# ==================================================================== # # TITLE: # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE CODE: # # https://github.com/msberends/AMR # # # # PLEASE CITE THIS SOFTWARE AS: # # Berends MS, Luz CF, Friedrich AW, et al. (2022). # # AMR: An R Package for Working with Antimicrobial Resistance Data. # # Journal of Statistical Software, 104(3), 1-31. # # https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # # colleagues from around the world, see our website. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # library(dplyr) # got EARS-Net codes (= ECDC/WHO codes) from here: # Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html), # opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access # and exported table 'DRGLST' to MS Excel library(readxl) DRGLST <- read_excel("DRGLST.xlsx") abx <- DRGLST %>% select( ab = WHON5_CODE, name = ANTIBIOTIC ) %>% # remove the ones without WHONET code filter(!is.na(ab)) %>% distinct(name, .keep_all = TRUE) %>% # add the ones without WHONET code bind_rows( DRGLST %>% select( ab = WHON5_CODE, name = ANTIBIOTIC ) %>% filter(is.na(ab)) %>% distinct(name, .keep_all = TRUE) # add new ab code later ) %>% arrange(name) # add old ATC codes ab_old <- AMR::antibiotics %>% mutate( official = gsub("( and |, )", "/", official), abbr = tolower(paste(ifelse(is.na(abbr), "", abbr), ifelse(is.na(certe), "", certe), ifelse(is.na(umcg), "", umcg), sep = "|" )) ) for (i in 1:nrow(ab_old)) { abbr <- ab_old[i, "abbr"] abbr <- strsplit(abbr, "|", fixed = TRUE) %>% unlist() %>% unique() abbr <- abbr[abbr != ""] # print(abbr) if (length(abbr) == 0) { ab_old[i, "abbr"] <- NA_character_ } else { ab_old[i, "abbr"] <- paste(abbr, collapse = "|") } } # create reference data set: to be able to map ab to atc abx_atc1 <- abx %>% mutate(name_lower = tolower(name)) %>% left_join(ab_old %>% select(ears_net, atc), by = c(ab = "ears_net")) %>% rename(atc1 = atc) %>% left_join(ab_old %>% mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>% transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>% rename(atc2 = atc) %>% left_join(ab_old %>% mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>% mutate(official = gsub("f", "ph", official)) %>% transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>% rename(atc3 = atc) %>% left_join(ab_old %>% mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>% mutate(official = gsub("t", "th", official)) %>% transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>% rename(atc4 = atc) %>% left_join(ab_old %>% mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>% mutate(official = gsub("f", "ph", official)) %>% mutate(official = gsub("t", "th", official)) %>% transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>% rename(atc5 = atc) %>% left_join(ab_old %>% mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>% mutate(official = gsub("f", "ph", official)) %>% mutate(official = gsub("t", "th", official)) %>% mutate(official = gsub("ine$", "in", official)) %>% transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>% rename(atc6 = atc) %>% mutate(atc = case_when( !is.na(atc1) ~ atc1, !is.na(atc2) ~ atc2, !is.na(atc3) ~ atc3, !is.na(atc4) ~ atc4, !is.na(atc4) ~ atc5, TRUE ~ atc6 )) %>% distinct(ab, name, .keep_all = TRUE) %>% select(ab, atc, name) abx_atc2 <- ab_old %>% filter( !atc %in% abx_atc1$atc, is.na(ears_net), !is.na(atc_group1), atc_group1 %unlike% ("virus|vaccin|viral|immun"), official %unlike% "(combinations| with )" ) %>% mutate(ab = NA_character_) %>% as.data.frame(stringsAsFactors = FALSE) %>% select(ab, atc, name = official) abx2 <- bind_rows(abx_atc1, abx_atc2) rm(abx_atc1) rm(abx_atc2) abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate( gsub( "[/0-9-]", " ", abx2$name[is.na(abx2$ab)] ), minlength = 3, method = "left.kept", strict = TRUE )) n_distinct(abx2$ab) abx2 <- abx2 %>% arrange(ab) seqnr <- 0 # add follow up nrs for (i in 2:nrow(abx2)) { if (abx2[i, "ab", drop = TRUE] == abx2[i - 1, "ab", drop = TRUE]) { seqnr <- seqnr + 1 abx2[i, "seqnr"] <- seqnr } else { seqnr <- 0 } } for (i in 2:nrow(abx2)) { if (!is.na(abx2[i, "seqnr"])) { abx2[i, "ab"] <- paste0(abx2[i, "ab", drop = TRUE], abx2[i, "seqnr", drop = TRUE]) } } abx2 <- abx2 %>% select(-seqnr) %>% arrange(name) # everything unique?? nrow(abx2) == n_distinct(abx2$ab) # get ATC properties abx2 <- abx2 %>% left_join(ab_old %>% select( atc, abbr, atc_group1, atc_group2, oral_ddd, oral_units, iv_ddd, iv_units )) abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixed = TRUE))) # Update Compound IDs and Synonyms ---- # vector with official names, returns vector with CIDs get_CID <- function(ab) { CID <- rep(NA_integer_, length(ab)) p <- AMR:::progress_ticker(n = length(ab), min_time = 0) for (i in 1:length(ab)) { p$tick() CID[i] <- tryCatch( data.table::fread( paste0( "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/", URLencode(ab[i], reserved = TRUE), "/cids/TXT?name_type=complete" ), showProgress = FALSE )[[1]][1], error = function(e) NA_integer_ ) if (is.na(CID[i])) { # try with removing the text in brackets CID[i] <- tryCatch( data.table::fread( paste0( "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/", URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE), "/cids/TXT?name_type=complete" ), showProgress = FALSE )[[1]][1], error = function(e) NA_integer_ ) } if (is.na(CID[i])) { # try match on word and take the lowest CID value (sorted) ab[i] <- gsub("[^a-z0-9]+", " ", ab[i], ignore.case = TRUE) CID[i] <- tryCatch( data.table::fread( paste0( "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/", URLencode(ab[i], reserved = TRUE), "/cids/TXT?name_type=word" ), showProgress = FALSE )[[1]][1], error = function(e) NA_integer_ ) } Sys.sleep(0.1) } CID } # get CIDs (4-5 min) CIDs <- get_CID(antibiotics$name) # take missing from previously found CIDs CIDs[is.na(CIDs) & !is.na(antibiotics$cid)] <- antibiotics$cid[is.na(CIDs) & !is.na(antibiotics$cid)] # These could not be found: antibiotics[is.na(CIDs), ] %>% View() # returns list with synonyms (brand names), with CIDs as names get_synonyms <- function(CID, clean = TRUE) { synonyms <- rep(NA_character_, length(CID)) p <- AMR:::progress_ticker(n = length(CID), min_time = 0) for (i in 1:length(CID)) { p$tick() synonyms_txt <- "" if (is.na(CID[i])) { next } # we will now get the closest compounds with a 96% threshold similar_cids <- tryCatch( data.table::fread( paste0( "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/cid/", CID[i], "/cids/TXT?Threshold=96&MaxRecords=5" ), sep = "\n", showProgress = FALSE )[[1]], error = function(e) NA_character_ ) all_cids <- unique(c(CID[i], similar_cids)) # for each one, we are getting the synonyms current_syns <- character(0) for (j in seq_len(length(all_cids))) { synonyms_txt <- tryCatch( data.table::fread( paste0( "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/", all_cids[j], "/synonyms/TXT" ), sep = "\n", showProgress = FALSE )[[1]], error = function(e) NA_character_ ) Sys.sleep(0.05) if (clean == TRUE) { # remove text between brackets synonyms_txt <- trimws(gsub( "[(].*[)]", "", gsub( "[[].*[]]", "", gsub( "[(].*[]]", "", gsub("[[].*[)]", "", synonyms_txt) ) ) )) synonyms_txt <- gsub("Co-", "Co", synonyms_txt, fixed = TRUE) synonyms_txt <- gsub(" ?(mono)?sodium ?", "", ignore.case = TRUE, synonyms_txt) synonyms_txt <- gsub(" ?injection ?", "", ignore.case = TRUE, synonyms_txt) # only length 6 to 20 and no txt with reading marks or numbers and must start with capital letter (= brand) synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(5:20) & !grepl("[-&{},_0-9/:]", synonyms_txt) & grepl("^[A-Z]", synonyms_txt, ignore.case = FALSE)] synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE)) } current_syns <- c(current_syns, synonyms_txt) } current_syns <- unique(trimws(current_syns[tolower(current_syns) %in% unique(tolower(current_syns))])) synonyms[i] <- list(sort(current_syns)) } names(synonyms) <- CID synonyms } # get brand names from PubChem (3-4 min) synonyms <- get_synonyms(CIDs) synonyms.bak <- synonyms # add existing ones (will be cleaned later) for (i in seq_len(length(synonyms))) { old <- antibiotics$synonyms[[i]] if (old %like% "^c[()]") { old <- eval(parse(text = old)) } synonyms[[i]] <- c(synonyms[[i]], old) } antibiotics$synonyms <- synonyms stop("remember to remove co-trimoxazole as synonyms from SMX (Sulfamethoxazole), so it only exists in SXT!") sulfa <- antibiotics[which(antibiotics$ab == "SMX"), "synonyms", drop = TRUE][[1]] cotrim <- antibiotics[which(antibiotics$ab == "SXT"), "synonyms", drop = TRUE][[1]] sulfa <- sulfa[!sulfa %in% cotrim] antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]][[1]] <- sulfa # now go to end of this file # ----- # add them to data set antibiotics <- abx2 %>% left_join(DRGLST %>% select(ab = WHON5_CODE, CLASS, SUBCLASS) %>% distinct(ab, .keep_all = TRUE), by = "ab") %>% transmute(ab, atc, cid = CIDs, # no capital after a slash: Ampicillin/Sulbactam -> Ampicillin/sulbactam name = name %>% gsub("([/-])([A-Z])", "\\1\\L\\2", ., perl = TRUE) %>% gsub("edta", "EDTA", ., ignore.case = TRUE), group = case_when( paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "am(ph|f)enicol" ~ "Amphenicols", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "aminoglycoside" ~ "Aminoglycosides", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "carbapenem" | name %like% "(imipenem|meropenem)" ~ "Carbapenems", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "First-generation cephalosporin" ~ "Cephalosporins (1st gen.)", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Second-generation cephalosporin" ~ "Cephalosporins (2nd gen.)", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Third-generation cephalosporin" ~ "Cephalosporins (3rd gen.)", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Fourth-generation cephalosporin" ~ "Cephalosporins (4th gen.)", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(tuberculosis|mycobacter)" ~ "Antimycobacterials", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "cephalosporin" ~ "Cephalosporins", name %like% "^Ce" & is.na(atc_group1) & paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "beta-?lactam" ~ "Cephalosporins", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(beta-?lactam|penicillin)" ~ "Beta-lactams/penicillins", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "quinolone" ~ "Quinolones", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "glycopeptide" ~ "Glycopeptides", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "macrolide" ~ "Macrolides/lincosamides", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "tetracycline" ~ "Tetracyclines", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "trimethoprim" ~ "Trimethoprims", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "polymyxin" ~ "Polymyxins", paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(fungal|mycot)" ~ "Antifungals/antimycotics", TRUE ~ "Other antibacterials" ), atc_group1, atc_group2, abbreviations = unname(abbr), synonyms = unname(synonyms), oral_ddd, oral_units, iv_ddd, iv_units ) %>% as.data.frame(stringsAsFactors = FALSE) # some exceptions antibiotics[which(antibiotics$ab == "DOX"), "abbreviations"][[1]] <- list(c("dox", "doxy")) antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]] <- list(c("clox")) antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]], "CFC")) # cefaclor old WHONET4 code antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]], "Amoxy"))) # 'Polymixin B' (POL) and 'Polymyxin B' (PLB) both exist, so: antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "POL", "Polymixin", "Polymixin B", "Poly B")) antibiotics <- filter(antibiotics, ab != "POL") # 'Latamoxef' (LTM) and 'Moxalactam (Latamoxef)' (MOX) both exist, so: antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c("MOX", "moxa")) antibiotics <- filter(antibiotics, ab != "MOX") # RFP and RFP1 (the J0 one) both mean 'rifapentine', although 'rifp' is not recognised, so: antibiotics <- filter(antibiotics, ab != "RFP") antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP" antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp")) # Rifampicin is better known as a drug than Rifampin (Rifampin is still listed as a brand name), so: antibiotics[which(antibiotics$ab == "RIF"), "name"] <- "Rifampicin" # PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so: antibiotics <- filter(antibiotics, ab != "PME") antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME" # Remove Sinecatechins antibiotics <- filter(antibiotics, ab != "SNC") # GLIMS codes antibiotics[which(antibiotics$ab == as.ab("cefuroxim")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefuroxim")), "abbreviations"][[1]], "cfrx")) antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]], "cftx")) antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]], "cftz")) antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]], "cfpi")) antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt")) # Add cefoxitin screening class(antibiotics$ab) <- "character" antibiotics <- rbind(antibiotics, data.frame( ab = "FOX1", atc = NA, cid = NA, name = "Cefoxitin screening", group = "Cephalosporins (2nd gen.)", atc_group1 = NA, atc_group2 = NA, abbreviations = "cfsc", synonyms = NA, oral_ddd = NA, oral_units = NA, iv_ddd = NA, iv_units = NA, loinc = NA, stringsAsFactors = FALSE )) # More GLIMS codes antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]], "amf")) antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz")) antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]], "cst")) antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr")) antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "cftx")) antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]], "cfrx")) antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]], "cfzl")) antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]], "fcu")) antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]], "fluy")) antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]], "flz")) antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]], "fof")) antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]], "cfxt")) antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]], "fa")) antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]], "g_h")) antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]], "k_h")) antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]], "ktc")) antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "pipc")) antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "PIPC")) antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]], "spa")) antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]], "s_h")) antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]], "stm")) antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "COTRIM")) antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "trsx")) antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]], "tig")) antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]], "tri")) antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "PIPTAZ")) antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pit")) antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pita")) antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]], "vrc")) # official RIVM codes (Dutch National Health Institute) # https://www.rivm.nl/sites/default/files/2019-09/Bijlage_4_Lijst_antibiotica%202020%201.0.pdf antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FCT"), "abbreviations"][[1]], "5flc")) antibiotics[which(antibiotics$ab == "AMC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMC"), "abbreviations"][[1]], "amcl")) antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]], "amfb")) antibiotics[which(antibiotics$ab == "AMH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMH"), "abbreviations"][[1]], "amhl")) antibiotics[which(antibiotics$ab == "AMK"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMK"), "abbreviations"][[1]], "amik")) antibiotics[which(antibiotics$ab == "AMX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMX"), "abbreviations"][[1]], "amox")) antibiotics[which(antibiotics$ab == "AMP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMP"), "abbreviations"][[1]], "ampi")) antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]], "amsu")) antibiotics[which(antibiotics$ab == "ANI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ANI"), "abbreviations"][[1]], "anid")) antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SAM"), "abbreviations"][[1]], "apsu")) antibiotics[which(antibiotics$ab == "AZM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AZM"), "abbreviations"][[1]], "azit")) antibiotics[which(antibiotics$ab == "AZL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AZL"), "abbreviations"][[1]], "azlo")) antibiotics[which(antibiotics$ab == "ATM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ATM"), "abbreviations"][[1]], "aztr")) antibiotics[which(antibiotics$ab == "PNV"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PNV"), "abbreviations"][[1]], "bepe")) antibiotics[which(antibiotics$ab == "CAP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAP"), "abbreviations"][[1]], "capr")) antibiotics[which(antibiotics$ab == "CRB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRB"), "abbreviations"][[1]], "carb")) antibiotics[which(antibiotics$ab == "CAS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAS"), "abbreviations"][[1]], "casp")) antibiotics[which(antibiotics$ab == "CDC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CDC"), "abbreviations"][[1]], "cecl")) antibiotics[which(antibiotics$ab == "CXA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXA"), "abbreviations"][[1]], "cfax")) antibiotics[which(antibiotics$ab == "CTB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTB"), "abbreviations"][[1]], "cfbu")) antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]], "cfcl")) antibiotics[which(antibiotics$ab == "CFR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFR"), "abbreviations"][[1]], "cfdx")) antibiotics[which(antibiotics$ab == "CEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEP"), "abbreviations"][[1]], "cflt")) antibiotics[which(antibiotics$ab == "LEX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LEX"), "abbreviations"][[1]], "cflx")) antibiotics[which(antibiotics$ab == "MAN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MAN"), "abbreviations"][[1]], "cfmn")) antibiotics[which(antibiotics$ab == "CPD"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPD"), "abbreviations"][[1]], "cfpd")) antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]], "cfpi")) antibiotics[which(antibiotics$ab == "CPO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPO"), "abbreviations"][[1]], "cfpr")) antibiotics[which(antibiotics$ab == "CFP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFP"), "abbreviations"][[1]], "cfpz")) antibiotics[which(antibiotics$ab == "CED"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CED"), "abbreviations"][[1]], "cfrd")) antibiotics[which(antibiotics$ab == "CPT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPT"), "abbreviations"][[1]], "cfro")) antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]], "cfrx")) antibiotics[which(antibiotics$ab == "CFS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFS"), "abbreviations"][[1]], "cfsl")) antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr")) antibiotics[which(antibiotics$ab == "CTT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTT"), "abbreviations"][[1]], "cftt")) antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "cftx")) antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz")) antibiotics[which(antibiotics$ab == "CFM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CFM"), "abbreviations"][[1]], "cfxm")) antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]], "cfxt")) antibiotics[which(antibiotics$ab == "CZA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZA"), "abbreviations"][[1]], "cfav")) antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]], "cfzl")) antibiotics[which(antibiotics$ab == "CZX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZX"), "abbreviations"][[1]], "cfzx")) antibiotics[which(antibiotics$ab == "CHL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CHL"), "abbreviations"][[1]], "chlo")) antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]], "cicl")) antibiotics[which(antibiotics$ab == "CIN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CIN"), "abbreviations"][[1]], "cino")) antibiotics[which(antibiotics$ab == "CIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CIP"), "abbreviations"][[1]], "cipr")) antibiotics[which(antibiotics$ab == "CIX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CIX"), "abbreviations"][[1]], "cipx")) antibiotics[which(antibiotics$ab == "CLR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CLR"), "abbreviations"][[1]], "clar")) antibiotics[which(antibiotics$ab == "CLI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CLI"), "abbreviations"][[1]], "clin")) antibiotics[which(antibiotics$ab == "CTR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTR"), "abbreviations"][[1]], "clot")) antibiotics[which(antibiotics$ab == "CLO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CLO"), "abbreviations"][[1]], "clox")) antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "COL"), "abbreviations"][[1]], "coli")) antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]], "cxcl")) antibiotics[which(antibiotics$ab == "CYC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CYC"), "abbreviations"][[1]], "cycl")) antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]], "czcl")) antibiotics[which(antibiotics$ab == "DAP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DAP"), "abbreviations"][[1]], "dapt")) antibiotics[which(antibiotics$ab == "DIC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DIC"), "abbreviations"][[1]], "dicl")) antibiotics[which(antibiotics$ab == "DOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DOR"), "abbreviations"][[1]], "dori")) antibiotics[which(antibiotics$ab == "DOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "DOX"), "abbreviations"][[1]], "doxy")) antibiotics[which(antibiotics$ab == "ENX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ENX"), "abbreviations"][[1]], "enox")) antibiotics[which(antibiotics$ab == "ETP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ETP"), "abbreviations"][[1]], "erta")) antibiotics[which(antibiotics$ab == "ERY"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ERY"), "abbreviations"][[1]], "eryt")) antibiotics[which(antibiotics$ab == "PHE"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PHE"), "abbreviations"][[1]], "fene")) antibiotics[which(antibiotics$ab == "PHN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PHN"), "abbreviations"][[1]], "fepe")) antibiotics[which(antibiotics$ab == "FLE"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLE"), "abbreviations"][[1]], "fler")) antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLU"), "abbreviations"][[1]], "fluc")) antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]], "flux")) antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOS"), "abbreviations"][[1]], "fosf")) antibiotics[which(antibiotics$ab == "FRM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FRM"), "abbreviations"][[1]], "fram")) antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FUS"), "abbreviations"][[1]], "fusi")) antibiotics[which(antibiotics$ab == "GAT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GAT"), "abbreviations"][[1]], "gati")) antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]], "gehl")) antibiotics[which(antibiotics$ab == "GEN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GEN"), "abbreviations"][[1]], "gent")) antibiotics[which(antibiotics$ab == "GRX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "GRX"), "abbreviations"][[1]], "grep")) antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]], "imci")) antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]], "imip")) antibiotics[which(antibiotics$ab == "ISV"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ISV"), "abbreviations"][[1]], "isav")) antibiotics[which(antibiotics$ab == "ITR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "ITR"), "abbreviations"][[1]], "itra")) antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KAH"), "abbreviations"][[1]], "kahl")) antibiotics[which(antibiotics$ab == "KAN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KAN"), "abbreviations"][[1]], "kana")) antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "KET"), "abbreviations"][[1]], "keto")) antibiotics[which(antibiotics$ab == "LVX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LVX"), "abbreviations"][[1]], "levo")) antibiotics[which(antibiotics$ab == "LIN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LIN"), "abbreviations"][[1]], "linc")) antibiotics[which(antibiotics$ab == "LNZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LNZ"), "abbreviations"][[1]], "line")) antibiotics[which(antibiotics$ab == "LOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LOR"), "abbreviations"][[1]], "lora")) antibiotics[which(antibiotics$ab == "MEM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MEM"), "abbreviations"][[1]], "mero")) antibiotics[which(antibiotics$ab == "MET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MET"), "abbreviations"][[1]], "meti")) antibiotics[which(antibiotics$ab == "MTR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MTR"), "abbreviations"][[1]], "metr")) antibiotics[which(antibiotics$ab == "MEZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MEZ"), "abbreviations"][[1]], "mezl")) antibiotics[which(antibiotics$ab == "MIF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MIF"), "abbreviations"][[1]], "mica")) antibiotics[which(antibiotics$ab == "MCZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MCZ"), "abbreviations"][[1]], "mico")) antibiotics[which(antibiotics$ab == "MNO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MNO"), "abbreviations"][[1]], "mino")) antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]], "moxa", "moxalactam")) antibiotics[which(antibiotics$ab == "MFX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MFX"), "abbreviations"][[1]], "moxi")) antibiotics[which(antibiotics$ab == "NAL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NAL"), "abbreviations"][[1]], "nali")) antibiotics[which(antibiotics$ab == "NEO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NEO"), "abbreviations"][[1]], "neom")) antibiotics[which(antibiotics$ab == "NET"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NET"), "abbreviations"][[1]], "neti")) antibiotics[which(antibiotics$ab == "NIT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NIT"), "abbreviations"][[1]], "nitr")) antibiotics[which(antibiotics$ab == "NOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NOR"), "abbreviations"][[1]], "norf")) antibiotics[which(antibiotics$ab == "NYS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NYS"), "abbreviations"][[1]], "nyst")) antibiotics[which(antibiotics$ab == "OFX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "OFX"), "abbreviations"][[1]], "oflo")) antibiotics[which(antibiotics$ab == "OXA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "OXA"), "abbreviations"][[1]], "oxal")) antibiotics[which(antibiotics$ab == "PEF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PEF"), "abbreviations"][[1]], "pefl")) antibiotics[which(antibiotics$ab == "PEN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PEN"), "abbreviations"][[1]], "peni")) antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "pipc")) antibiotics[which(antibiotics$ab == "PPA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PPA"), "abbreviations"][[1]], "pipz")) antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pita")) antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "polb")) antibiotics[which(antibiotics$ab == "POS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "POS"), "abbreviations"][[1]], "posa")) antibiotics[which(antibiotics$ab == "PRI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PRI"), "abbreviations"][[1]], "pris")) antibiotics[which(antibiotics$ab == "QDA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "QDA"), "abbreviations"][[1]], "quda")) antibiotics[which(antibiotics$ab == "RIF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "RIF"), "abbreviations"][[1]], "rifa")) antibiotics[which(antibiotics$ab == "RXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "RXT"), "abbreviations"][[1]], "roxi")) antibiotics[which(antibiotics$ab == "SMX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SMX"), "abbreviations"][[1]], "sfmx")) antibiotics[which(antibiotics$ab == "SLF4"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SLF4"), "abbreviations"][[1]], "sfmz")) antibiotics[which(antibiotics$ab == "SSS"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SSS"), "abbreviations"][[1]], "sfna")) antibiotics[which(antibiotics$ab == "SLF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SLF"), "abbreviations"][[1]], "sfsz")) antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPX"), "abbreviations"][[1]], "spar")) antibiotics[which(antibiotics$ab == "SPT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPT"), "abbreviations"][[1]], "spec")) antibiotics[which(antibiotics$ab == "SPI"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SPI"), "abbreviations"][[1]], "spir")) antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]], "sthl")) antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "STR1"), "abbreviations"][[1]], "stre")) antibiotics[which(antibiotics$ab == "TAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TAZ"), "abbreviations"][[1]], "tazo")) antibiotics[which(antibiotics$ab == "TEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TEC"), "abbreviations"][[1]], "teic")) antibiotics[which(antibiotics$ab == "TLT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TLT"), "abbreviations"][[1]], "teli")) antibiotics[which(antibiotics$ab == "TMX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TMX"), "abbreviations"][[1]], "tema")) antibiotics[which(antibiotics$ab == "TEM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TEM"), "abbreviations"][[1]], "temo")) antibiotics[which(antibiotics$ab == "TRB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TRB"), "abbreviations"][[1]], "terb")) antibiotics[which(antibiotics$ab == "TCY"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TCY"), "abbreviations"][[1]], "tetr")) antibiotics[which(antibiotics$ab == "TIC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TIC"), "abbreviations"][[1]], "tica")) antibiotics[which(antibiotics$ab == "TCC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TCC"), "abbreviations"][[1]], "ticl")) antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TGC"), "abbreviations"][[1]], "tige")) antibiotics[which(antibiotics$ab == "TIN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TIN"), "abbreviations"][[1]], "tini")) antibiotics[which(antibiotics$ab == "TOB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TOB"), "abbreviations"][[1]], "tobr")) antibiotics[which(antibiotics$ab == "TOH"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TOH"), "abbreviations"][[1]], "tohl")) antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TMP"), "abbreviations"][[1]], "trim")) antibiotics[which(antibiotics$ab == "TVA"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TVA"), "abbreviations"][[1]], "trov")) antibiotics[which(antibiotics$ab == "SLT4"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SLT4"), "abbreviations"][[1]], "trsm")) antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "trsx")) antibiotics[which(antibiotics$ab == "VAN"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "VAN"), "abbreviations"][[1]], "vanc")) antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "VOR"), "abbreviations"][[1]], "vori")) antibiotics[which(antibiotics$ab == "FOS"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "FOS"), "synonyms"][[1]], "Monuril"))) antibiotics[which(antibiotics$ab == "FOS"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "FOS"), "synonyms"][[1]], "Monurol"))) antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "piptazo"))) antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]], "RPT"))) antibiotics[which(antibiotics$ab == "RTP"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "RTP"), "abbreviations"][[1]], "RET"))) antibiotics[which(antibiotics$ab == "TYL1"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TYL1"), "abbreviations"][[1]], "TVN"))) antibiotics <- antibiotics %>% mutate(ab = as.character(ab)) %>% rbind(antibiotics %>% filter(ab == "GEH") %>% mutate( ab = "AMH", name = "Amphotericin B-high", abbreviations = list(c("amhl", "amfo b high", "ampho b high", "amphotericin high")) )) %>% rbind(antibiotics %>% filter(ab == "GEH") %>% mutate( ab = "TOH", name = "Tobramycin-high", abbreviations = list(c("tohl", "tobra high", "tobramycin high")) )) %>% rbind(antibiotics %>% filter(ab == "BUT") %>% mutate( ab = "CIX", atc = "D01AE14", name = "Ciclopirox", group = "Antifungals/antimycotics", atc_group1 = "Antifungals for topical use", atc_group2 = "Other antifungals for topical use", abbreviations = list(c("cipx")) )) antibiotics[which(antibiotics$ab == "SSS"), "name"] <- "Sulfonamide" # ESBL E-test codes: antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl")) antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta")) antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]] <- list(c("xpml")) antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]], "xpm")) antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl")) antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct")) # High level Gentamcin and Streptomycin antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high", "gehi")) antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high", "sthi")) # add imi and "imipenem/cilastatine" to imipenem antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp")) antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]], "imipenem/cilastatin"))) # add synonyms of ones not found antibiotics[which(antibiotics$ab == "TZP"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TZP"), "synonyms"][[1]], "Tazocel", "tazocillin", "Tazocin", "Zosyn"))) antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Colisticin", "Polymyxin E", "Colimycin", "Coly-Mycin", "Totazina", "Colistimethate", "Promixin", "Colistimethate Sodium")))) # remove incorrect synonyms from rifampicin (RIF) and add them to the combination rifampicin/isoniazid (RFI) old_sym <- antibiotics[which(antibiotics$ab == "RIF"), "synonyms"][[1]] old_sym <- old_sym[!old_sym %in% c("Rifinah", "Rimactazid")] antibiotics[which(antibiotics$ab == "RIF"), "synonyms"][[1]] <- list(old_sym) antibiotics[which(antibiotics$ab == "RFI"), "synonyms"][[1]] <- list(sort(c("Rifinah", "Rimactazid"))) # remove incorrect synonyms from sulfamethoxazole (SMX) and add them to the combination trimethoprim/sulfamethoxazole (SXT) old_sym <- antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")] antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym) antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole")))) # Fix penicillins antibiotics[which(antibiotics$ab == "PEN"), "abbreviations"][[1]] <- list(c("bepe", "pg", "pen", "peni", "peni g", "penicillin", "penicillin g")) antibiotics[which(antibiotics$ab == "PEN"), "name"] <- "Benzylpenicillin" antibiotics[which(antibiotics$ab == "PHN"), "abbreviations"][[1]] <- list(c("fepe", "peni v", "pv", "penicillin v", "PNV")) antibiotics <- subset(antibiotics, antibiotics$ab != "PNV") # New DDDs antibiotics[which(antibiotics$ab == "PEN"), "iv_ddd"] <- 3.6 antibiotics[which(antibiotics$ab == "PEN"), "iv_units"] <- "g" ## new ATC codes # ceftaroline antibiotics[which(antibiotics$ab == "CPT"), "atc"] <- "J01DI02" # faropenem antibiotics[which(antibiotics$ab == "FAR"), "atc"] <- "J01DI03" # ceftobiprole antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01" # ceftazidime / avibactam antibiotics[which(antibiotics$ab == "CZA"), "atc"] <- "J01DD52" antibiotics[which(antibiotics$ab == "CZA"), "cid"] <- 90643431 antibiotics[which(antibiotics$ab == "CZA"), "atc_group1"] <- "Other beta-lactam antibacterials" antibiotics[which(antibiotics$ab == "CZA"), "atc_group2"] <- "Third-generation cephalosporins" antibiotics[which(antibiotics$ab == "CZA"), "iv_ddd"] <- 6 antibiotics[which(antibiotics$ab == "CZA"), "iv_units"] <- "g" antibiotics[which(antibiotics$ab == "CZA"), "synonyms"] <- list(c("Avycaz", "Zavicefta")) # typo antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin" antibiotics[which(antibiotics$ab == "PEN"), "atc"] <- "J01CE01" # WHONET cleanup antibiotics[which(antibiotics$ab == "BCZ"), "name"] <- "Bicyclomycin" antibiotics[which(antibiotics$ab == "CCL"), "name"] <- "Cefetecol" antibiotics[which(antibiotics$ab == "ENV"), "name"] <- "Enviomycin" antibiotics[which(antibiotics$ab == "KIT"), "name"] <- "Kitasamycin" antibiotics[which(antibiotics$ab == "LSP"), "name"] <- "Linco-spectin" antibiotics[which(antibiotics$ab == "MEC"), "name"] <- "Mecillinam" antibiotics[which(antibiotics$ab == "PMR"), "name"] <- "Pimaricin" antibiotics[which(antibiotics$ab == "BCZ"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "BCZ"), "abbreviations"][[1]], "Bicozamycin")))) antibiotics[which(antibiotics$ab == "CCL"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "CCL"), "abbreviations"][[1]], "Cefcatacol")))) antibiotics[which(antibiotics$ab == "ENV"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "ENV"), "abbreviations"][[1]], "Tuberactinomycin")))) antibiotics[which(antibiotics$ab == "KIT"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "KIT"), "abbreviations"][[1]], "Leucomycin")))) antibiotics[which(antibiotics$ab == "LSP"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "LSP"), "abbreviations"][[1]], "lincomycin/spectinomycin")))) antibiotics[which(antibiotics$ab == "MEC"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "MEC"), "abbreviations"][[1]], "Amdinocillin")))) antibiotics[which(antibiotics$ab == "PMR"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "PMR"), "abbreviations"][[1]], "Natamycin")))) # set cephalosporins groups for the ones that could not be determined automatically: antibiotics <- antibiotics %>% mutate(group = case_when( name == "Cefcapene" ~ "Cephalosporins (3rd gen.)", name == "Cefcapene pivoxil" ~ "Cephalosporins (3rd gen.)", name == "Cefditoren pivoxil" ~ "Cephalosporins (3rd gen.)", name == "Cefepime/clavulanic acid" ~ "Cephalosporins (4th gen.)", name == "Cefepime/tazobactam" ~ "Cephalosporins (4th gen.)", name == "Cefetamet pivoxil" ~ "Cephalosporins (3rd gen.)", name == "Cefetecol (Cefcatacol)" ~ "Cephalosporins (4th gen.)", name == "Cefetrizole" ~ "Cephalosporins (unclassified gen.)", name == "Cefoselis" ~ "Cephalosporins (4th gen.)", name == "Cefotaxime/clavulanic acid" ~ "Cephalosporins (3rd gen.)", name == "Cefotaxime/sulbactam" ~ "Cephalosporins (3rd gen.)", name == "Cefotiam hexetil" ~ "Cephalosporins (3rd gen.)", name == "Cefovecin" ~ "Cephalosporins (3rd gen.)", name == "Cefozopran" ~ "Cephalosporins (4th gen.)", name == "Cefpimizole" ~ "Cephalosporins (3rd gen.)", name == "Cefpodoxime proxetil" ~ "Cephalosporins (3rd gen.)", name == "Cefpodoxime/clavulanic acid" ~ "Cephalosporins (3rd gen.)", name == "Cefquinome" ~ "Cephalosporins (4th gen.)", name == "Cefsumide" ~ "Cephalosporins (unclassified gen.)", name == "Ceftaroline" ~ "Cephalosporins (5th gen.)", name == "Ceftaroline/avibactam" ~ "Cephalosporins (5th gen.)", name == "Ceftazidime/avibactam" ~ "Cephalosporins (3rd gen.)", name == "Cefteram" ~ "Cephalosporins (3rd gen.)", name == "Cefteram pivoxil" ~ "Cephalosporins (3rd gen.)", name == "Ceftiofur" ~ "Cephalosporins (3rd gen.)", name == "Ceftizoxime alapivoxil" ~ "Cephalosporins (3rd gen.)", name == "Ceftobiprole" ~ "Cephalosporins (5th gen.)", name == "Ceftobiprole medocaril" ~ "Cephalosporins (5th gen.)", name == "Ceftolozane/enzyme inhibitor" ~ "Cephalosporins (5th gen.)", name == "Ceftolozane/tazobactam" ~ "Cephalosporins (5th gen.)", name == "Cefuroxime axetil" ~ "Cephalosporins (2nd gen.)", TRUE ~ group )) antibiotics[which(antibiotics$ab %in% c("CYC", "LNZ", "THA", "TZD")), "group"] <- "Oxazolidinones" # add clindamycin inducible screening clin <- antibiotics |> filter(ab == "FOX1") |> mutate(ab = as.character("CLI1"), name = "Clindamycin inducible screening", group = "Macrolides/lincosamides") antibiotics <- antibiotics |> mutate(ab = as.character(ab)) |> bind_rows(clin) class(antibiotics$ab) <- c("ab", "character") antibiotics[which(antibiotics$ab == "CLI1"), "abbreviations"][[1]] <- list(c("clindamycin inducible", "clinda inducible", "clin inducible")) # add pretomanid antibiotics <- antibiotics %>% mutate(ab = as.character(ab)) %>% bind_rows(antibiotics %>% mutate(ab = as.character(ab)) %>% filter(ab == "SMF") %>% mutate( ab = "PMD", atc = "J04AK08", cid = 456199, name = "Pretomanid", abbreviations = list(""), oral_ddd = NA_real_ )) # update ATC codes from WHOCC website ------------------------------------- # last time checked: 2024-02-22 library(rvest) updated_atc <- as.list(antibiotics$atc) get_atcs <- function(ab_name, type = "human") { if (type == "human") { url <- "https://atcddd.fhi.no/atc_ddd_index/" } else if (type == "veterinary") { url <- "https://atcddd.fhi.no/atcvet/atcvet_index/" } else { stop("invalid type") } ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE) # we will do a search on their website, which means: # go to the url atc_tbl <- read_html(url) %>% # get all forms html_form() %>% # get the second form (the first form is a global website form) .[[2]] %>% # set the name input box to our search parameter html_form_set(name = ab_name) %>% # hit Submit html_form_submit() %>% # read the resulting page read_html() %>% # retrieve the table on it html_node("table") %>% # transform it to an R data set html_table(header = FALSE) # and get the ATCs (first column) of only exact hits unique(as.character(atc_tbl[which(tolower(atc_tbl[, 2, drop = TRUE]) == ab_name), 1, drop = TRUE])) } # this takes around 4 minutes (some are skipped and go faster) for (i in seq_len(nrow(antibiotics))) { message(percentage(i / nrow(antibiotics), digits = 1), " - Downloading ", antibiotics$name[i], appendLF = FALSE ) atcs <- get_atcs(antibiotics$name[i], type = "human") if (all(is.na(atcs))) { atcs <- get_atcs(antibiotics$name[i], type = "veterinary") } if (length(atcs) > 0) { updated_atc[[i]] <- atcs message(" (", length(atcs), " results)") # let the WHO server rest for a second - they might have a limitation on the queries per second Sys.sleep(1) } else { message(" (skipping)") } } antibiotics$atc <- updated_atc # update DDDs from WHOCC website ------------------------------------------ # last time checked: 2024-02-22 ddd_oral <- rep(NA_real_, nrow(antibiotics)) ddd_oral_units <- rep(NA_character_, nrow(antibiotics)) ddd_iv <- rep(NA_real_, nrow(antibiotics)) ddd_iv_units <- rep(NA_character_, nrow(antibiotics)) progress <- progress_ticker(nrow(antibiotics)) for (i in seq_len(nrow(antibiotics))) { on.exit(close(progress)) progress$tick() atcs <- antibiotics$atc[[i]] if (!all(is.na(atcs))) { for (j in seq_len(length(atcs))) { # oral if (is.na(ddd_oral[i])) { ddd_oral[i] <- atc_online_ddd(atcs[j], administration = "O") if (!is.na(ddd_oral[i])) { ddd_oral_units[i] <- atc_online_ddd_units(atcs[j], administration = "O") } } # parenteral if (is.na(ddd_iv[i])) { ddd_iv[i] <- atc_online_ddd(atcs[j], administration = "P") if (!is.na(ddd_iv[i])) { ddd_iv_units[i] <- atc_online_ddd_units(atcs[j], administration = "P") } } } } if (!is.na(ddd_oral[i]) | !is.na(ddd_iv[i])) { # let the WHO server rest for 0.25 second - they might have a limitation on the queries per second Sys.sleep(0.25) } } antibiotics$oral_ddd <- ddd_oral antibiotics$oral_units <- ddd_oral_units antibiotics$iv_ddd <- ddd_iv antibiotics$iv_units <- ddd_iv_units # Wrap up ----------------------------------------------------------------- # set as data.frame again antibiotics <- dataset_UTF8_to_ASCII(as.data.frame(antibiotics, stringsAsFactors = FALSE)) class(antibiotics$ab) <- c("ab", "character") antibiotics <- dplyr::arrange(antibiotics, name) # REFER TO data-raw/loinc.R FOR ADDING LOINC CODES # make all abbreviations and synonyms lower case, unique and alphabetically sorted ---- for (i in 1:nrow(antibiotics)) { abb <- as.character(sort(unique(tolower(antibiotics[i, "abbreviations", drop = TRUE][[1]])))) abb <- abb[abb != "" & abb %unlike% ":"] syn <- as.character(sort(unique(tolower(antibiotics[i, "synonyms", drop = TRUE][[1]])))) syn <- syn[syn != "" & syn %unlike% ":"] antibiotics[i, "abbreviations"][[1]] <- ifelse(length(abb) == 0, list(""), list(abb)) antibiotics[i, "synonyms"][[1]] <- ifelse(length(syn) == 0, list(""), list(syn)) if ("loinc" %in% colnames(antibiotics)) { loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc", drop = TRUE][[1]])))) loinc <- loinc[loinc != ""] antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc)) } } usethis::use_data(antibiotics, overwrite = TRUE, version = 2, compress = "xz") rm(antibiotics)