Drivers for emerging issues in animal and plant health

Richardson, Jane; Lockhart, Caryl; Pongolini, Stefano; Karesh, William B.; Baylis, Matthew; Goldberg, Tony; Slingenbergh, Jan; Gale, Paul; Venturini, Tommaso; Catchpole, Mike; de Balogh, Katinka; Pautasso, Marco; Broglia, Alessandro; Berthe, Franck; Schans, Jan; Poppy, Guy

Relations between pathogens, hosts and environments: joining the dots Understanding the risks and drivers of emergence of pests and pathogens requires extensive knowledge of the types of microbes present in plants, animals and the environment, and their potential for cross-species/domain spread of disease-causing organisms, as well as the risk of commensals becoming pathogens. For example, human foodborne pathogens include microbes present in food-producing animals or the wider environment that we acquire by eating contaminated food. There is, however, a significant under-representation of plant, animal and environmental pathogens in the scientific literature compared to pathogens of human beings. Studies of pathogen diversity report over 40% more pathogen species known in humans alone than in up to 50 domestic animal species combined. A key research challenge is to identify the characteristics of pathogens that give them the propensity to be infectious, or be infectious to species or groups of species other than those already known to be susceptible. Considering the specific issue of zoonotic risk, key questions are: are some pathogen types (such as bacteria, viruses) more or less likely to spread from animals to humans? Are we humans most likely to acquire zoonotic pathogens from the animals that we eat (livestock), the ones we share our homes with (pets) or the ones we are most similar to genetically (primates)? And what about the few plant pathogens affecting humans (e.g. Cryptococcus gattii; Hagen et al., 2013) ? And is the transmission route important? Are we more likely to share foodborne pathogens with animals, than those that are transmitted by direct contact, by aerosol or by sexual contact? Are we overlooking the consequences for human health of regional outbreaks of exotic plant pests and pathogens (e.g. emerald ash borer) (Donovan et al., 2013) ? Data on pathogens and hosts can be acquired using automated procedures applied to online data sources, such as the metadata uploaded with gene sequences, and the abstracts of biomedical papers. Media monitoring and social media are also a source of unstructured data (Galaz et al., 2010; Daume et al., 2014; Alomar et al., 2015; Daume, 2016) . A pathogen/host database, such as the Enhanced Infectious Disease Database (EID2) can be used to address questions about the relationships between pathogens, hosts and their environment. At present, for example, the EID2 database holds information on 1,606 human pathogens, of which half are zoonotic, and 1,038 pathogens of domestic animals. Using network analysis, the human and animal hosts (dots) can be joined by the pathogens that they share, with the strongest joins for those that share the most pathogens. Joining the dots creates pathogen networks that can then be used to assess which types of host are the major source of pathogens for humans; and the network properties can be compared for different types of pathogen and those with different properties, such as transmission route. Such an approach should be further expanded to include more plants and environmental isolates.