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Thongseesuksai T, Boonmars T, Laummaunwai P. Comparison of Three Methods to Extract Plasmodium falciparum DNA from Whole Blood and Dried Blood Spots. Am J Trop Med Hyg 2024; 110:220-227. [PMID: 38227960 PMCID: PMC10859813 DOI: 10.4269/ajtmh.23-0612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/01/2023] [Indexed: 01/18/2024] Open
Abstract
This study aimed to compare the effectiveness of three DNA extraction methods: the GF-1 Blood DNA Extraction Kit (GF-1 BD Kit), which employs a spin column along with lysing and washing buffers; the tris-ethylenediaminetetraacetic acid and proteinase K (TE-pK) method, which utilizes a combination of TE buffer and proteinase K for cell lysis; and DNAzol® Direct (DN 131), a single reagent combined with heating for the extraction process. Plasmodium falciparum DNA was extracted from both whole blood and dried blook spots (DBSs), with consideration of DNA concentration, purity, cost, time requirement, and limit of parasite detection (LOD) for each method. The target gene in this study was 18S rRNA, resulting in a 395-bp product using specific primers. In the comparative analysis, the DN 131 method yielded significantly higher DNA quantities from whole blood and DBSs than the GF-1 BD Kit and TE-pK methods. In addition, the DNA purity obtained from whole blood and DBSs using the GF-1 BD Kit significantly exceeded that obtained using the TE-pK and DN 131 methods. For LOD, the whole blood extracted using the DN 131, GF-1 BD Kit, and TE-pK methods revealed 0.012, 0.012, and 1.6 parasites/µL, respectively. In the case of DBSs, the LODs for the DN 131, GF-1 BD Kit, and TE-pK methods were 1.6, 8, and 200 parasites/µL, respectively. The results revealed that the TE-pK method was the most cost-effective, whereas the DN 131 method showed the simplest protocol. These findings offer alternative approaches for extracting Plasmodium DNA that are particularly well-suited for large-scale studies conducted in resource-limited settings.
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Affiliation(s)
| | - Thidarut Boonmars
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Neglected Zoonosis and Vector-Borne Disease Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Porntip Laummaunwai
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Neglected Zoonosis and Vector-Borne Disease Research Group, Khon Kaen University, Khon Kaen, Thailand
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Lai MY, Abdul Hamid MH, Jelip J, Mudin RN, Lau YL. Evaluation of A Simple DNA Extraction Method and Its Combination with Loop-Mediated Isothermal Amplification Assays for Rapid Plasmodium knowlesi Diagnosis. Trop Med Infect Dis 2023; 8:389. [PMID: 37624327 PMCID: PMC10458645 DOI: 10.3390/tropicalmed8080389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/24/2023] [Accepted: 07/01/2023] [Indexed: 08/26/2023] Open
Abstract
The initial and vital stage in the diagnosis of malaria involves extracting DNA. The efficiency of malaria testing is restricted by the multiple steps involved in commercial DNA extraction kits. We attempted to improve an existing loop-mediated isothermal amplification (LAMP) for the detection of Plasmodium knowlesi by using a simple DNA extraction approach, making it a feasible option for mass screening. We utilized a simple nucleic acid extraction method directly from whole blood for the detection of P. knowlesi, taking only 5 min to complete. The extracted DNA was evaluated by two fluorescent-based LAMP and one colorimetric-based LAMP assay. The detection limit for both SYTO-LAMP and SYBR green-LAMP was 0.00001% and 0.0001% parasitemia, respectively. Meanwhile, neutral red-LAMP had a detection limit of 0.01% parasitemia. Combining this simple and inexpensive DNA extraction method, SYTO-LAMP could serve as an alternative molecular diagnosis for the detection of P. knowlesi and other human Plasmodium spp.
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Affiliation(s)
- Meng-Yee Lai
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | | | - Jenarun Jelip
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62000, Malaysia
| | - Rose Nani Mudin
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62000, Malaysia
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
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Dieki R, Eyang-Assengone ER, Makouloutou-Nzassi P, Bangueboussa F, Nsi Emvo E, Akue JP. Comparison of six methods for Loa loa genomic DNA extraction. PLoS One 2022; 17:e0265582. [PMID: 35312712 PMCID: PMC8936488 DOI: 10.1371/journal.pone.0265582] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/05/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Good-quality and sufficient DNA is essential for diagnostics and vaccine development. We aimed to compare six DNA extraction techniques applied to Loa loa microfilariae in order to evaluate the purity and integrity of extracts in terms of quality and quantity. METHODS The microfilariae were purified via a Percoll gradient procedure with blood from hyper-microfilaremic individuals (> 30,000 microfilaria [mf]/ml). DNA extraction was carried out in duplicate at a rate of 350,000 mf/tube for each technique: phenol/chloroform, commercial Qiagen kit, salting out, Tris-EDTA, methanol, and cetyltrimethylammonium bromide (CTAB). The integrity, purity, concentration, and quality of the DNA extracts were successively verified by agarose gel electrophoresis, spectrophotometry (A260/A280 and A260/A230 wavelength ratio), Qubit fluorometry, and endonuclease and polymerase activity. The six techniques were compared on the basis of the following parameters: concentration, purity, efficiency, effectiveness, integrity, safety of the technique, as well as cost and duration of the protocol. RESULTS The ratios of the optical densities of the extracts A260/A280 and A260/A230 were, respectively: phenol/chloroform (1.82; 1.11), Qiagen (1.93; 1.36), salting-out (1.9; 2.04), Tris-EDTA (1.99; 1.183), methanol (2.126; 1.343), and CTAB (2.01; 2.426). The DNA yield was: phenol/chloroform (3.920 μg), Qiagen (10.280 μg), salting-out (10.390 μg), Tris-EDTA (0.5528 μg), methanol (0.1036 μg), and CTAB (1.115 μg). Endonuclease and polymerase activity was demonstrated by digestion of DNA and through amplicons obtained via polymerase chain reaction assays with phenol/chloroform, Qiagen, and salting-out extracts. CONCLUSION The phenol/chloroform, Qiagen, and salting-out DNA extracts were all of good quality. Salting out had the best yield followed by Qiagen and then phenol/chloroform. Endonuclease and polymerase activity was effective in all three extracts despite the presence of some contaminants. These methods are therefore suitable for the extraction of DNA from Loa loa microfilariae. Tris-EDTA and methanol did not show adequate sensitivity, while CTAB was found to be unsuitable.
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Affiliation(s)
- Roland Dieki
- Département de Parasitologie, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Laboratoire de Recherche en Biochimie (LAREBIO), Faculté des Sciences, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon
| | | | | | - Félicien Bangueboussa
- Unité de Recherches en Ecologie de la Santé (URES/CIRMF), BP. 769 Franceville, Gabon
| | - Edouard Nsi Emvo
- Laboratoire de Recherche en Biochimie (LAREBIO), Faculté des Sciences, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon
| | - Jean Paul Akue
- Département de Parasitologie, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
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Saidi Q, Minja D, Njau J, Hansson H, Kavishe R, Alifrangis M. Ultrasensitive qPCR-Based Detection of Plasmodium falciparum in Pregnant Women Using Dried Blood or Whole Blood Pellet Samples Processed through Different DNA Extraction Methods. Am J Trop Med Hyg 2022; 106:846-849. [PMID: 34872057 PMCID: PMC8922499 DOI: 10.4269/ajtmh.21-0496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/23/2021] [Indexed: 11/07/2022] Open
Abstract
Highly sensitive molecular techniques for the detection of low-level Plasmodium falciparum parasitemia are highly useful for various clinical and epidemiological studies. However, differences in how blood samples are preserved, the quantity of blood stored, as well as genomic DNA extraction methods used may compromise the potential usefulness of these methodologies. This study compared diagnostic sensitivity based on microscopy and malaria rapid diagnostic tests (mRDTs), with quantitative polymerase chain reaction (qPCR) P. falciparum positivity of dried blood spots (DBS) or whole blood pellets (WBP) from pregnant women using different DNA extraction protocols (Chelex-saponin or a commercial kit). Samples from 129 pregnant women were analyzed, of which 13 were P. falciparum positive by mRDT and 5 by microscopy. By using extraction kit on WBP and on DBS, qPCR positivity was 27 (20.9%) and 16 (12.4%), respectively, whereas Chelex extraction on DBS only resulted in 4 (3.1%) P. falciparum positive samples. Thus, extraction using commercial kits greatly improve the likelihood of detecting P. falciparum infections.
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Affiliation(s)
- Queen Saidi
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania;,Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark;,Address correspondence to Queen Saidi, Kilimanjaro Clinical Research Institute, P.O. Box 2236, Moshi, Tanzania. E-mail:
| | - Daniel Minja
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Judith Njau
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Helle Hansson
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Reginald Kavishe
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania;,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
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Ozturk EA, Caner A. Liquid Biopsy for Promising Non-invasive Diagnostic Biomarkers in Parasitic Infections. Acta Parasitol 2022; 67:1-17. [PMID: 34176040 DOI: 10.1007/s11686-021-00444-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Liquid biopsy refers to the sampling and molecular analysis of body fluids such as blood, saliva, and urine in contrast to conventional tissue biopsies. Liquid biopsy approach can offer powerful non-invasive biomarkers (circulating markers) for diagnosis and monitoring treatment response of a variety of diseases, including parasitic infections. METHODS In this review, we concentrate on cell-free DNA (cfDNA), microRNA (miRNA), and exosomes in the published literature. RESULTS Considering the high prevalence and severity of parasitic infections worldwide, circulating biomarkers can provide a new insight into the diagnosis and prognosis of parasites in the near future. Moreover, identifying and characterizing parasite- or host-derived circulating markers are important for a better understanding of the pathogenesis of parasite infection and host-parasite relationship at the molecular level. Profiling of biomarkers for parasitic diseases is a promising potential field, though further studies and optimization strategies are required, both in vitro and in vivo. CONCLUSION In this review, we discuss three approaches in the liquid biopsy including circulating cfDNA, miRNAs, and exosomes for diagnosis and evaluation of parasites and summarize circulating biomarkers in non-invasive samples during parasitic infections.
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Affiliation(s)
- Eylem Akdur Ozturk
- Department of Parasitology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - Ayse Caner
- Department of Parasitology, Ege University Faculty of Medicine, 35100, Izmir, Turkey.
- Cancer Research Center, Ege University, Izmir, Turkey.
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Schumann R, Bischoff E, Klaus S, Möhring S, Flock J, Keller S, Remans K, Ganter M, Deponte M. Protein abundance and folding rather than the redox state of Kelch13 determine the artemisinin susceptibility of Plasmodium falciparum. Redox Biol 2021; 48:102177. [PMID: 34773836 PMCID: PMC8600086 DOI: 10.1016/j.redox.2021.102177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/25/2021] [Accepted: 10/30/2021] [Indexed: 12/30/2022] Open
Abstract
Decreased susceptibilities of the human malaria parasite Plasmodium falciparum towards the endoperoxide antimalarial artemisinin are linked to mutations of residue C580 of PfKelch13, a homologue of the redox sensor Keap1 and other vertebrate BTB-Kelch proteins. Here, we addressed whether mutations alter the artemisinin susceptibility by modifying the redox properties of PfKelch13 or by compromising its native fold or abundance. Using selection-linked integration and the glmS ribozyme, efficient down-regulation of PfKelch13 resulted in ring-stage survival rates around 40%. While the loss of the thiol group of C469 or of the potential disulfide bond between residues C580 and C532 had no effect on the artemisinin susceptibility, the thiol group of C473 could not be replaced. Furthermore, we detected two different forms of PfKelch13 with distinct electrophoretic mobilities around 85 and 95 kDa, suggesting an unidentified post-translational modification. We also established a protocol for the production of recombinant PfKelch13 and produced an antibody against the protein. Recombinant PfKelch13 adopted alternative oligomeric states and only two of its seven cysteine residues, C469 and C473, reacted with Ellman's reagent. While common field mutations resulted in misfolded and completely insoluble recombinant PfKelch13, cysteine-to-serine replacements had no effect on the solubility except for residue C473. In summary, in contrast to residues C469, C532, and C580, the surface-exposed thiol group of residue C473 appears to be essential. However, not the redox properties but impaired folding of PfKelch13, resulting in a decreased PfKelch13 abundance, alters the artemisinin susceptibility and is the central parameter for mutant selection.
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Affiliation(s)
- Robin Schumann
- Faculty of Chemistry, Comparative Biochemistry, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Eileen Bischoff
- Faculty of Chemistry, Comparative Biochemistry, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Severina Klaus
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, D-69120, Heidelberg, Germany
| | - Sophie Möhring
- Faculty of Chemistry, Comparative Biochemistry, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Julia Flock
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory (EMBL), D-69117, Heidelberg, Germany
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern, D-67663, Kaiserslautern, Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010, Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Kim Remans
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory (EMBL), D-69117, Heidelberg, Germany
| | - Markus Ganter
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, D-69120, Heidelberg, Germany
| | - Marcel Deponte
- Faculty of Chemistry, Comparative Biochemistry, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany.
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