The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance A sudden increase in the number of Mpox virus (MPXV) cases worldwide prompted the WHO to declare a Public Health Emergency of International Concern in 2022 and again in 2024. Public health genomic sur...

Harmonizing and integrating metadata across labs and systems can be difficult. In our new publication we describe an open source One Health data standard to support collaborative genomic surveillance of MPXV (Mpox virus).
www.microbiologyresearch.org/content/jour...
@microbiologysociety.org

Lockout @dalhousieu.bsky.social covered in the Globe and Mail. Seems like the whole country is watching the results of the Board's reckless decisions. #KeepDalStrong

12th Microbial Bioinformatics Hackathon Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).

immem hackthon registration closes 31st May. www.escmid.org/congress-events/immem-xi...

Invited & Abstract Programme Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).

There is still time to submit an abstract for #IMMEMXIV so don’t miss this chance and join us in Porto! Link for submission: www.escmid.org/congress-eve...

Graph depicts suration checkpoints, indicated by stoplight symbols, along the data generation and sharing continuum.

The latest Editor's Choice in Canadian Journal of Microbiology 🔬🦠 is by Griffiths et al
📖 Crossing the streams: improving data quality and integration across the One Health genomics continuum with data standards and implementation strategies
🔗 buff.ly/PVbgooj
@griffiemma.bsky.social
#OneHealth #AMR

San Diego to take a $40 million hit in federal funding for public health Ninety-one grant-funded positions could be affected by cancellation of grants.

Just as our new Public Health Lab - which was built on key lessons learned during COVID - was set to open, the necessary funding for its operation was just pulled by DOGE/HHS.

That operation, critical to safety and public health in San Diego.

Gone.

www.sandiegouniontribune.com/2025/04/04/s...

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🧬🦠

Screenshot of the virological post on the Ebolavirus sequence

Screenshot of the sequence on pathoplexus

Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC, & SANBI, UWC the sequence from the Ebola Sudan case in Kampala is now available on Pathoplexus pathoplexus.org/seq/PP_0011C... w full analysis here: virological.org/t/near-real-...

Excellent, rapid work by Uganda’s CPHL and partners and also a great use case for @pathoplexus.org

Annual Conference 2025 31 March - 03 April 2025

It’s Race Equality Week and we want to shine a light on a very important drop-in session the Black Microbiologists Association will be hosting during #Microbio25 on 31 March. Find out more via our programme and join them on the day: https://microb.io/Microbio25 #REW25 #BlackInMicro

Shoutout to all of the exceptional Black scientists who have contributed to and are currently contributing to virology research! Your work is vitally important to understanding basic virology controlling viral diseases worldwide! #BlackHistoryMonth

Update: the web page on ASM IDEAA leadership is now active (asm.org/PIAA-Committ...). However, other IDEAA content still is missing. Please keep applying pressure!! #MicroSky

@charlesgaba.com is a hero and downloaded CDC’s entire website. A small group of us has come together to preserve this critical resource and make it accessible to the scientific community.

More to come. These data are public and they are ours. Deletion disobedience is one way to fight back.

Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...

First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.

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

@cidgoh and @pha4ge are developing ISO-based, modular, interoperable contextual data standards supporting global Mpox genomic surveillance and sharing. To learn more, find them here: One Health Mpox: github.com/cidgoh/MPox_..., Wastewater: github.com/pha4ge/Waste....

Integrating different types of data across sectors can be challenging. The Canadian One Health AMR genomics contextual data standard, built in partnership with the Can gov't, is readily adapted for international use and supports public data sharing. #GRDI osf.io/preprints/os...

Pathoplexus | Two Weeks of Pathoplexus Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

Happy to celebrate two weeks of @pathoplexus.org ! 🎉
Read a quick overview of what's happened since launch (and upcoming talks!) in the News section of our website:

pathoplexus.org/news/2024-09-13-two-weeks

#OpenScience #Pathoplexus

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!