Senior Data Scientist @sangerinstitute | Antimicrobial resistance evolution | Researcher and coffee drinker
Cambridge, UK
Joined June 2013
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Most AMR data is still collapsed to “resistant vs susceptible.”
But resistance often shows gradual shifts before cut-offs.
AMR Cartography maps full profiles in 2D — revealing co-resistance, sub-breakpoint changes & lineage patterns.
🔗 biorxiv.org/content/10.1101/…
🚨 New paper in eLife!
We analysed >100k malaria parasite samples to track the rise of artemisinin resistance.
Resistance is now emerging in Africa, echoing SE Asia 10–15 yrs ago.
Genomic surveillance is key to staying one step ahead!
elifesciences.org/articles/1…
The framework works across species & drug classes — and the code is open-source. Would love feedback from anyone working in AMR surveillance!
Preprint: biorxiv.org/content/10.1101/…
Applied to 3,600+ pneumococcal isolates, AMR Cartography revealed lineage-specific resistance and the genetic changes driving multidrug resistance.
Instead of treating correlations between drugs as noise, we use them as insight.
That lets us see:
• subtle shifts before breakpoints
• co-resistance patterns
• collateral sensitivity trade-offs
• genetic markers of resistance
In our new preprint we introduce AMR Cartography: a way to map full resistance profiles into simple 2D maps.
By ignoring that structure, we lose the early warning signs of resistance emerging — and miss how resistance evolves in real populations.
New Preprint! 🚨:
Most AMR data gets collapsed into “resistant” vs “susceptible.”
But resistance isn’t a simple switch — it changes gradually, and often in correlated ways across drugs.
Andrew Balmer retweeted
[New pre-print🚨] When a single genotype (pbp) confer resistance to multiple antibiotics (penicillin and cephalosporins), how do we make sense of genetic changes and their impact on AMR?
A new concept - AMR cartography is invented by @Quackscience
biorxiv.org/content/10.1101/…
We’ve just posted AMR Cartography on bioRxiv: a way to study multivariate drug resistance and connect it to genotypes. Would love feedback from people working with surveillance MIC data! @AntibioticResis @crypticproject
biorxiv.org/content/10.1101/…
Just posted our new preprint:
Antimicrobial Resistance Cartography – A generalisable framework for studying multivariate drug resistance @CamInfectDis @CambridgeDDU
biorxiv.org/content/10.1101/…
AMR Cartography lets us visualise how different pneumococcal lineages have distinct multivariate resistance phenotypes. @pneumowatch
New preprint: Antimicrobial Resistance Cartography — a simple way to map multivariate drug-resistance phenotypes, using data from @CDCgov.
biorxiv.org/content/10.1101/…
Andrew Balmer retweeted
Antimicrobial Resistance Cartography: A Generalisable Framework for Studying Multivariate Drug Resistance biorxiv.org/content/10.1101/… #biorxiv_genomic
Andrew Balmer retweeted
Announcing the latest version of MalariaGEN’s world-leading malaria parasite data resource: Pf8! 📢
In this release, you’ll find:
🦠 33,325 parasite whole genomes
🌍 Samples from 122 different locations
🗓️ 56 years of data
Read more:
malariagen.net/article/pf8-r…
Andrew Balmer retweeted
Our next Journal Club will be all about the new Pf8 data release!
Join Dr Nina White, Senior Data Scientist at the Genomic Surveillance Unit (@sangerinstitute) to learn to make the most of this unique malaria parasite data resource.
📅July 22, 1:30pm
sanger.zoom.us/webinar/regis…
ALT Malaria Genomic Epidemiology Journal Club, 22 July, 1:30pm, on Zoom. It will feature Dr Nina White, a Senior Data Scientist at the Genomic Surveillance Unit at the Wellcome Sanger Institute. The talk description is: Nina will showcase the Pf8 data resource, the latest MalariaGEN release of curated genome variation data on over 33,000 Plasmodium falciparum samples from 99 partner studies and 122 locations over more than 50 years. She will walk through the suite of tools which accompany Pf8, guiding users on how to get the most out of this resource.