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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling
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128
R/mdro.R
128
R/mdro.R
@ -51,7 +51,11 @@
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#'
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#' Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) ([link](https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext))
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#'
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#' * `guideline = "EUCAST3.2"` (or simply `guideline = "EUCAST"`)
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#' * `guideline = "EUCAST3.3"` (or simply `guideline = "EUCAST"`)
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#'
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#' The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf))
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#'
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#' * `guideline = "EUCAST3.2"`
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#'
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#' The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf))
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#'
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@ -73,7 +77,6 @@
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#'
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#' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
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#'
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#'
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#' @section Using Custom Guidelines:
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#'
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#' Custom guidelines can be set with the [custom_mdro_guideline()] function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
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@ -325,10 +328,17 @@ mdro <- function(x = NULL,
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} else if (guideline$code == "eucast3.2") {
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guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
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guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
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guideline$version <- "3.2, 2020"
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guideline$version <- "3.2, February 2020"
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guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"
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guideline$type <- "EUCAST Unusual Phenotypes"
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} else if (guideline$code == "eucast3.3") {
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guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
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guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
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guideline$version <- "3.3, October 2021"
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guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf"
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guideline$type <- "EUCAST Unusual Phenotypes"
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} else if (guideline$code == "tb") {
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guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
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guideline$author <- "WHO (World Health Organization)"
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@ -474,6 +484,7 @@ mdro <- function(x = NULL,
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verbose = verbose,
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info = info,
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only_rsi_columns = only_rsi_columns,
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fn = "mdro",
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...)
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} else if (guideline$code == "eucast3.2") {
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cols_ab <- get_column_abx(x = x,
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@ -502,6 +513,36 @@ mdro <- function(x = NULL,
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verbose = verbose,
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info = info,
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only_rsi_columns = only_rsi_columns,
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fn = "mdro",
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...)
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} else if (guideline$code == "eucast3.3") {
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cols_ab <- get_column_abx(x = x,
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soft_dependencies = c("AMP",
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"AMX",
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"CIP",
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"DAL",
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"DAP",
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"ERV",
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"FDX",
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"GEN",
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"LNZ",
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"MEM",
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"MTR",
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"OMC",
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"ORI",
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"PEN",
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"QDA",
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"RIF",
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"TEC",
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"TGC",
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"TLV",
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"TOB",
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"TZD",
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"VAN"),
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verbose = verbose,
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info = info,
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only_rsi_columns = only_rsi_columns,
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fn = "mdro",
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...)
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} else if (guideline$code == "tb") {
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cols_ab <- get_column_abx(x = x,
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@ -516,6 +557,7 @@ mdro <- function(x = NULL,
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verbose = verbose,
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info = info,
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only_rsi_columns = only_rsi_columns,
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fn = "mdro",
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...)
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} else if (guideline$code == "mrgn") {
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cols_ab <- get_column_abx(x = x,
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@ -528,12 +570,14 @@ mdro <- function(x = NULL,
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verbose = verbose,
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info = info,
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only_rsi_columns = only_rsi_columns,
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fn = "mdro",
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...)
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} else {
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cols_ab <- get_column_abx(x = x,
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verbose = verbose,
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info = info,
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only_rsi_columns = only_rsi_columns,
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fn = "mdro",
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...)
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}
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if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) {
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@ -1171,10 +1215,80 @@ mdro <- function(x = NULL,
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which(x$genus == "Streptococcus" & x$species == "pneumoniae"),
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c(carbapenems, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC, RIF),
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"any")
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streps <- MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE]
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streps_ABCG <- streps[as.mo(streps, Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")]
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trans_tbl(3, # Sr. groups A/B/C/G
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which(x$mo %in% streps_ABCG),
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which(x$mo %in% MO_STREP_ABCG),
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c(PEN, cephalosporins, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
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"any")
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trans_tbl(3,
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which(x$genus == "Enterococcus"),
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c(DAP, LNZ, TGC, ERV, OMC, TEC),
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"any")
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trans_tbl(3,
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which(x$genus == "Enterococcus" & x$species == "faecalis"),
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c(AMP, AMX),
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"any")
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# Table 8
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trans_tbl(3,
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which(x$genus == "Bacteroides"),
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MTR,
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"any")
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trans_tbl(3,
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which(x$genus == "Clostridium" & x$species == "difficile"),
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c(MTR, VAN, FDX),
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"any")
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}
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if (guideline$code == "eucast3.3") {
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# EUCAST 3.3 --------------------------------------------------------------
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# note: this guideline is equal to EUCAST 3.2 - no MDRO insights changed
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# Table 6
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trans_tbl(3,
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which((x$order == "Enterobacterales" &
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!x$family == "Morganellaceae" &
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!(x$genus == "Serratia" & x$species == "marcescens"))
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| (x$genus == "Pseudomonas" & x$species == "aeruginosa")
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| x$genus == "Acinetobacter"),
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COL,
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"all")
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trans_tbl(3,
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which(x$genus == "Salmonella" & x$species == "Typhi"),
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c(carbapenems),
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"any")
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trans_tbl(3,
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which(x$genus == "Haemophilus" & x$species == "influenzae"),
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c(cephalosporins_3rd, carbapenems, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(x$genus == "Moraxella" & x$species == "catarrhalis"),
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(x$genus == "Neisseria" & x$species == "meningitidis"),
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c(cephalosporins_3rd, fluoroquinolones),
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"any")
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trans_tbl(3,
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which(x$genus == "Neisseria" & x$species == "gonorrhoeae"),
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SPT,
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"any")
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# Table 7
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trans_tbl(3,
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which(x$genus == "Staphylococcus" & x$species == "aureus"),
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c(VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
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"any")
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trans_tbl(3,
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which(x$mo %in% MO_CONS), # coagulase-negative Staphylococcus
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c(VAN, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
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"any")
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trans_tbl(3,
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which(x$genus == "Corynebacterium"),
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c(VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC),
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"any")
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trans_tbl(3,
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which(x$genus == "Streptococcus" & x$species == "pneumoniae"),
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c(carbapenems, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC, RIF),
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"any")
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trans_tbl(3, # Sr. groups A/B/C/G
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which(x$mo %in% MO_STREP_ABCG),
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c(PEN, cephalosporins, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
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"any")
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trans_tbl(3,
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@ -1435,7 +1549,7 @@ mdro <- function(x = NULL,
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# Results ----
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if (guideline$code == "cmi2012") {
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if (any(x$MDRO == -1, na.rm = TRUE)) {
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if (message_not_thrown_before("mdro.availability")) {
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if (message_not_thrown_before("mdro", "availability")) {
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warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
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percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
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}
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