Parkhill Group

Pathogen Genomics

Archive Page

This page is maintained as a historical record and is no longer being updated.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 This page is being maintained as historical record of the group’s research at the Sanger Institute and is no longer being updated.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.

Core team

Photo of Professor Stephen D. Bentley

Professor Stephen D. Bentley

Principal Staff Scientist and Team Leader

Photo of Dr Dorota Jamrozy

Dr Dorota Jamrozy

Principal Bioinformatician

Photo of Neil MacAlasdair

Neil MacAlasdair

PhD Student

Previous team members

Photo of Isobel Everall

Isobel Everall

PhD Student

Photo of Theresa Feltwell

Theresa Feltwell

Advance Research Assistant

Photo of Dr Nick Grayson

Dr Nick Grayson


Photo of Dr Simon Harris

Dr Simon Harris

Senior Staff Scientist

Photo of John Lees

John Lees

Former PhD Student at the Sanger Institute

Photo of Susannah J Salter

Susannah J Salter

Advanced Research Assistant

Photo of Dr Josef Wagner

Dr Josef Wagner

Postdoctoral Fellow

Photo of Dr Nicole Wheeler

Dr Nicole Wheeler

Data Scientist

Photo of Dr Andries van Tonder

Dr Andries van Tonder

Postdoctoral Fellow



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