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Kane J, Li X, Kumar S, Button-Simons KA, Brenneman KMV, Dahlhoff H, Sievert MA, Checkley LA, Shoue DA, Singh PP, Abatiyow BA, Haile MT, Nair S, Reyes A, Tripura R, Peto T, Lek D, Kappe SH, Dhorda M, Nkhoma SC, Cheeseman IH, Vaughan AM, Anderson TJC, Ferdig MT. A Plasmodium falciparum genetic cross reveals the contributions of pfcrt and plasmepsin II/III to piperaquine drug resistance. bioRxiv 2023:2023.06.06.543862. [PMID: 37745488 PMCID: PMC10515748 DOI: 10.1101/2023.06.06.543862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Piperaquine (PPQ) is widely used in combination with dihydroartemisinin (DHA) as a first-line treatment against malaria parasites. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multi-drug resistant KEL1/PLA1 lineage isolate (KH004) and a drug susceptible parasite isolated in Malawi (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and four copies of pm2/3. We recovered 104 unique recombinant progeny and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3 for detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes, including PPQ survival assay (PSA), area under the dose-response curve (AUC), and a limited point IC50 (LP-IC50). We find that inheritance of the KH004 pfcrt allele is required for PPQ resistance, whereas copy number variation in pm2/3 further enhances resistance but does not confer resistance in the absence of PPQ-R-associated mutations in pfcrt. Deeper investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background, to a range of PPQ-related traits and confirm the critical role of the PfCRT G367C substitution in PPQ resistance.
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Affiliation(s)
- John Kane
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Katrina A. Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Haley Dahlhoff
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Mackenzie A.C. Sievert
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Lisa A. Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Puspendra P. Singh
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ann Reyes
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Rupam Tripura
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Tom Peto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Dysoley Lek
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
- School of Public Health, National Institute of Public Health, Phnom Penh, Cambodia
| | - Stefan H.I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Standwell C Nkhoma
- BEI Resources, American Type Culture Collection (ATCC), Manassas, VA, USA
| | - Ian H. Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Timothy J. C. Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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Nkhoma SC, Ahmed AOA, Porier D, Rashid S, Bradford R, Molestina RE, Stedman TT. Dynamics of parasite growth in genetically diverse Plasmodium falciparum isolates. Mol Biochem Parasitol 2023; 254:111552. [PMID: 36731750 PMCID: PMC10149587 DOI: 10.1016/j.molbiopara.2023.111552] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/29/2022] [Revised: 10/24/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023]
Abstract
Multiple parasite lineages with different proliferation rates or fitness may coexist within a clinical malaria isolate, resulting in complex growth interactions and variations in phenotype. To elucidate the dynamics of parasite growth in multiclonal isolates, we measured growth rates (GRs) of three Plasmodium falciparum Cambodian isolates, including IPC_3445 (MRA-1236), IPC_5202 (MRA-1240), IPC_6403 (MRA-1285), and parasite lineages previously cloned from each of these isolates by limiting dilution. Following synchronization, in vitro cultures of each parasite line were maintained over four consecutive asexual cycles (192 h), with thin smears prepared at each 48-h cycle to estimate GR and fold change in parasitemia (FCP). Cell cycle time (CCT), the duration it takes for ring-stage parasites to develop into mature schizonts, was measured by monitoring the development of 0-3-h post-invasion rings for up to 52 h post-incubation. Laboratory lines 3D7 (MRA-102) and Dd2 (MRA-150) were used as controls. Significant differences in GR, FCP, and CCT were observed between parasite isolates and clonal lineages from each isolate. The parasite lines studied here have well-defined growth phenotypes and will facilitate basic malaria research and development of novel malaria interventions. These lines are available to malaria researchers through the MR4 collection of NIAID's BEI Resources Program.
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Affiliation(s)
- Standwell C Nkhoma
- BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA.
| | - Amel O A Ahmed
- BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Danielle Porier
- BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Sujatha Rashid
- BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Rebecca Bradford
- BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Robert E Molestina
- BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Timothy T Stedman
- BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209, USA
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Nair S, Li X, Nkhoma SC, Anderson T. Fitness Costs of pfhrp2 and pfhrp3 Deletions Underlying Diagnostic Evasion in Malaria Parasites. J Infect Dis 2022; 226:1637-1645. [PMID: 35709327 PMCID: PMC10205895 DOI: 10.1093/infdis/jiac240] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/28/2022] [Accepted: 06/14/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Rapid diagnostic tests based on detection of histidine-rich proteins (HRPs) are widely used for malaria diagnosis, but parasites carrying pfhrp deletions can evade detection and are increasing in frequency in some countries. Models aim to predict conditions under which pfhrp2 and/or pfhrp3 deletions will increase, but a key parameter-the fitness cost of deletions-is unknown. METHODS We removed pfhrp2 and/or pfhrp3 from a Malawian parasite clone using gene editing approaches) and measured fitness costs by conducting pairwise competition experiments. RESULTS We observed significant fitness costs of 0.087 ± 0.008 (1 standard error) per asexual cycle for pfhrp2 deletion and 0.113 ± 0.008 for the pfhrp2/3 double deletion, relative to the unedited progenitor parasite. Selection against deletions is strong and comparable to that resulting from drug resistance mutations. CONCLUSIONS Prior modeling suggested that diagnostic selection may drive increased frequency of pfhrp deletions only when fitness costs are mild. Our experiments show that costs of pfhrp deletions are higher than these thresholds, but modeling and empirical results can be reconciled if the duration of infection is short. These results may inform future modeling to understand why pfhrp2/3 deletions are increasing in some locations (Ethiopia and Eritrea) but not in others (Mekong region).
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Affiliation(s)
- Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Standwell C Nkhoma
- BEI Resources, American Type Culture Collection, Manassas, Virginia, USA
| | - Tim Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
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Brenneman KV, Li X, Kumar S, Delgado E, Checkley LA, Shoue DA, Reyes A, Abatiyow BA, Haile MT, Tripura R, Peto T, Lek D, Button-Simons KA, Kappe SH, Dhorda M, Nosten F, Nkhoma SC, Cheeseman IH, Vaughan AM, Ferdig MT, Anderson TJ. Optimizing bulk segregant analysis of drug resistance using Plasmodium falciparum genetic crosses conducted in humanized mice. iScience 2022; 25:104095. [PMID: 35372813 PMCID: PMC8971943 DOI: 10.1016/j.isci.2022.104095] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 01/15/2023] Open
Abstract
Classical malaria parasite genetic crosses involve isolation, genotyping, and phenotyping of progeny parasites, which is time consuming and laborious. We tested a rapid alternative approach-bulk segregant analysis (BSA)-that utilizes sequencing of bulk progeny populations with and without drug selection for rapid identification of drug resistance loci. We used dihydroartemisinin (DHA) selection in two genetic crosses and investigated how synchronization, cryopreservation, and the drug selection regimen impacted BSA success. We detected a robust quantitative trait locus (QTL) at kelch13 in both crosses but did not detect QTLs at four other candidate loci. QTLs were detected using synchronized, but not unsynchronized progeny pools, consistent with the stage-specific action of DHA. We also successfully applied BSA to cryopreserved progeny pools, expanding the utility of this approach. We conclude that BSA provides a powerful approach for investigating the genetic architecture of drug resistance in Plasmodium falciparum.
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Affiliation(s)
- Katelyn Vendrely Brenneman
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Elizabeth Delgado
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Lisa A. Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Ann Reyes
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Meseret T. Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Rupam Tripura
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Tom Peto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Dysoley Lek
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
- School of Public Health, National Institute of Public Health, Phnom Penh, Cambodia
| | - Katrina A. Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stefan H.I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Ian H. Cheeseman
- Program in Host Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Corresponding author
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- Corresponding author
| | - Tim J.C. Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA
- Corresponding author
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5
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Nkhoma SC, Ahmed AOA, Zaman S, Porier D, Baker Z, Stedman TT. Dissection of haplotype-specific drug response phenotypes in multiclonal malaria isolates. Int J Parasitol Drugs Drug Resist 2021; 15:152-161. [PMID: 33780700 PMCID: PMC8039770 DOI: 10.1016/j.ijpddr.2021.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 10/28/2022]
Abstract
Natural infections of Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, often comprise multiple parasite lineages (haplotypes). Multiclonal parasite isolates may exhibit variable phenotypes including different drug susceptibility profiles over time due to the presence of multiple haplotypes. To test this hypothesis, three P. falciparum Cambodian isolates IPC_3445 (MRA-1236), IPC_5202 (MRA-1240) and IPC_6403 (MRA-1285) suspected to be multiclonal were cloned by limiting dilution, and the resulting clones genotyped at 24 highly polymorphic single nucleotide polymorphisms (SNPs). Isolates harbored up to three constituent haplotypes, and exhibited significant variability (p < 0.05) in susceptibility to chloroquine, mefloquine, artemisinin and piperaquine as measured by half maximal drug inhibitory concentration (IC50) assays and parasite survival assays, which measure viability following exposure to pharmacologically relevant concentrations of antimalarial drugs. The IC50 of the most abundant haplotype frequently reflected that of the uncloned parental isolate, suggesting that a single haplotype dominates the antimalarial susceptibility profile and masks the effect of minor frequency haplotypes. These results indicate that phenotypic variability in parasite isolates is often due to the presence of multiple haplotypes. Depending on intended end-use, clinical isolates should be cloned to yield single parasite lineages with well-defined phenotypes and genotypes. The availability of such standardized clonal parasite lineages through NIAID's BEI Resources program will aid research directed towards the development of diagnostics and interventions including drugs against malaria.
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Affiliation(s)
- Standwell C Nkhoma
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA.
| | - Amel O A Ahmed
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Sharmeen Zaman
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Danielle Porier
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Zachary Baker
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Timothy T Stedman
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA.
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McDew-White M, Li X, Nkhoma SC, Nair S, Cheeseman I, Anderson TJC. Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment. Genome Biol Evol 2020; 11:1971-1985. [PMID: 31273388 PMCID: PMC6644851 DOI: 10.1093/gbe/evz140] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2019] [Indexed: 12/12/2022] Open
Abstract
Malaria parasites have small extremely AT-rich genomes: microsatellite repeats (1–9 bp) comprise 11% of the genome and genetic variation in natural populations is dominated by repeat changes in microsatellites rather than point mutations. This experiment was designed to quantify microsatellite mutation patterns in Plasmodium falciparum. We established 31 parasite cultures derived from a single parasite cell and maintained these for 114–267 days with frequent reductions to a single cell, so parasites accumulated mutations during ∼13,207 cell divisions. We Illumina sequenced the genomes of both progenitor and end-point mutation accumulation (MA) parasite lines in duplicate to validate stringent calling parameters. Microsatellite calls were 99.89% (GATK), 99.99% (freeBayes), and 99.96% (HipSTR) concordant in duplicate sequence runs from independent sequence libraries, whereas introduction of microsatellite mutations into the reference genome revealed a low false negative calling rate (0.68%). We observed 98 microsatellite mutations. We highlight several conclusions: microsatellite mutation rates (3.12 × 10−7 to 2.16 × 10−8/cell division) are associated with both repeat number and repeat motif like other organisms studied. However, 41% of changes resulted from loss or gain of more than one repeat: this was particularly true for long repeat arrays. Unlike other eukaryotes, we found no insertions or deletions that were not associated with repeats or homology regions. Overall, microsatellite mutation rates are among the lowest recorded and comparable to those in another AT-rich protozoan (Dictyostelium). However, a single infection (>1011 parasites) will still contain over 2.16 × 103 to 3.12 × 104 independent mutations at any single microsatellite locus.
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Affiliation(s)
| | - Xue Li
- Texas Biomedical Research Institute, San Antonio, Texas
| | - Standwell C Nkhoma
- Texas Biomedical Research Institute, San Antonio, Texas.,Malaria Research and Reference Reagent Resource Center (MR4), BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA
| | - Shalini Nair
- Texas Biomedical Research Institute, San Antonio, Texas
| | - Ian Cheeseman
- Texas Biomedical Research Institute, San Antonio, Texas
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Nkhoma SC, Trevino SG, Gorena KM, Nair S, Khoswe S, Jett C, Garcia R, Daniel B, Dia A, Terlouw DJ, Ward SA, Anderson TJC, Cheeseman IH. Co-transmission of Related Malaria Parasite Lineages Shapes Within-Host Parasite Diversity. Cell Host Microbe 2020; 27:93-103.e4. [PMID: 31901523 PMCID: PMC7159252 DOI: 10.1016/j.chom.2019.12.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 04/19/2019] [Revised: 10/17/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022]
Abstract
In high-transmission regions, we expect parasite lineages within complex malaria infections to be unrelated due to parasite inoculations from different mosquitoes. This project was designed to test this prediction. We generated 485 single-cell genome sequences from fifteen P. falciparum malaria patients from Chikhwawa, Malawi-an area of intense transmission. Patients harbored up to seventeen unique parasite lineages. Surprisingly, parasite lineages within infections tend to be closely related, suggesting that superinfection by repeated mosquito bites is rarer than co-transmission of parasites from a single mosquito. Both closely and distantly related parasites comprise an infection, suggesting sequential transmission of complex infections between multiple hosts. We identified tetrads and reconstructed parental haplotypes, which revealed the inbred ancestry of infections and non-Mendelian inheritance. Our analysis suggests strong barriers to secondary infection and outbreeding amongst malaria parasites from a high transmission setting, providing unexpected insights into the biology and transmission of malaria.
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Affiliation(s)
- Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Liverpool, UK; Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK; Texas Biomedical Research Institute, San Antonio, TX, USA.
| | | | - Karla M Gorena
- University of Texas Health Science Center San Antonio, San Antonio, TX, USA
| | - Shalini Nair
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Stanley Khoswe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Catherine Jett
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Roy Garcia
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Benjamin Daniel
- University of Texas Health Science Center San Antonio, San Antonio, TX, USA
| | - Aliou Dia
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Dianne J Terlouw
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Liverpool, UK
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8
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Nkhoma SC, Banda RL, Khoswe S, Dzoole-Mwale TJ, Ward SA. Intra-host dynamics of co-infecting parasite genotypes in asymptomatic malaria patients. Infect Genet Evol 2018; 65:414-424. [PMID: 30145390 PMCID: PMC6219893 DOI: 10.1016/j.meegid.2018.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 11/22/2022]
Abstract
Malaria-infected individuals often harbor mixtures of genetically distinct parasite genotypes. We studied intra-host dynamics of parasite genotypes co-infecting asymptomatic adults in an area of intense malaria transmission in Chikhwawa, Malawi. Serial blood samples (5 ml) were collected over seven consecutive days from 25 adults with asymptomatic Plasmodium falciparum malaria and analyzed to determine whether a single peripheral blood sample accurately captures within-host parasite diversity. Blood samples from three of the participants were also analyzed by limiting dilution cloning and SNP genotyping of the parasite clones isolated to examine both the number and relatedness of co-infecting parasite haplotypes. We observed rapid turnover of co-infecting parasite genotypes in 88% of the individuals sampled (n = 22) such that the genetic composition of parasites infecting these individuals changed dramatically over the course of seven days of follow up. Nineteen of the 25 individuals sampled (76%) carried multiple parasite genotypes at baseline. Analysis of serial blood samples from three of the individuals revealed that they harbored 6, 12 and 17 distinct parasite haplotypes respectively. Approximately 70% of parasite haplotypes recovered from the three extensively sampled individuals were unrelated (proportion of shared alleles <83.3%) and were deemed to have primarily arisen from superinfection (inoculation of unrelated parasite haplotypes through multiple mosquito bites). The rest were related at the half-sib level or greater and were deemed to have been inoculated into individual human hosts via parasite co-transmission from single mosquito bites. These findings add further to the growing weight of evidence indicating that a single blood sample poorly captures within-host parasite diversity and underscore the importance of repeated blood sampling to accurately capture within-host parasite ecology. Our data also demonstrate a more pronounced role for parasite co-transmission in generating within-host parasite diversity in high transmission settings than previously assumed. Taken together, these findings have important implications for understanding the evolution of drug resistance, malaria transmission, parasite virulence, allocation of gametocyte sex ratios and acquisition of malaria immunity.
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Affiliation(s)
- Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; Wellcome Trust-Liverpool-Glasgow Centre for Global Health Research, 70 Pembroke Place, Liverpool L69 3GF, UK.
| | - Rachel L Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stanley Khoswe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tamika J Dzoole-Mwale
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stephen A Ward
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
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9
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Trevino SG, Nkhoma SC, Nair S, Daniel BJ, Moncada K, Khoswe S, Banda RL, Nosten F, Cheeseman IH. High-Resolution Single-Cell Sequencing of Malaria Parasites. Genome Biol Evol 2018; 9:3373-3383. [PMID: 29220419 PMCID: PMC5737330 DOI: 10.1093/gbe/evx256] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2017] [Indexed: 12/13/2022] Open
Abstract
Single-cell genomics is a powerful tool for determining the genetic architecture of complex communities of unicellular organisms. In areas of high transmission, malaria patients are often challenged by the activities of multiple Plasmodium falciparum lineages, which can potentiate pathology, spread drug resistance loci, and also complicate most genetic analysis. Single-cell sequencing of P. falciparum would be key to understanding infection complexity, though efforts are hampered by the extreme nucleotide composition of its genome (∼80% AT-rich). To counter the low coverage achieved in previous studies, we targeted DNA-rich late-stage parasites by Fluorescence-Activated Cell Sorting and whole genome sequencing. Our method routinely generates accurate, near-complete capture of the 23 Mb P. falciparum genome (mean breadth of coverage 90.7%) at high efficiency. Data from 48 single-cell genomes derived from a polyclonal infection sampled in Chikhwawa, Malawi allowed for unambiguous determination of haplotype diversity and recent meiotic events, information that will aid public health efforts.
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Affiliation(s)
- Simon G Trevino
- Genetics Department, Texas Biomedical Research Institute, San Antonio, Texas
| | - Standwell C Nkhoma
- Malawi-Wellcome-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, United Kingdom
| | - Shalini Nair
- Genetics Department, Texas Biomedical Research Institute, San Antonio, Texas
| | - Benjamin J Daniel
- University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Karla Moncada
- University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Stanley Khoswe
- Malawi-Wellcome-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, Blantyre, Malawi
| | - Rachel L Banda
- Malawi-Wellcome-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, Blantyre, Malawi
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand.,Nuffield Department of Medicine, Centre for Tropical Medicine, University of Oxford, United Kingdom
| | - Ian H Cheeseman
- Genetics Department, Texas Biomedical Research Institute, San Antonio, Texas
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10
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Fulakeza JRM, Banda RL, Lipenga TR, Terlouw DJ, Nkhoma SC, Hodel EM. Comparison of Two Genotyping Methods for Distinguishing Recrudescence from Reinfection in Antimalarial Drug Efficacy/Effectiveness Trials. Am J Trop Med Hyg 2018; 99:84-86. [PMID: 29785925 PMCID: PMC6085787 DOI: 10.4269/ajtmh.18-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 01/10/2023] Open
Abstract
Genotyping of allelic variants of Plasmodium falciparum merozoite surface proteins 1 and 2 (msp-1 and msp-2), and the glutamate-rich protein is the gold standard for distinguishing reinfections from recrudescences in antimalarial drug trials. We compared performance of the recently developed 24-single-nucleotide polymorphism (SNP) Barcoding Assay against msp-1 and msp-2 genotyping in a cluster-randomized effectiveness trial of artemether-lumefantrine and dihydroartemisinin-piperaquine in Malawi. Rates of recrudescence and reinfection estimated by the two methods did not differ significantly (Fisher's exact test; P = 0.887 and P = 0.768, respectively). There was a strong agreement between the two methods in predicting treatment outcomes and resolving the genetic complexity of malaria infections in this setting. These results support the use of this SNP assay as an alternative method for correcting antimalarial efficacy/effectiveness data.
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Affiliation(s)
| | - Rachel L Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Trancizeo R Lipenga
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Dianne J Terlouw
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Eva Maria Hodel
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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11
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Taylor AR, Schaffner SF, Cerqueira GC, Nkhoma SC, Anderson TJC, Sriprawat K, Pyae Phyo A, Nosten F, Neafsey DE, Buckee CO. Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. PLoS Genet 2017; 13:e1007065. [PMID: 29077712 PMCID: PMC5678785 DOI: 10.1371/journal.pgen.1007065] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/08/2017] [Accepted: 10/10/2017] [Indexed: 01/18/2023] Open
Abstract
With the rapidly increasing abundance and accessibility of genomic data, there is a growing interest in using population genetic approaches to characterize fine-scale dispersal of organisms, providing insight into biological processes across a broad range of fields including ecology, evolution and epidemiology. For sexually recombining haploid organisms such as the human malaria parasite P. falciparum, however, there have been no systematic assessments of the type of data and methods required to resolve fine scale connectivity. This analytical gap hinders the use of genomics for understanding local transmission patterns, a crucial goal for policy makers charged with eliminating this important human pathogen. Here we use data collected from four clinics with a catchment area spanning approximately 120 km of the Thai-Myanmar border to compare the ability of divergence (FST) and relatedness based on identity by descent (IBD) to resolve spatial connectivity between malaria parasites collected from proximal clinics. We found no relationship between inter-clinic distance and FST, likely due to sampling of highly related parasites within clinics, but a significant decline in IBD-based relatedness with increasing inter-clinic distance. This association was contingent upon the data set type and size. We estimated that approximately 147 single-infection whole genome sequenced parasite samples or 222 single-infection parasite samples genotyped at 93 single nucleotide polymorphisms (SNPs) were sufficient to recover a robust spatial trend estimate at this scale. In summary, surveillance efforts cannot rely on classical measures of genetic divergence to measure P. falciparum transmission on a local scale. Given adequate sampling, IBD-based relatedness provides a useful alternative, and robust trends can be obtained from parasite samples genotyped at approximately 100 SNPs.
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Affiliation(s)
- Aimee R. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Stephen F. Schaffner
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Gustavo C. Cerqueira
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Standwell C. Nkhoma
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Timothy J. C. Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Oxford, United Kingdom
| | - Daniel E. Neafsey
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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12
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Cheeseman IH, Miller B, Tan JC, Tan A, Nair S, Nkhoma SC, De Donato M, Rodulfo H, Dondorp A, Branch OH, Mesia LR, Newton P, Mayxay M, Amambua-Ngwa A, Conway DJ, Nosten F, Ferdig MT, Anderson TJC. Population Structure Shapes Copy Number Variation in Malaria Parasites. Mol Biol Evol 2015; 33:603-20. [PMID: 26613787 PMCID: PMC4760083 DOI: 10.1093/molbev/msv282] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
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Affiliation(s)
- Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Becky Miller
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Hectorina Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Oralee H Branch
- Division of Parasitology, Department of Microbiology, New York University School of Medicine
| | - Lastenia Ruiz Mesia
- Laboratorio De Investigaciones De Productos Naturales Y Antiparasitarios, Universidad Nacional De La Amazonia Peruana, Iquitos, Peru
| | - Paul Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | | | - David J Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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13
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Sisya TJ, Kamn'gona RM, Vareta JA, Fulakeza JM, Mukaka MFJ, Seydel KB, Laufer MK, Taylor TE, Nkhoma SC. Subtle changes in Plasmodium falciparum infection complexity following enhanced intervention in Malawi. Acta Trop 2015; 142:108-14. [PMID: 25460345 PMCID: PMC4296692 DOI: 10.1016/j.actatropica.2014.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/25/2014] [Accepted: 11/17/2014] [Indexed: 11/29/2022]
Abstract
We examined impact of intense malaria control on parasite genetic structure in Malawi. Malaria infections sampled before and after intense control were genotyped at 24 SNPs. Despite intense control efforts, parasite genetic diversity was unchanged over time. Only the mean number of heterozygous SNPs within infections showed change over time. Findings suggest minimal or no change in malaria transmission despite intense control.
With support from the Global Fund, the United States President's Malaria Initiative (PMI) and other cooperating partners, Malawi is implementing a comprehensive malaria control programme involving indoor residual spraying in targeted districts, universal coverage with insecticide-treated bed nets, use of rapid diagnostic tests to confirm the clinical diagnosis of malaria and use of the highly effective artemisinin-based combination therapy, artemether-lumefantrine (AL), as the first-line treatment for malaria. We genotyped 24 genome-wide single nucleotide polymorphisms (SNPs) in Plasmodium falciparum infections (n = 316) sampled from a single location in Malawi before (2006 and 2007) and after enhanced intervention (2008 and 2012). The SNP data generated were used to examine temporal changes in the proportion of multiple-genotype infections (MIs), mean number of heterozygous SNPs within MIs, parasite genetic diversity (expected heterozygosity and genotypic richness), multilocus linkage disequilibrium and effective population size (Ne). While the proportion of MIs, expected heterozygosity, genotypic richness, multilocus linkage disequilibrium and Ne were unchanged over time, the mean number (±standard deviation) of heterozygous SNPs within MIs decreased significantly (p = 0.01) from 9(±1) in 2006 to 7(±1) in 2012. These findings indicate that the genetic diversity of P. falciparum malaria parasites in this area remains high, suggesting that only subtle gains, if any, have been made in reducing malaria transmission. Continued surveillance is required to evaluate the impact of malaria control interventions in this area and the rest of Malawi, and to better target control interventions.
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Affiliation(s)
- Tamika J Sisya
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Raphael M Kamn'gona
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Jimmy A Vareta
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Joseph M Fulakeza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Mavuto F J Mukaka
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Karl B Seydel
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi; Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Miriam K Laufer
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi; Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Terrie E Taylor
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi; Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, UK.
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14
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Nair S, Nkhoma SC, Serre D, Zimmerman PA, Gorena K, Daniel BJ, Nosten F, Anderson TJC, Cheeseman IH. Single-cell genomics for dissection of complex malaria infections. Genome Res 2014; 24:1028-38. [PMID: 24812326 PMCID: PMC4032849 DOI: 10.1101/gr.168286.113] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [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: 12/20/2022]
Abstract
Most malaria infections contain complex mixtures of distinct parasite lineages. These multiple-genotype infections (MGIs) impact virulence evolution, drug resistance, intra-host dynamics, and recombination, but are poorly understood. To address this we have developed a single-cell genomics approach to dissect MGIs. By combining cell sorting and whole-genome amplification (WGA), we are able to generate high-quality material from parasite-infected red blood cells (RBCs) for genotyping and next-generation sequencing. We optimized our approach through analysis of >260 single-cell assays. To quantify accuracy, we decomposed mixtures of known parasite genotypes and obtained highly accurate (>99%) single-cell genotypes. We applied this validated approach directly to infections of two major malaria species, Plasmodium falciparum, for which long term culture is possible, and Plasmodium vivax, for which no long-term culture is feasible. We demonstrate that our single-cell genomics approach can be used to generate parasite genome sequences directly from patient blood in order to unravel the complexity of P. vivax and P. falciparum infections. These methods open the door for large-scale analysis of within-host variation of malaria infections, and reveal information on relatedness and drug resistance haplotypes that is inaccessible through conventional sequencing of infections.
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Affiliation(s)
- Shalini Nair
- Texas Biomedical Research Institute, San Antonio, Texas 78227-5301, USA
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, Blantyre 3, Malawi
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA
| | - Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Karla Gorena
- University of Texas Health Science Center San Antonio, San Antonio, Texas 78229, USA
| | - Benjamin J Daniel
- University of Texas Health Science Center San Antonio, San Antonio, Texas 78229, USA
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak 63110, Thailand; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford 0X3 7LJ, United Kingdom
| | | | - Ian H Cheeseman
- Texas Biomedical Research Institute, San Antonio, Texas 78227-5301, USA
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15
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Nkhoma SC, Stepniewska K, Nair S, Phyo AP, McGready R, Nosten F, Anderson TJC. Genetic evaluation of the performance of malaria parasite clearance rate metrics. J Infect Dis 2013; 208:346-50. [PMID: 23592863 PMCID: PMC3685230 DOI: 10.1093/infdis/jit165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Accurate measurement of malaria parasite clearance rates (CRs) following artemisinin (ART) treatment is critical for resistance surveillance and research, and various CR metrics are currently used. We measured 13 CR metrics in 1472 ART-treated hyperparasitemia infections for which 6-hour parasite counts and parasite genotypes (93 single nucleotide polymorphisms [SNPs]) were available. We used heritability to evaluate the performance of each metric. Heritability ranged from 0.06 ± 0.06 (SD) for 50% parasite clearance times to 0.67 ± 0.04 (SD) for clearance half-lives estimated from 6-hour parasite counts. These results identify the measures that should be avoided and show that reliable clearance measures can be obtained with abbreviated monitoring protocols.
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16
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Nkhoma SC, Nair S, Al-Saai S, Ashley E, McGready R, Phyo AP, Nosten F, Anderson TJC. Population genetic correlates of declining transmission in a human pathogen. Mol Ecol 2012; 22:273-85. [PMID: 23121253 PMCID: PMC3537863 DOI: 10.1111/mec.12099] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [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: 07/09/2012] [Revised: 09/14/2012] [Accepted: 09/19/2012] [Indexed: 12/17/2022]
Abstract
Pathogen control programs provide a valuable, but rarely exploited, opportunity to directly examine the relationship between population decline and population genetics. We investigated the impact of an ~12-fold decline in transmission on the population genetics of Plasmodium falciparum infections (n = 1731) sampled from four clinics on the Thai-Burma border over 10 years and genotyped using 96 genome-wide SNPs. The most striking associated genetic change was a reduction in the frequency of infections containing multiple parasite genotypes from 63% in 2001 to 14% in 2010 (P = 3 × 10(-15)). Two measures of the clonal composition of populations (genotypic richness and the β-parameter of the Pareto distribution) declined over time as more people were infected by parasites with identical multilocus genotypes, consistent with increased selfing and a reduction in the rate at which multilocus genotypes are broken apart by recombination. We predicted that the reduction in transmission, multiple clone carriage and outbreeding would be mirrored by an increased influence of genetic drift. However, geographical differentiation and expected heterozygosity remained stable across the sampling period. Furthermore, N(e) estimates derived from allele frequencies fluctuation between years remained high (582 to ∞) and showed no downward trend. These results demonstrate how genetic data can compliment epidemiological assessments of infectious disease control programs. The temporal changes in a single declining population parallel to those seen in comparisons of parasite genetics in regions of differing endemicity, strongly supporting the notion that reduced opportunity for outbreeding is the key driver of these patterns.
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Affiliation(s)
- Standwell C Nkhoma
- Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA
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17
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Nkhoma SC, Nair S, Cheeseman IH, Rohr-Allegrini C, Singlam S, Nosten F, Anderson TJC. Close kinship within multiple-genotype malaria parasite infections. Proc Biol Sci 2012; 279:2589-98. [PMID: 22398165 PMCID: PMC3350702 DOI: 10.1098/rspb.2012.0113] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [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: 11/12/2022] Open
Abstract
Malaria infections containing multiple parasite genotypes are ubiquitous in nature, and play a central role in models of recombination, intra-host dynamics, virulence, sex ratio, immunity and drug resistance evolution in Plasmodium. While these multiple infections (MIs) are often assumed to result from superinfection (bites from multiple infected mosquitoes), we know remarkably little about their composition or generation. We isolated 336 parasite clones from eight patients from Malawi (high transmission) and six from Thailand (low transmission) by dilution cloning. These were genotyped using 384 single-nucleotide polymorphisms, revealing 22 independent haplotypes in Malawi (2–6 per MI) and 15 in Thailand (2–5 per MI). Surprisingly, all six patients from Thailand and six of eight from Malawi contained related haplotypes, and haplotypes were more similar within- than between-infections. These results argue against a simple superinfection model. Instead, the observed kinship patterns may be explained by inoculation of multiple related haploid sporozoites from single mosquito bites, by immune suppression of parasite subpopulations within infections, and serial transmission of related parasites between people. That relatedness is maintained in endemic areas in the face of repeated bites from infected mosquitoes has profound implications for understanding malaria transmission, immunity and intra-host dynamics of co-infecting parasite genotypes.
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Affiliation(s)
- Standwell C Nkhoma
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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