Theodore Pak

#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...

Impact of removing the healthcare mask mandate on hospital-acquired COVID-19 rates Mandatory mask-wearing policies were one of several measures employed to reduce hospital-acquired SARS-CoV-2 infection throughout the pandemic. Many nations have removed healthcare mask mandates, but ...

I've seen this study. It used <1yr of data for 1 hospital, rather than 3.5yrs for 10 hospitals. IMO, it was underpowered.

The 95% CI for the primary IRR was huge (0.52–2.33). Something close to a 2x change would be falsely missed by this design.

www.journalofhospitalinfection.com/article/S019...

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...

Thanks! I agree, it’s very hard to do a masking RCT in a healthcare setting, for ethical and practical reasons. So it’s all too easy to use absence of RCTs as a strawman, despite plenty of other evidence to the contrary. And no, I don’t think I’ve had the privilege 😌

First author here, happy to answer questions!

For those of you reacting: Duh, why was this study necessary? I have a thread for you... bsky.app/profile/tedp...

#MedSky #IDsky

First author here, happy to answer questions!

For more, check out this thread for the backstory of the study and a walkthru of the results: bsky.app/profile/tedp... #MedSky #IDsky

Testing and Masking Policies and Hospital-Onset Respiratory Viral Infections This cohort study examines the ratio between hospital- and community-onset respiratory viral infections at different levels of testing and masking from 2020 to 2024.

New: Universal masking&testing reduce hospital infections, so does staff masking

Stopping universal masking&testing led to 25% increase in respiratory viral infections
Restarting staff masking led to 33% decrease

8 out of 100 (random sample) died in the hospital
jamanetwork.com/journals/jam...

All three viruses (flu, COVID, RSV) are combined for the plotted points. The vast majority of respiratory viruses and hospital-onset cases in those two periods was COVID, so this is why the combined measure changes when the variant changes.