Details
-
This data set is currently based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
+
This data set is currently strictly follows 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). The
This data set is internally used by:
not_intrinsic_resistant() (an antimicrobial selector)
mo_is_intrinsic_resistant()
wisca() to model \(\beta(1, 9999)\) for resistant bug-drug combinations, per doi:10.1093/jac/dkv397
Examples
intrinsic_resistant
-#> # A tibble: 294,079 × 2
-#> mo ab
-#> <mo> <ab>
-#> 1 B_GRAMP ATM
-#> 2 B_GRAMP COL
-#> 3 B_GRAMP NAL
-#> 4 B_GRAMP PLB
-#> 5 B_GRAMP TEM
-#> 6 B_ANAER-POS ATM
-#> 7 B_ANAER-POS COL
-#> 8 B_ANAER-POS NAL
-#> 9 B_ANAER-POS PLB
-#> 10 B_ANAER-POS TEM
+#> # A tibble: 294,079 × 3
+#> mo ab version
+#> <mo> <ab> <chr>
+#> 1 B_GRAMP ATM 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 2 B_GRAMP COL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 3 B_GRAMP NAL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 4 B_GRAMP PLB 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 5 B_GRAMP TEM 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 6 B_ANAER-POS ATM 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 7 B_ANAER-POS COL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 8 B_ANAER-POS NAL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 9 B_ANAER-POS PLB 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 10 B_ANAER-POS TEM 'EUCAST Expected Resistant Phenotypes' v1.2
#> # ℹ 294,069 more rows
diff --git a/reference/intrinsic_resistant.md b/reference/intrinsic_resistant.md
index 8dedfbac7..7af29f388 100644
--- a/reference/intrinsic_resistant.md
+++ b/reference/intrinsic_resistant.md
@@ -15,7 +15,7 @@ intrinsic_resistant
## Format
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
-079 observations and 2 variables:
+079 observations and 3 variables:
- `mo`
Microorganism ID which occurs in
@@ -29,12 +29,15 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
Names can be retrieved using
[`ab_name()`](https://amr-for-r.org/reference/ab_property.md).
+- `version`
+ Guideline name and version.
+
## Details
-This data set is currently based on ['EUCAST Expected Resistant
+This data set is currently strictly follows ['EUCAST Expected Resistant
Phenotypes'
v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
-(2023).
+(2023). The
This data set is internally used by:
@@ -68,18 +71,18 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
intrinsic_resistant
-#> # A tibble: 294,079 × 2
-#> mo ab
-#>
-#> 1 B_GRAMP ATM
-#> 2 B_GRAMP COL
-#> 3 B_GRAMP NAL
-#> 4 B_GRAMP PLB
-#> 5 B_GRAMP TEM
-#> 6 B_ANAER-POS ATM
-#> 7 B_ANAER-POS COL
-#> 8 B_ANAER-POS NAL
-#> 9 B_ANAER-POS PLB
-#> 10 B_ANAER-POS TEM
+#> # A tibble: 294,079 × 3
+#> mo ab version
+#>
+#> 1 B_GRAMP ATM 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 2 B_GRAMP COL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 3 B_GRAMP NAL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 4 B_GRAMP PLB 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 5 B_GRAMP TEM 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 6 B_ANAER-POS ATM 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 7 B_ANAER-POS COL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 8 B_ANAER-POS NAL 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 9 B_ANAER-POS PLB 'EUCAST Expected Resistant Phenotypes' v1.2
+#> 10 B_ANAER-POS TEM 'EUCAST Expected Resistant Phenotypes' v1.2
#> # ℹ 294,069 more rows
```
diff --git a/reference/italicise_taxonomy.html b/reference/italicise_taxonomy.html
index 8a5f393e2..8a68f2165 100644
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@@ -7,7 +7,7 @@
AMR (for R)
- 3.0.1.9087
+ 3.0.1.9088
mo_ref() returns the abbreviated authority of the nomenclatural act that created the queried name combination. When keep_synonyms = FALSE (default), this is the authority of the currently accepted name. When keep_synonyms = TRUE, this is the authority under which the queried (possibly outdated) name was published. Emendations (changes to the species description without a name change) are not reflected; only the combination or original description authority is returned.
-
The short name (mo_shortname()) returns the first character of the genus and the full species, such as "E. coli", for species and subspecies. Exceptions are abbreviations of staphylococci (such as "CoNS", Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as "GBS", Group B Streptococci). Please bear in mind that e.g. E. coli could mean Escherichia coli (kingdom of Bacteria) as well as Entamoeba coli (kingdom of Protozoa). Returning to the full name will be done using as.mo() internally, giving priority to bacteria and human pathogens, i.e. "E. coli" will always be considered Escherichia coli. As a result, mo_fullname(mo_shortname("Entamoeba coli")) returns "Escherichia coli".
+
The short name (mo_shortname()) returns the first character of the genus and the full species, such as "E. coli", for species and subspecies. Exceptions are abbreviations of staphylococci (such as "CoNS", Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as "GBS", Group B Streptococci). Please bear in mind that e.g. E. coli could mean Escherichia coli (domain of Bacteria) as well as Entamoeba coli (domain of Protozoa). Returning to the full name will be done using as.mo() internally, giving priority to bacteria and human pathogens, i.e. "E. coli" will always be considered Escherichia coli. As a result, mo_fullname(mo_shortname("Entamoeba coli")) returns "Escherichia coli".
Following the formal introduction of the new kingdom rank into prokaryotic nomenclature in 2024 (doi:10.1099/ijsem.0.006242
), mo_kingdom() and mo_domain() return different results for bacteria and archaea: mo_kingdom() returns the new formal kingdom (e.g. "Pseudomonadati", "Bacillati"), while mo_domain() returns the new domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both functions return identical results.
Determination of human pathogenicity (mo_pathogenicity()) is strongly based on Bartlett et al. (2022, doi:10.1099/mic.0.001269
). This function returns a factor with the levels Pathogenic, Potentially pathogenic, Non-pathogenic, and Unknown.
-
Determination of the Gram stain (mo_gramstain() is based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, PMID 11837318), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, PMID 34694987). Bacteria in these phyla are considered Gram-positive in this AMR package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value NA. Functions mo_is_gram_negative() and mo_is_gram_positive() always return TRUE or FALSE (or NA when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.
-
Determination of yeasts (mo_is_yeast()) is based on the taxonomic kingdom and class. Budding yeasts are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. True yeasts quite specifically refers to yeasts in the underlying order Saccharomycetales (such as Saccharomyces cerevisiae). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return TRUE. It returns FALSE otherwise (or NA when the input is NA or the MO code is UNKNOWN).
+
Determination of the Gram stain (mo_gramstain() is based on the taxonomic domain and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, PMID 11837318), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, PMID 34694987). Bacteria in these phyla are considered Gram-positive in this AMR package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value NA. Functions mo_is_gram_negative() and mo_is_gram_positive() always return TRUE or FALSE (or NA when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.
+
Determination of yeasts (mo_is_yeast()) is based on the taxonomic domain and class. Budding yeasts are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. True yeasts quite specifically refers to yeasts in the underlying order Saccharomycetales (such as Saccharomyces cerevisiae). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return TRUE. It returns FALSE otherwise (or NA when the input is NA or the MO code is UNKNOWN).
Determination of intrinsic resistance (mo_is_intrinsic_resistant()) is based on the intrinsic_resistant data set, which is based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). The mo_is_intrinsic_resistant() function can be vectorised over both argument x (input for microorganisms) and ab (input for antimicrobials).
-
Determination of both bacterial oxygen tolerance (mo_oxygen_tolerance()) and morphology (mo_morphology()) are based on BacDive, see Source. The function mo_is_anaerobic() only returns TRUE if the oxygen tolerance is "anaerobe", indicating an obligate anaerobic species or genus. It always returns FALSE for species outside the taxonomic kingdom of Bacteria.
+
Determination of both bacterial oxygen tolerance (mo_oxygen_tolerance()) and morphology (mo_morphology()) are based on BacDive, see Source. The function mo_is_anaerobic() only returns TRUE if the oxygen tolerance is "anaerobe", indicating an obligate anaerobic species or genus. It always returns FALSE for species outside the taxonomic domain of Bacteria.
The function mo_url() will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. This MycoBank URL is used for fungi wherever available , this LPSN URL for bacteria wherever available, and this GBIF link otherwise.
SNOMED codes (mo_snomed()) was last updated on 16th of July, 2024. See Source and the microorganisms data set for more info.
Old taxonomic names (so-called 'synonyms') can be retrieved with mo_synonyms() (which will have the scientific reference as name), the current taxonomic name can be retrieved with mo_current(). Both functions return full names.
diff --git a/reference/mo_property.md b/reference/mo_property.md
index d329ad3e7..ff83b3a3c 100644
--- a/reference/mo_property.md
+++ b/reference/mo_property.md
@@ -400,9 +400,9 @@ genus and the full species, such as `"E. coli"`, for species and
subspecies. Exceptions are abbreviations of staphylococci (such as
*"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic
streptococci (such as *"GBS"*, Group B Streptococci). Please bear in
-mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of
-Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning
-to the full name will be done using
+mind that e.g. *E. coli* could mean *Escherichia coli* (domain of
+Bacteria) as well as *Entamoeba coli* (domain of Protozoa). Returning to
+the full name will be done using
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, giving
priority to bacteria and human pathogens, i.e. `"E. coli"` will always
be considered *Escherichia coli*. As a result,
@@ -426,7 +426,7 @@ function returns a
*Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.
Determination of the Gram stain (`mo_gramstain()` is based on the
-taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
+taxonomic domain and phylum. Originally, Cavalier-Smith defined the
so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID
11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
considered these phyla as Posibacteria: Actinobacteria, Chloroflexi,
@@ -443,7 +443,7 @@ is `UNKNOWN`), thus always return `FALSE` for species outside the
taxonomic kingdom of Bacteria.
Determination of yeasts (`mo_is_yeast()`) is based on the taxonomic
-kingdom and class. *Budding yeasts* are yeasts that reproduce asexually
+domain and class. *Budding yeasts* are yeasts that reproduce asexually
through a process called budding, where a new cell develops from a small
protrusion on the parent cell. Taxonomically, these are members of the
phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes)
@@ -468,7 +468,7 @@ Determination of both bacterial oxygen tolerance
on BacDive, see *Source*. The function `mo_is_anaerobic()` only returns
`TRUE` if the oxygen tolerance is `"anaerobe"`, indicating an obligate
anaerobic species or genus. It always returns `FALSE` for species
-outside the taxonomic kingdom of Bacteria.
+outside the taxonomic domain of Bacteria.
The function `mo_url()` will return the direct URL to the online
database entry, which also shows the scientific reference of the
diff --git a/reference/mo_source.html b/reference/mo_source.html
index 9da576eb7..2232eff22 100644
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
AMR (for R)
-
3.0.1.9087
+
3.0.1.9088