📢 New preprint from the PHA4GE Infrastructure Working Group on compute infrastructure for pathogen genomics.

Exploring practical approaches and best practices to support timely, secure public health genomic analysis.

Read here: verixiv.org/articles/3-6...

#PHA4GE #GenomicEpidemiology

A novel virulent core genome multilocus sequence type CT 11424 of Listeria monocytogenes isolate causing stillbirth in Bangladesh | BMC Microbiology

We published a stillbirth case by novel Listeria monocytogenes in Bangladesh. It seems a distinct genotype is living in the country in absence of genomic investigation.

#Listeria #Stillbirth #GenomicEpidemiology #Bangladesh

Participants will:

• Understand MLST, cgMLST, SNP-based, LIN and k-mer systems
• Apply these to classify bacterial isolates at species, lineage and outbreak level
• Design or adapt cgMLST schemes
• Evaluate pros and cons for public health surveillance

#GenomicEpidemiology #Bioinformatics

GitHub - lskatz/pdtk: NCBI Pathogen Detection Portal toolkit NCBI Pathogen Detection Portal toolkit. Contribute to lskatz/pdtk development by creating an account on GitHub.

I don’t think I’ve ever advertised this, but I built pdtk - a CLI toolkit for parsing NCBI Pathogens.
It downloads from the NCBI Pathogens FTP, builds a local database, and lets you query the results.

🛠️ Useful for outbreak surveillance
📍 github.com/lskatz/pdtk
#Bioinformatics #GenomicEpidemiology

📣Public health just got a major upgrade! Say hello to Mk1D, our powerful portable sequencer💪 Real-time genomics now at Dr Vasylyeva Lab in UCI! 💥🧬 @ucirvine.bsky.social @nanoporetech.com #globalhealth #genomicsurveillance #genomicepidemiology

Great news for those of us using #ONT for #bacterial genome reconstruction and epidemiological surveillance! According to these authors, we now have sufficient quality to achieve the reproducibility and accuracy required for effective bacterial surveillance. #genomicepidemiology

Can we track epidemics at the individual level without invading privacy? New article by @odorg.bsky.social & @martonkarsai.bsky.social finds signs of epidemic awareness behavior in SARS-CoV-2 genetic data.
Read more: go.nature.com/3SRuw05

#GenomicEpidemiology #BehavioralEpidemiology #HumanDynamics

Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans - Nature Communications This study reveals prior undetected transmission events of Corynebacterium ulcerans, suggesting pets play an intermediary role between wildlife and humans. Two main sublineages were identified, showin...

Thrilled to share our new @natcomms.nature.com paper “Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans” with @sylvainbrisse.bsky.social!

Read more ▶️ www.nature.com/articles/s41...

@pasteur.fr #GenomicEpidemiology #Zoonoses #OneHealth

6/7 Why are we excited? We believe our method helps bridge the gap between broad epidemic data & detailed local observations. It's a simple tool to monitor local awareness without privacy concerns, which could be invaluable for future pandemic responses. #GenomicEpidemiology #NetworkScience

6/7 Why are we excited? We believe our method helps bridge the gap between broad epidemic data & detailed local observations. It's a simple tool to monitor local awareness without privacy concerns, which could be invaluable for future pandemic responses. #GenomicEpidemiology #NetworkScience

Why are we excited? We believe our method helps bridge the gap between broad epidemic data & detailed local observations. It's a simple tool to monitor local awareness without privacy concerns, which could be invaluable for future pandemic responses. #GenomicEpidemiology #NetworkScience

My supervisor, Prof. Rachel Thomson, head of the NTM Research Group at UQ (medical-school.uq.edu.au/research/ntm...), has recently published excellent work on the role of drinking water in MABS transmission.
#NTM #GenomicEpidemiology #Abscessus #IDSky #IDEpi

Build software better, together GitHub is where people build software. More than 150 million people use GitHub to discover, fork, and contribute to over 420 million projects.

🖥️ TB-AMRpred is #opensource as a web server & command-line tool for predicting drug resistance in M. tuberculosis based on whole-genome sequencing.
Web: http://www.nii.ac.in/TB-AMRpred.html
GitHub: https://github.com/Ankitapal1995/TB-AMRprd

#GenomicEpidemiology #AntimicrobialResistance

Thrilled to see the results of our work out in the world!
Be sure to check out Natàlia's great overview of the main findings as well as the full paper. ⬇️

#WomensHealth #GenomicEpidemiology

Strange man standing in front of a bronze triceratops skull.

Hi, #episky!

I work with an incredible team, laser focused on expanding pathogen genomics and other innovative technologies across the public health system.

Ask me about #genomicepidemiology, #fellowships, #opendata, #datastandards, #surveillance and #outbreakresponse

On the web: www.cdc.gov/amd

The ARTIC gang at the #nanoporeconf #oxfordnanopore #sequencing #genomicepidemiology

https://www.amazon.com/dp/103253026X?psc=1&ref=ppx_yo2ov_dt_b_product_details

"The Applied Genomic Epidemiology Handbook" - a game-changer for public health pros! Kudos to Alli Black, @evogytis.bsky.social, with contributions from Taj Azarian, and Janeece Pourroy. A must-read for anyone in #PublicHealth or #GenomicEpidemiology. And even better - you can get it on Amazon.

Early and Sensitive Detection of Pathogens for Public Health and Biosafety: An Example of Surveillan... Infectious diseases severely threaten public health and global biosafety. In addition to transmission through the air, pathogenic microorganisms have also been detected in environmental liquid samples...

My morning reading cued up: “Early and Sensitive Detection of Pathogens for Public Health and Biosafety: An Example of Surveillance and Genotyping of SARS-CoV-2 in Sewage Water by Cas12a-Facilitated Portable Plasmonic Biosensor” #OneHealth #GenomicEpidemiology spj.science.org/doi/10.34133...