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(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples.

mo_name(x, language = get_locale(), ...)

mo_fullname(x, language = get_locale(), ...)

mo_shortname(x, language = get_locale(), ...)

mo_subspecies(x, language = get_locale(), ...)

mo_species(x, language = get_locale(), ...)

mo_genus(x, language = get_locale(), ...)

mo_family(x, language = get_locale(), ...)

mo_order(x, language = get_locale(), ...)

mo_class(x, language = get_locale(), ...)

mo_phylum(x, language = get_locale(), ...)

mo_kingdom(x, language = get_locale(), ...)

mo_domain(x, language = get_locale(), ...)

mo_type(x, language = get_locale(), ...)

mo_gramstain(x, language = get_locale(), ...)

mo_is_gram_negative(x, language = get_locale(), ...)

mo_is_gram_positive(x, language = get_locale(), ...)

mo_is_intrinsic_resistant(x, ab, language = get_locale(), ...)

mo_snomed(x, language = get_locale(), ...)

mo_ref(x, language = get_locale(), ...)

mo_authors(x, language = get_locale(), ...)

mo_year(x, language = get_locale(), ...)

mo_rank(x, language = get_locale(), ...)

mo_taxonomy(x, language = get_locale(), ...)

mo_synonyms(x, language = get_locale(), ...)

mo_info(x, language = get_locale(), ...)

mo_url(x, open = FALSE, language = get_locale(), ...)

mo_property(x, property = "fullname", language = get_locale(), ...)

Arguments

x	any character (vector) that can be coerced to a valid microorganism code with `as.mo()`. Can be omitted for auto-guessing in `mo_is_()` functions when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`, please see Examples*.
language	language of the returned text, defaults to system language (see `get_locale()`) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see translate. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
...	other parameters passed on to `as.mo()`, such as 'allow_uncertain' and 'ignore_pattern'
ab	any (vector of) text that can be coerced to a valid antibiotic code with `as.ab()`
open	browse the URL using `utils::browseURL()`
property	one of the column names of the microorganisms data set: "`mo`", "`fullname`", "`kingdom`", "`phylum`", "`class`", "`order`", "`family`", "`genus`", "`species`", "`subspecies`", "`rank`", "`ref`", "`species_id`", "`source`", "`prevalence`", "`snomed`", or must be `"shortname"`

Value

An integer in case of mo_year()
A list in case of mo_taxonomy() and mo_info()
A named character in case of mo_url()
A double in case of mo_snomed()
A character in all other cases

Details

All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for mo_ref(), mo_authors() and mo_year(). Please refer to this example, knowing that Escherichia blattae was renamed to Shimwellia blattae in 2010:

mo_name("Escherichia blattae") will return "Shimwellia blattae" (with a message about the renaming)
mo_ref("Escherichia blattae") will return "Burgess et al., 1973" (with a message about the renaming)
mo_ref("Shimwellia blattae") will return "Priest et al., 2010" (without a message)

The short name - mo_shortname() - almost always returns the first character of the genus and the full species, like "E. coli". 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. In other words, 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.

The Gram stain - mo_gramstain() - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, PMID 11837318), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - 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 (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.

Intrinsic resistance - mo_is_intrinsic_resistant() - will be determined based on the intrinsic_resistant data set, which is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 from 2020. The mo_is_intrinsic_resistant() can be vectorised over parameters x (input for microorganisms) and over ab (input for antibiotics).

All output will be translated where possible.

The function mo_url() will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.

Stable lifecycle

The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

Matching score for microorganisms

With ambiguous user input in as.mo() and all the mo_* functions, the returned results are chosen based on their matching score using mo_matching_score(). This matching score $m$, is calculated as:

$$m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}$$

where:

$x$ is the user input;
$n$ is a taxonomic name (genus, species, and subspecies);
$l_n$ is the length of $n$;
lev is the Levenshtein distance function, which counts any insertion, deletion and substitution as 1 that is needed to change $x$ into $n$;
$p_n$ is the human pathogenic prevalence group of $n$, as described below;
$k_n$ is the taxonomic kingdom of $n$, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.

The grouping into human pathogenic prevalence ($p$) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is Enterococcus, Staphylococcus or Streptococcus. This group consequently contains all common Gram-negative bacteria, such as Pseudomonas and Legionella and all species within the order Enterobacterales. Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is Absidia, Acremonium, Actinotignum, Alternaria, Anaerosalibacter, Apophysomyces, Arachnia, Aspergillus, Aureobacterium, Aureobasidium, Bacteroides, Basidiobolus, Beauveria, Blastocystis, Branhamella, Calymmatobacterium, Candida, Capnocytophaga, Catabacter, Chaetomium, Chryseobacterium, Chryseomonas, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Cryptococcus, Curvularia, Exophiala, Exserohilum, Flavobacterium, Fonsecaea, Fusarium, Fusobacterium, Hendersonula, Hypomyces, Koserella, Lelliottia, Leptosphaeria, Leptotrichia, Malassezia, Malbranchea, Mortierella, Mucor, Mycocentrospora, Mycoplasma, Nectria, Ochroconis, Oidiodendron, Phoma, Piedraia, Pithomyces, Pityrosporum, Prevotella,\Pseudallescheria, Rhizomucor, Rhizopus, Rhodotorula, Scolecobasidium, Scopulariopsis, Scytalidium,Sporobolomyces, Stachybotrys, Stomatococcus, Treponema, Trichoderma, Trichophyton, Trichosporon, Tritirachium or Ureaplasma. Group 3 consists of all other microorganisms.

All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., "E. coli" will return the microbial ID of Escherichia coli ($m = 0.688$, a highly prevalent microorganism found in humans) and not Entamoeba coli ($m = 0.079$, a less prevalent microorganism in humans), although the latter would alphabetically come first.

Catalogue of Life

This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, http://www.catalogueoflife.org). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, lpsn.dsmz.de). This supplementation is needed until the CoL+ project is finished, which we await.

Click here for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with catalogue_of_life_version().

Source

Becker K et al. Coagulase-Negative Staphylococci. 2014. Clin Microbiol Rev. 27(4): 870–926. https://dx.doi.org/10.1128/CMR.00109-13
Becker K et al. Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS). 2019. Clin Microbiol Infect. https://doi.org/10.1016/j.cmi.2019.02.028
Becker K et al. Emergence of coagulase-negative staphylococci 2020. Expert Rev Anti Infect Ther. 18(4):349-366. https://dx.doi.org/10.1080/14787210.2020.1730813
Lancefield RC A serological differentiation of human and other groups of hemolytic streptococci. 1933. J Exp Med. 57(4): 571–95. https://dx.doi.org/10.1084/jem.57.4.571
Catalogue of Life: Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org (check included annual version with catalogue_of_life_version()).

Reference data publicly available

All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.

Examples

# taxonomic tree -----------------------------------------------------------
mo_kingdom("E. coli")         # "Bacteria"
mo_phylum("E. coli")          # "Proteobacteria"
mo_class("E. coli")           # "Gammaproteobacteria"
mo_order("E. coli")           # "Enterobacterales"
mo_family("E. coli")          # "Enterobacteriaceae"
mo_genus("E. coli")           # "Escherichia"
mo_species("E. coli")         # "coli"
mo_subspecies("E. coli")      # ""

# colloquial properties ----------------------------------------------------
mo_name("E. coli")            # "Escherichia coli"
mo_fullname("E. coli")        # "Escherichia coli" - same as mo_name()
mo_shortname("E. coli")       # "E. coli"

# other properties ---------------------------------------------------------
mo_gramstain("E. coli")       # "Gram-negative"
mo_snomed("E. coli")          # 112283007, 116395006, ... (SNOMED codes)
mo_type("E. coli")            # "Bacteria" (equal to kingdom, but may be translated)
mo_rank("E. coli")            # "species"
mo_url("E. coli")             # get the direct url to the online database entry
mo_synonyms("E. coli")        # get previously accepted taxonomic names

# scientific reference -----------------------------------------------------
mo_ref("E. coli")             # "Castellani et al., 1919"
mo_authors("E. coli")         # "Castellani et al."
mo_year("E. coli")            # 1919

# abbreviations known in the field -----------------------------------------
mo_genus("MRSA")              # "Staphylococcus"
mo_species("MRSA")            # "aureus"
mo_shortname("VISA")          # "S. aureus"
mo_gramstain("VISA")          # "Gram-positive"

mo_genus("EHEC")              # "Escherichia"
mo_species("EHEC")            # "coli"

# known subspecies ---------------------------------------------------------
mo_name("doylei")             # "Campylobacter jejuni doylei"
mo_genus("doylei")            # "Campylobacter"
mo_species("doylei")          # "jejuni"
mo_subspecies("doylei")       # "doylei"

mo_fullname("K. pneu rh")     # "Klebsiella pneumoniae rhinoscleromatis"
mo_shortname("K. pneu rh")    # "K. pneumoniae"

# \donttest{
# Becker classification, see ?as.mo ----------------------------------------
mo_fullname("S. epi")                     # "Staphylococcus epidermidis"
mo_fullname("S. epi", Becker = TRUE)      # "Coagulase-negative Staphylococcus (CoNS)"
mo_shortname("S. epi")                    # "S. epidermidis"
mo_shortname("S. epi", Becker = TRUE)     # "CoNS"

# Lancefield classification, see ?as.mo ------------------------------------
mo_fullname("S. pyo")                     # "Streptococcus pyogenes"
mo_fullname("S. pyo", Lancefield = TRUE)  # "Streptococcus group A"
mo_shortname("S. pyo")                    # "S. pyogenes"
mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" (='Group A Streptococci')


# language support  --------------------------------------------------------
mo_gramstain("E. coli", language = "de")  # "Gramnegativ"
mo_gramstain("E. coli", language = "nl")  # "Gram-negatief"
mo_gramstain("E. coli", language = "es")  # "Gram negativo"

# mo_type is equal to mo_kingdom, but mo_kingdom will remain official
mo_kingdom("E. coli")                     # "Bacteria" on a German system
mo_type("E. coli")                        # "Bakterien" on a German system
mo_type("E. coli")                        # "Bacteria" on an English system

mo_fullname("S. pyogenes",
            Lancefield = TRUE,
            language = "de")              # "Streptococcus Gruppe A"
mo_fullname("S. pyogenes",
            Lancefield = TRUE,
            language = "nl")              # "Streptococcus groep A"


# other --------------------------------------------------------------------

# gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
if (require("dplyr")) {
  example_isolates %>%
    filter(mo_is_gram_positive())
    
  example_isolates %>%
    filter(mo_is_intrinsic_resistant(ab = "vanco"))
}


# get a list with the complete taxonomy (from kingdom to subspecies)
mo_taxonomy("E. coli")
# get a list with the taxonomy, the authors, Gram-stain and URL to the online database
mo_info("E. coli")
# }