P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 21:22:01 +02:00
Code Releases Activity

Updated mo_gramstain() to reflect current taxonomy, fixes #83

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-12-09 10:30:25 +01:00
parent 6017f81e74
commit 510140fc55
5 changed files with 51 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
R/mo_property.R
View File

@ -45,9 +45,9 @@
#'
#' 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](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all 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.
#' The Gram stain - [mo_gramstain()] - will be determined 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. All of these phyla were 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 fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`).
#' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`).
#'
#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
#'
@ -400,13 +400,17 @@ mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
# overwrite these 4 phyla with Gram-positives
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002)
x[(mo_phylum(x.mo, language = NULL, keep_synonyms = keep_synonyms) %in% c(
# no longer in use, does not hurt to keep here:
"Actinobacteria",
"Chloroflexi",
"Firmicutes",
"Tenericutes",
"Bacillota" # this one is new! It was renamed from Firmicutes by Gibbons et al., 2021
"Actinomycetota", # since 2021, old name was Actinobacteria
"Chloroflexota", # since 2021, old name was Chloroflexi
"Bacillota", # since 2021, old name was Firmicutes
"Mycoplasmatota" # since 2021, old name was Tenericutes
) &
# but class Negativicutes (of phylum Firmicutes) are Gram-negative!
# but class Negativicutes (of phylum Bacillota) are Gram-negative!
mo_class(x.mo, language = NULL, keep_synonyms = keep_synonyms) != "Negativicutes")
# and of course our own ID for Gram-positives
| x.mo == "B_GRAMP"] <- "Gram-positive"