1. Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates
- Author
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Antoine Claessens, Lindsay B. Stewart, Eleanor Drury, Ambroise D. Ahouidi, Alfred Amambua-Ngwa, Mahamadou Diakite, Dominic P. Kwiatkowski, Gordon A. Awandare, David J. Conway, Laboratory of Pathogen and Host Immunity [Montpellier] (LPHI), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), London School of Hygiene and Tropical Medicine (LSHTM), London School of Hygiene and Tropical Medicine [Fajara, Gambia], The Wellcome Trust Sanger Institute [Cambridge], Hôpital Aristide-Le-Dantec, Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), University of Bamako [Mali], West African Centre for Cell Biology of Infectious Pathogens [Legon, Ghana] (WACCBIP), University of Ghana, and This study was supported by funding from the European Research Council (AdG-2011–294428), the Royal Society (AA110050) and the UK Medical Research Council (MR/S009760/1). Support for A.C. was provided by a joint MRC Gambia-LSHTM fellowship. Genome sequencing was conducted at the Wellcome Sanger Institute, with funding from The Wellcome Trust (grants 098051, 206194, 090770).
- Subjects
MESH: Humans ,MESH: Genomics ,MESH: Malaria ,mixed genotypes ,adaptation ,General Medicine ,MESH: Protein Serine-Threonine Kinases ,culture ,MESH: Genotype ,loss-of-function mutants ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,MESH: Guanine Nucleotide Exchange Factors ,genomic relatedness ,MESH: Plasmodium falciparum ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology - Abstract
Experimental studies on the biology of malaria parasites have mostly been based on laboratory-adapted lines, but there is limited understanding of how these may differ from parasites in natural infections. Loss-of-function mutants have previously been shown to emerge during culture of some Plasmodium falciparum clinical isolates in analyses focusing on single-genotype infections. The present study included a broader array of isolates, mostly representing multiple-genotype infections, which are more typical in areas where malaria is highly endemic. Genome sequence data from multiple time points over several months of culture adaptation of 28 West African isolates were analysed, including previously available sequences along with new genome sequences from additional isolates and time points. Some genetically complex isolates eventually became fixed over time to single surviving genotypes in culture, whereas others retained diversity, although proportions of genotypes varied over time. Drug resistance allele frequencies did not show overall directional changes, suggesting that resistance-associated costs are not the main causes of fitness differences among parasites in culture. Loss-of-function mutants emerged during culture in several of the multiple-genotype isolates, affecting genes (including AP2-HS, EPAC and SRPK1) for which loss-of-function mutants were previously seen to emerge in single-genotype isolates. Parasite clones were derived by limiting dilution from six of the isolates, and sequencing identified de novo variants not detected in the bulk isolate sequences. Interestingly, several of these were nonsense mutants and frameshifts disrupting the coding sequence of EPAC, the gene with the largest number of independent nonsense mutants previously identified in laboratory-adapted lines. Analysis of genomic identity by descent to explore relatedness among clones revealed co-occurring non-identical sibling parasites, illustrative of the natural genetic structure within endemic populations.
- Published
- 2023