Centre for Genomic Pathogen Surveillance
The Centre for Genomic Pathogen Surveillance (CGPS) is dedicated to tracking pathogen dynamics, data flow, and the use of genome sequencing for microbial pathogen surveillance. It collaborates with global partners, supports capacity building in genomics, and develops software tools for public health and research. CGPS is involved in various initiatives including genomic surveillance of antimicrobial resistance, outbreak investigation, and pathogen classification, with a focus on global health security and scientific collaboration. It actively partners with international health organizations and research institutions to enhance genomic epidemiology and response to infectious diseases.
Industries
Nr. of Employees
small (1-50)
Centre for Genomic Pathogen Surveillance
Oxford, Oxfordshire, United Kingdom, Europe
Products
Metadata uploader web application
Authenticated web application for sequencing sites to upload, validate and synchronise sample metadata with central repository APIs, with embedded field documentation.
Lineage and variant assignment web application
Web-accessible application to assign phylogenetic lineage or variant labels to genome sequences and display placement, temporal trends and geographic distribution for interpretation.
Curated protocols and resource collections
Collections of standardised laboratory protocols, training materials and guidance documents for implementation of genomic surveillance and for supporting grant and operational practices.
Metadata uploader web application
Authenticated web application for sequencing sites to upload, validate and synchronise sample metadata with central repository APIs, with embedded field documentation.
Lineage and variant assignment web application
Web-accessible application to assign phylogenetic lineage or variant labels to genome sequences and display placement, temporal trends and geographic distribution for interpretation.
Curated protocols and resource collections
Collections of standardised laboratory protocols, training materials and guidance documents for implementation of genomic surveillance and for supporting grant and operational practices.
Services
Genomic epidemiology and surveillance support
Technical collaboration with sequencing centres and public-health agencies to deliver genomic surveillance workflows, data integration, analysis and interpretation for outbreak response; includes coordination between local and large-scale sequencing facilities.
Training and capacity-building courses
Non-laboratory courses and workshops on designing and delivering pathogen genomics training, genomic data analysis, and capacity building for sequencing and bioinformatics.
EQA / proficiency testing for AMR prediction
Design and distribution of blinded bacterial strain panels and assessment frameworks to evaluate laboratory ability to report phenotypic species/AST and genomic AMR-prediction results.
Software deployment and hosting support
Installation, configuration and post-installation support for genomic data platforms including private/local instances and integration with local authentication services.
Public engagement activities
Interactive events and materials that use real datasets and web tools to communicate concepts around antimicrobial resistance and pathogen spread to general audiences.
Genomic epidemiology and surveillance support
Technical collaboration with sequencing centres and public-health agencies to deliver genomic surveillance workflows, data integration, analysis and interpretation for outbreak response; includes coordination between local and large-scale sequencing facilities.
Training and capacity-building courses
Non-laboratory courses and workshops on designing and delivering pathogen genomics training, genomic data analysis, and capacity building for sequencing and bioinformatics.
EQA / proficiency testing for AMR prediction
Design and distribution of blinded bacterial strain panels and assessment frameworks to evaluate laboratory ability to report phenotypic species/AST and genomic AMR-prediction results.
Software deployment and hosting support
Installation, configuration and post-installation support for genomic data platforms including private/local instances and integration with local authentication services.
Public engagement activities
Interactive events and materials that use real datasets and web tools to communicate concepts around antimicrobial resistance and pathogen spread to general audiences.
Expertise Areas
- Genomic surveillance
- Outbreak genomics and phylogenetic analysis
- Bioinformatics and genomic data visualisation
- Antimicrobial resistance (AMR) surveillance and genomic prediction
Key Technologies
- Whole-genome sequencing (WGS)
- Phylogenetic analysis
- Genomic data visualization platforms
- Metadata validation and ingestion pipelines