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Background  The eastern part of the Tibetan Plateau is now recognized as an endemic region with the highest reported human infection rates in the world of human alveolar echinococcosis (AE) caused by  Echinococcus multilocularis . Existing epidemiological studies on AE have mainly focused on the synanthropic environment, while basic parasitological and ecological aspects in wildlife host species remain largely unknown, especially for small mammal hosts. Therefore, we examined small mammal host species composition, occurrence, and the prevalence of both  E. multilocularis  and  E. shiquicus  in Shiqu County (Sichuan Province, China), eastern Tibetan Plateau.    Results  In total, 346 small mammals from five rodent and one pika species were trapped from four randomly set 0.25 ha square plots. Two vole species,  Lasiopodomys fuscus  ( n  = 144) and  Microtus limnophilus  ( n  = 44), and the plateau pika ( Ochotona curzoniae ) ( n  = 135), were the three most-dominant species trapped. Although protoscoleces of  E. multilocularis  and  E. shiquicus  were only observed in  L. fuscus  and  O. curzoniae , respectively,  cox 1 and  nad 1 gene DNA of  E. shiquicus  was detected in all the small mammal species except for  Neodon irene , whereas  E. multilocularis  was detected in the three most-dominant species. The overall molecular prevalence of  Echinococcus  species was 5.8 (95% CI: 3.3–8.2%) ~ 10.7% (95% CI: 7.4–14.0%) (the conservative prevalence to the maximum prevalence with 95% CI in parentheses), whereas for  E. multilocularis  it was 4.3 (95% CI: 2.2–6.5%) ~ 6.7% (95% CI: 4.0–9.3%), and 1.5 (95% CI: 0.2–2.7%) ~ 4.1% (95% CI: 2.0–6.1%) for  E. shiquicus . The prevalence of both  E. multilocularis  and  E. shiquicus , was significantly higher in rodents (mainly voles) than in pikas. Phylogenetic analyses revealed that  Echinococcus  haplotypes of  cox 1 from small mammal hosts were actively involved in the sylvatic and anthropogenic transmission cycles of  E. multilocularis  in the eastern Tibetan Plateau.    Conclusions  In contrast to previous studies, the current results indicated that rodent species, rather than pikas, are probably more important natural intermediate hosts of  E. multilocularis  and  E. shiquicus  in the eastern Tibetan Plateau. Thus, understanding interspecific dynamics between rodents and pikas is essential to studies of the echinococcosis transmission mechanism and human echinococcosis prevention in local communities.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2873-x) contains supplementary material, which is available to authorized users.

parasites and vectors

Echinococcus multilocularis and Echinococcus shiquicus in a small mammal community on the eastern Tibetan Plateau: host species composition, molecular prevalence, and epidemiological implications