Qianxuan(Sean) She

This work wouldn’t have been possible without my incredible PIs @pjplanet.bsky.social @joeyzacks.bsky.social @ahmedmicrobes.bsky.social and Dr. Lakshmi Srinivasan, who initiated and led the surveillance. An amazing collaboration across the CHOP NICU, IDDL, IPC, and @centermicrobialmed.bsky.social!

GitHub - microbialARC/THRESHER: THRESHER is a bacterial phylogenomics toolkit for strain and/or transmission clusters identification, genome profiling of substitution rates and MGEs, and bacterial evo... THRESHER is a bacterial phylogenomics toolkit for strain and/or transmission clusters identification, genome profiling of substitution rates and MGEs, and bacterial evolution simulation. - microbia...

We’ve made our analytical pipeline THRESHER publicly available! Just provide your genomes and it handles strain and/or cluster composition, and generates quality visualizations for you. Easy to install,thoroughly documented,and validated on published datasets and simulations. Manuscript coming soon!

We dedicated a lot of effort to the visualizations in this paper to present insights from genomics, phylogenetics, and epidemiology in a more accessible way, not just specialists, but healthcare workers, IPC teams, and anyone interested in understanding how S. aureus transmits in a clinical setting.

S. aureus is a universal challenge, which happens in hospitals everywhere, not just ours. What’s different here is that we have the resolution to actually see it. By WGS surveillance in near real time, we can perform targeted infection prevention, making NICU a safer place for vulnerable babies.

How does S. aureus move? We found that physical proximity and shared caregivers are major routes of transmission. We also found environmental reservoirs harboring persistent strains. But the key finding: strain spreading to more babies over time were the same ones linked to invasive infections.

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.

Thrilled to share this study tracking Staph aureus carriage and transmission across the NICU using genomics! Work done w @pjplanet.bsky.social & @ahmedmicrobes.bsky.social and made possible by @centermicrobialmed.bsky.social.

Study co-led by the amazing @qianxuan.bsky.social & Lakshmi Srinivasan!

This study was made possible through an amazing collaboration across the CHOP NICU, CHOP Infectious Disease Diagnostics Lab (IDDL), CHOP Infection Prevention and Control, the Microbial Archive and Cryocollection at CHOP (MicrobialARC), and @centermicrobialmed.bsky.social.

In this study we tracked carriage, transmission, and invasive infection with S. aureus across 33 months in the NICU. Using longitudinal WGS, we identify risk factors for transmission of invasive clones, and show strains that are transmitted more rapidly are more likely to cause invasive disease

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 (N...

Excited to share our work with @pjplanet.bsky.social and @ahmedmicrobes.bsky.social tracking Staph aureus transmission across the NICU using genomics!!

This study was co-led by the amazing @qianxuan.bsky.social and Lakshmi Srinivasan, and made possible by the @centermicrobialmed.bsky.social

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...