Today, I started my fellowship in Inst of Systems, Molecular & Integrative Biology at @LivUni. I am grateful to HPRU AMR at Imperial, managers (@Grampospath Dr Elita Jauneikaite A. Holmes), collaborators (@bugsinblood Yana Vieira Xavier Didelot Juliana Coelho etc), and HPRU’s admin team, for supports over the last 4 years.

Today we met with Professor Jahangir Alam, Director of dhaka shishu (children) hospital, the largest children’s hospital in Bangladesh, to discuss its collaboration with Child Health Research Foundation (CHRF) and how Centres for Antimicrobial Optimisation Network can help support its development. This work is genuinely life changing Wellcome #AMR 🇧🇩🤝🇬🇧

Our wonderful team in Bangladesh 🇧🇩 at the Child Health Research Foundation (CHRF), where our shadow national site is engaged in vital work on preventing infections and addressing AMR around Bangladesh.
Wellcome

Colonisation of hospital surfaces from low- and middle-income countries by extended spectrum β-lactamase- and carbapenemase-producing bacteria dlvr.it/T4rGKW

PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Read the full article in #MGen : doi.org/10.1099/mgen.0…

It’s time to demote vancomycin

blogs.jwatch.org/hiv-id-observa…

Bactopia now supports AllTheBacteria assemblies! 🎉

If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia.

To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies

bactopia.github.io/latest/blog/20…

Mandatory reading and surprising results from Michael Hall and colleagues - much better SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work
biorxiv.org/content/10.110…

Luckily came across this place by chance on a night walk along River Ouse in Oct 2022. The All Saints’ Church next to the pump is the place where John Snow was baptised.

Very excited to announce our transdisciplinary AMR workshop 🎉

Join us to hear perspectives and discussion from patient activists, journalists, philosophers, microbiologists, historians, clinicians, policy makers, and artists. More info: torch.ox.ac.uk/event/communic…

Interested in AMR modelling for policy? Consider joining the RESIST3 workshop organised by
Gwen Knight LSHTM AMR Centre April 22!

Now taking submissions for short talks (15 mins), attendee registration open soon. #AMR2024

lshtm.ac.uk/newsevents/eve…

So proud to share our commentary that's out in Cell today. We discuss the historical context for the systems that oppress trans people, how this has shaped research, and how individuals and institutions can support trans people in STEMM.
cell.com/cell/fulltext/…

Excited to share our Streptococcus dysgalactiae subsp. equisimilis (group C/G strep, SDSE) population genomics study highlighting its overlap with S. pyogenes (group A strep). Made possible by many partners Mark_Davies_Lab Steven Tong David McMillan Doherty Institute rdcu.be/dA6Ye

Ryan Wick, myself and the team (@JuddLmj Tim Stinear Rob Edwards & Sarah) have recently looked at the effect of depth on short-read polishing almost-perfect Nanopore bacterial genomes

biorxiv.org/content/10.110…

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Before you burn any more CPU assembling bacterial genomes from reads in the public archives, please consider using this fantastic resource of consistently assembled and QC’d bacterial genomes!

How could I miss this thread... This is wonderful 🤣🦠

New preprint in collaboration with Alfonso Santos-López lab and led by Jorge Sastre Domínguez. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8
biorxiv.org/content/10.110…

Two years ago we published a Nature Milestone project on Genomic sequencing in the 21st century - for anyone new to the topic, you can download a PDF of the Milestones here: go.nature.com/3PahHMD

The immersive Milestone timeline is here:
go.nature.com/3IKcvvD