Polymorphic markers for identification of parasite population in Plasmodium malariae
Abstract Background Molecular genotyping in Plasmodium serves many aims including providing tools for studying parasite population genetics and distinguishing recrudescence from reinfection. Microsatellite typing, insertion-deletion (INDEL) and single nucleotide polymorphisms is used for genotyping,...
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | Malaria Journal |
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| Online Access: | https://doi.org/10.1186/s12936-020-3122-2 |
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| author | Vivek Bhakta Mathema Supatchara Nakeesathit Watcharee Pagornrat Frank Smithuis Nicholas J. White Arjen M. Dondorp Mallika Imwong |
| author_facet | Vivek Bhakta Mathema Supatchara Nakeesathit Watcharee Pagornrat Frank Smithuis Nicholas J. White Arjen M. Dondorp Mallika Imwong |
| author_sort | Vivek Bhakta Mathema |
| collection | DOAJ |
| description | Abstract Background Molecular genotyping in Plasmodium serves many aims including providing tools for studying parasite population genetics and distinguishing recrudescence from reinfection. Microsatellite typing, insertion-deletion (INDEL) and single nucleotide polymorphisms is used for genotyping, but only limited information is available for Plasmodium malariae, an important human malaria species. This study aimed to provide a set of genetic markers to facilitate the study of P. malariae population genetics. Methods Markers for microsatellite genotyping and pmmsp1 gene polymorphisms were developed and validated in symptomatic P. malariae field isolates from Myanmar (N = 37). Fragment analysis was used to determine allele sizes at each locus to calculate multiplicity of infections (MOI), linkage disequilibrium, heterozygosity and construct dendrograms. Nucleotide diversity (π), number of haplotypes, and genetic diversity (H d ) were assessed and a phylogenetic tree was constructed. Genome-wide microsatellite maps with annotated regions of newly identified markers were constructed. Results Six microsatellite markers were developed and tested in 37 P. malariae isolates which showed sufficient heterozygosity (0.530–0.922), and absence of linkage disequilibrium (I A S =0.03, p value > 0.05) (N = 37). In addition, a tandem repeat (VNTR)-based pmmsp1 INDEL polymorphisms marker was developed and assessed in 27 P. malariae isolates showing a nucleotide diversity of 0.0976, haplotype gene diversity of 0.698 and identified 14 unique variants. The size of VNTR consensus repeat unit adopted as allele was 27 base pairs. The markers Pm12_426 and pmmsp1 showed greatest diversity with heterozygosity scores of 0.920 and 0.835, respectively. Using six microsatellites markers, the likelihood that any two parasite strains would have the same microsatellite genotypes was 8.46 × 10−4 and was further reduced to 1.66 × 10−4 when pmmsp1 polymorphisms were included. Conclusions Six novel microsatellites genotyping markers and a set of pmmsp1 VNTR-based INDEL polymorphisms markers for P. malariae were developed and validated. Each marker could be independently or in combination employed to access genotyping of the parasite. The newly developed markers may serve as a useful tool for investigating parasite diversity, population genetics, molecular epidemiology and for distinguishing recrudescence from reinfection in drug efficacy studies. |
| first_indexed | 2024-12-18T00:53:05Z |
| format | Article |
| id | doaj.art-20a98e39c7694ddfad120f4a73b30332 |
| institution | Directory Open Access Journal |
| issn | 1475-2875 |
| language | English |
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| publishDate | 2020-01-01 |
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| spelling | doaj.art-20a98e39c7694ddfad120f4a73b303322022-12-21T21:26:36ZengBMCMalaria Journal1475-28752020-01-0119111210.1186/s12936-020-3122-2Polymorphic markers for identification of parasite population in Plasmodium malariaeVivek Bhakta Mathema0Supatchara Nakeesathit1Watcharee Pagornrat2Frank Smithuis3Nicholas J. White4Arjen M. Dondorp5Mallika Imwong6Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol UniversityMahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityMahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityMahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityMahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityMahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityDepartment of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol UniversityAbstract Background Molecular genotyping in Plasmodium serves many aims including providing tools for studying parasite population genetics and distinguishing recrudescence from reinfection. Microsatellite typing, insertion-deletion (INDEL) and single nucleotide polymorphisms is used for genotyping, but only limited information is available for Plasmodium malariae, an important human malaria species. This study aimed to provide a set of genetic markers to facilitate the study of P. malariae population genetics. Methods Markers for microsatellite genotyping and pmmsp1 gene polymorphisms were developed and validated in symptomatic P. malariae field isolates from Myanmar (N = 37). Fragment analysis was used to determine allele sizes at each locus to calculate multiplicity of infections (MOI), linkage disequilibrium, heterozygosity and construct dendrograms. Nucleotide diversity (π), number of haplotypes, and genetic diversity (H d ) were assessed and a phylogenetic tree was constructed. Genome-wide microsatellite maps with annotated regions of newly identified markers were constructed. Results Six microsatellite markers were developed and tested in 37 P. malariae isolates which showed sufficient heterozygosity (0.530–0.922), and absence of linkage disequilibrium (I A S =0.03, p value > 0.05) (N = 37). In addition, a tandem repeat (VNTR)-based pmmsp1 INDEL polymorphisms marker was developed and assessed in 27 P. malariae isolates showing a nucleotide diversity of 0.0976, haplotype gene diversity of 0.698 and identified 14 unique variants. The size of VNTR consensus repeat unit adopted as allele was 27 base pairs. The markers Pm12_426 and pmmsp1 showed greatest diversity with heterozygosity scores of 0.920 and 0.835, respectively. Using six microsatellites markers, the likelihood that any two parasite strains would have the same microsatellite genotypes was 8.46 × 10−4 and was further reduced to 1.66 × 10−4 when pmmsp1 polymorphisms were included. Conclusions Six novel microsatellites genotyping markers and a set of pmmsp1 VNTR-based INDEL polymorphisms markers for P. malariae were developed and validated. Each marker could be independently or in combination employed to access genotyping of the parasite. The newly developed markers may serve as a useful tool for investigating parasite diversity, population genetics, molecular epidemiology and for distinguishing recrudescence from reinfection in drug efficacy studies.https://doi.org/10.1186/s12936-020-3122-2GenotypingINDELNucleotide diversityTandem repeats |
| spellingShingle | Vivek Bhakta Mathema Supatchara Nakeesathit Watcharee Pagornrat Frank Smithuis Nicholas J. White Arjen M. Dondorp Mallika Imwong Polymorphic markers for identification of parasite population in Plasmodium malariae Malaria Journal Genotyping INDEL Nucleotide diversity Tandem repeats |
| title | Polymorphic markers for identification of parasite population in Plasmodium malariae |
| title_full | Polymorphic markers for identification of parasite population in Plasmodium malariae |
| title_fullStr | Polymorphic markers for identification of parasite population in Plasmodium malariae |
| title_full_unstemmed | Polymorphic markers for identification of parasite population in Plasmodium malariae |
| title_short | Polymorphic markers for identification of parasite population in Plasmodium malariae |
| title_sort | polymorphic markers for identification of parasite population in plasmodium malariae |
| topic | Genotyping INDEL Nucleotide diversity Tandem repeats |
| url | https://doi.org/10.1186/s12936-020-3122-2 |
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