So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

🚨 Tomorrow! 🧬NCBI Pathogen Detection is hosting a public seminar showcasing how their open data resource is being used by researchers and public health professionals.

📅 April 11 | 🕒 12:00 p.m.–1:00p.m. ET
datascience.nih.gov/news/april-2...

#PathogenSurveillance #DataSharing #RadicalTransparency

Suffice to say - if you are a local philanthropist and would like to see infectious disease surveillance continue here in San Diego County, please reach out.

Without continued support, we'll lose our eyes on infectious diseases in our county, just as they're likely to surge.

Email on website 👇.

A Critical FDA Program Has Helped Solve Thousands of Foodborne Outbreaks For over a decade, GenomeTrakr has helped scientists trace contaminants from Salmonella to E. coli in the food system.

@fda.gov's #GenomeTrakr is in the news! This program collects genomic data from foodborne pathogens to rapidly stop outbreaks and support long-term prevention strategies to ensure a safer U.S. food supply.

www.the-scientist.com/a-critical-f... #FoodSafety🧬🦠

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

Our new commentary out today in @asm.org AAC: "Pathogen genomics in healthcare: overcoming barriers to proactive surveillance"!

Here, my colleagues and I discuss the promises, barriers, and potential solutions for genomic surveillance in healthcare 🦠

#IDSky #PublicHealth

doi.org/10.1128/aac....

About the detection of bird flu virus in raw milk in CA:
CDC, others warn against drinking raw milk.
CDFA routinely tests raw milk in bulk tanks.
This batch discovered because Santa Clara County health staff buy and test raw milk from retail stores for another line of defense.
Public health, y’all.

Big congrats to the @who.int IPSN for coordinating a substantial collection of tools for enhancing the development of pathogen surveillance & organising a great Global Partners Forum. This complements the work of PHA4GE & of course many others. Lots of "homework" for us all & see you next year!!

📣 New Manuscript from #FDA and #APHL 📣

The human health and broad economic benefits of funding genomic surveillance for foodborne pathogens are clear, yet significant challenges remain to sustaining and advancing this critical public health work in the US.

journals.lww.com/jphmp/fullte...

PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization...

Seq data of varying quality can be used for different public health applications (analysis, training, more). @pha4ge standardized QC tags help users share, triage, and identify a wider array of data in public repos. For more info, see: shorturl.at/1yaCw hot off the presses!

First post on the sky app!

Our local paper, #Oaklandside, joined our Christmas bird count team this year 🐦🦆📈:
oaklandside.org/2023/12/21/h...