No wonder institutions, and whole countries, are refusing to pay exorbitant fees to Elsevier to access this utter nonsense

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

Ever struggled with a good SNP threshold for transmission analysis? As part of our paper, we made the bioinformatics pipeline available and we deeply investigated and developed new methods for this purpose. Check it out!

Over 3 years we performed WGS-based surveillance of S. aureus in the NICU at @childrensphila.bsky.social, sequencing both surveillance and bloodstream infection isolates, to understand how colonization, transmission, and persistence are associated with invasive infection in high-risk neonates.

Researchers from @centermicrobialmed.bsky.social @chopresearch.bsky.social identify strategies for preventing the most infectious strains of Staph aureus.

@pjplanet.bsky.social @ahmedmicrobes.bsky.social @qianxuan.bsky.social @joeyzacks.bsky.social

This work was made possible through an amazing collaboration across @chopresearch.bsky.social including CHOP NICU, CHOP Infectious Disease Diagnostics Lab (IDDL), CHOP Infection Prevention & Control, the MicrobialARC at CHOP, the CHOP MIcrobiome Center, and
@centermicrobialmed.bsky.social!!

We tracked S. aureus using whole genome sequencing over 3 years in the NICU and identify spatial and temporal links for transmission between babies. We also demonstrate a strong association between colonization, transmission, persistence, and the development of invasive infections.

It’s a great honor to be part of these efforts. Check out our new paper co-led by our talented co-mentored PhD student @qianxuan.bsky.social & our colleague from the CHOP NICU Lakshmi Srinivasan! This would not happen without amazing collaborations across multiple departments & divisions at CHOP.

🚼 New research by @lshtm.bsky.social researchers and global partners shows how a vaccine could prevent newborn sepsis 💉🌍

@shaunkeegan.bsky.social, @neleshg.bsky.social, @childrensphila.bsky.social, @ahmedmicrobes.bsky.social, @kemriwellcome.bsky.social

Read more 👇
www.lshtm.ac.uk/research/cen...

Really happy to have this study led by @ashleyweiss.bsky.social and Jilarie Santos-Santiago published in the Journal of Bacteriology (@asm.org) over the holiday break!! Always awesome to team up with the amazing @ritatamayo.bsky.social lab! #Cdiff #enterococci

journals.asm.org/doi/10.1128/...

Happy New Year, all! Reminder that the deadline for abstract selected talks is Jan 7th for @keystonesymposia.bsky.social meeting "Beyond Antibiotics: Emerging Strategies Combating Bacterial Infection." Register today and join us in Breckenridge!! It is going to be an awesome meeting!

Constructing a “periodic table” of bacteria to map diversity in trait space Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen

New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...

Our study of neonatal sepsis in a NICU in Botswana underscores the value of integrating colonization surveillance, environmental investigation, and genomics to uncover hidden reservoirs and strengthen infection prevention and control (IPC) practices in resource-limited settings.

Proud to be part of a global effort focused on protecting our most vulnerable patients. Thanks @katholt.bsky.social for leading this global effort!

figure showing estimated proportion of cases in clusters, for each site. range from 0.04 to 0.93, mean estimate in random effects model is 0.57 [0.46,0.68]

#AMR #Klebsiella cause >100,000 neonatal deaths globally each year.

Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW

doi.org/10.1101/2025...

Research Technician III-Microbiome Center in Philadelphia, Pennsylvania, United States of America | Research at Children’s Hospital of Philadelphia Apply for Research Technician III-Microbiome Center job with Children’s Hospital of Philadelphia in Philadelphia, Pennsylvania, United States of America. Research at Children’s Hospital of Philadelphi...

Join my team at Children’s Hospital of Philadelphia, Research Technician III-Microbiome Center careers.chop.edu/70oyDxL

Research Technician IV in Philadelphia, Pennsylvania, United States of America | Research at Children’s Hospital of Philadelphia Apply for Research Technician IV job with Children’s Hospital of Philadelphia in Philadelphia, Pennsylvania, United States of America. Research at Children’s Hospital of Philadelphia

Join the CHOP Microbiome Center as a Research Technician IV!
We are seeking a motivated individual with hands-on experience in next-generation sequencing (NGS) to support our innovative microbiome research.
careers.chop.edu/us/en/job/10...

Microbial bellwether: Community-scale metabolic modeling to predict infection Microbial colonization is shaped by a complex network of interactions that influence both commensals and pathogens, including the public-health threat…

Happy to see the preview @joeyzacks.bsky.social and I wrote on the excellent paper recently published by the Gibbons Lab @gibbological.bsky.social is in press! I'd encourage folks interested in bacterial pathogenesis or microbial ecology to check out the preview and the research article!

Happy to team up with @microbe-enjoyer.bsky.social to highlight fantastic work by @gibbological.bsky.social, Alex Carr, and colleagues using community scale metabolic models to predict risk for C. difficile colonization!

See the initial study here: www.cell.com/cell-systems...

Very excited to attend this new @keystonesymposia.bsky.social meeting "Beyond #Antibiotics: Emerging Strategies Combating #BacterialInfection."
co-organized by
@joeyzacks.bsky.social
@kimingeneva.bsky.social
,
@maribyndloss.bsky.social
and
@dariavantyne.bsky.social . #KSAntibiotics26

Important 🧵 if your research depends on genome assemblies from long (PacBio / ONT) reads. As @merenbey.bsky.social says, these may not be the genomes you are looking for. TLDR: the assemblers are wrong and predict too many small circular contigs.

Check out this exciting preprint from @pjplanet.bsky.social @ahmedmicrobes.bsky.social @joeyzacks.bsky.social!! Study led by @qianxuan.bsky.social looking at Staphylococcus aureus transmission across the NICU.

Check our recent work tracking the transmission of Staph aureus in the NICU for 33 months.

Transmission of Staphylococcus aureus in the neonatal intensive care unit predicts invasive infection Background : Staphylococcus aureus is a leading cause of healthcare-associated infection and is one of the most common pathogens causing serious invasive infection in the neonatal intensive care unit ...

Our preprint on genomic epidemiology in the NICU! Strains that transmit faster also cause more invasive disease! nam10.safelinks.protection.outlook.com?url=https%3A...

Pretty good ROI...

Whenever you hear someone sneer about scientific research that seems useless to them — “they’re studying the spit of lizards?!” — remind them that’s exactly how we got Ozempic.

globalnews.ca/news/9793403...

Apologies for this long post I put together to explain to non-scientists the impact of NIH cuts: Last night, an “atomic bomb” was dropped on the biomedical science community. We were informed that effective immediately, indirect costs on NIH grants (both current and future) would be fixed at 15%.

Biomedical research institutions are major local employers. Take the University of Pennsylvania, Philadelphia’s largest employer—this policy threatens jobs across multiple sectors, such as health care, construction, food services and cleaning staff....

400,000 jobs at risk in red and blue states across the country.

“The N.I.H. funding also supports about 412,000 jobs, from research assistants to grant managers to people who dispose of toxic chemicals”

Excited to share updates to Microbiocode, the code repository for the PennCHOP Microbiome program. Numerous well curated software packages to enable Microbiome research. Check it out!
www.med.upenn.edu/microbiocode/