Centre for Genomic Pathogen Surveillance

Data, insight and tools for local and global value - Based at Uni Oxford Big Data Institute

[Centre for Genomic Pathogen Surveillance @TheCGPS]

This afternoon at our GHRU AGM, we’re diving into challenges and opportunities of structured surveys through a World Café format.

From communicating results beyond journals to measuring impact, colleagues from across the GHRU network are exchanging insights and solutions that will make a valuable contribution to our future work.

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Kicking off Day 2 of #GHRU2025 in Bohol 🇵🇭 with a focus on structured surveys.
Our @NIHRresearch-funded Global Health Research Unit teams are sharing updates on the KlebSurvey and developing rapid reports to support public health decision-making.

[Centre for Genomic Pathogen Surveillance @TheCGPS]

We’re in the Philippines 🇵🇭 this week for the 6th NIHR Global Health Research Unit Annual Meeting on Genomic Surveillance of AMR.
Hosted by our partners at @RITMPH, teams from across the GHRU network are sharing progress and planning for the future.

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Our @NIHRresearch funded GHRU together in Bohol, Philippines.

Colleagues from Colombia, India, Nigeria, the Philippines & the UK working together to strengthen genomic surveillance of AMR at the Unit’s annual general meeting. 🌍🤝🧬

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Future planned updates include a) incorporation and filtering of additional metadata (e.g. isolate source), b) adding the ability to display data from bespoke genome collections (including user-defined) and c) extending to additional pathogens/vaccine targets.

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Pleased to share our new preprint describing https://t.co/SHQ7a2yFUq, an interactive platform enabling exploration of vaccine target diversity from global genome data: https://t.co/p72GCpCfBq

[Centre for Genomic Pathogen Surveillance @TheCGPS]

https://t.co/TlO2nswEUA currently displays data for >100k high-quality genomes with geotemporal sampling information (post-2010), but we demonstrate that substantial biases and geographic gaps remain in the coverage of available genomes.

[Centre for Genomic Pathogen Surveillance @TheCGPS]

By combining survey data with additional public data, we also found substantial global spread of high-risk E. coli clones with NDM-5 and other carbapenemases. We found many introductions of these into European hospitals in 2019, albeit with limited onward nosocomial transmission.

[Centre for Genomic Pathogen Surveillance @TheCGPS]

We’re pleased to share two new preprints with results from a structured survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE), conducted in 37 European countries in 2019.
E. coli: https://t.co/mlh3IV8G5E
K. pneumoniae: https://t.co/zmFxFfhr2N
@ECDC_EU

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Our findings suggest that the situation with carbapenem-resistant K. pneumoniae has continued to worsen and that control measures have not been able to interrupt transmission of high-risk lineages circulating within European hospital networks.

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Huge disparity in genomic data: We support all efforts to increase the genomic surveillance of pathogens on a global scale as dynamics differ locally: what happens in one place does not translate to another and high-risk clones can emerge anywhere. https://t.co/x7XlcXutbi can be used to assess the representation of geographic regions, e.g. with countries here in white currently lacking any public genomes. See more at: https://t.co/IywIToFcbO

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Our latest preprint is out describing https://t.co/x7XlcXutbi – a platform for monitoring AMR trends from global genomics data. Supporting all WHO priority pathogens (2017), https://t.co/x7XlcXutbi summarises the geographic and temporal distribution of genotypic variants (e.g. STs) in the context of AMR to aid monitoring and prioritisation efforts. https://t.co/nUJtVzL0HF

[Centre for Genomic Pathogen Surveillance @TheCGPS]

Always-on: all QC’d genomes with geotemporal metadata, are ingested from archives, analysed in https://t.co/unoU08iIUL and results visualised within https://t.co/x7XlcXutbi. Data are extracted and updated every 4h, with observed trends therefore only delayed by time to genome deposition. See more on filtering here : https://t.co/5sHT5uxvNO