GRF 2nd One Health Summit 2013: Presentation by RISLEY, Dr. Claire Louise, University of Liverpool

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)
Causes of disease
Pathogens
Micro-organisms
Claire Risley clr25@aber.ac.uk

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

5. Pathogens Biodiversity of
microorganisms
Claire Risley 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. Host
Pathogen
Location
Niche
Models
Maps Info
Links
EID2
Taxon hierarchy
of organisms
Geodata
Climate
Layers
Disease
heirarchy
Claire Risley 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 host-
pathogen 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)
Correct
91.11%
Water
1.46%
Incorrect
5.95%
Irrelevant
0.91% Unidentifi
able
0.56%
Country
Correct
99.81%
Water
Bodies
0.19%
Incorrect
0.0019%
2012 country level disambiguation 2012 Sub country level disambiguation
e.g.
Yugoslavia,
USSR
Claire Risley clr25@aber.ac.uk

16. Quality of organism matching
(nucleotide data)
29%
16%
26%
26%
3%
Unidentifyable
Unidentified
Correct to species level
Correct to genus level
Incorrect
Claire Risley 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
bacillus
subtilis
rabies
virus
wolbachi
a
pipientis
cucumb
er
mosaic
virus
west nile
virus
bacillus
pumilus
corynes
pora
cassiicol
a
bemisia
tabaci
fusarium
oxyspor
um
bacillus
cereus
carrierPerCargo 89 86 80 74 71 70 68 67 61 59
0
10
20
30
40
50
60
70
80
90
100
Claire Risley clr25@aber.ac.uk

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