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(v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR)

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-03-03 15:41:08 +01:00
parent 12cf144b19
commit b6211931f8
25 changed files with 162 additions and 74 deletions
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24
data-raw/_pre_commit_checks.R
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@@ -366,7 +366,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
# antibiotic groups
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
filter(group %like% "aminoglycoside") %>%
filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
pull(ab)
pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
@@ -400,6 +400,12 @@ pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[
pre_commit_lst$AB_GLYCOPEPTIDES <- antimicrobials %>%
filter(group %like% "glycopeptide") %>%
pull(ab)
pre_commit_lst$AB_FUSIDANES <- antimicrobials %>%
filter(name %like% "fusi") %>%
pull(ab)
pre_commit_lst$AB_IONOPHORES<- antimicrobials %>%
filter(name %like% "alamethicin|beauvericin|calcimycin|chloroquine|clioquinol|diiodohydroxyquinoline|dithiocarbamates|enniatin|epigallocatechin|gramicidin|hinokitiol|ionomycin|laidlomycin|lasalocid|maduramicin|monensin|narasin|nigericin|nonactin|nystatin|pyrazole|pyrithione|quercetin|salinomycin|semduramicin|valinomycin|zincophorin") %>%
pull(ab)
pre_commit_lst$AB_ISOXAZOLYLPENICILLINS <- antimicrobials %>%
filter(name %like% "oxacillin|cloxacillin|dicloxacillin|flucloxacillin|meth?icillin") %>%
pull(ab)
@@ -412,7 +418,7 @@ pre_commit_lst$AB_MACROLIDES <- antimicrobials %>%
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2)) | name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|primycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)") %>%
pull(ab)
pre_commit_lst$AB_MONOBACTAMS <- antimicrobials %>%
filter(group %like% "monobactam") %>%
filter(group %like% "monobactam" | name %like% "aztreonam|carumonam|tigemonam") %>%
pull(ab)
pre_commit_lst$AB_NITROFURANS <- antimicrobials %>%
filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
@@ -423,12 +429,18 @@ pre_commit_lst$AB_OXAZOLIDINONES <- antimicrobials %>%
pre_commit_lst$AB_PENICILLINS <- antimicrobials %>%
filter(group %like% "penicillin" & !(name %unlike% "/" & name %like% ".*bactam$")) %>%
pull(ab)
pre_commit_lst$AB_PEPTIDES <- antimicrobials %>%
filter(ab %in% pre_commit_lst$AB_GLYCOPEPTIDES | name %like% "thiostrepton|actinomycin|bacitracin|daptomycin|vancomycin|teixobactin|tyrocidine|gramicidin|zwittermicin|epothilone|fabclavine|bleomycin|ciclosporin|cyclosporine|siderophores|pyoverdine|enterobactin|myxochelin") %>%
pull(ab)
pre_commit_lst$AB_PHENICOLS <- antimicrobials %>%
filter(group %like% "phenicol" | atc_group1 %like% "phenicol" | atc_group2 %like% "phenicol") %>%
pull(ab)
pre_commit_lst$AB_PHOSPHONICS <- antimicrobials %>%
filter(group %like% "phosphonic" | name %like% "fosfo") %>%
pull(ab)
pre_commit_lst$AB_PLEUROMUTILINS <- antimicrobials %>%
filter(name %like% "retapamulin|tiamulin|pleuromutilin") %>%
pull(ab)
pre_commit_lst$AB_POLYMYXINS <- antimicrobials %>%
filter(group %like% "polymyxin") %>%
pull(ab)
@@ -446,7 +458,7 @@ pre_commit_lst$AB_SPIROPYRIMIDINETRIONES <- antimicrobials %>%
filter(name %like% "zoliflodacin") %>%
pull(ab)
pre_commit_lst$AB_STREPTOGRAMINS <- antimicrobials %>%
filter(atc_group2 %like% "streptogramin") %>%
filter(atc_group2 %like% "streptogramin" | name %like% "streptogramin|virginiamycin|ostreogrycin") %>%
pull(ab)
pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>%
filter(atc_group1 %like% "tetracycline" | atc_group2 %like% "tetracycline" | name %like% "chlortetracycline|cetocycline|demeclocycline|doxycycline|eravacycline|lymecycline|meclocycline|meth?acycline|minocycline|omadacycline|oxytetracycline|rolitetracycline|sarecycline|tetracycline|tigecycline") %>%
@@ -500,7 +512,7 @@ for (i in seq_along(group_map)) {
if (is.null(group_map[[i]])) {
group_map[[i]] <- "Other"
if (antimicrobials$group[i] %unlike% "other") {
usethis::ui_warn("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i]))
usethis::ui_warn(paste0("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i])))
}
}
group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))]
@@ -523,6 +535,7 @@ pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
"Aminoglycosides",
"Lipoglycopeptides",
"Glycopeptides",
"Peptides",
"Lincosamides",
"Streptogramins",
"Macrolides",
@@ -537,10 +550,13 @@ pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
"Trimethoprims",
"Sulfonamides",
"Tetracyclines",
"Ionophores",
"Antifungals",
"Antimycobacterials",
"Fusidanes",
"Beta-lactams",
"Beta-lactamase inhibitors",
"Pleuromutilins",
"Other")
if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))