EC-K-Typing v4.0.0 is out! 🧬 The E. coli group 2/3 capsule database now includes 109 K-loci (up from 90), updated phenotype assignments, curated annotations, provenance docs, and a reproducible private-DB builder. github.com/rgladstone/E...

Release EC-K-Typing database v4.0.0 · rgladstone/EC-K-typing

EC-K-Typing database v4.0.0 This release expands the group 2 and group 3 reference database from 90 to 109 K-locus records. Database changes Added 16 sequence-defined loci assigned EC-K-Typing ide...

github.com

#ISPPD14 is "local" this time 🤩 In the spirit of Copenhagen I have set off by bike fully loaded and I am now relaxing on the ferry from Oslo🚴🏼‍♀️⛴️🚴🏼‍♀️ #ISPPD2026 Really looking forward to the conference and seeing old friends 😁 #pneumo

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...

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…

sciencedirect.com

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

"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

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...

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...

biorxiv.org

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👇

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...

doi.org

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...

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...

biorxiv.org

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.

Wellcome Sanger Institute@sangerinstitute.bsky.social · last yr.

Read ‘Plasmid-driven strategies for clone success in Escherichia coli.’ From @sangerinstitute.bsky.social @uitnorgesarktiske.bsky.social, the University of Oslo, and others, in @naturecomms.bsky.social, here ⤵️ www.nature.com/articles/s41...

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

Altmetric@altmetric.com · 2y ago

BLUESKY MEGA-THREAD Altmetric is thrilled and also LITERALLY RELIEVED to officially announce: We are now tracking research attention as it happens on Bluesky! We have been picking up posts on the site since late Oct. Our team is on Bluesky all day answering questions. Let's get into it!

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...

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…

sciencedirect.com

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/...