maidenlab

odile.harrison@zoo.ox.ac.uk

Senior Research Associate

Bidmos,F.A., Chan,H., Praekelt,U., Tauseef,I., Ali,Y.M., Kaczmarski,E.B., Feavers,I. and Bayliss,C.D. (2015) Investigation into the Antigenic Properties and Contributions to Growth in Blood of the Meningococcal Haemoglobin Receptors, HpuAB and HmbR. PLoS One 10: e0133855

Sanders,H., Norheim,G., Chan,H., Dold,C., Vipond,C., Derrick,J.P., Pollard,A.J., Maiden,M.C. and Feavers,I.M. (2015) FetA Antibodies Induced by an Outer Membrane Vesicle Vaccine Derived from a Serogroup B Meningococcal Isolate with Constitutive FetA Expression. PLoS One 10: e0140345

Norheim,G., Sanders,H., Mellesdal,J.W., Sundfor,I., Chan,H., Brehony,C., Vipond,C., Dold,C., Care,R., Saleem,M., Maiden,M.C., Derrick,J.P., Feavers,I. and Pollard,A.J. (2015) An OMV Vaccine Derived from a Capsular Group B Meningococcus with Constitutive FetA Expression: Preclinical Evaluation of Immunogenicity and Toxicity. PLoS One 10: e0134353

Marsay,L., Dold,C., Green,C.A., Rollier,C.S., Norheim,G., Sadarangani,M., Shanyinde,M., Brehony,C., Thompson,A.J., Sanders,H., Chan,H., Haworth,K., Derrick,J.P., Feavers,I.M., Maiden,M.C. and Pollard,A.J. (2015) A novel meningococcal outer membrane vesicle vaccine with constitutive expression of FetA: A phase I clinical trial. J. Infect. 71; 326-337

Maharjan,S., Saleem,M., Feavers,I.M., Wheeler,J.X., Care,R. and Derrick,J.P. (2015) Dissection of the function of the RmpM periplasmic protein from Neisseria meningitidis. Microbiology 162: 364-375.

Vipond,C., Findlay,L., Feavers,I. and Care,R. (2016) Limitations of the rabbit pyrogen test for assessing meningococcal OMV based vaccines. ALTEX. 33: 47-53

Wetzler, L.M., Feavers, I.M., Gray-Owen, S.D., Jerse, A.E., Rice, P.A. and Deal, C.D. (2016) Summary and Recommendations from the National Institute of Allergy and Infectious Diseases (NIAID) Workshop "Gonorrhea Vaccines: the Way Forward". Clin.Vaccine Immunol. 23: 656-663

Feavers, I.M. and Maiden, M.C.J. (2017) Recent Progress in the Prevention of Serogroup B Meningococcal Disease. Clin.Vaccine Immunol. 24: e00566-16

Bryan, P., Seabroke, S., Wong, J., Donegan, K., Webb, E., Goldsmith, C., Vipond, C. and Feavers, I. (2018) Safety of multicomponent meningococcal group B vaccine (4CMenB) in routine infant immunisation in the UK: a prospective surveillance study. The Lancet: Child and Adolescent Health. 2(6): 395-403

Markey, K., C. Asokanathan, and I. Feavers (2019) Assays for Determining Pertussis Toxin Activity in Acellular Pertussis Vaccines. Toxins (Basel). 11(7).

Dr Odile Harrison

Read more about Dr Odile Harrison

My work explores the population genomics of bacterial pathogens. I am particularly interested in defining bacterial lineages using genome data as this has the potential to allow strains associated with distinct pathologies including antimicrobial resistance to be more rapidly identified. Such information brings with it opportunities for improving diagnostics, preventing infection through vaccination and the capacity to limit antimicrobial resistance. My research involves the analysis of whole genome sequence data belonging to the sexually transmitted pathogens Neisseria gonorrhoeae and Chlamydia trachomatis as well as the meningitis causing pathogens Neisseria meningitidis, Haemophilus influenzae and Streptococcus agalactiae.

I am an editorial board member for the Journal of Infection and a fellow of the Higher Education academy.

@OdileHarrison

Senior Researcher

keith.jolley@zoo.ox.ac.uk

Dr Keith Jolley

Read more about Dr Keith Jolley

I studied biochemistry at the University of Bath, graduating in 1993 and stayed on to complete a PhD studying halophilic proteins from Archaea. In 1996, I undertook a postdoctoral position at the University of Southampton working on meningococcal surface proteins involved in eliciting immune responses. Continuing this interest in meningococcal biology, I moved to the Maiden Group in Oxford in 1998, where I worked on the genetic characterization of bacterial carrier populations.

I now work mainly on software development and database design, including development of the PubMLST website and the underlying genomics platform, BIGSdb.

james.bray@biology.ox.ac.uk

Senior Researcher

Dr James Bray

Read more about Dr James Bray

I am a bioinformatics scientist working in the bacterial genomics field.

Bacterial species identification using ribosomal multilocus sequence typing (rMLST)

I curate the ribosomal multilocus sequence typing (rMLST) scheme and associated databases. The goal of rMLST is the accurate taxonomic classification of all bacterial isolates using the DNA sequences found within the ribosomal protein-encoding genes (pubmlst.org/species-id).

My research involves applying rMLST in three ways:
1. Performing phylogenetic analysis for taxonomic investigations
2. Defining ribosomal sequence types for the rapid species identification of bacterial isolates
3. Developing and maintaining a 'one-click' species identification server

Large-scale bacterial genomics projects

I am responsible for assembling high-throughput DNA sequencing data for the large-scale genomic projects with the Maiden Group (with a focus on Campylobacter, Neisseria and Streptococcus). As a result, I manage the exchange of large amounts of data between sequencing centres, different labs and the ENA Sequence Read Archive (SRA).

Assembled genomes are accessible on the PubMLST website (pubmlst.org) for bacterial population studies, pathogen surveillance and gene-by-gene analysis.

My research interests include:

Pathogen strain identification
Bacterial genome annotation and protein structure/function prediction

Knowledge-based structural genomics target selection

ORCID Link to Publications

Department of Biology Profile

Bioinformatics Research Scientist

frances.colles@zoo.ox.ac.uk

Bacterial Genomics

Mulhall R, Bennett D, Bratcher H, Jolley K, Bray J, O'Lorcain P, Cotter S, Maiden M, Cunney R. (2019) cgMLST characterisation of invasive Neisseria meningitidis serogroup C and W strains associated with increasing disease incidence in the Republic of Ireland. PLoS One. 14 (5). e0216771. PMID: 31141820

van Tonder A, Bray J, Jolley K, Jansen van Rensburg M, Quirk S, Haraldsson G, Maiden M, Bentley S, Haraldsson Á, Erlendsdóttir H, Kristinsson K, Brueggemann A. (2019) Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions. Frontiers in Microbiology. 10:317. PMID: 30858837

Jolley A, Bray J, Maiden M. (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Research. 3:124. PMID: 30345391

Cody A, Bray J, Jolley K, McCarthy N, Maiden M (2017) Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates. Journal of Clinical Microbiology. 55 (7), 2086-2097. PMID: 28446571

Sharp C, Bray J, Housden N, Maiden M, Kleanthous C (2017) Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models. PLoS Computational Biology. 13 (7), e1005652. PMID: 28715501

Hill D, Lucidarme J, Gray S, Newbold L, Ure R, Brehony C, Harrison O, Bray J, Jolley K, Bratcher H, Parkhill J, Tang C, Borrow R, Maiden M. (2015) Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. The Lancet Infectious Diseases. 15 (12), 1420-1428. PMID: 26515523

Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson T, Rolo J, Lamble S, Bray J, Jolley K, Hanage W, Bowden R, Maiden M, Mack D, de Lencastre H, Feil E, Corander J, Sheppard S. (2015) Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol. PMID: 25888688

Bull M, Jolley K, Bray J, Aerts M, Vandamme P, Maiden M, Marchesi J, Mahenthiralingam E. (2014) The domestication of the probiotic bacterium Lactobacillus acidophilus. Science Reports 4:7202. PMID: 25425319

Vaz C, Francisco A, Silva M, Jolley K, Bray J, Pouseele H, Rothganger J, Ramirez M, Carriço J. (2014) TypOn: the microbial typing ontology. Journal of Biomedical Semantics.  5(1):43. PMID: 25584183

Maiden M, Jansen van Rensburg M, Bray J, Earle S, Ford S, Jolley A, McCarthy N (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nature Reviews Microbiology 11(10):728-36. PMID: 23979428

Structural Genomics

Bray J. (2012) Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome. Journal of Structural and Functional Genomics. 13(1):37-46. PMID: 22354707

Hillringhaus L, Yue W, Rose N, Ng S, Gileadi C, Loenarz C, Bello S, Bray J, Schofield CJ, Oppermann U. (2011) Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family. Journal of Biological Chemistry. 286(48):41616-25. PMID: 21914792

Savitsky P, Bray J, Cooper C, Marsden B, Mahajan P, Burgess-Brown N, Gileadi O. (2010) High-throughput production of human proteins for crystallization: the SGC experience. Journal of Structural Biology. 172(1):3-13. PMID: 20541610

Bray J, Marsden B, Oppermann U. (2009) The human short-chain dehydrogenase/reductase (SDR) superfamily: a bioinformatics summary. Chemico-Biological Interactions 178(1-3):99-109. PMID: 19061874

Gräslund S Nordlund P, Weigelt J, Hallberg B, Bray J, et al. (2008) Protein production and purification. Nature Methods. 5(2):135-46. PMID: 18235434

Ng S, Kavanagh K, McDonough M, Butler D, Pilka E, Lienard B, Bray J, Savitsky P, Gileadi O, von Delft F, Rose N, Offer J, Scheinost J, Borowski T, Sundstrom M, Schofield C, Oppermann U. (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature. 448(7149):87-91. PMID: 17589501

Krogan J, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440(7084):637-43. PMID: 16554755

Dobrovetsky E, Lu M, Andorn-Broza R, Khutoreskaya G, Bray J, Savchenko A, Arrowsmith CH, Edwards A, Koth C. (2005) High-throughput production of prokaryotic membrane proteins. Journal of Structural and Functional Genomics. 6(1):33-50. PMID:15909233

Bray J, Marsden R, Rison S, Savchenko A, Edwards A, Thornton J, Orengo C. (2004) A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics. 20(14):2288-95. PMID: 15201178

Protein Structure & Function Resources

Buchan D, Rison S, Bray J, Lee D, Pearl F, Thornton J, Orengo C. (2003) Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Research. 31(1):469-73. PMID: 12520054

Bray J, Todd A, Pearl F, Thornton J, Orengo C. (2000) The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues. Protein Engineering. 13(3):153-65. PMID: 10775657

Orengo C, Pearl F, Bray J, Todd A, Martin A, Lo Conte L and Thornton J (1999) The CATH database provides insights into protein structure/function relationships. Nucleic Acids Research, 27 (1), 275-279. PMID: 9847200

Dr Frances Colles

Read more about Dr Frances Colles

Campylobacter is the principal organism I work on. It can cause severe gastrointestinal disease in humans, with the yearly number of reported UK cases being equivalent to one person becoming infected every two minutes.  Contaminated chicken meat has been identified as a major source of infection, and effective ‘on-farm’ intervention strategies are urgently sought to support the biosecurity measures that are currently used. 

Work for my DPhil demonstrated that, contrary to popular belief, wild birds are not a major source of contamination for broiler chicken flocks, with Campylobacter strains more likely to colonise particular bird species across disparate continents, than to cross host species barriers on the same farm.  Current research forms part of a multidisciplinary approach using state of the art technology to formally test links between chicken flock behaviour, welfare and Campylobacter prevalence, and to explore good husbandry as a potential measure to reduce colonisation of chicken flocks by Campylobacter, and ultimately to reduce the incidence of human disease.

Senior Researcher

Departmental Lecturer in Microbiology and Infectious diseases

Retained lecturer Magdalen College

charlene.rodrigues@zoo.ox.ac.uk

Dr Charlene Rodrigues

Read more about Dr Charlene Rodrigues

I am a clinician specialising in Paediatric Infectious Diseases and trained in the UK. I undertook a Wellcome Trust funded DPhil (2015-18), supervised by Profs. Martin Maiden and Chris Tang (Dunn School of Pathology) in genomic epidemiology of meningococcal disease in the UK using Meningitis Research Foundation Meningococcal Genome Library. The focus of my DPhil was to develop scalable genomic methods to study the diversity and distribution of meningococcal protein-based vaccine antigens and how this can inform vaccine strategy. I am now interested in developing applications that aid translation of genomic data for use in the clinical setting, in particular for non-genomics specialists. An example of such work includes a genomic based application to assess MenB vaccines for deployment in public health settings, the MenDeVAR Index.

Research interests
Genomics is making increasing contributions to infectious diseases and microbiology. Infection caused by Neisseria meningitidis serves as a useful disease model (carriage, vaccination, recognising clinical signs, optimal treatment of sepsis), as well as an important paediatric infection with significant morbidity and mortality in the UK and globally. My training and experience in microbial genomics has allowed me to combine my interests in infectious diseases, microbiology, public health, and vaccinology, to address important clinical questions in the prevention and management of other childhood infections, including Klebsiella pneumoniae. With collaborators in research institutes and public health reference laboratories globally, our work impacts children and young people in many settings.

Teaching

Having received formal training in microbial genomics I am enthusiastic about contributing to transferring this knowledge and experience to clinical and non-clinical colleagues, particularly where it helps inform patient care ad clinical decision-making. I am a course instructor on the Wellcome Trust Advanced Course for "Genomics and Clinical Microbiology" and teach on the MSc in Genomics at St George’s University, London.

Experience

I graduated from Leicester University medical school in 2007 having also completed an Intercalated BSc in breast cancer pathology.
On completion of the Academic Foundation Programme, I entered paediatric training in London as an NIHR Academic Clinical Fellow at Imperial College London.
I completed core registrar training and obtained a GRID sub-specialty infectious diseases, immunology and allergy training post in Newcastle upon Tyne in September 2014.
I trained in microbiology for 6 months following my DPhil, alongside adult ID and microbiology colleagues at St George’s Hospital, London.
I obtained CCT in paediatrics and subspecialty infectious diseases, immunology and allergy in February 2019.
I spend part of my time as a Paediatric Infectious Diseases Consultant in London.

@cmc_rodrigues

Post-doctoral Clinical Fellow

Paediatric Infectious Diseases Specialist

(2021) Tzanakaki G, Xirogianni A, Tsitsika A, Clark SA, Kesanopoulos K, Bratcher HB, Papandreou A, Rodrigues CMC, Maiden MCJ, Borrow R, Tsolia M. Estimated strain coverage of serogroup B meningococcal vaccines: A retrospective study for disease and carrier strains in Greece (2010-2017). Vaccine. 2021 Mar 12;39(11):1621-1630. doi: 10.1016/j.vaccine.2021.01.073.

(2021) MacLennan JM, Rodrigues CMC, Bratcher HB, Lekshmi A, Finn A, Oliver J, Wootton M, Ray S, Cameron C, Smith A, Heath PT, Bartolf A, Nolan T, Hughes S, Varghese A, Snape MD, Sewell R, Cunningham R, Stolton A, Kay C, Palmer K, Baxter D, Suggitt D, Zipitis CS, Pemberton N, Jolley KA, Bray JE, Harrison OB, Ladhani SN, Pollard AJ, Borrow R, Gray SJ, Trotter C, Maiden MCJ. Meningococcal carriage in periods of high and low invasive meningococcal disease incidence in the UK: comparison of UKMenCar1-4 cross-sectional survey results. Lancet Infectious Diseases. 2021 Jan 19:S1473-3099(20)30842-2. doi: 10.1016/S1473-3099(20)30842-2.

(2020) Rodrigues CMC, Jolley KA, Smith A, Cameron JC, Feavers IM, Maiden MCJ. Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool that Exploits Genomic Data in Public Health and Clinical Microbiology Applications. J Clin Microbiol. 2020 Oct 14:JCM.02161-20. doi: 10.1128/JCM.02161-20.

(2020) Rodrigues CMC and Plotkin SA. Impact of Vaccines on Human, Health; Health, Economic and Social Perspectives. Frontiers in Microbiology 2020 11:1526.

(2020) Rodgers, E., Bentley, S. D., Borrow, R., Bratcher, H. B., Brisse, S., Brueggemann, A. B., Caugant, D. A., Findlow, J., Fox, L., Glennie, L., Harrison, L. H., Harrison, O. B., Heyderman, R. S., van Rensburg, M. J., Jolley, K. A., Kwambana-Adams, B., Ladhani, S., LaForce, M., Levin, M., Lucidarme, J., MacAlisdair N., MacLennan J., Maiden MCJ., Maynard-Smith L., Muzzi A., Oster P., Rodrigues CMC., Ronveaux O., Serino L., Smoth V., van der Ende A., Vazquez J., Wang X., Yezli S., Stuart, J. M. (2020). The global meningitis genome partnership. Journal of infection, S0163-4453(20)30446-1.

(2019) Bratcher HB, Rodrigues CMC, Finn A, Wootton M, Cameron JC, Smith A, Heath P, Ladhani S, Snape MD, Pollard AJ, Cunningham R, Borrow R, Trotter C, Gray SJ, Maiden MCJ, MacLennan JM. UKMenCar4: A cross-sectional survey of asymptomatic meningococcal carriage amongst UK adolescents at a period of low invasive meningococcal disease incidence. Version 2. Wellcome Open Res. 2019 Oct 28 [revised 2019 Jan 1];4:118.

(2019) Rodrigues CMC, Handy L, Plotkin S. Vaccine Innovation and Development, Maxey-Rosenau-Last Public Health and Preventive Medicine. In press.

(2018) Rodrigues CMC, Chan H, Vipond C, Jolley K, Harrison OB, Wheeler J, Whiting G, Feavers IM and Maiden MCJ Typing complex meningococcal vaccines to understand diversity and population structure of key vaccine antigens. Wellcome Open Research. 2018 Nov 29;3:151.

(2018) Chen M, Rodrigues CMC, Harrison OB, Zhang C, Tan T, Chen J, Zhang X, Chen M, Maiden MCJ. Invasive meningococcal disease in Shanghai, China from 1950 to 2016: implications for serogroup B vaccine implementation. Scientific Reports. 2018 Aug 17;8(1):12334.

(2018) Rodrigues CMCand Maiden MCJ. A world without bacterial meningitis: how genomic epidemiology can inform vaccination strategy. F1000Research. 2018 Mar 27;7:401.

(2018) Rodrigues CMC, Lucidarme J, Borrow R, Smith A, Cameron JC, Moxon ER, Maiden MCJ. Genomic Surveillance of 4CMenB Vaccine Antigenic Variants among Disease-Causing Neisseria meningitidis Isolates, United Kingdom, 2010-2016. Emerging Infectious Diseases. 2018 Apr;24(4):673-682.

Books:

Rodrigues CMC, Handy L, Plotkin S. Vaccine Innovation and Development, Maxey-Rosenau-Last Public Health and Preventive Medicine. In pres 

Podcast:

http://www.scienceforthepeople.ca/episodes/meningitis

Dr Holly Bratcher

Read more about Dr Holly Bratcher

As a pathogen research specialist, I have a multidisciplinary background in public health, forensics, and translational research. At Colorado State University, USA I received a BSc in genetics and received a WHO Research Training Fellowship at the Centers for Disease Control and Prevention (CDC), USA. I studied bacterial populations of Yersinia pestis and Francisella tularensis and helped to develop genetic and molecular tools for reference typing and diagnostic testing. In 1999 I was recruited by the FBI as a Forensic Biologist and served in both the Laboratory Division and the Counterterrorism Division. I returned to research in 2005 and completed a MSc with honours for biomedical studies in forensics at the University of Manchester, UK. I joined the Maiden Group at the University of Oxford in 2008 and completed my PhD in the genomic evolutionary development of meningococcal lineage structures. As laboratory manager I supervise undergraduate research projects.

genomic epidemiology and evolution of bacterial population structure
strain typing of bacterial pathogens

holly.bratcher@zoo.ox.ac.uk

www.twitter.com

Senior Researcher and Laboratory Manager

Dr Margaret Varga

Read more about Dr Margaret Varga

I received my PhD in statistical pattern recognition from the University of Cambridge, UK. I joined the Maiden Lab as a visual analytics specialist in February 2018. I research, develop and apply visual analytics and visualisation techniques to infectious diseases such as Campylobacter and Neisseria meningitidis.

I am Chairman of the NATO Exploratory Visual Analytics Research Task Group and I am a Director of various engineering companies including Seetru Limited.

I was the recipient of the 2019 NATO Scientific Achievement Award.

Research interests

I have very wide ranging research interests which, in addition to visualisation and visual analytics, include; uncertainty analysis, network analysis, big data analysis, provenance analysis and visualisation, Bayesian reasoning, evidential reasoning, situation awareness and decision support, pattern and image processing, as well as financial systemic risk and stability monitoring.

In recent years I have worked extensively on the application of many of the above technologies to cyber security and I have also developed an interest in symbology to support situation awareness, for instance, in the cyber domain. Another of my interests is in the navigation of knowledge landscapes.

I also have a major interest in medical image processing: I led the team that developed the world’s first automated breast cancer histopathology diagnosis systems - I was granted seven patents for this system.

I have published widely, with well over one hundred and thirty publications.

Memberships: Fellow of the Institution of Engineering and Technology (IET); CEng

Award: 2019 NATO Scientific Achievement Award

margaret.varga@zoo.ox.ac.uk

Analytics Researcher