High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology

Abstract Genetic polymorphisms in P. falciparum can be used to indicate the parasite’s susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR,...

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Autores principales:	Sidsel Nag, Marlene D. Dalgaard, Poul-Erik Kofoed, Johan Ursing, Marina Crespo, Lee O’Brien Andersen, Frank Møller Aarestrup, Ole Lund, Michael Alifrangis
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e639319d64b942d0836b9370fc6a25d1
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spelling	oai:doaj.org-article:e639319d64b942d0836b9370fc6a25d12021-12-02T11:40:13ZHigh throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology10.1038/s41598-017-02724-x2045-2322https://doaj.org/article/e639319d64b942d0836b9370fc6a25d12017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02724-xhttps://doaj.org/toc/2045-2322Abstract Genetic polymorphisms in P. falciparum can be used to indicate the parasite’s susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well as the entire length of pfK13, and the mitochondrial barcode for parasite origin. SNPs of interest were sequenced with an average depth of 2,043 reads, and bases were called for the various SNP-positions with a p-value below 0.05, for 89.8–100% of samples. The SNP data indicates that artemisinin resistance-conferring SNPs in pfK13 are absent from the studied area of Guinea-Bissau, while the pfmdr1 86 N allele is found at a high prevalence. The mitochondrial barcodes are unanimous and accommodate a West African origin of the parasites. With this method, very reliable high throughput surveillance of antimalarial drug resistance becomes more affordable than ever before.Sidsel NagMarlene D. DalgaardPoul-Erik KofoedJohan UrsingMarina CrespoLee O’Brien AndersenFrank Møller AarestrupOle LundMichael AlifrangisNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sidsel Nag Marlene D. Dalgaard Poul-Erik Kofoed Johan Ursing Marina Crespo Lee O’Brien Andersen Frank Møller Aarestrup Ole Lund Michael Alifrangis High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
description	Abstract Genetic polymorphisms in P. falciparum can be used to indicate the parasite’s susceptibility to antimalarial drugs as well as its geographical origin. Both of these factors are key to monitoring development and spread of antimalarial drug resistance. In this study, we combine multiplex PCR, custom designed dual indexing and Miseq sequencing for high throughput SNP-profiling of 457 malaria infections from Guinea-Bissau, at the cost of 10 USD per sample. By amplifying and sequencing 15 genetic fragments, we cover 20 resistance-conferring SNPs occurring in pfcrt, pfmdr1, pfdhfr, pfdhps, as well as the entire length of pfK13, and the mitochondrial barcode for parasite origin. SNPs of interest were sequenced with an average depth of 2,043 reads, and bases were called for the various SNP-positions with a p-value below 0.05, for 89.8–100% of samples. The SNP data indicates that artemisinin resistance-conferring SNPs in pfK13 are absent from the studied area of Guinea-Bissau, while the pfmdr1 86 N allele is found at a high prevalence. The mitochondrial barcodes are unanimous and accommodate a West African origin of the parasites. With this method, very reliable high throughput surveillance of antimalarial drug resistance becomes more affordable than ever before.
format	article
author	Sidsel Nag Marlene D. Dalgaard Poul-Erik Kofoed Johan Ursing Marina Crespo Lee O’Brien Andersen Frank Møller Aarestrup Ole Lund Michael Alifrangis
author_facet	Sidsel Nag Marlene D. Dalgaard Poul-Erik Kofoed Johan Ursing Marina Crespo Lee O’Brien Andersen Frank Møller Aarestrup Ole Lund Michael Alifrangis
author_sort	Sidsel Nag
title	High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
title_short	High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
title_full	High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
title_fullStr	High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
title_full_unstemmed	High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
title_sort	high throughput resistance profiling of plasmodium falciparum infections based on custom dual indexing and illumina next generation sequencing-technology
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/e639319d64b942d0836b9370fc6a25d1
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High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology

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