Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast

English version

Autoři: Aimee R. Taylor ^aff001; Diego F. Echeverry ^aff003; Timothy J. C. Anderson ^aff006; Daniel E. Neafsey ^aff002; Caroline O. Buckee ^aff001
Působiště autorů: Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA ^aff001; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA ^aff002; Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia ^aff003; Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia ^aff004; Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia ^aff005; Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA ^aff006; Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA ^aff007
Vyšlo v časopise: Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast. PLoS Genet 16(11): e1009101. doi:10.1371/journal.pgen.1009101
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1009101

Souhrn

Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between malaria parasite populations, with implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). However, uncertainty around estimated relatedness has not been accounted for. IBD-based relatedness estimates with uncertainty were computed for pairs of monoclonal Plasmodium falciparum samples collected from five cities on the Colombian-Pacific coast where long-term clonal propagation of P. falciparum is frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically but connected by frequent marine traffic. Fractions of highly-related sample pairs (whose classification using a threshold accounts for uncertainty) were greater within cities versus between. However, based on both highly-related fractions and on a threshold-free approach (Wasserstein distances between parasite populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura-Tumaco connectivity was consistent with transmission events involving parasites from five clonal components (groups of statistically indistinguishable parasites identified under a graph theoretic framework). To conclude, P. falciparum population connectivity on the Colombian-Pacific coast abides by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with opportunities for targeted intervention. Further investigations are required to test this hypothesis. For the first time in malaria epidemiology (and to our knowledge in ecological and epidemiological studies more generally), we account for uncertainty around estimated relatedness (an important consideration for studies that plan to use genotype versus whole genome sequence data to estimate IBD-based relatedness); we also use threshold-free methods to compare parasite populations and identify clonal components. Threshold-free methods are especially important in analyses of malaria parasites and other recombining organisms with mixed mating systems where thresholds do not have clear interpretation (e.g. due to clonal propagation) and thus undermine the cross-comparison of studies.

Klíčová slova:

Cities – Colombia – DNA recombination – Malaria – Malarial parasites – Parasitic diseases – Plasmodium – Single nucleotide polymorphisms

Zdroje

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