ArticleGenome medicine2023
Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control.
Article in Genome medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 20 citations in OpenAlex.
- Rapid whole-genome sequencing of Plasmodium DNA from cryptic malaria cases in UK travellers provides insights into infection origins, transmission and antimalarial resistance.Journal of travel medicine · 2026Article
- Estimating probabilities of malaria importation in southern Mozambique through modellingeLife · 2026Article
- Global-scale population genetic analysis of Plasmodium falciparum identifies region-specific patterns of malaria parasite adaptation.Nature communications · 2026Article
- Unveiling the overlooked burden of malaria misdiagnosis using lamp-based re-evaluation of routine malaria diagnosis in health centers: implications for public health and clinical practice in Northwest Ethiopia.BMC infectious diseases · 2026Article
- NovelmBio · 2026Article
- Current and emerging molecular diagnostic approaches in the detection of human parasites.Parasitology research · 2026Review
- Whole genome sequencing to inform the epidemiology of Plasmodium falciparum malaria in the elimination setting of Malaysia.BMC genomics · 2026Article
- Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites.Genome medicine · 2026Article
- Malaria-GENOMAP: a web-based tool for exploring genomic variation of malaria parasites.Bioinformatics (Oxford, England) · 2026Article
- Enhancing whole genome DNA amplification of Plasmodium falciparum for advanced molecular surveillance in malaria control.Malaria journal · 2025Article
- Gametocyte production and transmission fitness of African and AsianAntimicrobial agents and chemotherapy · 2025Article
- Preferential transmission of minority and drug-resistant clones in polyclonal infections in Mali.Malaria journal · 2025Article
- Gametocyte production and transmission fitness of African and AsianbioRxiv : the preprint server for biology · 2025Article
- Detecting imported malaria infections in endemic settings using molecular surveillance: current state and challenges.Frontiers in epidemiology · 2025Review
- Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.Frontiers in genetics · 2024Article
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Authors and funding
18 authors at 5 institutions in 5 countries.
Funding
Abstract
backgroundMalaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settings, where the profiling of co-infections, identification of imported malaria parasites, and detection of drug resistance are crucial for infection control and disease elimination. To support this informatically, we have developed the Malaria-Profiler tool, which rapidly (within minutes) predicts Plasmodium species, geographical source, and resistance to antimalarial drugs directly from WGS data.
resultsThe online and command line versions of Malaria-Profiler detect ~ 250 markers from genome sequences covering Plasmodium speciation, likely geographical source, and resistance to chloroquine, sulfadoxine-pyrimethamine (SP), and other anti-malarial drugs for P. falciparum, but also providing mutations for orthologous resistance genes in other species. The predictive performance of the mutation library was assessed using 9321 clinical isolates with WGS and geographical data, with most being single-species infections (P. falciparum 7152/7462, P. vivax 1502/1661, P. knowlesi 143/151, P. malariae 18/18, P. ovale ssp. 5/5), but co-infections were identified (456/9321; 4.8%). The accuracy of the predicted geographical profiles was high to both continental (96.1%) and regional levels (94.6%). For P. falciparum, markers were identified for resistance to chloroquine (49.2%; regional range: 24.5% to 100%), sulfadoxine (83.3%; 35.4- 90.5%), pyrimethamine (85.4%; 80.0-100%) and combined SP (77.4%). Markers associated with the partial resistance of artemisinin were found in WGS from isolates sourced from Southeast Asia (30.6%).
conclusionsMalaria-Profiler is a user-friendly tool that can rapidly and accurately predict the geographical regional source and anti-malarial drug resistance profiles across large numbers of samples with WGS data. The software is flexible with modifiable bioinformatic pipelines. For example, it is possible to select the sequencing platform, display specific variants, and customise the format of outputs. With the increasing application of next-generation sequencing platforms on Plasmodium DNA, Malaria-Profiler has the potential to be integrated into point-of-care and surveillance settings, thereby assisting malaria control. Malaria-Profiler is available online (bioinformatics.lshtm.ac.uk/malaria-profiler) and as standalone software ( https://github.com/jodyphelan/malaria-profiler ).
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