Health Systems Implementation and Molecular Surveillance of Multiple First-Line Treatments for Uncomplicated Malaria in Western Kenya

Spatiotemporal Dynamics of Antimalarial Drug Resistance in Western Kenya During a Pilot Multiple First-line Treatment for Uncomplicated Malaria Study: Molecular Evidence of Resistance Saturation and Emerging Artemisinin Tolerance

This implementation study evaluated the health systems feasibility, economic costs, and stakeholder acceptability of deploying multiple first-line therapies (MFTs) that were of the artemisinin-based combination therapies (ACTs) type, for uncomplicated malaria in Western Kenya. The study included a nested observational molecular surveillance of antimalarial resistance markers in Plasmodium falciparum parasites. The implementation program involved adaptive cycling of four ACTs across 28 health facilities over 28 months (June 2020 - October 2022) with and extension to January 2024 in one geographic area (Mfangano Island). Health systems outcomes (feasibility, costs, acceptability) are reported in Cole et al., Malaria Journal 2024. Molecular surveillance outcomes (resistance marker prevalence and temporal trends) are reported in a companion manuscript currently under peer-review.

BACKGROUND: Artemisinin-based combination therapies (ACTs) are first-line treatment for uncomplicated malaria in sub-Saharan Africa, but emerging artemisinin partial resistance threatens efficacy. Multiple first-line treatments (MFTs) represent a proposed strategy to delay resistance emergence by deploying several ACTs simultaneously, sequentially, or using other strategies rather than relying on a single first-line therapy.

STUDY DESIGN: This 28-month implementation program (June 2020 - October 2022) with and extension only on Mfangano Island until January 2024, deployed adaptive cycling of four artemisinin-based combinations across health facilities in Western Kenya using geographic allocation:

INTERVENTION COUNTY - HOMA BAY:

• Homa Bay Mainland (n=approximately 40,000 patients treated): Sequential deployment with 8-month cycling using crowding-out approach: Baseline (AL) → DHA-PIP (8 months) → AS+AQ (8 months) → AL (8 months)
• Mfangano Island (n=approximately 21,000 patients treated): Extended single MFT deployment: Baseline (AL) → AS+PYD (39 months). This extension allowed longer follow-up surveillance of the most recent combination ACT in Kenya where data was not previously monitored.

COMPARISON COUNTY - MIGORI:

- Continued artemether-lumefantrine (AL) monotherapy throughout study period (n=32,835 patients treated) PARTICIPANTS: Adults and children ≥5 years diagnosed with uncomplicated Plasmodium falciparum malaria at participating health facilities. Excluded: pregnant women and children <5 years due to medication restrictions and lack of pediatric formulations.

OUTCOMES MEASURED:

Primary Outcomes (reported in Cole et al., Malaria Journal 2024):

1. Health systems feasibility was assessed through commodity management, human resources adequacy, information system functionality, and implementation barriers/facilitators analysis
2. Economic costs of MFT deployment including start-up and implementation phases, calculated per facility and per patient were sought after
3. Stakeholder acceptability among policymakers, healthcare workers, and patients assessed through key informant interviews and surveys was analyzed.

Secondary Outcomes (reported in companion manuscript recently submitted for peer-review):

1. Prevalence of antimalarial resistance markers in dhfr (N51I, C59R, S108N, I164L), dhps (S436H, A437G, K540E, A581G), mdr1 (N86Y, Y184F), and k13 (A578S, A675V) genes
2. Temporal trends in resistance marker prevalence over four timepoints (September 2020, August-October 2021, May-July 2022, November 2023-January 2024)
3. Geographic distribution of resistance patterns across study sites
4. Complexity of infection (COI) determined by molecular methods

METHODS:

• Sample collection: Dried blood spots (n=310) from malaria-positive patients at four timepoints
• Molecular analysis: Targeted amplicon deep sequencing using Oxford Nanopore Technology
• Health systems assessment: Semi-structured questionnaires, key informant interviews, exit interviews, cost analysis using activity-based costing
• Statistical analysis: Chi-square tests, Cochran-Armitage trend tests, machine learning models for resistance prediction SETTING: Government and faith-based health facilities in Homa Bay County facilities received MFTs and Migori County (control) where AL was the only ACT used in Western Kenya, a malaria-endemic region with high transmission intensity.

ETHICAL APPROVAL: Strathmore University Institutional Scientific and Ethics Review Committee (SU-ISERC 1730/20) and Kenya National Commission for Science, Technology and Innovation (NACOSTI).

Inclusion Criteria:

• Age 5 years or older
• Clinical diagnosis of uncomplicated malaria
• Confirmed Plasmodium falciparum infection by rapid diagnostic test (RDT) or microscopy
• Presenting at participating health facility for malaria treatment
• Able and willing to provide informed consent (or parental/guardian consent for minors under 18 years)
• Resident of study catchment area
• For molecular surveillance substudy: willingness to provide dried blood spot sample

Exclusion Criteria:

• Pregnant women (due to contraindications for some study medications in first trimester and lack of safety data)
• Children under 5 years of age (due to lack of pediatric formulations for some study medications)
• Severe or complicated malaria requiring parenteral treatment or hospitalization
• Known hypersensitivity or contraindication to any of the study artemisinin-based combination therapies
• Unable to take oral medications
• Previous participation in current treatment episode (repeat visits)
• Concurrent participation in other interventional malaria treatment studies