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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 This page is being maintained as historical record of the group’s research at the Sanger Institute and is no longer being updated.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. Our people Group lead 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. Core team Professor Stephen D. Bentley Principal Staff Scientist and Team Leader Dr Dorota Jamrozy Postdoctoral Fellow Neil MacAlasdair PhD Student Previous team members Marcus De Goffau Postdoctoral Fellow Isobel Everall PhD Student Theresa Feltwell Advance Research Assistant Dr Rebecca A Gladstone Senior Bioinformatician Dr Nick Grayson Bioinformatician Dr Simon Harris Senior Staff Scientist John Lees Former PhD Student at the Sanger Institute Susannah J Salter Advanced Research Assistant Dr Leonor Sánchez Busó Staff Scientist Dr Josef Wagner Postdoctoral Fellow Dr Nicole Wheeler Data Scientist Dr Andries van Tonder Postdoctoral Fellow previous members Associated research Collaborations Collaboration Clinical microbiology translation The Pathogen genomics group is collaborating with a number of external groups to explore and enable whole genome sequencing in ... Collaboration Global Pneumococcal Sequencing Project A worldwide genomic survey of the impact of vaccination on the pathogen population Collaboration Pathogen Overseas Courses Overseas courses in collaboration with the Wellcome Trust Advanced Courses Collaboration Public Health England reference collections The NCTC 3000 reference collection Tools & software Tool Artemis Genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the ... Tool DNAPlotter An interactive Java application for generating circular and linear representations of genomes. Tool Gubbins Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) can be used to identify recombination. Data Data set Bacteriophage Data All bacteriophage genomes sequenced by the Sanger Institute Data set Plasmid Data All plasmid data sequenced by the Sanger Institute previous data sets Data set Bacterial Data This Archived page provides historical information on the genome sequences of bacteria that were sequenced at the Wellcome Sanger Institute and ... Related groups Science group Lawley Lab Host-microbiota interactions The host-microbiota Interactions laboratory studies the mechanisms that underlie how micro-organisms in the gut, nasopharynx and uro-gential tract interact with their ... Science group Pathogen Informatics Parasites and Microbes The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the Parasites and Microbes ... Science group Thomson Group Bacterial genomics and evolution The bacterial genomics and evolution team focuses primarily on using whole-genome sequencing approaches to study the patterns and drivers for historical ... previous related groups Science group Aanensen Group Genomic Epidemiology of Infectious Diseases Our mission is to inform control strategies and interventions on a local, national and international scale. Our group consists of a ... Science group Dougan Group Microbial Pathogenesis The Microbial Pathogenesis team, under the leadership of Professor Gordon Dougan, focused on the genetic analysis of the interactions between ... Wellcome Sanger Institute Programmes and Facilities Programme Parasites and Microbes We use genomics to study important problems in infectious disease, with a strong desire to develop and refine tools for disease ... previous programmes and facilities Programme Infection Genomics The Infection Genomics Programme investigates the common underpinning mechanisms of evolution, infection and resistance to therapy in viruses, bacteria and parasites. ... See full index Publications Loading publications... Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA. UK +44 (0)1223 834244 About Legal Data sharing Careers Privacy Equality, Diversity, Inclusion Study Cookies Modern Slavery Statement Expand footer Wellcome Sanger Institute, Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457 2022 Wellcome Sanger Institute | All rights reserved
