Summary 1. Despite a growing interest in wildlife disease ecology, there is a surprising lack of knowledge about the exposure dynamics of individual animals to naturally circulating infectious agents and the impact of such agents on host life‐history traits. 2. The exploration of these questions requires detailed longitudinal data on individual animals that can be captured multiple times during their life but also requires being able to account for several sources of uncertainty, notably the partial observation or recapture of individuals at each sampling occasion. 3. We use a multi‐year dataset to (i) assess the potential effect of exposure to the tick‐borne agent of Lyme disease, Borrelia burgdorferi sensu lato (Bbsl), on adult apparent survival for one of its natural long‐lived hosts, the Black‐legged kittiwake (Rissa tridactyla), and (ii) investigate the temporal dynamics of individual immunological status in kittiwakes to infer the rate of new exposure and the persistence of the immune response. Using a multi‐event modelling approach, potential uncertainties arising from partial observations were explicitly taken into account. 4. The potential impact of Bbsl on kittiwake survival was also evaluated via an experimental approach: the apparent survival of a group of breeding birds treated with an antibiotic was compared with that of a control group. 5. No impact of exposure to Bbsl was detected on adult survival in kittiwakes, in either observational or experimental data. 6. An annual seroconversion rate (from negative to positive) of 1·5% was estimated, but once an individual became seropositive, it remained so with a probability of 1, suggesting that detectable levels of anti‐Bbsl antibodies persist for multiple years. 7. These results, in combination with knowledge on patterns of exposure to the tick vector of Bbsl, provide important information for understanding the spatio‐temporal nature of the interaction between this host and several of its parasites. Furthermore, our analyses highlight the utility of capture–mark–recapture approaches handling state uncertainty for disease ecology studies.

Abstract. Classifying the states of an individual and quantifying transitions between states are crucial while modeling animal behavior, movement, and physiologic status. When these states are hidden or imperfectly known, it is particularly convenient to relate them to appropriate quantitative measurements taken on the individual. This task is, however, challenging when quantitative measurements are not available at each sampling occasion. For capture-recapture data, various ways of incorporating such non-discrete information have been used, but they are either ad hoc and/or use a fraction of the available information by relying on a priori thresholds to assign individual states. Here we propose assigning discrete states based on a continuous measurement, and then modeled survival and transition probabilities based on these assignments. The main advantage of this new approach is that a more informative use of the non-discrete information is done. As an illustrative working example, we applied this approach to eco-epidemiological data collected across a series of years in which individuals of a long-lived seabird, the Black-legged Kittiwake (Rissa tridactyla), could either be visually detected or physically recaptured and blood sampled for subsequent immunological analyses. We discuss how this approach opens many perspectives in eco-epidemiology, but also more broadly, in population ecology.