دورية أكاديمية
Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control.
| العنوان: | Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control. |
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| المؤلفون: | Phelan JE; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK. jody.phelan@lshtm.ac.uk., Turkiewicz A; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK., Manko E; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK., Thorpe J; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK., Vanheer LN; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK., van de Vegte-Bolmer M; Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands., Ngoc NTH; Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam., Binh NTH; Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam., Thieu NQ; Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam., Gitaka J; Directorate of Research and Innovation, Mount Kenya University, Gen. Kago Rd, Thika, Kenya., Nolder D; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.; UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK., Beshir KB; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK., Dombrowski JG; Department of Parasitology, Institute of Biomedical Sciences, Univ. of São Paulo, São Paulo, Brazil., Di Santi SM; School of Medicine, Instituto de Medicina Tropical, University of São Paulo, São Paulo, Brazil., Bousema T; Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands., Sutherland CJ; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.; UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK., Campino S; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK. susana.campino@lshtm.ac.uk., Clark TG; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK. taane.clark@lshtm.ac.uk.; Faculty of Epidemiology and Population Health, LSHTM, London, WC1E 7HT, UK. taane.clark@lshtm.ac.uk. |
| المصدر: | Genome medicine [Genome Med] 2023 Nov 10; Vol. 15 (1), pp. 96. Date of Electronic Publication: 2023 Nov 10. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 101475844 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-994X (Electronic) Linking ISSN: 1756994X NLM ISO Abbreviation: Genome Med Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [London] : BioMed Central |
| مواضيع طبية MeSH: | Antimalarials*/pharmacology , Antimalarials*/therapeutic use , Parasites* , Coinfection*/drug therapy , Malaria*/drug therapy , Malaria*/parasitology , Plasmodium*/genetics , Malaria, Falciparum*/drug therapy , Malaria, Vivax*, Humans ; Animals ; Chloroquine/therapeutic use ; Drug Resistance/genetics ; Plasmodium falciparum/genetics |
| مستخلص: | Background: Malaria 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. Results: The 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%). Conclusions: Malaria-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 ). (© 2023. The Author(s).) |
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| معلومات مُعتمدة: | MR/R026297/1 United Kingdom MRC_ Medical Research Council; MR/T016124/1 United Kingdom MRC_ Medical Research Council; 214227/Z/18/Z United Kingdom WT_ Wellcome Trust; United Kingdom WT_ Wellcome Trust; MR/X005895/1 United Kingdom MRC_ Medical Research Council; IAA2129 United Kingdom MRC_ Medical Research Council |
| فهرسة مساهمة: | Keywords: Diagnostics; Drug resistance; Genomics; Malaria; Plasmodium parasites; Whole genome sequencing |
| المشرفين على المادة: | 0 (Antimalarials) 886U3H6UFF (Chloroquine) |
| تواريخ الأحداث: | Date Created: 20231111 Date Completed: 20231113 Latest Revision: 20240313 |
| رمز التحديث: | 20240313 |
| مُعرف محوري في PubMed: | PMC10636944 |
| DOI: | 10.1186/s13073-023-01247-7 |
| PMID: | 37950308 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1756-994X |
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| DOI: | 10.1186/s13073-023-01247-7 |