(v3.0.1.9149) Fix WHONET codes in microorganisms.codes that referred to unrelated microorganisms, let codes refer to the name they were named after and add a source column, and replace the fuzzy matching of WHONET names by exact matching with a guard against unreviewed remaps

WHONET names are now matched exactly (also outdated names, after removing qualifiers), then on GBIF identifier, and fuzzy results are only kept if consistent with that; otherwise the genus or UNKNOWN is used. A code refers to the record of the name it was named after (e.g. EAE is Enterobacter aerogenes) if that name refers to the same taxon. Every remap of an existing code to another taxon must be listed in data-raw/whonet_remaps_reviewed.csv; the 198 remaps of this rebuild were reviewed.
2026-11-15 22:20:47 +01:00 · 2026-10-15 21:08:04 +02:00
1 parent 179eec584f
commit eb9a9c2fa5
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9148
+Version: 3.0.1.9149
 Date: 2026-10-15
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@@ -1,4 +1,4 @@
-# AMR 3.0.1.9148
+# AMR 3.0.1.9149

 Planned as v3.1.0, mid October 2026.

@@ -55,6 +55,7 @@ Planned as v3.1.0, mid October 2026.
  * New function `amr_course()` to download and unpack course or webinar materials from GitHub in one call
  * New typed missing value constants `NA_ab_` and `NA_mo_`, for use in pipelines that need missing values of a specific class
  * A registry of all MO codes since v2.0.0 now prevents existing codes from being reused or mixed up. Codes of earlier releases are translated to the current code of the same taxon.
+  * New column `source` in the `microorganisms.codes` data set, stating the source of a code and the name it refers to, e.g., `"WHONET (Enterobacter aerogenes)"`

 ### Changed
 * SIR interpretation (`as.sir()`)
@@ -98,9 +99,14 @@ Planned as v3.1.0, mid October 2026.
  * Taxonomic update of all microorganisms, now based on COL 2026-04-18 XR, LPSN and BacDive of October 2026, and MycoBank of January 2026
  * Names listed twice by a source now take the correct record (e.g., *Eggerthella lenta*, *Gordonia amarae*, and *Anisakis simplex* were synonyms without a current name)
  * Synonyms without a current name are now linked via LPSN or removed, with their codes retired. The *M. tuberculosis* complex is always kept.
-  * Higher taxonomy and parent records are now consistent, and all data sets refer only to current names (except `intrinsic_resistant`)
+  * Higher taxonomy and parent records are now consistent, and all data sets refer only to current names (except `intrinsic_resistant` and `microorganisms.codes`)
  * *Erysipelatoclostridium* and its species are now synonyms of *Thomasclavelia*; *E. merdavium* is retired
  * Author references now strip `emend.` and everything after it, so that `ref` reflects the combination authority rather than the emendation author (e.g., *Rhodococcus equi* now returns "Goodfellow et al., 1977" instead of "Nouioui et al., 2018")
+* `microorganisms.codes` data set
+  * Fixed WHONET codes that referred to an unrelated microorganism, e.g., `VAG` ("Vaginal flora") to *Vagococcus*, `PAR` ("Parasite") to *Paracoccus*, the *Leptospira interrogans* serovars to *Legionella*, and *Salmonella* O-groups to *Salmonella* Group A. Codes for organisms that are not in the `microorganisms` data set, such as viruses, now refer to `UNKNOWN`, and names that only partly exist refer to the genus.
+  * WHONET codes for *Salmonella* serovars now refer to the serovar instead of *S. enterica* subsp. *enterica*, e.g., `SAT` to *Salmonella* Typhi
+  * Codes now refer to the name they were named after, also if that name is outdated, so that the code and the microorganism code remain relatable, e.g., `EAE` refers to *Enterobacter aerogenes* (`B_ENTRBC_AERG`). `as.mo()` still returns the current name, here *Klebsiella aerogenes*.
+  * Added 271 WHONET codes
 * Antimicrobial coercion (`as.ab()`) and `antimicrobials` data set
  * Considerably faster through the same session cache design as `as.mo()` (#313)
  * Input that is not a known name or code is now coerced up to 70 times faster, with identical results, as LOINC codes, synonyms, and abbreviations are looked up in one step instead of per antimicrobial, and translated names are built once per language
@@ -182,7 +182,8 @@
 #' A data set containing commonly used codes for microorganisms, from laboratory systems and [WHONET](https://whonet.org). Define your own with [set_mo_source()]. They will all be searched when using [as.mo()] and consequently all the [`mo_*`][mo_property()] functions.
 #' @format A [tibble][tibble::tibble] with `r format(nrow(microorganisms.codes), big.mark = " ")` observations and `r ncol(microorganisms.codes)` variables:
 #' - `code`\cr Commonly used code of a microorganism. ***This is a unique identifier.***
-#' - `mo`\cr ID of the microorganism in the [microorganisms] data set
+#' - `mo`\cr ID of the microorganism in the [microorganisms] data set. This is the record of the name that the code was named after, also if that name is outdated, so that the code and the microorganism ID remain relatable: e.g., the WHONET code `EAE` refers to *Enterobacter aerogenes* (`B_ENTRBC_AERG`). [as.mo()] returns the current name, here *Klebsiella aerogenes*. Codes for organisms that are not in the [microorganisms] data set, such as viruses, refer to `UNKNOWN`.
+#' - `source`\cr Source of the code, with the name it refers to, e.g. `"WHONET (Enterobacter aerogenes)"`, or `NA` if the source is unknown
 #' @inheritSection AMR Download Our Reference Data
 #' @seealso [as.mo()] [microorganisms]
 #' @examples
@@ -51,10 +51,12 @@ file_organisms <- file.path(github_repo, "Organisms.txt")
 file_breakpoints <- file.path(github_repo, "Breakpoints.txt")
 file_antibiotics <- file.path(github_repo, "Antibiotics.txt")

-whonet_organisms_raw <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
-  # remove old taxonomic names
-  filter(TAXONOMIC_STATUS == "C") |>
+# all names per WHONET code, i.e. the current name (TAXONOMIC_STATUS "C") and older names ("O")
+whonet_organisms_all <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
  mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
+# one row per code with its current name
+whonet_organisms_raw <- whonet_organisms_all |>
+  filter(TAXONOMIC_STATUS == "C")

 whonet_breakpoints_raw <- read_tsv(file_breakpoints, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
  filter(GUIDELINES %in% c("CLSI", "EUCAST"))
@@ -67,59 +69,157 @@ whonet_antibiotics_raw <- read_tsv(file_antibiotics, na = c("", "NA", "-"), show

 whonet_organisms <- whonet_organisms_raw |>
  select(ORGANISM_CODE, ORGANISM, SPECIES_GROUP, GBIF_TAXON_ID) |>
-  mutate(
-    # this one was called Issatchenkia orientalis, but it should be:
-    ORGANISM = if_else(ORGANISM_CODE == "ckr", "Candida krusei", ORGANISM)
-  ) |>
-  # try to match on GBIF identifier
-  left_join(microorganisms |> distinct(mo, gbif, status) |> filter(!is.na(gbif)), by = c("GBIF_TAXON_ID" = "gbif")) |>
+  # GBIF identifier, used if WHONET's name itself is not in the microorganisms data set
+  left_join(microorganisms |> distinct(mo_gbif = as.character(mo), gbif, status) |> filter(!is.na(gbif)), by = c("GBIF_TAXON_ID" = "gbif")) |>
  # remove duplicates
  arrange(ORGANISM_CODE, GBIF_TAXON_ID, status) |>
  distinct(ORGANISM_CODE, .keep_all = TRUE) |>
+  select(-status) |>
  # add Enterobacterales, which is a subkingdom code in their data
-  bind_rows(data.frame(ORGANISM_CODE = "ebc", ORGANISM = "Enterobacterales", mo = as.mo("Enterobacterales"))) |>
+  bind_rows(data.frame(ORGANISM_CODE = "ebc", ORGANISM = "Enterobacterales")) |>
  arrange(ORGANISM)


 ## Add new WHO codes to microorganisms.codes ----

-matched <- whonet_organisms |> filter(!is.na(mo))
-unmatched <- whonet_organisms |> filter(is.na(mo))
-
 # generate the mo codes and add their names
+# Fuzzy matching alone (as.mo() with minimum_matching_score = 0.55) mapped WHONET names that are not in the microorganisms data set to unrelated taxa, e.g. "Vaginal flora" to Vagococcus, "Parasite" to Paracoccus and "Babesia bigemina" to Babesia divergens. A WHONET name is therefore matched exactly (case-insensitive, including outdated names), first as is and then after removing qualifiers such as subspecies notation, serotypes, biovars, and "sp.", then on its GBIF identifier, and otherwise to its genus. The code of the matched record itself is used, also if it is an outdated name, so that the WHONET code and the microorganism code remain relatable (e.g. EAE is Enterobacter aerogenes, B_ENTRBC_AERG, which as.mo() returns as Klebsiella aerogenes). The fuzzy result of as.mo() is only used where it is consistent with that exact match: the exact match must be the same taxon or one of its ancestors, every epithet of the fuzzy result must be spelled within one character of a word in WHONET's name (e.g. "Pneumocystis jiroveci"), and for a group all its words apart from "group" and "complex" must occur in WHONET's name (e.g. "Streptococcus, beta-haem. Group A" for Streptococcus Group A). WHONET names that match nothing become UNKNOWN, apart from descriptive groups such as "Gram negative rods".
 message("Getting MO codes for WHONET input...")
-unmatched <- unmatched |>
-  mutate(
-    mo = as.mo(gsub("(sero[a-z]*| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
-      minimum_matching_score = 0.55,
-      keep_synonyms = TRUE,
-      language = "en"
-    ),
-    mo = case_when(
-      ORGANISM %like% "Anaerobic" & ORGANISM %like% "negative" ~ as.mo("B_ANAER-NEG"),
-      ORGANISM %like% "Anaerobic" & ORGANISM %like% "positive" ~ as.mo("B_ANAER-POS"),
-      ORGANISM %like% "Anaerobic" ~ as.mo("B_ANAER"),
-      TRUE ~ mo
-    ),
-    mo_name = mo_name(mo,
-      keep_synonyms = TRUE,
-      language = "en"
-    )
-  )
-# check if coercion at least resembles the first part (genus)
-unmatched <- unmatched |>
-  mutate(
-    first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
-    keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic"
-  ) |>
-  arrange(keep)
-if (interactive()) View(unmatched)
-unmatched <- unmatched |>
-  filter(keep == TRUE)
+# obvious errors in WHONET's names, corrected before matching
+whonet_name_fixes <- c(
+  "^Legionella interrogans" = "Leptospira interrogans", # the serovars of Leptospira interrogans are named "Legionella interrogans serovar ..."
+  "^Agchylostoma " = "Ancylostoma ", # old spelling
+  "^Salmonella Group ([A-Z])[0-9]+ " = "Salmonella Group \\1 " # subgroups such as C1 (O:7) belong to their group, e.g. Salmonella Group C
+)
+fix_whonet_name <- function(x) {
+  for (i in seq_along(whonet_name_fixes)) x <- sub(names(whonet_name_fixes)[i], whonet_name_fixes[i], x)
+  x
+}
+mo_fullname_lower <- tolower(microorganisms$fullname)
+# the code of the record with this name, also if it is an outdated name
+exact_mo <- function(x) {
+  i <- match(tolower(trimws(x)), mo_fullname_lower)
+  if (is.na(i)) NA_character_ else as.character(microorganisms$mo[i])
+}
+current_mo <- function(x) as.character(as.mo(as.character(x), keep_synonyms = FALSE, info = FALSE))
+whonet_name_candidates <- function(x) {
+  x <- gsub("\\s+", " ", trimws(x))
+  no_parentheses <- gsub("\\s*\\([^)]*\\)", "", x)
+  no_subsp <- gsub(" (ss|subsp)\\. ", " ", no_parentheses)
+  no_comma <- sub(",.*$", "", no_subsp)
+  as_complex <- sub(" group$", " complex", no_comma)
+  no_qualifier <- sub(" (serotype|serovar|serogroup|biotype|biovar|genomovar|genomospecies|type|group|var\\.|DT|phage type|strain) .*$", "", no_comma, ignore.case = TRUE)
+  no_sp <- sub(" spp?\\.?$", "", no_qualifier)
+  words <- strsplit(no_sp, " ")[[1]]
+  species <- if (length(words) >= 3) paste(words[1:2], collapse = " ") else no_sp
+  unique(c(x, no_parentheses, no_subsp, no_comma, as_complex, no_qualifier, no_sp, species))
+}
+exact_whonet_mo <- function(x, genus_fallback = TRUE) {
+  all_candidates <- whonet_name_candidates(x)
+  candidates <- all_candidates
+  # a candidate reduced to only the genus is a genus fallback, unless WHONET's name is the genus itself (e.g. "Arthrographis sp."), so that a consistent fuzzy result can still be more specific (e.g. "Streptococcus, beta-haemolytic")
+  if (!grepl("^[^ ]+( spp?\\.?)?$", gsub("\\s*\\([^)]*\\)", "", trimws(x)))) {
+    candidates <- candidates[grepl(" ", candidates)]
+  }
+  for (candidate in candidates) {
+    out <- exact_mo(candidate)
+    if (!is.na(out)) {
+      return(out)
+    }
+  }
+  # a complex named after several of its species, e.g. 'Mycobacterium avium-intracellulare complex'
+  if (grepl(" complex$", all_candidates[1])) {
+    out <- as.character(as.mo(all_candidates[1], info = FALSE))
+    if (grepl("-C$", out)) {
+      return(out)
+    }
+  }
+  if (!genus_fallback) {
+    return(NA_character_)
+  }
+  out <- exact_mo(strsplit(all_candidates[length(all_candidates)], " ")[[1]][1])
+  if (!is.na(out) && mo_rank(out, keep_synonyms = TRUE) %in% "genus") out else NA_character_
+}
+fuzzy_is_consistent <- function(fuzzy, exact, whonet_name) {
+  if (is.na(fuzzy) || is.na(exact) || fuzzy == "UNKNOWN") {
+    return(FALSE)
+  }
+  fuzzy_current <- current_mo(fuzzy)
+  ancestors <- c(fuzzy_current, current_mo(c(mo_genus(fuzzy_current), paste(mo_genus(fuzzy_current), mo_species(fuzzy_current)))))
+  if (!current_mo(exact) %in% ancestors) {
+    return(FALSE)
+  }
+  whonet_words <- strsplit(tolower(gsub("[^A-Za-z0-9 ]", " ", whonet_name)), " +")[[1]]
+  fuzzy_words <- strsplit(tolower(gsub("[^A-Za-z0-9 ]", " ", gsub("\\s*\\([^)]*\\)", "", mo_name(fuzzy, language = NULL)))), " +")[[1]]
+  fuzzy_words <- fuzzy_words[fuzzy_words != ""]
+  if (mo_rank(fuzzy) %in% c("species", "subspecies")) {
+    # every epithet within one character of a word in WHONET's name (the epithets, since the name of e.g. B_STRPT_MILL is "Milleri Group Streptococcus (MGS)")
+    epithets <- tolower(c(mo_species(fuzzy, keep_synonyms = TRUE), mo_subspecies(fuzzy, keep_synonyms = TRUE)))
+    epithets <- epithets[epithets != ""]
+    all(vapply(epithets, function(w) any(adist(w, whonet_words) <= 1), logical(1)))
+  } else {
+    # the generic words of a group name need not occur, e.g. "Streptococcus viridans, alpha-hem." for Viridans Group Streptococcus
+    all(fuzzy_words[!fuzzy_words %in% c("group", "complex")] %in% whonet_words)
+  }
+}
+# The name that a code was named after is used, so that the code and the microorganism code remain relatable: of all names of a code (current and older ones) that exist in the microorganisms data set and refer to the same taxon, the one whose initials form the code, preferring an older name, e.g. EAE is Enterobacter aerogenes (current WHONET name: Klebsiella aerogenes) and CKR is Candida krusei (current WHONET name: Issatchenkia orientalis). Without such a name, the current WHONET name is used.
+matches_code_initials <- function(code, name) {
+  words <- strsplit(tolower(gsub("[^A-Za-z ]", " ", name)), " +")
+  genus <- vapply(words, function(w) w[1], character(1))
+  species <- vapply(words, function(w) if (length(w) >= 2) w[2] else "", character(1))
+  code <- tolower(code)
+  nchar(code) == 3 & substr(genus, 1, 1) == substr(code, 1, 1) & startsWith(species, substr(code, 2, 3))
+}
+# An older name is only used if it is an outdated name of the same taxon as the current WHONET name, since some older WHONET names refer to another taxon in the microorganisms data set, e.g. PCA "Pneumocystis carinii" (current WHONET name: Pneumocystis jirovecii).
+current_whonet_mo <- whonet_organisms |>
+  transmute(ORGANISM_CODE, current_taxon = current_mo(vapply(fix_whonet_name(ORGANISM), exact_whonet_mo, character(1), genus_fallback = FALSE, USE.NAMES = FALSE)))
+whonet_name_by_initials <- whonet_organisms_all |>
+  filter(ORGANISM_CODE %in% whonet_organisms$ORGANISM_CODE, matches_code_initials(ORGANISM_CODE, ORGANISM)) |>
+  mutate(record = vapply(fix_whonet_name(ORGANISM), exact_whonet_mo, character(1), genus_fallback = FALSE, USE.NAMES = FALSE)) |>
+  filter(!is.na(record)) |>
+  left_join(current_whonet_mo, by = "ORGANISM_CODE") |>
+  filter(TAXONOMIC_STATUS == "C" | current_mo(record) == current_taxon) |>
+  arrange(ORGANISM_CODE, TAXONOMIC_STATUS != "O") |>
+  distinct(ORGANISM_CODE, .keep_all = TRUE)
+whonet_organisms <- whonet_organisms |>
+  mutate(ORGANISM = coalesce(whonet_name_by_initials$ORGANISM[match(ORGANISM_CODE, whonet_name_by_initials$ORGANISM_CODE)], ORGANISM))
+whonet_organisms |>
+  filter(ORGANISM_CODE %in% whonet_name_by_initials$ORGANISM_CODE[whonet_name_by_initials$TAXONOMIC_STATUS == "O"]) |>
+  select(ORGANISM_CODE, ORGANISM)

-organisms <- matched |>
-  transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo) |>
-  bind_rows(unmatched |> transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo)) |>
+whonet_organisms <- whonet_organisms |>
+  mutate(
+    name_to_match = fix_whonet_name(ORGANISM),
+    exact = vapply(name_to_match, exact_whonet_mo, character(1), genus_fallback = FALSE, USE.NAMES = FALSE),
+    genus = vapply(name_to_match, exact_whonet_mo, character(1), USE.NAMES = FALSE),
+    fuzzy = if_else(is.na(exact) & is.na(mo_gbif),
+      as.character(as.mo(gsub("(sero[a-z]*| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", name_to_match),
+        minimum_matching_score = 0.55,
+        keep_synonyms = TRUE,
+        language = "en",
+        info = FALSE
+      )),
+      NA_character_
+    ),
+    fuzzy_ok = mapply(fuzzy_is_consistent, fuzzy, genus, name_to_match, USE.NAMES = FALSE),
+    mo = as.mo(case_when(
+      ORGANISM %like% "Anaerobic" & ORGANISM %like% "negative" ~ "B_ANAER-NEG",
+      ORGANISM %like% "Anaerobic" & ORGANISM %like% "positive" ~ "B_ANAER-POS",
+      ORGANISM %like% "Anaerobic" ~ "B_ANAER",
+      ORGANISM %like% "^(Non-fermenting )?Gram negative" ~ "B_GRAMN",
+      ORGANISM %like% "^Gram positive" ~ "B_GRAMP",
+      !is.na(exact) ~ exact,
+      !is.na(mo_gbif) ~ mo_gbif,
+      fuzzy_ok ~ fuzzy,
+      !is.na(genus) ~ genus,
+      TRUE ~ "UNKNOWN"
+    ), keep_synonyms = TRUE),
+    mo_name = mo_name(mo, keep_synonyms = TRUE, language = "en")
+  )
+if (interactive()) View(whonet_organisms)
+
+organisms <- whonet_organisms |>
+  transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo, source = paste0("WHONET (", ORGANISM, ")")) |>
  mutate(name = mo_name(mo, keep_synonyms = TRUE)) |>
  arrange(code)

@@ -150,13 +250,18 @@ organisms <- organisms |>
  bind_rows(subspp) |>
  arrange(code)

-# add the groups
+# add the groups, unless the group code is also an organism code (e.g. ABX), which then already has its microorganism
+group_codes <- organisms |>
+  filter(!is.na(group), !group %in% code) |>
+  pull(group) |>
+  unique()
 organisms <- organisms |>
  bind_rows(tibble(
-    code = organisms |> filter(!is.na(group)) |> pull(group) |> unique(),
+    code = group_codes,
    group = NA,
-    mo = organisms |> filter(!is.na(group)) |> pull(group) |> unique() |> as.mo(keep_synonyms = TRUE),
-    name = mo_name(mo, keep_synonyms = TRUE)
+    mo = as.mo(group_codes, keep_synonyms = TRUE),
+    name = mo_name(mo, keep_synonyms = TRUE),
+    source = "WHONET (species group)"
  )) |>
  arrange(code, group) |>
  select(-group) |>
@@ -188,13 +293,44 @@ microorganisms.codes2 <- microorganisms.codes |>
  # remove all old WHONET codes, whether we (in the end) keep them or not
  filter(!toupper(code) %in% toupper(organisms$code)) |>
  # and add the new ones
-  bind_rows(organisms |> select(code, mo)) |>
+  bind_rows(organisms |> select(code, mo, source)) |>
  arrange(code) |>
  distinct(code, .keep_all = TRUE)
 # new codes:
 microorganisms.codes2$code[which(!microorganisms.codes2$code %in% microorganisms.codes$code)]
 mo_name(microorganisms.codes2$mo[which(!microorganisms.codes2$code %in% microorganisms.codes$code)], keep_synonyms = TRUE)
-microorganisms.codes <- microorganisms.codes2 |> distinct()
+microorganisms.codes2 <- microorganisms.codes2 |> distinct()
+
+# Remap guard: an existing code must not silently start to point to another taxon, since that changes the result of as.mo() for users' data. Remaps that follow a taxonomic update (the outdated and the new code have the same current name) are accepted. All other remaps must be listed in data-raw/whonet_remaps_reviewed.csv, after checking the WHONET name against the old and the new microorganism, with `reviewed = TRUE` to accept the new microorganism, or `reviewed = REJECT` to keep the old one.
+remaps <- microorganisms.codes |>
+  transmute(code, mo_old = as.character(mo)) |>
+  inner_join(microorganisms.codes2 |> transmute(code, mo_new = as.character(mo)), by = "code") |>
+  filter(current_mo(mo_old) != current_mo(mo_new)) |>
+  left_join(whonet_organisms |> transmute(code = ORGANISM_CODE, whonet_name = ORGANISM) |> distinct(code, .keep_all = TRUE), by = "code") |>
+  mutate(name_old = mo_name(mo_old, keep_synonyms = TRUE, language = NULL), name_new = mo_name(mo_new, keep_synonyms = TRUE, language = NULL))
+remaps_file <- "data-raw/whonet_remaps_reviewed.csv"
+# a reviewed remap applies to the taxa, i.e. to the current names of the old and the new microorganism, so it still holds if another record of the same taxon is used (e.g. an outdated name)
+remaps_listed <- read.csv(remaps_file, stringsAsFactors = FALSE, na.strings = "", colClasses = "character")
+remap_key <- function(df) paste(df$code, current_mo(df$mo_old), current_mo(df$mo_new))
+remaps_rejected <- remaps[remap_key(remaps) %in% remap_key(remaps_listed[remaps_listed$reviewed == "REJECT", ]), ]
+remaps_unreviewed <- remaps[!remap_key(remaps) %in% remap_key(remaps_listed[remaps_listed$reviewed %in% c("TRUE", "REJECT"), ]), ]
+if (nrow(remaps_unreviewed) > 0) {
+  # unreviewed remaps are added to the file with `reviewed = FALSE`, so that only `reviewed` needs to be changed after checking them
+  remaps_listed <- remaps_listed |>
+    bind_rows(remaps_unreviewed[!remap_key(remaps_unreviewed) %in% remap_key(remaps_listed), ] |> mutate(reviewed = "FALSE")) |>
+    select(code, whonet_name, mo_old, name_old, mo_new, name_new, any_of("assessment"), reviewed) |>
+    arrange(code)
+  write.csv(remaps_listed, remaps_file, row.names = FALSE, na = "")
+  print(as.data.frame(remaps_unreviewed |> select(code, whonet_name, name_old, name_new)))
+  stop(
+    nrow(remaps_unreviewed), " WHONET code(s) would point to another microorganism, see above. ",
+    "Review them in ", remaps_file, " and set `reviewed` to TRUE (accept) or REJECT (keep the old microorganism)."
+  )
+}
+# rejected remaps keep their old microorganism
+i <- match(remaps_rejected$code, microorganisms.codes2$code)
+microorganisms.codes2$mo[i] <- as.mo(remaps_rejected$mo_old, keep_synonyms = TRUE)
+microorganisms.codes <- microorganisms.codes2

 # Run this part to update ASIARS-Net:
 # 2024-06-14: file not available anymore
@@ -224,6 +360,7 @@ microorganisms.codes <- microorganisms.codes2 |> distinct()

 ## Save to package ----
 class(microorganisms.codes$mo) <- c("mo", "character")
+microorganisms.codes <- AMR:::dataset_UTF8_to_ASCII(microorganisms.codes)
 usethis::use_data(microorganisms.codes, overwrite = TRUE, compress = "xz", version = 2)
 rm(microorganisms.codes)
 devtools::load_all()
@@ -4947,7 +4947,8 @@ save_df <- function(...) {
    compress = "xz"
  )
 }
-microorganisms.codes <- fix_old_mos(AMR::microorganisms.codes, taxonomy, drop = TRUE)
+# microorganisms.codes keeps the record of the name that a code was named after, also if it is an outdated name (e.g. EAE is Enterobacter aerogenes), so that a code and its microorganism code remain relatable; as.mo() returns the current name
+microorganisms.codes <- fix_old_mos(AMR::microorganisms.codes, taxonomy, drop = TRUE, current = FALSE)
 if (!identical(microorganisms.codes, AMR::microorganisms.codes)) save_df(microorganisms.codes)
 rm(microorganisms.codes)

@@ -190,7 +190,8 @@ explained or fixed:
 Also verify the most used organisms in the package's own data sets: every `mo` in
 `clinical_breakpoints`, `intrinsic_resistant`, `microorganisms.groups`, `microorganisms.codes` and
 `example_isolates` must exist in the new `microorganisms`, and refer to a current name (except
-`intrinsic_resistant`, which lists synonyms on purpose); `tests/testthat/test-data.R` checks this.
+`intrinsic_resistant`, which lists synonyms on purpose, and `microorganisms.codes`, which keeps the record of the
+name a code was named after, e.g. EAE is *Enterobacter aerogenes*); `tests/testthat/test-data.R` checks this.
 `microorganisms.groups`, the EUCAST breakpoints in `clinical_breakpoints` and `intrinsic_resistant` are recreated
 from the new data set by `run_after_microorganisms_build.R`, which the script runs at its end. `intrinsic_resistant`
 is never an input of the build, as it is computed from the `microorganisms` data set itself.
@@ -1 +1 @@
-19deed740b29b33d288443a1528c0fcd
+bbd1671f1e29c7510e23471aeb3245d3
@@ -20574,6 +20574,7 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level
 "EUCAST 2021"	"human"	"human"	"MIC"		"B_ACHRMB_XYLS"	2	"TZP"	"A.xylosoxidans (file: Clinical Breakpoint Tables v. 11.0)"		4	4	FALSE	FALSE	"[1] For susceptibility testing purposes, the concentration of tazobactam is fixed at 4 mg/L."
 "EUCAST 2021"	"human"	"human"	"DISK"		"B_ACNTB"	3.1	"AMC"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
 "EUCAST 2021"	"human"	"human"	"MIC"		"B_ACNTB"	3.1	"AMC"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
+"EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB"	3	"AMK"	"ECOFF"		8	8	FALSE	FALSE	
 "EUCAST 2021"	"human"	"human"	"DISK"	"Infections originating from the urinary tract"	"B_ACNTB"	3	"AMK"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"	"30 mcg"	19	19	TRUE	FALSE	
 "EUCAST 2021"	"human"	"human"	"DISK"		"B_ACNTB"	3.1	"AMK"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives breakpoints in brackets only (S (19), R (19)) | [( )] Breakpoints in brackets are based on ECOFF values for relevant species. They are used to distinguish between organisms with and without acquired resistance mechanisms. ECOFFs do not predict clinical susceptibility but in some situations and/or when the agent is combined with another active agent, therapy may be considered. | [A] For systemic infections, aminoglycosides must be used in combination with other active therapy. In this circumstance, the breakpoint/ECOFF in brackets can be used to distinguish between organisms with and without acquired resistance mechanisms. For isolates without resistance mechanisms, include a comment in the report: \"Aminoglycosides are often given in combination with other agents, either to support the activity of the aminoglycoside or to broaden the spectrum of therapy. In systemic infections, the aminoglycoside must be supported by other active therapy.\" For more information, see http://www.eucast.org/guidance_documents/."
 "EUCAST 2021"	"human"	"human"	"MIC"	"Infections originating from the urinary tract"	"B_ACNTB"	3	"AMK"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"		8	8	TRUE	FALSE	
@@ -20680,6 +20681,7 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level
 "EUCAST 2021"	"human"	"human"	"MIC"		"B_ACNTB"	3.1	"LMU"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
 "EUCAST 2021"	"human"	"human"	"DISK"		"B_ACNTB"	3.1	"LNZ"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
 "EUCAST 2021"	"human"	"human"	"MIC"		"B_ACNTB"	3.1	"LNZ"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
+"EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB"	3	"LVX"	"ECOFF"		0.5	0.5	FALSE	FALSE	
 "EUCAST 2021"	"human"	"human"	"DISK"		"B_ACNTB"	3	"LVX"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"	"5 mcg"	23	20	FALSE	FALSE	
 "EUCAST 2021"	"human"	"human"	"DISK"	"Topical, Screen"	"B_ACNTB"	3	"LVX"	"Topical agents (file: Clinical Breakpoint Tables v. 11.0)"	"5 mcg"	23	23	FALSE	FALSE	
 "EUCAST 2021"	"human"	"human"	"MIC"		"B_ACNTB"	3	"LVX"	"Acinetobacter (file: Clinical Breakpoint Tables v. 11.0)"		0.5	1	FALSE	FALSE	
@@ -20801,10 +20803,6 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level
 "EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_LWFF"	2	"IPM"	"ECOFF"		1	1	FALSE	FALSE	
 "EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_LWFF"	2	"MEM"	"ECOFF"		2	2	FALSE	FALSE	
 "EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_LWFF"	2	"TOB"	"ECOFF"		2	2	FALSE	FALSE	
-"EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"AMK"	"ECOFF"		8	8	FALSE	FALSE	
-"EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"CIP"	"ECOFF"		1	1	FALSE	FALSE	
-"EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"LVX"	"ECOFF"		0.5	0.5	FALSE	FALSE	
-"EUCAST 2021"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"TOB"	"ECOFF"		4	4	FALSE	FALSE	
 "EUCAST 2021"	"human"	"human"	"DISK"		"B_AERCC_SNGN"	2	"AMP"	"A.sanguinicola_A.urinae (file: Clinical Breakpoint Tables v. 11.0)"	"2 mcg"	26	26	FALSE	FALSE	
 "EUCAST 2021"	"human"	"human"	"MIC"		"B_AERCC_SNGN"	2	"AMP"	"A.sanguinicola_A.urinae (file: Clinical Breakpoint Tables v. 11.0)"		0.25	0.25	FALSE	FALSE	
 "EUCAST 2021"	"human"	"human"	"DISK"		"B_AERCC_SNGN"	2.1	"AMX"	"A.sanguinicola_A.urinae (file: Clinical Breakpoint Tables v. 11.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives Note (see note) | [A] Infer susceptibility from ampicillin susceptibility."
@@ -25001,6 +24999,7 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level
 "EUCAST 2021"	"human"	"human"	"MIC"		"UNKNOWN"	7	"TZP"	"PK PD breakpoints (file: Clinical Breakpoint Tables v. 11.0)"		8	16	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\". | [3] For susceptibility testing purposes, the concentration of tazobactam is fixed at 4 mg/L."
 "EUCAST 2020"	"human"	"human"	"DISK"		"B_ACNTB"	3.1	"AMC"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
 "EUCAST 2020"	"human"	"human"	"MIC"		"B_ACNTB"	3.1	"AMC"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
+"EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB"	3	"AMK"	"ECOFF"		8	8	FALSE	FALSE	
 "EUCAST 2020"	"human"	"human"	"DISK"	"Infections originating from the urinary tract"	"B_ACNTB"	3	"AMK"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"	"30 mcg"	19	19	TRUE	FALSE	
 "EUCAST 2020"	"human"	"human"	"DISK"		"B_ACNTB"	3.1	"AMK"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives breakpoints in brackets only (S (19), R (19)) | [( )] Breakpoints in brackets are based on ECOFF values for relevant species. They are used to distinguish between organisms with and without acquired resistance mechanisms. ECOFFs do not predict clinical susceptibility but in some situations and/or when the agent is combined with another active agent, therapy may be considered. | [A] For systemic infections, aminoglycosides must be used in combination with other active therapy. In this circumstance, the breakpoint/ECOFF in brackets can be used to distinguish between organisms with and without acquired resistance mechanisms. For isolates without resistance mechanisms, include a comment in the report: \"Aminoglycosides are often given in combination with other agents, either to support the activity of the aminoglycoside or to broaden the spectrum of therapy. In systemic infections, the aminoglycoside must be supported by other active therapy.\" For more information, see http://www.eucast.org/guidance_documents/."
 "EUCAST 2020"	"human"	"human"	"MIC"	"Infections originating from the urinary tract"	"B_ACNTB"	3	"AMK"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"		8	8	TRUE	FALSE	
@@ -25101,6 +25100,7 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level
 "EUCAST 2020"	"human"	"human"	"MIC"		"B_ACNTB"	3.1	"LEX"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
 "EUCAST 2020"	"human"	"human"	"DISK"		"B_ACNTB"	3.1	"LNZ"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
 "EUCAST 2020"	"human"	"human"	"MIC"		"B_ACNTB"	3.1	"LNZ"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives - (susceptibility testing is not recommended)"
+"EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB"	3	"LVX"	"ECOFF"		0.5	0.5	FALSE	FALSE	
 "EUCAST 2020"	"human"	"human"	"DISK"		"B_ACNTB"	3	"LVX"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"	"5 mcg"	23	20	FALSE	FALSE	
 "EUCAST 2020"	"human"	"human"	"DISK"	"Topical, Screen"	"B_ACNTB"	3	"LVX"	"Topical agents (file: Clinical Breakpoint Tables v. 10.0)"	"5 mcg"	23	23	FALSE	FALSE	
 "EUCAST 2020"	"human"	"human"	"MIC"		"B_ACNTB"	3	"LVX"	"Acinetobacter (file: Clinical Breakpoint Tables v. 10.0)"		0.5	1	FALSE	FALSE	
@@ -25220,10 +25220,6 @@ Positive test: Isolates with gentamicin MIC >128 mg/L. The isolate is high-level
 "EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_LWFF"	2	"IPM"	"ECOFF"		1	1	FALSE	FALSE	
 "EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_LWFF"	2	"MEM"	"ECOFF"		2	2	FALSE	FALSE	
 "EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_LWFF"	2	"TOB"	"ECOFF"		2	2	FALSE	FALSE	
-"EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"AMK"	"ECOFF"		8	8	FALSE	FALSE	
-"EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"CIP"	"ECOFF"		1	1	FALSE	FALSE	
-"EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"LVX"	"ECOFF"		0.5	0.5	FALSE	FALSE	
-"EUCAST 2020"	"ECOFF"	"ECOFF"	"MIC"		"B_ACNTB_VNTN"	2	"TOB"	"ECOFF"		4	4	FALSE	FALSE	
 "EUCAST 2020"	"human"	"human"	"DISK"		"B_AERCC_SNGN"	2	"AMP"	"A.sanguinicola_A.urinae (file: Clinical Breakpoint Tables v. 10.0)"	"2 mcg"	26	26	FALSE	FALSE	
 "EUCAST 2020"	"human"	"human"	"MIC"		"B_AERCC_SNGN"	2	"AMP"	"A.sanguinicola_A.urinae (file: Clinical Breakpoint Tables v. 10.0)"		0.25	0.25	FALSE	FALSE	
 "EUCAST 2020"	"human"	"human"	"DISK"		"B_AERCC_SNGN"	2.1	"AMX"	"A.sanguinicola_A.urinae (file: Clinical Breakpoint Tables v. 10.0)"				FALSE	FALSE	"[No breakpoint] EUCAST gives Note (see note) | [A] Infer susceptibility from ampicillin susceptibility."
@@ -1 +1 @@
-e73b63cae3d1917d84e09b72f24fb0c2
+36873cd7a96ba8610d785f36b8bcf677
@@ -0,0 +1,199 @@
+"code","whonet_name","mo_old","name_old","mo_new","name_new","assessment","reviewed"
+"104","Salmonella Typhimurium DT 104","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_HMRM","Salmonella Typhimurium","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"AAN","Acinetobacter anitratus","B_ACNTB_VNTN","Acinetobacter venetianus","B_ACNTB","Acinetobacter","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"ADU","Agchylostoma duodenale","AN_ANCYL","Ancylostoma","AN_ANCYL_DDNL","Ancylostoma duodenale","Old spelling of Ancylostoma duodenale (name fix in script); old was the genus","TRUE"
+"AFB","Acid fast bacilli","B_ACDFR","Acidiferrobacter","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"AFN","Aphanoascus fulvescens","F_APHNS_RTCL","Aphanoascus reticulispora","F_APHNS_FLVS","Aphanoascus fulvescens","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"AKI","Sarocladium kiliense","F_ACRMN","Acremonium","F_SRCLD_KLNS","Sarocladium kiliense","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"APK","Trueperella pyogenes-like bacteria","B_AMYCS","Actinomyces","B_TRPRL","Trueperella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"APM","Anaplasma mesaeterum","B_ANPLS_PHGC","Anaplasma phagocytophilum","B_ANPLS","Anaplasma","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"ARF","Xenoacremonium recifei","F_ACRMN","Acremonium","F_XNCRM_RECF","Xenoacremonium recifei","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"ART","Arthrographis sp.","B_ARTHR","Arthrobacter","F_ARPHS","Arthrographis","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"ASC","Ascaris sp.","B_ACRCM","Acaricomes","AN_ASCRS","Ascaris","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"AVH","Aerococcus viridans var. homari","B_AERCC_VRDN","Aerococcus viridans","B_AERCC","Aerococcus","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"BCL","Balantidium coli","B_BCLLS","Bacillus","C_BNTDM_COLI","Balantidium coli","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"BFG","Bacteroides fragilis group","B_BCTRD_FRGL","Bacteroides fragilis","B_BCTRD_FRGL-C","Bacteroides fragilis complex","WHONET group is the B. fragilis complex; old was the species","TRUE"
+"BLA","Blastomyces sp.","F_CSPRM","Chrysosporium","F_BLSTM","Blastomyces","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"BOS","Borrelia suilla","B_BORRL_SPLM","Borrelia spielmanii","B_BORRL","Borrelia","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"C2C","Flavobacterium group IIc","B_ELZBT_MNNG","Elizabethkingia meningoseptica","B_FLVBC","Flavobacterium","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"C2E","Flavobacterium group IIe","B_SPHNGB_SPRT","Sphingobacterium spiritivorum","B_FLVBC","Flavobacterium","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"C2H","Flavobacterium group IIh","B_ELZBT_MNNG","Elizabethkingia meningoseptica","B_FLVBC","Flavobacterium","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"C2I","Flavobacterium group IIi","B_SPHNGB_SPRT","Sphingobacterium spiritivorum","B_FLVBC","Flavobacterium","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"CAE","Papiliotrema laurentii","F_CRYPT","Cryptococcus","F_PPLTR_LRNT","Papiliotrema laurentii","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CCI","Trichomonascus ciferrii","F_CANDD","Candida","F_TNSCS_CFRR","Trichomonascus ciferrii","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CCT","Diutina catenulata","F_CANDD","Candida","F_DIUTN_CTNL","Diutina catenulata","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CGA","Goffeauzyma gastrica","F_GFFZY","Goffeauzyma","F_GFFZY_GSTR","Goffeauzyma gastrica","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CHD","Chlamydophila sp.","B_CHLMY","Chlamydia","B_CPHLA","Chlamydophila","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"CHU","Vanrija humicola","F_CANDD","Candida","F_VANRJ_HMCL","Vanrija humicola","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CKR","Issatchenkia orientalis","F_ISSTC_BRMP","Issatchenkia brumptii","F_ISSTC_ORNT","Issatchenkia orientalis","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CLI","Hathewaya limosa","B_HTHWY","Hathewaya","B_HTHWY_LIMS","Hathewaya limosa","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CLL","Hannaella luteola","F_HNNLL_ALBA","Hannaella alba","F_HNNLL_LUTL","Hannaella luteola","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CME","Chilomastix mesnili","P_CHLMS_MTLL","Chilomastix motellae","P_CHLMS","Chilomastix","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"CNA","Clostridium novyi type A","B_CTRDM_NNTL","Clostridium neonatale","B_CTRDM_NOVY","Clostridium novyi","Clostridium novyi type A; old was an unrelated species (C. neonatale)","TRUE"
+"CNB","Clostridium novyi type B","B_CTRDM_NNTL","Clostridium neonatale","B_CTRDM_NOVY","Clostridium novyi","Clostridium novyi type B; old was an unrelated species (C. neonatale)","TRUE"
+"COP","Salmonella Copenhagen","B_SLMNL_CLNDL","Salmonella Colindale","B_SLMNL","Salmonella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"CPH","Capillaria philippinensis","AN_CPLLR_RKNS","Capillaria riukiuensis","AN_CPLLR","Capillaria","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"CPR","Ajellomyces crescens","F_CANDD_ASCL","Candida ascalaphidarum","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"CRU","Diutina rugosa","F_CANDD","Candida","F_DIUTN_RUGS","Diutina rugosa","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"CTU","Solicoccozyma terrea","F_SLCCC_ALBD","Solicoccozyma albidus","F_SLCCC_TERR","Solicoccozyma terrea","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"DCA","Taenia canina","AN_TAENI_SGNT","Taenia saginata","AN_TAENI","Taenia","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"DIP","Dipetalonema sp.","AN_DPHYL","Diphyllobothrium","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"EAT","Enterobacter catenibacterium","B_KLYVR_INTR","Kluyvera intermedia","B_ENTRBC","Enterobacter","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"ERO","Exophiala rostratum","F_EXPHL_PRST","Exophiala prostantherae","F_EXPHL","Exophiala","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"FAC","Fasciolopsis sp.","B_FCKLM","Facklamia","AN_FSCLP","Fasciolopsis","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"FDI","Bisifusarium dimerum","F_BSFSR_AQDC","Bisifusarium aquaeductuum","F_BSFSR_DMRM","Bisifusarium dimerum","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"FPL","Francisella tularensis biovar palearctica","B_FRNCS_TLRN_HLRC","Francisella tularensis holarctica","B_FRNCS_TLRN","Francisella tularensis","Biovar palearctica is subsp. holarctica, so old was more specific but not wrong; new is the species","TRUE"
+"G51","Salmonella Group 51 (O:51)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G52","Salmonella Group 52 (O:52)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G53","Salmonella Group 53 (O:53)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G54","Salmonella Group 54 (O:54)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G55","Salmonella Group 55 (O:55)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G56","Salmonella Group 56 (O:56)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G57","Salmonella Group 57 (O:57)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G58","Salmonella Group 58 (O:58)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G59","Salmonella Group 59 (O:59)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G60","Salmonella Group 60 (O:60)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G61","Salmonella Group 61 (O:61)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G62","Salmonella Group 62 (O:62)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G63","Salmonella Group 63 (O:63)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G64","Salmonella Group 64 (O:64)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G65","Salmonella Group 65 (O:65)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G66","Salmonella Group 66 (O:66)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"G67","Salmonella Group 67 (O:67)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GPE","Dipodascus klebahnii","F_DDSCS_LCTS","Dipodascus lactis","F_DDSCS_KLBH","Dipodascus klebahnii","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"GRI","Salmonella Group I (O:16)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRJ","Salmonella Group J (O:17)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRK","Salmonella Group K (O:18)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRL","Salmonella Group L (O:21)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRM","Salmonella Group M (O:28)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRN","Salmonella Group N (O:30)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRO","Salmonella Group O (O:35)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRP","Salmonella Group P (O:38)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRQ","Salmonella Group Q (O:39)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRR","Salmonella Group R (O:40)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRS","Salmonella Group S (O:41)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRT","Salmonella Group T (O:42)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRU","Salmonella Group U (O:43)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRV","Salmonella Group V (O:44)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRW","Salmonella Group W (O:45)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRX","Salmonella Group X (O:47)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRY","Salmonella Group Y (O:48)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"GRZ","Salmonella Group Z (O:50)","B_SLMNL_GRPA","Salmonella Group A","B_SLMNL","Salmonella","Salmonella O-group not in microorganisms; old was another group, now Salmonella","TRUE"
+"HAU","Haemonchus sp.","F_HNDRS_ASTR","Hendersonula astragalina","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"HDI","Taenia diminuta","AN_TAENI_SGNT","Taenia saginata","AN_TAENI_DMNT","Taenia diminuta","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"HPO","Ogataea polymorpha","F_OGATA","Ogataea","F_OGATA_PLYM","Ogataea polymorpha","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"HSP","Hanseniaspora sp.","F_HNDRS_ASTR","Hendersonula astragalina","F_HNSNS","Hanseniaspora","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"IND","Salmonella Indiana","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_INDN","Salmonella Indiana","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"INF","Salmonella Infantis","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_INFN","Salmonella Infantis","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"ISA","Salmonella Isangi","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_ISNG","Salmonella Isangi","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"JAV","Salmonella Paratyphi B var. Java","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_PRTB","Salmonella Paratyphi B","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"LAR","Salmonella Larochelle","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_LRCH","Salmonella Larochelle","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"LAU","Legionella interrogans serovar autumnalis","B_LGNLL_PNMP","Legionella pneumophila","B_LPTSP_INTR","Leptospira interrogans","WHONET writes Legionella for Leptospira; old was Legionella, now Leptospira interrogans","TRUE"
+"LBA","Legionella interrogans serovar ballum","B_LGNLL_PNMP_PSCL","Legionella pneumophila pascullei","B_LPTSP_INTR","Leptospira interrogans","WHONET writes Legionella for Leptospira; old was Legionella, now Leptospira interrogans","TRUE"
+"LBT","Legionella interrogans serovar bataviae","B_LGNLL_PNMP_PSCL","Legionella pneumophila pascullei","B_LPTSP_INTR","Leptospira interrogans","WHONET writes Legionella for Leptospira; old was Legionella, now Leptospira interrogans","TRUE"
+"LCC","Legionella interrogans serovar canicola","B_LGNLL_PNMP","Legionella pneumophila","B_LPTSP_INTR","Leptospira interrogans","WHONET writes Legionella for Leptospira; old was Legionella, now Leptospira interrogans","TRUE"
+"LDO","Leishmania donovani","P_LSHMN_LNSN","Leishmania lainsoni","P_LSHMN_DNVN","Leishmania donovani","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"LET","Lecythophora sp.","B_LPTTR","Leptotrichia","F_LCYTH","Lecythophora","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"LGP","Legionella interrogans serovar grippotyphosa","B_LGNLL_ANIS","Legionella anisa","B_LPTSP_INTR","Leptospira interrogans","WHONET writes Legionella for Leptospira; old was Legionella, now Leptospira interrogans","TRUE"
+"LIC","Legionella interrogans serovar icterohaemorrhagiae","B_LGNLL_ANIS","Legionella anisa","B_LPTSP_INTR","Leptospira interrogans","WHONET writes Legionella for Leptospira; old was Legionella, now Leptospira interrogans","TRUE"
+"LOM","Salmonella Lomita","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_LOMT","Salmonella Lomita","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"LPR","Leishmania peruviana","P_LSHMN_MXCN","Leishmania mexicana","P_LSHMN_PRVN","Leishmania peruviana","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"MCO","Paraphyton cookei","F_MCRSP","Microsporum","F_PRPHY_COOK","Paraphyton cookei","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"MPO","Moraxella mima polymorpha (var. oxidans)","B_MRXLL_CTRR","Moraxella catarrhalis","B_MRXLL","Moraxella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"MYE","Mycobacterium caprae","B_EPRYT_SUIS","Eperythrozoon suis","B_MYCBC_CAPR","Mycobacterium caprae","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"MYM","Myxozyma melibiosi","F_MYXZY","Myxozyma","F_MYXZY_MLBS","Myxozyma melibiosi","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"MYS","Mycobacterium suricattae","B_MYCBC_SRRC","Mycobacterium sarraceniae","B_MYCBC","Mycobacterium","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"NPE","Neisseria subflava biovar perflava","B_NESSR_ELNG","Neisseria elongata","B_NESSR_SBFL","Neisseria subflava","Neisseria subflava biovar; old was another species (N. elongata)","TRUE"
+"NRC","Anaerococcus sp.","B_ANRCC_HYDR","Anaerococcus hydrogenalis","B_ANRCC","Anaerococcus","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"NSB","Neisseria subflava biovar subflava","B_NESSR_ELNG","Neisseria elongata","B_NESSR_SBFL","Neisseria subflava","Neisseria subflava biovar; old was another species (N. elongata)","TRUE"
+"OCH","Ochrobactrum sp.","B_BRCLL","Brucella","B_OCHRB","Ochrobactrum","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"OCR","Ochroconis sp.","F_SCLCB","Scolecobasidium","F_OCHRC","Ochroconis","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"PAR","Parasite","B_PRCCC","Paracoccus","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"PAU","Salmonella Saintpaul","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_SNTP","Salmonella Saintpaul","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"PG1","Pseudomonas sp. group 1","B_PSDMN_PRFN","Pseudomonas profundi","B_PSDMN","Pseudomonas","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"PHO","Phocanema sp.","F_PHOMA","Phoma","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"POT","Salmonella Potsdam","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_PTSD","Salmonella Potsdam","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"PRC","Prototheca sp.","F_PICHI_MMBR","Pichia membranifaciens","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"PSA","Pseudallescheria sp.","F_SCDSP","Scedosporium","F_PSDLL","Pseudallescheria","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"PSS","Passalurus sp.","B_PSDSC","Pseudescherichia","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"PTY","Salmonella Paratyphi","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_PRTY","Salmonella Paratyphi","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"REU","Ralstonia euphora","B_CPRVD_RSPR","Cupriavidus respiraculi","B_RLSTN","Ralstonia","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"RMI","Cystobasidium minutum","F_RHDTR","Rhodotorula","F_CYSTBS_MNTM","Cystobasidium minutum","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"RO4","Roseomonas genomospecies 4","B_RSMNS_GLRD_ROSE","Roseomonas gilardii rosea","B_RSMNS","Roseomonas","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"RO5","Roseomonas genomospecies 5","B_RSMNS_GLRD_ROSE","Roseomonas gilardii rosea","B_RSMNS","Roseomonas","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"RO6","Roseomonas genomospecies 6","B_RSMNS_GLRD_ROSE","Roseomonas gilardii rosea","B_RSMNS","Roseomonas","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SAA","Salmonella Paratyphi A","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_PRTA","Salmonella Paratyphi A","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SAB","Salmonella Paratyphi B","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_PRTB","Salmonella Paratyphi B","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SAC","Salmonella Paratyphi C","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_PRTC","Salmonella Paratyphi C","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SAM","Salmonella Typhimurium","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_HMRM","Salmonella Typhimurium","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SAT","Salmonella Typhi","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_TYPH","Salmonella Typhi","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SBV","Streptococcus bovis-variant","B_STRPT_EQNS","Streptococcus equinus","B_STRPT","Streptococcus","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SDM","Neoscytalidium dimidiatum","F_SCYTL","Scytalidium","F_NSCYT_DMDT","Neoscytalidium dimidiatum","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"SHG","Salmonella Heidelberg","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_HDLB","Salmonella Heidelberg","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SHR","Salmonella Hadar","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_HADR","Salmonella Hadar","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SJV","Salmonella Javiana","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_JAVN","Salmonella Javiana","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SKA","Salmonella Kaapstad","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_KPST","Salmonella Kaapstad","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SKD","Salmonella Kedougou","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_KEDG","Salmonella Kedougou","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SKE","Salmonella Kentucky","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_KNTC","Salmonella Kentucky","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SKO","Salmonella Kottbus","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_KTTB","Salmonella Kottbus","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SKR","Salmonella Krefeld","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_KRFL","Salmonella Krefeld","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SLA","Salmonella Anatum","B_SLMNL_AMNT","Salmonella Aminatu","B_SLMNL","Salmonella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SLI","Salmonella Litchfield","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_LTCH","Salmonella Litchfield","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SLO","Salmonella London","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_LONDN","Salmonella London","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SLV","Salmonella Livingstone","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_LVNG","Salmonella Livingstone","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SLX","Salmonella Lexington","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_LXNG","Salmonella Lexington","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SMB","Salmonella Mbandaka","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_MBND","Salmonella Mbandaka","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SMH","Salmonella Manhattan","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_MNHT","Salmonella Manhattan","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SMN","Salmonella Muenchen","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_MCHN","Salmonella Muenchen","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SMO","Salmonella Montevideo","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_MNTV","Salmonella Montevideo","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SMR","Salmonella Muenster","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL","Salmonella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SNA","Salmonella Narashino","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_NRSH","Salmonella Narashino","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SNE","Salmonella Newport","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_NWPR","Salmonella Newport","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SOH","Salmonella Ohio","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL","Salmonella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SOI","Salmonella Orion","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_ORIN","Salmonella Orion","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SOR","Salmonella Oranienburg","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_ORNN","Salmonella Oranienburg","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SOU","Salmonella Ouakam","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_OUKM","Salmonella Ouakam","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SPG","Streptomyces paraguayensis","B_SMYCS_ASNS","Streptomyces asoensis","B_SMYCS","Streptomyces","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SPM","Salmonella Panama","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_PANM","Salmonella panama","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SPO","Salmonella Poona","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_POON","Salmonella Poona","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SRE","Salmonella Reading","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_RDNG","Salmonella Reading","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SRI","Salmonella Rissen","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_RSSN","Salmonella Rissen","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SRM","Spirillum minus","B_SPRLLM_VLTN","Spirillum volutans","B_SPRLLM","Spirillum","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SRO","Salmonella sp. (rough)","B_SLMNL_BRGH","Salmonella Broughton","B_SLMNL","Salmonella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SS1","Streptococcus sanguinis I","B_STRPT_GRPI","Streptococcus Group I","B_STRPT_SNGN","Streptococcus sanguinis","Streptococcus sanguinis I; old was Streptococcus Group I (Lancefield), which is unrelated","TRUE"
+"SSD","Salmonella Sandiego","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_SDGO","Salmonella Sandiego","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SSE","Salmonella Senftenberg","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_SNFT","Salmonella Senftenberg","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SSW","Salmonella Schwarzengrund","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_SRND","Salmonella Schwarzengrund","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SSY","Salmonella Stanley","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_STNL","Salmonella Stanley","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"STL","Stemphylium sp.","AN_STRNG","Strongyloides","F_SHYLM","Stemphylium","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"STS","Salmonella Typhisuis","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_THSS","Salmonella Typhisuis","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"STY","Salmonella sp., typhoidal","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL","Salmonella","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"SVC","Salmonella Typhimurium var. Copenhagen","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_HMRM","Salmonella Typhimurium","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SVG","Salmonella Virginia","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_VRGN","Salmonella Virginia","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SVR","Salmonella Virchow","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_VRCH","Salmonella Virchow","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SWD","Salmonella Wandsworth","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_WNDS","Salmonella Wandsworth","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SWE","Salmonella Weltevreden","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_WLTV","Salmonella Weltevreden","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SWO","Salmonella Worthington","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_WRTH","Salmonella Worthington","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"SWY","Salmonella Weybridge","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_WYBR","Salmonella Weybridge","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"TAL","Tatlockia sp.","B_LGNLL","Legionella","B_TTLCK","Tatlockia","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"TBE","Geotrichum beigelii","F_GTRCH_NDDM","Geotrichum candidum","F_GTRCH","Geotrichum","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"TCA","Debaryomyces hansenii","F_DBRYM_CHVL","Debaryomyces chevalieri","F_DBRYM_HNSN","Debaryomyces hansenii","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"TCT","Treponema carateum","B_GRCLN_CLDR","Gracilinema caldarium","B_TRPNM","Treponema","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"TEN","Treponema pallidum ss. endemicum","B_TRPNM_PRLS","Treponema paraluiscuniculi","B_TRPNM_PLLD_ENDM","Treponema pallidum endemicum","Treponema pallidum subsp. endemicum; old was another species","TRUE"
+"THM","Salmonella Thompson","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_THMP","Salmonella Thompson","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"THO","Trichomonas hominis","P_THMNS_VAG","Trichomonas vaginalis","P_THMNS","Trichomonas","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"TMU","Cutaneotrichosporon mucoides","F_CTNTR_HVNN","Cutaneotrichosporon heveanensis","F_CTNTR_MCDS","Cutaneotrichosporon mucoides","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"TNS","Salmonella Tennessee","B_SLMNL_ENTR_ENTR","Salmonella enterica enterica","B_SLMNL_TNNS","Salmonella Tennessee","Salmonella serovar now specific; old was S. enterica subsp. enterica","TRUE"
+"TPA","Treponema pallidum ss. pallidum","B_TRPNM_PRLS","Treponema paraluiscuniculi","B_TRPNM_PLLD","Treponema pallidum","Treponema pallidum subsp. pallidum (nominate subspecies, so the species); old was another species","TRUE"
+"TPI","Kazachstania telluris","F_KZCHS","Kazachstania","F_KZCHS_TLLR","Kazachstania telluris","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"TPP","Treponema pallidum ss. pertenue","B_TRPNM_SCRN_PRDS","Treponema socranskii paredis","B_TRPNM_PLLD_PRTN","Treponema pallidum pertenue","Treponema pallidum subsp. pertenue; old was another species","TRUE"
+"TPU","Tausonia pullulans","F_TAUSN","Tausonia","F_TAUSN_PLLL","Tausonia pullulans","New is the exact WHONET name; old was an unrelated fuzzy match or another species","TRUE"
+"TRF","Treponema refringens","B_TRPNM_SCRN_PRDS","Treponema socranskii paredis","B_TRPNM","Treponema","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"TRG","Trypanosoma congolense","P_TRYPN_SNGL","Trypanosoma senegalense","P_TRYPN","Trypanosoma","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"TRH","Trypanosoma brucei ss. rhodesiense","F_TRCHD","Trichoderma","P_TRYPN_BRUC","Trypanosoma brucei","Trypanosoma brucei subsp. rhodesiense is not in microorganisms, so the species; old was Trichoderma","TRUE"
+"TRV","Trypanosoma vivax","P_TRYPN_AVIM","Trypanosoma avium","P_TRYPN","Trypanosoma","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"TYE","Trypanosoma evansi","P_TRYPN_JNSN","Trypanosoma janseni","P_TRYPN","Trypanosoma","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"ULO","Ulocladium sp.","F_ALTRN","Alternaria","F_ULCLD","Ulocladium","WHONET name not in microorganisms (except genus); old was a fuzzy match to another taxon, now genus only","TRUE"
+"VAG","Vaginal flora","B_VGCCC","Vagococcus","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"XEN","Candidatus Xenohaliotis sp.","B_XNRHB","Xenorhabdus","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
+"XEP","No enteric pathogens found","B_XNPHL","Xenophilus","UNKNOWN","(unknown name)","WHONET name is no taxon in microorganisms; old was an unrelated fuzzy match, now UNKNOWN","TRUE"
@@ -5,7 +5,7 @@
 \alias{clinical_breakpoints}
 \title{Data Set with Clinical Breakpoints for SIR Interpretation}
 \format{
-A \link[tibble:tibble]{tibble} with 61 393 observations and 15 variables:
+A \link[tibble:tibble]{tibble} with 61 389 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"}
@@ -3,12 +3,13 @@
 \docType{data}
 \name{microorganisms.codes}
 \alias{microorganisms.codes}
-\title{Data Set with 6 022 Common Microorganism Codes}
+\title{Data Set with 6 293 Common Microorganism Codes}
 \format{
-A \link[tibble:tibble]{tibble} with 6 022 observations and 2 variables:
+A \link[tibble:tibble]{tibble} with 6 293 observations and 3 variables:
 \itemize{
 \item \code{code}\cr Commonly used code of a microorganism. \emph{\strong{This is a unique identifier.}}
-\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
+\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set. This is the record of the name that the code was named after, also if that name is outdated, so that the code and the microorganism ID remain relatable: e.g., the WHONET code \code{EAE} refers to \emph{Enterobacter aerogenes} (\code{B_ENTRBC_AERG}). \code{\link[=as.mo]{as.mo()}} returns the current name, here \emph{Klebsiella aerogenes}. Codes for organisms that are not in the \link{microorganisms} data set, such as viruses, refer to \code{UNKNOWN}.
+\item \code{source}\cr Source of the code, with the name it refers to, e.g. \code{"WHONET (Enterobacter aerogenes)"}, or \code{NA} if the source is unknown
 }
 }
 \usage{
@@ -486,7 +486,6 @@ test_that("data sets refer only to current names", {
  check <- list(
    "example_isolates$mo" = example_isolates$mo,
    "clinical_breakpoints$mo" = clinical_breakpoints$mo,
-    "microorganisms.codes$mo" = microorganisms.codes$mo,
    "microorganisms.groups$mo" = microorganisms.groups$mo,
    "microorganisms.groups$mo_group" = microorganisms.groups$mo_group
  )
@@ -572,11 +571,15 @@ test_that("microorganisms.groups: consistent groups of current names", {
  expect_identical(g$mo_group_name, microorganisms$fullname[match(g$mo_group, microorganisms$mo)])
 })

-test_that("microorganisms.codes: unique codes for existing current names", {
+test_that("microorganisms.codes: unique codes for existing names", {
  skip_on_cran()
  dup <- microorganisms.codes$code[duplicated(toupper(microorganisms.codes$code))]
  expect_true(length(dup) == 0, info = paste("Duplicated codes:", paste(utils::head(dup, 25), collapse = ", ")))
  expect_false(anyNA(microorganisms.codes$mo))
+  # a code keeps the record of the name it was named after, also if outdated, while as.mo() returns the current name
+  expect_identical(as.character(microorganisms.codes$mo[microorganisms.codes$code == "EAE"]), "B_ENTRBC_AERG")
+  expect_identical(as.character(as.mo("EAE")), "B_KLBSL_AERG")
+  expect_true(all(is.na(microorganisms.codes$source) | grepl("^WHONET \\(.+\\)$", microorganisms.codes$source)))
 })

 test_that("clinical_breakpoints: consistent and unambiguous", {