Oxford

Group Leads

Derrick Crook

Professor Derrick Crook qualified in medicine in 1977 at the University of Witwatersrand South Africa; he specialised in General Internal Medicine and Infectious Diseases at the University of Virginia, Tufts, New England Medical Center, USA. He became a Fellow of the Royal Colleges of Pathology and Physicians in 1998, a Professor of Microbiology in 2008 and obtained NIHR Senior Investigator status in 2009. He worked as a NHS Consultant in Infectious Diseases and Clinical Microbiology for the Oxford University Hospitals NHS Trust, and led the Infection Control Department. In 2015 he was appointed Director of Microbiology at Public Health England, and divides his time between this and continuing his commitments leading Modernising Medical Microbiology.

During the past 5 years developed a research programme in translating whole genome sequencing of pathogens and linkage of patient data contained in hospital databases. By linking whole genomic typing of pathogens with this patient data, his research is leading to more rapid and effective diagnosis, management and tracking of common infections such as MRSA, C. difficile, TB and Norovirus.
 

Tim Peto

Professor Tim Peto is a Professor of Medicine at the University of Oxford. He is the co-leader for the Infection Theme of the Oxford Biomedical Research Centre and a National Institute for Health Research Senior Investigator.

His research has included combination therapy for AIDS, the search for an effective AIDS vaccine, the transmission of methicillin-resistant Staphylococcus aureus in hospitals, and transmission mechanisms for Clostridium difficile infections.

Sarah Walker

Professor Sarah Walker has worked with the group since April 2006, originally on secondment from the MRC Clinical Trials Unit, but part-time with the University of Oxford from December 2011. Her work includes the design and analysis of studies investigating the epidemiology and management of infectious diseases (including healthcare-associated infections) and antimicrobial resistance, predominantly within the “Modernising Medical Microbiology” Consortium translating new whole genome sequencing approaches into microbiology practice and service. Sarah is also Associate Statistical Editor for the Journal of Infectious Diseases.

 

Collaborating Group Leads

Daniel Wilson

Daniel Wilson is a Sir Henry Dale Fellow at the University of Oxford, where his laboratory investigates pathogen evolution and epidemiology via whole genome sequencing. He is a collaborator in the Modernising Medical Microbiology consortium whose aim is to harness genomics for microbiological diagonostics and infection control in hospitals. His work currently focuses on the identification of genetic variants in pathogen genomes that explain differences in the frequency and severity of infections, in particular hospital-associated infections including Staphylococcus aureus, Clostridium difficile and norovirus.

He has previously held positions at Lancaster University and the University of Chicago.

More about Daniel here
 

Zam Iqbal

Zamin Iqbal is a computational biologist at the Wellcome Trust Centre for Human Genetics. Many of the abilities of bacteria and parasites,
such as the ability to avoid the human immune (i.e. defence) system or to not-be-killed by antibiotics, are determined by their DNA. In particular, they commonly “shuffle” their DNA, either by passing chunks between “individuals” (as if you gave some of your DNA to someone on the bus) or by "scrambling" their own DNA. This means that techniques that work for human genetics, where you can (mostly) just compare anyone’s DNA with a fixed “reference”, do not work for bacteria – they are just too different. Zam develops computational methods for comparing bacterial DNA. Some of this work is quite abstract, and some of it very pragmatic, such as this app for telling a doctor whether a patient’s infection is drug-resistant : https://www.youtube.com/watch?v=pM4yiirQD0c.

Links:
https://twitter.com/zaminiqbal
http://iqbal-lab.github.io/
http://www.well.ox.ac.uk/iqbal

Molecular Biologists and Laboratory

Teresa Street

Teresa’s research interests lie in the ability to utilise molecular techniques to improve the diagnosis of bacterial infections. Using whole genome sequencing techniques she is working on a project that aims to identify pathogenic bacteria directly from clinical samples, without the need for an initial culture step. Her interests have always been centred on high-throughput laboratory techniques and sequencing. Previously, Teresa has worked on gene expression profiling and re-sequencing projects using microarray technology.

Her current work uses a metagenomics sequencing approach to identify pathogenic organisms causing prosthetic joint infections, using both the Illumina Miseq sequencing platform and, more recently, Nanopore sequencing.

Teresa obtained both her BSc in Biochemistry and her PhD from the University of Bath.

Louise Pankhurst

Louise completed her PhD in 2010 and after working at University College London she joined the group in August 2011. She started her research with the Crook group working on MassCode (a multiplex PCR and mass spectrometry based method) for faecal diagnostics.

She is currently working to translate WGS into the routine diagnostic setting for mycobacterial and blood stream infections. In addition she is assisting in the development of methodologies for plasmid sequencing for the identification of antibiotic resistance determinants on mobile genetic elements.

Sophie George

Sophie is assisting at the lab bench to optimize and develop methodologies for sequencing antibiotic resistance genes in human pathogens.

She explores the medical microbiology field after completing an MSc in molecular ecology at UiT The Arctic University of Norway and assisting in DNA damage repair research at the Genome Damage and Stability Centre in Brighton.

Alasdair Hubbard

Alasdair completed his Ph.D in 2015 and, after working for a molecular diagnostic company as a postdoctoral scientist for a year, joined the group as a Research Assistant in October 2016.  Before his Ph.D, Alasdair had worked in a number of different roles at the Health Protection Agency and the Defence Science and Technology Laboratory at Porton Down.

He is currently working on the REHAB: The Environmental Resistome study, as well as being involved in other projects within the group, including whole genome sequencing Mycobacterium tuberculosis direct from clinical samples.

Kevin Chau


Ali Vaughan

Ali has worked for Professor Crook at the NDM since 2009 and has a dual role within the group:

Research Assistant - currently working in the lab, on Mycobacterium tuberculosis and Gram-negative bacteraemia; and Assistant Lab Manager - assisting with the day-to-day running of the lab and organising social and corporate events (rounders matches, weekly cake rota, celebration/leaving lunches, Christmas functions and our Annual Conference).

Research Clinicians

Nicole Stoesser

Nicole qualified as a clinician in 2004, and started specialty training in infectious diseases and microbiology on the Oxford rotation in 2008. She has been involved in full- or part-time research with the Crook/Peto group since 2008, initially acting as the study doctor and coordinator for the three Oxfordshire sites of a multi-centre international clinical trial investigating the efficacy of Fidaxomicin in the management of Clostridium difficile-associated infection, and set up the group’s study on the molecular epidemiology and risk factors for carriage/acquisition of C. difficile in children < 2 years.

She currently studies antimicrobial resistance in major gram-negative pathogens, such as Escherichia coli and Klebsiella pneumoniae, and is leading the REHAB: The Environmental Resistome study.

Nicola Fawcett

Nicola is an MRC Clinical Research Fellow, and Chief Investigator of the Antibiotic Resistance in the Microbiome OxfoRD (ARMORD) Study.

She is interested in the use of DNA sequencing to measure the effects of antibiotics on the gut bacteria, as well as antimicrobial stewardship, behaviour change, and quality improvement in clinical practice. She also contributes to the MMM public engagement programme and the MMM website.

Study website: http://armordstudy.wordpress.com
Twitter: @drnjfawcett

Timothy Walker

Tim is an Academic Clinical Lecturer and clinician (an infectious disease / microbiology registrar) who has been with the group since 2010. His research has been into tuberculosis, it’s transmission and the genetic determinants of drug resistance.

Bernadette Young

Bernadette qualified as a clinician in 2006, and started specialty training in Infectious Diseases and Microbiology as an Academic Clinical Fellow in 2009. As part of this scheme she spent 12 months working with the MMM group from August 2010, then returned in November 2013 to begin DPhil studies as a Wellcome Trust Clinical Training Fellow.

Bernadette’s work investigates the role that bacterial genetics play in the variation of virulence in Staphylococcus aureus.

Ana L Gibertoni Cruz

Ana qualified as an Infectious Disease physician in Brazil in 2009, and that was followed by a master’s degree in, and subsequent experience of, global public health. She has been working in the UK since 2012 as an ID/micro specialty registrar, and in 2014 she joined MMM to work on tuberculosis-related research.

Since 2016 Ana is the clinical research fellow with Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC); she is frequently liaising with mycobacterial reference laboratories all over the world to help setting up lab infra-structure and training staff. When genotypic and phenotypic data of dozens of thousands of TB strains from 5 continents start coming in, Ana will also be involved with analysis at Oxford.

Leon Peto

Timothy Davies

Natasha Hough

David Eyre

David Eyre is a National Institute for Health Research and Public Health England clinical lecturer in the Nuffield Department of Medicine. He is also an honorary specialist registrar in Infectious Diseases and Medical Microbiology. His main research interest are the application of whole-genome sequencing to understanding the transmission of infectious diseases, both at an individual level and within healthcare systems; and the use of whole-genome sequencing as a routine diagnostic microbiology tool. His current work focuses on a number of pathogens including Clostridium difficile, Neisseria gonorrhoeae, and enterobacteriaceae.

Population Genomics

Sarah Earle

DPhil student, currently studying the use of bacterial Genome-wide association Studies

Read more here


 

Nicola de Maio

Nicola has joined the group in September 2013. He is funded by a James Martin research fellowship and studies within-host evolution of viruses causing chronic disease.
His work includes the design, development, testing, and application of statistical and computational methods for the analysis of viral genomes sequence data. He is currently collaborating to a project regarding the study of norovirus mixed infections and recombination."

Rosalind Harding

My research investigates the evolution of genetic diversity in human and bacterial populations, with a current focus on bacterial species that have high profile clinical significance in the UK. I use an interdisciplinary approach that combines statistical population genetics, medical microbiology and biological anthropology, and I collaborate with researchers located in the Oxford Departments of Zoology and Statistics and at the John Radcliffe Hospital. We want to understand how antibiotic resistance and pathogenicity emerges from benign human commensal species, and how rapidly can newly evolving lineages attain a global reach across human host populations.

Statistics and large dataset analysis

Phuong Quan

Phuong is a Research Methodology Fellow and completed her MSc in Applied Statistics in 2013. She conducts epidemiological research using both primary and secondary data sources, with recent projects covering pneumonia incidence and risk factors for urinary tract infections.

She is particularly interested in the application of machine learning techniques to medical datasets.

Karina Vihta

Eric Budgell

Eric Budgell joined the group as a Medical Statistician in April 2016. He currently investigates antimicrobial use and resistance in large observational cohorts in the UK. This work is helping to optimize the design of clinical interventions and randomised studies that will explore ways to reduce antibiotic burden in acute/general care, with the ultimate long-term goal of reducing antimicrobial resistance. Prior to this he worked as an epidemiologist in South Africa and as a consultant to the World Health Organization in Switzerland. He completed his MSc here at the University of Oxford in 2012

Tjibbe Donker

Tjibbe Donker is a infectious disease modeller whose research focusses on the influence of health care networks, formed by exchanged patients, on the spread of antibiotic-resistant bacteria and other hospital-associated pathogens.

Other Postdoctoral Researchers

Clara Grazian

Clara is a Postdoctoral Scientist who has joined the group in January 2017, after completing a double PhD in Applied Mathematics and Statistics in Université Paris-Dauphine and Sapienza Università di Roma, where she studied methods to perform Bayesian inference for complicated models, such as dependence and mixture models. She is currently involved in studying the mechanisms of development of drug resistance in Mycobacterium Tuberculosis, by using genome-wide association studies. In her work, she tries to use both frequentist and Bayesian methodologies to work with large datasets.

Philip W Fowler

Philip is a Senior Researcher at the University of Oxford. He is a computational biophysicist and is leading efforts to predict by simulating the protein-antibiotic complex whether novel mutations are susceptible or resistant to different antibiotics. Examining the genome of a bacterium to determine its susceptibility to different antibiotics currently relies on knowing the effect of each genotype; hence being able to predict the effect of previously unseen mutations will further improve the utility of whole-genome sequencing based clinical microbiology.

He is experienced at using a wide range of High Performance Computing, including clouds and conventional clusters and is also a Software Carpentry Instructor. Before joining the group he worked in the Department of Biochemistry for ten years.

Twitter: @philipwfowler
Blog: http://philipwfowler.me

Bioinformatics

Alex Orlek

Alex joined the group as a DPhil student in October 2015. He is investigating the spread of antibiotic resistance in gram-negative bacteria, focusing on plasmids as vectors of transmission. Ultimately, he is interested in addressing questions such as whether plasmids found in livestock populations are an important source of antibiotic resistance in human populations. The project is funded by the NIHR Health Protection Research Unit and involves a collaboration with Public Health England and the Animal and Plant Health Agency.

Anna Sheppard

Anna completed her PhD in Adelaide, Australia, and after working for several years as a postdoctoral researcher in Kiel, Germany, she joined the group's bioinformatics team in June 2013. Her current research includes investigation of antibiotic resistance plasmids in Gram-negative bacteria, as well as genomic and phylogeographic analyses of Group B Streptococcus.

Hang Phan

Hang is senior bioinformatician, in charge of several microbial projects using Next Generation Sequencing data to understand the transmission routes of antimicrobial resistance mechanisms in infectious diseases within hospital outbreaks.

“I am particularly interested in the movement of antimicrobial resistance genes within populations. I have recently developed a method to predict phenotypic AR which can be applied to blood stream infection. I am also assessing the use of Oxford Nanopore Technologies' MinION for gram-negative species, particularly for plasmid detection. I have collaborations with scientists within the UK and internationally, including China and Vietnam.”

Yifei Xu

Yifei joined MMM is April 2017 after completing his PhD at Mississippi State University, in the USA. His research was directed towards studying the epidemiology, ecology, genetic and antigenic evolution, and interspecies transmission dynamics of influenza A virus. He is interested in the use of genome sequencing to diagnose infectious diseases.

Nicholas Sanderson

Nick completed his PhD at the Pirbright Institute and Imperial College London working on NK cell receptor diversity in ruminant species. His current research involves using computational metagenomic techniques to determine the infectious agents from directly sequenced clinical samples.

Informatics

John Finney

John is currently working with a small team on a number of major health informatics initiatives at the University of Oxford in collaboration with the NHS and the HPA.
The four major projects aim to combine large scale clinical records with microbial genetics records together in real time for the purpose of understanding, managing and potentially minimising infection outbreaks. This work is being done at both the local level (Oxfordshire) and at a national level (multiple hospital trusts).
 

Trien Do

Jeremy Swann

Jeremy joined the group in October 2016 after completing his PhD at the University of Leeds. He has previously worked at the University of Leeds and Linköping University developing tools to allow interactive registration of 3D pathology and MRI volumes and is currently a Software Engineer developing the bioinformatics pipeline of the group.

Fan Yang-Turner

Fan joined the group in April 2017. She was trained as a software engineer in China and obtained her PhD in University of Birmingham in 2006. Since then she has worked both in Universities and Industry, developing enterprise software systems. Before joining the team, she has worked for University of Leeds (2011-2013) on EU-funded big data project DICODE (Data-intensive collaboration and decision making) and NHS Digital (2013-2016), delivering a few national software systems of Health and Social Care, such as NCMP (National Child Measurement Program), MIDAS (Medical Information and Data Analysis System), DES (Data Exchange System). Click here for LinkedIn profile and blog.

Project Management

Dona Foster

Sarah Hoosdally

Sarah completed her PhD at MRC Clinical Sciences Centre, Imperial College London and moved to Oxford University in 2009 spending a few years as a post-doc exploring the role of master transcriptional regulators in primary haematopoiesis. She moved to the University’s Research Services team in 2012 before joining MMM in October 2015 as a Project Manager, primarily overseeing CRyPTIC and HICF projects. Sarah is also a College Lecturer in Biomedical Sciences at St Catherine’s College, Oxford.

Elizabeth Darwin

Elizabeth joined the MMM consortium in 2015 as Project Manager, and has primary responsibility for the Oxford NIHR Health Protection Research Unit (HPRU) and the ARK-Hospital programme. The latter is a major initiative to tackle antibiotic resistance, by safely reducing the unnecessary use of antibiotics in hospitals. Her background is in the life sciences industry, as a management consultant leading commercial strategy projects for pharmaceutical and biotech clients, and in a commercial effectiveness role within Pharma. She holds an MPhil in Bioscience Enterprise from the University of Cambridge and is a Chartered Financial Analyst (CFA).

Public Engagement

Cliff Gorton

Cliff Gorton - Retired Surveyor and Housing Association Property Services Director (15 years). Joined the then Patient panel in 2008. Active member of the Hospital Infection Control Committee (HICC) since Nov. 2009. Involved in various activities for OUH, including Trust Environmental Audit Reviews (TEAR), Patient Led Assessment of the Care Environment (PLACE), Staff Recognition Rewards, Antibiotic Reduction & Conservation (ARK). Lay member of a Clinical Trial Steering Group for the Blood and Transfusion Service - benefits of liberal or restrictive use of blood for those patients with Acute Upper Gastro Intestinal Bleeding. Plus many other areas of involvement too numerous to mention.

 

 

 

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