Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Life Identification Numbers: A bacterial strain nomenclature approach

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

doi.org

Our paper reporting a highly conserved mechanism by which arginine positively regulates hypervirulent K. pneumoniae mucoid phenotype is now fully online. rdcu.be/euiWG Summary picture is below, but details in the 🧵

Este 10 de abril, saludamos a quienes investigan, y en este marco, a pensarse como trabajadores. Tiene que haber un horizonte común entre quienes investigan y el resto de los trabajadores. Porque sin ciencias no hay futuro deseable. Y sin condiciones dignas, no hay ciencias.

Este 20 de febrero se cumple un nuevo aniversario del nacimiento del científico y pensador Rolando García. Doctor en Meteorología, vicepresidente fundador del CONICET, cofundador de la Universidad Nacional del Sur,y recordado decano de Exactas en la UBA entre 1957 y 1966.

Pasteur Course: Tuberculosis 🧫 Join a 2-week intensive course at the Institut Pasteur from June 2–13, 2025 to gain expertise in TB diagnosis, treatment & epidemiology. Including hands-on trainings & insights from leading experts. Limited to 20 participants - apply by March 1, 2025 👉bit.ly/3Cr0ift

🌊 Food Traceability Using Genomic Tools 🧬 Join us for an online course with @marianilab.bsky.social & @shump.bsky.social , in February, to learn how cutting-edge genomic technologies (@illumina, @nanoporetech.com & qPCR) are revolutionising seafood traceability and sustainability shorturl.at/Wsdyz

✨ Apoyan: @okfn.bsky.social, @nerdearla.bsky.social, @latambioimaging.bsky.social, UNC CCAD Supercómputo, Conectorial, LA-CoNGA Physics, ILDA, R-Ladies Buenos Aires, @abrir.bsky.social, PsiNet Lab, ARPHAI, DiploCientífica. ¡Gracias por acompañarnos! 🚀

🚨 GLLVMs: Advanced Multivariate Analysis of Ecological Communities in R with @vdveenb.bsky.social 🚨 📅 20-23 May Learn to master Generalized Linear Latent Variable Models (GLLVMs)-a cutting-edge, flexible alternative to classical ordination methods for ecological data analysis📊 shorturl.at/WfdXK

What do you think are the critical features pathogen genomic data-sharing platforms require to meet the public health need? Please participate in this public consultation!

silargi.bsky.social@silargi.bsky.social · 2y ago

Does your team deposit and access pathogen genomic data via data-sharing platforms for public health use? Participate in WHO's online consultation on the critical features of pathogen genomic data-sharing platforms to meet public health needs. All info here: www.who.int/news-room/ar...

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social

A phylogenetic approach to comparative genomics

Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

rdcu.be

Join us for a new season of #KlebCkub! @klebclub.bsky.social New speakers & new research! Registration is FREE but mandatory. Abstracts due by February 16! Please share ! Link below👇🏻👇🏻

Caity Holmes@caityholmes.bsky.social · 2y ago

It's that time of year! Registration and abstract submission for the 6th Klebsiella Seminar Series is now open. Participation is free and abstracts are due by February 16th. See the link below for details, and reach out to the organizers with any questions: forms.gle/gxbvaC6FjzuS... #KlebClub

#KLEBS2024 replay now available at www.klebs-2024.conferences-pasteur.org/replay - great opportunity to catch-up about #Klebsiella or to relive the conference - enjoy!

Replay - Klebsiella Epidemiology and Biology Symposium 2024

Klebsiella Epidemiology and Biology Symposium 2024

klebs-2024.conferences-pasteur.org

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... (1/5)

Home

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

github.com

Good day to recall some milestones in US polio history 1953 Worst recorded US outbreak kills more than 3000 1955 First polio vaccine licensed 1979 Polio considered eliminated from the United States 1994 Polio considered eliminated in North and South America ourworldindata.org/grapher/repo...

Really exciting development from the @pathoplexus.org team, with a new curated database for mpox genomic data. Glad to see these rapid data sharing efforts taking shape, guided by consistent, transparent governance and an ongoing commitment to equity and fairness.

Pathoplexus@pathoplexus.org · 2y ago

Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox). Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response. 1/7

Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox). Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response. 1/7

🚨 We’re thrilled to kick off the eDNA Metabarcoding course, funded by @ednacollab.bsky.social! 🌍 Researchers worldwide are joining us this week to learn how to analyse their eDNA data with guidance from an exceptional team of instructors. @leeselab.bsky.social @shump.bsky.social

I started an #eDNA starter pack as one didn’t exist yet. Feel free to message me to get your name added. Open to all! go.bsky.app/U2vgV5Q

Please join us at 13:00 CET December 12th for the next edition of the IPSN webinar series 'Pathogen Genomics in Health Emergencies' to hear how genomics can contribute to the understanding of Cholera outbreaks. Register here:

How best to avoid the costs of bearing a #plasmid? Rosanna Wright @brockhurstlab.bsky.social @jpjhall.bsky.social &co find that #bacteria benefit from compensating plasmids by chromosomal (rather than plasmid-borne) mutations @plosbiology.bsky.social plos.io/3ODbXdN

A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation

Plasmids spread important traits in microbiomes but impose fitness costs on their hosts. This study of the ecological consequences of plasmid-bacterial compensatory evolution reveals benefits to bacte...

plos.io

Back in Argentina after the #KlebsiellaSymposium at @pasteur.fr. Grateful to the organizers @sylvainbrisse.bsky.social and @chcrestani.bsky.social for the opportunity to present my work on #Klebsiella in #Wastewater and to connect with brilliant researchers. Inspired and honored!

often overlooked in EDI strategies and key to perceptions of excellence. Language coaching not the only solution (takes extra time too): need to normalise non-native accents/accept different ways of expressing oneself

Madhu Pai, MD, PhD@madhupai.bsky.social · 2y ago

Non-native English speakers need 50% more time to write a paper When they do, they face a 2.5 times higher chance of being rejected because of language journals.plos.org/plosbiology/...

From here #Klebsiella genomics really ramped up, and we now have >100,000 genomes in NCBI! There’s too much to cover here, but we summarised some of it in this 2020 review pubmed.ncbi.nlm.nih.gov/32055025/ & will hear a lot of new stuff at #KLEBS week. Look our for a conference report!

A small history lesson in #Klebsiella genomics in honour of #KLEBS24… 2009 was a big year for Klebs! - First genome published - First description of ST258 KPC-producing clone pubmed.ncbi.nlm.nih.gov/19218573/ - First description of NDM-1 beta-lactamase pubmed.ncbi.nlm.nih.gov/19770275/

Let's increase #klebclub chatter on 🔵🦋! Klebsiella aficionados add your handle below and we will build a starter pack. 🔁 to spread the word

Lots of people are missing, let us know if you want to be included by replying! You can also share to help us gain visibility #MicroSky go.bsky.app/EdereoU

Very much enjoying #Klebsiella2024 with great talks. Some absolutely shocking data around AMR and mortality in neonatal infections in LMICs, which do not have access to new (and very few) drugs that still work.

Interesting One Health study on Klebsiella pneumonie in Norway, which seems to confirm that there is little (but not no) spillover between human and non-human niches www.biorxiv.org/content/10.1... Presented by Marit Hetland #Klebsiella2024

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relev...

biorxiv.org