Search for genetic determinants of Plasmodium falciparum malaria drug resistance in vitro and in vivo

Malaria remains the most deadly disease in the world with nearly 627 000 deaths and more than 200 million new clinical cases every year, the large majority occurring in sub Saharan Africa children aged < 5 years. This represents anyway a significant decrease as compared with the situation in the start of the Millennium. This is due in part to the worldwide adoption of artemisinin-based combination therapy (ACT). However these gains are being threatened. A pattern of progressive decreased susceptibility of the parasite to the ACT key drugs, the artemisinin derivatives is emerging. Another central drug is quinine, still the mainstay for the treatment of severe malaria in Africa. The aim of this thesis was to contribute to the understanding of the genetic determinants of Plasmodium falciparum resistance to two key short half-life antimalarials, quinine and artesunate and to assess the parasite susceptibility to these drugs in Mali. In a clinical study on the efficacy of quinine 100% of severe Plasmodium falciparum infected patients were cured. For the first time, the pfnhe1 microsatellite allele ms4760-1, previously proposed to be involved with parasite in vitro resistance to this drug was selected post treatment pointing for this marker as also involved in the in vivo sensitivity of the parasite to quinine. Conversely, t he ms4760 status of the initial infections was not predictive of the clinical outcome, leading to the conclusion that the ms4760-1 is likely a secondary factor of quinine resistance. The pfcrt K76T SNP was not shown to be under selection. In conclusion, albeit pfnhe1 has an undeniable contribution to the parasite response in vivo, other factors must be involved, supporting the view of quinine resistance as a complex multigenic trait. P. falciparum decreased sensitivity to artemisinin and its derivatives have been recently reported in SE Asia, including Thailand. We therefore performed an explorative study based on the determination of the in vitro sensitivity (IC 50 ) of 47 culture adapted parasites from Mae Sot (Thai-Myanmar boarder) to a number of ACT drugs. These included artemisinin and dihydroartemisinin (DHA), the key metabolite of both artemether and artesunate. The open reading frames of the drug transporter genes pfcrt, pfmdr1, pfmrp1 and pfmrp2 were further studied. Correlation analyses revealed two novel candidate markers of multidrug resistance: the pfmdr1 F1226Y and pfmrp1 F1390I SNPs, which were associated with 2-3 fold, increases in the IC50 s of artemisinin and also the ACT partner drugs lumefantrine and mefloquine. An artesunate monotherapy (7 days) efficacy trial was performed at Malian malaria setting with the objective of detecting possible delayed P. falciparum clearance phenotypes, an early sign of decreased drug susceptibility. The microscopic based assessment of the infections did not reveal any extended parasitaemia clearance times with a median clearance time of 32 hours. Nevertheless there were clear int er-individual differences in the clearance dynamics. Recently, SNPs in the P.falciparum K13 propeller gene has been proposed to be markers of artemisinin resistance, i.e. of significantly increased clearance time in SE Asia. We therefore studied the polymorphisms in this gene in Mali and any possible association with the range of clearance times observed above. In addition, a set of samples from a previous cross section survey study, conducted prior to ACTs implementation, were analyzed in order to try to detect temporal changes in the sequence of the K13 propeller gene. The SE Asian mutations associated with artemisinin resistance were not found in Mali in any of the periods. Nevertheless, the K13 gene was found to be polymorphic in Mali even before the wide use of ACTs. No association was however found between polymorphism and parasite clearance rate. Interestingly, the SNPs found in the early cross-sectional study were different from those found in the later study . Further, the later study revealed mutations present near one of the key a.a. positions linked with resistance in Asia. These patterns merit further investigations. Finally, a new qPCR based approach was used to revisit the artesunate monotherapy study. This had the aim of increasing the sensitivity of parasite detection, in order to obtain an improved phenotype of parasite clearance, and hence improved conditions to search for a correlation between the presence of K13 mutation and the trend of prolonged parasite clearance. No clear association could be found even though the qPCR approach was able to find evidence of parasites 72 hours after artesunate treatment in more than 46% of infections previously considered as cleared by microscopy. Intriguingly no mutations in the K13 propeller gene were found among the parasites classified as fast clearers by this method (parasites cleared at 24 hours after treatment). The result of the clinical trials showed high in vivo efficacies for both artesunate and quinine. However, this situation can rapidly change, as demonstrated by the recent emergence of artemisinin resistance in Asia. Molecular monitoring of any possible evolution and selection of antimalarial drug tolerance/resistance associated polymorphisms of genes such as Pfnhe-1 or K13 propeller are critical for optimal drug policies and sustained efficacy

Efficacy of chloroquine, amodiaquine and sulphadoxine-pyrimethamine for the treatment of uncomplicated falciparum malaria: revisiting molecular markers in an area of emerging AQ and SP resistance in Mali

<p>Abstract</p> <p>Background</p> <p>To update the National Malaria Control Programme of Mali on the efficacy of chloroquine, amodiaquine and sulphadoxine-pyrimethamine in the treatment of uncomplicated <it>falciparum </it>malaria.</p> <p>Methods</p> <p>During the malaria transmission seasons of 2002 and 2003, 455 children – between six and 59 months of age, with uncomplicated malaria in Kolle, Mali, were randomly assigned to one of three treatment arms. <it>In vivo </it>outcomes were assessed using WHO standard protocols. Genotyping of <it>msp1</it>, <it>msp2 </it>and CA1 polymorphisms were used to distinguish reinfection from recrudescent parasites (molecular correction).</p> <p>Results</p> <p>Day 28 adequate clinical and parasitological responses (ACPR) were 14.1%, 62.3% and 88.9% in 2002 and 18.2%, 60% and 85.2% in 2003 for chloroquine, amodiaquine and sulphadoxine-pyrimethamine, respectively. After molecular correction, ACPRs (cACPR) were 63.2%, 88.5% and 98.0% in 2002 and 75.5%, 85.2% and 96.6% in 2003 for CQ, AQ and SP, respectively. Amodiaquine was the most effective on fever. Amodiaquine therapy selected molecular markers for chloroquine resistance, while in the sulphadoxine-pyrimethamine arm the level of <it>dhfr </it>triple mutant and <it>dhfr</it>/<it>dhps </it>quadruple mutant increased from 31.5% and 3.8% in 2002 to 42.9% and 8.9% in 2003, respectively. No infection with <it>dhps </it>540E was found.</p> <p>Conclusion</p> <p>In this study, treatment with sulphadoxine-pyrimethamine emerged as the most efficacious on uncomplicated falciparum malaria followed by amodiaquine. The study demonstrated that sulphadoxine-pyrimethamine and amodiaquine were appropriate partner drugs that could be associated with artemisinin derivatives in an artemisinin-based combination therapy.</p

Genome-wide SNP analysis of Plasmodium falciparum shows differentiation at drug-resistance-associated loci among malaria transmission settings in southern Mali.

Plasmodium falciparum malaria cases in Africa represent over 90% of the global burden with Mali being amongst the 11 highest burden countries that account for 70% of this annual incidence. The persistence of P. falciparum despite massive global interventions is because of its genetic diversity that drives its ability to adapt to environmental changes, develop resistance to drugs, and evade the host immune system. Knowledge on P. falciparum genetic diversity across populations and intervention landscape is thus critical for the implementation of new strategies to eliminate malaria. This study assessed genetic variation with 12,177 high-quality SNPs from 830 Malian P. falciparum isolates collected between 2007 and 2017 from seven locations. The complexity of infections remained high, varied between sites, and showed a trend toward overall decreasing complexity over the decade. Though there was no significant substructure, allele frequencies varied geographically, partly driven by temporal variance in sampling, particularly for drug resistance and antigen loci. Thirty-two mutations in known drug resistance markers (pfcrt, pfdhps, pfdhfr, pfmdr1, pfmdr2, and pfk13) attained a frequency of at least 2% in the populations. SNPs within and around the major markers of resistance to quinolines (pfmdr1 and pfcrt) and antifolates (pfdhfr and pfdhps) varied temporally and geographically, with strong linkage disequilibrium and signatures of directional selection in the genome. These geo-temporal populations also differentiated at alleles in immune-related loci, including, protein E140, pfsurfin8, pfclag8, and pfceltos, as well as pftrap, which showed signatures of haplotype differentiation between populations. Several regions across the genomes, including five known drug resistance loci, showed signatures of differential positive selection. These results suggest that drugs and immune pressure are dominant selective forces against P. falciparum in Mali, but their effect on the parasite genome varies temporally and spatially. Interventions interacting with these genomic variants need to be routinely evaluated as malaria elimination strategies are implemented

Different Plasmodium falciparum clearance times in two Malian villages following artesunate monotherapy.

BACKGROUND: Artemisinin resistance described as increased parasite clearance time (PCT) is rare in Africa. More sensitive methods such as qPCR might better characterize the clearance phenotype in sub-Saharan Africa. METHODS: PCT is explored in Mali using light microscopy and qPCR after artesunate for uncomplicated malaria. In two villages, patients were followed for 28 days. Blood smears and spots were collected respectively for microscopy and qPCR. Parasitemia slope half-life was calculated after microscopy. Patient residual parasitemia were measured by qPCR. RESULTS: Uncorrected adequate clinical and parasitological responses (ACPR) observed in Faladje and Bougoula-Hameau were 78% and 92%, respectively (p=0.01). This reached 100% for both after molecular correction. Proportions of 24H microscopy positive patients in Faladje and Bougoula-Hameau were 97.2% and 72%, respectively (p<0.0001). Slope half-life was 2.8h in Faladje vs 2H in Bougoula-Hameau (p<0.001) and Proportions of 72H patients with residual parasitemia were 68.5% and 40% in Faladje and Bougoula-Hameau, respectively (p=0.003). The mean residual parasitemia was 2.9 in Faladje vs. 0.008 in Bougoula-Hameau (p=0.002). Although artesunate is efficacious in Mali, the longer parasite clearance time with submicroscopic parasitemia observed may represent early signs of developing P. falciparum resistance to artemisinins

Quinine Treatment Selects the pfnhe-1 ms4760-1 Polymorphism in Malian Patients with Falciparum Malaria

Background. The mechanism of Plasmodium falciparum resistance to quinine is not known. In vitro quantitative trait loci mapping suggests involvement of a predicted P. falciparum sodium-hydrogen exchanger (pfnhe-1) on chromosome 13. Methods. We conducted prospective quinine efficacy studies in 2 villages, Kolle and Faladie, Mali. Cases of clinical malaria requiring intravenous therapy were treated with standard doses of quinine and followed for 28 days. Treatment outcomes were classified using modified World Health Organization protocols. Molecular markers of parasite polymorphisms were used to distinguish recrudescent parasites from new infections. The prevalence of pfnhe-1 ms4760-1 among parasites before versus after quinine treatment was determined by direct sequencing. Results. Overall, 163 patients were enrolled and successfully followed. Without molecular correction, the mean adequate clinical and parasitological response (ACPR) was 50.3% (n = 163). After polymerase chain reaction correction to account for new infections, the corrected ACPR was 100%. The prevalence of ms4760-1 increased significantly, from 26.2% (n = 107) before quinine treatment to 46.3% (n = 54) after therapy (P = .01). In a control sulfadoxine-pyrimethamine study, the prevalence of ms4760-1 was similar before and after treatment. Conclusions. This study supports a role for pfnhe-1 in decreased susceptibility of P. falciparum to quinine in the field.Howard Hughes Medical Institute [55005502]; Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health; European and Developing Countries Clinical Trials Partnership [EDCTP IP_07_31060_002]info:eu-repo/semantics/publishedVersio

Novel Polymorphisms in Plasmodium falciparum ABC Transporter Genes Are Associated with Major ACT Antimalarial Drug Resistance

Chemotherapy is a critical component of malaria control. However, the most deadly malaria pathogen, Plasmodium falciparum, has repeatedly mounted resistance against a series of antimalarial drugs used in the last decades. Southeast Asia is an epicenter of emerging antimalarial drug resistance, including recent resistance to the artemisinins, the core component of all recommended antimalarial combination therapies. Alterations in the parasitic membrane proteins Pgh-1, PfCRT and PfMRP1 are believed to be major contributors to resistance through decreasing intracellular drug accumulation. The pfcrt, pfmdr1 and pfmrp1 genes were sequenced from a set of P.falciparum field isolates from the Thai-Myanmar border. In vitro drug susceptibility to artemisinin, dihydroartemisinin, mefloquine and lumefantrine were assessed. Positive correlations were seen between the in vitro susceptibility responses to artemisinin and dihydroartemisinin and the responses to the arylamino-alcohol quinolines lumefantrine and mefloquine. The previously unstudied pfmdr1 F1226Y and pfmrp1 F1390I SNPs were associated significantly with artemisinin, mefloquine and lumefantrine in vitro susceptibility. A variation in pfmdr1 gene copy number was also associated with parasite drug susceptibility of artemisinin, mefloquine and lumefantrine. Our work unveils new candidate markers of P. falciparum multidrug resistance in vitro, while contributing to the understanding of subjacent genetic complexity, essential for future evidence-based drug policy decisions

Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website

Table1_Genome-wide SNP analysis of Plasmodium falciparum shows differentiation at drug-resistance-associated loci among malaria transmission settings in southern Mali

Plasmodium falciparum malaria cases in Africa represent over 90% of the global burden with Mali being amongst the 11 highest burden countries that account for 70% of this annual incidence. The persistence of P. falciparum despite massive global interventions is because of its genetic diversity that drives its ability to adapt to environmental changes, develop resistance to drugs, and evade the host immune system. Knowledge on P. falciparum genetic diversity across populations and intervention landscape is thus critical for the implementation of new strategies to eliminate malaria. This study assessed genetic variation with 12,177 high-quality SNPs from 830 Malian P. falciparum isolates collected between 2007 and 2017 from seven locations. The complexity of infections remained high, varied between sites, and showed a trend toward overall decreasing complexity over the decade. Though there was no significant substructure, allele frequencies varied geographically, partly driven by temporal variance in sampling, particularly for drug resistance and antigen loci. Thirty-two mutations in known drug resistance markers (pfcrt, pfdhps, pfdhfr, pfmdr1, pfmdr2, and pfk13) attained a frequency of at least 2% in the populations. SNPs within and around the major markers of resistance to quinolines (pfmdr1 and pfcrt) and antifolates (pfdhfr and pfdhps) varied temporally and geographically, with strong linkage disequilibrium and signatures of directional selection in the genome. These geo-temporal populations also differentiated at alleles in immune-related loci, including, protein E140, pfsurfin8, pfclag8, and pfceltos, as well as pftrap, which showed signatures of haplotype differentiation between populations. Several regions across the genomes, including five known drug resistance loci, showed signatures of differential positive selection. These results suggest that drugs and immune pressure are dominant selective forces against P. falciparum in Mali, but their effect on the parasite genome varies temporally and spatially. Interventions interacting with these genomic variants need to be routinely evaluated as malaria elimination strategies are implemented