Pathogenwatch

UPDATES: SARS-CoV-2 - Pangolin has been updated to PangoLEARN 2021-11-04

Shown in the tree and map are 51 genomes carrying either acrB_R717Q or R717L

AMR UPDATE: We have added “Intermediate” resistance predictions for Typhi genomes with 1-2 mutations within QRDR, and “Resistant” prediction for the triple mutant gyrA_S83F-gyrA_D87N-parC_S80I.

UPDATE: Addition of 937 Salmonella Typhi genomes and 7 new collections (thanks @silargi). Screenshot shows tree of 4389 public genomes with MDR strains highlighted (pathogen.watch/collection/07…). Add your own genomes for automatic contextualisation and prediction of AMR determinants.

The AMR library is available at gitlab.com/cgps/pathogenwatc… (@leosanbu & @corinyeats). The reads were downloaded from the ENA and assembled using our pipeline: gitlab.com/cgps/ghru/pipelin… (@bioinformAnt & @benmadeit). Manuscript in preparation.

The new AMR panel has 88 genotypes with 36 genes & >50 variants extracted from ~4000 genomes with associated MIC values and verified using Town et al (2019), Kwong et al (2018) and Yahara et al (2019). Thanks to all our collaborators including @yhgrad @thisiskatytown @gfspiteri.

We're excited to announce Pathogenwatch now has 14,444 N. gonorrhoeae genome assemblies (pathogen.watch/genomes/all?g…) with location metadata and 25 new curated collections based on publications. All annotated with a new antimicrobial resistance library developed at the @TheCGPS.

View the current set of genomes at pathogen.watch/genomes/all?g….

We're excited to announce S. pneumoniae penicillin resistance prediction and PBP typing, along with major improvements to the current AMR library. Many thanks to Ben Metcalf and the CDC for the software and libraries and Stephanie Lo (@stephlo_lo) for validation.

Thanks for the mention, folks. Just to clarify, we provide clustering with a network visualisation for those cgMLST schemes. We provide neighbour-joining trees for select species (see attached), with more details of the method here: cgps.gitbook.io/pathogenwatc…

Trees and networks can now be exported as png or svg, and the timeline can be exported as png, for external use. Try out the tree and timeline with datasets at pathogen.watch/collections! 🔗 (4/4)

The tree component has also been upgraded! It brings a long list of features present in Microreact including 2-dimensional scaling, internal nodes (pictured), and re-rooting. It's also generally faster, prettier, and more consistent. 🦾 (3/4)

The timeline is available in both collection and clustering views. This example illustrates the map and network updating while filtering by time. (2/4)

Do not adjust your monitors. Pathogenwatch now has timelines! 🕰️📈 This is part of a series of upgrades designed to include functionality from @MyMicroreact, so it should feel familiar. More details below 🧵 (1/4)

Thanks! Follow the project directly with @Pathogenwatch 👍