Molecular assays for antimalarial drug resistance surveillance: A target product profile

Abstract

Antimalarial drug resistance is a major constraint for malaria control and elimination efforts. Artemisinin-based combination therapy is now the mainstay for malaria treatment. However, delayed parasite clearance following treatment with artemisinin derivatives has now spread in the Greater Mekong Sub region and may emerge or spread to other malaria endemic regions. This spread is of great concern for malaria control programmes, as no alternatives to artemisinin-based combination therapies are expected to be available in the near future. There is a need to strengthen surveillance systems for early detection and response to the antimalarial drug resistance threat. Current surveillance is mainly done through therapeutic efficacy studies; however these studies are complex and both time- and resource-intensive. For multiple common antimalarials, parasite drug resistance has been correlated with specific genetic mutations, and the molecular markers associated with antimalarial drug resistance offer a simple and powerful tool to monitor the emergence and spread of resistant parasites. Different techniques to analyse molecular markers associated with antimalarial drug resistance are available, each with advantages and disadvantages. However, procedures are not adequately harmonized to facilitate comparisons between sites. Here we describe the target product profiles for tests to analyse molecular markers associated with antimalarial drug resistance, discuss how use of current techniques can be standardised, and identify the requirements for an ideal product that would allow malaria endemic countries to provide useful spatial and temporal information on the spread of resistance.

Targeted deep amplicon sequencing of kelch 13 and cytochrome b in Plasmodium falciparum isolates from an endemic African country using the Malaria Resistance Surveillance (MaRS) protocol

“…Active surveillance of imported malaria cases is an important public health activity in the USA and the EU [27,28]: it plays a pivotal role in estimating the incidence in imported malaria cases, preventing malaria reintroduction, and providing chemoprophylaxis guidelines to travelers to malaria endemic regions. Historically, anti-malaria drug resistance genotyping was performed using traditional low throughput sequencing methodologies, such as Sanger sequencing [29]. However, currently, next-generation sequencing and accompanying standardized bioinformatics tools provide advanced and rapid protocols for monitoring molecular marker genes involved in P. falciparum drug resistance [24].…”

Proof of concept: Malaria rapid diagnostic tests and massively parallel sequencing for surveillance of molecular markers of antimalarial resistance in Bissau, Guinea-Bissau during 2014-2017

“…Therapeutic efficacy studies are often not feasible due to economic and practical constraints in many settings in Sub-Saharan Africa (SSA). It has been suggested that molecular surveillance of genetic polymorphisms associated with antimalarial resistance could complement therapeutic efficacy studies (4-15) because these can provide early warning signs of decreasing antimalarial efficacy (5). Molecular surveillance only requires sampling of P. falciparum infected blood, which in turn can be acquired from finger prick samples, as used for malaria rapid diagnostic tests (RDTs) (16, 17).…”

Strengthening Surveillance Systems for Malaria Elimination by Integrating Molecular and Genomic Data

“…However, the use of NGS could be centralized to very few sub-regional reference laboratories located in malaria endemic countries [36,83,84]. This requires a lot of effort to develop the capacity not only for sequencing but more importantly for data analysis, a critical part in the path for developing countries to get access to these techniques [85][86][87]. This should be a concerted effort not only from the malaria community but from the global health community, as other diseases such as tuberculosis (TB), human immunodeficiency virus (HIV), and other bacterial and viral infections may benefit as well from these centers of excellence [88].…”