Browsing by Author "Kaneko,Akira"

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    PublicationOpen Access
    Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next-generation sequencing
    (Scientific Reports, 2023-07-14) Osborne, Ashley; Chan,Chim; Kagaya, Wataru; Kaneko,Akira; Clark, Taane G.; Campino, Susana; Gitaka, Jesse; Kita, Kiyoshi; Kongere, James; Ngara, Mtakai; Phelan,Jody E.
    Malaria control initiatives require rapid and reliable methods for the detection and monitoring of molecular markers associated with antimalarial drug resistance in Plasmodium falciparum parasites. Ngodhe island, Kenya, presents a unique malaria profile, with lower P. falciparum incidence rates than the surrounding region, and a high proportion of sub-microscopic and low-density infections. Here, using custom dual-indexing and Illumina next generation sequencing, we generate resistance profiles on seventy asymptomatic and low-density P. falciparum infections from a mass drug administration program implemented on Ngodhe island between 2015 and 2016. Our assay encompasses established molecular markers on the Pfcrt, Pfmdr1, Pfdhps, Pfdhfr, and Pfk13 genes. Resistance markers for sulfadoxine-pyrimethamine were identified at high frequencies, including a quintuple mutant haplotype (Pfdhfr/Pfdhps: N51I, C59R, S108N/A437G, K540E) identified in 62.2% of isolates. The Pfdhps K540E biomarker, used to inform decision making for intermittent preventative treatment in pregnancy, was identified in 79.2% of isolates. Several variants on Pfmdr1, associated with reduced susceptibility to quinolones and lumefantrine, were also identified (Y184F 47.1%; D1246Y 16.0%; N86 98%). Overall, we have presented a low-cost and extendable approach that can provide timely genetic profiles to inform clinical and surveillance activities, especially in settings with abundant low-density infections, seeking malaria elimination.
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    PublicationOpen Access
    High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing
    (Scientific Reports, 2023-07-26) Osborne, Ashley; Phelan, Jody E; Vanheer, Leen; Manjurano, Alphaxard; Gitaka, Jesse; Drakeley, Chris; Kaneko,Akira; Kita,Kiyoshi; Campino, Susana; Clark, Taane G.
    Malaria has exhibited the strongest known selective pressure on the human genome in recent history and is the evolutionary driving force behind genetic conditions, such as sickle-cell disease, glucose-6-phosphatase deficiency, and some other erythrocyte defects. Genomic studies (e.g., The 1000 Genomes project) have provided an invaluable baseline for human genetics, but with an estimated two thousand ethno-linguistic groups thought to exist across the African continent, our understanding of the genetic differences between indigenous populations and their implications on disease is still limited. Low-cost sequencing-based approaches make it possible to target specific molecular markers and genes of interest, leading to potential insights into genetic diversity. Here we demonstrate the versatility of custom dual-indexing technology and Illumina next generation sequencing to generate a genetic profile of human polymorphisms associated with malaria pathology.For 100 individuals diagnosed with severe malaria in Northeast Tanzania, variants were successfully characterised on the haemoglobin subunit beta (HBB), glucose-6-phosphate dehydrogenase (G6PD), atypical chemokine receptor 1 (ACKR1) genes, and the intergenic Dantu genetic blood variant, then validated using pre-existing genotyping data. High sequencing coverage was observed across all amplicon targets in HBB, G6PD, ACKR1, and the Dantu blood group, with variants identified at frequencies previously observed within this region of Tanzania. Sequencing data exhibited high concordance rates to pre-existing genotyping data (> 99.5%). Our work demonstrates the potential utility of amplicon sequencing for applications in human genetics, including to personalise medicine and understand the genetic diversity of loci linked to important host phenotypes, such as malaria susceptibility.
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    PublicationOpen Access
    Potential application of the hematology analyzer XN-31 prototype for field malaria surveillance in Kenya
    (Research Square, 2022-04-14) Kagaya, Wataru; Takehara, Ikki; Kurihara, Kyoko; Okomo, Gordon; Gitaka, Jesse; Kaneko,Akira; Kongere James
    Early and accurate diagnosis is a key component in malaria control programs. Microscopy is the current gold standard, however it requires extensive training and the results largely rely on the skill of the microscopists. Malaria rapid diagnostic tests (RDT) can be performed with minimal training and offer timely diagnosis, but results are not quantitative. Moreover, some Plasmodium falciparum parasites have evolved to evade detection by RDT. Developed by the Sysmex Corporation, the XN-31 prototype (XN-31p) is an automated hematology analyzer capable of detecting Plasmodium-infected erythrocytes and providing species differentiation and stage specific parasite counts in venous blood samples in a minute without any sample preparation. Here we tested the performance of the XN-31p with capillary blood samples and evaluated the effect of sample storage time and temperature on the stability of results. Paired capillary and venous blood samples were collected from 169 outpatients with clinical malaria symptoms in Homa Bay County Referral Hospital, Kenya. Malaria infections were diagnosed with the XN-31p, microscopy, RDT, and PCR. Capillary blood samples were remeasured on the XN-31p after 24 hours of storage at either room (15 to 25°C) or chilled temperatures (2 to 8°C). Identical results in malaria diagnosis were observed between venous and capillary blood samples processed with the XN-31p. The sensitivity and specificity of XN-31p with capillary blood sample relative to PCR were 0.857 and 1.000 and those relative to microscopy and RDT were 1.000 and 0.986 to 1.000, respectively. Parasitemia and complete blood count (CBC) results were stable in capillary blood samples after 24 hours at room or chilled temperatures. These results showed that the XN-31p can be a useful tool to complement existing methods for routine malaria diagnosis in remote settings.