Theodore Pak

Infectious Diseases Society of America (IDSA) Position Statement: Why IDSA Did Not Endorse the Community-Acquired Pneumonia Guidelines 2025 Update The Infectious Diseases Society of America (IDSA) did not endorse updated community-acquired pneumonia guidelines because they recommend antibiotics for pa

A @idsainfo.bsky.social position statement in @cidjournal.bsky.social describing why the society backed out of ATS CAP guidelines.

[In viral pneumonia] “briefly withholding antibiotics for patients with nonsevere illness to clarify the diagnosis is safe”

#IDSky

academic.oup.com/cid/advance-...

Today I am very proud to announce the release of the Antibiotic Resistance Microbiology Dataset - Mass General Brigham (ARMD-MGB; physionet.org/content/armd...) , as part of an NIH-funded collaboration led by Jonathan Chen at Stanford. (1/6)

When plotting, LLMs see what they expect to see - Posit Data science agents need to accurately read plots even when the content contradicts their expectations. Our testing shows today's LLMs still struggle here.

To be effective, data science agents need to be able to read plots reliably. @sara-altman.bsky.social and I wrote about some concerning findings on LLMs' ability to interpret plots when the content contradicts their expectations on the @posit.co blog.

posit.co/blog/introdu...

Gave my 1st talk in NL: how to make multicenter data analysis with patient data actually work.

tl;dr: common data models (global interoperability) + LLMs (data harmonization, mapping, future-proofing) + federated learning (privacy)

Let me know what you think!

drive.google.com/file/d/1N3yk...

Heatmaps show symptom co-occurrence and infection sources. Panel A charts 30 signs/symptoms (skin, cardiopulmonary, gastrointestinal, dizziness, constitutional), with red indicating high co-occurrence. Panel B links infection sources to symptoms via ICD-10-CM codes.

An #LLM extracted signs and symptoms for patients with sepsis with similar accuracy to humans, and identified 7 syndromes differentially correlating with multidrug-resistant infection risk and mortality. ja.ma/47onWVE

Syndromic Analysis of Sepsis Cohorts Using Large Language Models This cohort study compares the performance of a large language model against manual medical record review for extracting presenting signs and symptoms data from hospital admission notes and uses these...

Maybe AI Knows Something That We Do Not!
🆕💫 Cohort study
LLM accurately extracted presenting signs & symptoms from admission notes that clustered into syndromes differentially correlated with infection sources, MDR infections, and mortality #IDsky
jamanetwork.com/journals/jam...

Opinion | We Can Stop Deadly Hospital Outbreaks -- So Why Aren't We? Genomic surveillance can help contain local and nationwide threats

My new piece in @medpagetoday.com

We Can Stop Deadly Hospital Outbreaks - So Why Aren't We?

Genomic surveillance can prevent outbreaks from spreading, save lives, and costs.

So what’s holding it back from being implemented in hospitals?

#IDSky

www.medpagetoday.com/opinion/seco...

#IDsky #Medsky 🧪🦠

New preprint from our lab by Rangachar Srinivasa et al:

We WGS 4 major respiratory viruses in 3 hospitals (RSV, influenza, rhinovirus, HMPV) & found silent transmission happening under the radar

Genomics uncovered hidden spread, complex transmission chains #IDSky
📄: www.medrxiv.org/content/10.1...

How many hospitalized patients need care in the ICU? How many of them survive? What interventions do they receive there?

These are some of the questions I had two years ago while trying to write the "background" section for my masters thesis. But I couldn't find the answers... they did not exist.

The amount of green on this level of evidence guiding antifungal treatment duration demonstrates nicely the research knowledge gap in this field!

#IDSky #ClinMicro #AMR @drneilstone.bsky.social

ondering how this year’s measles outbreaks compare to previous years? This chart shows that 2025 (dark purple) is already about 4x higher than this time last year (light purple), which was itself a sharp increase over 2023. The trend is alarming. Prevention—including vaccination—is critical.

Agree that individual vs population-level goals often get conflated, to ASPs’ detriment

But even for #2, even at an individual level, a decision of which MDROs to prevent pivots on colonization burden, pathogenicity, and ∆ harm once MDR

This still puts Staph aureus and PsA near the top of the list

OK but then to keep going with this…

Staph aureus is just one of thousands of bacteria species in people’s noses, should we base our whole GPC coverage on it?

ID - Return to Basics:

This was the 1st reported case of an adult immunocompetent host who survived measles complicated by ARDS. A 36 yo female ED nurse, unvaccinated, who was exposed to a patient w active measles in October 1989. Ten days later, she developed measles

Your AI can't see gorillas – A comparison of LLMs' ability to perform exploratory data analysis

chiraaggohel.com/posts/llms-e...

Clever tricks with token sampling can guide a "reasoning" LLM like Deepseek's R1 (and the many new models it is already inspiring) into <think>'ing longer, and thereby producing more accurate output

There is a lot more juice to squeeze from these kinds of models.

timkellogg.me/blog/2025/02...

Use of Machine Learning to Assess the Management of Uncomplicated UTI This cohort study examines the effectiveness and adverse event profile for first-line antibiotics, fluoroquinolones, and oral β-lactams for treating uncomplicated urinary tract infection (UTI) in cont...

New paper in JAMA Network Open!

jamanetwork.com/journals/jam...

The IDSA released their guidelines for treatment of uncomplicated UTI back in 2011. We looked at a large claims database formatted into the OMOP common data model to see whether the recommendations still hold

tl;dr They do.

(1/7)

The removal of #HIV- and #LGBTQ-related resources from the websites of CDC and other health agencies is deeply concerning.

Access to this information is crucial for ID and HIV health care professionals.

Our full statement: https://buff.ly/42AO8LI

It is simply not enough for universities to say, “Our grants & research offices are looking into how research will be affected by the latest directive.”

University leaders must actively and very publicly make the case for the kind of work many of us do. The silence on this front is deafening.

It appears that the CDC has removed its guidelines for contraception and STIs. www.cdc.gov/contraceptio...

The entire website for the NIH Office of Research on Women's Health (ORWH) is very nearly stripped bare. This is so, so devastating. orwh.od.nih.gov/research/fun...

CDC removes data on sexual orientation, gender identity from website Data from an expansive federal survey on youth behavioral habits, including their sexual orientation and gender identity, have been removed from the website of the CDC.

It's one thing to take down pages talking about diversity in science.

It's another thing entirely to take down research databases that are used for observational studies.

That is exactly what it seems just happened at the CDC.

www.statnews.com/2025/01/31/c... www.statnews.com/2025/01/31/c...

🚨If you use public data products from the CDC or other US federal agencies 🚨

Download them NOW

[This is how I’m spending my Friday]

I'm just here to say for the 2nd week in a row, the CDC has not released its morbidly and mortality weekly report on schedule. Everyone who provides healthcare to patients in the US is less informed and less up to date as a direct result. This impacts negatively at the population level.

The communications pause for federal health agencies meant that the CDC couldn't publish the MMWR this week -- the first time in the publication's 60+ year history this has happened.

Unhappy about this! Getting good data published on infectious threats is critical, especially as H5N1 looms. #IDSky

💯 The sanewashing needs to stop. Active disinformation does not deserve the grace of the "both sides" framing that legacy media eternally, fatalistically obligates itself to.

When that framing gets baked into the vocabulary of headlines and discourse, they are doing the public a disservice.

💯 The sanewashing needs to stop. Active disinformation does not deserve the grace of the "both sides" framing that legacy media eternally, fatalistically obligates itself to.

When that framing gets baked into the vocabulary of headlines and discourse, it is doing the public a disservice.

Board certified!

Glad that I'm now officially qualified to wear sunglasses while ranting about doxycycline, the definition of "FUO," and Streptococcus taxonomy controversies 😎

Author of the study here, happy to answer questions!

For those of you reacting: Duh! Why is this kind of study even necessary? I have a thread for you... bsky.app/profile/tedp...