AMR

• Fix for selecting first isolates using the phenotype-based method
  • This included too many isolates when patients had altering antibiograms within the same bacterial species
  • See for more info our issue #122
• Added 1,366 LOINC codes to the antibiotics data set and updated to the latest version (LOINC v2.76)
• MICs can now be used in complex number calculations and allow scientific number format as input (e.g., as.mic("1.28e-2"))
• Fix rounding MICs on latest R beta ('R-devel')
• Removed unneeded note about the used language when option AMR_locale is set
• Fixed non-ASCII characters in documentation, according to CRAN maintainers

New

• Regarding clinical breakpoints:
  • Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added to the clinical_breakpoints data set for usage in as.sir(). EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations
  • The EUCAST dosage guideline of v13.0 has been added to the dosage data set
  • The clinical_breakpoints data set now also contains epidemiological cut-off (ECOFF) values and CLSI animal breakpoints. These two new breakpoint types can be used for MIC/disk interpretation using as.sir(..., breakpoint_type = "ECOFF") oras.sir(..., breakpoint_type = "animal"), which is an important new addition for veterinary microbiology.
• Added support for 30 species groups / complexes. They are gathered in a new data set microorganisms.groups and are used in clinical breakpoint interpretation. For example, CLSI 2023 contains breakpoints for the RGM group (Rapidly Growing Mycobacterium, containing over 80 species) which is now supported by our package.
• Added oxygen tolerance from BacDive to over 25,000 bacteria in the microorganisms data set
  • Added mo_oxygen_tolerance() to retrieve the values
  • Added mo_is_anaerobic() to determine which genera/species are obligate anaerobic bacteria
• Added LPSN and GBIF identifiers, and oxygen tolerance to mo_info()
• Added SAS Transport files (file extension .xpt) to our download page to use in SAS software
• Added microbial codes for Gram-negative/positive anaerobic bacteria

Changed

• Updated algorithm of as.mo() by giving more weight to fungi
• Fixed clinical breakpoints errors introduced by the source we import the rules from
• mo_rank() now returns NA for 'unknown' microorganisms (B_ANAER, B_ANAER-NEG, B_ANAER-POS, B_GRAMN, B_GRAMP, F_FUNGUS, F_YEAST, and UNKNOWN)
• When printing microorganism or antibiotic codes in a tibble, a mouse-hover now shows the full name of the code
• Plots for MIC and disk diffusion values:
  • Now have settable arguments for breakpoint type and PK/PD, like as.sir()
  • Will now contain the name of the guideline table in the subtitle of the plot
• Fixed formatting for sir_interpretation_history()
• Fixed some WHONET codes for microorganisms and consequently a couple of entries in clinical_breakpoints
• Fixed a bug for as.mo() that led to coercion of NA values when using custom microorganism codes
• Fixed usage of icu_exclude in first_isolates()
• Improved as.mo() algorithm:
  • Now allows searching on only species names
  • Fix for using the keep_synonyms argument when using MO codes as input
  • Fix for using the minimum_matching_score argument
• Updated the code table in microorganisms.codes
• Fixed an endless loop if using reference_df in as.mo()
• Fixed bug for indicating UTIs in as.sir()
• Greatly improved speed of as.sir()