Bio-banking and Metagenomics Platforms for Pathogen
Discovery at ILRI
George Michuki, Absolomon Kihara, Alan Orth, Cecilia Rumberia and Steve Kemp
Introduction
There has been documented increase of emergence and re-emergence of zoonotic infectious diseases in Africa in the past years. The
pathogen discovery team at the International Livestock Research Institute (ILRI) addresses the problem in Kenya and beyond. The
genomics platform at ILRI which is an integration of the bio-repository (Biobank), first and second generation sequencing platforms
and high performance computing systems facilitates the pathogen discovery work.
Pictures
Conclusion
The biobank currently has 340,000 samples which include blood, tissues and semen among others from livestock, wildlife, human
and insects collected from East, West and Central Africa among other regions. The genomics platform at ILRI has generated outputs
ranging from whole/partial genome sequences of Rift Valley Fever, Equine Encephalosis, Blue Tongue, African Swine Fever, Ndumu,
Semliki forest, Dugbe, Bunyamwera, Chikungunya, Newcastle disease and Pigeon Paramyxo - viruses among other organisms
including, bacteria, plants and protozoan parasites. A number of the genomes are also available to the public on NCBI database.
George N. Michuki
g.michuki@cgiar.org ● Box 30709 Nairobi Kenya ● +254 20 422 3467
● www.ilri.org
This document is licensed for use under a Creative Commons Attribution –Non commercial-Share Alike 3.0
Unported License June 2012
August 24-29, 2014 for
TTP8/STVM12
Sampling is a very time-consuming and expensive exercise. We have an ethical and scientific responsibility to make the
best use of that effort and money.
Source of samples: Field sampling and collaborators
Collaborating Institutions
Bio-Bank System
Genebank, Pubmed
(NCBI), MGRAST
The system is under fulltime
surveillance and monitoring
Metagenomics platform has first and second generation sequencers
The Bioinformatics platform has 88 compute
cores, 31TB of network-attached GlusterFS
storage and back up systems.
Access to samples
they have provided
Provide samples
to genomics
platform and
receive back data
Data captured
by LIMS
Processed and
analyzed data
linked to sample
LIMS captures
all sample
metadata, storage
and all data is
backed up
Data
transferred
to HPC
Metadata
and sample
source
Sample
location
Analysed
data