Meet the Team
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.
Building on her experience as a postdoctoral researcher at the Wellcome Sanger Institute and Imperial College London, where she studied the emergence and spread of antimicrobial resistance in Gram-positive bacteria, Monica is now designing and applying new methods of training and teaching others in Bioinformatics and Genomic Epidemiology.
Monica’s main role in CGPS is to design and develop courses in data science and pathogen genomics for healthcare professionals in the UK, as part of the T3CONNECT project (https://t3connect.org/). In the past years, she was a mentor and trainer in Bioinformatics-related courses organised by Wellcome Connecting Science, EMBL-EBI and the University of Cambridge.
Monica holds a PhD in Microbial Ecology and Evolution from the University of Manchester (2015), an MSc in Computer Science (2010, University of Leicester, UK) and a BSc also in Computer Science (2008, Babes-Bolyai University, Romania).
Full publication list: Google Scholar Profile
Abrudan, M., A. Matimba, D. Nikolic, D. Hughes, S. Argimon, M. Kekre, A. Underwood, D. M. Aanensen, and Nihr Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance. “Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of Antimicrobial Resistance (Amr).” Clinical Infectious Diseases 73, no. Supplement_4 (Dec 1 2021): S283-S89. https://doi.org/10.1093/cid/ciab770. https://www.ncbi.nlm.nih.gov/pubmed/34850831.
Miller, E. L., M. Kjos, M. I. Abrudan, I. S. Roberts, J. W. Veening, and D. E. Rozen. “Eavesdropping and Crosstalk between Secreted Quorum Sensing Peptide Signals That Regulate Bacteriocin Production in Streptococcus Pneumoniae.” ISME J 12, no. 10 (Oct 2018): 2363-75. https://doi.org/10.1038/s41396-018-0178-x. https://www.ncbi.nlm.nih.gov/pubmed/29899510.
Miller, E. L., M. I. Abrudan, I. S. Roberts, and D. E. Rozen. “Diverse Ecological Strategies Are Encoded by Streptococcus Pneumoniae Bacteriocin-Like Peptides.” Genome Biology and Evolution 8, no. 4 (Apr 13 2016): 1072-90. https://doi.org/10.1093/gbe/evw055. https://www.ncbi.nlm.nih.gov/pubmed/26983823.
Abrudan M., You L., Staňková K., Thuijsman F. “A game theoretical approach to microbial coexistence” Advances in Dynamic and Evolutionary Games : Theory, Applications, and Numerical Methods. 1st ed. Cham: Springer International Publishing : Imprint: Birkhäuser, 2016. https://doi.org/10.1007/978-3-319-28014-1.
Abrudan, M. I., F. Smakman, A. J. Grimbergen, S. Westhoff, E. L. Miller, G. P. van Wezel, and D. E. Rozen. “Socially Mediated Induction and Suppression of Antibiosis During Bacterial Coexistence.” The Proceedings of the National Academy of Sciences (PNAS) 112, no. 35 (Sep 1 2015): 11054-9. https://doi.org/10.1073/pnas.1504076112. https://www.ncbi.nlm.nih.gov/pubmed/26216986.
Abrudan, M. I., S. Brown, and D. E. Rozen. “Killing as Means of Promoting Biodiversity.” Biochemical Society Transactions 40, no. 6 (Dec 1 2012): 1512-6. https://doi.org/10.1042/BST20120196. https://www.ncbi.nlm.nih.gov/pubmed/23176508.
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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/).
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.
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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.
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.
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).
- 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).
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- Hadfield J, David S. A bit of a mouthful. Nat Rev Microbiol. 2016;14(9):548.
- 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.
- David S, Hadfield J. It’s diversity all the way down. Nat Rev Microbiol. 2015;13(12):740.
- 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.
- 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 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.
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
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.
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.
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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)
- 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
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.
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.
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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