Timo Saratto

Clinical significance and antifungal susceptibility profile of 103 clinical isolates of Scedosporium species complex and Lomentospora prolificans obtained from NIH patients | Journal of Clinical Micro... Understanding the epidemiology and clinical spectrum of infections caused by Scedosporium species complex and Lomentospora prolificans is integral to improving outcomes, particularly in severely ill a...

Clinical significance and antifungal susceptibility profile of 103 clinical isolates of Scedosporium species complex and Lomentospora prolificans obtained from NIH patients | Journal of Clinical Microbiology journals.asm.org/doi/10.1128/...

Congats!

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

NZJMLS V.79 N0. 1 March 2025 New Zealand Journal of Medical Laboratory Science. Volume 79, Number 1, March 2025

Hospital infections are a problem & 'go-to' methods have limits. We trailed @nanoporetech.com in outbreak detection & response

📌Implementing nanopore sequencing in a clinical laboratory: a social systems case study | NZ J Med Lab Sci

issuu.com/sharontozer/...

🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠

New name, same old me! Me and my wife decided to take Saratto, from her father’s side, as our new surname. The wedding itself was already in September, we just were a bit slow with the name change 🎉

New pre-print from folks @ Copenhagen University Hospital:

🔬 28-month WGS surveillance
🦠 7,760 patient infections
📊 27.1% genetically related, 69% w/ epi link
💰 €1.25M net savings/year if acted upon/prevented!

#IDSky more great evidence for WGS for IP&C

📄: www.medrxiv.org/content/10.1...

Link to original preprint by @rhystwhite.bsky.social, @maxgbloomfield.bsky.social & co:

bsky.app/profile/rhys...

How New Zealand’s ESR and Awanui Labs achieve ultrafast outbreak detection with Solu and Nanopore sequencing | Solu New Zealand’s Institute of Environmental Science and Research (ESR) and Awanui Labs present an ultrafast outbreak surveillance model using nanopore sequencing and Solu's bioinformatics

Exciting news from New Zealand!⚡️
Read how ESR and Awanui Labs run genomic surveillance with Solu and @nanoporetech.com, speeding up analysis from weeks to minutes. What’s best, the system is in routine use protecting #NICU patients

#IDSky #MicroSky #IPSky #ClinMicro 🧬🖥️🧫
tinyurl.com/solu-4c8a

Kia ora koutou! 👋

I’ve put together a starter pack of amazing people working in #Genomics across Aotearoa New Zealand.

If I’ve missed anyone, please let me know!

go.bsky.app/KhMbQxK

Excited to see this out! This truly is the forefront of outbreak surveillance. Congrats for the whole author team!

Brilliant new preprint! Genomic outbreak analysis in minutes instead of weeks, by using the Solu Platform.

This is exactly what we built it for: fast onsite genomic analysis, paired with data sharing with national public health experts.

The future is here!

#IPSky #EpiSky #ClinMicro
🧬💻🧪🧫🦠

The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates dela...

📌The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory |@medrxivpreprint

See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays

doi.org/10.1101/2025...

🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠

The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing - Antimicrobial Resistance & Infection Control Background Klebsiella variicola has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as Klebsiella pneumoniae. An increased incidence of K. pneumoni...

K. variicola can be misID as K. pneumoniae. Our #OpenAccess paper reports an NICU #Outbreak

📌The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing

doi.org/10.1186/s137...

@nanoporetech.com

🖥️🧬💻
#AcademicSky
#Microsky
🧪🧫🦠

NEW Publication🥳 Solu enables easy genome-scale pathogen surveillance!

Solu is a cloud-based real-time #pathogen surveillance platform integrating privacy, speed & usability. It automatically assembles, characterizes & compares WGS data—no bioinformatics expertise required.

🔗: tinyurl.com/y8p24uya

Was an absolute pleasure to work with you on this. Thousand thanks!

So excited about our new publication with @jlsteenwyk.bsky.social & co 🎉

Senior post at LSHTM closes in 2 days (31st Jan). Do apply if you want to lead/join a department focussed on infectious disease epi and dynamics.

Unrelated: the UK doesn’t have executive orders.

In London for the amazing Festival of Genomics and Biodata! Looking forward to all the amazing talks and encounters. If you’re also here, DM me for a chat on pathogen genomic surveillance
🧬💻🦠

Interested in bacterial/fungal sequencing for epidemiology?

We’re piloting a new service with ONT sequencing, DNA extraction and analysis with Solu platform for €95/sample. Results within a week. Limited batch available!

See more: solu-bio.notion.site/18561663af81...

#IDSky #MicroSky #IPSky 🧬💻

Our publication on Solu Platform is now out in BMC Bioinformatics! So excited and proud to see this out. A huge thanks for the whole author team 🥳
rdcu.be/d57Cd #IDSky #MicroSky #IPSky 🧬🖥️
PS. I'm changing my surname to Saratto due to getting married, just in time for this publication!

Exciting times ahead! Our manuscript for Solu Platform just got accepted and is in final proofreading 🧬🖥️ 🦠

Don't miss out on the free registration for the The Festival of Genomics & Biodata in London!
I will be speaking at The Festival, taking place on the 29th-30th of January 2025 at ExCeL London.

Register now ! hubs.la/Q02TptWZ0
#FOG2025

One of today’s highlights: Iain Johnston explaining AMR evolution inference using Pokemon analogy 😄
#NCMG24 #MicroSky

Helen Wang on plasmid copy number variation as a tradeoff between resistance and fitness. Fascinating!
#NCMG24 #ClinMicro

The perfect outbreak...for showcasing the value of sequencing Pseudomonas outbreak brings genomics to the forefront

Sequencing is an important tool for connecting across disciplines, organization types, geography, human/animal, and time. In this article I use the 2022-2023 Pseudomonas outbreak in artificial tears as a case study on the power of sequencing for surveillance. genomicepi.substack.com/p/the-perfec...

Great example of the power of genomic pathogen surveillance. A balance between sharing data & privacy must be found.

Awesome, thanks!

As the great migration from Twitter to Bluesky begins, I have created the "Clinical Microbiology" starter pack to help you find your colleagues. Please let me know if you would like to be added!

go.bsky.app/VTpSjBL

Thanks for making this! Can I join? (if you accept bioinformaticians working on the topic 🤓)