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# Get Properties of a Microorganism
Use these functions to return a specific property of a microorganism
based on the latest accepted taxonomy. All input values will be
evaluated internally with
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md), which makes it
possible to use microbial abbreviations, codes and names as input. See
*Examples*.
## Usage
``` r
mo_name(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_fullname(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_shortname(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_subspecies(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_species(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_genus(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_family(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_order(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_class(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_phylum(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_kingdom(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_domain(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_type(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_status(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_pathogenicity(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_gramstain(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_gram_negative(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_gram_positive(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_yeast(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_oxygen_tolerance(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_anaerobic(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_snomed(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_ref(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_authors(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_year(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_lpsn(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_mycobank(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_gbif(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_rank(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_taxonomy(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_synonyms(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_current(x, language = get_AMR_locale(), ...)
mo_group_members(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_info(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_url(x, open = FALSE, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_property(x, property = "fullname", language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
```
## Arguments
- x:
Any [character](https://rdrr.io/r/base/character.html) (vector) that
can be coerced to a valid microorganism code with
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md). Can be left
blank for auto-guessing the column containing microorganism codes if
used in a data set, see *Examples*.
- language:
Language to translate text like "no growth", which defaults to the
system language (see
[`get_AMR_locale()`](https://amr-for-r.org/reference/translate.md)).
- keep_synonyms:
A [logical](https://rdrr.io/r/base/logical.html) to indicate if
outdated, previously valid taxonomic names must be preserved and not
be corrected to currently accepted names. Do note that the term
"synonym" is in this case jargon from the field of microbial
taxonomy - it is not in place to denote that e.g. "Streptococcus Group
A" is a synonym of *S. pyogenes*. Though this is practically the case,
taxonomically it is not as "Streptococcus Group A" is not even a valid
taxonomic name.
The default is `FALSE`, which will return a note if outdated taxonomic
names were processed. The default can be set with the package option
[`AMR_keep_synonyms`](https://amr-for-r.org/reference/AMR-options.md),
i.e. `options(AMR_keep_synonyms = TRUE)` or
`options(AMR_keep_synonyms = FALSE)`.
- ...:
Other arguments passed on to
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md), such as
'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'.
- ab:
Any (vector of) text that can be coerced to a valid antibiotic drug
code with [`as.ab()`](https://amr-for-r.org/reference/as.ab.md).
- open:
Browse the URL using
[`browseURL()`](https://rdrr.io/r/utils/browseURL.html).
- property:
One of the column names of the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
data set: `"mo"`, `"fullname"`, `"status"`, `"kingdom"`, `"phylum"`,
`"class"`, `"order"`, `"family"`, `"genus"`, `"species"`,
`"subspecies"`, `"rank"`, `"ref"`, `"oxygen_tolerance"`, `"source"`,
`"lpsn"`, `"lpsn_parent"`, `"lpsn_renamed_to"`, `"mycobank"`,
`"mycobank_parent"`, `"mycobank_renamed_to"`, `"gbif"`,
`"gbif_parent"`, `"gbif_renamed_to"`, `"prevalence"`, or `"snomed"`,
or must be `"shortname"`.
## Value
\- An \[integer\] in case of \[mo_year()\] - An \[ordered
factor\]\[factor\] in case of \[mo_pathogenicity()\] - A \[list\] in
case of \[mo_taxonomy()\], \[mo_synonyms()\], \[mo_snomed()\], and
\[mo_info()\] - A \[logical\] in case of \[mo_is_anaerobic()\],
\[mo_is_gram_negative()\], \[mo_is_gram_positive()\],
\[mo_is_intrinsic_resistant()\], and \[mo_is_yeast()\] - A named
\[character\] in case of \[mo_synonyms()\] and \[mo_url()\] - A
\[character\] in all other cases
## Details
All functions will, at default, \*\*not\*\* keep old taxonomic
properties, as synonyms are automatically replaced with the current
taxonomy. Take for example \*Enterobacter aerogenes\*, which was
initially named in 1960 but renamed to \*Klebsiella aerogenes\* in
2017: - \`mo_genus("Enterobacter aerogenes")\` will return
\`"Klebsiella"\` (with a note about the renaming) -
\`mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
\`"Enterobacter"\` (with a once-per-session warning that the name is
outdated) - \`mo_ref("Enterobacter aerogenes")\` will return \`"Tindall
et al., 2017"\` (with a note about the renaming) -
\`mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
\`"Hormaeche et al., 1960"\` (with a once-per-session warning that the
name is outdated)
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 be
considered \*Escherichia coli\*. As a result,
\`mo_fullname(mo_shortname("Entamoeba coli"))\` returns \`"Escherichia
coli"\`.
Since the top-level of the taxonomy is sometimes referred to as
'kingdom' and sometimes as 'domain', the functions \[mo_kingdom()\] and
\[mo_domain()\] return the exact same results.
Determination of human pathogenicity (\[mo_pathogenicity()\]) is
strongly based on Bartlett \*et al.\* (2022,
[doi:10.1099/mic.0.001269](https://doi.org/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 (\[mo_gramstain()\]) will be based on
the taxonomic kingdom 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,
Firmicutes, and Tenericutes. These phyla were later renamed to
Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021,
\[PMID 34694987\](https://pubmed.ncbi.nlm.nih.gov/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 (\[mo_is_yeast()\]) will be 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 intrinsic resistance (\[mo_is_intrinsic_resistant()\])
will be based on the \[intrinsic_resistant\] data set, which is based on
\`r
format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES\[1\]))\`.
The \[mo_is_intrinsic_resistant()\] function can be vectorised over both
argument \`x\` (input for microorganisms) and \`ab\` (input for
antimicrobials).
Determination of bacterial oxygen tolerance (\[mo_oxygen_tolerance()\])
will be based on BacDive, see \*Source\*. The function
\[mo_is_anaerobic()\] only returns \`TRUE\` if the oxygen tolerance is
\`"anaerobe"\`, indicting an obligate anaerobic species or genus. It
always returns \`FALSE\` for species outside the taxonomic kingdom 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. \[This MycoBank URL\](\`r
TAXONOMY_VERSION\$MycoBank\$url\`) will be used for fungi wherever
available , \[this LPSN URL\](\`r TAXONOMY_VERSION\$MycoBank\$url\`) for
bacteria wherever available, and \[this GBIF link\](\`r
TAXONOMY_VERSION\$GBIF\$url\`) otherwise.
SNOMED codes (\[mo_snomed()\]) was last updated on \`r
documentation_date(TAXONOMY_VERSION\$SNOMED\$accessed_date)\`. 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
\[name\]\[base::names()\]), the current taxonomic name can be retrieved
with \[mo_current()\]. Both functions return full names.
All output \[will be translated\]\[translate\] where possible.
## Matching Score for Microorganisms
This function uses [`as.mo()`](https://amr-for-r.org/reference/as.mo.md)
internally, which uses an advanced algorithm to translate arbitrary user
input to valid taxonomy using a so-called matching score. You can read
about this public algorithm on the [MO matching score
page](https://amr-for-r.org/reference/mo_matching_score.md).
## Source
- Berends MS *et al.* (2022). **AMR: An R Package for Working with
Antimicrobial Resistance Data**. *Journal of Statistical Software*,
104(3), 1-31;
[doi:10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)
- Parte, AC *et al.* (2020). **List of Prokaryotic names with Standing
in Nomenclature (LPSN) moves to the DSMZ.** International Journal of
Systematic and Evolutionary Microbiology, 70, 5607-5612;
[doi:10.1099/ijsem.0.004332](https://doi.org/10.1099/ijsem.0.004332) .
Accessed from <https://lpsn.dsmz.de> on June 24th, 2024.
- Vincent, R *et al* (2013). **MycoBank gearing up for new horizons.**
IMA Fungus, 4(2), 371-9;
[doi:10.5598/imafungus.2013.04.02.16](https://doi.org/10.5598/imafungus.2013.04.02.16)
. Accessed from <https://www.mycobank.org> on June 24th, 2024.
- GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset
[doi:10.15468/39omei](https://doi.org/10.15468/39omei) . Accessed from
<https://www.gbif.org> on June 24th, 2024.
- Reimer, LC *et al.* (2022). ***BacDive* in 2022: the knowledge base
for standardized bacterial and archaeal data.** Nucleic Acids Res.,
50(D1):D741-D74;
[doi:10.1093/nar/gkab961](https://doi.org/10.1093/nar/gkab961) .
Accessed from <https://bacdive.dsmz.de> on July 16th, 2024.
- Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020.
Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).
URL: <https://www.cdc.gov/phin/php/phinvads/>
- Bartlett A *et al.* (2022). **A comprehensive list of bacterial
pathogens infecting humans** *Microbiology* 168:001269;
[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269)
## Download Our Reference Data
All reference data sets in the AMR package - including information on
microorganisms, antimicrobials, and clinical breakpoints - are freely
available for download in multiple formats: R, MS Excel, Apache Feather,
Apache Parquet, SPSS, and Stata.
For maximum compatibility, we also provide machine-readable,
tab-separated plain text files suitable for use in any software,
including laboratory information systems.
Visit [our website for direct download
links](https://amr-for-r.org/articles/datasets.html), or explore the
actual files in [our GitHub
repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
## See also
Data set
[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
## Examples
``` r
# taxonomic tree -----------------------------------------------------------
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_phylum("Klebsiella pneumoniae")
#> [1] "Pseudomonadota"
mo_class("Klebsiella pneumoniae")
#> [1] "Gammaproteobacteria"
mo_order("Klebsiella pneumoniae")
#> [1] "Enterobacterales"
mo_family("Klebsiella pneumoniae")
#> [1] "Enterobacteriaceae"
mo_genus("Klebsiella pneumoniae")
#> [1] "Klebsiella"
mo_species("Klebsiella pneumoniae")
#> [1] "pneumoniae"
mo_subspecies("Klebsiella pneumoniae")
#> [1] ""
# full names and short names -----------------------------------------------
mo_name("Klebsiella pneumoniae")
#> [1] "Klebsiella pneumoniae"
mo_fullname("Klebsiella pneumoniae")
#> [1] "Klebsiella pneumoniae"
mo_shortname("Klebsiella pneumoniae")
#> [1] "K. pneumoniae"
# other properties ---------------------------------------------------------
mo_pathogenicity("Klebsiella pneumoniae")
#> [1] Pathogenic
#> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown
mo_gramstain("Klebsiella pneumoniae")
#> [1] "Gram-negative"
mo_snomed("Klebsiella pneumoniae")
#> [[1]]
#> [1] "1098101000112102" "446870005" "1098201000112108" "409801009"
#> [5] "56415008" "714315002" "713926009"
#>
mo_type("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_rank("Klebsiella pneumoniae")
#> [1] "species"
mo_url("Klebsiella pneumoniae")
#> Klebsiella pneumoniae
#> "https://lpsn.dsmz.de/species/klebsiella-pneumoniae"
mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
#> [1] TRUE FALSE FALSE
mo_group_members(c(
"Streptococcus group A",
"Streptococcus group C",
"Streptococcus group G",
"Streptococcus group L"
))
#> $`Streptococcus Group A`
#> [1] "Streptococcus pyogenes"
#>
#> $`Streptococcus Group C`
#> [1] "Streptococcus dysgalactiae"
#> [2] "Streptococcus dysgalactiae dysgalactiae"
#> [3] "Streptococcus dysgalactiae equisimilis"
#> [4] "Streptococcus equi"
#> [5] "Streptococcus equi equi"
#> [6] "Streptococcus equi ruminatorum"
#> [7] "Streptococcus equi zooepidemicus"
#>
#> $`Streptococcus Group G`
#> [1] "Streptococcus canis"
#> [2] "Streptococcus dysgalactiae"
#> [3] "Streptococcus dysgalactiae dysgalactiae"
#> [4] "Streptococcus dysgalactiae equisimilis"
#>
#> $`Streptococcus Group L`
#> [1] "Streptococcus dysgalactiae"
#> [2] "Streptococcus dysgalactiae dysgalactiae"
#> [3] "Streptococcus dysgalactiae equisimilis"
#>
# scientific reference -----------------------------------------------------
mo_ref("Klebsiella aerogenes")
#> [1] "Tindall et al., 2017"
mo_authors("Klebsiella aerogenes")
#> [1] "Tindall et al."
mo_year("Klebsiella aerogenes")
#> [1] 2017
mo_synonyms("Klebsiella aerogenes")
#> Hormaeche et al., 1960 Bascomb et al., 1971
#> "Enterobacter aerogenes" "Klebsiella mobilis"
mo_lpsn("Klebsiella aerogenes")
#> [1] "777146"
mo_gbif("Klebsiella aerogenes")
#> [1] "9281703"
mo_mycobank("Candida albicans")
#> [1] "256187"
mo_mycobank("Candida krusei")
#> [1] "337013"
mo_mycobank("Candida krusei", keep_synonyms = TRUE)
#> Warning: `as.mo()` returned one outdated taxonomic name. Use `keep_synonyms = FALSE` to
#> clean the input to currently accepted taxonomic names, or set the R option
#> `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.
#> [1] "268707"
# abbreviations known in the field -----------------------------------------
mo_genus("MRSA")
#> [1] "Staphylococcus"
mo_species("MRSA")
#> [1] "aureus"
mo_shortname("VISA")
#> [1] "S. aureus"
mo_gramstain("VISA")
#> [1] "Gram-positive"
mo_genus("EHEC")
#> [1] "Escherichia"
mo_species("EIEC")
#> [1] "coli"
mo_name("UPEC")
#> [1] "Escherichia coli"
# known subspecies ---------------------------------------------------------
mo_fullname("K. pneu rh")
#> [1] "Klebsiella pneumoniae rhinoscleromatis"
mo_shortname("K. pneu rh")
#> [1] "K. pneumoniae"
# \donttest{
# Becker classification, see ?as.mo ----------------------------------------
mo_fullname("Staph epidermidis")
#> [1] "Staphylococcus epidermidis"
mo_fullname("Staph epidermidis", Becker = TRUE)
#> [1] "Coagulase-negative Staphylococcus (CoNS)"
mo_shortname("Staph epidermidis")
#> [1] "S. epidermidis"
mo_shortname("Staph epidermidis", Becker = TRUE)
#> [1] "CoNS"
# Lancefield classification, see ?as.mo ------------------------------------
mo_fullname("Strep agalactiae")
#> [1] "Streptococcus agalactiae"
mo_fullname("Strep agalactiae", Lancefield = TRUE)
#> [1] "Streptococcus Group B"
mo_shortname("Strep agalactiae")
#> [1] "S. agalactiae"
mo_shortname("Strep agalactiae", Lancefield = TRUE)
#> [1] "GBS"
# language support --------------------------------------------------------
mo_gramstain("Klebsiella pneumoniae", language = "de") # German
#> [1] "Gramnegativ"
mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
#> [1] "Gram-negatief"
mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
#> [1] "Gram negativo"
mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
#> [1] "Αρνητικό κατά Gram"
mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#> [1] "Грамнегативні"
# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
#> [1] "细菌"
mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
#> [1] "Streptococcus Gruppe A"
mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
#> [1] "Streptococcus Група A"
# other --------------------------------------------------------------------
# gram stains and intrinsic resistance can be used as a filter in dplyr verbs
if (require("dplyr")) {
example_isolates %>%
filter(mo_is_gram_positive()) %>%
count(mo_genus(), sort = TRUE)
}
#> ℹ Using column mo as input for `mo_is_gram_positive()`
#> ℹ Using column mo as input for `mo_genus()`
#> # A tibble: 18 × 2
#> `mo_genus()` n
#> <chr> <int>
#> 1 Staphylococcus 840
#> 2 Streptococcus 275
#> 3 Enterococcus 83
#> 4 Corynebacterium 17
#> 5 Micrococcus 6
#> 6 Gemella 3
#> 7 Aerococcus 2
#> 8 Cutibacterium 1
#> 9 Dermabacter 1
#> 10 Fusibacter 1
#> 11 Globicatella 1
#> 12 Granulicatella 1
#> 13 Lactobacillus 1
#> 14 Leuconostoc 1
#> 15 Listeria 1
#> 16 Paenibacillus 1
#> 17 Rothia 1
#> 18 Schaalia 1
if (require("dplyr")) {
example_isolates %>%
filter(mo_is_intrinsic_resistant(ab = "vanco")) %>%
count(mo_genus(), sort = TRUE)
}
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Using column mo as input for `mo_genus()`
#> # A tibble: 19 × 2
#> `mo_genus()` n
#> <chr> <int>
#> 1 Escherichia 467
#> 2 Klebsiella 77
#> 3 Proteus 39
#> 4 Pseudomonas 30
#> 5 Serratia 25
#> 6 Enterobacter 23
#> 7 Citrobacter 11
#> 8 Haemophilus 9
#> 9 Acinetobacter 6
#> 10 Morganella 6
#> 11 Pantoea 4
#> 12 Salmonella 3
#> 13 Neisseria 2
#> 14 Stenotrophomonas 2
#> 15 Campylobacter 1
#> 16 Enterococcus 1
#> 17 Hafnia 1
#> 18 Leuconostoc 1
#> 19 Pseudescherichia 1
# get a list with the complete taxonomy (from kingdom to subspecies)
mo_taxonomy("Klebsiella pneumoniae")
#> $kingdom
#> [1] "Bacteria"
#>
#> $phylum
#> [1] "Pseudomonadota"
#>
#> $class
#> [1] "Gammaproteobacteria"
#>
#> $order
#> [1] "Enterobacterales"
#>
#> $family
#> [1] "Enterobacteriaceae"
#>
#> $genus
#> [1] "Klebsiella"
#>
#> $species
#> [1] "pneumoniae"
#>
#> $subspecies
#> [1] ""
#>
# get a list with the taxonomy, the authors, Gram-stain,
# SNOMED codes, and URL to the online database
mo_info("Klebsiella pneumoniae")
#> $mo
#> [1] "B_KLBSL_PNMN"
#>
#> $rank
#> [1] "species"
#>
#> $kingdom
#> [1] "Bacteria"
#>
#> $phylum
#> [1] "Pseudomonadota"
#>
#> $class
#> [1] "Gammaproteobacteria"
#>
#> $order
#> [1] "Enterobacterales"
#>
#> $family
#> [1] "Enterobacteriaceae"
#>
#> $genus
#> [1] "Klebsiella"
#>
#> $species
#> [1] "pneumoniae"
#>
#> $subspecies
#> [1] ""
#>
#> $status
#> [1] "accepted"
#>
#> $synonyms
#> NULL
#>
#> $gramstain
#> [1] "Gram-negative"
#>
#> $oxygen_tolerance
#> [1] "facultative anaerobe"
#>
#> $url
#> [1] "https://lpsn.dsmz.de/species/klebsiella-pneumoniae"
#>
#> $ref
#> [1] "Trevisan, 1887"
#>
#> $snomed
#> [1] "1098101000112102" "446870005" "1098201000112108" "409801009"
#> [5] "56415008" "714315002" "713926009"
#>
#> $lpsn
#> [1] "777151"
#>
#> $mycobank
#> [1] NA
#>
#> $gbif
#> [1] "3221874"
#>
#> $group_members
#> character(0)
#>
# }
```
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