Genomic Surveillance Reveals Clusters of Plasmodium falciparum Antimalarial Resistance Markers in Eswatini, A Low-Transmission Setting
11 affiliations
- 1Laboratory Department, National Malaria Programme, Manzini, Eswatini
- 2EPPIcenter Research Program, Department of Medicine, University of California, San Francisco, California, USA
- 3Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco, California, USA
- 4ISGlobal, Barcelona, Spain
- 5Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- 6Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research, Centre of Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
- 7SADC Malaria Elimination Eight Secretariat, Windhoek, Namibia
- 8Wits Research Institute for Malaria, University of Witwatersrand, Johannesburg, South Africa
- 9University of Pretoria Institute for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
- 10Department of Epidemiology & Biostatistics, University of California, San Francisco, California
- 11Parasitology Department, Faculty of Health Sciences, University of Eswatini, Mbabane, Eswatini
Abstract
The elimination of Plasmodium falciparum malaria in Eswatini remains elusive because of ongoing importation and sustained local transmission. The current status of antimalarial and diagnostic resistance in the country remains unknown. Genomic surveillance can complement routine surveillance by characterizing the prevalence and distribution of resistance markers and revealing granular patterns of transmission. Between March and December 2023, dried blood spots, demographic data, and travel history were collected from individuals who tested positive for malaria on a rapid diagnostic test (RDT) and from symptomatic RDT-negative individuals across Eswatini. Multiplexed amplicon deep sequencing was used to genotype 12 genes associated with antimalarial resistance, detect histidine-rich protein (hrp) 2/3 deletions, estimate genetic relatedness, and detect non-falciparum species. Data from 437 samples revealed significant clustering of parasites carrying resistance markers. A validated marker of artemisinin partial resistance, kelch13 P553L, was identified in a cluster of four infections (0.9% of all samples), likely linked to importation. The dihydropteroate synthase/dihydrofolate reductase sextuple mutant haplotype, associated with high-level sulfadoxine–pyrimethamine resistance, was found in 7.8% of the samples, also within clusters. The multidrug resistance 1 N86 genotype associated with reduced susceptibility to lumefantrine was nearly fixed. More than 60% of the infections were polyclonal, with higher complexity observed in imported cases. No hrp2/3 deletions were detected; most false-negative RDTs were attributed to subpatent parasitemia. Non-falciparum coinfections were rare (<1%). These findings shed light on the dynamics of resistance emergence in low-transmission settings. Integrating routine genomic surveillance into national malaria programs is essential for detecting, tracking, and responding to resistance threats in countries nearing elimination.
Related
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BibTeX
@article{nhlengethwa2026genomic,
title = {{Genomic Surveillance Reveals Clusters of Plasmodium falciparum Antimalarial Resistance Markers in Eswatini, A Low-Transmission Setting}},
author = {Nomcebo Nhlengethwa and Andrés Aranda-Díaz and Sibonakaliso Vilakati and Alfred Hubbard and Isobel Routledge and Sonja B. Lauterbach and Takalani I. Makhanthisa and Faith De Amaral and Mukosha Chisenga and Brighton Mangena and Chadwick Sikaala and John Chimumbwa and Quinton Dlamini and Jaishree Raman and Jennifer L. Smith and Sabelo V. Dlamini},
journal = {The American Journal of Tropical Medicine and Hygiene},
year = {2026},
month = may,
doi = {10.4269/ajtmh.25-0487},
url = {https://doi.org/10.4269/ajtmh.25-0487},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genomic Surveillance Reveals Clusters of Plasmodium falciparum Antimalarial Resistance Markers in Eswatini, A Low-Transmission Setting
AU - Nomcebo Nhlengethwa
AU - Andrés Aranda-Díaz
AU - Sibonakaliso Vilakati
AU - Alfred Hubbard
AU - Isobel Routledge
AU - Sonja B. Lauterbach
AU - Takalani I. Makhanthisa
AU - Faith De Amaral
AU - Mukosha Chisenga
AU - Brighton Mangena
AU - Chadwick Sikaala
AU - John Chimumbwa
AU - Quinton Dlamini
AU - Jaishree Raman
AU - Jennifer L. Smith
AU - Sabelo V. Dlamini
PY - 2026
DA - 2026/05/19
JO - The American Journal of Tropical Medicine and Hygiene
DO - 10.4269/ajtmh.25-0487
UR - https://doi.org/10.4269/ajtmh.25-0487
AB - The elimination of Plasmodium falciparum malaria in Eswatini remains elusive because of ongoing importation and sustained local transmission. The current status of antimalarial and diagnostic resistance in the country remains unknown. Genomic surveillance can complement routine surveillance by characterizing the prevalence and distribution of resistance markers and revealing granular patterns of transmission. Between March and December 2023, dried blood spots, demographic data, and travel history were collected from individuals who tested positive for malaria on a rapid diagnostic test (RDT) and from symptomatic RDT-negative individuals across Eswatini. Multiplexed amplicon deep sequencing was used to genotype 12 genes associated with antimalarial resistance, detect histidine-rich protein (hrp) 2/3 deletions, estimate genetic relatedness, and detect non-falciparum species. Data from 437 samples revealed significant clustering of parasites carrying resistance markers. A validated marker of artemisinin partial resistance, kelch13 P553L, was identified in a cluster of four infections (0.9% of all samples), likely linked to importation. The dihydropteroate synthase/dihydrofolate reductase sextuple mutant haplotype, associated with high-level sulfadoxine–pyrimethamine resistance, was found in 7.8% of the samples, also within clusters. The multidrug resistance 1 N86 genotype associated with reduced susceptibility to lumefantrine was nearly fixed. More than 60% of the infections were polyclonal, with higher complexity observed in imported cases. No hrp2/3 deletions were detected; most false-negative RDTs were attributed to subpatent parasitemia. Non-falciparum coinfections were rare (<1%). These findings shed light on the dynamics of resistance emergence in low-transmission settings. Integrating routine genomic surveillance into national malaria programs is essential for detecting, tracking, and responding to resistance threats in countries nearing elimination.
SN - 0002-9637
SN - 1476-1645
ER -