Using open-access taxonomic and spatial information to create a comprehensive database for the study of Mammalian and avian livestock and pet infections
Using open-access taxonomic and spatial information to create a comprehensive database for the study of Mammalian and avian livestock and pet infections
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DOI：
10.1016/j.prevetmed.2013.07.002
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发表时间：
2014-10-01
影响因子：
2.6
通讯作者：
Baylis, M.
中科院分区：
文献类型：
--
作者：
McIntyre, K. M.;Setzkorn, C.;Baylis, M.
影响我们牲畜的病原体种类有哪些？由于每10个人类病原体中就有6个来自动物，其中很大一部分来自牲畜和宠物，因此未来出现的可能威胁或破坏人类健康的大多数病原体可能来自动物。仅在10年前，第一份针对人类的全面病原体清单才编制出来;我们仍然没有针对动物的相应清单。在这里，我们描述了一个新型病原体数据库的创建，并展示了该数据库的输出，证明了其价值。ENHanCEd传染病数据库（EID 2）是开放访问且基于证据的，它描述了人类和动物的病原体、其宿主和媒介物种，以及它们在全球的发生情况。EID 2系统地整理病原体的信息到一个单一的资源，使用NCBI分类数据库，NCBI核苷酸数据库，NCBI MeSH（医学主题词）库和PubMed的证据。使用元数据的数据挖掘和半自动化文献检索来分配有关病原体的信息。在这里，我们关注47种哺乳动物和鸟类宿主，包括在欧洲通常用作食物或宠物的人类和动物。目前，EID 2证据表明：在这些宿主物种中，病原菌为细菌395种，占30.5%;真菌705例，占15.2%（27.1%）蠕虫，372原虫占14.3%，（12.8%）病毒。病原体出现与不出现的几率因分类学划分而异，当病原体有更多数量的宿主物种与它们相关，并且是人畜共患病而不是非人畜共患病时，病原体出现与不出现的几率会增加。病原体是人畜共患病与非人畜共患病的几率因分类学划分而异，并且当与更大数量的宿主相关时也会增加。影响最大数量的宿主的病原体包括：大肠杆菌、贾第鞭毛虫、刚地弓形虫、嗜吞噬细胞无形体、微小隐孢子虫、狂犬病病毒、金黄色葡萄球菌、犬新孢子虫和细粒棘球绦虫。人类和家畜宿主的病原体的特征在于病原体和宿主物种之间的4223种相互作用，在人类、绵羊/山羊、牛、小型哺乳动物、猪、狗和马科动物中发现的数量最多。病原体种类的数量因欧洲国家而异。与世界其他地区相比，在欧洲发现病原体的几率因分类学而异，如果它们正在出现与未出现相比，或者与它们相关的宿主物种数量更多，则会增加。(C)2013作者Elsevier B. V.出版，保留所有权利。
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. (C) 2013 The Authors. Published by Elsevier B.V. All rights reserved.