EID2 Database: New Tools for One Health Research and Policy Development

EID2 Database: New tools for One Health research and policy

development

Claire Risley

Maya Wardeh, K. Marie McIntyre, Christian Setzkorn, Alan Radford, Matthew Baylis

University of LiverpoolUniversity of Aberystwyth: [email protected]

Some One Health Questions

• Which hosts are likely to transmit pathogens to my host of interest?

• Where is my pathogen and all its hosts found?– Where has it been found– Where else is it likely to be found

Claire Risley [email protected]

What is a pathogen (1)Causes of disease

Pathogens

Micro-organisms


Non-infectious causes of disease or deathPathogens


Pathogens Biodiversity of microorganisms


What is a pathogen (2)


Organisms can be both pathogens and hosts

• We use only a statement about interaction• There are only ‘cargoes’ & ‘carriers’– Which is which?• Specified directly in nucleotide db• Hierarchy for identification in papers


How Can We Know Who infects What and Where?

• Nucleotide & paper information– Uploaded metadata can be as important as

sequence– Useable data also in paper titles, keywords etc.

• Built on tree of life– Links pairs of organisms– Recursive; can get info on higher level taxa


HostPathogen

Location

Niche Models

Maps InfoLinks

EID2

Taxon hierarchy of organisms

GeodataClimate Layers

DiseaseheirarchyClaire Risley [email protected]


HostPathogen

Location

EID2



Extent of EID2

• 762,361 organisms (~250,000 species)• 276,426 country interactions (all countries

represented)• 122,524 organism interactions (~25,000 host-

pathogen species interactions)• 31,953 organism interactions in countries


Data have undergone rounds of “Disambiguation”

Host ambiguity:/host=“Prostitute”/host=“German shepherd”/host=“24 year old male”

Geolocation ambiguity:/country=“Middle east”/country=“UK:north sea”

NCBI heirarchy ambiguitiesWolbachia sp.


Quality of country matching (nucleotide data)

Correct91.11%

Water1.46%

Incorrect5.95%

Irrelevant0.91% Unidentifiable

0.56%

Country Correct99.81%

Water Bodies0.19%

Incorrect0.0019%

2012 country level disambiguation 2012 Sub country level disambiguation

e.g. Yugoslavia, USSR


Quality of organism matching (nucleotide data)

29%

16%26%

26%

3%

UnidentifyableUnidentifiedCorrect to species levelCorrect to genus levelIncorrect








Borrelia burgdorferi:Evidence of presence


Borrelia burgdorferi: Distribution of Predicted niche


Pathogens with the broadest host range

bacillu

s subtilis

rabies viru

s

wolbachia pipientis

cucu

mber mosaic v

irus

west nile

virus

bacillu

s pumilu

s

corynesp

ora cassi

icola

bemisia

tabaci

fusarium oxys

porum

bacillus c

ereus

0

10

20

30

40

50

60

70

80

90

100


(non human) hosts with the most pathogen entries

bos tau

rus

picea a

bies

sus scro

fa

ovis ar

ies

equus c

aball

us

zea m

ays

gallu

s gall

us

pinus sylv

estris

capra

hircus

felis c

atus

0

50

100

150

200

250

300


Using EID2

• Investigate NCBI’s output– Radford et al. J Gen Virol. 2012 September; 93(Pt

9): 1853–1868.• Comparing predictors of pathogen sharing– Sandoval et al. (in prep) : Felid pathogens,

relatedness and proximity• Large-scale comparisons of climate predictions• Etc.

EID2: a new, useful resource:

• EID2 updated:– More records– Greater sensitivity and specificity for Enhance hosts– Improved sub-country level recognition

• Now very useful to all researchers:– Host/Pathogen/Location Information easily available– Location and climatic niche maps available– Interesting for many types of studies e.g. network

analyses


Further Information

• Maya’s contact info to log in: [email protected]

• Database URL: http://zoonosis.ac.uk/eid2• McIntyre KM, Setzkorn C, Wardeh M, Hepworth PJ,

Radford AD, Baylis M (2013) Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections. Preventive Veterinary Medicine (in press)


mailto:[email protected]

http://zoonosis.ac.uk/eid2

EID2 Database: New Tools for One Health Research and Policy Development

Health & Medicine