Dissecting the molecular basis of PfCRT-mediated antimalarial drug resistance

The protozoan parasite Plasmodium falciparum is responsible for the deadliest form of malaria, which causes 584,000 fatalities annually and whose complications include coma, anemia, respiratory distress, and renal failure. Although malaria eradication efforts were hindered by the rise of chloroquine (CQ) resistance (CQR), CQ continues to be clinically deployed in resistance-free regions. CQR is primarily mediated by mutations in the P. falciparum chloroquine resistance transporter (pfcrt) gene, which also modulates parasite susceptibility to first-line artemisinin-based combination therapies (ACTs). In certain geographical regions (e.g. Africa), mutant pfcrt alleles display considerable fitness costs and have undergone attrition in the absence of CQ pressure. Surveillance of resistant field isolates presently centers on the PfCRT mutation K76T, ubiquitous among CQ-resistant parasites and always accompanied by ≥3 additional mutations. Despite the global adoption of K76T as a molecular marker of CQR, the contributions of this and other mutations to P. falciparum drug resistance versus fitness had not been previously defined. AIMS: We aimed to address the following: (1) Do PfCRT mutations beyond PfCRT K76T directly contribute to CQR? (2) Do PfCRT mutations contribute to parasite fitness during the pathogenic asexual blood stage? (3) Are there predictable mutational paths in the evolution of pfcrt-mediated drug resistance? (4) How do PfCRT mutations impact current antimalarials, including the first-line ACTs? APPROACH: Using zinc finger nucleases, we generated isogenic, pfcrt-modified blood-stage P. falciparum parasites encoding wild-type (CQ-sensitive) or variant PfCRT haplotypes. Variants included a combinatorial library of alleles harboring 1-4 mutations comprising the simplest CQ-resistant haplotype (Ecu1110). Additional genetic dissections of full-length or partial pfcrt alleles encompassed the most common variants found in Africa and Asia, including a unique fitness-neutral mutant allele (Cam734) that has undergone expansion in Southeast Asia. Parasite antimalarial drug susceptibility was determined using IC50-based (cytostatic) assays or parasite survival-based (cytocidal) assays and was combined with data from flow cytometric parasite growth competition assays to computationally model mutant pfcrt evolution. To further define the biochemical impacts of PfCRT mutations, our studies leveraged metabolomic, heme fractionation, and drug transport studies. RESULTS: Key findings emerging from our studies included the following: (1) PfCRT K76T is insufficient for CQR and an inaccessible first mutational step in pfcrt evolution; (2) Alongside proliferation rates, parasite resistance gains dictate a constrained pfcrt mutational landscape and predict important roles for the active metabolites of CQ and amodiaquine in guiding pfcrt evolution; (3) To various degrees, PfCRT polymorphisms beyond K76T increase the potency of both the artemisinin and partner drug components of first-line ACT regimens; (4) Emerging PfCRT mutations (e.g. A144F) directly contribute to the enhanced fitness of pfcrt alleles and are necessary for multidrug resistance, independent of K76T. CONCLUSIONS: Our studies uncovered multiple pleiotropic contributions of PfCRT mutations to antimalarial drug resistance, countering earlier dogma that non-K76T mutations are merely compensatory. Evolutionary modeling revealed parasites’ ability to navigate constrained mutational landscapes and evolve drug resistance via rare mutational bursts. These results collectively highlight the capacity of PfCRT to acquire novel mutations that successfully balance parasite multidrug resistance with the essential role of PfCRT in maintaining digestive vacuole physiology. Our studies are of direct relevance to the regional recommendations of antimalarials, whose activity is influenced by, and in certain cases enhanced against, pfcrt-mutant parasites

Evolution of Fitness Cost-Neutral Mutant PfCRT Conferring P. falciparum 4-Aminoquinoline Drug Resistance Is Accompanied by Altered Parasite Metabolism and Digestive Vacuole Physiology

Southeast Asia is an epicenter of multidrug-resistant Plasmodium falciparum strains. Selective pressures on the subcontinent have recurrently produced several allelic variants of parasite drug resistance genes, including the P. falciparum chloroquine resistance transporter (pfcrt). Despite significant reductions in the deployment of the 4-aminoquinoline drug chloroquine (CQ), which selected for the mutant pfcrt alleles that halted CQ efficacy decades ago, the parasite pfcrt locus is continuously evolving. This is highlighted by the presence of a highly mutated allele, Cam734 pfcrt, which has acquired the singular ability to confer parasite CQ resistance without an associated fitness cost. Here, we used pfcrt-specific zinc-finger nucleases to genetically dissect this allele in the pathogenic setting of asexual blood-stage infection. Comparative analysis of drug resistance and growth profiles of recombinant parasites that express Cam734 or variants thereof, Dd2 (the most common Southeast Asian variant), or wild-type pfcrt, revealed previously unknown roles for PfCRT mutations in modulating parasite susceptibility to multiple antimalarial agents. These results were generated in the GC03 strain, used in multiple earlier pfcrt studies, and might differ in natural isolates harboring this allele. Results presented herein show that Cam734-mediated CQ resistance is dependent on the rare A144F mutation that has not been observed beyond Southeast Asia, and reveal distinct impacts of this and other Cam734-specific mutations on CQ resistance and parasite growth rates. Biochemical assays revealed a broad impact of mutant PfCRT isoforms on parasite metabolism, including nucleoside triphosphate levels, hemoglobin catabolism and disposition of heme, as well as digestive vacuole volume and pH. Results from our study provide new insights into the complex molecular basis and physiological impact of PfCRT-mediated antimalarial drug resistance, and inform ongoing efforts to characterize novel pfcrt alleles that can undermine the efficacy of first-line antimalarial drug regimens

Staphylococcus aureus small colony variants impair host immunity by activating host cell glycolysis and inducing necroptosis

Staphylococcus aureus small colony variants (SCVs) are frequently associated with chronic infection, yet they lack expression of many virulence determinants associated with the pathogenicity of wild-type strains. We found that both wild-type S. aureus and a ΔhemB SCV prototype potently activate glycolysis in host cells. Glycolysis and the generation of mitochondrial reactive oxygen species were sufficient to induce necroptosis, a caspase-independent mechanism of host cell death that failed to eradicate S. aureus and instead promoted ΔhemB SCV pathogenicity. To support ongoing glycolytic activity, the ΔhemB SCV induced over a 100-fold increase in the expression of fumC, which encodes an enzyme that catalyses the degradatin of fumarate, an inhibitor of glycolysis. Consistent with fumC-dependent depletion of local fumarate, the ΔhemB SCV failed to elicit trained immunity and protection from a secondary infectious challenge in the skin. The reliance of the S. aureus SCV population on glycolysis accounts for much of its role in the pathogenesis of S. aureus skin infection

Global Spread of Mutant PfCRT and Its Pleiotropic Impact on Plasmodium falciparum Multidrug Resistance and Fitness

Our study defines the allelic distribution of pfcrt, an important mediator of multidrug resistance in Plasmodium falciparum, in Africa and Asia. We leveraged whole-genome sequence analysis and gene editing to demonstrate how current drug combinations can select different allelic variants of this gene and shape region-specific parasite population structures. We document the ability of PfCRT mutations to modulate parasite susceptibility to current antimalarials in dissimilar, pfcrt allele-specific ways. This study underscores the importance of actively monitoring pfcrt genotypes to identify emerging patterns of multidrug resistance and help guide region-specific treatment options.The global spread of Plasmodium falciparum chloroquine resistance transporter (PfCRT) variant haplotypes earlier caused the widespread loss of chloroquine (CQ) efficacy. In Asia, novel PfCRT mutations that emerged on the Dd2 allelic background have recently been implicated in high-level resistance to piperaquine, and N326S and I356T have been associated with genetic backgrounds in which resistance emerged to artemisinin derivatives. By analyzing large-scale genome sequencing data, we report that the predominant Asian CQ-resistant Dd2 haplotype is undetectable in Africa. Instead, the GB4 and previously unexplored Cam783 haplotypes predominate, along with wild-type, drug-sensitive PfCRT that has reemerged as the major haplotype. To interrogate how these alleles impact drug susceptibility, we generated pfcrt-modified isogenic parasite lines spanning the mutational interval between GB4 and Dd2, which includes Cam783 and involves amino acid substitutions at residues 326 and 356. Relative to Dd2, the GB4 and Cam783 alleles were observed to mediate lower degrees of resistance to CQ and the first-line drug amodiaquine, while resulting in higher growth rates. These findings suggest that differences in growth rates, a surrogate of parasite fitness, influence selection in the context of African infections that are frequently characterized by high transmission rates, mixed infections, increased immunity, and less recourse to treatment. We also observe that the Asian Dd2 allele affords partial protection against piperaquine yet does not directly impact artemisinin efficacy. Our results can help inform the regional recommendations of antimalarials, whose activity is influenced by and, in certain cases, enhanced against select PfCRT variant haplotypes

Combinatorial Genetic Modeling of pfcrt

The emergence of drug resistance continuously threatens global control of infectious diseases, including malaria caused by the protozoan parasite Plasmodium falciparum. A critical parasite determinant is the P. falciparum chloroquine resistance transporter (PfCRT), the primary mediator of chloroquine (CQ) resistance (CQR), and a pleiotropic modulator of susceptibility to several first-line artemisinin-based combination therapy partner drugs. Aside from the validated CQR molecular marker K76T, P. falciparum parasites have acquired at least three additional pfcrt mutations, whose contributions to resistance and fitness have been heretofore unclear. Focusing on the quadruple-mutant Ecuadorian PfCRT haplotype Ecu1110 (K76T/A220S/N326D/I356L), we genetically modified the pfcrt locus of isogenic, asexual blood stage P. falciparum parasites using zinc-finger nucleases, producing all possible combinations of intermediate pfcrt alleles. Our analysis included the related quintuple-mutant PfCRT haplotype 7G8 (Ecu1110 + C72S) that is widespread throughout South America and the Western Pacific. Drug susceptibilities and in vitro growth profiles of our combinatorial pfcrt-modified parasites were used to simulate the mutational trajectories accessible to parasites as they evolved CQR. Our results uncover unique contributions to parasite drug resistance and growth for mutations beyond K76T and predict critical roles for the CQ metabolite monodesethyl-CQ and the related quinoline-type drug amodiaquine in driving mutant pfcrt evolution. Modeling outputs further highlight the influence of parasite proliferation rates alongside gains in drug resistance in dictating successful trajectories. Our findings suggest that P. falciparum parasites have navigated constrained pfcrt adaptive landscapes by means of probabilistically rare mutational bursts that led to the infrequent emergence of pfcrt alleles in the field

Balancing drug resistance and growth rates via compensatory mutations in the Plasmodium falciparum chloroquine resistance transporter

The widespread use of chloroquine to treat Plasmodium falciparum infections has resulted in the selection and dissemination of variant haplotypes of the primary resistance determinant PfCRT. These haplotypes have encountered drug pressure and within-hos

Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt.

Comment in : Fusion of field studies and the laboratory solves a puzzle in antimalarial resistance. [Proc Natl Acad Sci U S A. 2015]International audienceIn regions with high malaria endemicity, the withdrawal of chloroquine (CQ) as first-line treatment of Plasmodium falciparum infections has typically led to the restoration of CQ susceptibility through the reexpansion of the wild-type (WT) allele K76 of the chloroquine resistance transporter gene (pfcrt) at the expense of less fit mutant alleles carrying the CQ resistance (CQR) marker K76T. In low-transmission settings, such as South America, drug resistance mutations can attain 100% prevalence, thereby precluding the return of WT parasites after the complete removal of drug pressure. In French Guiana, despite the fixation of the K76T allele, the prevalence of CQR isolates progressively dropped from >90% to <30% during 17 y after CQ withdrawal in 1995. Using a genome-wide association study with CQ-sensitive (CQS) and CQR isolates, we have identified a single mutation in pfcrt encoding a C350R substitution that is associated with the restoration of CQ susceptibility. Genome editing of the CQR reference strain 7G8 to incorporate PfCRT C350R caused a complete loss of CQR. A retrospective molecular survey on 580 isolates collected from 1997 to 2012 identified all C350R mutant parasites as being CQS. This mutation emerged in 2002 and rapidly spread throughout the P. falciparum population. The C350R allele is also associated with a significant decrease in piperaquine susceptibility in vitro, suggesting that piperaquine pressure in addition to potential fitness costs associated with the 7G8-type CQR pfcrt allele may have selected for this mutation. These findings have important implications for understanding the evolutionary dynamics of antimalarial drug resistance