📆 Join next week's webinar on Salmonella Typhia genomics & #AMR surveillance being given by @msmicrobiocode.bsky.social

London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.

PhD position (London, UK)
Generating microbiology data and paired mathematical modelling
with @msmicrobiocode.bsky.social @gmknght.bsky.social @sergemostowylab.bsky.social
at @lshtm.bsky.social
More details: http://iddjobs.org/jobs/2405

AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance Abstract. Antimicrobial resistance (AMR) poses a substantial threat to global public health. Whole genome sequencing is increasingly used as a core method

🚨 New paper out on @narjournal.bsky.social.
Many thanks to everyone involved, especially the project leader Professor @katholt.bsky.social and the wonderful #AMRnet team: @msmicrobiocode.bsky.social, Vandana Sharma, Mary Maranga, Ebenezer Foster-Nyarko, Megan Carey
academic.oup.com/nar/advance-...

Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage www.medrxiv.org/content/10.1101/2025.06....

🚨 Last chance to sign up for an online space at Thursday's symposium on target trial emulation (TTE) and other frameworks

Sign up 🔽

Wonderful presentation @nisbetalice.bsky.social !

Coming up next at #I3S #I3Scongress is @nisbetalice.bsky.social showing a summary of 20 years of #typhoidal #Salmonella in England & Wales. She is excited to present here as she prepares this for publication and as this is her first international talk. We are hanging around if you have any Qs.

Outbreak of Ceftriaxone-Resistant <em>Salmonella enterica</em> Serovar Typhi, Bangladesh, 2024 Ceftriaxone-Resistant <em>Salmonella</em> Typhi, Bangladesh

One ceftriaxone-resistant #typhoid case last year set us on a path that is now live on Emerging Infectious Diseases.
47 cases in months, resistance rose from 0 to 5%. We spoke with patients, sequenced samples. 4.3.1.2.B1 lineage+blaCTX-M-15 on pCROB1. #AMR #PublicHealth
wwwnc.cdc.gov/eid/article/...

🥇 Congratulations to @msmicrobiocode.bsky.social
who was one of the winners of the @lshtmamrcentre.bsky.social Publication Prize

She received the Staff Prize for her work analysing AMR typhoid infections in Bangladesh, Nepal, and Malawi

Find out why 🔽
www.lshtm.ac.uk/research/cen...

A huge thank you to all involved - especially members of the Global Typhoid Genomics Consortium, @katholt.bsky.social , @meganecarey.bsky.social , @louisecerdeira.bsky.social, and Vandana Sharma!

The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health - Genome Medicine Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; ...

🧬 Out today 🧬 - our TyphiNET
#AMR surveillance dashboard for #typhoid

Use TyphiNET to view genome-derived data on global and national annual trends in AMR and circulating pathogen genotypes via any standard web browser.

genomemedicine.biomedcentral.com/articles/10....

📣 🎉 Congratulations to Ms Gladys and @msmicrobiocode.bsky.social on winning our 2025 Publication Prize at @lshtm.bsky.social 🏆

Read more about their winning papers and impactful AMR research🔬 👇
bit.ly/4iM7uCh

@msmicrobiocode.bsky.social won the Staff Prize for her work revealing that most AMR typhoid infections in Bangladesh, Nepal, and Malawi are driven by ongoing local transmission of existing resistant strains—not new variants.

Good luck ☺️

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
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