publication . Article . Other literature type . 2016

A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections

Oksana Kharabora; Jonathan J. Juliano; Steven R. Meshnick; Andrew F. Read; Anders Björkman; Billy Ngasala; David L. Saunders; Andrew Jamnik; Jeffrey A. Bailey; Chanthap Lon; ...
Open Access English
  • Published: 01 Jan 2016 Journal: Evolution, Medicine, and Public Health, volume 2,016, issue 1, pages 21-36 (eissn: 2050-6201, Copyright policy)
  • Publisher: Oxford University Press
  • Country: Sweden
Abstract
Background and objectives: Current tools struggle to detect drug-resistant malaria parasites when infections contain multiple parasite clones, which is the norm in high transmission settings in Africa. Our aim was to develop and apply an approach for detecting resistance that overcomes the challenges of polyclonal infections without requiring a genetic marker for resistance. Methodology: Clinical samples from patients treated with artemisinin combination therapy were collected from Tanzania and Cambodia. By deeply sequencing a hypervariable locus, we quantified the relative abundance of parasite subpopulations (defined by haplotypes of that locus) within infecti...
Subjects
Medical Subject Headings: parasitic diseases
free text keywords: Original Research Article, malaria, within-host selection, ecology, amplicon sequencing, artemisinin, drug resistance, Occupational Health and Environmental Health, Arbetsmedicin och miljömedicin, Clearance rate, Locus (genetics), Immunology, Parasite hosting, Deep sequencing, medicine.drug, medicine, medicine.disease, Genetic marker, Biology
Funded by
NSERC
Project
  • Funder: Natural Sciences and Engineering Research Council of Canada (NSERC)
,
NIH| Human copy number polymorphism and severe malaria
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI099473-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Genomics Core
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19AI089676-04
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Within Host Selection of P. falciparum Variants by Artemisinin Combination Therap
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01AI089819-01
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
45 references, page 1 of 3

1 World Health Organization. World Malaria Report 2014 http://www.who.int/malaria/publications/world_malaria_report_2014/report/en/ (2 June 2015, date last accessed).

2 Amaratunga C Sreng S Suon S Artemisinin-resistant Plasmodium falciparum in Pursat province, western Cambodia: a parasite clearance rate study. Lancet Infect Dis 2012;12:851–8.22940027 [OpenAIRE] [PubMed]

3 Ashley EA Dhorda M Fairhurst RM Spread of artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med 2014;371:411–23.25075834 [OpenAIRE] [PubMed]

4 Dondorp AM Nosten F Yi P Artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med 2009;361:455–67.19641202 [OpenAIRE] [PubMed]

5 Dondorp AM Yeung S White L Artemisinin resistance: current status and scenarios for containment. Nat Rev Microbiol 2010;8:272–80.20208550 [OpenAIRE] [PubMed]

6 Phyo AP Nkhoma S Stepniewska K Emergence of artemisinin-resistant malaria on the western border of Thailand: a longitudinal study. Lancet 2012;379:1960–6.22484134 [OpenAIRE] [PubMed]

7 Mideo N Kennedy DA Carlton JM Ahead of the curve: next generation estimators of drug resistance in malaria infections. Trends Parasitol 2013;29:321–8.23746748 [OpenAIRE] [PubMed]

8 Ariey F Witkowski B Amaratunga C A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. Nature 2014;505:50–5.24352242 [OpenAIRE] [PubMed]

9 Witkowski B Amaratunga C Khim N Novel phenotypic assays for the detection of artemisinin-resistant Plasmodium falciparum malaria in Cambodia: in-vitro and ex-vivo drug-respon se studies. Lancet Infect Dis 2013;13:1043–9.24035558 [OpenAIRE] [PubMed]

10 Kamau E Campino S Amenga-Etego L K13-propeller polymorphisms in Plasmodium falciparum p arasites from sub-Saharan Africa. J Infect Dis 2015;211:1352–5.25367300 [OpenAIRE] [PubMed]

11 Taylor SM Parobek CM DeConti DK Absence of putative artemisinin resistance mutations among Plasmodium falciparum in sub-Saharan Africa: a molecular epidemiologic study. J Infect Dis 2015;211:680–8.25180240 [OpenAIRE] [PubMed]

12 Straimer J Gnadig NF Witkowski B Drug resistance. K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates. Science 2015;347:428–31.25502314 [OpenAIRE] [PubMed]

13 Miotto O Amato R Ashley EA Genetic architecture of artemisinin-resistant Plasmodium falciparum. Nature Genet 2015;47:226–34.25599401 [OpenAIRE] [PubMed]

14 Andriantsoanirina V Ratsimbasoa A Bouchier C Chloroquine clinical failures in P. falciparum malaria are associated with mutant Pfmdr-1, not Pfcrt in Madagascar. PLoS One 2010;5:e13281.20967251 [OpenAIRE] [PubMed]

15 Ngalah BS Ingasia LA Cheruiyot AC Analysis of major genome loci underlying artemisinin resistance and pfmdr1 copy number in pre- and post-ACTs in western Kenya. Sci Rep 2015;5:8308.25655315 [OpenAIRE] [PubMed]

45 references, page 1 of 3
Abstract
Background and objectives: Current tools struggle to detect drug-resistant malaria parasites when infections contain multiple parasite clones, which is the norm in high transmission settings in Africa. Our aim was to develop and apply an approach for detecting resistance that overcomes the challenges of polyclonal infections without requiring a genetic marker for resistance. Methodology: Clinical samples from patients treated with artemisinin combination therapy were collected from Tanzania and Cambodia. By deeply sequencing a hypervariable locus, we quantified the relative abundance of parasite subpopulations (defined by haplotypes of that locus) within infecti...
Subjects
Medical Subject Headings: parasitic diseases
free text keywords: Original Research Article, malaria, within-host selection, ecology, amplicon sequencing, artemisinin, drug resistance, Occupational Health and Environmental Health, Arbetsmedicin och miljömedicin, Clearance rate, Locus (genetics), Immunology, Parasite hosting, Deep sequencing, medicine.drug, medicine, medicine.disease, Genetic marker, Biology
Funded by
NSERC
Project
  • Funder: Natural Sciences and Engineering Research Council of Canada (NSERC)
,
NIH| Human copy number polymorphism and severe malaria
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI099473-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Genomics Core
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19AI089676-04
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Within Host Selection of P. falciparum Variants by Artemisinin Combination Therap
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01AI089819-01
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
45 references, page 1 of 3

1 World Health Organization. World Malaria Report 2014 http://www.who.int/malaria/publications/world_malaria_report_2014/report/en/ (2 June 2015, date last accessed).

2 Amaratunga C Sreng S Suon S Artemisinin-resistant Plasmodium falciparum in Pursat province, western Cambodia: a parasite clearance rate study. Lancet Infect Dis 2012;12:851–8.22940027 [OpenAIRE] [PubMed]

3 Ashley EA Dhorda M Fairhurst RM Spread of artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med 2014;371:411–23.25075834 [OpenAIRE] [PubMed]

4 Dondorp AM Nosten F Yi P Artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med 2009;361:455–67.19641202 [OpenAIRE] [PubMed]

5 Dondorp AM Yeung S White L Artemisinin resistance: current status and scenarios for containment. Nat Rev Microbiol 2010;8:272–80.20208550 [OpenAIRE] [PubMed]

6 Phyo AP Nkhoma S Stepniewska K Emergence of artemisinin-resistant malaria on the western border of Thailand: a longitudinal study. Lancet 2012;379:1960–6.22484134 [OpenAIRE] [PubMed]

7 Mideo N Kennedy DA Carlton JM Ahead of the curve: next generation estimators of drug resistance in malaria infections. Trends Parasitol 2013;29:321–8.23746748 [OpenAIRE] [PubMed]

8 Ariey F Witkowski B Amaratunga C A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. Nature 2014;505:50–5.24352242 [OpenAIRE] [PubMed]

9 Witkowski B Amaratunga C Khim N Novel phenotypic assays for the detection of artemisinin-resistant Plasmodium falciparum malaria in Cambodia: in-vitro and ex-vivo drug-respon se studies. Lancet Infect Dis 2013;13:1043–9.24035558 [OpenAIRE] [PubMed]

10 Kamau E Campino S Amenga-Etego L K13-propeller polymorphisms in Plasmodium falciparum p arasites from sub-Saharan Africa. J Infect Dis 2015;211:1352–5.25367300 [OpenAIRE] [PubMed]

11 Taylor SM Parobek CM DeConti DK Absence of putative artemisinin resistance mutations among Plasmodium falciparum in sub-Saharan Africa: a molecular epidemiologic study. J Infect Dis 2015;211:680–8.25180240 [OpenAIRE] [PubMed]

12 Straimer J Gnadig NF Witkowski B Drug resistance. K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates. Science 2015;347:428–31.25502314 [OpenAIRE] [PubMed]

13 Miotto O Amato R Ashley EA Genetic architecture of artemisinin-resistant Plasmodium falciparum. Nature Genet 2015;47:226–34.25599401 [OpenAIRE] [PubMed]

14 Andriantsoanirina V Ratsimbasoa A Bouchier C Chloroquine clinical failures in P. falciparum malaria are associated with mutant Pfmdr-1, not Pfcrt in Madagascar. PLoS One 2010;5:e13281.20967251 [OpenAIRE] [PubMed]

15 Ngalah BS Ingasia LA Cheruiyot AC Analysis of major genome loci underlying artemisinin resistance and pfmdr1 copy number in pre- and post-ACTs in western Kenya. Sci Rep 2015;5:8308.25655315 [OpenAIRE] [PubMed]

45 references, page 1 of 3
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