Merge remote-tracking branch 'origin/main' into breakpoints

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.1.0.9015
-Date: 2026-11-03
+Version: 3.1.0.9016
+Date: 2026-11-04
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.1.0.9015
+# AMR 3.1.0.9016
 
 This version fixes a critical bug in WISCA that biased all coverage estimates of `wisca()` and `antibiogram(..., wisca = TRUE)` downwards since AMR 3.0.0. Users are strongly advised to re-run their WISCA analyses.
 
@@ -11,6 +11,9 @@ It also adds a `site` argument to `as.sir()`, stores EUCAST MIC breakpoints exac
 * EUCAST breakpoints of *Vibrio* now apply only to the species that EUCAST states: *V. alginolyticus*, *V. cholerae*, *V. fluvialis*, *V. parahaemolyticus* and *V. vulnificus*. Other species and isolates identified at genus level now give `NA`, or use PK/PD breakpoints in EUCAST 2022-2023
 * With unknown `uti`, a blocking row without UTI status no longer overrides a UTI breakpoint at the same taxonomic level, e.g., amikacin in *Acinetobacter* now gives S or R instead of `NA`, which is noted in `sir_interpretation_history()`. Use `uti = FALSE` to prevent this
 * If several breakpoints fit and no `site` is set, `as.sir()` now takes the one for the most systemic site, instead of the first one in the data set. This means, e.g., that a meningitis breakpoint now precedes a non-meningitis breakpoint, such as for benzylpenicillin in *S. pneumoniae*. Use `site` to choose another one
+* `mo_shortname()` now returns the serovar for *Salmonella* serovars, e.g., `"S. Typhi"` and `"S. Goldcoast"` instead of `"S. enterica"`. As this is the default for `bug_drug_combinations()` and short names in `antibiogram()`, serovars are no longer merged in their results. Use `FUN = function(x) paste(mo_genus(x), mo_species(x))` in `bug_drug_combinations()` to group them by species (#341)
+* `mo_shortname()` now returns e.g. `"S. Group B"` for *Salmonella* groups instead of the abbreviations of streptococci, such as `"GBS"`, so that they are no longer merged with streptococci in `bug_drug_combinations()` and `antibiogram()`. *Streptococcus* groups E, I, J and L are now also abbreviated, e.g., `"GES"`, and `"B_STRPT_ABCG"` now returns `"S. Group A, B, C, G"` instead of the malformed `"GA, B, C, GS"` (#341)
+* `mdro()` now applies the rule for *Salmonella* Typhi in the EUCAST guidelines, i.e., resistance to carbapenems (and fluoroquinolones in `"EUCAST3.1"`). This rule never applied before, so these isolates were wrongly classified as negative (#341)
 
 ### New
 * **Site of infection**

R/mdro.R

@@ -1156,7 +1156,7 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      which(x$genus == "Salmonella" & x$species == "Typhi"),
+      which(x$genus == "Salmonella" & x$subspecies == "Typhi"),
       c(carbapenems, fluoroquinolones),
       "any"
     )
@@ -1251,7 +1251,7 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      which(x$genus == "Salmonella" & x$species == "Typhi"),
+      which(x$genus == "Salmonella" & x$subspecies == "Typhi"),
       c(carbapenems),
       "any"
     )
@@ -1353,7 +1353,7 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      which(x$genus == "Salmonella" & x$species == "Typhi"),
+      which(x$genus == "Salmonella" & x$subspecies == "Typhi"),
       c(carbapenems),
       "any"
     )

R/mo_property.R

@@ -44,7 +44,7 @@
 #'
 #' [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* (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"`.
+#' 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 *Salmonella* serovars, which return the serovar (such as `"S. Typhi"`), and 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.
 #'
@@ -262,13 +262,19 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
   genera <- mo_genus(x.mo, language = NULL, keep_synonyms = keep_synonyms, ...)
   shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL, keep_synonyms = keep_synonyms, ...)))
 
+  # exceptions for Salmonella serovars, that are stored as subspecies of S. enterica: return e.g. "S. Typhi"
+  subspecies <- mo_subspecies(x.mo, language = NULL, keep_synonyms = keep_synonyms, ...)
+  serovars <- which(genera == "Salmonella" & subspecies %like_case% "^[A-Z]")
+  shortnames[serovars] <- paste0("S. ", subspecies[serovars])
+
   # exceptions for where no species is known
   shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"]
   # exceptions for staphylococci
   shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
   shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
   # exceptions for streptococci: Group A Streptococcus -> GAS
-  shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"] <- paste0("G", gsub("S. Group ([ABCDFGHK])", "\\1", shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"], perl = TRUE), "S")
+  streptococci_groups <- which(genera == "Streptococcus" & shortnames %like_case% "^S[.] Group [A-L]$")
+  shortnames[streptococci_groups] <- paste0("G", gsub("S. Group ([A-L])", "\\1", shortnames[streptococci_groups], perl = TRUE), "S")
   # unknown species etc.
   shortnames[shortnames %like% "unknown"] <- paste0("(", trimws2(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
 

man/mo_property.Rd

@@ -349,7 +349,7 @@ All functions will, at default, \strong{not} keep old taxonomic properties, as s
 
 \code{\link[=mo_ref]{mo_ref()}} returns the abbreviated authority of the nomenclatural act that created the queried name combination. When \code{keep_synonyms = FALSE} (default), this is the authority of the currently accepted name. When \code{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 (\code{\link[=mo_shortname]{mo_shortname()}}) returns the first character of the genus and the full species, such as \code{"E. coli"}, for species and subspecies. Exceptions are abbreviations of staphylococci (such as \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (domain of Bacteria) as well as \emph{Entamoeba coli} (domain of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will always be considered \emph{Escherichia coli}. As a result, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
+The short name (\code{\link[=mo_shortname]{mo_shortname()}}) returns the first character of the genus and the full species, such as \code{"E. coli"}, for species and subspecies. Exceptions are \emph{Salmonella} serovars, which return the serovar (such as \code{"S. Typhi"}), and abbreviations of staphylococci (such as \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (domain of Bacteria) as well as \emph{Entamoeba coli} (domain of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will always be considered \emph{Escherichia coli}. As a result, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
 
 Following the formal introduction of the new kingdom rank into prokaryotic nomenclature in 2024 (\doi{10.1099/ijsem.0.006242}), \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return different results for bacteria and archaea: \code{\link[=mo_kingdom]{mo_kingdom()}} returns the new formal kingdom (e.g. "Pseudomonadati", "Bacillati"), while \code{\link[=mo_domain]{mo_domain()}} returns the new domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both functions return identical results.
 

tests/testthat/test-mdro.R

@@ -56,6 +56,27 @@ test_that("test-mdro.R", {
     mdro(example_isolates, guideline = "BRMO", info = FALSE)
   )
 
+  # test EUCAST rule for Salmonella Typhi, which is stored as subspecies of S. enterica
+  typhi <- data.frame(
+    mo = as.mo(rep("Salmonella Typhi", 2)),
+    CIP = as.sir(c("R", "S")),
+    IPM = as.sir(c("S", "S")),
+    MEM = as.sir(c("S", "S")),
+    AMX = as.sir(c("S", "S"))
+  )
+  expect_equal(
+    as.character(suppressWarnings(mdro(typhi, guideline = "EUCAST3.1", col_mo = "mo", info = FALSE))),
+    c("Positive", "Negative")
+  )
+  typhi$CIP <- as.sir(c("S", "S"))
+  typhi$MEM <- as.sir(c("R", "S"))
+  for (gl in c("EUCAST3.2", "EUCAST3.3")) {
+    expect_equal(
+      as.character(suppressWarnings(mdro(typhi, guideline = gl, col_mo = "mo", info = FALSE))),
+      c("Positive", "Negative")
+    )
+  }
+
   # test Dutch P. aeruginosa MDRO
   expect_equal(
     as.character(mdro(

tests/testthat/test-mo_property.R

@@ -45,6 +45,25 @@ test_that("test-mo_property.R", {
   expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
   expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
   expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
+  # Salmonella serovars return the serovar, and all stay distinct
+  expect_equal(
+    mo_shortname(c("Salmonella Typhi", "Salmonella Goldcoast", "Salmonella Paratyphi A", "Salmonella enterica", "Salmonella enterica enterica", NA), language = NULL),
+    c("S. Typhi", "S. Goldcoast", "S. Paratyphi A", "S. enterica", "S. enterica", NA)
+  )
+  # Salmonella groups must not be abbreviated as streptococci
+  expect_equal(
+    mo_shortname(c("Salmonella group B", "Streptococcus group B"), language = NULL),
+    c("S. Group B", "GBS")
+  )
+  # all Lancefield groups are abbreviated, also when they share a letter with a Salmonella group
+  expect_equal(
+    mo_shortname(paste0("B_STRPT_GRP", LETTERS[1:12]), language = NULL),
+    paste0("G", LETTERS[1:12], "S")
+  )
+  expect_equal(mo_shortname("B_SLMNL_GRPE", language = NULL), "S. Group E")
+  expect_equal(mo_shortname("B_STRPT_ABCG", language = NULL), "S. Group A, B, C, G")
+  serovars <- microorganisms$mo[microorganisms$genus == "Salmonella" & microorganisms$subspecies %like_case% "^[A-Z]" & microorganisms$status == "accepted"]
+  expect_false(anyDuplicated(mo_shortname(serovars, language = NULL)) > 0)
 
   # check gram stain determination, to prevent we lag after a taxonomic renaming
   current_grampos_phyla <- c(