Bio-banking and Metagenomics Platforms for Pathogen Discovery

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 animals. 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

Presented at the Sequencing, Finishing and Analysis in the Future (SFAF) meeting, Santa Fe, New Mexico, 29-31 May 2013

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