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Background  Forests in urban landscapes differ from their rural counterparts in ways that may alter vector-borne disease dynamics. In urban forest fragments, tick-borne pathogen prevalence is not well characterized; mitigating disease risk in densely-populated urban landscapes requires understanding ecological factors that affect pathogen prevalence. We trapped blacklegged tick ( Ixodes scapularis ) nymphs in urban forest fragments on the East Coast of the United States and used multiplex real-time PCR assays to quantify the prevalence of four zoonotic, tick-borne pathogens. We used Bayesian logistic regression and WAIC model selection to understand how vegetation, habitat, and landscape features of urban forests relate to the prevalence of  B. burgdorferi  (the causative agent of Lyme disease) among blacklegged ticks.    Results  In the 258 nymphs tested, we detected  Borrelia burgdorferi  (11.2% of ticks),  Borrelia miyamotoi  (0.8%) and  Anaplasma phagocytophilum  (1.9%), but we did not find  Babesia microti  (0%). Ticks collected from forests invaded by non-native multiflora rose ( Rosa multiflora ) had greater  B. burgdorferi  infection rates (mean = 15.9%) than ticks collected from uninvaded forests (mean = 7.9%). Overall,  B. burgdorferi  prevalence among ticks was positively related to habitat features (e.g. coarse woody debris and total understory cover) favorable for competent reservoir host species.    Conclusions  Understory structure provided by non-native, invasive shrubs appears to aggregate ticks and reservoir hosts, increasing opportunities for pathogen transmission. However, when we consider pathogen prevalence among nymphs in context with relative abundance of questing nymphs, invasive plants do not necessarily increase disease risk. Although pathogen prevalence is greater among ticks in invaded forests, the probability of encountering an infected tick remains greater in uninvaded forests characterized by thick litter layers, sparse understories, and relatively greater questing tick abundance in urban landscapes.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2623-0) contains supplementary material, which is available to authorized users.

Multiflora rose invasion amplifies prevalence of Lyme disease pathogen, but not necessarily Lyme disease risk