Hi everyone 🖖
If you are thinkging about using #nanopore for genomic surveillance in #hospitals, but don't have the #bioinformatics nor command-line skills, don't let that put you off.
'Modernising Medical Microbiology', at @NDMOxford in #Oxford, has developed `OxBreaker': a graphical tool that can help identify budding #outbreaks by #healthcare professionals without having to upload your data to external servers and compromise patient privacy. Worth a read 👇
https://www.biorxiv.org/content/10.64898/2026.03.18.709804
OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing
Real-time genomic surveillance may mitigate the spread of health-care-associated infections, but whole-genome sequencing costs and the need for specialised expertise constrain its wide implementation in public health. Here we present ‘ OxBreaker ’, an automated and species-agnostic pipeline optimised for the high-resolution analysis of bacterial and plasmid genomes sequenced via Oxford Nanopore Technologies (ONT). ‘ OxBreaker ’ streamlines the transition from raw reads to phylogenetic inference through automated reference selection and high-accuracy variant calling. It is accessible via a graphical user interface (GUI) that can be easily installed locally and operated by non-specialists. Benchmarking against technical and biological replicates of high-priority pathogens demonstrates high accuracy, with false positive variant rates reduced to 0–4 single-nucleotide polymorphisms (SNPs) for common species. We further validated the pipeline by accurately characterising previously published clonal and plasmid-mediated outbreaks, reproducing established phylogenies with improved accessibility. By providing a stable, scalable, open-source offline-compatible solution that matches the resolution of short-read platforms while maintaining the speed of long-read technology, ‘ OxBreaker ’ is designed to facilitate the adoption of local, real-time genomic surveillance for frontline infection prevention and control.
### Competing Interest Statement
The authors have declared no competing interest.
NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, NIHR207397
NIHR Biomedical Research Centre, Oxford, GB
A Model For HHS: New Mexico Measles Outbreak Was Curtailed With Mass Vaccination Campaign
With RFK Jr. and his version of HHS entirely out to lunch on the ongoing measles issue in America, it’s been left to states and local medical professionals to try to figure out how to do comb…
#BrownUniversity’s
#Pandemic Center studies
#pandemics, and the
#US resurgence of
#measles is a grim sign of what’s coming
Low levels of
#vaccination across the country mean measles
#outbreaks will continue to occur, needlessly hospitalizing and killing the unvaccinated. But beyond these harms, the disease’s resurgence serves as a serious warning about the country’s capacity to manage
#infectiousdisease threats of all kinds.
https://arstechnica.com/science/2026/03/we-study-pandemics-and-the-resurgence-of-measles-is-a-grim-sign-of-whats-coming/ 
We study pandemics, and the resurgence of measles is a grim sign of what’s coming
The US eliminated measles in 2000, but the disease is once again circulating.
Europe sees decline in bird flu case detections, report finds
Between November 29 and February 27, authorities recorded 406 outbreaks of bird flu in domestic birds in 32 European countries and 2,108 outbreaks in wild birds, they said.
#Health #birdflu #Influenza https://globalnews.ca/news/11727714/europe-decline-bird-flu/Europe sees decline in bird flu case detections, report finds
Between November 29 and February 27, authorities recorded 406 outbreaks of bird flu in domestic birds in 32 European countries and 2,108 outbreaks in wild birds, they said.
#Health #birdflu #Influenza https://globalnews.ca/news/11727714/europe-decline-bird-flu/Europe sees decline in bird flu case detections, report finds
Between November 29 and February 27, authorities recorded 406 outbreaks of bird flu in domestic birds in 32 European countries and 2,108 outbreaks in wild birds, they said.
#Health #birdflu #Influenza https://globalnews.ca/news/11727714/europe-decline-bird-flu/Viral
#Outbreaks Take a Common Path from Animals to People, Study Finds How
#Pandemics Are Made
Scientists compared seven viral outbreaks that occurred in recent decades, including epidemics of Covid, Ebola and influenza. The outbreaks were not preceded by any unusual genetic changes in the viruses. In all but one case, in 1977, the viruses circulated in animals and gained the ability to spread to and among people only by unfortunate coincidence.
https://www.nytimes.com/2026/03/09/science/covid-coronavirus-evolution.htmlhttps://archive.ph/UjxJ0
Viral Outbreaks Take a Common Path from Animals to People, Study Finds
Researchers have devised a new tool for discerning between naturally occurring viral outbreaks and those resulting from lab accidents.
The funds are administered through the #CDC. They include grants given to #states for a variety of purposes, including hiring staffs, modernizing data systems & managing #disease #outbreaks. Some programs are aimed at the needs of specific communities.
Some of the cuts will be finalized this week & others over the coming weeks, totaling roughly $600 million.
#law #PublicHealth #Trump #Congress #TheCrueltyIsThePoint
The withdrawal will hurt the global response to new #outbreaks & will hobble the ability of #US #scientists & #pharmaceutical companies to develop #vaccines & #medicines against new threats, said Lawrence Gostin, a #PublicHealth #law expert at Georgetown University.
The #WHO is the #UnitedNations’ specialized #health agency & is mandated to coordinate the response to global health threats.
#Trump #idiocracy
#US #vaccination rates are plunging. Look up where your
#school stands.
Rocked by pandemic politics, the nation’s shield against infectious disease is shrinking.
Before the pandemic, roughly half of counties had
#kindergarten #vaccinationrates high enough to prevent
#measles #outbreaks.
After, many lost ground, leaving only about a quarter of the counties with
#herdimmunity in kindergartners.
https://www.washingtonpost.com/health/interactive/2025/measles-vaccine-schools-outbreaks-public-health/https://archive.ph/b9DqZ 
As U.S. vaccination rates fall, see how your school compares
Take a look to see what the kindergarten measles vaccination rates are in your area.
Carlos Reding
Techdirt
Benjamin Carr, Ph.D. 👨🏻💻🧬
Global News National
Global News Health
Global News
Nonilex