Pretzel
@krispyhajkowicz.bsky.social
Infectious Diseases Physician, Clinical Metagenomics and Virology PhD Student, Arsenal FC, Trail Running.
Reposted by Pretzel
So nohuman now ships an unmasked HPRC.r2 DB by default, with optional dataset selection.
If you’ve used nohuman before, I highly recommend updating to v0.5.0 and re-downloading the new DB.
Repo: github.com/mbhall88/nohuman
Keep your metagenomes clean 🧹🧬
If you’ve used nohuman before, I highly recommend updating to v0.5.0 and re-downloading the new DB.
Repo: github.com/mbhall88/nohuman
Keep your metagenomes clean 🧹🧬
GitHub - mbhall88/nohuman: Remove human reads from a sequencing run
Remove human reads from a sequencing run. Contribute to mbhall88/nohuman development by creating an account on GitHub.
github.com
November 20, 2025 at 6:50 AM
So nohuman now ships an unmasked HPRC.r2 DB by default, with optional dataset selection.
If you’ve used nohuman before, I highly recommend updating to v0.5.0 and re-downloading the new DB.
Repo: github.com/mbhall88/nohuman
Keep your metagenomes clean 🧹🧬
If you’ve used nohuman before, I highly recommend updating to v0.5.0 and re-downloading the new DB.
Repo: github.com/mbhall88/nohuman
Keep your metagenomes clean 🧹🧬
Reposted by Pretzel
Day 4 of the metagenomic virus discovery workshop is all about phylogenetics and virus evolution! Thanks to Eduan Wilkinson, Jackie Mahar and @spyroslytras.bsky.social
@ceri-news.bsky.social
@ceri-news.bsky.social
November 20, 2025 at 12:37 PM
Day 4 of the metagenomic virus discovery workshop is all about phylogenetics and virus evolution! Thanks to Eduan Wilkinson, Jackie Mahar and @spyroslytras.bsky.social
@ceri-news.bsky.social
@ceri-news.bsky.social
Go @eakarlsson.bsky.social knocking it out of the park at the @virus-metagenomics.bsky.social workshop at CERI in Stellenbosch.
November 19, 2025 at 3:06 PM
Go @eakarlsson.bsky.social knocking it out of the park at the @virus-metagenomics.bsky.social workshop at CERI in Stellenbosch.
Reposted by Pretzel
Tomorrow evening we have our keynote lecture session from 16:00 in the Neelsie Cinema, Stellenbosch University. Dr Maja Vukovikj will be speaking about Africas ancient disease landscape and Dr Erik Karlsson will talk about metagenomics and high-risk interfaces tinyurl.com/ytj3sppm
November 18, 2025 at 11:36 AM
Tomorrow evening we have our keynote lecture session from 16:00 in the Neelsie Cinema, Stellenbosch University. Dr Maja Vukovikj will be speaking about Africas ancient disease landscape and Dr Erik Karlsson will talk about metagenomics and high-risk interfaces tinyurl.com/ytj3sppm
Reposted by Pretzel
Viruses and bacteria jumping from animals to people became a real problem when humans started keeping livestock, according to a massive genomic analysis of ancient pathogens 🧪
Animal diseases leapt to humans when we started keeping livestock
When hunter-gatherers began living close to animals, the pathogens that cause the plague and leprosy got closer too.
www.nature.com
July 10, 2025 at 4:46 AM
Viruses and bacteria jumping from animals to people became a real problem when humans started keeping livestock, according to a massive genomic analysis of ancient pathogens 🧪
Reposted by Pretzel
First isolation of a mammalian chuvirus, bizarrely from Tasmanian Devil facial tumour cells. Work led by @julienmelade.bsky.social and @erinharvey.bsky.social. www.sciencedirect.com/science/arti...
Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii)
Jingchuvirales are single-stranded negative-sense RNA viruses classified into five families, including the Chuviridae.1 Jingchuviruses were first foun…
www.sciencedirect.com
June 26, 2025 at 10:28 PM
First isolation of a mammalian chuvirus, bizarrely from Tasmanian Devil facial tumour cells. Work led by @julienmelade.bsky.social and @erinharvey.bsky.social. www.sciencedirect.com/science/arti...
academic.oup.com/cid/article-...
This is a disappointing but predictable outcome of doxyPEP to prevent STIs. Drives AMR not only in Gonococcus, but in Staph aureus and Group A Strep.
This is a disappointing but predictable outcome of doxyPEP to prevent STIs. Drives AMR not only in Gonococcus, but in Staph aureus and Group A Strep.
May 29, 2025 at 12:25 AM
academic.oup.com/cid/article-...
This is a disappointing but predictable outcome of doxyPEP to prevent STIs. Drives AMR not only in Gonococcus, but in Staph aureus and Group A Strep.
This is a disappointing but predictable outcome of doxyPEP to prevent STIs. Drives AMR not only in Gonococcus, but in Staph aureus and Group A Strep.
Reposted by Pretzel
Great session this morning at #ESCMIDGlobal 2025 discussing the use of whole genome sequencing in outbreak resposne.
We have amazing scientific tools and should use them to better define and characterize outbreaks
We have amazing scientific tools and should use them to better define and characterize outbreaks
April 13, 2025 at 3:22 PM
Great session this morning at #ESCMIDGlobal 2025 discussing the use of whole genome sequencing in outbreak resposne.
We have amazing scientific tools and should use them to better define and characterize outbreaks
We have amazing scientific tools and should use them to better define and characterize outbreaks
Happy days at @escmid.bsky.social Global 2025 Vienna, presenting our posters on HDV and RSV epidemiology and viral metagenomics for community flu-like illness. Nice to meet the @esgrev-escmid.bsky.social committee too!
April 13, 2025 at 9:47 AM
Happy days at @escmid.bsky.social Global 2025 Vienna, presenting our posters on HDV and RSV epidemiology and viral metagenomics for community flu-like illness. Nice to meet the @esgrev-escmid.bsky.social committee too!
Reposted by Pretzel
Another zoonotic (alpha) coronavirus. Closely related to the rodent virus AcCoV-JC34 that contains a putative furin cleavage site. www.tandfonline.com/doi/full/10....
Novel human coronavirus in an infant patient with pneumonia, Republic of Korea
Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequ...
www.tandfonline.com
April 2, 2025 at 11:48 PM
Another zoonotic (alpha) coronavirus. Closely related to the rodent virus AcCoV-JC34 that contains a putative furin cleavage site. www.tandfonline.com/doi/full/10....
@tstinear.bsky.social discusses the expansion of the very successful Austrakka to “Pathogen Trakka” which will enable secure, consistent sharing of microbial genomics data within LMICs and enhance access to bioinformatics/ visualisation tools. Looks like a winner! At Institut Pasteur New Caledonia.
March 18, 2025 at 11:21 PM
@tstinear.bsky.social discusses the expansion of the very successful Austrakka to “Pathogen Trakka” which will enable secure, consistent sharing of microbial genomics data within LMICs and enhance access to bioinformatics/ visualisation tools. Looks like a winner! At Institut Pasteur New Caledonia.
Scientists, clinicians and public health from across the Pacific are discussing pathogen genomic surveillance at the Institut Pasteur de Novelle Caledonie at the stunning Pacific Community Building in Noumea. Here, @eakarlsson.bsky.social leads a discussion of wet lab technical requirements.
March 18, 2025 at 1:33 AM
Scientists, clinicians and public health from across the Pacific are discussing pathogen genomic surveillance at the Institut Pasteur de Novelle Caledonie at the stunning Pacific Community Building in Noumea. Here, @eakarlsson.bsky.social leads a discussion of wet lab technical requirements.
Reposted by Pretzel
New preprint on canine viromes in Australia led by @jonathonmifsud.bsky.social. Includes the first RNA virus reported in dingoes - an unusual rotavirus A. Domestic dogs worldwide seem to carry a pretty similar set of viruses. www.biorxiv.org/content/10.1...
Diverse Viral Pathogens in Australian Canines: Limited Geographic Structure and the First Detection of an RNA Virus in Dingoes
Viruses impose a substantial disease burden on dogs and the close relationship between dogs and humans may facilitate zoonotic disease emergence. Australia's geographic isolation, strict biosecurity m...
www.biorxiv.org
February 19, 2025 at 6:41 AM
New preprint on canine viromes in Australia led by @jonathonmifsud.bsky.social. Includes the first RNA virus reported in dingoes - an unusual rotavirus A. Domestic dogs worldwide seem to carry a pretty similar set of viruses. www.biorxiv.org/content/10.1...
Reposted by Pretzel
💪
HIV/AIDS and COVID-19: Shared Lessons from Two Pandemics
Anthony Fauci and Greg Folkers
@cidjournal.bsky.social #IDSky
academic.oup.com/cid/advance-...
Anthony Fauci and Greg Folkers
@cidjournal.bsky.social #IDSky
academic.oup.com/cid/advance-...
HIV/AIDS and COVID-19: Shared Lessons from Two Pandemics
The HIV/AIDS and COVID-19 pandemics hold important lessons for preparing for, and responding to, future infectious disease outbreaks. Eight lessons common
academic.oup.com
November 29, 2024 at 4:20 AM
💪
Reposted by Pretzel
I will not hide my inner convictions anymore. Be the change you want to see in the world !
#AcademicSky 🧪
#AcademicSky 🧪
November 20, 2024 at 11:04 AM
I will not hide my inner convictions anymore. Be the change you want to see in the world !
#AcademicSky 🧪
#AcademicSky 🧪
Reposted by Pretzel
It is time for "...routine use of diagnostic mNGS testing for hospitalized patients with suspected CNS infection."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections - Nature Medicine
Next-generation metagenomic testing increases the accuracy and sensitivity of the etiology of central nervous system infections in hospitalized patients.
www.nature.com
November 17, 2024 at 7:48 PM
It is time for "...routine use of diagnostic mNGS testing for hospitalized patients with suspected CNS infection."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
journals.asm.org/doi/10.1128/.... This is another “fail” for poorly selected CSF samples for clinical metagenomics - with low yields, even fewer changes in patient management/antibiotics. Metagenomics on plasma samples however performed very well - looks like a good target for BSIs and beyond.
A retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers | Journal of Clinical Microbiology
Metagenomic next-generation sequencing (mNGS) stewardship practices remain poorly
standardized. This study aims to provide actionable insights for institutions that
seek to reduce the unnecessary usag...
journals.asm.org
October 15, 2024 at 12:44 AM
journals.asm.org/doi/10.1128/.... This is another “fail” for poorly selected CSF samples for clinical metagenomics - with low yields, even fewer changes in patient management/antibiotics. Metagenomics on plasma samples however performed very well - looks like a good target for BSIs and beyond.
Florian Krammer unpacks the entire history of human influenza viruses at OPTIONS XII in Brisbane.
September 28, 2024 at 11:41 PM
Florian Krammer unpacks the entire history of human influenza viruses at OPTIONS XII in Brisbane.
Reposted by Pretzel
We and others have been subject to relentless harassment. Here Nickels presents "supporting evidence" for our origins cover-up and we're not even discussing origins...we're discussing the lack of available SARS2 sequence data for surveillance.
March 16, 2024 at 4:50 AM
We and others have been subject to relentless harassment. Here Nickels presents "supporting evidence" for our origins cover-up and we're not even discussing origins...we're discussing the lack of available SARS2 sequence data for surveillance.
A routine clinical metagenomics service using nanopore sequencing @ St Thomas' Hospital ICU🇬🇧 performed extremely well - 93% sens and 94% spec cf. routine microbiol testing. Median turnaround time = 6.7h. This is the beginning of the end of conventional microbiology. pubmed.ncbi.nlm.nih.gov/37938162/
January 29, 2024 at 6:01 AM
A routine clinical metagenomics service using nanopore sequencing @ St Thomas' Hospital ICU🇬🇧 performed extremely well - 93% sens and 94% spec cf. routine microbiol testing. Median turnaround time = 6.7h. This is the beginning of the end of conventional microbiology. pubmed.ncbi.nlm.nih.gov/37938162/
