Chronic infections can shape epidemic exposure: Pathogen co-occurrence networks in the Serengeti lions

Nicholas M. Fountain-Jones; Craig Packer; Maude Jacquot; F. Guillaume Blanchet; Karen Terio; Meggan E. Craft

Discriminating between positive or negative interactions between pathogens in populations is complicated by the short time window that an acute pathogen is shedding (and thus detectable with molecular methods) and by potentially confounding host environments (Tompkins et al. 2011) . This is particularly the case for microparasites where pathogen detection often relies on serology, and, thus, without resampling the same individual, the precise timing of exposure cannot be estimated. Detection of chronic pathogens may be more straightforward as the infection is active for more extended periods, but deducing pathogen interactions is difficult without extensive longitudinal data (Tompkins et al. 2011; Fenton et al. 2014) . Identifying whether two pathogens interact due to host-habitat preferences, the increasing likelihood of exposure with age, or infra-community processes such as competition is methodologically challenging (Poulin 2007; Johnson & Buller 2011; Fenton et al. 2014; Clark et al. 2016) .