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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.
PMID
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Authors

Mayor MeshTerms

Animal Diseases

Databases, Factual

Livestock

Pets

Keywords

Database

Disease

Emerging

Pathogen

Surveillance

Zoonosis

Journal Title preventive veterinary medicine
Publication Year Start
%A McIntyre, K. M.; Setzkorn, C.; Wardeh, M.; Hepworth, P. J.; Radford, A. D.; Baylis, M.
%T Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.
%J Preventive veterinary medicine, vol. 116, no. 3, pp. 325-335
%D 10/2014
%V 116
%N 3
%M eng
%B 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.
%K Animal Diseases, Animals, Birds, Databases, Factual, Livestock, Mammals, Pets
%P 325
%L 335
%Y 10.1016/j.prevetmed.2013.07.002
%W PHY
%G AUTHOR
%R 2014......116..325M

@Article{McIntyre2014,
author="McIntyre, K. M.
and Setzkorn, C.
and Wardeh, M.
and Hepworth, P. J.
and Radford, A. D.
and Baylis, M.",
title="Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.",
journal="Preventive veterinary medicine",
year="2014",
month="Oct",
day="01",
volume="116",
number="3",
pages="325--335",
keywords="Animal Diseases",
keywords="Animals",
keywords="Birds",
keywords="Databases, Factual",
keywords="Livestock",
keywords="Mammals",
keywords="Pets",
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: {\textbullet} 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. {\textbullet} 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. {\textbullet} The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. {\textbullet} 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. {\textbullet} 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. {\textbullet} 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.",
issn="1873-1716",
doi="10.1016/j.prevetmed.2013.07.002",
url="http://www.ncbi.nlm.nih.gov/pubmed/23906393",
language="eng"
}

%0 Journal Article
%T Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.
%A McIntyre, K. M.
%A Setzkorn, C.
%A Wardeh, M.
%A Hepworth, P. J.
%A Radford, A. D.
%A Baylis, M.
%J Preventive veterinary medicine
%D 2014
%8 Oct 01
%V 116
%N 3
%@ 1873-1716
%G eng
%F McIntyre2014
%X 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.
%K Animal Diseases
%K Animals
%K Birds
%K Databases, Factual
%K Livestock
%K Mammals
%K Pets
%U http://dx.doi.org/10.1016/j.prevetmed.2013.07.002
%U http://www.ncbi.nlm.nih.gov/pubmed/23906393
%P 325-335

PT Journal
AU McIntyre, KM
   Setzkorn, C
   Wardeh, M
   Hepworth, PJ
   Radford, AD
   Baylis, M
TI Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.
SO Preventive veterinary medicine
JI Prev. Vet. Med.
PD Oct
PY 2014
BP 325
EP 335
VL 116
IS 3
DI 10.1016/j.prevetmed.2013.07.002
LA eng
DE Animal Diseases; Animals; Birds; Databases, Factual; Livestock; Mammals; Pets
AB 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.
ER

PMID- 23906393
OWN - NLM
STAT- MEDLINE
DA  - 20140910
DCOM- 20150520
LR  - 20150708
IS  - 1873-1716 (Electronic)
IS  - 0167-5877 (Linking)
VI  - 116
IP  - 3
DP  - 2014 Oct 1
TI  - Using open-access taxonomic and spatial information to create a comprehensive
      database for the study of mammalian and avian livestock and pet infections.
PG  - 325-35
LID - 10.1016/j.prevetmed.2013.07.002 [doi]
LID - S0167-5877(13)00228-6 [pii]
AB  - 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.
CI  - Copyright (c) 2013 The Authors. Published by Elsevier B.V. All rights reserved.
FAU - McIntyre, K M
AU  - McIntyre KM
AD  - 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: [email protected]
FAU - Setzkorn, C
AU  - Setzkorn C
AD  - Department of Epidemiology and Population Health, Institute of Infection and
      Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston,
      Cheshire CH64 7TE, UK.
FAU - Wardeh, M
AU  - Wardeh M
AD  - Department of Epidemiology and Population Health, Institute of Infection and
      Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston,
      Cheshire CH64 7TE, UK.
FAU - Hepworth, P J
AU  - Hepworth PJ
AD  - Department of Epidemiology and Population Health, Institute of Infection and
      Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston,
      Cheshire CH64 7TE, UK.
FAU - Radford, A D
AU  - Radford AD
AD  - Department of Infection Biology, IGH, UoL, UK.
FAU - Baylis, M
AU  - Baylis M
AD  - Department of Epidemiology and Population Health, Institute of Infection and
      Global Health (IGH), University of Liverpool (UoL), Leahurst Campus, Neston,
      Cheshire CH64 7TE, UK.
LA  - eng
GR  - BB/K003798/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20130730
PL  - Netherlands
TA  - Prev Vet Med
JT  - Preventive veterinary medicine
JID - 8217463
SB  - IM
MH  - *Animal Diseases/epidemiology/etiology/transmission
MH  - Animals
MH  - Birds
MH  - *Databases, Factual
MH  - *Livestock
MH  - Mammals
MH  - *Pets
OTO - NOTNLM
OT  - Database
OT  - Disease
OT  - Emerging
OT  - Pathogen
OT  - Surveillance
OT  - Zoonosis
EDAT- 2013/08/03 06:00
MHDA- 2015/05/21 06:00
CRDT- 2013/08/03 06:00
PHST- 2013/03/05 [received]
PHST- 2013/06/21 [revised]
PHST- 2013/07/03 [accepted]
PHST- 2013/07/30 [aheadofprint]
AID - S0167-5877(13)00228-6 [pii]
AID - 10.1016/j.prevetmed.2013.07.002 [doi]
PST - ppublish
SO  - Prev Vet Med. 2014 Oct 1;116(3):325-35. doi: 10.1016/j.prevetmed.2013.07.002.
      Epub 2013 Jul 30.
TY  - JOUR
AU  - McIntyre, K. M.
AU  - Setzkorn, C.
AU  - Wardeh, M.
AU  - Hepworth, P. J.
AU  - Radford, A. D.
AU  - Baylis, M.
PY  - 2014/Oct/01
TI  - Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.
T2  - Prev. Vet. Med.
JO  - Preventive veterinary medicine
SP  - 325
EP  - 335
VL  - 116
IS  - 3
KW  - Animal Diseases
KW  - Animals
KW  - Birds
KW  - Databases, Factual
KW  - Livestock
KW  - Mammals
KW  - Pets
N2  - 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.
SN  - 1873-1716
UR  - http://dx.doi.org/10.1016/j.prevetmed.2013.07.002
UR  - http://www.ncbi.nlm.nih.gov/pubmed/23906393
ID  - McIntyre2014
ER  - 
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