2016
Polymorphisms in K13, pfcrt, pfmdr1, pfdhfr, and pfdhps in parasites isolated from symptomatic malaria patients in Burkina Faso
Somé A, Sorgho H, Zongo I, Bazié T, Nikiéma F, Sawadogo A, Zongo M, Compaoré Y, Ouédraogo J. Polymorphisms in K13, pfcrt, pfmdr1, pfdhfr, and pfdhps in parasites isolated from symptomatic malaria patients in Burkina Faso. Parasite 2016, 23: 60. PMID: 28004634, PMCID: PMC5178381, DOI: 10.1051/parasite/2016069.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAntigens, BacterialAntigens, SurfaceAntimalarialsArtemisininsBurkina FasoChildChild, PreschoolDrug ResistanceDrug Therapy, CombinationHumansInfantMalaria, FalciparumMembrane Transport ProteinsMultidrug Resistance-Associated ProteinsPlasmodium falciparumPolymorphism, Single NucleotideProtozoan ProteinsYoung AdultConceptsPolymerase chain reactionUncomplicated malariaDrug resistance polymorphismsPfcrt 76TResistance-mediating polymorphismsPrevalence of polymorphismsSymptomatic malaria patientsAntimalarial drug resistanceGlobal malaria controlEmergence of resistancePfmdr1 184FPfmdr1 86YMalaria patientsPfdhps genesBaseline prevalenceCombination therapyHealth centersBlood samplesWestern CambodiaBetter efficacyGene polymorphismsCodon 540Malaria controlDrug resistancePfdhpsArtesunate-Amodiaquine and Artemether-Lumefantrine Therapies and Selection of Pfcrt and Pfmdr1 Alleles in Nanoro, Burkina Faso
Sondo P, Derra K, Nakanabo S, Tarnagda Z, Kazienga A, Zampa O, Valéa I, Sorgho H, Owusu-Dabo E, Ouédraogo J, Guiguemdé T, Tinto H. Artesunate-Amodiaquine and Artemether-Lumefantrine Therapies and Selection of Pfcrt and Pfmdr1 Alleles in Nanoro, Burkina Faso. PLOS ONE 2016, 11: e0151565. PMID: 27031231, PMCID: PMC4816516, DOI: 10.1371/journal.pone.0151565.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAllelesAmodiaquineAntimalarialsArtemether, Lumefantrine Drug CombinationArtemisininsBurkina FasoChildDrug CombinationsEthanolaminesFemaleFluorenesGene FrequencyGenotypeHost-Parasite InteractionsHumansMalaria, FalciparumMaleMembrane Transport ProteinsMiddle AgedMultidrug Resistance-Associated ProteinsMultivariate AnalysisParasitemiaPlasmodium falciparumPolymorphism, Single NucleotideProtozoan ProteinsTreatment OutcomeConceptsPfmdr1 allelesTreatment failureArtemether-lumefantrine therapyPfcrt K76TSingle nucleotide polymorphismsRestriction fragment length polymorphism methodFragment length polymorphism methodPotential beneficial effectsLength polymorphism methodArtesunate-AmodiaquineRecurrent parasitaemiaTreatment regimenACT resistanceCombination therapyK76TPfmdr1 geneClinical trialsTreatment outcomesMultivariate analysisDay 0PfcrtMalaria controlBlood spotsBeneficial effectsPolymorphism method
2015
Dynamic of plasmodium falciparum chloroquine resistance transporter gene Pfcrt K76T mutation five years after withdrawal of chloroquine in Burkina Faso
Sondo P, Derra K, Tarnagda Z, Nakanabo S, Zampa O, Kazienga A, Valea I, Sorgho H, Ouedraogo J, Guiguemde T, Tinto H. Dynamic of plasmodium falciparum chloroquine resistance transporter gene Pfcrt K76T mutation five years after withdrawal of chloroquine in Burkina Faso. Pan African Medical Journal 2015, 21: 101. PMID: 26516402, PMCID: PMC4606025, DOI: 10.11604/pamj.2015.21.101.6437.Peer-Reviewed Original ResearchMeSH KeywordsAntimalarialsBurkina FasoChloroquineDrug ResistanceHumansMalaria, FalciparumMembrane Transport ProteinsMutationPlasmodium falciparumPolymorphism, Single NucleotidePrevalenceProtozoan Proteins
2014
A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
Preston M, Campino S, Assefa S, Echeverry D, Ocholla H, Amambua-Ngwa A, Stewart L, Conway D, Borrmann S, Michon P, Zongo I, Ouédraogo J, Djimde A, Doumbo O, Nosten F, Pain A, Bousema T, Drakeley C, Fairhurst R, Sutherland C, Roper C, Clark T. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nature Communications 2014, 5: 4052. PMID: 24923250, PMCID: PMC4082634, DOI: 10.1038/ncomms5052.Peer-Reviewed Original ResearchMeSH KeywordsGenome, ProtozoanGeographyHumansMalaria, FalciparumPhylogenyPlasmodium falciparumPolymorphism, Single NucleotideConceptsMajor public health problemValuable public health toolSingle nucleotide polymorphismsPublic health problemDrug-resistant parasitesPublic health toolPlasmodium falciparum strainsGlobal eradication campaignHealth problemsFalciparum strainsCase managementHealth toolsPlasmodium falciparumParasite migrationElimination areaEradication campaignApicoplast genomeParasitesPolymorphismInfectionMalariaInternational air travelFalciparum
2013
PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
Preston M, Assefa S, Ocholla H, Sutherland C, Borrmann S, Nzila A, Michon P, Hien T, Bousema T, Drakeley C, Zongo I, Ouédraogo J, Djimde A, Doumbo O, Nosten F, Fairhurst R, Conway D, Roper C, Clark T. PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation. The Journal Of Infectious Diseases 2013, 209: 1808-1815. PMID: 24338354, PMCID: PMC4017360, DOI: 10.1093/infdis/jit812.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceDNA, ProtozoanGenome, ProtozoanHumansInternetMalaria, FalciparumMolecular Sequence AnnotationPlasmodium falciparumPolymorphism, Single NucleotideConceptsGenomic variationSingle nucleotide polymorphismsHigh-quality single nucleotide polymorphismsHigh-throughput sequencingInter-population differencesGenetic barcodesPlasmodium biologyGenetic variabilityGenomic dataInformative variantsDrug resistanceParasite populationsDifferential phenotypesLaboratory strainsMalaria parasitesNovel mutationsGlobal public health challengeNew insightsPf isolatesMalaria-endemic regionsPublic health challengePlasmodium falciparum speciesMedicine applicationsWeb-based resourcesClinical studiesMultiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia
Miotto O, Almagro-Garcia J, Manske M, MacInnis B, Campino S, Rockett K, Amaratunga C, Lim P, Suon S, Sreng S, Anderson J, Duong S, Nguon C, Chuor C, Saunders D, Se Y, Lon C, Fukuda M, Amenga-Etego L, Hodgson A, Asoala V, Imwong M, Takala-Harrison S, Nosten F, Su X, Ringwald P, Ariey F, Dolecek C, Hien T, Boni M, Thai C, Amambua-Ngwa A, Conway D, Djimdé A, Doumbo O, Zongo I, Ouedraogo J, Alcock D, Drury E, Auburn S, Koch O, Sanders M, Hubbart C, Maslen G, Ruano-Rubio V, Jyothi D, Miles A, O'Brien J, Gamble C, Oyola S, Rayner J, Newbold C, Berriman M, Spencer C, McVean G, Day N, White N, Bethell D, Dondorp A, Plowe C, Fairhurst R, Kwiatkowski D. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nature Genetics 2013, 45: 648-655. PMID: 23624527, PMCID: PMC3807790, DOI: 10.1038/ng.2624.Peer-Reviewed Original Research
2012
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
Preston M, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo J, Nosten F, Anderson T, Clark T. VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. Bioinformatics 2012, 28: 2983-2985. PMID: 22976080, PMCID: PMC3496337, DOI: 10.1093/bioinformatics/bts557.Peer-Reviewed Original ResearchMeSH KeywordsGenetic VariationGenome, ProtozoanHigh-Throughput Nucleotide SequencingINDEL MutationPlasmodium falciparumPolymorphism, Single NucleotideSequence Analysis, DNASoftwareConceptsNext-generation sequencing dataUser-defined groupsGenomic regionsVariant call format filesSingle nucleotide polymorphismsDrug resistance genesSequence dataSequencing dataStructural variantsImportant antigenicSequence file formatsInformative markersPlasmodium falciparumDifferent continentsFile formatFormat fileUser manualReal timeAnalysis toolsGenesVariantsDeletionPolymorphismVarBFalciparumAnalysis of Plasmodium falciparum diversity in natural infections by deep sequencing
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O’Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo J, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara S, Marsh K, Jiang H, Su X, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White N, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail M, Turner D, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan J, Ferdig M, Amambua-Ngwa A, Conway D, Takala-Harrison S, Plowe C, Rayner J, Rockett K, Clark T, Newbold C, Berriman M, MacInnis B, Kwiatkowski D. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 2012, 487: 375-379. PMID: 22722859, PMCID: PMC3738909, DOI: 10.1038/nature11174.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBiodiversityGenome, ProtozoanGenotypeHigh-Throughput Nucleotide SequencingHumansMalaria, FalciparumPhylogenyPlasmodium falciparumPolymorphism, Single NucleotidePrincipal Component AnalysisCharacterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data
Auburn S, Campino S, Miotto O, Djimde A, Zongo I, Manske M, Maslen G, Mangano V, Alcock D, MacInnis B, Rockett K, Clark T, Doumbo O, Ouédraogo J, Kwiatkowski D. Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data. PLOS ONE 2012, 7: e32891. PMID: 22393456, PMCID: PMC3290604, DOI: 10.1371/journal.pone.0032891.Peer-Reviewed Original ResearchConceptsHost diversityIllumina GA platformMultiplicity of infectionGenome-wide datasetsPopulation-level diversitySingle-molecule sequencing technologiesNext-generation sequence dataPlasmodium falciparum diversityMsp-1 locusGenetic divergenceSequence dataSequencing technologiesNumber of clonesLevel diversityNovel insightsDiversityP. falciparum fieldLociMSP-1PCRRelative proportionsNew statistical approachSNPsClonesReduced sensitivity
2011
Host candidate gene polymorphisms and clearance of drug-resistant Plasmodium falciparum parasites
Diakite M, Achidi E, Achonduh O, Craik R, Djimde A, Evehe M, Green A, Hubbart C, Ibrahim M, Jeffreys A, Khan B, Kimani F, Kwiatkowski D, Mbacham W, Jezan S, Ouedraogo J, Rockett K, Rowlands K, Tagelsir N, Tekete M, Zongo I, Ranford-Cartwright L. Host candidate gene polymorphisms and clearance of drug-resistant Plasmodium falciparum parasites. Malaria Journal 2011, 10: 250. PMID: 21867552, PMCID: PMC3177816, DOI: 10.1186/1475-2875-10-250.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAfricaAntimalarialsChildChild, PreschoolDrug ResistanceFemaleGenomicsHumansMalaria, FalciparumMaleMass SpectrometryPlasmodium falciparumPolymorphism, Single NucleotideConceptsDrug-resistant parasitesHuman genomeAnti-malarial drugsSignificant associationDrug treatmentResistant parasitesAnti-inflammatory cytokine responseTh1/Th2 balanceDrug-resistant Plasmodium falciparum parasitesDrug-resistant P. falciparumMolecular testsPlasmodium falciparum infectionPlasmodium falciparum parasitesDrug resistance profilesDrug-resistant infectionsImmune response lociCandidate gene polymorphismsAbility of parasitesTh2 balanceFalciparum infectionCytokine responsesMalaria infectionOdds ratioClearance phenotypeEnhanced clearancePopulation Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay
Campino S, Auburn S, Kivinen K, Zongo I, Ouedraogo J, Mangano V, Djimde A, Doumbo O, Kiara S, Nzila A, Borrmann S, Marsh K, Michon P, Mueller I, Siba P, Jiang H, Su X, Amaratunga C, Socheat D, Fairhurst R, Imwong M, Anderson T, Nosten F, White N, Gwilliam R, Deloukas P, MacInnis B, Newbold C, Rockett K, Clark T, Kwiatkowski D. Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay. PLOS ONE 2011, 6: e20251. PMID: 21673999, PMCID: PMC3108946, DOI: 10.1371/journal.pone.0020251.Peer-Reviewed Original ResearchMeSH KeywordsCloning, OrganismCulture TechniquesDNA, ProtozoanGenetic LociGenotypeHigh-Throughput Nucleotide SequencingLaboratoriesMalaria, FalciparumPlasmodium falciparumPolymorphism, Single NucleotideTime FactorsConceptsPopulation genetic studiesIllumina GoldenGateGenetic studiesSingle nucleotide polymorphism (SNP) discoveryLarge-scale population genetic studiesLaboratory clonesPopulation genetic diversityPopulation genetic analysesGenome sequencing projectsPlasmodium falciparum genomeTotal genomic DNAParasite population dynamicsMinor frequency allelesFalciparum genomePolymorphism discoveryGenetic diversitySequencing projectsWhole genomeP. falciparumGenetic analysisImportant phenotypesGenomic DNAHigh SNPPopulation dynamicsMultiple-clone infections
2010
Selection of Known Plasmodium falciparum Resistance-Mediating Polymorphisms by Artemether-Lumefantrine and Amodiaquine- Sulfadoxine-Pyrimethamine but Not Dihydroartemisinin- Piperaquine in Burkina Faso
Somé A, Séré Y, Dokomajilar C, Zongo I, Rouamba N, Greenhouse B, Ouédraogo J, Rosenthal P. Selection of Known Plasmodium falciparum Resistance-Mediating Polymorphisms by Artemether-Lumefantrine and Amodiaquine- Sulfadoxine-Pyrimethamine but Not Dihydroartemisinin- Piperaquine in Burkina Faso. Antimicrobial Agents And Chemotherapy 2010, 54: 1949-1954. PMID: 20231394, PMCID: PMC2863637, DOI: 10.1128/aac.01413-09.Peer-Reviewed Original ResearchAmodiaquineAntimalarialsArtemetherArtemisininsBurkina FasoDrug CombinationsDrug Resistance, BacterialEthanolaminesFluorenesGenotypeHumansInfantLumefantrineMalaria, FalciparumMembrane Transport ProteinsMultidrug Resistance-Associated ProteinsPlasmodium falciparumPolymorphism, Single NucleotideProtozoan ProteinsPyrimethamineQuinolinesRandomized Controlled Trials as TopicRecurrenceSulfadoxine