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Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 PMCID: PMC11009618 DOI: 10.1073/pnas.2310859121] [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] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Mark P. Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ONM5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CCLeiden, The Netherlands
| | - Hendrik N. Poinar
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ONL8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Megan B. Brickley
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
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Srisutham S, Rattanakoch P, Kijprasong K, Sugaram R, Kantaratanakul N, Srinulgray T, Dondorp AM, Imwong M. A novel sensitive hexaplex high-resolution melt assay for identification of five human Plasmodium species plus internal control. Acta Trop 2023; 248:107020. [PMID: 37739253 PMCID: PMC10641754 DOI: 10.1016/j.actatropica.2023.107020] [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: 06/28/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND The diagnosis of malaria infection in humans remains challenging, further complicated by mixed Plasmodium species infections, potentially altering disease severity and morbidity. To facilitate appropriate control measures and treatment, rapid, sensitive, and specific detection assays, including those for the second minor species, would be required. This study aimed to develop a multiplex high-resolution melting (hexaplex PCR-HRM) assay with seven distinct peaks corresponding to five Plasmodium species of the Plasmodium genus, and an internal control to limit false negatives providing quality assurance testing results. METHODS Five species-specific primers for human malaria species were designed targeting on the Plasmodium 18 small subunit ribosomal RNA (18S rRNA) and mitochondrial genes. The hexaplex PCR-HRM was developed for the simultaneous and rapid detection and differentiation of five human Plasmodium spp. The limit of detection (LoD), sensitivity, and specificity of the assay were evaluated. Artificial mixing was used to assess the ability to determine the second minor species. Furthermore, a hexaplex PCR-HRM assay was used to identify 120 Plasmodium-infected clinical isolates from Kanchanaburi, Western Thailand, where malaria is endemic. RESULTS The hexaplex PCR-HRM assay detected the targeted genome of five Plasmodium species at levels as low as 2.354-3.316 copies/uL with 91.76 % sensitivity and 98.04 % specificity. In artificial mixing, the assay could detect minority parasite species at 0.001 % of the predominant parasite population. Plasmodium vivax infections (99 %) accounted for the majority of malaria cases in Kanchanaburi, Thailand. CONCLUSIONS The developed hexaplex PCR-HRM assay we present in this study is a novel approach for multiplexing the Plasmodium genus and detecting five Plasmodium species with the advantage of detecting second minority parasite species. The developed one-step assay without any nesting protocols would reduce the risks of cross-contamination. Moreover, it also provides a simple, sensitive, specific, and low-cost approach for optional molecular detection of malaria.
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Affiliation(s)
- Suttipat Srisutham
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
| | - Paweesuda Rattanakoch
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Rungniran Sugaram
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | | | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, Northern Ireland UK
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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3
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Matsubara J, Chang M, Seilie AM, Murphy SC. Flow Cytometric Sorting of Infected Erythrocytes Demonstrates Reliable Detection of Individual Ring-Stage Plasmodium falciparum Parasites by Plasmodium 18S rRNA Reverse Transcription Polymerase Chain Reaction. Am J Trop Med Hyg 2022; 106:tpmd211226. [PMID: 35405648 PMCID: PMC9209910 DOI: 10.4269/ajtmh.21-1226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 11/12/2022] Open
Abstract
Molecular diagnostic tests for Plasmodium falciparum parasites are increasingly used to enable ultrasensitive detection of infection in clinical trials and field surveillance studies. Ribonucleic acid (RNA)-based assays targeting 18S rRNA are particularly sensitive with limits of detection reported to comprise a single infected red blood cell (RBC) in a relatively large volume of blood. However, the validation testing at such limiting concentrations is hampered by the so-called Poisson distribution of such rare events, which can lead laboratorians to inaccurately set the limit of detection higher (i.e., less sensitive) than the assay can actually detect. Here we set out to formally demonstrate the analytical sensitivity of the Plasmodium 18S rRNA quantitative reverse transcription PCR (qRT-PCR). Fluorescence-activated cell sorting (FACS) was used on synchronous P. falciparum cultures doubly stained for DNA and RNA and was followed by qRT-PCR on the individual sorted cells spiked with negative whole blood. Over 95% of individual single-ring infected RBCs were detected by qRT-PCR. The formally measured median 18S rRNA content per individual ring-stage P. falciparum parasite was 9,550 copies (interquartile range 8,130-12,300). Thus, one can confidently rely on Plasmodium 18S rRNA qRT-PCR to detect one parasite per 50-µL blood sample.
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Affiliation(s)
- Jokichi Matsubara
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington
| | - Ming Chang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington
| | - Annette M Seilie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington
| | - Sean C Murphy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington
- Department of Microbiology, University of Washington, Seattle, Washington
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Makunin A, Korlević P, Park N, Goodwin S, Waterhouse RM, von Wyschetzki K, Jacob CG, Davies R, Kwiatkowski D, St Laurent B, Ayala D, Lawniczak MKN. A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus. Mol Ecol Resour 2022; 22:28-44. [PMID: 34053186 PMCID: PMC7612955 DOI: 10.1111/1755-0998.13436] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 05/19/2021] [Indexed: 01/04/2023]
Abstract
Anopheles is a diverse genus of mosquitoes comprising over 500 described species, including all known human malaria vectors. While a limited number of key vector species have been studied in detail, the goal of malaria elimination calls for surveillance of all potential vector species. Here, we develop a multilocus amplicon sequencing approach that targets 62 highly variable loci in the Anopheles genome and two conserved loci in the Plasmodium mitochondrion, simultaneously revealing both the mosquito species and whether that mosquito carries malaria parasites. We also develop a cheap, nondestructive, and high-throughput DNA extraction workflow that provides template DNA from single mosquitoes for the multiplex PCR, which means specimens producing unexpected results can be returned to for morphological examination. Over 1000 individual mosquitoes can be sequenced in a single MiSeq run, and we demonstrate the panel's power to assign species identity using sequencing data for 40 species from Africa, Southeast Asia, and South America. We also show that the approach can be used to resolve geographic population structure within An. gambiae and An. coluzzii populations, as the population structure determined based on these 62 loci from over 1000 mosquitoes closely mirrors that revealed through whole genome sequencing. The end-to-end approach is quick, inexpensive, robust, and accurate, which makes it a promising technique for very large-scale mosquito genetic surveillance and vector control.
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Affiliation(s)
- Alex Makunin
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Petra Korlević
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Naomi Park
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | | | | | | | - Diego Ayala
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- CIRMF, Franceville, Gabon
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5
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Silva-do-Nascimento TF, Sánchez-Ribas J, Oliveira TMP, Bourke BP, Oliveira-Ferreira J, Rosa-Freitas MG, Lourenço-de-Oliveira R, Marinho-e-Silva M, Neves MSAS, Conn JE, Sallum MAM. Molecular Analysis Reveals a High Diversity of Anopheline Mosquitoes in Yanomami Lands and the Pantanal Region of Brazil. Genes (Basel) 2021; 12:1995. [PMID: 34946944 PMCID: PMC8701885 DOI: 10.3390/genes12121995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Identifying the species of the subfamily Anophelinae that are Plasmodium vectors is important to vector and malaria control. Despite the increase in cases, vector mosquitoes remain poorly known in Brazilian indigenous communities. This study explores Anophelinae mosquito diversity in the following areas: (1) a Yanomami reserve in the northwestern Amazon Brazil biome and (2) the Pantanal biome in southwestern Brazil. This is carried out by analyzing cytochrome c oxidase (COI) gene data using Refined Single Linkage (RESL), Assemble Species by Automatic Partitioning (ASAP), and tree-based multi-rate Poisson tree processes (mPTP) as species delimitation approaches. A total of 216 specimens collected from the Yanomami and Pantanal regions were sequenced and combined with 547 reference sequences for species delimitation analyses. The mPTP analysis for all sequences resulted in the delimitation of 45 species groups, while the ASAP analysis provided the partition of 48 groups. RESL analysis resulted in 63 operational taxonomic units (OTUs). This study expands our scant knowledge of anopheline species in the Yanomami and Pantanal regions. At least 18 species of Anophelinae mosquitoes were found in these study areas. Additional studies are now required to determine the species that transmit Plasmodium spp. in these regions.
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Affiliation(s)
- Teresa Fernandes Silva-do-Nascimento
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Jordi Sánchez-Ribas
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Distrito Sanitário Especial Indígena Yanomami, Roraima 69301-080, Brazil
| | - Tatiane M. P. Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil;
| | - Brian Patrick Bourke
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746, USA;
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, 10th St. NE & Constitution Ave. NE, Washington, DC 20002, USA
| | - Joseli Oliveira-Ferreira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Maria Goreti Rosa-Freitas
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
- Geniac Ltd., São Paulo 01031-902, Brazil
| | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Mariana Marinho-e-Silva
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
- Instituto Nacional da Propriedade Industrial, Rio de Janeiro 20090-910, Brazil
| | - Maycon Sebastião Alberto Santos Neves
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Jan E. Conn
- Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA;
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, NY 12222, USA
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil;
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Molina-Cruz A, Raytselis N, Withers R, Dwivedi A, Crompton PD, Traore B, Carpi G, Silva JC, Barillas-Mury C. A genotyping assay to determine geographic origin and transmission potential of Plasmodium falciparum malaria cases. Commun Biol 2021; 4:1145. [PMID: 34593959 PMCID: PMC8484479 DOI: 10.1038/s42003-021-02667-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 09/07/2021] [Indexed: 11/08/2022] Open
Abstract
As countries work towards malaria elimination, it is important to monitor imported cases to prevent reestablishment of local transmission. The Plasmodium falciparum Pfs47 gene has strong geographic population structure, because only those parasites with Pfs47 haplotypes compatible with the mosquito vector species in a given continent are efficiently transmitted. Analysis of 4,971 world-wide Pfs47 sequences identified two SNPs (at 707 and 725 bp) as sufficient to establish the likely continent of origin of P. falciparum isolates. Pfs47 sequences from Africa, Asia, and the New World presented more that 99% frequency of distinct combinations of the SNPs 707 and 725 genotypes. Interestingly, Papua New Guinea Pfs47 sequences have the highest diversity in SNPs 707 and 725. Accurate and reproducible High-Resolution Melting (HRM) assays were developed to genotype Pfs47 SNPs 707 and 725 in laboratory and field samples, to assess the geographic origin and risk of local transmission of imported P. falciparum malaria cases.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
| | - Nadia Raytselis
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Roxanne Withers
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, 20852, USA
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
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Rapid detection of Mycoplasma mycoides subsp. capri and Mycoplasma capricolum subsp. capripneumoniae using high-resolution melting curve analysis. Sci Rep 2021; 11:15329. [PMID: 34321522 PMCID: PMC8319336 DOI: 10.1038/s41598-021-93981-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/17/2021] [Indexed: 01/01/2023] Open
Abstract
Mycoplasma capricolum subsp.subsp. capripneumonia (Mccp) and Mycoplasma mycoides subsp.sbusp. capri (Mmc) cause caprine pleuropneumonia (CCPP) and mycoplasmal pneumonia in goats and sheep (MPGS), respectively. These diseases cannot be identified on clinical symptoms alone and it is laborious to distinguish them using biochemical methods. It is therefore important to establish a simple, rapid identification method for Mccp and Mmc. Here, we report a high-resolution melting (HRM) curve analysis using specific primers based on the Mmc 95010 strain MLC_0560 and Mccp F38 strain MCCPF38_00984 gene sequences. The method was highly specific with intra- and inter-batch coefficients of variation < 1%. The lower limit of detection for Mccp and Mmc was 55 copies/μL and 58 copies/μL, respectively. HRM and fluorescence qPCR results were compared using 106 nasal swabs and 47 lung tissue samples from goats (HRM-qPCR coincidence rate 94.8%; 145/153). Mycoplasma isolation and identification was performed on 30 lung tissue samples and 16 nasal swabs (HRM-culturing coincidence rate 87.0%; 40/46). HRM analysis was more sensitive than fluorescence qPCR and Mycoplasma isolation, indicating the practicality of HRM for accurate and rapid identification of Mccp and Mmc, and diagnosis and epidemiology of CCPP and MPGS.
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Lamien-Meda A, Fuehrer HP, Leitsch D, Noedl H. A powerful qPCR-high resolution melting assay with taqman probe in plasmodium species differentiation. Malar J 2021; 20:121. [PMID: 33639949 PMCID: PMC7916309 DOI: 10.1186/s12936-021-03662-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of highly sensitive molecular tools in malaria diagnosis is currently largely restricted to research and epidemiological settings, but will ultimately be essential during elimination and potentially eradication. Accurate diagnosis and differentiation down to species levels, including the two Plasmodium ovale species and zoonotic variants of the disease, will be important for the understanding of changing epidemiological patterns of the disease. METHODS A qPCR-high resolution melting (HRM) method was to detect and differentiate all human Plasmodium species with one forward and one reverse primer set. The HRM detection method was further refined using a hydrolysis probe to specifically discriminate Plasmodium falciparum. RESULTS Out of the 113 samples tested with the developed HRM-qPCR- P. falciparum probe assay, 96 (85.0 %) single infections, 12 (10.6 %) mixed infections, and 5 (4.4 %) were Plasmodium negative. The results were concordant with those of the nested PCR at 98.2 %. The assay limit of detection was varied from 21.47 to 46.43 copies /µl, equivalent to 1-2.11 parasites/µl. All P. falciparum infections were confirmed with the associated Taqman probe. CONCLUSIONS Although the dependence on qPCR currently limits its deployment in resource-limited environments, this assay is highly sensitive and specific, easy to perform and convenient for Plasmodium mono-infection and may provide a novel tool for rapid and accurate malaria diagnosis also in epidemiological studies.
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Affiliation(s)
- Aline Lamien-Meda
- Institute for Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria.
| | - Hans-Peter Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - David Leitsch
- Institute for Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Harald Noedl
- Malaria Research Initiative Bandarban, Vienna, Austria
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Kassaza K, Long AC, McDaniels JM, Andre M, Fredrickson W, Nyehangane D, Orikiriza P, Operario DJ, Bazira J, Mwanga-Amumpaire JA, Moore CC, Guler JL, Boum Y. Surveillance of Plasmodium falciparum pfcrt haplotypes in southwestern uganda by high-resolution melt analysis. Malar J 2021; 20:114. [PMID: 33632242 PMCID: PMC7908690 DOI: 10.1186/s12936-021-03657-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Chloroquine (CQ) resistance is conferred by mutations in the Plasmodium falciparum CQ resistance transporter (pfcrt). Following CQ withdrawal for anti-malarial treatment, studies across malaria-endemic countries have shown a range of responses. In some areas, CQ sensitive parasites re-emerge, and in others, mutant haplotypes persist. Active surveillance of resistance mutations in clinical parasites is essential to inform treatment regimens; this effort requires fast, reliable, and cost-effective methods that work on a variety of sample types with reagents accessible in malaria-endemic countries. METHODS Quantitative PCR followed by High-Resolution Melt (HRM) analysis was performed in a field setting to assess pfcrt mutations in two groups of clinical samples from Southwestern Uganda. Group 1 samples (119 in total) were collected in 2010 as predominantly Giemsa-stained slides; Group 2 samples (125 in total) were collected in 2015 as blood spots on filter paper. The Rotor-Gene Q instrument was utilized to assess the impact of different PCR-HRM reagent mixes and the detection of mixed haplotypes present in the clinical samples. Finally, the prevalence of the wild type (CVMNK) and resistant pfcrt haplotypes (CVIET and SVMNT) was evaluated in this understudied Southwestern region of Uganda. RESULTS The sample source (i.e. Giemsa-stained slides or blood spots) and type of LCGreen-based reagent mixes did not impact the success of PCR-HRM. The detection limit of 10- 5 ng and the ability to identify mixed haplotypes as low as 10 % was similar to other HRM platforms. The CVIET haplotype predominated in the clinical samples (66 %, 162/244); however, there was a large regional variation between the sample groups (94 % CVIET in Group 1 and 44 % CVIET in Group 2). CONCLUSIONS The HRM-based method exhibits the flexibility required to conduct reliable assessment of resistance alleles from various sample types generated during the clinical management of malaria. Large regional variations in CQ resistance haplotypes across Southwestern Uganda emphasizes the need for continued local parasite genotype assessment to inform anti-malarial treatment policies.
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Affiliation(s)
- Kennedy Kassaza
- Epicentre Mbarara Research Centre, Mbarara, Uganda
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Anna C Long
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Jennifer M McDaniels
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Mharlove Andre
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Wasswa Fredrickson
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | | | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Juliet A Mwanga-Amumpaire
- Epicentre Mbarara Research Centre, Mbarara, Uganda
- Department of Pediatrics and Child Health, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA.
| | - Yap Boum
- Epicentre Mbarara Research Centre, Mbarara, Uganda.
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda.
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Van der Heyden H, Fortier AM, Savage J. A HRM Assay for Rapid Identification of Members of the Seedcorn Maggot Complex (Delia florilega and D. platura) (Diptera: Anthomyiidae) and Evidence of Variation in Temporal Patterns of Larval Occurrence. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:2920-2930. [PMID: 33080027 DOI: 10.1093/jee/toaa230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 06/11/2023]
Abstract
The seedcorn maggot Delia platura (Meigen), and the bean seed maggot Delia florilega (Zetterstedt) can cause considerable feeding damage to a wide range of cultivated crops. The recent discovery of two distinct genetic lines of D. platura, each with a unique distribution pattern overlapping only in eastern Canada, suggests the presence of a new cryptic species for the group. The reliable identification of the three species/lines in the seedcorn maggot complex is crucial to our understanding of their distribution, phenology, and respective contribution to crop damage as well as to the development of specific integrated pest management approaches. As these taxa are morphologically indistinguishable in the immature stages, we developed a high-resolution melting PCR (HRM) assay using primers amplifying a variable 96-bp PCR product in the CO1 mitochondrial gene for rapid and economical identification of specimens. The three species/lines exhibited distinguishable melting profiles based on their different Tm values (between 0.4 and 0.9°C) and identification results based on HRM and DNA sequencing were congruent for all specimens in the validation data set (n = 100). We then used the new, highly sensitive HRM assay to identify survey specimens from the seedcorn maggot complex collected in Quebec, Canada, between 2017 and 2019. Progress curves developed to document the temporal occurrence patterns of each species/lines indicate differences between taxa, with the N-line (BOLD:AAA3453) of D. platura appearing approximately 17 d before D. florilega (BOLD:ACR4394) and the H-line (BOLD:AAG2511) of D. platura.
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Affiliation(s)
| | | | - Jade Savage
- Department of Biological Sciences, Bishop's University, Sherbrooke, QC, Canada
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Sikkel PC, Pagan JA, Santos JL, Hendrick GC, Nicholson MD, Xavier R. Molecular detection of apicomplexan blood parasites of coral reef fishes from free-living stages of ectoparasitic gnathiid isopods. Parasitol Res 2020; 119:1975-1980. [PMID: 32333110 DOI: 10.1007/s00436-020-06676-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/24/2020] [Indexed: 11/25/2022]
Abstract
Gnathiid isopods are marine ectoparasites that feed on the blood of fishes that have been implicated as vectors of blood parasites, with transmission possibly occurring through biting during their parasitic life-stages, or through ingestion by fishes. However, evidence for their role as vectors is limited, reflecting the small number of research groups working on them. Here, we used a molecular barcode approach to identify fish hosts and apicomplexan parasites in free-living gnathiids from the eastern Caribbean Sea, with the goal of further evaluating their potential role as reservoirs and/or vectors for these parasites. Apicomplexa were only identified in 8% of the Gnathia analyzed, and in four cases we could identify both Apicomplexa and fish host DNA. The results further suggest that Gnathia spp. in this region may serve as reservoirs for Apicomplexa, but whether they are vectors for this parasite remains uncertain.
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Affiliation(s)
- Paul C Sikkel
- Department of Biological Sciences and Environmental Sciences Program, Arkansas State University, PO Box 599, State University, Jonesboro, AR, 72467, USA. .,Water Research Group, Unit for Environmental Sciences and Management, Potchefstroom Campus, North West University, Private Bag X6001, Potchefstroom, 2520, South Africa.
| | - J Andres Pagan
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Joana L Santos
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Gina C Hendrick
- Department of Biological Sciences and Environmental Sciences Program, Arkansas State University, PO Box 599, State University, Jonesboro, AR, 72467, USA
| | - Matthew D Nicholson
- Department of Biological Sciences and Environmental Sciences Program, Arkansas State University, PO Box 599, State University, Jonesboro, AR, 72467, USA
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
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Arbabi M, Hooshyar H, Lotfinia M, Bakhshi MA. Molecular detection of Trichostrongylus species through PCR followed by high resolution melt analysis of ITS-2 rDNA sequences. Mol Biochem Parasitol 2020; 236:111260. [PMID: 31958470 DOI: 10.1016/j.molbiopara.2020.111260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
Abstract
Polymerase chain reaction followed by high resolution melting (PCR-HRM) analysis is a simple, rapid and accurate method for molecular detection of various nematode species. The objective of the present study was, for the first time, to develop a PCR-HRM assay for the detection of various animal Trichostrongylus spp. A pair of primers targeting the ITS-2 rDNA region of the Trichostrongylus spp. was designed for the development of the HRM assay. DNA samples were extracted from 30 adult worms of Trichostrongylus spp., the ITS-2-rDNA region was amplified using PCR, and the resultant products were sequenced and characterized. Afterwards, the PCR-HRM analysis was conducted to detect and discriminate Trichostrongylus spp. Molecular sequence analysis revealed that 24, 4, and 1 of the samples were T. colubriformis, T. vitrinus and T. capricola, respectively. Results from PCR-HRM indicated that complete agreement was relatively found between speciation by HRM analysis and DNA sequencing for the detection of Trichostrongylus species. The PCR-HRM analysis method developed in the present study is fast and low-cost; the method can be comparable with other molecular detection techniques, representing a reliable tool for the identification of various species within the Trichostrongylus genus.
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Affiliation(s)
- Mohsen Arbabi
- Department of Medical Parasitology, Kashan University of Medical Sciences, Kashan, Iran; Core Research Lab, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hossein Hooshyar
- Department of Medical Parasitology, Kashan University of Medical Sciences, Kashan, Iran
| | - Majid Lotfinia
- Physiology Research Center, Basic Sciences Research Institute, Kashan University of Medical Sciences, Kashan, Iran; Core Research Lab, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohamad Ali Bakhshi
- Department of Medical Parasitology, Kashan University of Medical Sciences, Kashan, Iran
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