Genetic Relatedness of Cambodian Plasmodium falciparum Isolates Was Associated with Geography and Occupation

Cambodia is nearing Plasmodium falciparum (P. falciparum) elimination, but targeted interventions are needed to prevent resurgence. Identity-by-descent (IBD)-based methods offer insight into parasite relatedness and transmission dynamics. Pairwise genetic relatedness was estimated among 107 P. falciparum isolates collected from military personnel and farmers during two clinical trials in Cambodia from 2014 to 2016. Using existing whole-genome sequence data, IBD relatedness was estimated as the proportion of the genome shared IBD between isolates. Associations between relatedness and epidemiological factors, including occupation, location, time, age, and sex, were evaluated. Network-based clustering was used to identify highly related isolate groups and associated covariates. High mean IBD sharing (40%) suggested clonal expansion or low transmission; isolates from Oddar Meanchey Province shared >20% more of their genome IBD than Kratie Province isolates (P <2.2e-16). Within Oddar Meanchey, isolates from individuals with different occupations shared 7.2% less of their genome IBD than farmer pairs (probability of direction [pd] = 0.999), after adjusting for age. Highly related clusters (>90% IBD) were associated with occupation, K13 mutation (C580Y versus R539T), and P. falciparum chloroquine resistance transporter mutation (P = 0.0027, 0.0001, and 0.0001, respectively). Isolates from mixed-occupation pairs had lower odds of being highly related (>90% IBD) than farmer pairs (pd = 0.958). High overall IBD sharing may reflect elimination efforts and the expansion of drug-resistant lineages. Differences in between-province relatedness underscore how geography shapes relatedness patterns. Lower relatedness among mixed-occupation pairs compared with farmer pairs suggests occupation-associated exposure differences, with occupation potentially acting as a proxy for micro-epidemiological exposure factors such as location or behavior, highlighting the need for locally tailored interventions.