Professor David Aanensen
Director of The Centre for Genomic Pathogen Surveillance
- Professor and Senior Group Leader in Genomic Surveillance
- Group Leader at Wellcome Sanger Institute
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 for Genomic Pathogen Surveillance David and team 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 surveys and sequencing of microbes with delivery of information for decision making.
Working with major public health agencies such as the US CDC, the European CDC, Public Health England and the WHO, systems are utilised to interpret and aid decision making for infection control.
David is also Director of the NIHR funded Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance working with partners leading National AMR strategies in The Phillipines, Colombia, Nigeria and India to implement genomic surveillance and linking to routine phenotypic and epidemiological data for priority pathogens.
Major Applications include:
Epicollect5 - Mobile data gathering platform used globally and by major health agencies, citizen scientists, ecologists, epidemiologists, business analytics, schools and colleges (..largely initiatives outside of the initial use cases..) over 14,000 projects and > 28Million data points.
Microreact - Open data visualisation and sharing for genomic epidemiology. Used by major agencies such as CDC, eCDC and PHE for routine investigation of public health incidents.
Pathogenwatch - A global platform for genomic surveillance of microbial pathogens (including all major WHO Priority bacterial pathogens) Rapid prediction of resistant genotypes, and clustering giving epidemiological context.
Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae.
David S. et al, (2020), Proceedings of the National Academy of Sciences of the United States of America
Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines.
Argimón S. et al, (2020), Nature communications, 11
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.
David S. et al, (2019), Nature microbiology
Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study.
Lo SW. et al, (2019), The Lancet. Infectious diseases
Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.
McNally A. et al, (2019), mBio, 10