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20
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Vidic J, Vizzini P, Manzano M, Kavanaugh D, Ramarao N, Zivkovic M, Radonic V, Knezevic N, Giouroudi I, Gadjanski I. Point-of-Need DNA Testing for Detection of Foodborne Pathogenic Bacteria. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1100. [PMID: 30836707 PMCID: PMC6427207 DOI: 10.3390/s19051100] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
Foodborne pathogenic bacteria present a crucial food safety issue. Conventional diagnostic methods are time-consuming and can be only performed on previously produced food. The advancing field of point-of-need diagnostic devices integrating molecular methods, biosensors, microfluidics, and nanomaterials offers new avenues for swift, low-cost detection of pathogens with high sensitivity and specificity. These analyses and screening of food items can be performed during all phases of production. This review presents major developments achieved in recent years in point-of-need diagnostics in land-based sector and sheds light on current challenges in achieving wider acceptance of portable devices in the food industry. Particular emphasis is placed on methods for testing nucleic acids, protocols for portable nucleic acid extraction and amplification, as well as on the means for low-cost detection and read-out signal amplification.
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Affiliation(s)
- Jasmina Vidic
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Priya Vizzini
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Devon Kavanaugh
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nalini Ramarao
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Milica Zivkovic
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, 11000 Belgrade, Serbia.
| | - Vasa Radonic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Nikola Knezevic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ioanna Giouroudi
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ivana Gadjanski
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
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21
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Duncan R, Grigorenko E, Fisher C, Hockman D, Lanning B. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls - an update. Expert Rev Mol Diagn 2018; 19:15-25. [DOI: 10.1080/14737159.2019.1559055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Robert Duncan
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Carolyn Fisher
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Bryan Lanning
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
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22
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Golparian D, Donà V, Sánchez-Busó L, Foerster S, Harris S, Endimiani A, Low N, Unemo M. Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer. Sci Rep 2018; 8:17596. [PMID: 30514867 PMCID: PMC6279828 DOI: 10.1038/s41598-018-35750-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/10/2018] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day. However, accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench including de novo assembly and optimised BLAST algorithms, we show that 2D ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended antimicrobials in gonococcal isolates. We also show that the 2D ONT-derived sequences are useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Valentina Donà
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Leonor Sánchez-Busó
- Pathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Sunniva Foerster
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simon Harris
- Pathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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23
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Malpartida-Cardenas K, Rodriguez-Manzano J, Yu LS, Delves MJ, Nguon C, Chotivanich K, Baum J, Georgiou P. Allele-Specific Isothermal Amplification Method Using Unmodified Self-Stabilizing Competitive Primers. Anal Chem 2018; 90:11972-11980. [PMID: 30226760 PMCID: PMC6195307 DOI: 10.1021/acs.analchem.8b02416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Rapid and specific detection of single nucleotide polymorphisms (SNPs) related to drug resistance in infectious diseases is crucial for accurate prognostics, therapeutics and disease management at point-of-care. Here, we present a novel amplification method and provide universal guidelines for the detection of SNPs at isothermal conditions. This method, called USS-sbLAMP, consists of SNP-based loop-mediated isothermal amplification (sbLAMP) primers and unmodified self-stabilizing (USS) competitive primers that robustly delay or prevent unspecific amplification. Both sets of primers are incorporated into the same reaction mixture, but always targeting different alleles; one set specific to the wild type allele and the other to the mutant allele. The mechanism of action relies on thermodynamically favored hybridization of totally complementary primers, enabling allele-specific amplification. We successfully validate our method by detecting SNPs, C580Y and Y493H, in the Plasmodium falciparum kelch 13 gene that are responsible for resistance to artemisinin-based combination therapies currently used globally in the treatment of malaria. USS-sbLAMP primers can efficiently discriminate between SNPs with high sensitivity (limit of detection of 5 × 101 copies per reaction), efficiency, specificity and rapidness (<35 min) with the capability of quantitative measurements for point-of-care diagnosis, treatment guidance, and epidemiological reporting of drug-resistance.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Ling-Shan Yu
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Michael J Delves
- Department of Life Sciences, Imperial College London , South Kensington Campus , SW7 2AZ , London , United Kingdom
| | - Chea Nguon
- National Centre for Parasitology , Entomology and Malaria Control , Phnom Penh 12302 , Cambodia
| | - Kesinee Chotivanich
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine , Mahidol University , Bangkok 10400 , Thailand
| | - Jake Baum
- Department of Life Sciences, Imperial College London , South Kensington Campus , SW7 2AZ , London , United Kingdom
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
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Kollenda H, Hagen RM, Hanke M, Rojak S, Hinz R, Wassill L, Poppert S, Tannich E, Frickmann H. Poor Diagnostic Performance of a Species-Specific Loop-Mediated Isothermal Amplification (LAMP) Platform for Malaria. Eur J Microbiol Immunol (Bp) 2018; 8:112-118. [PMID: 30719327 PMCID: PMC6348705 DOI: 10.1556/1886.2018.00020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/31/2022] Open
Abstract
Background The objective of this study was to assess an in-house loop-mediated isothermal amplification (LAMP) platform for malaria parasite detection and identification on species level. Methods LAMP primers specific for the human Plasmodium spp., namely, P. falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi, as well as genus-specific primers, were tested against a composite gold standard comprising microscopy from thick and thin blood films, commercial genus-specific Meridian illumigene Malaria LAMP, in-house real-time polymerase chain reaction (PCR), and commercial fast-track diagnostics (FTD) Malaria differentiation PCR. Results Of the 523 blood samples analyzed, the composite gold standard indicated 243 Plasmodium-species-DNA-containing samples (46.5%). Sensitivity and specificity of the analyzed genus- and species-specific LAMP primers were 71.0%–100.0% and 90.8%–100.0%, respectively. The influence of parasitemia was best documented for P. falciparum-specific LAMP with sensitivity values of 35.5% (22/62) for microscopically negative samples containing P. falciparum DNA, 50% (19/38) for parasitemia ≤50/μL, 84% (21/25) for parasitemia ≤500/μL, and 100% (92/92) for parasitemia >500/μL. Conclusions In our hands, performance characteristics of species-specific in-house LAMP for malaria lack reliability required for diagnostic laboratories. The use of the easy-to-apply technique for surveillance purposes may be considered.
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Affiliation(s)
- Hans Kollenda
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Ralf Matthias Hagen
- Department of Preventive Medicine, Bundeswehr Medical Academy, Munich, Germany
| | - Miriam Hanke
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Sandra Rojak
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany.,Department of Infectious Diseases and Tropical Medicine, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Rebecca Hinz
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | | | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Faculty of Medicine, University Basel, Basel, Switzerland
| | - Egbert Tannich
- National Reference Centre for Tropical Pathogens, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Tropical Microbiology and Entomology Unit, Bundeswehr Hospital Hamburg, Hamburg, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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25
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Mallepaddi PC, Lai MY, Podha S, Ooi CH, Liew JWK, Polavarapu R, Lau YL. Development of Loop-Mediated Isothermal Amplification-Based Lateral Flow Device Method for the Detection of Malaria. Am J Trop Med Hyg 2018; 99:704-708. [PMID: 29943720 DOI: 10.4269/ajtmh.18-0177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The present study aims to develop a method for rapid diagnosis of malaria using loop-mediated isothermal amplification (LAMP) combined with a lateral flow device (LFD). By adding the biotin-labeled and fluorescein amidite-labeled loop primers to the LAMP reaction solution, the end product can be visualized on a LFD. The entire procedure takes approximately 42 minutes to complete, LAMP assay exhibited high sensitivity, as the detection limit was 0.01 pg/μL for all five Plasmodium species. It was demonstrated that all Plasmodium knowlesi (N = 90) and Plasmodium vivax (N = 56) were positively amplified by LAMP-LFD assay, whereas healthy donor samples (N = 8) were negative. However, not all mixed infections were positive, and other infected nonmalaria samples were negative. Loop-mediated isothermal amplification-LFD represents a robust approach with potential suitability for use in resource-constrained laboratories. We believe that LAMP-LFD has a potential to be developed as point-of-care diagnostic tool in future.
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Affiliation(s)
- Prudhvi Chand Mallepaddi
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India.,Genomix Molecular Diagnostics Pvt. Ltd., Hyderabad, India
| | - Meng-Yee Lai
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sudhakar Podha
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Choo-Huck Ooi
- Sarawak State Health Department, Jalan Diplomatik, Kuching, Malaysia
| | - Jonathan Wee-Kent Liew
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rathnagiri Polavarapu
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India.,Genomix Molecular Diagnostics Pvt. Ltd., Hyderabad, India
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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26
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Pattaradilokrat S, Trakoolsoontorn C, Simpalipan P, Warrit N, Kaewthamasorn M, Harnyuttanakorn P. Size and sequence polymorphisms in the glutamate-rich protein gene of the human malaria parasite Plasmodium falciparum in Thailand. Parasit Vectors 2018; 11:49. [PMID: 29357909 PMCID: PMC5778735 DOI: 10.1186/s13071-018-2630-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background The glutamate-rich protein (GLURP) of the malaria parasite Plasmodium falciparum is a key surface antigen that serves as a component of a clinical vaccine. Moreover, the GLURP gene is also employed routinely as a genetic marker for malarial genotyping in epidemiological studies. While extensive size polymorphisms in GLURP are well recorded, the extent of the sequence diversity of this gene is rarely investigated. The present study aimed to explore the genetic diversity of GLURP in natural populations of P. falciparum. Results The polymorphic C-terminal repetitive R2 region of GLURP sequences from 65 P. falciparum isolates in Thailand were generated and combined with the data from 103 worldwide isolates to generate a GLURP database. The collection was comprised of 168 alleles, encoding 105 unique GLURP subtypes, characterized by 18 types of amino acid repeat units (AAU). Of these, 28 GLURP subtypes, formed by 10 AAU types, were detected in P. falciparum in Thailand. Among them, 19 GLURP subtypes and 2 AAU types are described for the first time in the Thai parasite population. The AAU sequences were highly conserved, which is likely due to negative selection. Standard Fst analysis revealed the shared distributions of GLURP types among the P. falciparum populations, providing evidence of gene flow among the different demographic populations. Conclusions Sequence diversity causing size variations in GLURP in Thai P. falciparum populations were detected, and caused by non-synonymous substitutions in repeat units and some insertion/deletion of aspartic acid or glutamic acid codons between repeat units. The P. falciparum population structure based on GLURP showed promising implications for the development of GLURP-based vaccines and for monitoring vaccine efficacy. Electronic supplementary material The online version of this article (doi: 10.1186/s13071-018-2630-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sittiporn Pattaradilokrat
- Department of Biology, Faculty of Science, Chualongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand. .,Veterinary Parasitology Research Group, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Chawinya Trakoolsoontorn
- Department of Biology, Faculty of Science, Chualongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand
| | - Phumin Simpalipan
- Department of Biology, Faculty of Science, Chualongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand
| | - Natapot Warrit
- Department of Biology, Faculty of Science, Chualongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand
| | - Morakot Kaewthamasorn
- Veterinary Parasitology Research Group, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pongchai Harnyuttanakorn
- Department of Biology, Faculty of Science, Chualongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand
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Yacob NA, Mohd Noor NA, Mohd Yunus NY, Lob Yussof R, Zakaria SAKY. Advancements in Parasite Diagnosis and Challenges in the Management of Parasitic Infections: A Mini Review. REGIONAL CONFERENCE ON SCIENCE, TECHNOLOGY AND SOCIAL SCIENCES (RCSTSS 2016) 2018. [PMCID: PMC7121306 DOI: 10.1007/978-981-13-0074-5_64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Intestinal parasitic infections (IPIs) remain a widespread public health concern causing severe implications in both developed and developing countries. Globally, numerous studies have been carried out ranging from various communities to schoolchildren as well as indigenous communities. The infections are commonly caused by helminths (e.g. Ascaris lumbricoides, Trichuris trichiura and hookworm) and protozoa (e.g. Blastocystis hominis, Cryptosporidium sp., Entamoeba histolytica and Giardia duodenalis). Poor sanitation and poverty are some of the factors associated with IPIs. With the ever-increasing impact of IPIs, newer detection approaches have been developed and studied. The efficacy of diagnostic method is crucial to give an accurate identification of these parasites. Recent developments of diagnostic tools such as serology- and molecular-based assays are assisting the conventional method of microscopy in detecting and further confirming current or past infections and the specific species of parasites. Ongoing investigations in parasitic infections using these advanced tools will provide useful information that will enable the evaluation of the effectiveness of the current control program and thus, assist future planning for improved strategies in eradicating these parasitic infections.
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