Proud to see Theiagen’s @curtiskapsak.bsky.social coauthor a new paper on StxTyper, an open-source approach to typing Shiga toxin operons from genomic sequence. https://www.mdpi.com/2076-2607/14/8/1607 #PathogenGenomics #Bioinformatics #PublicHealth
Curtis Kapsak
@curtiskapsak.bsky.social
Bioinformatics Scientist @theiagen.bsky.social Likely swimming in a sea of pathogen genomes 🏊🧬 or riding my bike 🚴 Public Health | Infectious Diseases | Bioinformatics | Software Dev
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
Early versions were known as the Kapsak Spectac. Congratulations team!!
Jess Chen@drjesschen.bsky.social · 4mo agoHurray!! 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 · 4mo agoJust 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 agoExcited 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
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
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.
ONT read QC strategies for assembly
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
“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
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 · 10mo 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
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.
