diff --git a/DESCRIPTION b/DESCRIPTION index ad30edb04..75e335419 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9147 +Version: 3.0.1.9148 Date: 2026-10-15 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index c9ded65e0..e0a983603 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9147 +# AMR 3.0.1.9148 Planned as v3.1.0, mid October 2026. @@ -74,6 +74,8 @@ Planned as v3.1.0, mid October 2026. * Fixed streptomycin breakpoints imported from WHONET, which were coded as streptoduocin (`STR`) instead of streptomycin (`STR1`) * Fixed CLSI breakpoints for sulbactam/durlobactam, which were coded as sulfadimethoxine (`SUD`), and added the missing EUCAST 2011 breakpoints for roxithromycin (#308) * Fixed some EUCAST Expert Rules, mostly on *S. pneumoniae* + * Zone diameters for which the guideline has no S category (coded by WHONET as an S breakpoint of 80 or 99 mm) are now blocking rows for EUCAST, e.g. cefuroxime oral in *H. influenzae* in EUCAST 2011, and keep only the R breakpoint for CLSI, e.g. fluconazole in *C. glabrata*. Previously, these S breakpoints were stored as 50 mm. + * Breakpoints and ECOFFs for *Salmonella* serovars Typhi, Typhimurium, and Paratyphi, and ECOFFs for the *Bacteroides fragilis* complex, are now assigned to these taxa instead of to *S. enterica* subsp. *enterica* and *B. fragilis*, and ECOFFs of amphotericin B for *Neocosmospora solani* were added * Microorganism coercion (`as.mo()`) and properties (`mo_*()`) * Considerably faster through one consistent session cache design, which is cleared when lookup tables change, e.g., after `add_custom_microorganisms()` (#313) * `mo_*()` functions now retrieve properties of valid `mo` input directly, and only for unique values @@ -81,7 +83,7 @@ Planned as v3.1.0, mid October 2026. * Previously coerced input is now recognised again, e.g., for an unknown species of a known genus, instead of being matched again on every call (#313) * `mo_uncertainties()` now also lists uncertainties of previously coerced input * Translated names in the set language are now recognised, such as the output of `mo_name(x, language = "fr")`, and cached per language - * Input of the form `"X complex"` now falls back to `"X"` when the complex is not a distinct taxon, preventing `NA` for valid clinical descriptions such as `"Proteus vulgaris complex"` (#287) + * Input of the form `"X complex"` now falls back to `"X"` when the complex is not a distinct taxon, preventing `NA` for valid clinical descriptions such as `"Proteus vulgaris complex"`, while a complex named after several of its species returns the complex of one of them, e.g., `"Acinetobacter calcoaceticus-baumannii complex"` returns *A. baumannii* complex (#287) * Abbreviated genus input now ranks candidates with an exactly matching species epithet above more prevalent organisms, so that e.g. `"S. apiospermum"` returns *Scedosporium apiospermum* instead of a *Staphylococcus* species (#288) * Abbreviated genus input for species with subspecies (e.g., `"P. ovale"`) now returns the species instead of a more prevalent organism, while explicit subspecies (e.g., `"P. ovale curtisi"`) are preserved (#288) * *Salmonella* serovars written with the species, such as `"Salmonella enterica serovar Typhi"`, no longer return *Salmonella bongori* or another subspecies @@ -120,7 +122,7 @@ Planned as v3.1.0, mid October 2026. * MICs and disk diffusion * New argument `round_to_next_log2` in `as.mic()` and `rescale_mic()` to round values up to the nearest log2 dilution level (#255) * `as.mic()` now handles values in scientific notation (e.g., `1e-3`) correctly - * Input validation of `as.disk()` is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter + * Input validation of `as.disk()` is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter. Values higher than 50 mm now return `NA` with a warning, instead of being set to 50 mm. * MDRO determination (`mdro()`) * Resistance can now be inferred from a drug/inhibitor combination when the column of the base drug is absent (e.g., piperacillin inferred from piperacillin/tazobactam). This is controlled with the new argument `infer_from_combinations` (default: `TRUE`) (#209). * BRMO classification now includes bacterial complexes (#275) diff --git a/R/data.R b/R/data.R index 5dc7880c1..888f50e49 100755 --- a/R/data.R +++ b/R/data.R @@ -313,7 +313,9 @@ #' The default is `"human"`, which can also be set with the package option [`AMR_breakpoint_type`][AMR-options]. Use [`as.sir(..., breakpoint_type = ...)`][as.sir()] to interpret raw data using a specific breakpoint type, e.g. `as.sir(..., breakpoint_type = "ECOFF")` to use ECOFFs. #' #' ### Blocking Rows -#' Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", breakpoints in brackets, or an organism excluded with "except"), [as.sir()] must not fall back to the breakpoint of a broader taxon, such as the breakpoint for *Vibrio* spp. where EUCAST gives "IE" for *V. fluvialis*. Such cases are included as "blocking rows": rows in which `breakpoint_S` and `breakpoint_R` are both `NA` and the `note` starts with `"[No breakpoint]"` followed by the reason. [as.sir()] returns `NA` for these. This currently applies to `r format(sum(is.na(clinical_breakpoints$breakpoint_S) & is.na(clinical_breakpoints$breakpoint_R)), big.mark = " ")` rows. Remove them with `subset(clinical_breakpoints, !is.na(breakpoint_S))` if only actual breakpoints are needed. +#' Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", breakpoints in brackets, an organism excluded with "except", or no S category for a zone diameter), [as.sir()] must not fall back to the breakpoint of a broader taxon, such as the breakpoint for *Vibrio* spp. where EUCAST gives "IE" for *V. fluvialis*. Such cases are included as "blocking rows": rows in which `breakpoint_S` and `breakpoint_R` are both `NA` and the `note` starts with `"[No breakpoint]"` followed by the reason. [as.sir()] returns `NA` for these. This currently applies to `r format(sum(is.na(clinical_breakpoints$breakpoint_S) & is.na(clinical_breakpoints$breakpoint_R)), big.mark = " ")` rows. Remove them with `subset(clinical_breakpoints, !is.na(breakpoint_S))` if only actual breakpoints are needed. +#' +#' Where another guideline has no S category for a zone diameter, such as CLSI for fluconazole in *C. glabrata* (SDD and R only), only `breakpoint_R` is given, and the `note` starts with `"[No S category]"`. [as.sir()] then returns R where applicable, and `NA` otherwise. #' #' ### Imported From WHONET #' Some breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software. diff --git a/R/disk.R b/R/disk.R index c1b686445..8d95004db 100755 --- a/R/disk.R +++ b/R/disk.R @@ -35,7 +35,7 @@ #' @param na.rm A [logical] indicating whether missing values should be removed. #' @details Interpret disk values as SIR values with [as.sir()]. It supports guidelines from EUCAST and CLSI. #' -#' Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 0-50 range will return `NA`. +#' Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Decimal values are rounded up. All input values outside the 0-50 range, including values higher than 50, return `NA` with a warning. #' @return An [integer] with additional class [`disk`] #' @aliases disk #' @export diff --git a/R/mo.R b/R/mo.R index cb628c5ef..5f709f939 100755 --- a/R/mo.R +++ b/R/mo.R @@ -344,6 +344,16 @@ as.mo <- function(x, if (x_out %in% MO_lookup_current$fullname_lower) { return(as.character(MO_lookup_current$mo[match(x_out, MO_lookup_current$fullname_lower)])) } + # a complex named after several of its species, such as 'Acinetobacter calcoaceticus-baumannii complex', must return the complex of one of these species (here 'Acinetobacter baumannii complex') instead of being matched as one of the species after the " complex" was stripped + x_words <- strsplit(x_out, " ", fixed = TRUE)[[1]] + if (length(x_words) >= 2) { + x_epithets <- strsplit(paste(x_words[-1], collapse = " "), "[-/ ]+", perl = TRUE)[[1]] + x_complexes <- paste(x_words[1], x_epithets[x_epithets != ""], "complex") + x_complexes <- x_complexes[x_complexes %in% MO_lookup_current$fullname_lower] + if (length(x_complexes) > 0) { + return(as.character(MO_lookup_current$mo[match(x_complexes[1], MO_lookup_current$fullname_lower)])) + } + } } # Salmonella serovars are stored without species (e.g. 'Salmonella Typhi'), but are often written with it, as in diff --git a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R index a7e2acef2..8cbbb0299 100644 --- a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R +++ b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R @@ -113,7 +113,7 @@ unmatched <- unmatched |> keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic" ) |> arrange(keep) -unmatched |> View() +if (interactive()) View(unmatched) unmatched <- unmatched |> filter(keep == TRUE) @@ -171,8 +171,11 @@ organisms <- organisms |> filter(code != "XXX") organisms |> filter(code == "SGM") # organisms <- organisms |> # filter(!(code == "SGM" & name %like% "Streptococcus")) -# this must be empty: -organisms$code[organisms$code |> duplicated()] +# this must be empty, e.g. a species group code that as.mo() resolves to another taxon than its organism code: +if (anyDuplicated(organisms$code) > 0) { + print(organisms |> filter(code %in% code[duplicated(code)])) + stop("WHONET organism code(s) resolve to more than one microorganism, see above") +} saveRDS(organisms, "data-raw/organisms.rds", version = 2) @@ -230,22 +233,11 @@ devtools::load_all() # now that we have the correct MO codes, get the breakpoints and convert them -whonet_breakpoints_raw |> - count(GUIDELINES, BREAKPOINT_TYPE) |> - pivot_wider(names_from = BREAKPOINT_TYPE, values_from = n) |> - janitor::adorn_totals(where = c("row", "col")) -whonet_breakpoints_raw |> - filter(YEAR == format(Sys.Date(), "%Y")) |> - count(GUIDELINES, YEAR, BREAKPOINT_TYPE) |> - pivot_wider(names_from = BREAKPOINT_TYPE, values_from = n) |> - janitor::adorn_totals(where = c("row", "col")) +# overview tables with row and column totals, for inspection only +with(whonet_breakpoints_raw, addmargins(table(GUIDELINES, BREAKPOINT_TYPE))) +with(whonet_breakpoints_raw |> filter(YEAR == format(Sys.Date(), "%Y")), addmargins(table(GUIDELINES, BREAKPOINT_TYPE))) # compared to current -AMR::clinical_breakpoints |> - count(GUIDELINES = gsub("[^a-zA-Z]", "", guideline), type) |> - arrange(tolower(type)) |> - pivot_wider(names_from = type, values_from = n) |> - as.data.frame() |> - janitor::adorn_totals(where = c("row", "col")) +with(AMR::clinical_breakpoints, addmargins(table(GUIDELINES = gsub("[^a-zA-Z]", "", guideline), type))) breakpoints <- whonet_breakpoints_raw |> mutate(code = toupper(ORGANISM_CODE)) |> @@ -301,8 +293,11 @@ whonet_code_check <- breakpoints |> by_name = as.ab(ANTIBIOTIC, info = FALSE) ) |> filter(is.na(by_code) | is.na(by_name) | by_code != by_name) -# this should be empty: -whonet_code_check +# this must be empty: +if (nrow(whonet_code_check) > 0) { + print(whonet_code_check) + stop("WHONET antimicrobial code(s) do not match WHONET's own name of the agent, add them to `whonet_ab_recode`") +} ## Build new breakpoints table ---- @@ -333,7 +328,8 @@ breakpoints_new <- breakpoints |> breakpoint_S = ifelse(type == "ECOFF" & is.na(S) & !is.na(ECV_ECOFF), ECV_ECOFF, S), breakpoint_R = ifelse(type == "ECOFF" & is.na(R) & !is.na(ECV_ECOFF), ECV_ECOFF, R), uti = ifelse(is.na(site), FALSE, gsub(".*(UTI|urinary|urine).*", "UTI", site) == "UTI"), - is_SDD = !is.na(SDD) + is_SDD = !is.na(SDD), + note = NA_character_ ) |> # Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII: mutate(disk_dose = disk_dose %>% @@ -346,9 +342,11 @@ breakpoints_new <- breakpoints |> distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE) # fix reference table names -breakpoints_new |> - filter(guideline %like% "EUCAST", is.na(ref_tbl)) |> - View() +if (interactive()) { + breakpoints_new |> + filter(guideline %like% "EUCAST", is.na(ref_tbl)) |> + View() +} breakpoints_new <- breakpoints_new |> mutate(ref_tbl = case_when( is.na(ref_tbl) & guideline %like% "EUCAST 202" ~ lead(ref_tbl), @@ -357,6 +355,18 @@ breakpoints_new <- breakpoints_new |> )) # clean disk zones +# WHONET uses an S breakpoint above 50 mm (e.g. 80 or 99) where the guideline has no S category for a zone diameter, e.g. EUCAST 2011 for cefuroxime oral in H. influenzae. These cannot be stored as zone diameters (as.disk() returns NA for values above 50 mm), so the WHONET value is kept in `S_above_50` and handled under "Zone diameters without S category" below, after the fixes for WHONET errors. Any other value outside 0-50 mm must stop the script. +breakpoints_new <- breakpoints_new |> + mutate( + S_above_50 = if_else(method == "DISK" & type != "ECOFF" & breakpoint_S > 50, breakpoint_S, NA_real_), + breakpoint_S = if_else(is.na(S_above_50), breakpoint_S, NA_real_) + ) +invalid_disk <- breakpoints_new |> + filter(method == "DISK" & ((!is.na(breakpoint_S) & (breakpoint_S < 0 | breakpoint_S > 50)) | (!is.na(breakpoint_R) & (breakpoint_R < 0 | breakpoint_R > 50)))) +if (nrow(invalid_disk) > 0) { + print(invalid_disk |> select(guideline, type, mo, ab, breakpoint_S, breakpoint_R)) + stop(nrow(invalid_disk), " zone diameter breakpoint(s) outside 0-50 mm that are not an S breakpoint of a guideline without S category, see above") +} breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S", drop = TRUE])) breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R", drop = TRUE])) @@ -384,8 +394,6 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- m breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1] breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1] -# S breakpoints must never be missing: -anyNA(breakpoints_new$breakpoint_S) # a lot of R breakpoints are missing, but for CLSI this is required and can be set using as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...) # 2025-04-20/ For EUCAST, this should not be the case, only happens to old guideline now it seems @@ -452,7 +460,7 @@ kleb_tmp_disk <- breakpoints_new |> uncount(length(kleb_spp)) |> mutate(mo = kleb_spp) breakpoints_new <- breakpoints_new |> - filter(!(guideline == "EUCAST 2026" & method == "MIC" & ab == "TMP" & mo == as.mo("Klebsiella"))) |> + filter(!(guideline == "EUCAST 2026" & ab == "TMP" & mo == as.mo("Klebsiella"))) |> bind_rows( kleb_tmp_mic, kleb_tmp_disk @@ -472,13 +480,41 @@ breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpo breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1 breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1 +# Zone diameters without S category: for EUCAST, there is no breakpoint for the organism then, so these become blocking rows (see "Blocking rows" in the EUCAST script, reproduction_of_clinical_breakpoints_eucast.R). Other guidelines keep the R breakpoint, so that as.sir() can still return R, e.g. CLSI for fluconazole in C. glabrata (SDD >= 15 mm, R <= 14 mm, no S category). Rows whose S breakpoint was set by the fixes above are left alone. +no_S_category <- !is.na(breakpoints_new$S_above_50) & is.na(breakpoints_new$breakpoint_S) +breakpoints_new |> + filter(no_S_category) |> + select(guideline, type, mo, ab, S_above_50, breakpoint_R) +no_S_eucast <- no_S_category & breakpoints_new$guideline %like% "EUCAST" +breakpoints_new$note[no_S_eucast] <- paste0("[No breakpoint] EUCAST gives no S category for this zone diameter (S >= ", breakpoints_new$S_above_50[no_S_eucast], " mm in WHONET)") +breakpoints_new$breakpoint_R[no_S_eucast] <- NA_real_ +breakpoints_new$site[no_S_eucast] <- NA_character_ +no_S_other <- no_S_category & !no_S_eucast +breakpoints_new$note[no_S_other] <- paste0("[No S category] ", gsub(" .*", "", breakpoints_new$guideline[no_S_other]), " gives no S category for this zone diameter (S >= ", breakpoints_new$S_above_50[no_S_other], " mm in WHONET), so only R can be interpreted") +# a blocking row is only kept where the organism has no breakpoint of its own for that agent, method and UTI status +is_blocker <- grepl("^\\[No breakpoint\\] ", breakpoints_new$note) +has_own_bp <- breakpoints_new[!is_blocker, ] |> distinct(guideline, type, host, mo, ab, method, uti) +breakpoints_new <- bind_rows( + breakpoints_new[!is_blocker, ], + breakpoints_new[is_blocker, ] |> anti_join(has_own_bp, by = c("guideline", "type", "host", "mo", "ab", "method", "uti")) +) |> + select(-S_above_50) +# S breakpoints must never be missing, except in blocking rows and for zone diameters without S category +missing_S <- breakpoints_new |> + filter(is.na(breakpoint_S) & !grepl("^\\[(No breakpoint|No S category)\\] ", note)) +if (nrow(missing_S) > 0) { + print(missing_S |> select(guideline, type, mo, ab, method, breakpoint_S, breakpoint_R)) + stop(nrow(missing_S), " row(s) without S breakpoint, see above") +} + # WHONET still contains PK/PD rules for EUCAST >= 2024, but this was ended from v14 (2024) on +guideline_year <- function(x) as.integer(gsub("[^0-9]", "", x)) breakpoints_new <- breakpoints_new |> - filter(!(guideline %like% "EUCAST (2024|2025|2026)" & ref_tbl == "PK/PD")) + filter(!(guideline %like% "EUCAST" & guideline_year(guideline) >= 2024 & ref_tbl == "PK/PD")) # WHONET still contains generic anaerobic rules for EUCAST >= 2021, but this was ended from v12 (2022) on breakpoints_new <- breakpoints_new |> - filter(!(guideline %like% "EUCAST (2022|2023|2024|2025|2026)" & ref_tbl %like% "anaerob")) + filter(!(guideline %like% "EUCAST" & guideline_year(guideline) >= 2022 & ref_tbl %like% "anaerob")) # WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales: # EUCAST 2023 guideline: S <= 8 and R > 8 @@ -501,11 +537,13 @@ breakpoints_new <- breakpoints_new |> # check the strange duplicates -breakpoints_new |> - mutate(id = paste(guideline, type, host, method, site, mo, ab, uti)) %>% - filter(id %in% .$id[which(duplicated(id))]) |> - arrange(desc(guideline)) |> - View() +if (interactive()) { + breakpoints_new |> + mutate(id = paste(guideline, type, host, method, site, mo, ab, uti)) %>% + filter(id %in% .$id[which(duplicated(id))]) |> + arrange(desc(guideline)) |> + View() +} # 2024-06-19/ mostly ECOFFs, but there's no explanation in the whonet_breakpoints_raw df, we have to remove duplicates # 2025-04-20/ same, most important one seems M. tuberculosis in CLSI (also in 2025) breakpoints_new <- breakpoints_new |> @@ -547,7 +585,9 @@ breakpoints_new <- breakpoints_new |> mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5, mo != "UNKNOWN" ~ 6, # for B_ANAER, etc. TRUE ~ 7 - )) |> + ) + + # a breakpoint of the same organism always precedes its blocking row + if_else(grepl("^\\[No breakpoint\\] ", note), 0.1, 0)) |> # and arrange arrange(desc(guideline), mo, ab, type, host, method) diff --git a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R index 269880511..2fc9ea960 100644 --- a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R +++ b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R @@ -2750,10 +2750,9 @@ merge_eucast_breakpoints <- function(clinical_breakpoints, breakpoints_eucast, e paste(sort(unique(paste(replaced$guideline, replaced$scope))), collapse = ", "), ") with ", nrow(breakpoints_eucast), " rows from the EUCAST workbooks" ) - # rows without any breakpoint are only kept as the blocking rows of the - # EUCAST workbooks (see "Blocking rows") + # rows without any breakpoint are only kept as blocking rows (see "Blocking rows"), which also come from the WHONET-based rows for zone diameters without S category, e.g. EUCAST 2011 kept |> - filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) |> + filter((!(is.na(breakpoint_S) & is.na(breakpoint_R)) | grepl("^\\[No breakpoint\\] ", note)) & !is.na(mo) & !is.na(ab)) |> bind_rows(breakpoints_eucast) |> arrange(desc(guideline), mo, ab, type, host, method, rank_index) |> distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE) |> diff --git a/data-raw/clin_break.md5 b/data-raw/clin_break.md5 index be7f39491..abf95dac2 100644 --- a/data-raw/clin_break.md5 +++ b/data-raw/clin_break.md5 @@ -1 +1 @@ -48ce51f62aa57d2fc24ef71500874b31 +19deed740b29b33d288443a1528c0fcd diff --git a/data-raw/datasets/clinical_breakpoints.dta b/data-raw/datasets/clinical_breakpoints.dta index 664b448ab..becb80aa4 100644 Binary files a/data-raw/datasets/clinical_breakpoints.dta and b/data-raw/datasets/clinical_breakpoints.dta differ diff --git a/data-raw/datasets/clinical_breakpoints.feather b/data-raw/datasets/clinical_breakpoints.feather index 6878c287c..876a621be 100644 Binary files a/data-raw/datasets/clinical_breakpoints.feather and b/data-raw/datasets/clinical_breakpoints.feather differ diff --git a/data-raw/datasets/clinical_breakpoints.parquet b/data-raw/datasets/clinical_breakpoints.parquet index c8b46e774..1de268890 100644 Binary files a/data-raw/datasets/clinical_breakpoints.parquet and b/data-raw/datasets/clinical_breakpoints.parquet differ diff --git a/data-raw/datasets/clinical_breakpoints.rds b/data-raw/datasets/clinical_breakpoints.rds index d6cc899b2..fcb326b7b 100644 Binary files a/data-raw/datasets/clinical_breakpoints.rds and b/data-raw/datasets/clinical_breakpoints.rds differ diff --git a/data-raw/datasets/clinical_breakpoints.sav b/data-raw/datasets/clinical_breakpoints.sav index 50104bc34..579d9c555 100644 Binary files a/data-raw/datasets/clinical_breakpoints.sav and b/data-raw/datasets/clinical_breakpoints.sav differ diff --git a/data-raw/datasets/clinical_breakpoints.txt b/data-raw/datasets/clinical_breakpoints.txt index c4eb9c69b..3713de876 100644 --- a/data-raw/datasets/clinical_breakpoints.txt +++ b/data-raw/datasets/clinical_breakpoints.txt @@ -407,10 +407,12 @@ "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MFX" "ECOFF" 2 2 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_BCTRD_FRGL" 2 "MTR" "ECOFF" "5 mcg" 25 25 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MTR" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MTR" "ECOFF" 4 4 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "TGC" "ECOFF" 4 4 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_BCTRD_FRGL" 2 "TZP" "ECOFF" "30/6 mcg" 24 24 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "TZP" "ECOFF" 0.5 0.5 FALSE FALSE +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL-C" 2.5 "MTR" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL-C" 2.5 "TZP" "ECOFF" 0.5 0.5 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_OVTS" 2 "IPM" "ECOFF" 0.5 0.5 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_OVTS" 2 "MEM" "ECOFF" 0.25 0.25 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_BCTRD_THTT" 2 "IPM" "ECOFF" 2 2 FALSE FALSE @@ -3169,7 +3171,7 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm d "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AMP" "ECOFF" 4 4 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AMX" "ECOFF" 4 4 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" "15 mcg" 12 12 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 16 16 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "ECOFF" "10 mcg" 20 20 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "ECOFF" 2 2 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "CEP" "ECOFF" 16 16 FALSE FALSE @@ -3206,6 +3208,8 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm d "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TMP" "ECOFF" "5 mcg" 22 22 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "TMP" "ECOFF" 2 2 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 2 2 FALSE FALSE "EUCAST 2026" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "ATM" "S.maltophilia (file: Clinical Breakpoint Tables v. 16.1)" FALSE FALSE "[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)" "EUCAST 2026" "human" "human" "MIC" "B_STNTR_MLTP" 2.1 "ATM" "S.maltophilia (file: Clinical Breakpoint Tables v. 16.1)" FALSE FALSE "[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)" "EUCAST 2026" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "AZA" "S.maltophilia (file: Clinical Breakpoint Tables v. 16.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [A] The ECOFF can be used to exclude acquired resistance mechanisms (presence of resistance indicated by MICs >8 mg/L or aztreonam-avibactam 30-20 ug disk zone diameter <21 mm)." @@ -5198,14 +5202,6 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_CRYPT_NFRM" 2.1 "VOR" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence)" "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_FUSRM_JKRI" 2 "AMB" "Antifungal ECOFFs" 8 8 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE -"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "AMB" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE @@ -5222,6 +5218,7 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2026" "human" "human" "MIC" "F_MYRZY_GLLR" 2.1 "POS" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [5] The ECOFFs for these species are in general higher than for C. albicans." "EUCAST 2026" "human" "human" "MIC" "F_MYRZY_GLLR" 2.1 "RZF" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [7] Breakpoints apply for MICs determined with Tween 20 supplemented medium according to the EUCAST E.Def 7.4 method." "EUCAST 2026" "human" "human" "MIC" "F_MYRZY_GLLR" 2.1 "VOR" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence)" +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_NCSMS_SOLN" 2 "AMB" "Antifungal ECOFFs" 8 8 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" 1 1 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE @@ -5240,15 +5237,23 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2026" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "RZF" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" 0.016 0.016 FALSE FALSE "[7] Breakpoints apply for MICs determined with Tween 20 supplemented medium according to the EUCAST E.Def 7.4 method." "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_NKSMY_BRTS" 2.1 "VOR" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [5] The ECOFFs for these species are in general higher than for C. albicans." +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" 1 1 FALSE FALSE +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" 0.064 0.064 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2.1 "CAS" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives Note (see note) | [2] Isolates that are susceptible to anidulafungin as well as micafungin should be considered susceptible to caspofungin, until caspofungin breakpoints have been established. EUCAST breakpoints have not yet been established for caspofungin, due to significant inter-laboratory variation in MIC ranges for caspofungin." +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2.1 "FLU" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)" "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2.1 "ISV" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence)" +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2.1 "ITR" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [5] The ECOFFs for these species are in general higher than for C. albicans." +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2.1 "MIF" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [6] MICs for C. krusei are approximately three two-fold dilution steps higher than those for C. albicans and, similarly, those for C. guilliermondii are approximately eight two-fold dilutions higher. In addition, there were only a small number of cases involving these species in the clinical trials. This means there is insufficient evidence (IE) to indicate whether the wild-type population of these pathogens can be considered susceptible to micafungin." +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2.1 "POS" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [5] The ECOFFs for these species are in general higher than for C. albicans." +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" 0.032 0.032 FALSE FALSE "[7] Breakpoints apply for MICs determined with Tween 20 supplemented medium according to the EUCAST E.Def 7.4 method." +"EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2.1 "VOR" "5. Yeast (file: Antifungal Clinical Breakpoint Table v. 12.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [5] The ECOFFs for these species are in general higher than for C. albicans." "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "AMB" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "ITR" "Antifungal ECOFFs" 2 2 FALSE FALSE @@ -5668,10 +5673,12 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MFX" "ECOFF" 2 2 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "DISK" "B_BCTRD_FRGL" 2 "MTR" "ECOFF" "5 mcg" 25 25 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MTR" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "MTR" "ECOFF" 4 4 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "TGC" "ECOFF" 4 4 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "DISK" "B_BCTRD_FRGL" 2 "TZP" "ECOFF" "30/6 mcg" 24 24 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL" 2 "TZP" "ECOFF" 0.5 0.5 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL-C" 2.5 "MTR" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_FRGL-C" 2.5 "TZP" "ECOFF" 0.5 0.5 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_OVTS" 2 "IPM" "ECOFF" 0.5 0.5 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_OVTS" 2 "MEM" "ECOFF" 0.25 0.25 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_BCTRD_THTT" 2 "IPM" "ECOFF" 2 2 FALSE FALSE @@ -8196,7 +8203,7 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm d "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AMP" "ECOFF" 4 4 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AMX" "ECOFF" 4 4 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" "15 mcg" 12 12 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 16 16 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "ECOFF" "10 mcg" 20 20 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "ECOFF" 2 2 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "CEP" "ECOFF" 16 16 FALSE FALSE @@ -8233,6 +8240,8 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm d "EUCAST 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TMP" "ECOFF" "5 mcg" 22 22 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "TMP" "ECOFF" 2 2 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 2 2 FALSE FALSE "EUCAST 2025" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "ATM" "S.maltophilia (file: Clinical Breakpoint Tables v. 15.0)" FALSE FALSE "[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)" "EUCAST 2025" "human" "human" "MIC" "B_STNTR_MLTP" 2.1 "ATM" "S.maltophilia (file: Clinical Breakpoint Tables v. 15.0)" FALSE FALSE "[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)" "EUCAST 2025" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "AZA" "S.maltophilia (file: Clinical Breakpoint Tables v. 15.0)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence)" @@ -10138,23 +10147,13 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_FUSRM_JKRI" 2 "AMB" "Antifungal ECOFFs" 8 8 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "RZF" "Candida" 0.032 0.032 FALSE FALSE -"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "AMB" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "FLU" "Antifungal ECOFFs" 16 16 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "POS" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_NCSMS_SOLN" 2 "AMB" "Antifungal ECOFFs" 8 8 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2025" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE @@ -10168,6 +10167,17 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "RZF" "Antifungal ECOFFs" 0.016 0.016 FALSE FALSE "EUCAST 2025" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "RZF" "Candida" 0.016 0.016 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE +"EUCAST 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE +"EUCAST 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE +"EUCAST 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "AMB" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "ITR" "Antifungal ECOFFs" 2 2 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_TRCHP_INDT" 2 "AMO" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE @@ -12391,19 +12401,19 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm d "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AMP" "ECOFF" "10 mcg" 20 20 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" "15 mcg" 12 12 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 32 32 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "ECOFF" "10 mcg" 20 20 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CHL" "ECOFF" "30 mcg" 20 20 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTB" "ECOFF" "30 mcg" 25 25 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTX" "ECOFF" "5 mcg" 21 21 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "GEN" "ECOFF" "10 mcg" 14 14 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "NAL" "ECOFF" "30 mcg" 16 16 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "PEF" "ECOFF" "5 mcg" 24 24 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "SXT" "ECOFF" "1.25/23.75 mcg" 21 21 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TCY" "ECOFF" "30 mcg" 17 17 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TMP" "ECOFF" "5 mcg" 23 23 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 14.0)" FALSE FALSE "[No breakpoint] EUCAST gives Note (see note) | [A] Zone diameters of >=20 mm for the cefiderocol 30 ug disk correspond to MIC values below the PK-PD breakpoint of S <= 2 mg/L." "EUCAST 2024" "human" "human" "MIC" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 14.0)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [1] Broth microdilution MIC determination must be performed in iron-depleted Mueller-Hinton broth and specific reading instructions must be followed. For testing conditions and reading instructions, see https://www.eucast.org/eucastguidancedocuments/." "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_STNTR_MLTP" 2 "SXT" "ECOFF" "1.25/23.75 mcg" 16 16 FALSE FALSE @@ -13828,22 +13838,13 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_FUSRM_JKRI" 2 "AMB" "Antifungal ECOFFs" 8 8 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE -"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "AMB" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "FLU" "Antifungal ECOFFs" 16 16 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "POS" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_NCSMS_SOLN" 2 "AMB" "Antifungal ECOFFs" 8 8 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE @@ -13856,6 +13857,16 @@ Positive test: Isolates with gentamicin MIC >128 mg/L denote presence of aminogl "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "POS" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "RZF" "Antifungal ECOFFs" 0.016 0.016 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE +"EUCAST 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE +"EUCAST 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE +"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "AMB" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "ITR" "Antifungal ECOFFs" 2 2 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_TRCHP_INDT" 2 "AMO" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE @@ -15938,9 +15949,9 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm. "EUCAST 2023" "human" "human" "DISK" "B_SLMNL" 3.1 "CIP" "Enterobacterales (file: Clinical Breakpoint Tables v. 13.1)" FALSE FALSE "[No breakpoint] EUCAST gives Note (see note) | [A] Tests with a ciprofloxacin 5 ug disk will not reliably detect low-level resistance in Salmonella spp. Perform an MIC test, or infer susceptibility from the pefloxacin 5 ug screening test. | [1] There is clinical evidence for ciprofloxacin to indicate a poor response in systemic infections caused by Salmonella spp. with low-level ciprofloxacin resistance (MIC >0.06 mg/L). The available data relate mainly to Salmonella Typhi but there are also case reports of poor response with other Salmonella species." "EUCAST 2023" "human" "human" "MIC" "B_SLMNL" 3 "CIP" "Enterobacterales (file: Clinical Breakpoint Tables v. 13.1)" 0.064 0.064 FALSE FALSE "[1] There is clinical evidence for ciprofloxacin to indicate a poor response in systemic infections caused by Salmonella spp. with low-level ciprofloxacin resistance (MIC >0.06 mg/L). The available data relate mainly to Salmonella Typhi but there are also case reports of poor response with other Salmonella species." "EUCAST 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE -"EUCAST 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 32 32 FALSE FALSE -"EUCAST 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"EUCAST 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"EUCAST 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"EUCAST 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 13.1)" FALSE FALSE "[No breakpoint] EUCAST gives Note (see note) | [A] Zone diameters of >=20 mm for the cefiderocol 30 ug disk correspond to MIC values below the PK-PD breakpoint of S <= 2 mg/L." "EUCAST 2023" "human" "human" "MIC" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 13.1)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [1] Broth microdilution MIC determination must be performed in iron-depleted Mueller-Hinton broth and specific reading instructions must be followed. For testing conditions and reading instructions, see https://www.eucast.org/eucastguidancedocuments/." "EUCAST 2023" "human" "human" "DISK" "B_STNTR_MLTP" 2 "SXT" "S.maltophilia (file: Clinical Breakpoint Tables v. 13.1)" "1.25/23.75 mcg" 50 16 FALSE FALSE "[A] There may be growth within the inhibition zone. The density of growth may vary from a fine haze to substantial growth (see pictures below). If any zone edge can be seen, ignore growth within the inhibition zone and read the zone diameter. | [1] Trimethoprim:sulfamethoxazole in the ratio 1:19. Breakpoints are expressed as the trimethoprim concentration." @@ -17217,12 +17228,12 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level "EUCAST 2023" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.25 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "F_CRYPT_NFRM" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2023" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2023" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 1e-04 16 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 13.1)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based. More information is available in the EUCAST Guidance Document on how to test and interpret results when there are no breakpoints. | [2] For susceptibility testing purposes, the concentration of clavulanic acid is fixed at 2 mg/L." "EUCAST 2023" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 13.1)" 1 1 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based. More information is available in the EUCAST Guidance Document on how to test and interpret results when there are no breakpoints." "EUCAST 2023" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 13.1)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based. More information is available in the EUCAST Guidance Document on how to test and interpret results when there are no breakpoints." @@ -19228,9 +19239,9 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm. "EUCAST 2022" "human" "human" "DISK" "Screen" "B_SLMNL" 3 "PEF" "Enterobacterales (file: Clinical Breakpoint Tables v. 12.0)" "5 mcg" 24 24 FALSE FALSE "[2/C] The pefloxacin 5 ug breakpoint used to screen for clinical fluoroquinolone resistance in Salmonella spp., can also be used to detect fluoroquinolone resistance mechanisms in other Enterobacterales such as E. coli, K. pneumoniae and Shigella spp. | [B] Susceptibility of Salmonella spp. to ciprofloxacin can be inferred from the pefloxacin disk diffusion screening test. | [1] There is clinical evidence for ciprofloxacin to indicate a poor response in systemic infections caused by Salmonella spp. with low-level ciprofloxacin resistance (MIC >0.06 mg/L). The available data relate mainly to Salmonella Typhi but there are also case reports of poor response with other Salmonella species." "EUCAST 2022" "human" "human" "MIC" "B_SLMNL" 3.1 "PEF" "Enterobacterales (file: Clinical Breakpoint Tables v. 12.0)" FALSE FALSE "[No breakpoint] EUCAST gives NA (not applicable) | [1] There is clinical evidence for ciprofloxacin to indicate a poor response in systemic infections caused by Salmonella spp. with low-level ciprofloxacin resistance (MIC >0.06 mg/L). The available data relate mainly to Salmonella Typhi but there are also case reports of poor response with other Salmonella species. | [2] The pefloxacin 5 ug breakpoint used to screen for clinical fluoroquinolone resistance in Salmonella spp., can also be used to detect fluoroquinolone resistance mechanisms in other Enterobacterales such as E. coli, K. pneumoniae and Shigella spp." "EUCAST 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE -"EUCAST 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 32 32 FALSE FALSE -"EUCAST 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"EUCAST 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"EUCAST 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"EUCAST 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 12.0)" FALSE FALSE "[No breakpoint] EUCAST gives Note (see note) | [A] Zone diameters of >=20 mm for the cefiderocol 30 ug disk correspond to MIC values below the PK-PD breakpoint of S <= 2 mg/L." "EUCAST 2022" "human" "human" "MIC" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 12.0)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [1] Broth microdilution MIC determination must be performed in iron-depleted Mueller-Hinton broth and specific reading instructions must be followed. For testing conditions and reading instructions, see https://www.eucast.org/eucastguidancedocuments/." "EUCAST 2022" "human" "human" "DISK" "B_STNTR_MLTP" 2 "SXT" "S.maltophilia (file: Clinical Breakpoint Tables v. 12.0)" "1.25/23.75 mcg" 50 16 FALSE FALSE "[A] There may be growth within the inhibition zone. The density of growth may vary from a fine haze to substantial growth (see pictures below). If any zone edge can be seen, ignore growth within the inhibition zone and read the zone diameter. | [1] Trimethoprim:sulfamethoxazole in the ratio 1:19. Breakpoints are expressed as the trimethoprim concentration." @@ -20508,12 +20519,12 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level "EUCAST 2022" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.25 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "F_CRYPT_NFRM" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2022" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2022" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 1e-04 16 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 12.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based. More information is available in the EUCAST Guidance Document on how to test and interpret results when there are no breakpoints. | [2] For susceptibility testing purposes, the concentration of clavulanic acid is fixed at 2 mg/L." "EUCAST 2022" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 12.0)" 1 1 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based. More information is available in the EUCAST Guidance Document on how to test and interpret results when there are no breakpoints." "EUCAST 2022" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 12.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based. More information is available in the EUCAST Guidance Document on how to test and interpret results when there are no breakpoints." @@ -23259,11 +23270,17 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm. "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "FOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "TZP" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AMP" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "CXM" "ECOFF" 16 16 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "AMP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "CXM" "ECOFF" 16 16 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "FOX" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_PRTY" 1 "AMP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AMP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "CXM" "ECOFF" 16 16 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "TZP" "ECOFF" 8 8 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_STNTR_MLTP" 2 "DOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 11.0)" FALSE FALSE "[No breakpoint] EUCAST gives Note (see note) | [A] Zone diameters of >=20 mm for the cefiderocol 30 ug disk correspond to MIC values below the PK-PD breakpoint of S <= 2 mg/L." "EUCAST 2021" "human" "human" "MIC" "B_STNTR_MLTP" 2.1 "FDC" "S.maltophilia (file: Clinical Breakpoint Tables v. 11.0)" FALSE FALSE "[No breakpoint] EUCAST gives IE (insufficient evidence) | [1] Broth microdilution MIC determination must be performed in iron-depleted Mueller-Hinton broth and specific reading instructions must be followed. For testing conditions and reading instructions, see http://www.eucast.org/guidance_documents/." @@ -24920,14 +24937,6 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level "EUCAST 2021" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.25 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CLVSP_LSTN" 2 "ITR" "ECOFF" 0.125 0.125 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CLVSP_LSTN" 2 "VOR" "ECOFF" 0.064 0.064 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "ECOFF" 1 1 FALSE FALSE -"EUCAST 2021" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE -"EUCAST 2021" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "ECOFF" 128 128 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "ECOFF" 1 1 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE -"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "ECOFF" 1 1 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "FLU" "ECOFF" 16 16 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "ITR" "ECOFF" 2 2 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "VOR" "ECOFF" 0.25 0.25 FALSE FALSE @@ -24941,6 +24950,14 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "MIF" "ECOFF" 0.032 0.032 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "ECOFF" 1 1 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "ECOFF" 1 1 FALSE FALSE +"EUCAST 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE +"EUCAST 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "ECOFF" 128 128 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "ECOFF" 1 1 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE +"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "ECOFF" 1 1 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 11.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\". | [2] For susceptibility testing purposes, the concentration of clavulanic acid is fixed at 2 mg/L." "EUCAST 2021" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 11.0)" 1 1 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\"." "EUCAST 2021" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 11.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\"." @@ -27576,11 +27593,17 @@ Positive test: Isolates with gentamicin MIC >128 mg/L or a zone diameter <8 mm. "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "FOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "TZP" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AMP" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "CXM" "ECOFF" 16 16 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "ECOFF" 8 8 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "AMP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "CXM" "ECOFF" 16 16 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "FOX" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_PRTY" 1 "AMP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AMP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "CXM" "ECOFF" 16 16 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "MEM" "ECOFF" 0.125 0.125 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "TZP" "ECOFF" 8 8 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_STNTR_MLTP" 2 "DOX" "ECOFF" 8 8 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_STNTR_MLTP" 2 "MNO" "ECOFF" 1 1 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_STNTR_MLTP" 2 "SXT" "ECOFF" 2 2 FALSE FALSE @@ -29187,14 +29210,6 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level "EUCAST 2020" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.25 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CLVSP_LSTN" 2 "ITR" "ECOFF" 0.125 0.125 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CLVSP_LSTN" 2 "VOR" "ECOFF" 0.064 0.064 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "ECOFF" 1 1 FALSE FALSE -"EUCAST 2020" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE -"EUCAST 2020" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "ECOFF" 128 128 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "ECOFF" 1 1 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE -"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "ECOFF" 1 1 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "FLU" "ECOFF" 16 16 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "ITR" "ECOFF" 2 2 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "VOR" "ECOFF" 0.25 0.25 FALSE FALSE @@ -29208,6 +29223,14 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "MIF" "ECOFF" 0.032 0.032 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "ECOFF" 1 1 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "ECOFF" 1 1 FALSE FALSE +"EUCAST 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE +"EUCAST 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "ECOFF" 128 128 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "ECOFF" 1 1 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE +"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "ECOFF" 1 1 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 10.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\". | [2] For susceptibility testing purposes, the concentration of clavulanic acid is fixed at 2 mg/L." "EUCAST 2020" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 10.0)" 1 1 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\"." "EUCAST 2020" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 10.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\"." @@ -31987,12 +32010,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2019" "human" "human" "MIC" "F_CANDD_TRPC" 2 "ITR" "Candida" 0.125 0.125 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.25 FALSE FALSE -"EUCAST 2019" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2019" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 0.002 32 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 9.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\". | [2] For susceptibility testing purposes, the concentration of clavulanic acid is fixed at 2 mg/L." "EUCAST 2019" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 9.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\"." "EUCAST 2019" "human" "human" "MIC" "UNKNOWN" 7 "AMX" "PK PD breakpoints (file: Clinical Breakpoint Tables v. 9.0)" 2 8 FALSE FALSE "[PK-PD] These breakpoints are used only when there are no species-specific breakpoints or other recommendations (a dash or a note) in the species-specific tables. If the MIC is greater than the PK-PD resistant breakpoint, advise against use of the agent. If the MIC is less than or equal to the PK-PD susceptible breakpoint, suggest that the agent can be used with caution. The MIC may also be reported although this is not essential. Include a note that the guidance is based on PK-PD breakpoints only, and include the dosage on which PK-PD breakpoint is based.More information is available in the guidance document \"Antimicrobial susceptibility tests on groups of organisms or agents for which there are no EUCAST breakpoints\"." @@ -32799,12 +32822,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2018" "human" "human" "MIC" "F_CANDD_TRPC" 2 "ITR" "Candida" 0.125 0.125 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE -"EUCAST 2018" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2018" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 0.002 32 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2018" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2018" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 8 16 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE @@ -33605,12 +33628,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2017" "human" "human" "MIC" "F_CANDD_TRPC" 2 "ITR" "Candida" 0.125 0.125 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE -"EUCAST 2017" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2017" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 0.002 32 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2017" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2017" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 8 16 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE @@ -34350,12 +34373,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2016" "human" "human" "MIC" "F_CANDD_TRPC" 2 "ITR" "Candida" 0.125 0.125 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE -"EUCAST 2016" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2016" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 0.002 32 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2016" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2016" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 8 16 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE @@ -35068,12 +35091,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2015" "human" "human" "MIC" "F_CANDD_TRPC" 2 "ITR" "Candida" 0.125 0.125 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE -"EUCAST 2015" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2015" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 0.002 32 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2015" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2015" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 8 16 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE @@ -35783,12 +35806,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2014" "human" "human" "MIC" "F_CANDD_TRPC" 2 "FLU" "Candida" 2 4 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE -"EUCAST 2014" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2014" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Candida" 0.002 32 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE +"EUCAST 2014" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2014" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 8 16 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE @@ -36481,10 +36504,10 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2013" "human" "human" "MIC" "F_CANDD_TRPC" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "F_CANDD_TRPC" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE -"EUCAST 2013" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "AMB" "Candida" 1 1 FALSE FALSE -"EUCAST 2013" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "AMB" "Candida" 1 1 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE +"EUCAST 2013" "human" "human" "MIC" "F_PICHI_KDRV" 2 "AMB" "Candida" 1 1 FALSE FALSE +"EUCAST 2013" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "Unknown" 2 8 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "Unknown" 8 16 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "Unknown" 2 8 FALSE FALSE @@ -37146,14 +37169,14 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "CTB" "Unknown" 1 1 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2 "CTX" "Unknown" "5 mcg" 22 22 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "CTX" "Unknown" 0.125 0.125 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2 "CXA" "Unknown" "30 mcg" 50 25 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2.1 "CXA" "Unknown" "30 mcg" FALSE FALSE "[No breakpoint] EUCAST gives no S category for this zone diameter (S >= 99 mm in WHONET)" "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "CXA" "Unknown" 0.125 1 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2 "CXM" "Unknown" "30 mcg" 25 22 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "CXM" "Unknown" 1 2 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2 "DOR" "Unknown" "10 mcg" 20 20 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "DOR" "Unknown" 1 1 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "DOX" "Unknown" 1 2 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2 "ERY" "Unknown" "15 mcg" 50 12 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2.1 "ERY" "Unknown" "15 mcg" FALSE FALSE "[No breakpoint] EUCAST gives no S category for this zone diameter (S >= 99 mm in WHONET)" "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "ERY" "Unknown" 0.5 16 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_INFL" 2 "ETP" "Unknown" "10 mcg" 20 20 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_INFL" 2 "ETP" "Unknown" 0.5 0.5 FALSE FALSE @@ -37204,14 +37227,14 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "CTB" "Unknown" 1 1 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2 "CTX" "Unknown" "5 mcg" 22 22 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "CTX" "Unknown" 0.125 0.125 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2 "CXA" "Unknown" "30 mcg" 50 25 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2.1 "CXA" "Unknown" "30 mcg" FALSE FALSE "[No breakpoint] EUCAST gives no S category for this zone diameter (S >= 99 mm in WHONET)" "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "CXA" "Unknown" 0.125 1 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2 "CXM" "Unknown" "30 mcg" 25 22 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "CXM" "Unknown" 1 2 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2 "DOR" "Unknown" "10 mcg" 20 20 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "DOR" "Unknown" 1 1 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "DOX" "Unknown" 1 2 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2 "ERY" "Unknown" "15 mcg" 50 12 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2.1 "ERY" "Unknown" "15 mcg" FALSE FALSE "[No breakpoint] EUCAST gives no S category for this zone diameter (S >= 99 mm in WHONET)" "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "ERY" "Unknown" 0.5 16 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_HMPHL_PRNF" 2 "ETP" "Unknown" "10 mcg" 20 20 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_HMPHL_PRNF" 2 "ETP" "Unknown" 0.5 0.5 FALSE FALSE @@ -37298,7 +37321,7 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2011" "human" "human" "MIC" "B_NESSR_MNNG" 2 "TCY" "Unknown" 1 2 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_PSDMN" 3 "AMK" "Unknown" "30 mcg" 18 15 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_PSDMN" 3 "AMK" "Unknown" 8 16 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_PSDMN" 3 "ATM" "Unknown" "30 mcg" 50 16 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_PSDMN" 3.1 "ATM" "Unknown" "30 mcg" FALSE FALSE "[No breakpoint] EUCAST gives no S category for this zone diameter (S >= 99 mm in WHONET)" "EUCAST 2011" "human" "human" "MIC" "B_PSDMN" 3 "ATM" "Unknown" 1 16 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_PSDMN" 3 "CAZ" "Unknown" 8 8 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_PSDMN" 3 "CIP" "Unknown" "5 mcg" 25 22 FALSE FALSE @@ -37592,7 +37615,7 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2 "AMP" "Unknown" "2 mcg" 28 22 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "AMP" "Unknown" 0.5 2 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "AZM" "Unknown" 0.25 0.5 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2 "CEC" "Unknown" "30 mcg" 50 28 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2.1 "CEC" "Unknown" "30 mcg" FALSE FALSE "[No breakpoint] EUCAST gives no S category for this zone diameter (S >= 99 mm in WHONET)" "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "CEC" "Unknown" 0.032 0.5 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2 "CHL" "Unknown" "30 mcg" 20 20 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "CHL" "Unknown" 8 8 FALSE FALSE @@ -37623,7 +37646,7 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "MFX" "Unknown" 0.5 0.5 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "MNO" "Unknown" 0.5 1 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2 "NOR" "Unknown" "10 mcg" 12 12 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2 "OFX" "Unknown" "5 mcg" 50 15 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2.1 "OFX" "Unknown" "5 mcg" FALSE FALSE "[No breakpoint] EUCAST gives no S category for this zone diameter (S >= 99 mm in WHONET)" "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "OFX" "Unknown" 0.125 4 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_STRPT_PNMN" 2 "OXA" "Unknown" "1 mcg" 18 18 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STRPT_PNMN" 2 "PEN" "Unknown" 0.064 2 FALSE FALSE @@ -39226,21 +39249,21 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2026" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" 2 8 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AMP" "Copied from EUCAST 2024" "10 mcg" 20 20 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Copied from EUCAST 2024" "15 mcg" 12 12 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Copied from EUCAST 2024" 32 32 FALSE FALSE -"CLSI 2026" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A-2" "15 mcg" 13 12 FALSE FALSE -"CLSI 2026" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A-2" 16 32 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "Copied from EUCAST 2024" "10 mcg" 20 20 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CHL" "Copied from EUCAST 2024" "30 mcg" 20 20 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTB" "Copied from EUCAST 2024" "30 mcg" 25 25 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTX" "Copied from EUCAST 2024" "5 mcg" 21 21 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "Copied from EUCAST 2024" 8 8 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "GEN" "Copied from EUCAST 2024" "10 mcg" 14 14 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "Copied from EUCAST 2024" 0.064 0.064 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "NAL" "Copied from EUCAST 2024" "30 mcg" 16 16 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "PEF" "Copied from EUCAST 2024" "5 mcg" 24 24 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "SXT" "Copied from EUCAST 2024" "1.25/23.75 mcg" 21 21 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TCY" "Copied from EUCAST 2024" "30 mcg" 17 17 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TMP" "Copied from EUCAST 2024" "5 mcg" 23 23 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "Copied from EUCAST 2024" 0.064 0.064 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Copied from EUCAST 2024" 32 32 FALSE FALSE +"CLSI 2026" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A-2" "15 mcg" 13 12 FALSE FALSE +"CLSI 2026" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A-2" 16 32 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "Copied from EUCAST 2024" 8 8 FALSE FALSE "CLSI 2026" "human" "human" "MIC" "B_SMYCS" 3 "AMC" "M24 Table 7" 8 32 FALSE FALSE "CLSI 2026" "human" "human" "MIC" "B_SMYCS" 3 "AMK" "M24 Table 7" 8 16 FALSE FALSE "CLSI 2026" "human" "human" "MIC" "B_SMYCS" 3 "CIP" "M24 Table 7" 1 4 FALSE FALSE @@ -40241,22 +40264,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "POS" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_FUSRM_JKRI" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 8 8 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2026" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2026" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2026" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "Copied from EUCAST 2024 Antifungal ECOFFs" 128 128 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2026" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2026" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.032 0.032 FALSE FALSE -"CLSI 2026" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE -"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE -"CLSI 2026" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2026" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "ANI" "M59 Table 1" 0.25 0.25 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "M59 Table 1" 1 1 FALSE FALSE @@ -40275,12 +40282,13 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2026" "human" "human" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Table 1" "10 mcg" 16 13 FALSE FALSE "CLSI 2026" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "MIF" "M27 Table 1" 2 8 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NCSMS_SOLN" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 8 8 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE "CLSI 2026" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2026" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M59 Table 4" 8 8 FALSE FALSE -"CLSI 2026" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE TRUE +"CLSI 2026" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE TRUE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2026" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M27 Table 1" 1e-04 64 FALSE TRUE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ITR" "M59 Table 1" 4 4 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "MIF" "M59 Table 4" 0.032 0.032 FALSE FALSE @@ -40290,6 +40298,22 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.016 0.016 FALSE FALSE "CLSI 2026" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "RZF" "M27 Table 1" 0.5 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2026" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "Copied from EUCAST 2024 Antifungal ECOFFs" 128 128 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2026" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.032 0.032 FALSE FALSE +"CLSI 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE +"CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE +"CLSI 2026" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2026" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "ITR" "Copied from EUCAST 2024 Antifungal ECOFFs" 2 2 FALSE FALSE "CLSI 2026" "ECOFF" "ECOFF" "MIC" "F_TRCHP_INDT" 2 "AMO" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.5 0.5 FALSE FALSE @@ -41854,21 +41878,21 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2025" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" 2 8 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AMP" "Copied from EUCAST 2024" "10 mcg" 20 20 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Copied from EUCAST 2024" "15 mcg" 12 12 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Copied from EUCAST 2024" 32 32 FALSE FALSE -"CLSI 2025" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A-2" "15 mcg" 13 12 FALSE FALSE -"CLSI 2025" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A-2" 16 32 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "Copied from EUCAST 2024" "10 mcg" 20 20 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CHL" "Copied from EUCAST 2024" "30 mcg" 20 20 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTB" "Copied from EUCAST 2024" "30 mcg" 25 25 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTX" "Copied from EUCAST 2024" "5 mcg" 21 21 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "Copied from EUCAST 2024" 8 8 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "GEN" "Copied from EUCAST 2024" "10 mcg" 14 14 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "Copied from EUCAST 2024" 0.064 0.064 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "NAL" "Copied from EUCAST 2024" "30 mcg" 16 16 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "PEF" "Copied from EUCAST 2024" "5 mcg" 24 24 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "SXT" "Copied from EUCAST 2024" "1.25/23.75 mcg" 21 21 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TCY" "Copied from EUCAST 2024" "30 mcg" 17 17 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TMP" "Copied from EUCAST 2024" "5 mcg" 23 23 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "Copied from EUCAST 2024" 0.064 0.064 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Copied from EUCAST 2024" 32 32 FALSE FALSE +"CLSI 2025" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A-2" "15 mcg" 13 12 FALSE FALSE +"CLSI 2025" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A-2" 16 32 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "Copied from EUCAST 2024" 8 8 FALSE FALSE "CLSI 2025" "human" "human" "MIC" "B_SMYCS" 3 "AMC" "M24 Table 7" 8 32 FALSE FALSE "CLSI 2025" "human" "human" "MIC" "B_SMYCS" 3 "AMK" "M24 Table 7" 8 16 FALSE FALSE "CLSI 2025" "human" "human" "MIC" "B_SMYCS" 3 "CIP" "M24 Table 7" 1 4 FALSE FALSE @@ -42865,22 +42889,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "POS" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_FUSRM_JKRI" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 8 8 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2025" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "Copied from EUCAST 2024 Antifungal ECOFFs" 128 128 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2025" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.032 0.032 FALSE FALSE -"CLSI 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE -"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE -"CLSI 2025" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2025" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "ANI" "M59 Table 1" 0.25 0.25 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "M59 Table 1" 1 1 FALSE FALSE @@ -42899,12 +42907,13 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2025" "human" "human" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Table 1" "10 mcg" 16 13 FALSE FALSE "CLSI 2025" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "MIF" "M27 Table 1" 2 8 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NCSMS_SOLN" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 8 8 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE "CLSI 2025" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2025" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M59 Table 4" 8 8 FALSE FALSE -"CLSI 2025" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE TRUE +"CLSI 2025" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE TRUE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2025" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M27 Table 1" 1e-04 64 FALSE TRUE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ITR" "M59 Table 1" 4 4 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "MIF" "M59 Table 4" 0.032 0.032 FALSE FALSE @@ -42914,6 +42923,22 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.016 0.016 FALSE FALSE "CLSI 2025" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "RZF" "M27 Table 1" 0.5 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2025" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "Copied from EUCAST 2024 Antifungal ECOFFs" 128 128 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2025" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.032 0.032 FALSE FALSE +"CLSI 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE +"CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE +"CLSI 2025" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2025" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "ITR" "Copied from EUCAST 2024 Antifungal ECOFFs" 2 2 FALSE FALSE "CLSI 2025" "ECOFF" "ECOFF" "MIC" "F_TRCHP_INDT" 2 "AMO" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.5 0.5 FALSE FALSE @@ -44480,21 +44505,21 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2024" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" 2 8 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AMP" "Copied from EUCAST 2024" "10 mcg" 20 20 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Copied from EUCAST 2024" "15 mcg" 12 12 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Copied from EUCAST 2024" 32 32 FALSE FALSE -"CLSI 2024" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A-2" "15 mcg" 13 12 FALSE FALSE -"CLSI 2024" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A-2" 16 32 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CAZ" "Copied from EUCAST 2024" "10 mcg" 20 20 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CHL" "Copied from EUCAST 2024" "30 mcg" 20 20 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTB" "Copied from EUCAST 2024" "30 mcg" 25 25 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CTX" "Copied from EUCAST 2024" "5 mcg" 21 21 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "Copied from EUCAST 2024" 8 8 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "GEN" "Copied from EUCAST 2024" "10 mcg" 14 14 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "Copied from EUCAST 2024" 0.064 0.064 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "NAL" "Copied from EUCAST 2024" "30 mcg" 16 16 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "PEF" "Copied from EUCAST 2024" "5 mcg" 24 24 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "SXT" "Copied from EUCAST 2024" "1.25/23.75 mcg" 21 21 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TCY" "Copied from EUCAST 2024" "30 mcg" 17 17 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "DISK" "B_SLMNL_ENTR_ENTR" 1 "TMP" "Copied from EUCAST 2024" "5 mcg" 23 23 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "Copied from EUCAST 2024" 0.064 0.064 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Copied from EUCAST 2024" 32 32 FALSE FALSE +"CLSI 2024" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A-2" "15 mcg" 13 12 FALSE FALSE +"CLSI 2024" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A-2" 16 32 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "Copied from EUCAST 2024" 8 8 FALSE FALSE "CLSI 2024" "human" "human" "MIC" "B_SMYCS" 3 "AMC" "M24 Table 7" 8 32 FALSE FALSE "CLSI 2024" "human" "human" "MIC" "B_SMYCS" 3 "AMK" "M24 Table 7" 8 16 FALSE FALSE "CLSI 2024" "human" "human" "MIC" "B_SMYCS" 3 "CIP" "M24 Table 7" 1 4 FALSE FALSE @@ -45490,22 +45515,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "POS" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_FUSRM_JKRI" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 8 8 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2024" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2024" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2024" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "FLU" "Copied from EUCAST 2024 Antifungal ECOFFs" 128 128 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2024" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2024" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.032 0.032 FALSE FALSE -"CLSI 2024" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE -"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE -"CLSI 2024" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2024" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "ANI" "M59 Table 1" 0.25 0.25 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "M59 Table 1" 1 1 FALSE FALSE @@ -45524,12 +45533,13 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2024" "human" "human" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Table 1" "10 mcg" 16 13 FALSE FALSE "CLSI 2024" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "MIF" "M27 Table 1" 2 8 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_MYRZY_GLLR" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NCSMS_SOLN" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 8 8 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE "CLSI 2024" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2024" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M59 Table 4" 8 8 FALSE FALSE -"CLSI 2024" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE TRUE +"CLSI 2024" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE TRUE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2024" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M27 Table 1" 1e-04 64 FALSE TRUE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ITR" "M59 Table 1" 4 4 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "MIF" "M59 Table 4" 0.032 0.032 FALSE FALSE @@ -45539,6 +45549,22 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.016 0.016 FALSE FALSE "CLSI 2024" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "RZF" "M27 Table 1" 0.5 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2024" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "FLU" "Copied from EUCAST 2024 Antifungal ECOFFs" 128 128 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2024" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "RZF" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.032 0.032 FALSE FALSE +"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE +"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE +"CLSI 2024" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2024" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "AMB" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.5 0.5 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_SCCHR_CRVS" 2 "ITR" "Copied from EUCAST 2024 Antifungal ECOFFs" 2 2 FALSE FALSE "CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_TRCHP_INDT" 2 "AMO" "Copied from EUCAST 2024 Antifungal ECOFFs" 0.5 0.5 FALSE FALSE @@ -46863,12 +46889,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE "CLSI 2023" "animal" "swine" "DISK" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" "30 mcg" 21 17 FALSE FALSE "CLSI 2023" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" 2 8 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 32 32 FALSE FALSE -"CLSI 2023" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2023" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2023" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR_ENTR" 1 "FLR" "VET01 Table 2A" 4 16 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "ECOFF" 8 8 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"CLSI 2023" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2023" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 8 8 FALSE FALSE "CLSI 2023" "human" "human" "MIC" "B_SMYCS" 3 "AMC" "M24 Table 7" 8 32 FALSE FALSE "CLSI 2023" "human" "human" "MIC" "B_SMYCS" 3 "AMK" "M24 Table 7" 8 16 FALSE FALSE "CLSI 2023" "human" "human" "MIC" "B_SMYCS" 3 "CIP" "M24 Table 7" 1 4 FALSE FALSE @@ -47682,20 +47708,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "ITR" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "POS" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "M59 Table 2" 0.25 0.25 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2023" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2023" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2023" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2023" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2023" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE -"CLSI 2023" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE -"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE -"CLSI 2023" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2023" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "ANI" "M59 Table 1" 0.25 0.25 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "M59 Table 1" 1 1 FALSE FALSE @@ -47719,7 +47731,7 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "M27 Table 1" 0.125 0.5 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M59 Table 4" 8 8 FALSE FALSE -"CLSI 2023" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE FALSE +"CLSI 2023" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE FALSE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M27 Table 1" 1e-04 64 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ITR" "M59 Table 1" 4 4 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "MIF" "M59 Table 4" 0.032 0.032 FALSE FALSE @@ -47728,6 +47740,20 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE "CLSI 2023" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "RZF" "M27 Table 1" 0.5 FALSE FALSE "CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2023" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2023" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "M27 Table 1" 0.25 FALSE FALSE +"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE +"CLSI 2023" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE "CLSI 2022" "human" "human" "MIC" "B_ABTRP" 3 "AMP" "M45 Table 1" 0.25 8 FALSE FALSE "CLSI 2022" "human" "human" "MIC" "B_ABTRP" 3 "CHL" "M45 Table 1" 4 8 FALSE FALSE "CLSI 2022" "human" "human" "MIC" "B_ABTRP" 3 "CIP" "M45 Table 1" 1 4 FALSE FALSE @@ -48904,12 +48930,12 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR" 2 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE "CLSI 2022" "animal" "swine" "DISK" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" "30 mcg" 21 17 FALSE FALSE "CLSI 2022" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" 2 8 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "ECOFF" 32 32 FALSE FALSE -"CLSI 2022" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2022" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2022" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR_ENTR" 1 "FLR" "VET01 Table 2A" 4 16 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "FOX" "ECOFF" 8 8 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_ENTR_ENTR" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_HMRM" 1 "MEM" "ECOFF" 0.064 0.064 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "AZM" "ECOFF" 32 32 FALSE FALSE +"CLSI 2022" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2022" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "B_SLMNL_TYPH" 1 "FOX" "ECOFF" 8 8 FALSE FALSE "CLSI 2022" "human" "human" "MIC" "Parenteral" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2022" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2022" "human" "human" "DISK" "Parenteral" "B_STNTR_MLTP" 2 "FDC" "Table 2B-4" "30 mcg" 15 FALSE FALSE @@ -49673,19 +49699,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "ITR" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "POS" "M59 Table 2" 0.25 0.25 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CRYPT_NFRM" 2 "VOR" "M59 Table 2" 0.25 0.25 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2022" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2022" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2022" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE -"CLSI 2022" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2022" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE -"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_ISSTC_BRMP" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE -"CLSI 2022" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2022" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "ANI" "M59 Table 1" 0.25 0.25 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_KLYVR_RXNS" 2 "FLU" "M59 Table 1" 1 1 FALSE FALSE @@ -49709,7 +49722,7 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Table 1" 0.125 0.5 FALSE FALSE "CLSI 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "Table 1" 0.125 0.5 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "FLU" "M59 Table 4" 8 8 FALSE FALSE -"CLSI 2022" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE FALSE +"CLSI 2022" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE FALSE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "ITR" "M59 Table 1" 4 4 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "MIF" "M59 Table 4" 0.032 0.032 FALSE FALSE @@ -49717,6 +49730,19 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2022" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE "CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_NKSMY_BRTS" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2022" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE +"CLSI 2022" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE +"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_PICHI_KDRV" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE +"CLSI 2022" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "B_ABTRP" 3 "AMP" "M45 Table 1" 0.25 8 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "B_ABTRP" 3 "CHL" "M45 Table 1" 4 8 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "B_ABTRP" 3 "CIP" "M45 Table 1" 1 4 FALSE FALSE @@ -50571,9 +50597,9 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2021" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "FLR" "VET01 Table 2A" 4 16 FALSE FALSE "CLSI 2021" "animal" "swine" "DISK" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" "30 mcg" 21 17 FALSE FALSE "CLSI 2021" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET01 Table 2A" 2 8 FALSE FALSE -"CLSI 2021" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2021" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2021" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR_ENTR" 1 "FLR" "VET01 Table 2A" 4 16 FALSE FALSE +"CLSI 2021" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2021" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "Parenteral" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2021" "human" "human" "DISK" "Parenteral" "B_STNTR_MLTP" 2 "FDC" "Table 2B-4" "30 mcg" 17 12 FALSE FALSE @@ -51241,13 +51267,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2021" "human" "human" "MIC" "F_CANDD_TRPC" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE "CLSI 2021" "human" "human" "DISK" "F_CANDD_TRPC" 2 "VOR" "Table 1" "1 mcg" 17 14 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Table 1" 0.125 1 FALSE FALSE -"CLSI 2021" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2021" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2021" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2021" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2021" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2021" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2021" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Table 1" 2 8 FALSE FALSE "CLSI 2021" "human" "human" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Table 1" "5 mcg" 13 10 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Table 1" 2 8 FALSE FALSE @@ -51255,10 +51274,17 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2021" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Table 1" 2 8 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Table 1" 0.125 0.5 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "Table 1" 0.125 0.5 FALSE FALSE -"CLSI 2021" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE FALSE +"CLSI 2021" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE FALSE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2021" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE "CLSI 2021" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "MIF" "Table 1" "10 mcg" 30 27 FALSE FALSE "CLSI 2021" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE +"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2021" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2021" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2021" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "B_ABTRP" 3 "AMP" "M45 Table 1" 0.25 8 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "B_ABTRP" 3 "CHL" "M45 Table 1" 4 8 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "B_ABTRP" 3 "CIP" "M45 Table 1" 1 4 FALSE FALSE @@ -52108,9 +52134,9 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2020" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "FLR" "VET08 Table 2A" 4 16 FALSE FALSE "CLSI 2020" "animal" "swine" "DISK" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET08 Table 2A" "30 mcg" 21 17 FALSE FALSE "CLSI 2020" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET08 Table 2A" 2 8 FALSE FALSE -"CLSI 2020" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2020" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2020" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR_ENTR" 1 "FLR" "VET08 Table 2A" 4 16 FALSE FALSE +"CLSI 2020" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2020" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "Parenteral" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2020" "human" "human" "DISK" "Parenteral" "B_STNTR_MLTP" 2 "FDC" "Table 2B-4" "30 mcg" 17 12 FALSE FALSE @@ -52754,13 +52780,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2020" "human" "human" "MIC" "F_CANDD_TRPC" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE "CLSI 2020" "human" "human" "DISK" "F_CANDD_TRPC" 2 "VOR" "Table 1" "1 mcg" 17 14 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Table 1" 0.125 1 FALSE FALSE -"CLSI 2020" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2020" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2020" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2020" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2020" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2020" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2020" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Table 1" 2 8 FALSE FALSE "CLSI 2020" "human" "human" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Table 1" "5 mcg" 13 10 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Table 1" 2 8 FALSE FALSE @@ -52768,10 +52787,17 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2020" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Table 1" 2 8 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Table 1" 0.125 0.5 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "Table 1" 0.125 0.5 FALSE FALSE -"CLSI 2020" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE FALSE +"CLSI 2020" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE FALSE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2020" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE "CLSI 2020" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "MIF" "Table 1" "10 mcg" 30 27 FALSE FALSE "CLSI 2020" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE +"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2020" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2020" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2020" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "B_ABTRP" 3 "AMP" "M45 Table 1" 0.25 8 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "B_ABTRP" 3 "CHL" "M45 Table 1" 4 8 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "B_ABTRP" 3 "CIP" "M45 Table 1" 1 4 FALSE FALSE @@ -53618,9 +53644,9 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2019" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "FLR" "VET08 Table 2A" 4 16 FALSE FALSE "CLSI 2019" "animal" "swine" "DISK" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET08 Table 2A" "30 mcg" 21 17 FALSE FALSE "CLSI 2019" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR" 2 "TIO" "VET08 Table 2A" 2 8 FALSE FALSE -"CLSI 2019" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2019" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2019" "animal" "swine" "MIC" "Respiratory" "B_SLMNL_ENTR_ENTR" 1 "FLR" "VET08 Table 2A" 4 16 FALSE FALSE +"CLSI 2019" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2019" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "B_STNTR_MLTP" 2 "FDC" "Table 2B-4" 4 16 FALSE FALSE @@ -54126,13 +54152,6 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2019" "human" "human" "MIC" "F_CANDD_TRPC" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE "CLSI 2019" "human" "human" "DISK" "F_CANDD_TRPC" 2 "VOR" "Table 1" "1 mcg" 17 14 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "F_CANDD_TRPC" 2 "VOR" "Table 1" 0.125 1 FALSE FALSE -"CLSI 2019" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2019" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE -"CLSI 2019" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2019" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE -"CLSI 2019" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE -"CLSI 2019" "human" "human" "DISK" "F_ISSTC_BRMP" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE -"CLSI 2019" "human" "human" "MIC" "F_ISSTC_BRMP" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Table 1" 2 8 FALSE FALSE "CLSI 2019" "human" "human" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Table 1" "5 mcg" 13 10 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Table 1" 2 8 FALSE FALSE @@ -54140,10 +54159,17 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2019" "human" "human" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Table 1" 2 8 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "ANI" "Table 1" 0.125 0.5 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "CAS" "Table 1" 0.125 0.5 FALSE FALSE -"CLSI 2019" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 50 14 FALSE FALSE +"CLSI 2019" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "FLU" "Table 1" "25 mcg" 14 FALSE FALSE "[No S category] CLSI gives no S category for this zone diameter (S >= 80 mm in WHONET), so only R can be interpreted" "CLSI 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE "CLSI 2019" "human" "human" "DISK" "F_NKSMY_BRTS" 2 "MIF" "Table 1" "10 mcg" 30 27 FALSE FALSE "CLSI 2019" "human" "human" "MIC" "F_NKSMY_BRTS" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE +"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2019" "human" "human" "DISK" "F_PICHI_KDRV" 2 "CAS" "Table 1" "5 mcg" 17 14 FALSE FALSE +"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2019" "human" "human" "DISK" "F_PICHI_KDRV" 2 "MIF" "Table 1" "10 mcg" 22 19 FALSE FALSE +"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE +"CLSI 2019" "human" "human" "DISK" "F_PICHI_KDRV" 2 "VOR" "Table 1" "1 mcg" 15 12 FALSE FALSE +"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE "CLSI 2018" "human" "human" "MIC" "B_ABTRP" 3 "FEP" "M45 Table 1" 1 4 FALSE FALSE "CLSI 2018" "human" "human" "MIC" "B_ABTRP" 3 "GAT" "M45 Table 1" 1 4 FALSE FALSE "CLSI 2018" "human" "human" "MIC" "B_ABTRP" 3 "IPM" "M45 Table 1" 0.5 2 FALSE FALSE @@ -54854,8 +54880,8 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2018" "human" "human" "MIC" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2018" "human" "human" "MIC" "Extraintestinal" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2018" "human" "human" "DISK" "B_SLMNL" 3 "PEF" "Table 2A" "5 mcg" 24 23 FALSE FALSE -"CLSI 2018" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2018" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE +"CLSI 2018" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2018" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2018" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2018" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2018" "human" "human" "DISK" "B_STNTR_MLTP" 2 "LVX" "Table 2B-4" "5 mcg" 17 13 FALSE FALSE @@ -55824,8 +55850,8 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2017" "human" "human" "MIC" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2017" "human" "human" "MIC" "Extraintestinal" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2017" "human" "human" "DISK" "B_SLMNL" 3 "PEF" "Table 2A" "5 mcg" 24 23 FALSE FALSE -"CLSI 2017" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2017" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE +"CLSI 2017" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2017" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2017" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2017" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2017" "human" "human" "DISK" "B_STNTR_MLTP" 2 "LVX" "Table 2B-4" "5 mcg" 17 13 FALSE FALSE @@ -56794,8 +56820,8 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2016" "human" "human" "MIC" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2016" "human" "human" "MIC" "Extraintestinal" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2016" "human" "human" "DISK" "B_SLMNL" 3 "PEF" "Table 2A" "5 mcg" 24 23 FALSE FALSE -"CLSI 2016" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2016" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE +"CLSI 2016" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2016" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2016" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2016" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2016" "human" "human" "DISK" "B_STNTR_MLTP" 2 "LVX" "Table 2B-4" "5 mcg" 17 13 FALSE FALSE @@ -57770,8 +57796,8 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2015" "human" "human" "MIC" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2015" "human" "human" "MIC" "Extraintestinal" "B_SLMNL" 3 "OFX" "Table 2A" 0.125 2 FALSE FALSE "CLSI 2015" "human" "human" "DISK" "B_SLMNL" 3 "PEF" "Table 2A" "5 mcg" 24 23 FALSE FALSE -"CLSI 2015" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE -"CLSI 2015" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "AZM" "Table 2A" 16 32 FALSE FALSE +"CLSI 2015" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" "15 mcg" 13 12 FALSE FALSE +"CLSI 2015" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "AZM" "Table 2A" 16 32 FALSE FALSE "CLSI 2015" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2015" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2015" "human" "human" "DISK" "B_STNTR_MLTP" 2 "LVX" "Table 2B-4" "5 mcg" 17 13 FALSE FALSE @@ -60639,8 +60665,8 @@ Some countries prefer to categorise wild-type isolates of E. coli and P. mirabil "CLSI 2012" "human" "human" "DISK" "Extraintestinal" "B_SLMNL" 3 "CIP" "Table 2A" "5 mcg" 31 20 FALSE FALSE "CLSI 2012" "human" "human" "MIC" "Intestinal" "B_SLMNL" 3 "CIP" "Table 2A" 1 4 FALSE FALSE "CLSI 2012" "human" "human" "MIC" "Extraintestinal" "B_SLMNL" 3 "CIP" "Table 2A" 0.064 1 FALSE FALSE -"CLSI 2012" "human" "human" "DISK" "B_SLMNL_ENTR_ENTR" 1 "CIP" "Table 2A" "5 mcg" 31 20 FALSE FALSE -"CLSI 2012" "human" "human" "MIC" "B_SLMNL_ENTR_ENTR" 1 "CIP" "Table 2A" 0.064 1 FALSE FALSE +"CLSI 2012" "human" "human" "DISK" "B_SLMNL_TYPH" 1 "CIP" "Table 2A" "5 mcg" 31 20 FALSE FALSE +"CLSI 2012" "human" "human" "MIC" "B_SLMNL_TYPH" 1 "CIP" "Table 2A" 0.064 1 FALSE FALSE "CLSI 2012" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CAZ" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2012" "human" "human" "MIC" "B_STNTR_MLTP" 2 "CHL" "Table 2B-4" 8 32 FALSE FALSE "CLSI 2012" "human" "human" "DISK" "B_STNTR_MLTP" 2 "LVX" "Table 2B-4" "5 mcg" 17 13 FALSE FALSE diff --git a/data-raw/datasets/clinical_breakpoints.xlsx b/data-raw/datasets/clinical_breakpoints.xlsx index 1eb2382e6..bc46f6163 100644 Binary files a/data-raw/datasets/clinical_breakpoints.xlsx and b/data-raw/datasets/clinical_breakpoints.xlsx differ diff --git a/data/clinical_breakpoints.rda b/data/clinical_breakpoints.rda index b61bdf312..74af5040d 100644 Binary files a/data/clinical_breakpoints.rda and b/data/clinical_breakpoints.rda differ diff --git a/man/as.disk.Rd b/man/as.disk.Rd index 4a428e287..2331890c4 100644 --- a/man/as.disk.Rd +++ b/man/as.disk.Rd @@ -27,7 +27,7 @@ This transforms a vector to a new class \code{\link{disk}}, which is a disk diff \details{ Interpret disk values as SIR values with \code{\link[=as.sir]{as.sir()}}. It supports guidelines from EUCAST and CLSI. -Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 0-50 range will return \code{NA}. +Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Decimal values are rounded up. All input values outside the 0-50 range, including values higher than 50, return \code{NA} with a warning. \code{NA_disk_} is a missing value of the new \code{disk} class. } diff --git a/man/clinical_breakpoints.Rd b/man/clinical_breakpoints.Rd index 1026c5d3d..78ecc7040 100644 --- a/man/clinical_breakpoints.Rd +++ b/man/clinical_breakpoints.Rd @@ -5,7 +5,7 @@ \alias{clinical_breakpoints} \title{Data Set with Clinical Breakpoints for SIR Interpretation} \format{ -A \link[tibble:tibble]{tibble} with 61 367 observations and 15 variables: +A \link[tibble:tibble]{tibble} with 61 393 observations and 15 variables: \itemize{ \item \code{guideline}\cr Name of the guideline \item \code{type}\cr Breakpoint type, either \code{"ECOFF"}, \code{"animal"}, or \code{"human"} @@ -49,7 +49,9 @@ The default is \code{"human"}, which can also be set with the package option \co \subsection{Blocking Rows}{ -Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", breakpoints in brackets, or an organism excluded with "except"), \code{\link[=as.sir]{as.sir()}} must not fall back to the breakpoint of a broader taxon, such as the breakpoint for \emph{Vibrio} spp. where EUCAST gives "IE" for \emph{V. fluvialis}. Such cases are included as "blocking rows": rows in which \code{breakpoint_S} and \code{breakpoint_R} are both \code{NA} and the \code{note} starts with \code{"[No breakpoint]"} followed by the reason. \code{\link[=as.sir]{as.sir()}} returns \code{NA} for these. This currently applies to 15 653 rows. Remove them with \code{subset(clinical_breakpoints, !is.na(breakpoint_S))} if only actual breakpoints are needed. +Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", breakpoints in brackets, an organism excluded with "except", or no S category for a zone diameter), \code{\link[=as.sir]{as.sir()}} must not fall back to the breakpoint of a broader taxon, such as the breakpoint for \emph{Vibrio} spp. where EUCAST gives "IE" for \emph{V. fluvialis}. Such cases are included as "blocking rows": rows in which \code{breakpoint_S} and \code{breakpoint_R} are both \code{NA} and the \code{note} starts with \code{"[No breakpoint]"} followed by the reason. \code{\link[=as.sir]{as.sir()}} returns \code{NA} for these. This currently applies to 15 660 rows. Remove them with \code{subset(clinical_breakpoints, !is.na(breakpoint_S))} if only actual breakpoints are needed. + +Where another guideline has no S category for a zone diameter, such as CLSI for fluconazole in \emph{C. glabrata} (SDD and R only), only \code{breakpoint_R} is given, and the \code{note} starts with \code{"[No S category]"}. \code{\link[=as.sir]{as.sir()}} then returns R where applicable, and \code{NA} otherwise. } \subsection{Imported From WHONET}{ diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R index 41e920f9d..0624dcc2f 100644 --- a/tests/testthat/test-data.R +++ b/tests/testthat/test-data.R @@ -69,7 +69,10 @@ test_that("test-data.R", { expect_true(all(clinical_breakpoints$guideline[is_blocking] %like% "EUCAST")) expect_false(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF" & !is_blocking), "breakpoint_S", drop = TRUE]))) expect_true(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF" & !is_blocking), "breakpoint_R", drop = TRUE]))) - expect_false(anyNA(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF" & !is_blocking), "breakpoint_S", drop = TRUE]))) + # zone diameters without S category in the guideline (e.g. CLSI for fluconazole in C. glabrata) only have an R breakpoint, and must state this + no_S_category <- grepl("^\\[No S category\\] ", clinical_breakpoints$note) + expect_true(all(is.na(clinical_breakpoints$breakpoint_S[no_S_category]) & !is.na(clinical_breakpoints$breakpoint_R[no_S_category]) & clinical_breakpoints$method[no_S_category] == "DISK")) + expect_false(anyNA(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF" & !is_blocking & !no_S_category), "breakpoint_S", drop = TRUE]))) expect_true(anyNA(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF" & !is_blocking), "breakpoint_R", drop = TRUE]))) # antibiotic names must always be coercible to their original AB code diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index a33bf2e32..131e30110 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -87,6 +87,9 @@ test_that("test-mo.R", { # Issue #287: "X complex" fallback to "X" when complex is not a distinct taxon expect_identical(as.character(suppressWarnings(as.mo("Proteus vulgaris complex"))), as.character(suppressWarnings(as.mo("Proteus vulgaris")))) expect_identical(as.character(suppressWarnings(as.mo("Enterobacter cloacae complex"))), as.character(as.mo("Enterobacter cloacae complex"))) + # a complex named after several of its species returns the complex, not one of the species + expect_identical(as.character(as.mo(c("Acinetobacter calcoaceticus-baumannii complex", "Acinetobacter calcoaceticus/baumannii complex"))), c("B_ACNTB_BMNN-C", "B_ACNTB_BMNN-C")) + expect_identical(as.character(as.mo("Klebsiella pneumoniae-variicola complex")), "B_KLBSL_PNMN-C") # Issue #288: abbreviated genus with exact species epithet match should win expect_identical(