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(v2.1.1.9195) add BTL-S, fix ranks in unknown microorganisms

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dr. M.S. (Matthijs) Berends
2025-03-13 14:30:14 +01:00
parent a7ef22a21e
commit 9aab129ea6
48 changed files with 1789 additions and 1710 deletions
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NEWS.md
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# AMR 2.1.1.9194
# AMR 2.1.1.9195
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
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* The selectors `lincosamides()` and `macrolides()` do not overlap anymore - each antibiotic is now classified as either of these and not both
* Fixed selector `fluoroquinolones()`, which now really only selects second-generation quinolones and up (first-generation quinolones do not contain a fluorine group)
* `antimicrobials` data set
* Added agents used for screening, with an ID all ending with `-S`: benzylpenicillin screening test (`PEN-S`), clindamycin inducible screening test (`CLI-S`), nalidixic acid screening test (`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening test (`OXA-S`), pefloxacin screening test (`PEF-S`), and tetracycline screening test (`TCY-S`). The ID of cefoxitin screening was renamed from `FOX1` to `FOX-S`, while the old code remains to work.
* Since clindamycin is a lincosamide, the antimicrobial selector `lincosamides()` now contains the argument `only_treatable = TRUE` (similar to other antimicrobial selectors that contain non-treatable drugs)
* Added agents used for screening, with an ID all ending with `-S`: benzylpenicillin screening test (`PEN-S`), beta-lactamase screening test (`BTL-S`), clindamycin inducible screening test (`CLI-S`), nalidixic acid screening test (`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening test (`OXA-S`), pefloxacin screening test (`PEF-S`), and tetracycline screening test (`TCY-S`). The ID of cefoxitin screening was renamed from `FOX1` to `FOX-S`, while the old code remains to work.
* For this reason, the antimicrobial selectors `lincosamides()`, `isoxazolylpenicillins()`, `quinolones()`, `fluoroquinolones()`, `tetracyclines()` now contain the argument `only_treatable = TRUE` (similar to other antimicrobial selectors that contain non-treatable drugs)
* Added amorolfine (`AMO`, D01AE16), which is now also part of the `antifungals()` selector
* Added efflux (`EFF`), to allow mapping to AMRFinderPlus
* Added tigemonam (`TNM`), a monobactam