Using genome sequencing to understand the spread of disease and antimicrobial resistance

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Dr Kate Baker
Dr Kate Baker

Kate Baker joined the Institute at the end of 2016, from the Sanger Institute, a non-profit genomics and genetics research institute, based outside Cambridge.

Originally from Australia, Kate trained as a veterinarian before deciding to pursue an academic career. She studied for her PhD between the Institute of Zoology, London and the University of Cambridge, studying the emerging viruses of fruit bats, mostly working in Ghana. Some of this research ‘How Does Africa's Most Hunted Bat Vary Across the Continent? Population Traits of the Straw-Coloured Fruit Bat (Eidolon helvum) and Its Interactions with Humans’ was recently published in Acta Chiropterologica.

Having used next-generation sequencing technologies to discover novel viruses, Kate sought to further her bioinformatic skills, completing a postdoctoral fellowship at the Wellcome Trust Sanger Institute where she worked on large scale genomic sequencing projects of diarrhoeal bacterial pathogens (mostly Shigella).

The paper ‘Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses’ was recently published in Clinical Microbiology and Infection.

Kate says: “I worked with collections of newly emerging bacteria and older collections, which can give us a historical perspective on how diseases have been so successful.

“We used whole genome sequencing in an existing public health network to create a regional genomic-epidemiological overview of the diarrhoeal pathogen Shigella sonnei across Latin America, where the disease is endemic.

“We revealed novel diversity relevant on a global scale and demonstrated the transmission and expansion of antimicrobial resistant lineages across international borders. Most importantly, the manuscript demonstrates how we can advance public health surveillance within disease-endemic regions through the adaptation of whole genome sequencing within existing surveillance frameworks.”

Kate talks more about her work examining Shigella genomes which involved examining a bacterial sample from a World War I soldier which led to piecing together his story.

She says: “Antimicrobial resistance has been a key evolutionary pressure in shaping bacterial populations over the last 100 years and is a crucial public health crisis facing the world today. I’m fundamentally interested in picking apart what it is that makes diseases emerge and persist in populations and I am fascinated by the constant interplay of evolution and epidemiology seen through the oculus of bacterial genomics.

“At Liverpool, in addition to continuing my work using bacterial genomics to understand the emergence and persistence of diarrhoeal diseases, I am focusing on the dynamic processes that allow antimicrobial resistance genes to move within and among bacterial populations.”

As part of the research for another recent publication‘Brucella neotomae Infection in Humans, Costa Rica’, Kate, and other researchers used whole genome sequencing to identify the first cases of human neurobrucellosis attributable to Brucella neotomae, which was previously thought only to infect animals.

Kate has now received a £99,734.08 Springboard award from the Academy of Medical Sciences for “Multi-species models of antimicrobial resistance emergence and persistence, developed from real world epidemics.” It involves a collaboration is between IIB, Public Health England and the EPSRC-funded Liverpool Centre for Mathematics in Healthcare.

Kate plans to use the grant to employ a post-doc for 21 months to do laboratory work on the dynamics of AMR transfer among clinical strains of Shigella that are relevant on a public-health level.