1
|
Affiliation(s)
- Ian M Hastings
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| |
Collapse
|
2
|
Abstract
Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.
Collapse
Affiliation(s)
- Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| |
Collapse
|
3
|
Plasmodium berghei K13 Mutations Mediate In Vivo Artemisinin Resistance That Is Reversed by Proteasome Inhibition. mBio 2020; 11:mBio.02312-20. [PMID: 33173001 PMCID: PMC7667033 DOI: 10.1128/mbio.02312-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent successes in malaria control have been seriously threatened by the emergence of Plasmodium falciparum parasite resistance to the frontline artemisinin drugs in Southeast Asia. P. falciparum artemisinin resistance is associated with mutations in the parasite K13 protein, which associates with a delay in the time required to clear the parasites upon drug treatment. Gene editing technologies have been used to validate the role of several candidate K13 mutations in mediating P. falciparum artemisinin resistance in vitro under laboratory conditions. Nonetheless, the causal role of these mutations under in vivo conditions has been a matter of debate. Here, we have used CRISPR/Cas9 gene editing to introduce K13 mutations associated with artemisinin resistance into the related rodent-infecting parasite, Plasmodium berghei. Phenotyping of these P. berghei K13 mutant parasites provides evidence of their role in mediating artemisinin resistance in vivo, which supports in vitro artemisinin resistance observations. However, we were unable to introduce some of the P. falciparum K13 mutations (C580Y and I543T) into the corresponding amino acid residues, while other introduced mutations (M476I and R539T equivalents) carried pronounced fitness costs. Our study provides evidence of a clear causal role of K13 mutations in modulating susceptibility to artemisinins in vitro and in vivo using the well-characterized P. berghei model. We also show that inhibition of the P. berghei proteasome offsets parasite resistance to artemisinins in these mutant lines. The recent emergence of Plasmodium falciparum parasite resistance to the first line antimalarial drug artemisinin is of particular concern. Artemisinin resistance is primarily driven by mutations in the P. falciparum K13 protein, which enhance survival of early ring-stage parasites treated with the artemisinin active metabolite dihydroartemisinin in vitro and associate with delayed parasite clearance in vivo. However, association of K13 mutations with in vivo artemisinin resistance has been problematic due to the absence of a tractable model. Herein, we have employed CRISPR/Cas9 genome editing to engineer selected orthologous P. falciparum K13 mutations into the K13 gene of an artemisinin-sensitive Plasmodium berghei rodent model of malaria. Introduction of the orthologous P. falciparum K13 F446I, M476I, Y493H, and R539T mutations into P. berghei K13 yielded gene-edited parasites with reduced susceptibility to dihydroartemisinin in the standard 24-h in vitro assay and increased survival in an adapted in vitro ring-stage survival assay. Mutant P. berghei K13 parasites also displayed delayed clearance in vivo upon treatment with artesunate and achieved faster recrudescence upon treatment with artemisinin. Orthologous C580Y and I543T mutations could not be introduced into P. berghei, while the equivalents of the M476I and R539T mutations resulted in significant growth defects. Furthermore, a Plasmodium-selective proteasome inhibitor strongly synergized dihydroartemisinin action in these P. berghei K13 mutant lines, providing further evidence that the proteasome can be targeted to overcome artemisinin resistance. Taken together, our findings provide clear experimental evidence for the involvement of K13 polymorphisms in mediating susceptibility to artemisinins in vitro and, most importantly, under in vivo conditions.
Collapse
|
4
|
Rebelo M, Pawliw R, Gower J, Webb L, Mitchell H, Pava Z, Watts RE, Davenport MP, McCarthy JS, Khoury DS. Parasite Viability as a Superior Measure of Antimalarial Drug Activity in Humans. J Infect Dis 2020; 223:2154-2163. [PMID: 33119072 DOI: 10.1093/infdis/jiaa678] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Artemisinin derivatives are the leading class of antimalarial drugs due to their rapid onset of action and rapid clearance of circulating parasites. The parasite clearance half-life measures the rate of loss of parasites from blood after treatment, and this is currently used to assess antimalarial activity of novel agents and to monitor resistance. However, a number of recent studies have challenged the use of parasite clearance to measure drug activity, arguing that many circulating parasites may be nonviable. METHODS Plasmodium falciparum-infected subjects (n = 10) in a malaria volunteer infection study were administered a single dose of artesunate (2 mg/kg). Circulating parasite concentration was assessed by means of quantitative polymerase chain reaction (qPCR). Parasite viability after artesunate administration was estimated by mathematical modeling of the ex vivo growth of parasites collected from subjects. RESULTS We showed that in artemisinin-sensitive infection, viable parasites declined to <0.1% of baseline within 8 hours after artesunate administration, while the total number of circulating parasites measured with quantitative polymerase chain reaction remained unchanged. In artemisinin-resistant infections over the same interval, viable parasites declined to 51.4% (standard error of the mean, 4.6%) of baseline. CONCLUSIONS These results demonstrate that in vivo drug activity of artesunate is faster than is indicated by the parasite clearance half-life.
Collapse
Affiliation(s)
- Maria Rebelo
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rebecca Pawliw
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jeremy Gower
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Lachlan Webb
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hayley Mitchell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Zuleima Pava
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rebecca E Watts
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales (Sydney), Sydney, New South Wales, Australia
| | - James S McCarthy
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David S Khoury
- Kirby Institute, University of New South Wales (Sydney), Sydney, New South Wales, Australia
| |
Collapse
|
5
|
Artemisinin resistance phenotypes and K13 inheritance in a Plasmodium falciparum cross and Aotus model. Proc Natl Acad Sci U S A 2018; 115:12513-12518. [PMID: 30455312 DOI: 10.1073/pnas.1813386115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Concerns about malaria parasite resistance to treatment with artemisinin drugs (ARTs) have grown with findings of prolonged parasite clearance t 1/2s (>5 h) and their association with mutations in Plasmodium falciparum Kelch-propeller protein K13. Here, we describe a P. falciparum laboratory cross of K13 C580Y mutant with C580 wild-type parasites to investigate ART response phenotypes in vitro and in vivo. After genotyping >400 isolated progeny, we evaluated 20 recombinants in vitro: IC50 measurements of dihydroartemisinin were at similar low nanomolar levels for C580Y- and C580-type progeny (mean ratio, 1.00; 95% CI, 0.62-1.61), whereas, in a ring-stage survival assay, the C580Y-type progeny had 19.6-fold (95% CI, 9.76-39.2) higher average counts. In splenectomized Aotus monkeys treated with three daily doses of i.v. artesunate, t 1/2 calculations by three different methods yielded mean differences of 0.01 h (95% CI, -3.66 to 3.67), 0.80 h (95% CI, -0.92 to 2.53), and 2.07 h (95% CI, 0.77-3.36) between C580Y and C580 infections. Incidences of recrudescence were 57% in C580Y (4 of 7) versus 70% in C580 (7 of 10) infections (-13% difference; 95% CI, -58% to 35%). Allelic substitution of C580 in a C580Y-containing progeny clone (76H10) yielded a transformant (76H10C580Rev) that, in an infected monkey, recrudesced regularly 13 times over 500 d. Frequent recrudescences of ART-treated P. falciparum infections occur with or without K13 mutations and emphasize the need for improved partner drugs to effectively eliminate the parasites that persist through the ART component of combination therapy.
Collapse
|
6
|
Nguetse CN, Adegnika AA, Agbenyega T, Ogutu BR, Krishna S, Kremsner PG, Velavan TP. Molecular markers of anti-malarial drug resistance in Central, West and East African children with severe malaria. Malar J 2017; 16:217. [PMID: 28535801 PMCID: PMC5442681 DOI: 10.1186/s12936-017-1868-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background The Plasmodium falciparum multidrug resistance 1 (PfMDR1), P. falciparum Ca2+-ATPase (PfATP6) and Kelch-13 propeller domain (PfK13) loci are molecular markers of parasite susceptibility to anti-malarial drugs. Their frequency distributions were determined in the isolates collected from children with severe malaria originating from three African countries. Methods Samples from 287 children with severe malaria [(Gabon: n = 114); (Ghana: n = 89); (Kenya: n = 84)] were genotyped for pfmdr1, pfatp6 and pfk13 loci by DNA sequencing and assessing pfmdr1 copy number variation (CNV) by real-time PCR. Results Pfmdr1-N86Y mutation was detected in 48, 10 and 10% in Lambaréné, Kumasi and Kisumu, respectively. At codon 184, the prevalence of the mutation was 73% in Lambaréné, 63% in Kumasi and 49% Kisumu. The S1034C and N1042D variants were absent at all three sites, while the frequency of the D1246Y mutation was 1, 3 and 13% in Lambaréné, Kumasi and Kisumu, respectively. Isolates with two pfmdr1 gene copy number predominantly harboured the N86Y wild-type allele and were mostly found in Kumasi (10%) (P < 0.0001). Among the main pfmdr1 haplotypes (NFD, NYD and YFD), NYD was associated with highest parasitaemia (P = 0.04). At the pfatp6 locus, H243Y and A623E mutations were observed at very low frequency at all three sites. The prevalence of the pfatp6 E431K variant was 6, 18 and 17% in Lambaréné, Kumasi and Kisumu, respectively. The L263E and S769N mutations were absent in all isolates. The pfk13 variants associated with artemisinin resistance in Southeast Asia were not observed. Eleven novel substitutions in the pfk13 locus occurring at low frequency were observed. Conclusions Artemisinins are still highly efficacious in large malaria-endemic regions though declining efficacy has occurred in Southeast Asia. The return of chloroquine-sensitive strains following the removal of drug pressure is observed. However, selection of wild-type alleles in the multidrug-resistance gene and the increased gene copy number is associated with reduced lumefantrine sensitivity. This study indicates a need to constantly monitor drug resistance to artemisinin in field isolates from malaria-endemic countries.
Collapse
Affiliation(s)
- Christian N Nguetse
- Institute of Tropical Medicine, University Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany
| | - Ayola Akim Adegnika
- Institute of Tropical Medicine, University Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Tsiri Agbenyega
- Department of Physiology, University of Science and Technology, School of Medical Sciences, Kumasi, Ghana.,Departments of Child Health and Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Bernhards R Ogutu
- Centre for Clinical Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Sanjeev Krishna
- Institute of Tropical Medicine, University Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Institute for Infection and Immunity, St George's University of London, London, UK
| | - Peter G Kremsner
- Institute of Tropical Medicine, University Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, University Tübingen, Wilhelmstrasse 27, 72074, Tübingen, Germany. .,Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of Congo. .,Vietnamese-German Center for Medical Research, Hanoi, Vietnam. .,Faculty of Medicine, Duy Tan University, Da Nang, Vietnam.
| |
Collapse
|
7
|
Gil JP, Krishna S. pfmdr1 (Plasmodium falciparum multidrug drug resistance gene 1): a pivotal factor in malaria resistance to artemisinin combination therapies. Expert Rev Anti Infect Ther 2017; 15:527-543. [DOI: 10.1080/14787210.2017.1313703] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- J. Pedro Gil
- Physiology and Pharmacology Department, Karolinska Institutet, Stockholm, Sweden
| | - S. Krishna
- St George’s University Hospital, Institute for Infection and Immunity, London, United Kingdom
| |
Collapse
|
8
|
Phyo AP, Ashley EA, Anderson TJC, Carrara VI, Woodrow CJ, White NJ, Nosten F. Reply to Meshnick and Hastings et al. Clin Infect Dis 2016; 63:1528-1529. [PMID: 27553372 PMCID: PMC5106610 DOI: 10.1093/cid/ciw584] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Aung Pyae Phyo
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mae Sot.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Elizabeth A Ashley
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mae Sot.,Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | | | - Verena I Carrara
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mae Sot.,Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Charles J Woodrow
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Nicholas J White
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Francois Nosten
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mae Sot.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| |
Collapse
|