Samuel K. Sheppard

Professor of Microbial Genomics and Evolution

Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford
Tutorial Fellow: St. Anne’s College
Editor-in-chief for Microbial Genomics

Professional profiles:
ORCiD | Google Scholar 


Bacterial pathogens, and the rise of antimicrobial resistance, are among the greatest threats to human and animal health. The emergence and spread of these organisms is governed by basic evolutionary processes, whereby adaptive phenotypes are favoured by selection – leaving signatures in the genome. Analysing this genome variation, my group addresses complex questions in the ecology, epidemiology and evolution of bacteria including CampylobacterAcinetobacterEscherichia coliHelicobacterStaphylococcus and Streptococcus. Current research can be broadly defined in three overlapping areas:

GENOME EVOLUTION – The genetic basis of phenotype variation. Processes such as host adaptation, zoonotic transition and emergence of virulence and antimicrobial resistance leave signatures in genomes. We develop bioinformatics approaches, such bacterial genome-wide association studies and genome covariation analyses, to explore how mutation, recombination and selection shape coadapted genomes and ecological strategies. Where possible, we validate genotype-phenotype associations through gene inactivation, functional comparison to ‘wild-type’ strains, and complementation to re-instate phenotypes.

ECOLOGICAL GENOMICS – Pathogens in the wild. Using genomics to understand the niche distribution and transmission of pathogenic bacteria requires identification of strains, and genes within strains, associated with host source, food, the environment and human disease. Analysing very large genome collections, we explain cryptic disease networks and track transmission in source-sink populations.

GLOBAL HEALTH – Interventions. In many cases the people at greatest infection risk are the least studied, specifically those in low and middle income countries. Using microbial genomics approaches I am currently working with global partners to understand One Health dynamics of pathogens to develop genomic surveillance programs, decision support modelling tools, antigen discovery for enteric livestock vaccines, and CRISPR-based targeted killing of pathogens.