Molecular surveillance for operationally relevant genetic polymorphisms in Plasmodium falciparum in Southern Chad, 2016–2017

Abstract

Background Resistance to anti-malarials is a serious threat to the efforts to control and eliminate malaria. Surveillance based on simple field protocols with centralized testing to detect molecular markers associated with anti-malarial drug resistance can be used to identify locations where further investigations are needed. Methods Dried blood spots were collected from 398 patients (age range 5–59 years, 99% male) with Plasmodium falciparum infections detected using rapid diagnostic tests over two rounds of sample collection conducted in 2016 and 2017 in Komé, South-West Chad. Specimens were genotyped using amplicon sequencing or qPCR for validated markers of anti-malarial resistance including partner drugs used in artemisinin-based combination therapy (ACT). Results No mutations in the pfk13 gene known to be associated with artemisinin resistance were found but a high proportion of parasites carried other mutations, specifically K189T (190/349, 54.4%, 95%CI 49.0–59.8%). Of 331 specimens successfully genotyped for pfmdr1 and pfcrt, 52% (95%CI 46.4–57.5%) carried the NFD-K haplotype, known to be associated with reduced susceptibility to lumefantrine. Only 20 of 336 (6.0%, 95%CI 3.7–9.0%) had parasites with the pfmdr1-N86Y polymorphism associated with increased treatment failures with amodiaquine. Nearly all parasites carried at least one mutation in pfdhfr and/or pfdhps genes but ‘sextuple’ mutations in pfdhfr—pfdhps including pfdhps -A581G were rare (8/336 overall, 2.4%, 95%CI 1.2–4.6%). Only one specimen containing parasites with pfmdr1 gene amplification was detected. Conclusions These results provide information on the likely high efficacy of artemisinin-based combinations commonly used in Chad, but suggest decreasing levels of sensitivity to lumefantrine and high levels of resistance to sulfadoxine-pyrimethamine used for seasonal malaria chemoprevention and intermittent preventive therapy in pregnancy. A majority of parasites had mutations in the pfk13 gene, none of which are known to be associated with artemisinin resistance. A therapeutic efficacy study needs to be conducted to confirm the efficacy of artemether-lumefantrine.

Therapeutic efficacy of artesunate–amodiaquine and artemether–lumefantrine for the treatment of uncomplicated falciparum malaria in Chad: clinical and genetic surveillance

“…Most of the parasites carried the pfcrt wild type allele (79% to 89%). The proportion of pfcrt variant associated with resistance to chloroquine (CVIET, 11.2%) remains similar to previous report in 2016 (8/191, 4.2%) [ 50 ] and relatively low compared to other regions such as Ethiopia [ 51 ], Democratic Republic of the Congo [ 52 ], Equatorial Guinea [ 53 ], and Liberia [ 38 ]. For pfmdr-1 gene, the single 184F mutation, which is suspected to be involved in recrudescent infections after AL treatment, was highly frequent in Chad as usually reported in numerous African settings such as Ghana [ 54 ], Uganda [ 55 ], Madagascar [ 56 ], Tanzania [ 57 ], and Equatorial Guinea [ 58 ].…”

Meta-analysis on Plasmodium falciparum sulfadoxine-pyrimethamine resistance-conferring mutations in India identifies hot spots for genetic surveillance

“…These include districts classified into 5 clusters where a continuous vigil is warranted: AN, AP, AR, AS, CG, HA, MP, NA, OD, TR, UP and WB. Evidence from such malaria genetic surveillance 44,45,46,47,48 may be used as a reference model to develop a framework in India. Countries aiming malaria elimination have been strongly advised to adopt genetic surveillance as an intervention.…”