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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Last session pushed beyond bacteria. Azole-resistant Aspergillus linked to agricultural fungicides. C. auris likely accelerated by climate change. Almost no global capacity for fungal genomic surveillance. AMR is bigger than bacteria. www.amrsurveillance.org #AMRSurveillanceAddis

amrsurveillance.org

AMR Convening on Building Sustainable AMR Genomic Surveillance

A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Four national stories. Philippines: 38 years of AMR surveillance, now adding WGS. Uganda: 16 to 43 sites. Pakistan: building a genomic strategy. Brazil: mapping labs nationally. Start small, invest in quality, build government ownership. #AMRSurveillanceAddis Day 1 of www.amrsurveillance.org

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Sentinel site session was the most grounding. Surveillance fails when it's extractive — data goes up, nothing comes back. Labs engage when it improves their own practice. www.amrsurveillance.org #AMRSurveillanceAddis

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 05/03/2026

Reporting from the AMR Surveillance Convening at Africa CDC, Addis Ababa. Opening message was direct: the surveillance gap isn't about knowledge anymore, it's delivery and financing. Africa carries ~21% of the global AMR burden. Recap of Day 1 from www.amrsurveillance.org #AMRSurveillanceAddis

amrsurveillance.org

AMR Convening on Building Sustainable AMR Genomic Surveillance

A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 02/03/2026

In support of the UN General Assembly commitment to reduce AMR-related deaths by 10% by 2030, the meeting is centred on learning from real-world experience, identifying common challenges across diverse settings, and agreeing on practical next steps for nationally owned AMR surveillance.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 02/03/2026

Organised by Africa CDC, @thecgps.bsky.social , the Fleming Initiative, and the International Vaccine Institute, the convening brings together ministry and public health laboratory leads, regional networks, researchers, and global partners.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 02/03/2026

109 participants from 52 countries are convening at Africa CDC Headquarters in Addis Ababa for a focused, experience-led meeting on strengthening routine national antimicrobial resistance (AMR) surveillance systems, including the integration of pathogen genomic data. More at www.amrsurveillance.org

amrsurveillance.org

AMR Convening on Building Sustainable AMR Genomic Surveillance

A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 02/03/2026

Organised by Africa CDC, the Centre for Genomic Pathogen Surveillance, the Fleming Initiative, and the International Vaccine Institute, the convening brings together ministry and public health laboratory leads, regional networks, researchers, and global partners.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

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.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

vaccines.watch 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.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

With analytics powered by Pathogenwatch (pathogen.watch), the platform uses the same “always-on” pipeline as the sister tool, amr.watch (amr.watch), with new genomes assembled, analysed and incorporated on an ongoing basis (every 4h) as public data are newly deposited.

pathogen.watch

Pathogenwatch

A global platform for genomic surveillance.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

The interactive interface enables users to assess vaccine target types (e.g. serotypes) within a broader population context by enabling assessment of their relationships with associated variant types (e.g. STs) and AMR markers, and within the context of existing pneumococcal vaccine formulations.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

We’ve initially focused on showing data for existing/prospective multivalent polysaccharide-based vaccines for Streptococcus pneumoniae, Klebsiella pneumoniae (and related species) and Acinetobacter baumannii.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

As global representativeness of data grows from increased genomic surveillance, we have designed vaccines.watch to support different stages of the vaccine pipeline, although caution in interpretation is currently important due to data representativeness (see below).

vaccines.watch

Vaccines.watch

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

Pleased to share our latest preprint describing vaccines.watch (vaccines.watch), an interactive platform enabling exploration of vaccine target diversity from global genome data: www.biorxiv.org/content/10.1...

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 12/06/2025

By combining survey data with additional public data, we also found substantial global spread of high-risk E. coli clones (e.g. ST167) with NDM-5 and other carbapenemases. We found many introductions of these clones into European hospitals in 2019, albeit with limited onward nosocomial transmission.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 12/06/2025

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.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 12/06/2025

Special thanks also to the project leads and collaborators @ecdc.europa.eu and Public Health Agency of Sweden, especially Anke Kohlenberg, Alma Brolund and Inga Froding, with whom it has been a pleasure to work with and learn from over the many years spanning the project.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 12/06/2025

The work comes together from the valiant efforts of all participating hospitals and national reference laboratories, forming the EURGen-Net CCRE Survey Working Group, who were able to continue with the data collection even despite onset of the COVID-19 pandemic shortly after the survey period.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 12/06/2025

The manuscripts, which follow up on the 2013-14 EuSCAPE survey, describe the occurrence and spread of carbapenem-resistant K. pneumoniae and E. coli using epidemiological, microbiological and WGS data obtained for isolates from >300 hospitals.

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 12/06/2025

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: papers.ssrn.com/sol3/papers.... K. pneumoniae: papers.ssrn.com/sol3/papers....

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025

amr.watch can be used to assess representation of geographic regions, e.g. with countries here in white currently lacking any public genomes. See more at amr.watch/all (6/6)

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025

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. (5/6)

amr.watch

AMR.watch

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025

Always on: all QC-d genomes with geotemporal metadata are ingested from archives, analysed in pathogen.watch and results visualised in amr.watch. Data are extracted and updated every 4h, with observed trends thus only delayed by time to genome deposition. More on filtering: amr.watch/summary (4/6)

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025

We show disparities between high- and low-income settings, indicate vast gaps in our knowledge globally and highlight the need for ongoing, structured surveillance combined with timely data deposition (including metadata) to support public health. (3/6)

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025

Supporting all WHO priority pathogens (2017), amr.watch summarises the geographic and temporal distribution of genotypic variants (e.g. STs) in the context of AMR to aid monitoring and prioritisation efforts. (2/6)

amr.watch

AMR.watch

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025

Our latest preprint is out describing amr.watch - a platform for monitoring AMR trends from global genomics data: www.biorxiv.org/content/10.1... (1/6)

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Reposted by Centre for Genomic Pathogen Surveillance

Pathogenwatch @pathogenwatch.bsky.social · 12/02/2025

We’ve just released a public Pathogenwatch collection of the MRSN Diversity Panel comprising 100 diverse K. pneumoniae clinical isolates: pathogen.watch/collection/8... #KlebClub

pathogen.watch

Pathogenwatch

A global platform for genomic surveillance.

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Reposted by Centre for Genomic Pathogen Surveillance

Pathogenwatch @pathogenwatch.bsky.social · 12/02/2025

Hi Bluesky! We’re looking forward to engaging with the community and our users on here. Follow this account for updates on the Pathogenwatch platform (pathogen.watch), as well as our sister tools @microreact.bsky.social and @amrwatch.bsky.social developed by @thecgps.bsky.social

pathogen.watch

Pathogenwatch

A global platform for genomic surveillance.

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