iiinova — where your digital self keeps evolving

Sanjat Kanjilal @sanjatkanjilal.bsky.social · 02/09/2026

Started one year ago yesterday at @amsterdamumc.bsky.social in the Department of Medical Microbiology and Infection Prevention Next month we go live with MILES, our comprehensive Microbiology and Infectious Diseases Learning Health System What a year. The most exciting stuff is coming next year

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 17/06/2026

Tallinn; summer 2026 +1 for Odesa, a great Ukrainian restaurant somewhat hidden in the Old Town. Pictured is a herring pate with horseradish vodka compliments of the chef, and a red wine from a Ukrainian grape I’ve never heard of. All very lekker!

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 17/06/2026

It was a pleasure to talk at the @ampath.bsky.social #AMPEurope2026 conference in Tallinn this morning on the future of AI in CMID I presented a vision for pre- and post-analytic AI decision support and a key (missing) piece needed to get there Slides available at drive.google.com/file/d/1I5Ib...

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 16/06/2026

Yes it surprisingly peaceful! Thank you, it’s been awesome living here

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 28/04/2026

Shoutout to @microbecharmer.bsky.social for her excellent work leading this project as well as @nicolepecora.bsky.social and the rest of the team for making this happen! 7/7

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 28/04/2026

Our findings suggest FEP is safe when molecular panels are negative — with one key exception: bloodstream infections due to E. cloacae complex, where occult resistance reached 4.4%. Worth keeping in mind at the bedside. 6/7

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 28/04/2026

To answer this we analyzed ~19,000 AmpC-producing isolates. 1–5% were FEP-SDD or FEP-R, varying by organism, setting, and body site. Higher FEP MICs tracked with more beta-lactamase genes — but absolute numbers were low and mechanisms were remarkably diverse. 5/7

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 28/04/2026

To aid in decision making, many labs now use rapid molecular panels to flag resistance genes before MIC results return 2 days later. We asked: is it safe to use FEP when those panels come back negative? How often do these pathogens have other genes that could cause treatment failure? 4/7

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 28/04/2026

FEP MICs fall into 3 buckets: susceptible (S) → treat with FEP; resistant (R) → use carbapenems, as other enzymes are likely present; susceptible-dose-dependent (SDD) → the gray zone. SDD isolates may or may not carry additional resistance genes, raising the possibility of treatment failure 3/7

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 28/04/2026

AmpC-producing Enterobacterales are a tricky clinical problem. Cefepime (FEP) is the go-to treatment — it's a weak inducer of, and poor substrate for the AmpC enzyme, but the decision to treat is nuanced because... 2/7

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 21/04/2026

MGH/BWH ID fellow class of 2014 Same friends, different day

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 17/04/2026

I'll be on the train from the other direction tomorrow! Looking forward to seeing folks IRL

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

12/12 If you work in infection control, hospital epidemiology, or clinical ML — please dig in, replicate it, and tell us what you find.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

11/12 tl;dr — colonization pressure matters beyond ICUs and resistant pathogens, cross-organism effects exist, and sometimes the relationship flips. Nosocomial transmission is more complex than we thought.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

10/12 This was a 4-year project. Huge shoutout to @alexwei21.bsky.social @tedpak.bsky.social and all co-authors. Really proud of what this team pulled off.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

8/12 All of this used passively collected clinical data — no extra testing required. Just a robust data analytics infrastructure. And it scales automatically across an entire health system. Building this (and much much more) at my new institution @amsterdamumc.bsky.social

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

7/12 Key finding #3 (the weird one): In some cases CP was inversely associated with acquisition — controls had higher CP than cases. Novel and puzzling. Definitely worth following up on.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

6/12 Key finding #2: CP from one organism sometimes predicted acquisition of a different organism — typically ones sharing the same body niche. Cross-organism spillover effects are real and underappreciated.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

5/12 Key finding #1: CP predicts nosocomial acquisition for drug-susceptible organisms (e.g. MSSA) just as much as drug-resistant ones (e.g. ESBL Klebsiella). This isn't just a resistance problem — it's a transmission problem.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

4/12 We built prediction models using CP from 9 organism sets to predict acquisition of 11 organism types. We matched cases & controls carefully at ward entry to control for baseline risk. Rigorous design, real clinical data.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

3/12 We already knew CP — infection rates among your ward co-occupants — predicts your own risk of acquiring a pathogen. But this was thought to mainly apply to ICUs and drug-resistant bugs. We tested whether that's really true.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 01/04/2026

2/12 Getting an infection from being in the hospital (nosocomial infection) is one of the worst outcomes for patients. Even in hospitals with advanced infection control, it remains widespread.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 12/03/2026

Note to self: If your audience is nodding off, point to centuries old stained glass windows to liven things up

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Reposted by Sanjat Kanjilal

Nature Medicine @natmed.nature.com · 12/03/2026

Analyses of oral antibiotic use over 8 years in the Swedish Prescribed Drug Register and fecal metagenomes data of 14979 individuals found evidence that antibiotics can have long-lasting impacts on the gut microbiome. www.nature.com/articles/s41591-026-…

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 24/02/2026

"Biology is…about propensities, potentials, vulnerabilities, predispositions, proclivities, interactions, modulations, contingencies, if/then clauses, context dependencies, exacerbation or diminution of preexisting tendencies.” - Robert Sapolsky, from his book Behave What a f-in great quote!

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Reposted by Sanjat Kanjilal

Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here: www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

biorxiv.org

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Reposted by Sanjat Kanjilal

Philipp Markolin @philippmarkolin.eurosky.social · 12/02/2026

Here is an announcement for everybody who is sick and tired on the attacks on science and scientists. It has been months in the making, but now we are ready to fight back. First episode airs tomorrow 5pm UK. New episode every friday. Incredible guests lined up. open.substack.com/pub/protagon...

open.substack.com

Announcing: Science Counterpunch

Fighting back for science & scientists was never more urgent

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 31/12/2025

12:37 and still going strong…sounds like 112 is blitzed

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 31/12/2025

Learned today that New Year’s Eve in Amsterdam is absolutely insane

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 31/12/2025

Cornwall, Oxford and London Holidays!

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 12/12/2025

No just EHR data. Good idea for the next release

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 12/12/2025

This month's @natrevmicro.nature.com is fantastic! Here @amsterdamumc.bsky.social, my team is building from scratch a next-gen clinical micro informatics infrastructure to support real-time pathogen surveillance; explicitly connecting the hospital to public health www.nature.com/nrmicro/volu...

nature.com

Nature Reviews Microbiology - Volume 24 Issue 1, January 2026

Viral pathogens and global health, inspired by the Focus issue.

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 05/12/2025

Links to the other 3 datasets: Stanford: datadryad.org/dataset/doi:... University of Texas Southwestern: datadryad.org/dataset/doi:... Eastern Caroline University Health: datadryad.org/dataset/doi:... (6/6)

datadryad.org

Dryad | Data: Antibiotic Resistance Microbiology Dataset (ARMD): A resource for antimicrobial resistance from EHRs

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Sanjat Kanjilal @sanjatkanjilal.bsky.social · 05/12/2025

Thank you to Jonathan Chen at Stanford, Rich Medford at UTSW / ECU, @alexwei21.bsky.social, Physionet, Mass General Brigham, NIH and all other team members who worked on this monumental, multiyear effort! (5/6)

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