1. 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 Liverpool
University of Aberystwyth: clr25@aber.ac.uk

2. 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
clr25@aber.ac.uk

3. What is a pathogen (1) Micro-organisms
Causes of disease
Claire Risley
Pathogens
clr25@aber.ac.uk

4. Pathogens
Claire Risley
Non-infectious causes of
disease or death
clr25@aber.ac.uk

5. Pathogens
Claire Risley
Biodiversity of
microorganisms
clr25@aber.ac.uk

6. What is a pathogen (2)
Claire Risley
clr25@aber.ac.uk

7. 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
Claire Risley
clr25@aber.ac.uk

8. 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
Claire Risley
clr25@aber.ac.uk

9. Taxon hierarchy
of organisms
Host
Geodata
Climate
Layers
Location
EID2
Disease
heirarchy Maps
Claire Risley
Pathogen
Info
Niche
Models
Links
clr25@aber.ac.uk

10. Claire Risley
clr25@aber.ac.uk

11. Host
Pathogen
Location
EID2
Claire Risley
clr25@aber.ac.uk

12. Claire Risley
clr25@aber.ac.uk

13. Extent of EID2
• 762,361 organisms (~250,000 species)
• 276,426 country interactions (all countries
represented)
• 122,524 organism interactions (~25,000 hostpathogen species interactions)
• 31,953 organism interactions in countries
Claire Risley
clr25@aber.ac.uk

14. 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 ambiguities
Wolbachia sp.
Claire Risley
clr25@aber.ac.uk

15. Quality of country matching
(nucleotide data)
Water
Bodies
0.19%
Incorrect
0.0019%
Incorrect
5.95%
Water
1.46%
Country
Correct
99.81%
e.g.
Yugoslavia,
USSR
2012 country level disambiguation
Claire Risley
Irrelevant
0.91% Unidentifi
able
0.56%
Correct
91.11%
2012 Sub country level disambiguation
clr25@aber.ac.uk

16. Quality of organism matching
(nucleotide data)
3%
26%
29%
Unidentifyable
Unidentified
Correct to species level
Correct to genus level
26%
Claire Risley
16%
Incorrect
clr25@aber.ac.uk

17. Claire Risley
clr25@aber.ac.uk

18. Claire Risley
clr25@aber.ac.uk

19. Claire Risley
clr25@aber.ac.uk

20. Claire Risley
clr25@aber.ac.uk

21. Claire Risley
clr25@aber.ac.uk

22. Claire Risley
clr25@aber.ac.uk

23. Borrelia burgdorferi:
Evidence of presence
Claire Risley
clr25@aber.ac.uk

24. Borrelia burgdorferi:
Distribution of Predicted niche
Claire Risley
clr25@aber.ac.uk

25. Pathogens with the broadest
host range
100
90
80
70
60
50
40
30
20
10
0
bacillus
subtilis
carrierPerCargo
Claire Risley
89
cucumb
corynes
wolbach
fusarium
rabies
west nile bacillus pora bemisia
bacillus
er
ia
oxyspor
mosaic
virus
virus pumilus cassiicol tabaci
cereus
pipientis
um
virus
a
86
80
74
71
70
68
67
61
59
clr25@aber.ac.uk

26. (non human) hosts with the most
pathogen entries
300
250
200
150
100
50
0
equus
pinus
bos picea sus
ovis
zea gallus
capra felis
caball
sylvest
taurus abies scrofa aries
mays gallus
hircus catus
us
ris
CargosPerCarrier 265
Claire Risley
210
200
188
174
129
127
126
124
123
clr25@aber.ac.uk

27. 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.

28. 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
Claire Risley
clr25@aber.ac.uk

29. Further Information
• Maya’s contact info to log in:
Maya.Wardeh@liverpool.ac.uk
• Database URL: http://zoonosis.ac.uk/eid2
• McIntyre KM, Setzkorn C, Wardeh M, Hepworth
PJ, Radford AD, Baylis M (2013) Using openaccess 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)
Claire Risley
clr25@aber.ac.uk