Whole Genome Sequencing By Melissa Ward, CIIE Research Fellow

The power of next generation sequencing is allowing us to gain a more detailed understanding than ever before about how bacteria spread. I am hugely excited to be a part of the Urban Zoonoses project, which will generate a vast amount of bacterial isolates along with meta-data at an unprecedented level of detail.We will be performing whole genome sequence analysis of bacterial samples collected through many strands of the Urban Zoonoses project, from humans, livestock, food, wildlife and the environment. I will use state-of-the art methods for integrating the bacterial genetic sequence data with information about the time, loca-tion and host from which the bacteria were sampled. By combining epidemiological and demographic infor-mation with the genetic data, we will be able to under-stand the E. coli diversity within Nairobi, and how this differs across socioeconomic groups, in different housing types and in relation to livestock keeping practices.

From the bacterial genome sequences we can also look for genes of interest, such as those conferring bacterial virulence or resistance to antibiotics. By examining the set of genes carried by bacteria from different individuals, hosts or locations, we can make inferences about reservoirs of antibiotic resistance and pinpoint potential hotspots for disease outbreaks, with a particular emphasis on zoonotic transmissions.

I have previously used whole genome sequence analysis to investigate the transmission of S. aureus between livestock and humans, and have also used phylogenetic techniques to help understand the origins of the HIV-1 group M epidemic. I am currently assessing the utility of whole genome sequencing as a tool for identifying epidemiologically related E. coli infections in collaboration with the Scot-tish E. coli O157 Reference Laboratory.

My involvement with the Urban Zoonoses project is made possible through a Junior Research Fellowship at the Centre for Immunity, Infection and Evolution at the University of Edinburgh, and a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust.

Melissa Ward is a CIIE Research Fellow at the University of Edinburg.