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Deshmukh SS, Byaruhanga O, Tumwebaze P, Akin D, Greenhouse B, Egan ES, Demirci U. Automated Recognition of Plasmodium falciparum Parasites from Portable Blood Levitation Imaging. Adv Sci (Weinh) 2022; 9:e2105396. [PMID: 35957519 PMCID: PMC9534981 DOI: 10.1002/advs.202105396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/03/2022] [Indexed: 06/15/2023]
Abstract
In many malaria-endemic regions, current detection tools are inadequate in diagnostic accuracy and accessibility. To meet the need for direct, phenotypic, and automated malaria parasite detection in field settings, a portable platform to process, image, and analyze whole blood to detect Plasmodium falciparum parasites, is developed. The liberated parasites from lysed red blood cells suspended in a magnetic field are accurately detected using this cellphone-interfaced, battery-operated imaging platform. A validation study is conducted at Ugandan clinics, processing 45 malaria-negative and 36 malaria-positive clinical samples without external infrastructure. Texture and morphology features are extracted from the sample images, and a random forest classifier is trained to assess infection status, achieving 100% sensitivity and 91% specificity against gold-standard measurements (microscopy and polymerase chain reaction), and limit of detection of 31 parasites per µL. This rapid and user-friendly platform enables portable parasite detection and can support malaria diagnostics, surveillance, and research in resource-constrained environments.
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Affiliation(s)
- Shreya S. Deshmukh
- Department of BioengineeringStanford University Schools of Engineering and MedicineStanfordCA94305USA
- Canary Center for Early Cancer DetectionBioacoustic MEMS in Medicine LabDepartment of RadiologyStanford University School of MedicinePalo AltoCA94305USA
| | | | | | - Demir Akin
- Canary Center for Early Cancer DetectionBioacoustic MEMS in Medicine LabDepartment of RadiologyStanford University School of MedicinePalo AltoCA94305USA
| | - Bryan Greenhouse
- Department of MedicineUniversity of California San FranciscoSan FranciscoCA94110USA
| | - Elizabeth S. Egan
- Department of PediatricsStanford University School of MedicineStanfordCA94305USA
- Department of Microbiology and ImmunologyStanford University School of MedicineStanfordCA94305USA
| | - Utkan Demirci
- Canary Center for Early Cancer DetectionBioacoustic MEMS in Medicine LabDepartment of RadiologyStanford University School of MedicinePalo AltoCA94305USA
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2
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Taft BR, Yokokawa F, Kirrane T, Mata AC, Huang R, Blaquiere N, Waldron G, Zou B, Simon O, Vankadara S, Chan WL, Ding M, Sim S, Straimer J, Guiguemde A, Lakshminarayana SB, Jain JP, Bodenreider C, Thompson C, Lanshoeft C, Shu W, Fang E, Qumber J, Chan K, Pei L, Chen YL, Schulz H, Lim J, Abas SN, Ang X, Liu Y, Angulo-Barturen I, Jiménez-Díaz MB, Gamo FJ, Crespo-Fernandez B, Rosenthal PJ, Cooper RA, Tumwebaze P, Aguiar ACC, Campo B, Campbell S, Wagner J, Diagana TT, Sarko C. Discovery and Preclinical Pharmacology of INE963, a Potent and Fast-Acting Blood-Stage Antimalarial with a High Barrier to Resistance and Potential for Single-Dose Cures in Uncomplicated Malaria. J Med Chem 2022; 65:3798-3813. [PMID: 35229610 PMCID: PMC9278664 DOI: 10.1021/acs.jmedchem.1c01995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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A series of 5-aryl-2-amino-imidazothiadiazole (ITD) derivatives
were identified by a phenotype-based high-throughput screening using
a blood stage Plasmodium falciparum (Pf) growth inhibition assay. A lead optimization program focused on
improving antiplasmodium potency, selectivity against human kinases,
and absorption, distribution, metabolism, excretion, and toxicity
properties and extended pharmacological profiles culminated in the
identification of INE963 (1), which demonstrates
potent cellular activity against Pf 3D7 (EC50 = 0.006 μM) and achieves “artemisinin-like”
kill kinetics in vitro with a parasite clearance
time of <24 h. A single dose of 30 mg/kg is fully curative in the Pf-humanized severe combined immunodeficient mouse model. INE963 (1) also exhibits a high barrier to resistance
in drug selection studies and a long half-life (T1/2) across species. These properties suggest the significant
potential for INE963 (1) to provide a curative
therapy for uncomplicated malaria with short dosing regimens. For
these reasons, INE963 (1) was progressed
through GLP toxicology studies and is now undergoing Ph1 clinical
trials.
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Affiliation(s)
- Benjamin R Taft
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Fumiaki Yokokawa
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Tom Kirrane
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Anne-Catherine Mata
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Richard Huang
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Nicole Blaquiere
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Grace Waldron
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Bin Zou
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Oliver Simon
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Subramanyam Vankadara
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Wai Ling Chan
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Mei Ding
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Sandra Sim
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Judith Straimer
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Armand Guiguemde
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Suresh B Lakshminarayana
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Jay Prakash Jain
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Christophe Bodenreider
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Christopher Thompson
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christian Lanshoeft
- Novartis Institutes for Biomedical Research, Fabrikstrasse 14, Basel CH-4056, Switzerland
| | - Wei Shu
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Eric Fang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
| | - Jafri Qumber
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Katherine Chan
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Luying Pei
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Yen-Liang Chen
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Hanna Schulz
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Jessie Lim
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Siti Nurdiana Abas
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Xiaoman Ang
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Yugang Liu
- Technical Research and Development, Global Drug Development, Novartis Pharmaceuticals Corporation, One Health Plaza, East Hanover, New Jersey 07936, United States
| | - Iñigo Angulo-Barturen
- The Art of Discovery, Astondo Bidea, BIC Bizkaia building, no. 612 Derio 48160 Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- The Art of Discovery, Astondo Bidea, BIC Bizkaia building, no. 612 Derio 48160 Bizkaia, Basque Country, Spain
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Benigno Crespo-Fernandez
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Philip J Rosenthal
- Department of Medicine, University of California, 533 Parnassus Avenue, San Francisco, California 94143, Unites States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | - Patrick Tumwebaze
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road, P.O. Box 7475 Kampala, Uganda
| | | | - Brice Campo
- Medicines for Malaria Venture, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Simon Campbell
- Medicines for Malaria Venture, 20 Route de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Jürgen Wagner
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, no. 05-01, Chromos, Singapore 138670, Singapore
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, 5959 Horton Street, Emeryville, California 94608, United States
| | - Christopher Sarko
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 5959 Horton Street, Emeryville, California 94608, United States
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Murithi JM, Pascal C, Bath J, Boulenc X, Gnädig NF, Pasaje CFA, Rubiano K, Yeo T, Mok S, Klieber S, Desert P, Jiménez-Díaz MB, Marfurt J, Rouillier M, Cherkaoui-Rbati MH, Gobeau N, Wittlin S, Uhlemann AC, Price RN, Wirjanata G, Noviyanti R, Tumwebaze P, Cooper RA, Rosenthal PJ, Sanz LM, Gamo FJ, Joseph J, Singh S, Bashyam S, Augereau JM, Giraud E, Bozec T, Vermat T, Tuffal G, Guillon JM, Menegotto J, Sallé L, Louit G, Cabanis MJ, Nicolas MF, Doubovetzky M, Merino R, Bessila N, Angulo-Barturen I, Baud D, Bebrevska L, Escudié F, Niles JC, Blasco B, Campbell S, Courtemanche G, Fraisse L, Pellet A, Fidock DA, Leroy D. The antimalarial MMV688533 provides potential for single-dose cures with a high barrier to Plasmodium falciparum parasite resistance. Sci Transl Med 2021; 13:13/603/eabg6013. [PMID: 34290058 PMCID: PMC8530196 DOI: 10.1126/scitranslmed.abg6013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/02/2021] [Indexed: 01/13/2023]
Abstract
The emergence and spread of Plasmodium falciparum resistance to first-line antimalarials creates an imperative to identify and develop potent preclinical candidates with distinct modes of action. Here, we report the identification of MMV688533, an acylguanidine that was developed following a whole-cell screen with compounds known to hit high-value targets in human cells. MMV688533 displays fast parasite clearance in vitro and is not cross-resistant with known antimalarials. In a P. falciparum NSG mouse model, MMV688533 displays a long-lasting pharmacokinetic profile and excellent safety. Selection studies reveal a low propensity for resistance, with modest loss of potency mediated by point mutations in PfACG1 and PfEHD. These proteins are implicated in intracellular trafficking, lipid utilization, and endocytosis, suggesting interference with these pathways as a potential mode of action. This preclinical candidate may offer the potential for a single low-dose cure for malaria.
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Affiliation(s)
- James M. Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cécile Pascal
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - Jade Bath
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Nina F. Gnädig
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Kelly Rubiano
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sylvie Klieber
- Sanofi R&D, Translational Medicine & Early Development, Montpellier, France
| | | | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | | | | | - Sergio Wittlin
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Universität Basel, Basel, Switzerland
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Grennady Wirjanata
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | | | - Roland A. Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, USA
| | | | - Laura M. Sanz
- Global Health Pharma Research Unit, GSK, Tres Cantos, Madrid, Spain
| | | | | | | | | | | | - Elie Giraud
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - Tanguy Bozec
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - Thierry Vermat
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - Gilles Tuffal
- Sanofi R&D, Translational Medicine & Early Development, Montpellier, France
| | | | - Jérôme Menegotto
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - Laurent Sallé
- Sanofi R&D, Translational Medicine & Early Development, Montpellier, France
| | | | - Marie-José Cabanis
- Sanofi R&D, Translational Medicine & Early Development, Montpellier, France
| | | | | | - Rita Merino
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - Nadir Bessila
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | | | | | | | | | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | - Laurent Fraisse
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - Alain Pellet
- Sanofi, Infectious Diseases Therapeutic Area, Marcy l'Etoile, France
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Corresponding author. (D.A.F.); (D.L.)
| | - Didier Leroy
- Medicines for Malaria Venture, Geneva, Switzerland.,Corresponding author. (D.A.F.); (D.L.)
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4
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Asua V, Conrad MD, Aydemir O, Duvalsaint M, Legac J, Duarte E, Tumwebaze P, Chin DM, Cooper RA, Yeka A, Kamya MR, Dorsey G, Nsobya SL, Bailey J, Rosenthal PJ. Changing Prevalence of Potential Mediators of Aminoquinoline, Antifolate, and Artemisinin Resistance Across Uganda. J Infect Dis 2021; 223:985-994. [PMID: 33146722 PMCID: PMC8006419 DOI: 10.1093/infdis/jiaa687] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/27/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND In Uganda, artemether-lumefantrine is recommended for malaria treatment and sulfadoxine-pyrimethamine for chemoprevention during pregnancy, but drug resistance may limit efficacies. METHODS Genetic polymorphisms associated with sensitivities to key drugs were characterized in samples collected from 16 sites across Uganda in 2018 and 2019 by ligase detection reaction fluorescent microsphere, molecular inversion probe, dideoxy sequencing, and quantitative polymerase chain reaction assays. RESULTS Considering transporter polymorphisms associated with resistance to aminoquinolines, the prevalence of Plasmodium falciparum chloroquine resistance transporter (PfCRT) 76T decreased, but varied markedly between sites (0-46% in 2018; 0-23% in 2019); additional PfCRT polymorphisms and plasmepsin-2/3 amplifications associated elsewhere with resistance to piperaquine were not seen. For P. falciparum multidrug resistance protein 1, in 2019 the 86Y mutation was absent at all sites, the 1246Y mutation had prevalence ≤20% at 14 of 16 sites, and gene amplification was not seen. Considering mutations associated with high-level sulfadoxine-pyrimethamine resistance, prevalences of P. falciparum dihydrofolate reductase 164L (up to 80%) and dihydropteroate synthase 581G (up to 67%) were high at multiple sites. Considering P. falciparum kelch protein propeller domain mutations associated with artemisinin delayed clearance, prevalence of the 469Y and 675V mutations has increased at multiple sites in northern Uganda (up to 23% and 41%, respectively). CONCLUSIONS We demonstrate concerning spread of mutations that may limit efficacies of key antimalarial drugs.
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Affiliation(s)
- Victor Asua
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Melissa D Conrad
- University of California, San Francisco, San Francisco, California, USA
| | | | - Marvin Duvalsaint
- University of California, San Francisco, San Francisco, California, USA
| | - Jennifer Legac
- University of California, San Francisco, San Francisco, California, USA
| | - Elias Duarte
- University of California, San Francisco, San Francisco, California, USA
| | | | | | - Roland A Cooper
- Dominican University of California, San Rafael, California, USA
| | - Adoke Yeka
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Grant Dorsey
- University of California, San Francisco, San Francisco, California, USA
| | - Sam L Nsobya
- Infectious Diseases Research Collaboration, Kampala, Uganda
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5
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Conrad MD, Mota D, Foster M, Tukwasibwe S, Legac J, Tumwebaze P, Whalen M, Kakuru A, Nayebare P, Wallender E, Havlir DV, Jagannathan P, Huang L, Aweeka F, Kamya MR, Dorsey G, Rosenthal PJ. Impact of Intermittent Preventive Treatment During Pregnancy on Plasmodium falciparum Drug Resistance-Mediating Polymorphisms in Uganda. J Infect Dis 2017; 216:1008-1017. [PMID: 28968782 PMCID: PMC5853776 DOI: 10.1093/infdis/jix421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/17/2017] [Indexed: 11/13/2022] Open
Abstract
Background In a recent trial of intermittent preventive treatment in pregnancy (IPTp) in Uganda, dihydroartemisinin-piperaquine (DP) was superior to sulfadoxine-pyrimethamine (SP) in preventing maternal and placental malaria. Methods We compared genotypes using sequencing, fluorescent microsphere, and quantitative polymerase chain reaction assays at loci associated with drug resistance in Plasmodium falciparum isolated from subjects receiving DP or SP. Results Considering aminoquinoline resistance, DP was associated with increased prevalences of mutations at pfmdr1 N86Y, pfmdr1 Y184F, and pfcrt K76T compared to SP (64.6% vs 27.4%, P < .001; 93.9% vs 59.2%, P < .001; and 87.7% vs 75.4%, P = .03, respectively). Increasing plasma piperaquine concentration at the time of parasitemia was associated with increasing pfmdr1 86Y prevalence; no infections with the N86 genotype occurred with piperaquine >2.75 ng/mL. pfkelch13 propeller domain polymorphisms previously associated with artemisinin resistance were not identified. Recently identified markers of piperaquine resistance were uncommon and not associated with DP. Considering antifolate resistance, SP was associated with increased prevalence of a 5-mutation haplotype (pfdhfr 51I, 59R, and 108N; pfdhps 437G and 581G) compared to DP (90.8% vs 60.0%, P = .001). Conclusions IPTp selected for genotypes associated with decreased sensitivity to treatment regimens, but genotypes associated with clinically relevant DP resistance in Asia have not emerged in Uganda.
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Affiliation(s)
| | | | | | | | | | | | | | - Abel Kakuru
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | | | - Prasanna Jagannathan
- University of California, San Francisco,Stanford University, Palo Alto, California
| | | | | | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda,Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Philip J Rosenthal
- University of California, San Francisco,Correspondence: P. J. Rosenthal, University of California, San Francisco, Box 0811, San Francisco, CA 94143 ()
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6
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Tukwasibwe S, Tumwebaze P, Conrad M, Arinaitwe E, Kamya MR, Dorsey G, Nsobya SL, Greenhouse B, Rosenthal PJ. Drug resistance mediating Plasmodium falciparum polymorphisms and clinical presentations of parasitaemic children in Uganda. Malar J 2017; 16:125. [PMID: 28327148 PMCID: PMC5361791 DOI: 10.1186/s12936-017-1777-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/15/2017] [Indexed: 11/19/2022] Open
Abstract
Background Plasmodium falciparum genetic polymorphisms that mediate altered drug sensitivity may impact upon virulence. In a cross-sectional study, Ugandan children with infections mutant at pfcrt K76T, pfmdr1 N86Y, or pfmdr1 D1246Y had about one-fourth the odds of symptomatic malaria compared to those with infections with wild type (WT) sequences. However, results may have been confounded by greater likelihood in those with symptomatic disease of higher density mixed infections and/or recent prior treatment that selected for WT alleles. Methods Polymorphisms in samples from paired episodes of asymptomatic and symptomatic parasitaemia in 114 subjects aged 4–11 years were followed longitudinally in Tororo District, Uganda. Paired episodes occurred within 3–12 months of each other and had no treatment for malaria in the prior 60 days. The prevalence of WT, mixed, and mutant alleles was determined using multiplex ligase detection reaction-fluorescent microsphere assays. Results Considering paired episodes in the same subject, the odds of symptomatic malaria were lower for infections with mutant compared to WT or mixed sequence at N86Y (OR 0.26, 95% CI 0.09–0.79, p = 0.018), but not K76T or D1246Y. However, symptomatic episodes (which had higher densities) were more likely than asymptomatic to be mixed (for N86Y OR 2.0, 95% CI 1.04–4.0, p = 0.036). Excluding mixed infections, the odds of symptomatic malaria were lower for infections with mutant compared to WT sequence at N86Y (OR 0.33, 95% CI 0.11–0.98, p = 0.046), but not the other alleles. However, if mixed genotypes were grouped with mutants in this analysis or assuming that mixed infections consisted of 50% WT and 50% mutant genotypes, the odds of symptomatic infection did not differ between infections that were mutant or WT at the studied alleles. Conclusions Although infections with only the mutant pfmdr1 86Y genotype were associated with symptomatic infection, this association could primarily be explained by greater parasite densities and therefore greater prevalence of mixed infections in symptomatic children. These results indicate limited association between the tested polymorphisms and risk of symptomatic disease and highlight the value of longitudinal studies for assessing associations between parasite factors and clinical outcomes.
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Affiliation(s)
| | | | - Melissa Conrad
- Department of Medicine, University of California, Box 0811, San Francisco, CA, 94143, USA
| | | | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Grant Dorsey
- Department of Medicine, University of California, Box 0811, San Francisco, CA, 94143, USA
| | | | - Bryan Greenhouse
- Department of Medicine, University of California, Box 0811, San Francisco, CA, 94143, USA
| | - Philip J Rosenthal
- Department of Medicine, University of California, Box 0811, San Francisco, CA, 94143, USA.
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7
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Tumwebaze P, Tukwasibwe S, Taylor A, Conrad M, Ruhamyankaka E, Asua V, Walakira A, Nankabirwa J, Yeka A, Staedke SG, Greenhouse B, Nsobya SL, Kamya MR, Dorsey G, Rosenthal PJ. Changing Antimalarial Drug Resistance Patterns Identified by Surveillance at Three Sites in Uganda. J Infect Dis 2017; 215:631-635. [PMID: 28039354 PMCID: PMC5853976 DOI: 10.1093/infdis/jiw614] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/07/2016] [Indexed: 11/12/2022] Open
Abstract
We assessed Plasmodium falciparum drug resistance markers in parasites collected in 2012, 2013, and 2015 at 3 sites in Uganda. The prevalence and frequency of parasites with mutations in putative transporters previously associated with resistance to aminoquinolines, but increased sensitivity to lumefantrine (pfcrt 76T; pfmdr1 86Y and 1246Y), decreased markedly at all sites. Antifolate resistance mutations were common, with apparent emergence of mutations (pfdhfr 164L; pfdhps 581G) associated with high-level resistance. K13 mutations linked to artemisinin resistance were uncommon and did not increase over time. Changing malaria treatment practices have been accompanied by profound changes in markers of resistance.
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Affiliation(s)
| | | | - Aimee Taylor
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Melissa Conrad
- Department of Medicine, University of California, San Francisco, USA
| | | | - Victor Asua
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Adoke Yeka
- Makerere University School of Public Health, College of Health Sciences, Kampala, Uganda
| | - Sarah G Staedke
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, USA
| | | | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, USA
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Nankoberanyi S, Mbogo GW, LeClair NP, Conrad MD, Tumwebaze P, Tukwasibwe S, Kamya MR, Tappero J, Nsobya SL, Rosenthal PJ. Validation of the ligase detection reaction fluorescent microsphere assay for the detection of Plasmodium falciparum resistance mediating polymorphisms in Uganda. Malar J 2014; 13:95. [PMID: 24629020 PMCID: PMC4004386 DOI: 10.1186/1475-2875-13-95] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/21/2014] [Indexed: 01/19/2023] Open
Abstract
Background Malaria remains a major public health problem, and its control has been hampered by drug resistance. For a number of drugs, Plasmodium falciparum single nucleotide polymorphisms (SNPs) are associated with altered drug sensitivity and can be used as markers of drug resistance. Several techniques have been studied to assess resistance markers. The most widely used methodology is restriction fragment length polymorphism (RFLP) analysis. The ligase detection reaction fluorescent microsphere (LDR-FM) assay was recently shown to provide high throughput assessment of P. falciparum SNPs associated with drug resistance. The aim of this study was to validate the reliability and accuracy of the LDR-FM assay in a field setting. Methods For 223 samples from a clinical trial in Tororo, Uganda in which P. falciparum was identified by blood smear, DNA was extracted from dried blood spots, genes of interest were amplified by PCR, amplicons were analysed by both RFLP and LDR-FM assays, and results were compared. Results SNP prevalence (wild type/mixed/mutant) with RFLP analysis was 8/5/87% for pfcrt K76T, 34/37/29% for pfmdr1 N86Y, 64/17/19% for pfmdr1 Y184F, and 42/21/37% for pfmdr1 D1246Y. These prevalences with the LDR-FM assay were 7/5/88%, 31/24/45%, 62/20/18%, and 48/19/33% for the four SNPs, respectively. Combining mixed and mutant outcomes for analysis, agreement between the assays was 97% (K = 0.77) for pfcrt K76T, 79% (K = 0.55) for pfmdr1 N86Y, 83% (K = 0.65) for pfmdr1 Y184F, and 91% (K = 0.82) for pfmdr1 D1246Y, with most disagreements due to discrepant readings of mixed genotypes. Conclusion The LDR-FM assay provides a high throughput, relatively inexpensive and accurate assay for the surveillance of P. falciparum SNPs associated with drug resistance in resource-limited countries.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Philip J Rosenthal
- Department of Medicine, University of California, Box 0811, San Francisco, CA 94143, USA.
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De Niz M, Eziefula AC, Othieno L, Mbabazi E, Nabukeera D, Ssemmondo E, Gonahasa S, Tumwebaze P, Diliberto D, Maiteki-Sebuguzi C, Staedke SG, Drakeley C. Tools for mass screening of G6PD deficiency: validation of the WST8/1-methoxy-PMS enzymatic assay in Uganda. Malar J 2013; 12:210. [PMID: 23782846 PMCID: PMC3691584 DOI: 10.1186/1475-2875-12-210] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/11/2013] [Indexed: 01/03/2023] Open
Abstract
Background The distribution of the enzymopathy glucose-6-phosphate dehydrogenase (G6PD) deficiency is linked to areas of high malaria endemicity due to its association with protection from disease. G6PD deficiency is also identified as the cause of severe haemolysis following administration of the anti-malarial drug primaquine and further use of this drug will likely require identification of G6PD deficiency on a population level. Current conventional methods for G6PD screening have various disadvantages for field use. Methods The WST8/1-methoxy PMS method, recently adapted for field use, was validated using a gold standard enzymatic assay (R&D Diagnostics Ltd ®) in a study involving 235 children under five years of age, who were recruited by random selection from a cohort study in Tororo, Uganda. Blood spots were collected by finger-prick onto filter paper at routine visits, and G6PD activity was determined by both tests. Performance of the WST8/1-methoxy PMS test under various temperature, light, and storage conditions was evaluated. Results The WST8/1-methoxy PMS assay was found to have 72% sensitivity and 98% specificity when compared to the commercial enzymatic assay and the AUC was 0.904, suggesting good agreement. Misclassifications were at borderline values of G6PD activity between mild and normal levels, or related to outlier haemoglobin values (<8.0 gHb/dl or >14 gHb/dl) associated with ongoing anaemia or recent haemolytic crises. Although severe G6PD deficiency was not found in the area, the test enabled identification of low G6PD activity. The assay was found to be highly robust for field use; showing less light sensitivity, good performance over a wide temperature range, and good capacity for medium-to-long term storage. Conclusions The WST8/1-methoxy PMS assay was comparable to the currently used standard enzymatic test, and offers advantages in terms of cost, storage, portability and use in resource-limited settings. Such features make this test a potential key tool for deployment in the field for point of care assessment prior to primaquine administration in malaria-endemic areas. As with other G6PD tests, outlier haemoglobin levels may confound G6PD level estimation.
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Affiliation(s)
- Mariana De Niz
- Malaria Centre, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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De Niz M, Eziefula AC, Maiteki-Sebuguzi C, Gonahasa S, DiLiberto D, Tumwebaze P, Staedke SG, Drakeley CJ. Mass screening tools for glucose-6-phosphate dehydrogenase deficiency: validation of the WST8/1 -methoxy-PMS enzymatic assay in a highly malaria-endemic area in Uganda. Malar J 2012. [PMCID: PMC3472219 DOI: 10.1186/1475-2875-11-s1-o28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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