Meet the Team

Professor David Aanensen

Director

Leads the Centre, bringing together a unique blend of expertise in data modelling, software development, epidemiology, bioinformatics and machine learning, genomic technology, Good Financial Grant Practice (GFGP), training and capacity building.

For endemic pathogens (and outbreak scenarios), epidemiological data combined with genomics can inform control strategies and interventions on a local, national and international scale. Data generation, integration, analytical flow and interpretation in real-time is challenging, but crucial for decision making and action. Within the Centre we focus on data flow and the use of genome sequencing for surveillance of microbial pathogens through a combination of web application and software engineering, methods development and large-scale structured pathogen sequencing surveys – to deliver actionable information. Working with major public health agencies such as the US CDC, the European CDC, Public Health England, Wales, Scotland and the WHO, our systems are utilised globally to interpret and aid decision making for infection control.

The Centre also hosts an NIHR-funded Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance (AMR), working with partners leading National AMR strategies in The Philippines, Colombia, Nigeria and India to implement genomic surveillance and linking to routine phenotypic and epidemiological data for priority pathogens.

Richard Acton

Managing Director (DES)

Richard joined the group as the Managing Director of Digital Epidemiology Services – the non-profit organisation focussed on implementing the group capabilities globally.

He has extensive experience in building operational processes and transformation programmes from start up to scale up within life science businesses. In previous roles he has consistently evolved the products/services and solutions that dovetail with customer needs and organisational strategy. Richard brings with him the capability to understand the market requirements, regulatory landscape and internal cross-functional capabilities to maximise efficiencies and deliver the global programmes.

Richard previously held the position of Chief Scientific Officer at Cignpost Diagnostics where he established an operational structure, quality framework and scaled and evolved the organisation to meet market demand. Prior to working at Cignpost Diagnostics, Richard was the Operations Director at SRG, delivering scientific services across a wide range of life science businesses. He holds a BSc in Microbiology and Genetics from Leeds University.

Dr. Khalil Abudahab

Senior Web Software Engineer/Architect

Engineers software for data visualisation and integration.
Learn more about my work

After completing my PhD in belief rule-based knowledge modelling from Manchester Business School (https://mbs.ac.uk), I joined the CGPS as a software engineer. I develop and maintain various software including Microreact (https://microreact.org/), PhyloCanvas (http://phylocanvas.org/), Pathogen.watch (https://pathogen.watch/), and Data-flo (https://data-flo.io/).

Krisandra Allen

Genomic Epidemiology and Public Health Partnerships

Krisandra works with public health agencies that are using software developed by CGPS to help them creatively overcome the challenges associated with building genomic surveillance systems, with a special focus on helping integrate genomic data into epidemiologic investigations.

Krisandra has held a variety of roles within public health, with a guiding career focus of bridging between laboratory science and applied epidemiology. Her career began at a local health department in the United States, and she has spent time working in a public health laboratory, two state-level health departments (Virginia and Washington), and a wastewater-based epidemiology company.

With the emergence of SARS-CoV-2, Krisandra pivoted her work from investigating outbreaks of foodborne diseases to using genomic epidemiology to track SARS-CoV-2. In this capacity, she worked with the US CDC as a developer of their genomic epidemiology toolkit, and implemented strategies for SARS-CoV-2 variant surveillance for public reporting and epidemiologic analyses in Washington state.

Krisandra holds a MPH in Epidemiology from Virginia Commonwealth University, and a BS in Microbiology from the University of Idaho.

Selected Publications
Full publication list: Google Scholar Profile

Oltean, H. N., Allen, K. J., Frisbie, L., Lunn, S. M., Torres, L. M., Manahan, L., Painter, I., Russell, D., Singh, A., Peterson, J. M., Grant, K., Peter, C., Cao, R., Garcia, K., Mackellar, D., Jones, L., Halstead, H., Gray, H., Melly, G., Nickerson, D., … Lindquist, S. (2023). Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020-2021. Emerging infectious diseases, 29(2), 242–251. https://doi.org/10.3201/eid2902.221482

Paredes, M. I., Lunn, S. M., Famulare, M., Frisbie, L. A., Painter, I., Burstein, R., Roychoudhury, P., Xie, H., Mohamed Bakhash, S. A., Perez, R., Lukes, M., Ellis, S., Sathees, S., Mathias, P. C., Greninger, A., Starita, L. M., Frazar, C. D., Ryke, E., Zhong, W., Gamboa, L., … Allen, K.J.,Oltean, H. N. (2022). Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 75(1), e536–e544. https://doi.org/10.1093/cid/ciac279

Crowe, S. J., Bottichio, L., Shade, L. N., Whitney, B. M., Corral, N., Melius, B., Arends, K. D., Donovan, D., Stone, J., Allen, K., Rosner, J., Beal, J., Whitlock, L., Blackstock, A., Wetherington, J., Newberry, L. A., Schroeder, M. N., Wagner, D., Trees, E., Viazis, S., … Neil, K. P. (2017). Shiga Toxin-Producing E. coli Infections Associated with Flour. The New England journal of medicine, 377(21), 2036–2043. https://doi.org/10.1056/NEJMoa1615910

James Baker

Software Engineer

James, a highly experienced FullStack Software Developer, possesses more than 14 years of expertise in commercial web development. Throughout his career, he has focused on serving companies in the financial services and e-commerce sectors, demonstrating his ability to adapt to organizations of different sizes, from startups to global enterprises. With a strong background in designing and building complex applications and websites, James prioritises performance, user experience, and code quality.

In his current role at CGPS, James plays a significant role in the Pathogenwatch project. As an experienced team member, he takes on various critical responsibilities, including expanding the UI capabilities, ensuring code quality through automated testing, and actively engaging in user feedback sessions to enhance the product’s user experience.

Angela Blanton

Program Manager - Digital Epidemiology Pilot

Angie liaises with both stakeholders and site personnel, coordinating efforts within the CGPS project team to ensure timely reporting and achievement of deliverables. She led the CGPS’ CDC funded Digital Epidemiology Pilot which successfully deployed Data-flo and Microreact to five U.S. state departments of public health (ID, NM, UT, WA and WY) for SARS-CoV-2 genomic surveillance. Her extensive experience includes several years in public health as program manager for data management improvement projects for Florida DoH, Bureau of Public Health Laboratories, as well as several years experience as a senior clinical data analyst and team lead for multiple oncology studies and a program analyst supporting the U.S. government. She holds a BSPH from the Gillings School of Global Public Health, University of North Carolina at Chapel Hill.

Dale Bridges

Product Manager

Dale joined the group in January 2024. As the Product Manager for DES, Dale will ensure that we capture the essence of user feedback and latest technical developments to build a robust product roadmap. This will ensure that our technologies continue to be cutting edge and serve our core market’s needs. Dale thrives at the cutting edge of Scientific Discovery and Technology. She is committed to delivering solutions that empower researchers and accelerate scientific discoveries.Dale holds a MSc in Bioinformatics with Systems Biology from University of London – Birkbeck College. A Postgraduate Certificate in Education from UNISA and a BSc in Chemistry and Biochemistry from the University of the Witwatersrand.Dale has a solid background in Bioinformatics where her masters focused on Gibbs free energy changes at the interface of protein ligand interactions. She has worked with both Sanger and Illumina short read sequencing technologies for the development of pipelines, visualisation and reporting applications applied to these and drug discovery. And crossed over to the commercial side as a professional services bioinformatics consultant.

Dr. Julio Diaz Caballero

Lead Bioinformatician

Julio is a bioinformatician with a focus on bacterial genomics, evolutionary biology, and big data. He obtained his PhD from the Department of Cell and Systems Biology at the University of Toronto. During his PhD, Julio worked to better understand the within-patient evolution of infectious bacterial populations in cystic fibrosis lungs. Here, he combined deep sampling and next generation sequencing with bioinformatics and statistical methods to identify changes in the bacterial population diversity that could be associated with the clinical history of the patient. After his PhD, Julio joined the Zoology department at the University of Oxford to study bacterial infections in intensive care units across Europe.

Julio joined CGPS in November 2021 to work on the AMRwatch project. In this project, he leads the implementation of bioinformatics tools and the development of supporting material for the assembly and analysis of all the genomes of organisms in the WHO pathogen priority list. He is also interested in training fellow researchers in bioinformatics and bacterial genomics.

 

Learn more about my work

Nicole Dagata

Surveillance Program Manager

Nicole joined the group in 2023 as a surveillance program manager. She works closely with public health stakeholders across the US to optimise and implement digital surveillance tools for improved public health response.

 

She has a long standing drive to ensure global surveillance of pathogens is conducted with efficiency, providing access and knowledge to the right tools. Prior to joining the group, Nicole worked for the Clinton Health Access Initiative supporting national malaria surveillance programs throughout southern and western Africa. She provided project management and technical support to ministries of health in both regions to assess surveillance system performance, design optimal health information and data reporting workflows, analyse surveillance data, and promote the use of information for improved decision making and implementation.

 

Nicole holds an MSc in Epidemiology from the London School of Hygiene and Tropical Medicine; prior to that she completed her bachelor’s degree with the University of Florida.

 

Paul Carvalho

Good Financial Grant Practice Consultant

Paul is a Good Financial Grant Practice standard (GFGP) consultant within the CGPS team. As part of the NIHR Global Health Research Unit project, Paul assists partners in Nigeria, the Philippines, Colombia and India comply with the GFGP standard as well as working with other global partners to drive the uptake and utility of the standard.

Paul has a post graduate degree in finance and experience working with the Indian taxation system. Before joining CGPS, he completed a two year long fellowship offered by a mental health research organization called Sangath in Goa, India. In which he was part of the team that achieved the world’s first silver-tier GFGP certification, playing an important role in drafting and implementing the procedures that were part of the certification. Paul also has a diploma in applied financial risk management from the Indian Institute of Management, Kashipur, India.

Learn more about my work

Diana Connor

Head of Programme Management

Diana joined the CGPS team in January 2022 as a Project Manager and is currently the Head of Programme Manager. She is responsible for managing two specific projects focusing on assessing the global landscape of AMR genomic sequencing and increasing capacity of forward training in pathogen genomics within the UK. Diana is also responsible for overseeing the programme’s entire project portfolio, coordinating grant management, and ensuring stakeholder engagement.

Diana obtained her MPH of Infectious Disease and Microbiology at the University of Pittsburgh, USA and was the co-coordinator of a public health computational modelling group which conducted vaccine supply chain research in various countries across the globe. Her background also includes US specific experience working at the US-Centers for Disease Control and Prevention, the Hawaii State Department of Health and the Palm Beach County Health Department in Florida. Most recently, she was the consortium coordinator in Copenhagen, Denmark, for an EU wide One Health project through the OneHealth European Joint Programme. Diana has co-authored over 25 peer reviewed journal articles focusing on infectious disease and public health.

Dr Natacha Couto

Consultant Bioinformatician

Natacha is a veterinary doctor and got her PhD in 2016. Her research focuses on the molecular epidemiology, population genomics and ecology of a broad range of bacterial and viral pathogens of humans and animals. She uses next-generation sequencing (NGS) and bioinformatics to understand transmission of bacterial and viral pathogens and emergence and spread of antimicrobial resistance between humans and animals (One Health). She studies the distribution of certain species, lineages, or genetic features in different ecological niches, understand adaptation to specific sources and to quantify the degree of transmission events within and between different sources. She has also been involved in the optimization (both wetlab and elab) of shotgun metagenomics, transcriptomics, and long-read sequencing. Prior to joining the CGPS, Natacha was awarded her PhD by the University of Lisbon in 2016.

Wa Ode Dwi Daningrat

DPhil student

Wa Ode Dwi Daningrat is an Indonesian government scholar pursuing a DPhil in Clinical Medicine at the University of Oxford. Her main research interests are vaccine impact evaluation and antimicrobial resistance (AMR) profile of Streptococcus pneumoniae (S. pneumoniae) and the utilisation of whole-genome sequencing (WGS) to investigate the presence of genes and mutations in pneumococcal isolates related to AMR. Under the supervision of Prof David Aanensen and Dr Silvia Argimon, her DPhil research focuses on the genomic epidemiology of Streptococcus pneumoniae pre- and post-Pneumococcal Conjugate Vaccine Introduction in Indonesia.

Dr Sophia David

Senior Research Fellow

Sophia is a Senior Research Fellow in the Centre for Genomic Pathogen Surveillance (CGPS). Her research uses genomic approaches to study the evolution and spread of bacterial pathogens, most notably Klebsiella pneumoniae. Recently, her work has focused on the genomic epidemiology of carbapenem-resistant K. pneumoniae including the role of high-risk clones, the diversity and transmission dynamics of resistance plasmids, and resistance mechanisms involving porin channels (OmpK35/OmpK36).

Sophia holds a PhD in Bacterial Genomics from the University of Cambridge/Wellcome Sanger Institute (2016) and a BSc in Biology from Imperial College London (2012).

 

Publications

  1. Delgado-Blas JF, Ovejero CM, David S, Serna C, Pulido-Vadillo M, Montero N, et al. Global scenario of the RmtE pan-aminoglycoside-resistance mechanism: emergence of the rmtE4 gene in South America associated with a hospital-related IncL plasmid. Microb Genom. 2023;9(3).
  2. Foster-Nyarko E, Cottingham H, Wick RR, Judd LM, Lam MMC, Wyres KL, et al. Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. Microb Genom. 2023;9(2).
  3. David S, Wong JLC, Sanchez-Garrido J, Kwong HS, Low WW, Morecchiato F, et al. Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae. PLoS Pathog. 2022;18(7):e1010334.
  4. Low WW, Wong JLC, Beltran LC, Seddon C, David S, Kwong HS, et al. Mating pair stabilization mediates bacterial conjugation species specificity. Nat Microbiol. 2022;7(7):1016-27.
  5. Wong JLC, David S, Sanchez-Garrido J, Woo JZ, Low WW, Morecchiato F, et al. Recurrent emergence of Klebsiella pneumoniae carbapenem resistance mediated by an inhibitory ompK36 mRNA secondary structure. Proc Natl Acad Sci U S A. 2022;119(38):e2203593119.
  6. Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, et al. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nat Microbiol. 2022;7(12):2054-67.
  7. Argimón S, David S, Underwood A, Abrudan M, Wheeler NE, Kekre M, et al. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch. Clin Infect Dis. 2021;73(Suppl_4):S325-S35.
  8. Afolayan AO, Oaikhena AO, Aboderin AO, Olabisi OF, Amupitan AA, Abiri OV, et al. Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria. Clin Infect Dis. 2021;73(Suppl_4):S308-S15.
  9. Di Pilato V, Errico G, Monaco M, Giani T, Del Grosso M, Antonelli A, et al. The changing epidemiology of carbapenemase-producing Klebsiella pneumoniae in Italy: toward polyclonal evolution with emergence of high-risk lineages. J Antimicrob Chemother. 2021;76(2):355-61.
  10. Delgado-Blas JF, Ovejero CM, David S, Montero N, Calero-Caceres W, Garcillan-Barcia MP, et al. Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments. Commun Biol. 2021;4(1):457.
  11. Gibbon MJ, Couto N, David S, Barden R, Standerwick R, Jagadeesan K, et al. A high prevalence of blaOXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England. Microb Genom. 2021;7(3).
  12. Mentasti M, David S, Sands K, Khan S, Davies L, Turner L, et al. Rapid detection and differentiation of mobile colistin resistance (mcr-1 to mcr-10) genes by real-time PCR and melt-curve analysis. J Hosp Infect. 2021;110:148-55.
  13. David S, Cohen V, Reuter S, Sheppard AE, Giani T, Parkhill J, et al. Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae. Proc Natl Acad Sci U S A. 2020;117(40):25043-54.
  14. Ginevra C, Chastang J, David S, Mentasti M, Yakunin E, Chalker VJ, et al. A real-time PCR for specific detection of the Legionella pneumophila serogroup 1 ST1 complex. Clin Microbiol Infect. 2020;26(4):514.e1-.e6.
  15. Mäklin T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, et al. High-resolution sweep metagenomics using fast probabilistic inference. Wellcome Open Res. 2020;5:14.
  16. Zhou K, Xiao T, David S, Wang Q, Zhou Y, Guo L, et al. Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China. Emerg Infect Dis. 2020;26(2):289-97.
  17. David S, Reuter S, Harris SR, Glasner C, Feltwell T, Argimon S, et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nat Microbiol. 2019;4(11):1919-29.
  18. Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, et al. Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nat Genet. 2019;51(6):1035-43.
  19. David S, Mentasti M, Lai S, Vaghji L, Ready D, Chalker VJ, et al. Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building. Microb Genom. 2018;4(10).
  20. David S, Mentasti M, Parkhill J, Chalker VJ. Low genomic diversity of Legionella pneumophila within clinical specimens. Clin Microbiol Infect. 2018;24(9):1020.e1-.e4.
  21. David S, Afshar B, Mentasti M, Ginevra C, Podglajen I, Harris SR, et al. Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires’ Disease. Clinical Infectious Diseases. 2017;64(9):1251-9.
  22. David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, et al. Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLoS Genet. 2017;13(6):e1006855.
  23. Mentasti M, Cassier P, David S, Ginevra C, Gomez-Valero L, Underwood A, et al. Rapid detection and evolutionary analysis of Legionella pneumophila serogroup 1 sequence type 47. Clin Microbiol Infect. 2017;23(4):264.e1-.e9.
  24. Schjørring S, Stegger M, Kjelsø C, Lilje B, Bangsborg JM, Petersen RF, et al. Genomic investigation of a suspected outbreak of Legionella pneumophila ST82 reveals undetected heterogeneity by the present gold-standard methods, Denmark, July to November 2014. Euro Surveill. 2017;22(25).
  25. Crellen T, Allan F, David S, Durrant C, Huckvale T, Holroyd N, et al. Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. Sci Rep. 2016;6:20954.
  26. David S, Mentasti M, Tewolde R, Aslett M, Harris SR, Afshar B, et al. Evaluation of an optimal epidemiologic typing scheme for Legionella pneumophila with whole genome sequence data using validation guidelines. Journal of Clinical Microbiology. 2016;54(8):2135-48.
  27. David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, et al. Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently. Genome Research. 2016.
  28. Hadfield J, David S. A bit of a mouthful. Nat Rev Microbiol. 2016;14(9):548.
  29. Stine OC, Burrowes S, David S, Johnson JK, Roghmann MC. Transmission Clusters of Methicillin-Resistant Staphylococcus Aureus in Long-Term Care Facilities Based on Whole-Genome Sequencing. Infect Control Hosp Epidemiol. 2016;37(6):685-91.
  30. David S, Hadfield J. It’s diversity all the way down. Nat Rev Microbiol. 2015;13(12):740.
  31. Mentasti M, Kese D, Echahidi F, Uldum SA, Afshar B, David S, et al. Design and validation of a qPCR assay for accurate detection and initial serogrouping of Legionella pneumophila in clinical specimens by the ESCMID Study Group for Legionella Infections (ESGLI). Eur J Clin Microbiol Infect Dis. 2015;34(7):1387-93.
  32. Turner CE, Abbott J, Lamagni T, Holden MT, David S, Jones MD, et al. Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom. MBio. 2015;6(4):e00622.

Georgina Lewis-Woodhouse

Digital Epidemiologist - Data Scientist

Georgina works on the implementation of CGPS tools to facilitate the use of genomic epidemiology and data science in public health and infectious disease research. She joined CGPS in 2022 and works on a variety of projects within the group utilising a background in molecular biology, data science and epidemiology.

Previously, Georgina worked for the Global Research on Antimicrobial Resistance (GRAM) project at the University of Oxford with a focus on modelling the prevalence of resistance of Staphylococcus aureus and Streptococcus pneumoniae as well as possible factors that drive AMR. She has a Masters of Research (MRes) in Ecology, Evolution and Development and a BSc in Biology from Oxford Brookes University.

Publications
Murray, C. J., Ikuta, K. S., Sharara, F., Swetschinski, L., Aguilar, G. R., Gray, A., Han, C., Bisignano, C., Rao, P., Wool, E., Johnson, S. C., Browne, A. J., Chipeta, M. G., Fell, F., Hackett, S., Haines-Woodhouse, G., Hamadani, B. H. K., Kumaran, E. A. P., McManigal, B., … Naghavi, M. (2022). Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet, 399(10325), 629–655. https://doi.org/10.1016/S0140-6736(21)02724-0

Browne, A. J., Chipeta, M. G., Haines-Woodhouse, G.,Kumaran, E. P. A., Hamadani, B. H. K., Zaraa, S., Henry, N. J., Deshpande, A., Reiner, R. C., Day, N. P. J., Lopez, A. D., Dunachie, S., Moore, C. E., Stergachis, A., Hay, S. I., & Dolecek, C. (2021). Global antibiotic consumption and usage in humans, 2000-18: a spatial modelling study. The Lancet. Planetary Health, 5(12), e893–e904. https://doi.org/10.1016/S2542-5196(21)00280-1

Chipeta, M. G., Kumaran, E. P. A., Browne, A. J., Hamadani, B. H. K., Haines-Woodhouse, G., Sartorius, B., Reiner, R. C., Dolecek, C., Hay, S. I., & Moore, C. E. (2022). Mapping local variation in household overcrowding across Africa from 2000 to 2018: a modelling study. The Lancet. Planetary Health, 6(8), e670–e681. https://doi.org/10.1016/S2542-5196(22)00149-8

Steve Karp

Operations

Steve joined CGPS to assist in scaling up our capabilities, and is helping to establish one or more charitable companies to implement those capabilities sustainably across the globe.

He has extensive expertise in all aspects of alliance, program and operations management in the life sciences. He has directed development and tech transfer programs in a variety of technologies. Among these have been multiple immunology and cardiovascular therapeutics ranging from the pre-clinical stage through post marketing. He has run various collaborative research and development programs working with government, non-profits and private industry. Previously Steve was the Executive Director of theInnovation Services at the California Life Sciences Institute, building and managing its accelerator programs for early stage life science companies, both in the U.S. and internationally. Prior to joining CLSI, Steve worked for synthetic biology company Intrexon, the Neugenesis Corporation, where he was Chief Operating Officer, Genentech, and Discovery Partners International, among others. He attended Harvard College.

Dr Nabil-Fareed Alikhan

Senior Bioinformatician

Nabil-Fareed is a Senior Bioinformatician at the Centre for Genomic Pathogen Surveillance. Nabil-Fareed has over a decade of research experience, with bioinformatics and research positions at the University of Warwick and Quadram Institute Bioscience. He holds a PhD from the University of Queensland, Australia. Nabil-Fareed’s research interests include the population genetics and pathogenesis of enteric pathogens, including Salmonella and E. coli.

 

During the COVID-19 pandemic, Nabil-Fareed was involved in building the bioinformatics infrastructure for his organisation’s participation in the national COVID-19 genome sequencing (COG-UK). Through the infrastructure he developed and ran, they released more than 80,000 SARS-CoV-2 genomes. These data, along with genomes across the UK have been presented in technical briefings to the UK government.

 

Nabil-Fareed is an avid software developer and writes software to assist research in microbial genomics, he has co-authored bioinformatics software such as GrapeTree, EnteroBase and BRIG.

 

Selected Publications

Emmanuelle Kumaran

Digital Epidemiologist - Data Scientist

Emmanuelle joined CGPS in 2022 where she works closely with CGPS stakeholders within the public health community to support and facilitate the use of molecular/genomic epidemiological analysis of infectious disease for surveillance and other public health response activities. Prior to joining CGPS, Emmanuelle worked on the Global Research on Antimicrobial Resistance project at the University of Oxford where her work focused primarily on the global prevalence of drug resistant tuberculosis.

She holds a Master’s in Public Health from the London School of Hygiene and tropical medicine and an undergraduate degree from Imperial College London.

 

Learn more about my work

 

Fergus Maclean

Programme Budget Manager

Fergus joined CGPS in May 2023 fulfilling the financial reporting requirements for the NIHR Global Health Research Unit (GHRU) on Genomics and Enabling Data for Surveillance of Antimicrobial Resistance. As Programme Budget Manager, Fergus works closely with the wider project team with a focus on financial management and collaboration with our four research collaboration sites in Nigeria, India, Colombia and The Philippines. Fergus brings to the role a successful track record working with Australian government as a management consultant building resilient, compliant and successful projects. As a management consultant, Fergus worked across multiple departments to facilitate better outcomes for Australian Defence Force families, national security procurement officials, National Disability Insurance Scheme participants, and other public groups.

Fergus holds a Bachelor of Arts and a Bachelor of Business Administration from the Australian National University (ANU).

Mirko Menegazzo

Web & Mobile Developer

 

Lead software developer focused on web and mobile applications.

Mirko is a full-stack software developer focusing primarily on Web and Mobile applications, and is the Centre’s lead developer of Epicollect5, a web and mobile platform for the generation of forms and freely hosted project websites for data collection. (five.epicollect.net)

 

William Minchin

Project Manager - GHRU

Will joined the CGPS group in January 2024 as Project Manager for the NIHR Global Health Research Unit (GHRU) on Genomics and Enabling Data for Surveillance of Antimicrobial Resistance.  He facilitates the delivery of further great work in the space of Whole Genome Sequencing and Antimicrobial Resistance surveillance, coordinating activity within the UK, the funders, and with collaborators in India, the Philippines, Colombia, and Nigeria.

Previously Will worked as a process engineer and subsequently moved into data analysis at UK Research and Innovation, where he spent a number of years as a Project Manager. At UKRI, Will helped both improve the organisation’s approach to Peer Review, and to develop and test the organisation’s new Funding Service – including business change management and operating model scoping.

Dr Ben Pascoe

Head of Laboratory Implementation

Ben Pascoe is the Head of Laboratory Implementation for the NIHR Global Health Research Unit (GHRU) on Genomics and Enabling Data for Surveillance of Antimicrobial Resistance for the Centre for Genomic Pathogen Surveillance (CGPS). With over a decade of experience running sequencing laboratories, including establishing sequencing facilities at Swansea University Medical School and the Milner Centre for Evolution at the University of Bath, Ben leads on all aspects of laboratory operations across the project, both in the UK and across our international collaborators, to develop and help manage research activities with international partners and enhance practical implementation of whole genome sequencing for the surveillance of antimicrobial resistance,
As part of the Ineos Oxford Institute for Antimicrobial Research, Ben manages an active research portfolio, including research into Global Pathogen Genomics and Evolution, Global differences in Campylobacter epidemiology, and the emergence of multi-drug resistant Campylobacter coli.
Selected Publications (Google Scholar)
  • Post V*, Pascoe B*, […] Sheppard SK**, Moriarty TF** (2022) Multiple hypervirulent methicillin-sensitive Staphylococcus aureus lineages contribute towards poor patient outcomes in orthopaedic device-related infections. medRxiv [TBC]
  • Kittiwan N, […] Patchanee P*, Pascoe B* (2022) Non-serotype 2 isolates from healthy pigs are a potential zoonotic reservoir of Streptococcus suis genetic diversity and antimicrobial resistance. Microbial Genomics doi: 10.1099/mgen.0.00088
  • Mouftah SF*, Pascoe B*, […], Sheppard SK, Elhadidy M (2022) Local accessory gene sharing drives lineage-specific acquisition of antimicrobial resistance in Egyptian Campylobacter spp. Microbial Genomics 8(6):834; doi: 10.1099/mgen.0.000834
  • Mourkas E, Yahara K, Bayliss SC, […] Pascoe B & Sheppard SK* (2022) Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter. eLife 11:e73552
  • Peters S*, Pascoe B*, Wu Z, […] Sheppard SK**, Grover M** (2021) Campylobacter jejuni genotypes associated with post infection irritable bowel syndrome in humans. Communications Biology 4: 1015
  • Calland JK, Pascoe B, […], Falush D & Sheppard SK (2021) Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages. PLoS Genetics 17(9):e1009829

Heather Shane

Strategy & Alliances

Heather joined CGPS to lead strategy and corporate development, and is working closely with Steve Karp to establish one or more charitable companies to scale CGPS’ capabilities sustainably across the globe. Heather brings over 15 years of experience in the life sciences across multiple domains. Her focus and passion is infectious disease and harnessing data to benefit public health. Before joining CGPS, Heather was a strategic advisor to companies developing therapeutics, vaccines and diagnostics to address antimicrobial resistance (AMR) as well as academic researchers seeking to translate their tools and discoveries. Heather became part of the AMR community through her work with CARB-X, where she built the accelerator program at the California Life Science Institute to connect CARB-X portfolio companies to potential partners, funding sources, subject matter expertise and capabilities, and designed support programs customised to suit their individual needs. In a past life, Heather practised corporate transactional law, first forming and financing startups in Silicon Valley, and then for 10 years as VP & Assistant General Counsel at a public biotech company where she supported antibiotic drug discovery transitioning to and through preclinical and clinical development, the regulatory process and ultimately commercialization. Heather has a BA in English Literature from the University of California at Santa Barbara and a JD from NYU School of Law.

Pranit Shinde

Full Stack Software Engineer

Pranit works as a FullStack software engineer at CGPS. He works on web applications that help facilitate the research conducted at CGPS. He is primarily responsible for developing and maintaining Data-Flo, Micro-React, and Pathogenwatch.

Pranit has extensive experience developing large-scale web applications at his previous work for a US-based company. His area of expertise is building applications in the Javascript/Typescript ecosystem with a focus on the reliability, scalability, and accessibility of the software.

Pranit has a Master’s degree in Computer Science from the University of Oregon and a Bachelor’s degree in Computer Engineering from the University of Mumbai.

Jude Walker

Programme Coordinator

Jude provides practical and logistical support to the interdisciplinary CGPS team. Based at the Big Data Institute, Jude assists with onboarding new team members, monitoring grant expenditure, and facilitating collaboration with external agencies and internal departments within the University of Oxford. Jude qualified as a Legal Executive in 2008, and was awarded her Master’s in Human Rights Law in 2010. Jude worked in a number of public sector administrative, commissioning and legal roles before joining the CGPS in 2022.

Dr. Corin Yeats

Computational Biologist

 

Works across a wide range of genomics and sequence-based research both theoretical (e.g. protein function evolution) and for applied software development (e.g. antimicrobial resistance prediction). Currently focussed on the application of genomics analysis software in the public health context.

After completing a PhD in protein sequence domain analysis as part of the Pfam group at the Sanger Institute (2005), I continued in the structural world in the CATH-Gene3D group at UCL. Here I gained experience in a range of modern computational biology practices: from the large-scale via development of ontologies and web-based tools for linking primary databases through to the detailed analysis of individual proteins.

I then joined David Aanensen at Imperial College as part of the nascent CGPS team – and then onto the BDI at Oxford University – to apply this experience to building genomics analysis tools for public health researchers and decision makers. In particular I feel the rapidly growing volumes of genome-phenotype data for antimicrobial resistance is leading to a transformation in the possibilities for modelling and prediction.

Publications

Yeats C, Finn R, Bateman A “The PASTA domain: a beta-lactam-binding domain” (2002) Trends in biochemical sciences 27 (9): 438-440

Bateman A, Lachlan C et al “The Pfam protein families database.” (2004) Nucleic acids research 32 (suppl_1):D138-D141

Pain A, Renauld H et al “Genome of the host-cell transforming parasite Theileria annulata compared with T. parva” (2005) Science 309 (5731), 131-133

Bentley S, Maiwald M et al “Sequencing and analysis of the genome of the Whipple’s disease bacterium Tropheryma whipplei” (2004) Proceedings of the National Academy of Sciences 101 (39):14240-14245

Hunter S, Apweiler R et al “InterPro: the integrative protein signature database” (2009) Nucleic acids research 37 (suppl_1):D211-D215

Aanensen D, Feil E et al “Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive Staphylococcus aureus in Europe” (2016) MBio 7 (3):e00444-16

Gladstone R, Lo S et al “Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates” (2020) Microbial Genomics mgen000357

Google Scholar Link: https://scholar.google.com/citations?user=TUMUF9gAAAAJ&hl=en