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Wamae K, Ndwiga L, Kharabora O, Kimenyi K, Osoti V, de Laurent Z, Wambua J, Musyoki J, Ngetsa C, Kalume P, Mwambingu G, Hamaluba M, van der Pluijm R, Dondorp AM, Bailey J, Juliano J, Bejon P, Ochola-Oyier L. Targeted amplicon deep sequencing of ama1 and mdr1 to track within-host P. falciparum diversity throughout treatment in a clinical drug trial. Wellcome Open Res 2024; 7:95. [PMID: 37456906 PMCID: PMC10349275 DOI: 10.12688/wellcomeopenres.17736.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2024] [Indexed: 07/20/2023] Open
Abstract
Introduction Antimalarial therapeutic efficacy studies are routinely conducted in malaria-endemic countries to assess the effectiveness of antimalarial treatment strategies. Targeted amplicon sequencing (AmpSeq) uniquely identifies and quantifies genetically distinct parasites within an infection. In this study, AmpSeq of Plasmodium falciparum apical membrane antigen 1 ( ama1), and multidrug resistance gene 1 ( mdr1), were used to characterise the complexity of infection (COI) and drug-resistance genotypes, respectively. Methods P. falciparum-positive samples were obtained from a triple artemisinin combination therapy clinical trial conducted in 30 children under 13 years of age between 2018 and 2019 in Kilifi, Kenya. Nine of the 30 participants presented with recurrent parasitemia from day 26 (624h) onwards. The ama1 and mdr1 genes were amplified and sequenced, while msp1, msp2 and glurp data were obtained from the original clinical study. Results The COI was comparable between ama1 and msp1, msp2 and glurp; overall, ama1 detected more microhaplotypes. Based on ama1, a stable number of microhaplotypes were detected throughout treatment until day 3. Additionally, a recrudescent infection was identified with an ama1 microhaplotype initially observed at 30h and later in an unscheduled follow-up visit. Using the relative frequencies of ama1 microhaplotypes and parasitemia, we identified a fast (<1h) and slow (>5h) clearing microhaplotype. As expected, only two mdr1 microhaplotypes (NF and NY) were identified based on the combination of amino acid polymorphisms at codons 86 and 184. Conclusions This study highlights AmpSeq as a tool for highly-resolution tracking of parasite microhaplotypes throughout treatment and can detect variation in microhaplotype clearance estimates. AmpSeq can also identify slow-clearing microhaplotypes, a potential early sign of selection during treatment. Consequently, AmpSeq has the capability of improving the discriminatory power to distinguish recrudescences from reinfections accurately.
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Affiliation(s)
- Kevin Wamae
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Leonard Ndwiga
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Oksana Kharabora
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Kelvin Kimenyi
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Victor Osoti
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Juliana Wambua
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Jennifer Musyoki
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Caroline Ngetsa
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Peter Kalume
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Mainga Hamaluba
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rob van der Pluijm
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Arjen M. Dondorp
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jeffrey Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, 02903, USA
| | - Jonathan Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Philip Bejon
- Bioscience, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Wamae K, Ndwiga L, Kharabora O, Kimenyi K, Osoti V, de Laurent Z, Wambua J, Musyoki J, Ngetsa C, Kalume P, Mwambingu G, Hamaluba M, van der Pluijm R, Dondorp A, Bailey J, Juliano J, Bejon P, Ochola-Oyier L. Targeted Amplicon deep sequencing of ama1 and mdr1 to track within-host P. falciparum diversity throughout treatment in a clinical drug trial. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17736.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimalarial therapeutic efficacy studies are routinely conducted in malaria-endemic countries to assess the effectiveness of antimalarial treatment strategies. Targeted amplicon deep sequencing (TADS) uniquely identifies and quantifies genetically distinct parasites within an infection. In this study, TADS Plasmodium falciparum apical membrane antigen 1 (ama1), and multidrug resistance gene 1 (mdr1), were used to characterize the complexity of infection (COI) and drug-resistance genotypes, respectively. P. falciparum positive samples were obtained from a triple artemisinin combination therapy clinical trial conducted in 30 children under 13 years of age between 2018 and 2019 in Kilifi, Kenya. Of the 30 participants, 9 presented with recurrent parasitemia from day 26 (624h) onwards. The ama1 and mdr1 genes were amplified and sequenced, while msp1, msp2 and glurp data were obtained from the original clinical study. The COI was comparable between ama1 and msp1, msp2 and glurp, however, overall ama1 detected more haplotypes. Based on ama1, a stable number of haplotypes were detected throughout treatment up until day 3. Additionally, a recrudescent infection was identified with an ama1 haplotype initially observed at 30h and later in an unscheduled follow-up visit. Using the relative frequencies of ama1 haplotypes and parasitaemia, we identified a fast (<1h) and slow (>5h) clearing haplotype. As expected, only two mdr1 haplotypes (NF and NY) were identified based on the combination of amino acid polymorphisms at codons 86 and 184. This study highlights TADS as a sensitive tool for tracking parasite haplotypes throughout treatment and can detect variation in haplotype clearance estimates. TADS can also identify slow clearing haplotypes, a potential early sign of selection during treatment. Consequently, TADS has the capability of improving the discriminatory power to accurately distinguish recrudescences from reinfections.
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