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Background  Infectious keratoconjunctivitis (IKC) is an ocular infectious disease caused by  Mycoplasma conjunctivae  which affects small domestic and wild mountain ruminants. Domestic sheep maintain the pathogen but the detection of healthy carriers in wildlife has raised the question as to whether  M. conjunctivae  may also persist in the wild. Furthermore, the factors shaping the dynamics of IKC outbreaks in wildlife have remained largely unknown. The aims of this study were (1) to verify the etiological role of  M. conjunctivae  in IKC outbreaks recorded between 2002 and 2010 at four study sites in different regions of France (Pyrenees and Alps, samples from 159 Alpine ibex  Capra ibex , Alpine chamois  Rupicapra rupicapra  and Pyrenean chamois  Rupicapra pyrenaica ); (2) to establish whether there existed any epidemiological links between the different regions through a cluster analysis of the detected strains (from 80 out of the 159 animals tested); (3) to explore selected pathogen, host and environmental factors potentially influencing the dynamics of IKC in wildlife, by joining results obtained by molecular analyses and by field observations (16,609 animal observations). All of the samples were tested for  M. conjunctivae  by qPCR, and cluster analysis was based on a highly variable part of the  lppS  gene.    Results  We documented infections with  M. conjunctivae  in epidemic and endemic situations, both in symptomatic and asymptomatic animals. The identified  M. conjunctivae  strains were site-specific and persisted in the local wild population for at least 6 years. In epidemic situations, peaks of cases and disease resurgence were associated with the emergence of new similar strains in a given area. Social interactions, seasonal movements and the landscape structure such as natural and anthropogenic barriers influenced the spatio-temporal spread of IKC. Adults were more affected than young animals and host susceptibility differed depending on the involved strain.    Conclusion  Our study indicates that IKC is a multifactorial disease and that  M. conjunctivae  can persist in wildlife populations. The disease course in individual animals and populations is influenced by both host and mycoplasma characteristics, and the disease spread within and among populations is shaped by host behavior and landscape structure.    Electronic supplementary material  The online version of this article (doi:10.1186/s12917-017-0972-0) contains supplementary material, which is available to authorized users.

Infectious keratoconjunctivitis in wild Caprinae: merging field observations and molecular analyses sheds light on factors shaping outbreak dynamics