Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda

Abstract Antimalarial therapeutic efficacy studies are vital for monitoring drug efficacy in malaria-endemic regions. The WHO recommends genotyping polymorphic markers including msp-1, msp-2, and glurp for distinguishing recrudescences from reinfections. Recently, WHO proposed replacing glurp with m...

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Main Authors: Alex Mwesigwa, Monica Golumbeanu, Sam Jones, Sara L. Cantoreggi, Benson Musinguzi, Joaniter I. Nankabirwa, Everd Maniple Bikaitwoha, Joan N Kalyango, Charles Karamagi, Mateusz Plucinski, Samuel L. Nsobya, Christian Nsanzabana, Pauline Byakika-Kibwika
Format: Article
Language:English
Published: Nature Portfolio 2025-02-01
Series:Scientific Reports
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Online Access:https://doi.org/10.1038/s41598-025-88892-7
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author Alex Mwesigwa
Monica Golumbeanu
Sam Jones
Sara L. Cantoreggi
Benson Musinguzi
Joaniter I. Nankabirwa
Everd Maniple Bikaitwoha
Joan N Kalyango
Charles Karamagi
Mateusz Plucinski
Samuel L. Nsobya
Christian Nsanzabana
Pauline Byakika-Kibwika
author_facet Alex Mwesigwa
Monica Golumbeanu
Sam Jones
Sara L. Cantoreggi
Benson Musinguzi
Joaniter I. Nankabirwa
Everd Maniple Bikaitwoha
Joan N Kalyango
Charles Karamagi
Mateusz Plucinski
Samuel L. Nsobya
Christian Nsanzabana
Pauline Byakika-Kibwika
author_sort Alex Mwesigwa
collection DOAJ
description Abstract Antimalarial therapeutic efficacy studies are vital for monitoring drug efficacy in malaria-endemic regions. The WHO recommends genotyping polymorphic markers including msp-1, msp-2, and glurp for distinguishing recrudescences from reinfections. Recently, WHO proposed replacing glurp with microsatellites (Poly-α, PfPK2, TA1). However, suitable combinations with msp-1 and msp-2, as well as the performance of different algorithms for classifying recrudescence, have not been systematically assessed. This study investigated various microsatellites alongside msp-1 and msp-2 for molecular correction and compared different genotyping algorithms across three sites in Uganda. Microsatellites 313, Poly-α, and 383 exhibited the highest diversity, while PfPK2 and Poly-α revealed elevated multiplicity of infection (MOI) across all sites. The 3/3 match-counting algorithm classified significantly fewer recrudescences than both the ≥ 2/3 and Bayesian algorithms at probability cutoffs of ≥ 0.7 and ≥ 0.8 (P < 0.05). The msp-1/msp-2/2490 combination identified more recrudescences using the ≥ 2/3 and 3/3 algorithms in the artemether-lumefantrine (AL) treatment arm, while msp-1/msp-2/glurp combination classified more cases of recrudescence using the ≥ 2/3 in the dihydroartemisinin-piperaquine (DP) arm. Microsatellites PfPK2 and Poly-α, potentially sensitive to detecting minority clones, are promising replacements for glurp. Discrepancies in recrudescence classification between match-counting and Bayesian algorithms highlight the need for standardized PCR correction practices.
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spelling doaj-art-8a030f6293744b90a932be2f305c95742025-02-09T12:32:02ZengNature PortfolioScientific Reports2045-23222025-02-0115111010.1038/s41598-025-88892-7Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in UgandaAlex Mwesigwa0Monica Golumbeanu1Sam Jones2Sara L. Cantoreggi3Benson Musinguzi4Joaniter I. Nankabirwa5Everd Maniple Bikaitwoha6Joan N Kalyango7Charles Karamagi8Mateusz Plucinski9Samuel L. Nsobya10Christian Nsanzabana11Pauline Byakika-Kibwika12Clinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere UniversitySwiss Tropical and Public Health InstituteMMV Medicines for Malaria VentureSwiss Tropical and Public Health InstituteDepartent of Medical Laboratory Science, Faculty of Health Sciences, Muni UniversityClinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere UniversityDepartment of Community Health, School of Medicine, Kabale UniversityClinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere UniversityClinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere UniversityU.S. President’s Malaria Initiative, Centers for Disease Control and PreventionInfectious Diseases Research Collaboration, College of Health Sciences, Makerere UniversitySwiss Tropical and Public Health InstituteMbarara University of Science and TechnologyAbstract Antimalarial therapeutic efficacy studies are vital for monitoring drug efficacy in malaria-endemic regions. The WHO recommends genotyping polymorphic markers including msp-1, msp-2, and glurp for distinguishing recrudescences from reinfections. Recently, WHO proposed replacing glurp with microsatellites (Poly-α, PfPK2, TA1). However, suitable combinations with msp-1 and msp-2, as well as the performance of different algorithms for classifying recrudescence, have not been systematically assessed. This study investigated various microsatellites alongside msp-1 and msp-2 for molecular correction and compared different genotyping algorithms across three sites in Uganda. Microsatellites 313, Poly-α, and 383 exhibited the highest diversity, while PfPK2 and Poly-α revealed elevated multiplicity of infection (MOI) across all sites. The 3/3 match-counting algorithm classified significantly fewer recrudescences than both the ≥ 2/3 and Bayesian algorithms at probability cutoffs of ≥ 0.7 and ≥ 0.8 (P < 0.05). The msp-1/msp-2/2490 combination identified more recrudescences using the ≥ 2/3 and 3/3 algorithms in the artemether-lumefantrine (AL) treatment arm, while msp-1/msp-2/glurp combination classified more cases of recrudescence using the ≥ 2/3 in the dihydroartemisinin-piperaquine (DP) arm. Microsatellites PfPK2 and Poly-α, potentially sensitive to detecting minority clones, are promising replacements for glurp. Discrepancies in recrudescence classification between match-counting and Bayesian algorithms highlight the need for standardized PCR correction practices.https://doi.org/10.1038/s41598-025-88892-7Plasmodium falciparumRecrudescenceReinfectionMicrosatellitesmsp-1msp-2
spellingShingle Alex Mwesigwa
Monica Golumbeanu
Sam Jones
Sara L. Cantoreggi
Benson Musinguzi
Joaniter I. Nankabirwa
Everd Maniple Bikaitwoha
Joan N Kalyango
Charles Karamagi
Mateusz Plucinski
Samuel L. Nsobya
Christian Nsanzabana
Pauline Byakika-Kibwika
Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda
Scientific Reports
Plasmodium falciparum
Recrudescence
Reinfection
Microsatellites
msp-1
msp-2
title Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda
title_full Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda
title_fullStr Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda
title_full_unstemmed Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda
title_short Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda
title_sort assessment of different genotyping markers and algorithms for distinguishing plasmodium falciparum recrudescence from reinfection in uganda
topic Plasmodium falciparum
Recrudescence
Reinfection
Microsatellites
msp-1
msp-2
url https://doi.org/10.1038/s41598-025-88892-7
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