Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations

Antimalarial resistance surveillance in sub-Saharan Africa is often constrained by logistical and financial challenges limiting its breadth and frequency. At two sites in Ghana, we have piloted a streamlined sample pooling process created immediately by sequential addition of positive malaria cases at the time of diagnostic testing. This streamlined process involving a single tube minimized clinical and laboratory work and provided accurate frequencies of all known drug resistance mutations after highthroughput targeted sequencing using molecular inversion probes. Our study validates this method as a cost-efficient, accurate and highly-scalable approach for drug resistance mutation monitoring that can potentially be applied to other infectious diseases such as tuberculosis.

Automated summary

Antimalarial resistance surveillance in sub-Saharan Africa faces logistical and financial challenges, but a streamlined sample pooling process piloted in Ghana shows promise in providing accurate drug resistance mutation monitoring. This cost-efficient and highly-scalable approach could potentially be applied to other infectious diseases like tuberculosis.