This page is maintained as a historical record and is no longer being updated.
In 2019 the Parkhill group moved to the Department of Veterinary Medicine, University of Cambridge. This page is being maintained as historical record of the group’s research at the Sanger Institute and is no longer being updated.
The Pathogen genomics team, headed by Julian Parkhill, used high-throughput genomic and phenotypic analysis of bacteria to understand their virulence, evolution, transmission and host-interactions.
At the Sanger Institute, the team investigated a wide range of human and animal pathogens, and collaborate widely within the UK and global scientific community. The team had previously generated reference genomes of organisms that are of fundamental importance for human health, including the causative agents of tuberculosis, plague, typhoid fever, whooping cough, leprosy, diphtheria and meningitis. We used population genomics to investigate transmission and evolution in many of these pathogens.
The group’s approach to pathogen genome analysis was “broad and deep”. “Broad” meant that we were interested in a wide variety of human and animal pathogens, in order to study the wide diversity of mechanisms that are used to infect a host and cause disease. These broad analyses included, for example, related members of a group of organisms that can cause disease in humans, animals and even plants, and those that live in a host without causing disease. These comparisons allowed us to identify genes that are of key importance for specifying common functions, and those that are accessory for example responsible for interaction with specific hosts, or for causing specific pathologies. We carried out analyses on a range of species including the enteric bacteria Salmonella, Escherichia, Yersinia and Erwinia, and others such as Bordetella, Streptococcus and Staphylococcus. Broad investigations also allowed us to find the novel and unexpected in less well-studied pathogens, and laid the foundations for investigating neglected diseases.
“Deep” referred to multiple comparisons between very closely related strains within a species, or group of species. Such comparisons allowed us to look at the fine detail of how or why organisms specialise on particular hosts for example the host-restricted pathogen Salmonella Typhi, how they have evolved for example Bordetella pertussis or Yersinia pestis, how variation in DNA sequence corresponds to the degree to which the organism can cause disease for example Streptococcus pneumoniae or Neisseria meningitidis, and how drug resistant strains have emerged and spread globally (e.g. Staphylococcus aureus (MRSA) or Vibrio cholerae). Very fine detail comparisons also allow us to study very recent transmission, virulence or drug resistance in organisms such as Mycobacterium tuberculosis or Staphylococcus aureus.
The group also worked on the role of the human microbiota in health and disease, and contributed to the development of novel analysis techniques and tools in bacterial genomics.
Julian Parkhill, FMedSci FRS
Former Head of Infection Genomics and Senior Group Leader
Julian was the Board of Management representative for the Infection Genomics Programme at the Sanger Institute. During his time at the Sanger Institute, he used high-throughput sequencing and phenotyping to study pathogen diversity and variation, how they affected virulence and transmission, and what they told us about the evolution of pathogenicity and host interactions.
Previous team members
Clinical microbiology translation
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Global Pneumococcal Sequencing Project
A worldwide genomic survey of the impact of vaccination on the pathogen population
Pathogen Overseas Courses
Overseas courses in collaboration with the Wellcome Trust Advanced Courses
Genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the ...
An interactive Java application for generating circular and linear representations of genomes.
Genomic Epidemiology of Infectious Diseases
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Parasites and Microbes
The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the Parasites and ...