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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 old,
previously valid taxonomic names must be preserved and not be
corrected to currently accepted names. The default is `FALSE`, which
will return a note if old 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](https://rdrr.io/r/base/integer.html) in case of
`mo_year()`
- An [ordered factor](https://rdrr.io/r/base/factor.html) in case of
`mo_pathogenicity()`
- A [list](https://rdrr.io/r/base/list.html) in case of `mo_taxonomy()`,
`mo_synonyms()`, `mo_snomed()`, and `mo_info()`
- A [logical](https://rdrr.io/r/base/logical.html) 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](https://rdrr.io/r/base/character.html) in case of
`mo_synonyms()` and `mo_url()`
- A [character](https://rdrr.io/r/base/character.html) 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()`](https://amr-for-r.org/reference/as.mo.md) 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](https://rdrr.io/r/base/factor.html) 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](https://amr-for-r.org/reference/intrinsic_resistant.md)
data set, which is based on ['EUCAST Expected Resistant Phenotypes'
v1.2](https://www.eucast.org/expert_rules_and_expected_phenotypes)
(2023). 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](https://www.mycobank.org) will be
used for fungi wherever available , [this LPSN
URL](https://www.mycobank.org) for bacteria wherever available, and
[this GBIF link](https://www.gbif.org) otherwise.
SNOMED codes (`mo_snomed()`) was last updated on July 16th, 2024. See
*Source* and the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md) 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](https://rdrr.io/r/base/names.html)), the current taxonomic name
can be retrieved with `mo_current()`. Both functions return full names.
All output [will be
translated](https://amr-for-r.org/reference/translate.md) 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: Function `as.mo()` returned one old taxonomic name. Use `as.mo(...,
#> 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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