As a group, our fundamental interest is in bacterial evolution, particularly the emergence and transmission of bacterial pathogens. We are interested in how and when novel clones emerge, how they become resistant to antibiotics, how they interact with human and animal hosts, and what are their pathways of transmission. We predominantly use large-scale genomics, phylogenetics and population genomics to address these questions. As we are interested in fundamental processes, we do not limit ourselves to specific organisms, but try to look for similar processes operating in different organisms and different niches. The work of the group covers a diverse range of topics within this broad area:
We have developed tools to describe and understand the pangenome (e.g. Panaroo), and we are developing approaches to model and incorporate non-SNP variation in phylogenetic inference. We are very interested in applying mutational signatures to understanding bacterial niches, and have developed software to enable this. In the past we have developed novel GWAS methods, and have a continued interest in this area.
We use phylogenetic approaches to understand the emergence and evolution of bacterial clones, and the adaption of these clones to novel niches. These include lung pathogens affecting people with CF, such as Mycobacterium abscessus and Pseudomonas aeruginosa and respiratory pathogens such as Ornithobacterium hominis.
We use the same tools to study the transmission pathways of other human and animal pathogens, including Mycobacterium bovis, Campylobacter jejuni, Bordetella pertussis, Salmonella enterica, Escherichia coli, Streptococcus equi and many others. These studies overlap strongly with the use of genomics in clinical microbiology, where we have a long-standing collaboration with Prof. Sharon Peacock, investigating the implementation of transmission tracking for Staphylococcus aureus, amongst others.
We also use these phylogenies to study the temporal patterns of emergence and transmission, and to uncover phenotype-genotype associations using GWAS.
We have been involved in many metagenomics studies of the gut and the lung microbiota, and have a particular interest in low-biomass studies and the thorny issues of false-positive signals due to pervasive contamination.
We use high-throughput mutagenesis approaches (such as TraDIS, previously developed in our lab) and other ‘omics tools such as dual-RNA Seq, to study the interaction of pathogens with the host. This currently includes work on Streptococcus zooepidemicus and Klebsiella pneumoniae. We use similar approaches to study the mode of action of antimicrobials and the development of antibiotic resistance.
We have a number of ongoing collaborations with leading researchers around the globe including, but not limited, to the following:
| Collaborator | Affiliation |
|---|---|
| Dr Nuno Oliveira | DAMTP, University of Cambridge |
| Dr John Welch | Department of Genetics, University of Cambridge |
| Dr Josie Bryant | Department of Medicine, University of Cambridge |
| Prof. Andres Floto | Department of Medicine, University of Cambridge |
| Dr Ewan Harrison | Department of Medicine, University of Cambridge |
| Prof. Sharon Peacock | Department of Medicine, University of Cambridge |
| Prof. Steve Charnock-Jones | Department of Obstetrics and Gynaecology, University of Cambridge |
| Prof. Gordon Smith | Department of Obstetrics and Gynaecology, University of Cambridge |
| Prof. Clare Bryant | Department of Veterinary Medicine, University of Cambridge |
| Dr Andrew Conlan | Department of Veterinary Medicine, University of Cambridge |
| Prof. Mark Holmes | Department of Veterinary Medicine, University of Cambridge |
| Dr Lucy Weinert | Department of Veterinary Medicine, University of Cambridge |
| Prof. James Wood | Department of Veterinary Medicine, University of Cambridge |
| Prof. Glyn Hewinson | IBERS, University of Aberystwyth |
| Prof. Andrew Preston | Department of Biology & Biochemistry, University of Bath |
| Prof. Sam Sheppard | Department of Biology & Biochemistry, University of Bath |
| Dr Felix Dube | Molecular and Cell Biology, University of Cape Town |
| Prof. Eshwar Mahenthiralingam | School of Biosciences, Cardiff University |
| Prof. Mary Jackson | Department of Microbiology, Immunology and Pathology, Colorado State University |
| Prof. Dianne Ordway | College of Veterinary Medicine and Biomedical Sciences, Colorado State University |
| Dr Emmanuel Ngbede | Federal University of Agriculture Makurdi |
| Prof. Lance Price | Environmental and Occupational Health, The George Washington University |
| Prof. Jukka Corander | Department of Mathematics and Statistics, University of Helsinki |
| Prof. Bill Cookson | Faculty of Medicine, Imperial College London |
| Dr Andrew Waller | Intervacc AB |
| Dr Francesc Coll | Department of Infection Biology, Faculty of Infectious and Tropical Diseases, LSHTM |
| Dr Catherine Ludden | Department of Infection Biology, Faculty of Infectious and Tropical Diseases, LSHTM |
| Dr Robyn Marsh | Menzies School of Health Research |
| Dr Francesca Short | Monash University |
| Prof. David Aanensen | Big Data Institute, University of Oxford |
| Prof. Colin Kleanthous | Department of Biochemistry, University of Oxford |
| Dr Claire Chewapreecha | MORU Mahidol Oxford Tropical Medicine Research Unit |
| Prof. Tim Walsh | Department of Zoology, University of Oxford |
| Prof. Saheer Gharbia | UK Health Security Agency |
| Prof. Xavier Didelot | School of Life Sciences, University of Warwick |