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Background  Despite declining incidence over the past decade, malaria remains an important health burden in India. This study aimed to assess the village-level temporal patterns of  Plasmodium  infection in two districts of the north-eastern state of Meghalaya and evaluate risk factors that might explain these patterns.    Methods  Primary Health Centre passive malaria case data from 2014 to 2018 were analysed to characterize village-specific annual incidence and temporal trends. Active malaria case detection was undertaken in 2018 and 2019 to detect  Plasmodium  infections using PCR. A questionnaire collected socio-demographic, environmental, and behavioural data, and households were spatially mapped via GPS. Adult mosquitoes were sampled at a subset of subjects' houses, and  Anopheles  were identified by PCR and sequencing. Risk factors for  Plasmodium  infection were evaluated using bivariate and multivariate logistic regression analysis, and spatial cluster analysis was undertaken.    Results  The annual malaria incidence from PHC-based passive surveillance datasets in 2014–2018 was heterogenous but declining across villages in both districts. Active surveillance in 2018 enrolled 1468 individuals from 468 households (West Jaintia Hills) and 1274 individuals from 359 households (West Khasi Hills).  Plasmodium falciparum  prevalence per 100 people varied from 0 to 4.1% in the nine villages of West Jaintia Hills, and from 0 to 10.6% in the 12 villages of West Khasi Hills .  Significant clustering of  P. falciparum  infections [observed = 11, expected = 2.15, Relative Risk (RR) = 12.65;  p  < 0.001] was observed in West Khasi Hills. A total of 13  Anopheles  species were found at 53 houses in five villages, with  Anopheles jeyporiensis  being the most abundant. Risk of infection increased with presence of mosquitoes and electricity in the households [Odds Ratio (OR) = 1.19 and 1.11], respectively. Households with reported animals had reduced infection risk (OR = 0.91).    Conclusion  Malaria incidence during 2014–2018 declined in all study villages covered by the passive surveillance data, a period that includes the first widespread insecticide-treated net campaign. The survey data from 2018 revealed a significant association between  Plasmodium  infection and certain household characteristics. Since species of  Plasmodium -competent mosquito vectors continue to be abundant, malaria resurgence remains a threat, and control efforts should continue.

Spatial and temporal village-level prevalence of Plasmodium infection and associated risk factors in two districts of Meghalaya, India