Rapid profiling of <i>Plasmodium</i> parasites from genome sequences to assist malaria control

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dc.contributorSistema FMUSP-HC: Faculdade de Medicina da Universidade de São Paulo (FMUSP) e Hospital das Clínicas da FMUSP
dc.contributor.authorPHELAN, Jody E.
dc.contributor.authorTURKIEWICZ, Anna
dc.contributor.authorMANKO, Emilia
dc.contributor.authorTHORPE, Joseph
dc.contributor.authorVANHEER, Leen N.
dc.contributor.authorVEGTE-BOLMER, Marga van de
dc.contributor.authorNGOC, Nguyen Thi Hong
dc.contributor.authorBINH, Nguyen Thi Huong
dc.contributor.authorTHIEU, Nguyen Quang
dc.contributor.authorGITAKA, Jesse
dc.contributor.authorNOLDER, Debbie
dc.contributor.authorBESHIR, Khalid B.
dc.contributor.authorDOMBROWSKI, Jamille G.
dc.contributor.authorSANTI, Silvia Maria Di
dc.contributor.authorBOUSEMA, Teun
dc.contributor.authorSUTHERLAND, Colin J.
dc.contributor.authorCAMPINO, Susana
dc.contributor.authorCLARK, Taane G.
dc.date.accessioned2024-02-15T14:55:27Z
dc.date.available2024-02-15T14:55:27Z
dc.date.issued2023
dc.description.abstractBackground 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 similar to 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).eng
dc.description.indexMEDLINE
dc.description.indexPubMed
dc.description.indexWoS
dc.description.indexScopus
dc.description.sponsorshipWe thank members of the LSHTM Malaria Centre for their thoughts on the design of the tool.
dc.identifier.citationGENOME MEDICINE, v.15, n.1, article ID 96, 11p, 2023
dc.identifier.doi10.1186/s13073-023-01247-7
dc.identifier.issn1756-994X
dc.identifier.urihttps://observatorio.fm.usp.br/handle/OPI/58165
dc.language.isoeng
dc.publisherBMCeng
dc.relation.ispartofGenome Medicine
dc.rightsopenAccesseng
dc.rights.holderCopyright BMCeng
dc.subjectDrug resistanceeng
dc.subjectMalariaeng
dc.subjectPlasmodium parasiteseng
dc.subjectGenomicseng
dc.subjectDiagnosticseng
dc.subjectWhole genome sequencingeng
dc.subject.otherclassificationeng
dc.subject.otherresistanceeng
dc.subject.otherselectioneng
dc.subject.otherevolutioneng
dc.subject.wosGenetics & Heredityeng
dc.titleRapid profiling of <i>Plasmodium</i> parasites from genome sequences to assist malaria controleng
dc.typearticleeng
dc.type.categoryoriginal articleeng
dc.type.versionpublishedVersioneng
dspace.entity.typePublication
hcfmusp.affiliation.countryHolanda
hcfmusp.affiliation.countryVietnã
hcfmusp.affiliation.countryQuênia
hcfmusp.affiliation.countryInglaterra
hcfmusp.affiliation.countryisogb
hcfmusp.affiliation.countryisonl
hcfmusp.affiliation.countryisovn
hcfmusp.affiliation.countryisoke
hcfmusp.author.externalPHELAN, Jody E.:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England
hcfmusp.author.externalTURKIEWICZ, Anna:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England
hcfmusp.author.externalMANKO, Emilia:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England
hcfmusp.author.externalTHORPE, Joseph:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England
hcfmusp.author.externalVANHEER, Leen N.:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England
hcfmusp.author.externalVEGTE-BOLMER, Marga van de:Univ Nijmegen, Radboud Univ Med Ctr, Dept Med Microbiol, Nijmegen, Netherlands; Univ Nijmegen, Radboud Univ Med Ctr, Radboud Ctr Infect Dis, Nijmegen, Netherlands
hcfmusp.author.externalNGOC, Nguyen Thi Hong:Vietnam Natl Inst Malariol, Mol Biol Dept, Parasitol & Entomol, Hanoi, Vietnam
hcfmusp.author.externalBINH, Nguyen Thi Huong:Vietnam Natl Inst Malariol, Mol Biol Dept, Parasitol & Entomol, Hanoi, Vietnam
hcfmusp.author.externalTHIEU, Nguyen Quang:Vietnam Natl Inst Malariol, Mol Biol Dept, Parasitol & Entomol, Hanoi, Vietnam
hcfmusp.author.externalGITAKA, Jesse:Mt Kenya Univ, Directorate Res & Innovat, Gen Kago Rd, Thika, Kenya
hcfmusp.author.externalNOLDER, Debbie:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England; UK Hlth Secur Agcy Malaria Reference Lab, LSHTM, London WC1E 7HT, England
hcfmusp.author.externalBESHIR, Khalid B.:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England
hcfmusp.author.externalDOMBROWSKI, Jamille G.:Univ Sao Paulo, Inst Biomed Sci, Dept Parasitol, Sao Paulo, Brazil
hcfmusp.author.externalBOUSEMA, Teun:Univ Nijmegen, Radboud Univ Med Ctr, Dept Med Microbiol, Nijmegen, Netherlands; Univ Nijmegen, Radboud Univ Med Ctr, Radboud Ctr Infect Dis, Nijmegen, Netherlands
hcfmusp.author.externalSUTHERLAND, Colin J.:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England; UK Hlth Secur Agcy Malaria Reference Lab, LSHTM, London WC1E 7HT, England
hcfmusp.author.externalCAMPINO, Susana:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England
hcfmusp.author.externalCLARK, Taane G.:London Sch Hyg & Trop Med LSHTM, Fac Infect & Trop Dis, London WC1E 7HT, England; LSHTM, Fac Epidemiol & Populat Hlth, London WC1E 7HT, England
hcfmusp.citation.scopus1
hcfmusp.contributor.author-fmusphcSILVIA MARIA FATIMA DI SANTI
hcfmusp.description.articlenumber96
hcfmusp.description.issue1
hcfmusp.description.volume15
hcfmusp.origemWOS
hcfmusp.origem.pubmed37950308
hcfmusp.origem.scopus2-s2.0-85176250600
hcfmusp.origem.wosWOS:001103423700002
hcfmusp.publisher.cityLONDONeng
hcfmusp.publisher.countryENGLANDeng
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