title: Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.
abstract: What are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value. The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches. Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that: • Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses. • The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic. • The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. • The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus, Staphylococcus aureus, Neospora caninum and Echinococcus granulosus. • The pathogens of humans and domestic animal hosts are characterised by 4223 interactions between pathogen and host species, with the greatest number found in: humans, sheep/goats, cattle, small mammals, pigs, dogs and equids. • The number of pathogen species varied by European country. The odds of a pathogen being found in Europe compared to the rest of the world differed by taxonomic division, and increased if they were emerging compared to not emerging, or had a larger number of host species associated with them.
authors.affiliation: Department of Epidemiology and Population Health, Institute of Infection and Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston, Cheshire CH64 7TE, UK. Electronic address: k.m.mcintyre@liv.ac.uk.
authors.forename: K M
authors.initials: KM
authors.lastname: McIntyre
authors.affiliation: Department of Epidemiology and Population Health, Institute of Infection and Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston, Cheshire CH64 7TE, UK.
authors.forename: C
authors.initials: C
authors.lastname: Setzkorn
authors.affiliation: Department of Epidemiology and Population Health, Institute of Infection and Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston, Cheshire CH64 7TE, UK.
authors.forename: M
authors.initials: M
authors.lastname: Wardeh
authors.affiliation: Department of Epidemiology and Population Health, Institute of Infection and Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston, Cheshire CH64 7TE, UK.
authors.forename: P J
authors.initials: PJ
authors.lastname: Hepworth
authors.affiliation: Department of Infection Biology, IGH, UoL, UK.
authors.forename: A D
authors.initials: AD
authors.lastname: Radford
authors.affiliation: Department of Epidemiology and Population Health, Institute of Infection and Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston, Cheshire CH64 7TE, UK.
authors.forename: M
authors.initials: M
authors.lastname: Baylis
mesh_terms: D000820:Animal Diseases / Q000453:epidemiology / Q000209:etiology / Q000635:transmission; D000818:Animals; D001717:Birds; D016208:Databases, Factual; D058751:Livestock; D008322:Mammals; D057805:Pets
keywords: Database; Disease; Emerging; Pathogen; Surveillance; Zoonosis