(v3.1.0.9013) Add species groups and complexes to the intrinsic_resistant data set for every antimicrobial to which all their species are intrinsically resistant (fixes #338)

2026-11-16 00:10:57 +01:00 · 2026-10-30 13:37:25 +01:00
1 parent aab0fcc479
commit 7f3c75ece7
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.1.0.9012
+Version: 3.1.0.9013
 Date: 2026-10-30
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@@ -1,4 +1,4 @@
-# AMR 3.1.0.9012
+# AMR 3.1.0.9013

 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.

@@ -9,6 +9,8 @@ This version fixes a critical bug in WISCA that biased all coverage estimates of
  * A new warning is given when the prior weight of 1 per pathogen (Bielicki *et al.*, 2016) accounts for more than 5% of the pathogen incidence, i.e., with rare pathogens or small groups, as this can strongly lower the estimated coverage; consider `top_n_microorganisms()` or fewer and larger groups in that case
 * Microorganism coercion (`as.mo()`)
  * Fixed the misaligned arrows in the message on taxonomically renamed microorganisms in colour-supporting consoles, for old names whose author reference lacks "*et al.*" (#336)
+* `intrinsic_resistant` data set
+  * Species groups and complexes are now listed for every antimicrobial to which all their species are intrinsically resistant. This adds 62 bug-drug combinations for the *Burkholderia cepacia* complex, coryneform bacteria, the *Enterobacter cloacae* complex (e.g., amoxicillin and amoxicillin/clavulanic acid), the *Klebsiella pneumoniae* complex, and coagulase-negative staphylococci, which affects `mo_is_intrinsic_resistant()`, `not_intrinsic_resistant()`, and the priors of `wisca()` (#338)

 ### Other
 * The manual index on the website was rewritten to improve findability, with sections ordered by task and a filter field
@@ -58,6 +58,23 @@ int_resis3 <- int_resis2[which(!int_resis2$ab %in% untreatable), ]
 int_resis3$ab <- as.ab(int_resis3$ab)
 int_resis3

+# add species groups (e.g., complexes) for every antimicrobial to which all their species are intrinsically resistant (#338)
+groups <- microorganisms.groups[which(microorganisms$rank[match(microorganisms.groups$mo, microorganisms$mo)] == "species"), , drop = FALSE]
+int_resis_keys <- paste(int_resis3$mo, int_resis3$ab)
+groups_species <- split(as.character(groups$mo), as.character(groups$mo_group))
+int_resis_groups <- do.call(rbind, Map(function(group, species) {
+  abx <- unique(as.character(int_resis3$ab[int_resis3$mo %in% species]))
+  abx <- abx[vapply(abx, function(ab) all(paste(species, ab) %in% int_resis_keys), logical(1))]
+  data.frame(mo = rep(group, length(abx)), ab = abx, stringsAsFactors = FALSE)
+}, names(groups_species), groups_species))
+int_resis_groups <- int_resis_groups[which(!paste(int_resis_groups$mo, int_resis_groups$ab) %in% int_resis_keys), , drop = FALSE]
+int_resis_groups$mo <- as.mo(int_resis_groups$mo, keep_synonyms = TRUE)
+int_resis_groups$ab <- as.ab(int_resis_groups$ab)
+int_resis3 <- bind_rows(int_resis3, int_resis_groups)
+# keep the order of the microorganisms and antimicrobials data sets
+int_resis3 <- int_resis3[order(match(int_resis3$mo, microorganisms$mo), match(int_resis3$ab, antimicrobials$ab)), , drop = FALSE]
+rownames(int_resis3) <- NULL
+
 all(int_resis3$mo %in% microorganisms$mo)
 all(int_resis3$ab %in% antimicrobials$ab)

@@ -31323,8 +31323,19 @@
 "Burkholderia cepacia"	"Zorbamycin"
 "Burkholderia cepacia complex"	"Acetylmidecamycin"
 "Burkholderia cepacia complex"	"Acetylspiramycin"
+"Burkholderia cepacia complex"	"Amikacin"
+"Burkholderia cepacia complex"	"Amikacin/fosfomycin"
+"Burkholderia cepacia complex"	"Amoxicillin"
+"Burkholderia cepacia complex"	"Amoxicillin/clavulanic acid"
+"Burkholderia cepacia complex"	"Ampicillin"
+"Burkholderia cepacia complex"	"Ampicillin/sulbactam"
+"Burkholderia cepacia complex"	"Apramycin"
+"Burkholderia cepacia complex"	"Arbekacin"
+"Burkholderia cepacia complex"	"Astromicin"
 "Burkholderia cepacia complex"	"Avoparcin"
 "Burkholderia cepacia complex"	"Azithromycin"
+"Burkholderia cepacia complex"	"Aztreonam"
+"Burkholderia cepacia complex"	"Bekanamycin"
 "Burkholderia cepacia complex"	"Benzylpenicillin"
 "Burkholderia cepacia complex"	"Bleomycin"
 "Burkholderia cepacia complex"	"Cadazolid"
@@ -31342,54 +31353,87 @@
 "Burkholderia cepacia complex"	"Cefmetazole"
 "Burkholderia cepacia complex"	"Cefonicid"
 "Burkholderia cepacia complex"	"Ceforanide"
+"Burkholderia cepacia complex"	"Cefotaxime"
 "Burkholderia cepacia complex"	"Cefotetan"
 "Burkholderia cepacia complex"	"Cefotiam"
 "Burkholderia cepacia complex"	"Cefoxitin"
 "Burkholderia cepacia complex"	"Cefprozil"
 "Burkholderia cepacia complex"	"Cefroxadine"
 "Burkholderia cepacia complex"	"Ceftezole"
+"Burkholderia cepacia complex"	"Ceftriaxone"
 "Burkholderia cepacia complex"	"Cefuroxime"
 "Burkholderia cepacia complex"	"Cefuroxime axetil"
 "Burkholderia cepacia complex"	"Cephradine"
+"Burkholderia cepacia complex"	"Chloramphenicol"
+"Burkholderia cepacia complex"	"Ciprofloxacin"
 "Burkholderia cepacia complex"	"Clarithromycin"
 "Burkholderia cepacia complex"	"Clindamycin"
+"Burkholderia cepacia complex"	"Colistin"
 "Burkholderia cepacia complex"	"Cycloserine"
 "Burkholderia cepacia complex"	"Dalbavancin"
+"Burkholderia cepacia complex"	"Dibekacin"
 "Burkholderia cepacia complex"	"Dirithromycin"
+"Burkholderia cepacia complex"	"Ertapenem"
 "Burkholderia cepacia complex"	"Erythromycin"
 "Burkholderia cepacia complex"	"Flurithromycin"
+"Burkholderia cepacia complex"	"Fosfomycin"
+"Burkholderia cepacia complex"	"Framycetin"
 "Burkholderia cepacia complex"	"Fusidic acid"
 "Burkholderia cepacia complex"	"Gamithromycin"
+"Burkholderia cepacia complex"	"Gentamicin"
+"Burkholderia cepacia complex"	"Habekacin"
+"Burkholderia cepacia complex"	"Hygromycin"
+"Burkholderia cepacia complex"	"Isepamicin"
 "Burkholderia cepacia complex"	"Josamycin"
+"Burkholderia cepacia complex"	"Kanamycin"
+"Burkholderia cepacia complex"	"Kanamycin/cephalexin"
+"Burkholderia cepacia complex"	"Kasugamycin"
 "Burkholderia cepacia complex"	"Kitasamycin"
 "Burkholderia cepacia complex"	"Lincomycin"
 "Burkholderia cepacia complex"	"Linezolid"
 "Burkholderia cepacia complex"	"Loracarbef"
 "Burkholderia cepacia complex"	"Meleumycin"
+"Burkholderia cepacia complex"	"Micronomicin"
 "Burkholderia cepacia complex"	"Midecamycin"
 "Burkholderia cepacia complex"	"Miocamycin"
 "Burkholderia cepacia complex"	"Nafithromycin"
+"Burkholderia cepacia complex"	"Neomycin"
+"Burkholderia cepacia complex"	"Netilmicin"
 "Burkholderia cepacia complex"	"Norvancomycin"
 "Burkholderia cepacia complex"	"Oleandomycin"
 "Burkholderia cepacia complex"	"Oritavancin"
 "Burkholderia cepacia complex"	"Ostreogrycin"
+"Burkholderia cepacia complex"	"Pentisomicin"
+"Burkholderia cepacia complex"	"Piperacillin"
+"Burkholderia cepacia complex"	"Piperacillin/tazobactam"
 "Burkholderia cepacia complex"	"Pirlimycin"
+"Burkholderia cepacia complex"	"Plazomicin"
+"Burkholderia cepacia complex"	"Polymyxin B"
 "Burkholderia cepacia complex"	"Primycin"
 "Burkholderia cepacia complex"	"Pristinamycin"
+"Burkholderia cepacia complex"	"Propikacin"
 "Burkholderia cepacia complex"	"Quinupristin/dalfopristin"
 "Burkholderia cepacia complex"	"Ramoplanin"
+"Burkholderia cepacia complex"	"Ribostamycin"
 "Burkholderia cepacia complex"	"Rifampicin"
 "Burkholderia cepacia complex"	"Rokitamycin"
 "Burkholderia cepacia complex"	"Roxithromycin"
+"Burkholderia cepacia complex"	"Sisomicin"
 "Burkholderia cepacia complex"	"Solithromycin"
 "Burkholderia cepacia complex"	"Spiramycin"
+"Burkholderia cepacia complex"	"Streptoduocin"
+"Burkholderia cepacia complex"	"Streptomycin"
 "Burkholderia cepacia complex"	"Tedizolid"
 "Burkholderia cepacia complex"	"Teicoplanin"
 "Burkholderia cepacia complex"	"Telavancin"
 "Burkholderia cepacia complex"	"Telithromycin"
 "Burkholderia cepacia complex"	"Thiacetazone"
+"Burkholderia cepacia complex"	"Ticarcillin"
+"Burkholderia cepacia complex"	"Ticarcillin/clavulanic acid"
 "Burkholderia cepacia complex"	"Tildipirosin"
 "Burkholderia cepacia complex"	"Tilmicosin"
+"Burkholderia cepacia complex"	"Tobramycin"
+"Burkholderia cepacia complex"	"Trimethoprim"
 "Burkholderia cepacia complex"	"Troleandomycin"
 "Burkholderia cepacia complex"	"Tulathromycin"
 "Burkholderia cepacia complex"	"Tylosin"
@@ -65522,6 +65566,7 @@
 "Cnuibacter physcomitrellae"	"Polymyxin B"
 "Cnuibacter physcomitrellae"	"Temocillin"
 "Coagulase-negative Staphylococcus (CoNS)"	"Aztreonam"
+"Coagulase-negative Staphylococcus (CoNS)"	"Ceftazidime"
 "Coagulase-negative Staphylococcus (CoNS)"	"Colistin"
 "Coagulase-negative Staphylococcus (CoNS)"	"Nalidixic acid"
 "Coagulase-negative Staphylococcus (CoNS)"	"Polymyxin B"
@@ -67762,6 +67807,11 @@
 "Corynebacterium zhongnanshanii"	"Nalidixic acid"
 "Corynebacterium zhongnanshanii"	"Polymyxin B"
 "Corynebacterium zhongnanshanii"	"Temocillin"
+"Coryneform bacterium"	"Aztreonam"
+"Coryneform bacterium"	"Colistin"
+"Coryneform bacterium"	"Nalidixic acid"
+"Coryneform bacterium"	"Polymyxin B"
+"Coryneform bacterium"	"Temocillin"
 "Cosenzaea"	"Acetylmidecamycin"
 "Cosenzaea"	"Acetylspiramycin"
 "Cosenzaea"	"Avoparcin"
@@ -76494,11 +76544,20 @@
 "Enterobacter cloacae cloacae"	"Zorbamycin"
 "Enterobacter cloacae complex"	"Acetylmidecamycin"
 "Enterobacter cloacae complex"	"Acetylspiramycin"
+"Enterobacter cloacae complex"	"Amoxicillin"
+"Enterobacter cloacae complex"	"Amoxicillin/clavulanic acid"
+"Enterobacter cloacae complex"	"Ampicillin"
+"Enterobacter cloacae complex"	"Ampicillin/sulbactam"
 "Enterobacter cloacae complex"	"Avoparcin"
 "Enterobacter cloacae complex"	"Azithromycin"
 "Enterobacter cloacae complex"	"Benzylpenicillin"
 "Enterobacter cloacae complex"	"Bleomycin"
 "Enterobacter cloacae complex"	"Cadazolid"
+"Enterobacter cloacae complex"	"Cefadroxil"
+"Enterobacter cloacae complex"	"Cefalexin"
+"Enterobacter cloacae complex"	"Cefalotin"
+"Enterobacter cloacae complex"	"Cefazolin"
+"Enterobacter cloacae complex"	"Cefoxitin"
 "Enterobacter cloacae complex"	"Clarithromycin"
 "Enterobacter cloacae complex"	"Clindamycin"
 "Enterobacter cloacae complex"	"Cycloserine"
@@ -102515,6 +102574,8 @@
 "Klebsiella pneumoniae"	"Zorbamycin"
 "Klebsiella pneumoniae complex"	"Acetylmidecamycin"
 "Klebsiella pneumoniae complex"	"Acetylspiramycin"
+"Klebsiella pneumoniae complex"	"Amoxicillin"
+"Klebsiella pneumoniae complex"	"Ampicillin"
 "Klebsiella pneumoniae complex"	"Avoparcin"
 "Klebsiella pneumoniae complex"	"Azithromycin"
 "Klebsiella pneumoniae complex"	"Benzylpenicillin"
@@ -102556,6 +102617,7 @@
 "Klebsiella pneumoniae complex"	"Telavancin"
 "Klebsiella pneumoniae complex"	"Telithromycin"
 "Klebsiella pneumoniae complex"	"Thiacetazone"
+"Klebsiella pneumoniae complex"	"Ticarcillin"
 "Klebsiella pneumoniae complex"	"Tildipirosin"
 "Klebsiella pneumoniae complex"	"Tilmicosin"
 "Klebsiella pneumoniae complex"	"Troleandomycin"
@@ -1 +1 @@
-b32da210529081a8e0ab8874956739d1
+e17c4cf3ac9495a9ed832b64da96770a
@@ -5,7 +5,7 @@
 \alias{intrinsic_resistant}
 \title{Data Set Denoting Bacterial Intrinsic Resistance}
 \format{
-A \link[tibble:tibble]{tibble} with 307 684 observations and 3 variables:
+A \link[tibble:tibble]{tibble} with 307 746 observations and 3 variables:
 \itemize{
 \item \code{mo}\cr Microorganism ID which occurs in \code{\link[=microorganisms]{microorganisms$mo}}. Names can be retrieved using \code{\link[=mo_name]{mo_name()}}.
 \item \code{ab}\cr Antimicrobial ID which occurs in \code{\link[=antimicrobials]{antimicrobials$ab}}. Names can be retrieved using \code{\link[=ab_name]{ab_name()}}.
@@ -547,6 +547,25 @@ test_that("intrinsic_resistant: synonyms have exactly the resistances of their c
  expect_true(length(absent) == 0, info = paste("Current names missing while their synonym is listed:", describe_mo(absent)))
 })

+test_that("intrinsic_resistant: species groups have the resistances shared by all their species", {
+  skip_on_cran()
+  ir_keys <- paste(intrinsic_resistant$mo, intrinsic_resistant$ab)
+  groups <- microorganisms.groups[which(microorganisms$rank[match(microorganisms.groups$mo, microorganisms$mo)] == "species"), , drop = FALSE]
+  groups_species <- split(as.character(groups$mo), as.character(groups$mo_group))
+  missing <- unlist(Map(function(group, species) {
+    abx <- unique(as.character(intrinsic_resistant$ab[intrinsic_resistant$mo %in% species]))
+    abx <- abx[vapply(abx, function(ab) all(paste(species, ab) %in% ir_keys), logical(1))]
+    if (length(abx) == 0) {
+      return(NULL)
+    }
+    abx <- abx[!paste(group, abx) %in% ir_keys]
+    if (length(abx) > 0) paste0(group, " (", paste(abx, collapse = ", "), ")")
+  }, names(groups_species), groups_species), use.names = FALSE)
+  expect_true(length(missing) == 0, info = paste("Species groups missing resistances shared by all their species:", paste(missing, collapse = "; ")))
+  # Enterobacter cloacae complex (#338)
+  expect_true(all(mo_is_intrinsic_resistant(rep("B_ENTRBC_CLOC-C", 2), ab = c("AMX", "AMC"))))
+})
+
 test_that("interpretive rules name organisms that exist", {
  skip_on_cran()
  r <- AMR:::INTERPRETIVE_RULES_DF