katholt.bsky.social
Scientist… pathogen genomics & antimicrobial resistance, computational biology & infectious disease epidemiology.
Co-Director LSHTM AMR Centre @lshtmamrcentre.bsky.social
holtlab.net | klebnet.org | typhoidgenomics.org | amr.lshtm.ac.uk
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No story -- ZERO -- should take at face values that DOGE is or was about creating "efficiency" in government.
The MAGA project is to destroy the government. This is not a hidden agenda! Any story that ignores that and pretends DOGE is about cutting costs is an utter journalistic failure.
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I tested myloasm on a 50x Klebsiella isolate, and it was very fast - only took about 1 minute to complete (on my Macbook).
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Yikes this should really be open access
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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.
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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.
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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.
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If you have an example file of an older output format you would want to interpret, we can specifically check and prioritise that compatibility.
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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.
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Yep! There is an active TB group, looking to integrate rules from the WHO TB catalog and elsewhere, see github.com/interpretAMR....
So far nobody has volunteered to define rules for other mycobacteria, but we would welcome that.
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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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Thanks to the amazing @yekwah.bsky.social who is leading the bioinformatics for AMRrules, my wonderful ESGEM-AMR co-chair @natachacouto.bsky.social & the >100 ESGEM-AMR members who have volunteered their time and expertise to curate AMRrules for their favourite organisms
github.com/interpretAMR...
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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.
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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.
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AMRrules are curated by organism experts belonging to ESGEM-AMR, a working group of ESGEM, the ESCMID Study Group on Epidemiological Markers.
github.com/interpretAMR...
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AMRrules tells us how to interpret these, and our Python package can apply the rules to annotate your AMRfinderplus output with these interpretations.
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The AMRrules beta release focuses on core genes. These are reported by AMRfinderplus and other tools, but don’t all confer clinical resistance.
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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?