Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years

www.sciencedirect.com/science/arti...

Data from invasive neonatal infections showed a major difference in the proportion of transporter-dependent K-loci between Europe and LMICs, indicating different vaccine design requirements.

We created a database compatible with Kaptive3 of 90 distinct capsule (K) loci; 66% represented novel K-loci that did not correspond to the known phenotypic K-antigens. Give it a whirl, and get in touch to have novel K-loci added to the DB github.com/rgladstone/E...

Capsules K1, K5, and K2 were the most common transporter-dependent K-loci across infection types and geographical locations. In Europe, K1, K5 and K2, together with K100 and K52, accounted for 58% of multidrug-resistant infections.

Now published! 'Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli' www.nature.com/articles/s41... insights below.....

And special thanks to Handal and Kaspersen et al. (doi.org/10.1093/jac/...) for sharing their AST data to serve as a UTI validation set for this genomic dataset.

It's still largely infeasible for national genomic surveillance at the scale AST data is available (here 24,866 BSI and 28,639 UTI E. coli, 2006–2021), but combining existing 3254 BSI genomes and AST data allowed us to estimate the importance of this notorious MDR clone in Norwegian UTIs.

This was a really fun study in collaboration with Theodor A. Ross and colleagues @uitnorgesarktiske.bsky.social @sfi-vi.bsky.social, training a model to predict the ST131-C genotype from antimicrobial susceptibility testing data, providing insight into its UTI prevalence and context for BSI trends.

"Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for Escherichia coli sequence type 131 clade C surveillance across infection types" Spoiler: the MDR ST131-C is pervasive in UTIs, underlying BSI trends. doi.org/10.1099/mgen... @microbiologysociety.org

Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli Specific strains of Escherichia coli employ the polyketide synthase island to produce a metabolite called colibactin that is implicated in colorectal tumorigenesis via its genotoxic effect on human DN...

New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions.

www.biorxiv.org/content/10.1...

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics

We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...

If you like time travel & biology, this 🧵is for you👇

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

Being able to data plasmid acquisition, and to see the diversity of plasmids being gained and lost from lineages, was really eye opening! It was a pleasure to contribute my tiny bit to this huge paper and the data has so much more to give! @arredondo.bsky.social @gerrythill.bsky.social et al.

Fantastic! Can you add @themaklin.bsky.social too?

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

We are hiring remote bioinformaticians at @theiagen . If you have a passion for microbial bioinformatics or public health, send your CV to careers@theiagen.com . You can be based nearly anywhere but need to be available to work US business hours.

RTs much appreciated... would love to reach both AMR and biomath folks!
"Evolutionary accumulation modelling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance"
arxiv.org/abs/2411.00219
We think EvAM methods have some potential in AMR. 🧵

Interesting and useful post from Altmetric.

TDLR:

🎉 BlueSky is an awesome place to share research.

❌ Don’t use link shorteners (unless it’s the DOI one)

✅ Keep the link in the post (don’t remove it once you have the auto-preview)

#AcademicSky #PhDSky

Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli Biomedical research has implicated the bacterial metabolite colibactin as a causal risk factor for several cancer types, in particular, colorectal can…

New paper:

We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers.

www.sciencedirect.com/science/arti...

How invasive are different E .coli capsules and how many are there? Find out here and use the group 2 and 3 database to type your own!
medrxiv.org/cgi/content/...