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Goodwin J, Kajubi R, Wang K, Li F, Wade M, Orukan F, Huang L, Whalen M, Aweeka FT, Mwebaza N, Parikh S. Persistent and multiclonal malaria parasite dynamics despite extended artemether-lumefantrine treatment in children. Nat Commun 2024; 15:3817. [PMID: 38714692 PMCID: PMC11076639 DOI: 10.1038/s41467-024-48210-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/24/2024] [Indexed: 05/10/2024] Open
Abstract
Standard diagnostics used in longitudinal antimalarial studies are unable to characterize the complexity of submicroscopic parasite dynamics, particularly in high transmission settings. We use molecular markers and amplicon sequencing to characterize post-treatment stage-specific malaria parasite dynamics during a 42 day randomized trial of 3- versus 5 day artemether-lumefantrine in 303 children with and without HIV (ClinicalTrials.gov number NCT03453840). The prevalence of parasite-derived 18S rRNA is >70% in children throughout follow-up, and the ring-stage marker SBP1 is detectable in over 15% of children on day 14 despite effective treatment. We find that the extended regimen significantly lowers the risk of recurrent ring-stage parasitemia compared to the standard 3 day regimen, and that higher day 7 lumefantrine concentrations decrease the probability of ring-stage parasites in the early post-treatment period. Longitudinal amplicon sequencing reveals remarkably dynamic patterns of multiclonal infections that include new and persistent clones in both the early post-treatment and later time periods. Our data indicate that post-treatment parasite dynamics are highly complex despite efficacious therapy, findings that will inform strategies to optimize regimens in the face of emerging partial artemisinin resistance in Africa.
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Affiliation(s)
- Justin Goodwin
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Richard Kajubi
- Infectious Disease Research Collaboration, Kampala, Uganda
| | - Kaicheng Wang
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Fangyong Li
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Martina Wade
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Francis Orukan
- Infectious Disease Research Collaboration, Kampala, Uganda
| | - Liusheng Huang
- University of California, San Francisco, San Francisco, CA, USA
| | - Meghan Whalen
- University of California, San Francisco, San Francisco, CA, USA
| | | | - Norah Mwebaza
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Pharmacology and Therapeutics, Makerere University College of Health Sciences, Kampala, Uganda
| | - Sunil Parikh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Yale School of Medicine, New Haven, CT, USA.
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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] [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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Topazian HM, Moser KA, Ngasala B, Oluoch PO, Forconi CS, Mhamilawa LE, Aydemir O, Kharabora O, Deutsch-Feldman M, Read AF, Denton M, Lorenzo A, Mideo N, Ogutu B, Moormann AM, Mårtensson A, Odwar B, Bailey JA, Akala H, Ong'echa JM, Juliano JJ. Low Complexity of Infection Is Associated With Molecular Persistence of Plasmodium falciparum in Kenya and Tanzania. FRONTIERS IN EPIDEMIOLOGY 2022; 2:852237. [PMID: 38455314 PMCID: PMC10910917 DOI: 10.3389/fepid.2022.852237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/06/2022] [Indexed: 03/09/2024]
Abstract
Background Plasmodium falciparum resistance to artemisinin-based combination therapies (ACTs) is a threat to malaria elimination. ACT-resistance in Asia raises concerns for emergence of resistance in Africa. While most data show high efficacy of ACT regimens in Africa, there have been reports describing declining efficacy, as measured by both clinical failure and prolonged parasite clearance times. Methods Three hundred children aged 2-10 years with uncomplicated P. falciparum infection were enrolled in Kenya and Tanzania after receiving treatment with artemether-lumefantrine. Blood samples were taken at 0, 24, 48, and 72 h, and weekly thereafter until 28 days post-treatment. Parasite and host genetics were assessed, as well as clinical, behavioral, and environmental characteristics, and host anti-malarial serologic response. Results While there was a broad range of clearance rates at both sites, 85% and 96% of Kenyan and Tanzanian samples, respectively, were qPCR-positive but microscopy-negative at 72 h post-treatment. A greater complexity of infection (COI) was negatively associated with qPCR-detectable parasitemia at 72 h (OR: 0.70, 95% CI: 0.53-0.94), and a greater baseline parasitemia was marginally associated with qPCR-detectable parasitemia (1,000 parasites/uL change, OR: 1.02, 95% CI: 1.01-1.03). Demographic, serological, and host genotyping characteristics showed no association with qPCR-detectable parasitemia at 72 h. Parasite haplotype-specific clearance slopes were grouped around the mean with no association detected between specific haplotypes and slower clearance rates. Conclusions Identifying risk factors for slow clearing P. falciparum infections, such as COI, are essential for ongoing surveillance of ACT treatment failure in Kenya, Tanzania, and more broadly in sub-Saharan Africa.
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Affiliation(s)
- Hillary M. Topazian
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Kara A. Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter O. Oluoch
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Lwidiko E. Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Oksana Kharabora
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Molly Deutsch-Feldman
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Andrew F. Read
- Department of Entomology, Penn State University, University Park, PA, United States
| | - Madeline Denton
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Antonio Lorenzo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Bernhards Ogutu
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Boaz Odwar
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Hoseah Akala
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | | | - Jonathan J. Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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