Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight) interpretamr.github.io/AMRrules - ThreadSky

katholt.bsky.social • 11 days ago

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
https://interpretamr.github.io/AMRrules

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katholt.bsky.social•11 days ago

AMRrules encode organism-specific rules for interpreting AMR genotype calls: if I find this gene/mutation in this organism, what does it mean for clinical resistance?

katholt.bsky.social•11 days ago

The AMRrules beta release focuses on core genes. These are reported by AMRfinderplus and other tools, but don’t all confer clinical resistance.

katholt.bsky.social•11 days ago

AMRrules tells us how to interpret these, and our Python package can apply the rules to annotate your AMRfinderplus output with these interpretations.

katholt.bsky.social•11 days ago

AMRrules are curated by organism experts belonging to ESGEM-AMR, a working group of ESGEM, the ESCMID Study Group on Epidemiological Markers.
https://github.com/interpretAMR/AMRrulescuration

dutchscientist.bsky.social•11 days ago

Nice, I am going to try that.

katholt.bsky.social•11 days ago

The ESGEM-AMR subgroups have been busy encoding AMRrules for lots of pathogens - the beta release has core gene rules for all the ESKAPEE pathogens, plus Salmonella & Yersinia.

katholt.bsky.social•11 days ago

The AMRrules beta release also includes rules to interpret acquired mutations in Neisseria gonorrhoeae - thanks to a wonderful group led by Leonor Sanchez Busó!!

Acquired gene/mutation interpretation for other pathogens is coming later this year.

alanmcn1.bsky.social•10 days ago

Rules is a strong word

katholt.bsky.social•10 days ago

Haha I suppose it is in some ways

It is borrowed from ‘Expert rules’ and ‘Interpretive rules’ used in phenotypic susceptibility testing, and is intended to be analogous.

sylvainbrisse.bsky.social•8 days ago

AMR will rule us all 😬

alanmcn1.bsky.social•8 days ago

Only if you allow it

marvig.bsky.social•10 days ago

Great work.
Does it take amrfinderplus v3 results as input or only newest armfinderplus v4 ?

katholt.bsky.social•10 days ago

If you have an example file of an older output format you would want to interpret, we can specifically check and prioritise that compatibility.

marvig.bsky.social•7 days ago

Thanks for reply.
My old files were generated without --print_node option so I generated new files.
I tried on 100 P. aeruginosa and gets "0 hits matched a rule" for all. Same for test_ecoli_genome.tsv so it must be problem at my end. I may create an issue at github to get onwards from here.

katholt.bsky.social•6 days ago

Please do post an issue! This is a bleeding edge beta release, as an open science project, and we haven’t had time yet to test widely and find edge cases. So it’s very helpful to know if you have an issue, and hopefully it’s easily fixed.

katholt.bsky.social•6 days ago

If the test command is not working, it’s probably an issue with installation of the Python package itself, but please post so we can help figure it out.

marvig.bsky.social•6 days ago

Yep.
The test command/dataset works now. So I am one step further :)
I have created an issue: https://github.com/interpretAMR/AMRrules/issues/4
Thanks and sure that I will work for me and be a success for many.

katholt.bsky.social•10 days ago

TBH this is a bleeding edge release that is tested with the newest version. We will aim for compatibility with different versions of AMRfp code and DB in the first full release, but need to review the specific changes to output field names etc.

luizcarvalholab.bsky.social•11 days ago

Very cool and useful, no doubt. It would be great to see M. tuberculosis and perhaps other important mycobacterial pathogens there too.

katholt.bsky.social•10 days ago

Yep! There is an active TB group, looking to integrate rules from the WHO TB catalog and elsewhere, see https://github.com/interpretAMR/AMRrulescuration?tab=readme-ov-file#member-list-by-subgroup.
So far nobody has volunteered to define rules for other mycobacteria, but we would welcome that.

luizcarvalholab.bsky.social•10 days ago

Awesome! Thanks Kat.

aldertzomer.bsky.social•11 days ago

This looks super useful. Will it also include logic for aminoglycoside resistance, with combinations of genes giving a specific drug resistance? there used to be a website with details of combinations ( https://web.archive.org/web/20021206082002/http:/www.warn.cas.cz/Topics/miller/amg_neg.html ), and this paper as well https://journals.asm.org/doi/10.1128/aac.43.4.727

katholt.bsky.social•11 days ago

Yes. We focused first on rules for core genes, as it causes a lot of confusion when users get loads of genes reported for a strain that actually has no/little acquired resistance. But we are moving on to acquired genes and expect aminoglycosides & B-lactamases will be most tricky & interesting.

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