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Background  The malaria burden of Myanmar still remains high within the Greater Mekong Subregion of Southeast Asia. An important indicator of progress towards malaria elimination is the prevalence of parasite infections in endemic populations. Information about malaria epidemiology is mostly derived from reports of confirmed acute malaria cases through passive case detection, whereas the prevalence of baseline subclinical malaria infections is much less known.    Methods  In this study, cross-sectional surveys were conducted during the rainy season of 2017 in four townships (Bilin, Thabeikkyin, Banmauk and Paletwa) of Myanmar with divergent annual malaria incidences. A total of 1991 volunteers were recruited from local villages and  Plasmodium  subclinical infections were estimated by light microscopy (LM), rapid diagnostic tests (RDTs) and nested PCR. The nested PCR analysis was performed with a modified pooling strategy that was optimized based on an initial estimate the infection prevalence.    Results  The overall malaria infection prevalence based on all methods was 13.9% (277/1991) and it differed drastically among the townships, with Paletwa in the western border having the highest infection rate (22.9%) and Thabeikkyin in central Myanmar having the lowest (3.9%). As expected, nested PCR was the most sensitive and identified 226 (11.4%) individuals with parasite infections. Among the parasite species,  Plasmodium vivax  was the most prevalent in all locations, while  Plasmodium falciparum  also accounted for 32% of infections in the western township Paletwa. Two RDTs based on the detection of the hrp2 antigen detected a total of 103  P. falciparum  infections, and the ultrasensitive RDT detected 20% more  P. falciparum  infections than the conventional RDT. In contrast, LM missed the majority of the subclinical infections and only identified 14  Plasmodium  infections.    Conclusions  Cross-sectional surveys identified considerable levels of asymptomatic  Plasmodium  infections in endemic populations of Myanmar with  P. vivax  becoming the predominant parasite species. Geographical heterogeneity of subclinical infections calls for active surveillance of parasite infections in endemic areas. The pooling scheme designed for nested PCR analysis offers a more practical strategy for large-scale epidemiological studies of parasite prevalence. Such information is important for decision-makers to put forward a more realistic action plan for malaria elimination.    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3330-1) contains supplementary material, which is available to authorized users.

Geographical heterogeneity in prevalence of subclinical malaria infections at sentinel endemic sites of Myanmar