journals.plos.org/digitalhealt... Congratulations to @rahilryder.bsky.social @jelder099.bsky.social and Team!! Great work!!!

The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California

Author summary In California, the COVID‑19 pandemic generated an unprecedented volume of anonymized viral genomic data, creating a critical need to link sequencing results with patient information for...

journals.plos.org

FDA Recalls 40,000 Gallons Of RFK Jr. Milk

FDA Recalls 40,000 Gallons Of RFK Jr. Milk

WASHINGTON—In what experts are already calling one of the worst outbreaks of foodborne illness in decades, the U.S. Food and Drug Administration issued an urgent recall Tuesday for 40,000 gallons of R...

theonion.com

Early versions were known as the Kapsak Spectac. Congratulations team!!

Jess Chen@drjesschen.bsky.social · 3mo ago

Hurray!! Big congrats to Arzoo and Mo from my team for developing this pipeline and getting it out there! Thanks to Justin, Peyton, @curtiskapsak.bsky.social and @lskatz.github.io their support of this work!

Hurray!! Big congrats to Arzoo and Mo from my team for developing this pipeline and getting it out there! Thanks to Justin, Peyton, @curtiskapsak.bsky.social and @lskatz.github.io their support of this work!

Journal of Open Source Software@joss-openjournals.bsky.social · 3mo ago

Just published in JOSS: 'stylo: a lightweight nanopore assembly pipeline optimized for enteric bacteria' https://doi.org/10.21105/joss.09695

Proud to have played a small role in this work regarding the linking of SARS-CoV-2 WGS data with epidemiological data for >800k samples! California's COVIDNet program & IGED has enabled impactful studies and actionable public health insights. Can't wait to expand to other pathogens!

Rahil Ryder@rahilryder.bsky.social · 4mo ago

Excited to share a preprint on how CA linked almost 1 million SARS-CoV-2 sequencing data to the patient data. This was a huge effort by multiple groups and we hope this can be used as a model for other emerging pathogens to enhance genomic epidemiology. www.medrxiv.org/content/10.6...

The CDC warns that extensively drug-resistant (XDR) Shigella is on the rise in US. The prevalence of XDR Shigella isolates in US surveillance data rose from 0% during 2011-2015 to 8.5% in 2023. Read more: ow.ly/VXee50YLphl 📷: CDC, Stephanie Rossow

www.cdc.gov/mmwr/volumes...

Emergence of Extensively Drug-Resistant Shigellosis

This report describes the emergence of drug-resistant shigellosis in the United States during 2011-2023.

cdc.gov

One way we use pathogen genomics for public health here in Utah. www.deseret.com/lifestyle/20...

Why Utah uses sewage to find measles, COVID, flu outbreaks

Cutting-edge system was built during COVID but can pivot to other diseases

deseret.com

A Decade of Docker Containers dl.acm.org/doi/10.1145/...

Sorry, kid, the government cancelled research into a cure for your disease. The man who swims in sewage and snorts cocaine in public restrooms said it's bad for you. Besides, there's no money now that we're locking up your friend's parents and the guys who mowed our lawn.

New blog post: ONT read QC strategies for assembly rrwick.github.io/2026/02/05/r... Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.

“We are grieving the realization that dedication alone cannot protect an agency from leaders determined to destroy it…. Still, CDC scientists will keep showing up. We will keep doing good science for as long as we are allowed to.”

Opinion | The CDC Shooting Isn't What Broke Me

Continuing to show up to work at an agency I no longer trust is devastating

medpagetoday.com

cov-spectrum.org/news/2025-12...

covSPECTRUM

covSPECTRUM is an interactive platform aiming to help scientists investigate and identify variants of SARS-CoV-2.

cov-spectrum.org

Hi.

Bari Weiss: Last Week Tonight with John Oliver (HBO)

YouTube video by LastWeekTonight

youtube.com

Congrats @efosternyarko.bsky.social and team for this great work building capacity for public health genomics to investigate cholera and other enteric bacteria, across Africa 👏 www.lshtm.ac.uk/research/cen...

Concerning levels of antibiotic resistance detected in cholera-causing bacteria

Concerning levels of antibiotic resistance detected in cholera-causing bacteria across Africa | LSHTM

lshtm.ac.uk

Microbiology Society@microbiologysociety.org · 9mo ago

📢Persistent antibiotic resistance of cholera-causing bacteria in Africa revealed from a multinational workshop for strengthening disease surveillance, hosted by PulseNet Africa and @lshtmamrcentre.bsky.social. Read more here: microb.io/4aDdPze%F0%9... #MGEN #AntimicrobialResistance #Microbiology

1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN). 👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name... #EVD68 #Enterovirus #OpenData

Please join us for the @who.int EPI-WIN webinar introducing WHO’s report on Attributes and Principles of Pathogen Genomic Data-Sharing Platforms. 24 November 2025, 1-2pm CET. 🔗 Register: who.zoom.us/webinar/regi... 👉 Webinar info: www.who.int/news-room/ev... 📄 Report: iris.who.int/bitstreams/f...

Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...

Ecology and spread of the North American H5N1 epizootic - Nature

The panzootic of highly pathogenic H5N1 since 2021 was driven by around nine introductions into the Atlantic and Pacific flyways, followed by rapid dissemination through wild migratory birds, primaril...

nature.com

apple.news/AfbRCeaNOR_q...

First locally acquired U.S. cases of more severe mpox strain reported — CBS News

California health officials have reported two cases of a potentially more severe form of mpox that appear to be locally acquired.

apple.news

RFK Jr. Promotes Natural Immunity With Invitation To Touch His Festering Sore https://theonion.com/rfk-jr-promotes-natural-immunity-with-invitation-to-touch-his-festering-sore/

Rocky start for new #CDC director Susan Monarez, whose first week was punctuated by Friday's attack. Her first all-hands meeting lasted ~13 minutes, with technical challenges with dead air for a time & some staff unable to join the call. "This is a mess," one said. www.statnews.com/2025/08/12/c...

CDC leaders attempt to reassure staff after shooting, but meeting is brief

An all-hands meeting at the CDC to discuss the attack on the agency on Friday was brief and chaotic, staffers say.

statnews.com

@kevinlibuit.bsky.social & @curtiskapsak.bsky.social were two of the co-authors on a new paper on Freyja 2 — a bioinformatics tool for real-time, multi-pathogen wastewater surveillance. Read about it here: www.medrxiv.org/content/10.1...

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2

Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...

medrxiv.org

A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵  doi.org/10.1101/2025...

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2

Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...

doi.org

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...

Schrier to RFK Jr: You gave Cassidy the answer he needed to hear in order to get his confirmation vote, then as soon as you were secretary you turned around & fired all 17 members. You lied. I also want to be clear that I will lay all responsibility for every vaccine-preventable death at your feet.

RUIZ: Did you read the report & fact-check its sources prior to publication? RFK JR: I did not fact check RUIZ: It included citations to sources that don't exist. How does that happen? RFK JR: All of the foundational assertions are accurate RUIZ: They did not exist. How can they be accurate?

Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance wwwnc.cdc.gov/eid/article/... 🧬🖥️🧪

You might be wondering why we haven't updated outbreak.info for months. Well, the reason is that GISAID cut our access in January - as they did others. Without telling us. After a ♾️ back and forth, that is now permanent. More on that soon - and why GISAID should not be trusted with critical data.