Planned as v3.1.0, end of September 2026.
The former kingdoms Bacteria and Archaea are now each divided into four kingdoms with new top-level domains ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new domain column in the microorganisms data set was added, and more importantly, mo_kingdom() now returns the formal kingdom (e.g. "Pseudomonadati" instead of "Bacteria"). Use mo_domain() for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), kingdom and domain are identical.
domain
microorganisms
mo_kingdom()
"Pseudomonadati"
"Bacteria"
mo_domain()
kingdom
Faster parallel computing via the future package for as.sir() and wisca(): a non-sequential plan (e.g. future::plan(future::multisession)) must be active before using parallel = TRUE.
future
as.sir()
wisca()
future::plan(future::multisession)
parallel = TRUE
clinical_breakpoints
breakpoint_type = "ECOFF"
wisca_plot()
options(AMR_guideline = "EUCAST 2012")
interpretive_rules()
resistance()
susceptibility()
count_resistant()
count_susceptible()
top_n_microorganisms()
property_for_each
property = NULL
The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".
"3.3"
"3.2"
"3.1"
The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3".
(only applies when rules contains "expert" or "all") a character value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is NA. Currently only works when version_expertrules is 3.2 and higher; these versions of 'EUCAST Expert Rules on Enterobacterales' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of NA (the default) for this argument will remove results for these three drugs, while e.g. a value of "R" will make the results for these drugs resistant. Use NULL or FALSE to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using TRUE is equal to using "R". For EUCAST Expert Rules v3.2, this rule applies to: Citrobacter braakii, Citrobacter freundii, Citrobacter gillenii, Citrobacter murliniae, Citrobacter rodenticum, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Enterobacter, Hafnia alvei, Klebsiella aerogenes, Morganella morganii, Providencia, and Serratia.
rules
"expert"
"all"
NA
version_expertrules
3.2
"R"
NULL
FALSE
TRUE
(only applies when rules contains "expert" or "all") a character value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is NA. Currently only works when version_expertrules is 3.2 and higher; these versions of 'EUCAST Expert Rules on Enterobacterales' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of NA (the default) for this argument will remove results for these three drugs, while e.g. a value of "R" will make the results for these drugs resistant. Use NULL or FALSE to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using TRUE is equal to using "R". For EUCAST Expert Rules v3.2, this rule applies to: Citrobacter braakii, Citrobacter freundii, Citrobacter gillenii, Citrobacter murliniae, Citrobacter rodenticum, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Enterobacter, Hafnia alvei, and Klebsiella aerogenes.