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Background  Scrub typhus is an important neglected vector-borne zoonotic disease across the Asia–Pacific region, with an expanding known distribution. The disease ecology is poorly understood, despite the large global burden of disease. The key determinants of high-risk areas of transmission to humans are unknown.    Methods  Small mammals and chiggers were collected over an 18-month period at three sites of differing ecological profiles with high scrub typhus transmission in Chiang Rai Province, northern Thailand. Field samples were identified and tested for  Orientia tsutsugamushi  by real-time PCR. The rates and dynamics of infection were recorded, and positive and negative individuals were mapped over time at the scale of single villages. Ecological analyses were performed to describe the species richness, community structure and interactions between infected and uninfected species and habitats. Generalised linear modelling (GLM) was applied to examine these interactions.    Results  The site with the highest rates of human infection was associated with the highest number of infected chigger pools (41%), individual chiggers (16%), proportion of the known vector species  Leptotrombidium deliense  (71%) and chigger index (151). Chigger species diversity was lowest (Shannon diversity index  H ′: 1.77) and rodent density appeared to be high. There were no consistent discrete foci of infection identified at any of the study sites. The small mammals  Rattus tanezumi  and  Bandicota indica  and the chiggers  L. deliense  and  Walchia kritochaeta  emerged as central nodes in the network analysis. In the GLM, the end of the dry season, and to a lesser extent the end of the wet season, was associated with  O. tsutsugamushi -infected small mammals and chiggers. A clear positive association was seen between  O. tsutsugamushi- positive chigger pools and the combination of  O. tsutsugamushi- positive chigger pools and  O. tsutsugamushi- positive small mammals with lowland habitats.    Conclusions  These findings begin to reveal some of the factors that may determine high-risk foci of scrub typhus at a fine local scale. Understanding these factors may allow practical public health interventions to reduce disease risk. Further studies are needed in areas with diverse ecology.    Graphical abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-05042-4.

Orientia tsutsugamushi dynamics in vectors and hosts: ecology and risk factors for foci of scrub typhus transmission in northern Thailand