2022
Application of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin gene
George S, Suwondo P, Akorli J, Otchere J, Harrison LM, Bilguvar K, Knight JR, Humphries D, Wilson MD, Caccone A, Cappello M. Application of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin gene. Scientific Reports 2022, 12: 11459. PMID: 35794459, PMCID: PMC9259660, DOI: 10.1038/s41598-022-15718-1.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsPeriodic mass drug administrationHigh-risk groupCross-sectional studyDrug resistance markersMass drug administrationResistance-associated mutationsHookworm Necator americanusPost-treatment samplesIsotype-1 β-tubulin geneHookworm infectionPersistent infectionResistance markersDrug AdministrationNecator americanusInfection statusVeterinary nematodesInfectionMarkersNucleotide polymorphismsSensitive toolBenzimidazole drugsNucleotide alleles
2018
Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities
Combs M, Byers K, Ghersi B, Blum M, Caccone A, Costa F, Himsworth C, Richardson J, Munshi-South J. Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities. Proceedings Of The Royal Society B 2018, 285: 20180245. PMID: 29875297, PMCID: PMC6015871, DOI: 10.1098/rspb.2018.0245.Peer-Reviewed Original ResearchConceptsGene flowGenome-wide single nucleotide polymorphismsSpatial population genomicsGenome-wide diversityShortest distance classesGenerality of predictionsPopulation genomicsGenetic discontinuityLimited dispersalNeutral evolutionSingle nucleotide polymorphismsMultiple speciesPest managementSame speciesBrown ratsDifferent biomesDistance classesNucleotide polymorphismsAnimal movementSpeciesGenomicsMajor waterwaysCoancestryClustering analysisDispersal
2017
Population genomics of the Asian tiger mosquito, Aedes albopictus: insights into the recent worldwide invasion
Kotsakiozi P, Richardson J, Pichler V, Favia G, Martins A, Urbanelli S, Armbruster P, Caccone A. Population genomics of the Asian tiger mosquito, Aedes albopictus: insights into the recent worldwide invasion. Ecology And Evolution 2017, 7: 10143-10157. PMID: 29238544, PMCID: PMC5723592, DOI: 10.1002/ece3.3514.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsGenetic structureRecent invasionRestriction Site-Associated DNA SequencingAsian tiger mosquitoGenomics-based approachesTiger mosquitoPopulation genomicsInvasive populationsNative rangeWorldwide invasionMultiple invasionsGenomic diversityRange populationsPopulation clustersMajor clustersDNA sequencingNucleotide polymorphismsAedes albopictusVector control strategiesInvasionMosquitoesLocal scaleDifferentiationGenomicsGenomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification
Richardson JB, Lee KY, Mireji P, Enyaru J, Sistrom M, Aksoy S, Zhao H, Caccone A. Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification. PLOS Neglected Tropical Diseases 2017, 11: e0005949. PMID: 28961238, PMCID: PMC5636163, DOI: 10.1371/journal.pntd.0005949.Peer-Reviewed Original ResearchConceptsAfrican trypanosomesHigh genetic similarityMaximum likelihood phylogenyStrain identificationGenomic resourcesGenetic structureEvolutionary relationshipsGenetic clustersPhylogenetic analysisGenomic analysisSingle nucleotide polymorphismsTaxonomic classificationGenetic similarityLarge comparative analysisGenetic markersHigh similarityGeographic originEvansi strainsSNPsNucleotide polymorphismsT. brucei bruceiPhylogenyTrypanosomesTrypanosomaTrypanozoon
2016
Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection
Richardson JB, Evans B, Pyana PP, Van Reet N, Sistrom M, Büscher P, Aksoy S, Caccone A. Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection. Evolutionary Applications 2016, 9: 381-393. PMID: 26834831, PMCID: PMC4721075, DOI: 10.1111/eva.12338.Peer-Reviewed Original ResearchSame patientHuman African trypanosomiasisHigh incidencePatientsTrypanosoma brucei gambienseHAT casesDrug resistanceDisease controlRelapseSingle nucleotide polymorphismsBrucei gambienseWhole-genome sequencingAfrican trypanosomiasisPathogenic levelsSaharan AfricaNucleotide polymorphismsOriginal strainRecent studiesTreatmentPromising new setFunctional studiesNovel insightsReinfectionFuture functional studiesNew strain