P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-04-26 15:18:52 +02:00
Code Releases Activity

(v2.1.1.9081) HUGE microorganisms update for fungi!

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
parent a558f4c121
commit ac1c40d8bb
119 changed files with 36445 additions and 67400 deletions
Download Patch File Download Diff File Expand all files Collapse all files

52
data-raw/_pre_commit_checks.R
View File

@@ -158,10 +158,11 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
"group a", "group b", "group c", "group g"
))]
pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
pre_commit_lst$MO_PREVALENT_GENERA <- c(
pre_commit_lst$MO_RELEVANT_GENERA <- c(
"Absidia",
"Acanthamoeba",
"Acremonium",
"Actinomucor",
"Aedes",
"Alternaria",
"Amoeba",
@@ -175,20 +176,31 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Aureobasidium",
"Basidiobolus",
"Beauveria",
"Bipolaris",
"Blastobotrys",
"Blastocystis",
"Blastomyces",
"Candida",
"Capillaria",
"Chaetomium",
"Chilomastix",
"Chrysonilia",
"Chrysosporium",
"Cladophialophora",
"Cladosporium",
"Clavispora",
"Coccidioides",
"Cokeromyces",
"Conidiobolus",
"Coniochaeta",
"Contracaecum",
"Cordylobia",
"Cryptococcus",
"Cryptosporidium",
"Cunninghamella",
"Curvularia",
"Cyberlindnera",
"Debaryozyma",
"Demodex",
"Dermatobia",
"Dientamoeba",
@@ -197,6 +209,8 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Echinostoma",
"Entamoeba",
"Enterobius",
"Epidermophyton",
"Exidia",
"Exophiala",
"Exserohilum",
"Fasciola",
@@ -204,6 +218,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Fusarium",
"Geotrichum",
"Giardia",
"Graphium",
"Haloarcula",
"Halobacterium",
"Halococcus",
@@ -212,16 +227,19 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Heterophyes",
"Histomonas",
"Histoplasma",
"Hortaea",
"Hymenolepis",
"Hypomyces",
"Hysterothylacium",
"Kloeckera",
"Kluyveromyces",
"Kodamaea",
"Lacazia",
"Leishmania",
"Lichtheimia",
"Lodderomyces",
"Lomentospora",
"Madurella",
"Malassezia",
"Malbranchea",
"Metagonimus",
@@ -232,6 +250,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Mortierella",
"Mucor",
"Mycocentrospora",
"Nannizzia",
"Necator",
"Nectria",
"Ochroconis",
@@ -239,8 +258,12 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Oidiodendron",
"Opisthorchis",
"Paecilomyces",
"Paracoccidioides",
"Pediculus",
"Penicillium",
"Phaeoacremonium",
"Phaeomoniella",
"Phialophora",
"Phlebotomus",
"Phoma",
"Pichia",
@@ -252,24 +275,34 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Pseudoscopulariopsis",
"Pseudoterranova",
"Pulex",
"Purpureocillium",
"Quambalaria",
"Rhinocladiella",
"Rhizomucor",
"Rhizopus",
"Rhodotorula",
"Saccharomyces",
"Saksenaea",
"Saprochaete",
"Sarcoptes",
"Scedosporium",
"Schistosoma",
"Schizosaccharomyces",
"Scolecobasidium",
"Scopulariopsis",
"Scytalidium",
"Spirometra",
"Sporobolomyces",
"Sporopachydermia",
"Sporothrix",
"Sporotrichum",
"Stachybotrys",
"Strongyloides",
"Syncephalastrum",
"Syngamus",
"Taenia",
"Talaromyces",
"Teleomorph",
"Toxocara",
"Trichinella",
"Trichobilharzia",
@@ -283,8 +316,15 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Trombicula",
"Trypanosoma",
"Tunga",
"Ulocladium",
"Ustilago",
"Verticillium",
"Wuchereria"
"Wallemia",
"Wangiella",
"Wickerhamomyces",
"Wuchereria",
"Yarrowia",
"Zygosaccharomyces"
)
# antibiotic groups
@@ -450,7 +490,6 @@ if (changed_md5(clin_break)) {
write_md5(clin_break)
try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(clin_break, "data-raw/clinical_breakpoints.xpt"), silent = TRUE)
try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
@@ -466,7 +505,6 @@ if (changed_md5(microorganisms)) {
mo <- microorganisms
mo$snomed <- max_50_snomed
mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
try(haven::write_xpt(mo, "data-raw/microorganisms.xpt"), silent = TRUE)
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@@ -481,7 +519,6 @@ if (changed_md5(microorganisms.codes)) {
write_md5(microorganisms.codes)
try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.codes, "data-raw/microorganisms.codes.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
@@ -494,7 +531,6 @@ if (changed_md5(microorganisms.groups)) {
write_md5(microorganisms.groups)
try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.groups, "data-raw/microorganisms.groups.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
@@ -507,7 +543,6 @@ if (changed_md5(ab)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
write_md5(ab)
try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(ab, "data-raw/antibiotics.xpt"), silent = TRUE)
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
ab_lists <- antibiotics %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@@ -522,7 +557,6 @@ if (changed_md5(av)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
write_md5(av)
try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(av, "data-raw/antivirals.xpt"), silent = TRUE)
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@@ -543,7 +577,6 @@ if (changed_md5(intrinsicR)) {
write_md5(intrinsicR)
try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(intrinsicR, "data-raw/intrinsic_resistant.xpt"), silent = TRUE)
try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
@@ -556,7 +589,6 @@ if (changed_md5(dosage)) {
write_md5(dosage)
try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(dosage, "data-raw/dosage.xpt"), silent = TRUE)
try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE)
try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)

2
data-raw/ab.md5
View File

@@ -1 +1 @@
5ad894790ad048110f8eb9207b89501f
6f6b49606c2c51f8344fbb9e186a3ad3

BIN
data-raw/antibiotics.dta
View File

Binary file not shown.

BIN
data-raw/antibiotics.feather
View File

Binary file not shown.

BIN
data-raw/antibiotics.parquet
View File

Binary file not shown.

BIN
data-raw/antibiotics.rds
View File

Binary file not shown.

BIN
data-raw/antibiotics.sav
View File

Binary file not shown.

2
data-raw/antibiotics.txt
View File

@@ -76,7 +76,7 @@
"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "NA" "" "cefetamet pivoxyl,globocef" ""
"CCL" 71719688 "Cefetecol" "Cephalosporins (4th gen.)" "NA" "cefcatacol" "cefetecol,cefetecol anhydrous" ""
"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "NA" "" "cefetrizole,cefetrizolum" ""
"FDC" 77843966 "Cefiderocol" "Other antibacterials" "J01DI04" "" "cefiderocol" 6 "g" "95767-0,99280-0,99503-5"
"FDC" 77843966 "Cefiderocol" "Cephalosporins (unclassified gen.)" "J01DI04" "" "cefiderocol" 6 "g" "95767-0,99280-0,99503-5"
"CFM" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "J01DD08" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cfe,cfix,cfxm,dcfm,fix,ix" "anhydrous cefixime,cefixim,cefixima,cefixime,cefixime anhydrous,cefixime hydrate,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oroken,suprax,tricef,unixime" 0.4 "g" "16567-0,18880-5,25236-1,35766-5,79-4,80-2,81-0,82-8"
"CEO" "Cefixime/ornidazole" "Other antibacterials" "J01RA15" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
"CMX" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "J01DD05,S01AA31,S02AA18" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "bestron,cefmax,cefmenoxima,cefmenoxime,cefmenoximum" 2 "g" "32375-8,54174-8,54203-5,55641-5"

BIN
data-raw/antibiotics.xlsx
View File

Binary file not shown.

BIN
data-raw/antibiotics.xpt
View File

Binary file not shown.

BIN
data-raw/antivirals.xpt
View File

Binary file not shown.

2
data-raw/clin_break.md5
View File

@@ -1 +1 @@
c79b6e112dc3ab478b990f0689b685b6
10fd88018ca098a76a8b1e9c86d2e40c

BIN
data-raw/clinical_breakpoints.dta
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.feather
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.parquet
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.rds
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.sav
View File

Binary file not shown.

212
data-raw/clinical_breakpoints.txt
View File

@@ -1845,16 +1845,16 @@
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "RZF" "Antifungal ECOFFs" 0.016 0.016 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "Antifungal ECOFFs" 0.064 0.064 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "FLU" "Antifungal ECOFFs" 128 128 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "Antifungal ECOFFs" 0.5 0.5 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "RZF" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 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_CANDD_PRPS" 2 "AMB" "Antifungal ECOFFs" 1 1 FALSE FALSE
"EUCAST 2024" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "ANI" "Antifungal ECOFFs" 4 4 FALSE FALSE
@@ -3399,8 +3399,8 @@
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 1e-04 16 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 4 4 FALSE FALSE
"EUCAST 2023" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -4833,8 +4833,8 @@
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 1e-04 16 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 4 4 FALSE FALSE
"EUCAST 2022" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -7019,14 +7019,14 @@
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "MIF" "ECOFF" 0.032 0.032 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "FLU" "ECOFF" 128 128 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 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" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2021" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2021" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "ANI" "ECOFF" 4 4 FALSE FALSE
@@ -9139,14 +9139,14 @@
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "MIF" "ECOFF" 0.032 0.032 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "ECOFF" 0.064 0.064 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "FLU" "ECOFF" 128 128 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "ECOFF" 0.25 0.25 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 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" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "AMB" "ECOFF" 1 1 FALSE FALSE
"EUCAST 2020" "human" "human" "MIC" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2020" "ECOFF" "ECOFF" "MIC" "F_CANDD_PRPS" 2 "ANI" "ECOFF" 4 4 FALSE FALSE
@@ -9989,8 +9989,8 @@
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -10805,8 +10805,8 @@
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2018" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -11611,8 +11611,8 @@
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2017" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -12356,8 +12356,8 @@
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2016" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -13074,8 +13074,8 @@
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2015" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -13791,8 +13791,8 @@
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Candida" 0.002 32 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Candida" 0.032 0.032 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Candida" 0.064 0.064 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Candida" 0.002 4 FALSE FALSE
"EUCAST 2014" "human" "human" "MIC" "F_CANDD_PRPS" 2 "FLU" "Candida" 2 4 FALSE FALSE
@@ -14491,8 +14491,8 @@
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_ALBC" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_GLBR" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_GLBR" 2 "ANI" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_KRUS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_KRUS" 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" "F_CANDD_PRPS" 2 "AMB" "Candida" 1 1 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_PRPS" 2 "POS" "Candida" 0.064 0.064 FALSE FALSE
"EUCAST 2013" "human" "human" "MIC" "F_CANDD_PRPS" 2 "VOR" "Candida" 0.125 0.125 FALSE FALSE
@@ -17856,20 +17856,20 @@
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_GLBR" 2 "RZF" "M27 Table 1" 0.5 4096 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "RZF" "M27 Table 1" 0.25 4096 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2024" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2024" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "M27 Table 1" 0.5 2 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" "5ug" 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 "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" "10ug" 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" "human" "human" "MIC" "F_PICHI_KDRV" 2 "RZF" "M27 Table 1" 0.25 4096 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" "1ug" 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_CANDD_MTPS" 2 "AMB" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "ANI" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2024" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "CAS" "M59 Table 1" 0.25 0.25 FALSE FALSE
@@ -20022,20 +20022,20 @@
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_GLBR" 2 "RZF" "M27 Table 1" 0.5 4096 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "M27 Table 1" 0.25 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "RZF" "M27 Table 1" 0.25 4096 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2023" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "M27 Table 1" 0.5 2 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" "5ug" 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" "10ug" 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 4096 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" "1ug" 15 12 FALSE FALSE
"CLSI 2023" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "M27 Table 1" 0.5 2 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "AMB" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "ANI" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2023" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "CAS" "M59 Table 1" 0.25 0.25 FALSE FALSE
@@ -22001,19 +22001,19 @@
"CLSI 2022" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "POS" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_GLBR" 2 "VOR" "M59 Table 1" 0.25 0.25 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "AMB" "M59 Table 1" 2 2 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ANI" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "ITR" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "MIF" "M59 Table 4" 0.25 0.25 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "POS" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_KRUS" 2 "VOR" "M59 Table 4" 0.5 0.5 FALSE FALSE
"CLSI 2022" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 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" "5ug" 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" "10ug" 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" "1ug" 15 12 FALSE FALSE
"CLSI 2022" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "AMB" "M59 Table 1" 1 1 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "ANI" "M59 Table 1" 0.5 0.5 FALSE FALSE
"CLSI 2022" "ECOFF" "ECOFF" "MIC" "F_CANDD_MTPS" 2 "CAS" "M59 Table 1" 0.25 0.25 FALSE FALSE
@@ -23602,13 +23602,13 @@
"CLSI 2021" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_GLBR" 2 "MIF" "Table 1" "10ug" 30 27 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 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" "5ug" 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" "10ug" 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" "1ug" 15 12 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Table 1" 2 8 FALSE FALSE
"CLSI 2021" "human" "human" "DISK" "F_CANDD_PRPS" 2 "CAS" "Table 1" "5ug" 13 10 FALSE FALSE
"CLSI 2021" "human" "human" "MIC" "F_CANDD_PRPS" 2 "CAS" "Table 1" 2 8 FALSE FALSE
@@ -25115,13 +25115,13 @@
"CLSI 2020" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_GLBR" 2 "MIF" "Table 1" "10ug" 30 27 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 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" "5ug" 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" "10ug" 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" "1ug" 15 12 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Table 1" 2 8 FALSE FALSE
"CLSI 2020" "human" "human" "DISK" "F_CANDD_PRPS" 2 "CAS" "Table 1" "5ug" 13 10 FALSE FALSE
"CLSI 2020" "human" "human" "MIC" "F_CANDD_PRPS" 2 "CAS" "Table 1" 2 8 FALSE FALSE
@@ -26487,13 +26487,13 @@
"CLSI 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "FLU" "Table 1" 1e-04 64 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_GLBR" 2 "MIF" "Table 1" "10ug" 30 27 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_GLBR" 2 "MIF" "Table 1" 0.064 0.25 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "ANI" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_KRUS" 2 "CAS" "Table 1" "5ug" 17 14 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "CAS" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_KRUS" 2 "MIF" "Table 1" "10ug" 22 19 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "MIF" "Table 1" 0.25 1 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_KRUS" 2 "VOR" "Table 1" "1ug" 15 12 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_KRUS" 2 "VOR" "Table 1" 0.5 2 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" "5ug" 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" "10ug" 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" "1ug" 15 12 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_PICHI_KDRV" 2 "VOR" "Table 1" 0.5 2 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "ANI" "Table 1" 2 8 FALSE FALSE
"CLSI 2019" "human" "human" "DISK" "F_CANDD_PRPS" 2 "CAS" "Table 1" "5ug" 13 10 FALSE FALSE
"CLSI 2019" "human" "human" "MIC" "F_CANDD_PRPS" 2 "CAS" "Table 1" 2 8 FALSE FALSE

BIN
data-raw/clinical_breakpoints.xlsx
View File

Binary file not shown.

BIN
data-raw/clinical_breakpoints.xpt
View File

Binary file not shown.

BIN
data-raw/dosage.xpt
View File

Binary file not shown.

2
data-raw/intrinsicR.md5
View File

@@ -1 +1 @@
e8c57a559ad846e72c700c88929e880d
930e15623071edb2196fcf8b2a259380

BIN
data-raw/intrinsic_resistant.dta
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.feather
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.parquet
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.rds
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.sav
View File

Binary file not shown.

62861
data-raw/intrinsic_resistant.txt
View File

File diff suppressed because it is too large Load Diff

BIN
data-raw/intrinsic_resistant.xlsx
View File

Binary file not shown.

BIN
data-raw/intrinsic_resistant.xpt
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.dta
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.feather
View File

Binary file not shown.

2
data-raw/microorganisms.codes.md5
View File

@@ -1 +1 @@
c9ba186023a0003c8153215646983621
cbf15fce0784e20b87aaa33b88b97f3f

BIN
data-raw/microorganisms.codes.parquet
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.rds
View File

Binary file not shown.

BIN
data-raw/microorganisms.codes.sav
View File

Binary file not shown.

120
data-raw/microorganisms.codes.txt
View File

@@ -341,7 +341,7 @@
"7001" "F_CANDD_ALBC"
"7002" "F_CANDD_TRPC"
"7003" "F_CANDD_GLBR"
"7005" "F_CANDD_KRUS"
"7005" "F_PICHI_KDRV"
"7006" "F_MYRZY_GLLR"
"7007" "F_CANDD_DBLN"
"7110" "F_CRYPT"
@@ -393,7 +393,7 @@
"7531" "B_CTRMN_SLNR"
"7540" "F_HSTPL"
"7541" "F_HSTPL_CPSL"
"7550" "F_BLSTM"
"7550" "F_CSPRM"
"7551" "B_BLSTM_DLFL"
"7560" "B_PSYCH_CCCD"
"7561" "B_PHYTB"
@@ -429,8 +429,8 @@
"9051" "B_BFDBC_COLB"
"9070" "P_THMNS"
"9071" "P_THMNS_VAG"
"9080" "P_TXPL"
"9081" "P_TXPL_GOND"
"9080" "C_TXPL"
"9081" "C_TXPL_GOND"
"9801" "B_ACHLP"
"9802" "B_ACDMNC"
"9803" "B_ACDVR"
@@ -1014,7 +1014,7 @@
"BARHEN" "B_BRTNL_HNSL"
"BARSPP" "B_BRTNL"
"BAS" "F_BSDBL"
"BAU" "F_CRVLR_ASTR"
"BAU" "F_BPLRS_ASTR"
"BAV" "B_BRDTL_AVIM"
"BAY" "B_EXGBC_ACTY"
"BBA" "B_BRTNL_BCLL"
@@ -1099,7 +1099,7 @@
"BHA" "F_CRVLR_HWNS"
"BHE" "B_BRTNL_HNSL"
"BHM" "B_BRDTL_HLMS"
"BHO" "F_BLSTC_HMNS"
"BHO" "C_BLSTC_HMNS"
"BHR" "B_BORRL_HRMS"
"BHZ" "B_BRDTL_HINZ"
"BIF" "B_BFDBC"
@@ -1118,14 +1118,14 @@
"BILSPP" "B_BLPHL"
"BILWAD" "B_BLPHL_WDSW"
"BIN" "B_BFDBC_LNGM_INFN"
"BLA" "F_BLSTM"
"BLAHOM" "F_BLSTC_HMNS"
"BLASPP" "F_BLSTC"
"BLA" "F_CSPRM"
"BLAHOM" "C_BLSTC_HMNS"
"BLASPP" "C_BLSTC"
"BLE" "B_PRPHYR_LEVI"
"BLI" "B_BCLLS_LCHN"
"BLN" "B_LDRBR_LENT"
"BLO" "B_BFDBC_LNGM"
"BLS" "F_BLSTC"
"BLS" "C_BLSTC"
"BLT" "B_BRVBC_LTRS"
"BLTSPP" "B_BCLLS"
"BMA" "B_BRKHL_MALL"
@@ -1223,7 +1223,7 @@
"BSF" "B_STRPT_GRPF"
"BSG" "B_STRPT_GRPG"
"BSH" "B_LYSNB_SPHR"
"BSI" "F_CRVLR_SPCF"
"BSI" "F_BPLRS_SPCF"
"BSL" "B_BCLLS_SBTL"
"BSP" "B_ODRBC_SPLN"
"BSR" "B_GBCLL_STRT"
@@ -1340,13 +1340,13 @@
"CANFIR" "F_CANDD"
"CANFRE" "F_CANDD_FRYS"
"CANGLA" "F_CANDD_GLBR"
"CANGUI" "F_CANDD_GLLR"
"CANGUI" "F_MYRZY_GLLR"
"CANINC" "F_CANDD_INCN"
"CANINT" "F_CANDD_INTR"
"CANKEF" "F_CANDD_KFYR"
"CANKRU" "F_CANDD_KRUS"
"CANKRU" "F_PICHI_KDRV"
"CANLAB" "F_CANDD"
"CANLAM" "F_CANDD_LMBC"
"CANLAM" "F_PICHI_FRMN"
"CANMAR" "F_CANDD_MARS"
"CANMEL" "F_CANDD_MLBS"
"CANMEM" "F_CANDD_MMBR"
@@ -1385,7 +1385,7 @@
"CATHON" "B_CHRST_HNGK"
"CATSPP" "B_CHRST"
"CAU" "B_CTRDM_SRDN"
"CAV" "B_ANRCL_LRCM"
"CAV" "B_ANRCL_AMNV"
"CAX" "F_CANDD_ALBC-C"
"CAY" "B_CRYPH"
"CAYSPP" "B_CRYPH"
@@ -1459,14 +1459,14 @@
"CFA" "B_CTRBC_FRMR"
"CFE" "B_CMPYL_FETS"
"CFL" "B_CHLMY_FELS"
"CFN" "F_CANDD_AFRC"
"CFN" "F_CANDD_ALBC"
"CFR" "B_CTRBC_FRND"
"CFV" "B_CMPYL_FETS_VNRL"
"CFX" "B_CTRDM_FLLX"
"CGA" "F_CRYPT"
"CGASPP" "F_CRYPT"
"CGC" "B_TRRSP_GLYC"
"CGH" "B_PNCLS_GHONI"
"CGH" "B_PRCLS_GHON"
"CGI" "B_CPNCY_GNGV"
"CGL" "F_CANDD_GLBR"
"CGM" "B_CRYNB_GLTM"
@@ -1550,7 +1550,7 @@
"CHDSPP" "B_CHLMY"
"CHE" "B_CTRDM_HMLY"
"CHF" "B_TSSRL_PRCT"
"CHI" "B_HTHWY_HSTLY"
"CHI" "B_HTHWY_HSTL"
"CHL" "B_CHLMY"
"CHLSPP" "B_CHLMY"
"CHM" "B_CHRMB"
@@ -1600,7 +1600,7 @@
"CJ2" "B_CMPYL_JEJN"
"CJD" "B_CMPYL_JEJN_DOYL"
"CJK" "B_CRYNB_JEKM"
"CKR" "F_CANDD_KRUS"
"CKR" "F_PICHI_KDRV"
"CKRSPP" "F_CANDD"
"CKU" "B_CRYNB_KTSC"
"CLA" "F_CLDSP"
@@ -1615,7 +1615,7 @@
"CLL" "B_CLLLSM"
"CLLCEL" "B_CLLLSM_CLLL"
"CLLSPP" "B_CLLLSM"
"CLM" "F_CANDD_LMBC"
"CLM" "F_PICHI_FRMN"
"CLMSPP" "F_CANDD"
"CLN" "F_CRYPT"
"CLNSPP" "F_CRYPT"
@@ -1761,7 +1761,7 @@
"CORVAR" "B_CRYNB_VRBL"
"CORXER" "B_CRYNB_XRSS"
"COT" "AN_CNTRC"
"COU" "B_FCLCT_RTCM"
"COU" "B_FCLCT_ORTC"
"COX" "B_COXLL"
"COXSPP" "B_COXLL"
"CPA" "F_CANDD_PRPS"
@@ -1975,7 +1975,7 @@
"EAF" "B_CLLNS_AERF"
"EAG" "B_PANTO_AGGL"
"EAL" "B_ERWIN_AMYL"
"EAM" "B_LLLTT_NGNS"
"EAM" "B_LLLTT_AMNG"
"EAN" "B_ENTRC_ASIN"
"EAR" "B_EWNGL_AMRC"
"EAS" "B_ENTRBC_ASBR"
@@ -1994,7 +1994,7 @@
"ECI" "P_ENTMB_COLI"
"ECL" "B_ENTRBC_CLOC"
"ECM" "B_CTRDM_CMBS"
"ECN" "B_FCLCT_TRTM"
"ECN" "B_FCLCT_CNTR"
"ECO" "B_ESCHR_COLI"
"ECR" "B_EKNLL_CRRD"
"ECS" "AN_ECHNS"
@@ -2054,7 +2054,7 @@
"ELA" "B_ELZBT_ANPH"
"ELE" "B_EGGRT_LENT"
"ELI" "B_EBCTRM_LMSM"
"ELIMEN" "B_ELZBT_PTCM"
"ELIMEN" "B_ELZBT_MNNG"
"ELIMIR" "B_ELZBT_MRCL"
"ELISPP" "B_ELZBT"
"ELZ" "B_ELZBT"
@@ -2163,14 +2163,14 @@
"EPO" "P_ENTMB_PLCK"
"EPS" "B_ENTRC_PSDV"
"ERA" "B_ENTRC_RFFN"
"ERE" "B_AGTHB_RECTL"
"ERE" "B_AGTHB_RCTL"
"ERH" "B_ERYSP_RHSP"
"ERO" "F_EXPHL"
"EROSPP" "F_EXPHL"
"ERU" "B_EHRLC_RMNN"
"ERW" "B_ERWIN"
"ERWAMY" "B_ERWIN_AMYL"
"ERWANA" "B_ERWIN_ANNT"
"ERWANA" "B_PANTO_ANNT"
"ERWCAR" "B_PCTBC_CRTV"
"ERWCHR" "B_DICKY_CHRY"
"ERWCYP" "B_ERWIN"
@@ -2378,7 +2378,7 @@
"FOD" "B_MYRDS_DRTS"
"FON" "F_FONSC"
"FOR" "B_PSDMN_ORYZ"
"FPA" "F_FUSRM_PLLD"
"FPA" "F_FUSRM_INCR"
"FPD" "F_FONSC_PDRS"
"FPE" "B_FSBCTR_PRDN"
"FPH" "B_FRNCS_PHLM"
@@ -2728,7 +2728,7 @@
"KOCKRI" "B_ROTHI_KRST"
"KOCPAL" "B_KOCUR_PLST"
"KOCRHI" "B_KOCUR_RHZP"
"KOCROS" "B_KOCUR_ROSS"
"KOCROS" "B_KOCUR_ROSE"
"KOCSPP" "B_KOCUR"
"KOCVAR" "B_KOCUR_VRNS"
"KOL" "B_KGLLA_ORLS"
@@ -2756,7 +2756,7 @@
"LAC" "B_LCTBC"
"LACACI" "B_LCTBC_ACDPH"
"LACCAS" "B_LCTCS_CASE"
"LACCAT" "B_LCTBC_CTNFR"
"LACCAT" "B_ERTHA_CTNF"
"LACCRI" "B_LCTBC_CRSP"
"LACCUR" "B_LTLCT_CRVT"
"LACDEL" "B_LCTBC_DLBR"
@@ -2866,7 +2866,7 @@
"LEIMEX" "P_LSHMN_MXCN"
"LEITRO" "P_LSHMN_TRPC"
"LEL" "B_LLLTT"
"LELAMN" "B_LLLTT_NGNS"
"LELAMN" "B_LLLTT_AMNG"
"LELNIM" "B_LLLTT_NMPR"
"LELSPP" "B_LLLTT"
"LEM" "B_LMNRL"
@@ -3024,7 +3024,7 @@
"MCT" "B_MYCBC_CHIT"
"MCU" "B_MBLNC_CRTS"
"MDE" "B_MYCBC_DRNH"
"MDI" "F_MCRSP_DSTR"
"MDI" "F_MCRSP_EQNM"
"MDU" "B_MYCBC_DUVL"
"MEA" "AN_MTGNM"
"MEASPP" "AN_MTGNM"
@@ -3098,9 +3098,9 @@
"MIO" "F_CANDD_PLML"
"MIP" "B_NOCRD"
"MIPAUD" "F_MCRSP_AUDN"
"MIPBOU" "F_MCRSP_BLLR"
"MIPBOU" "F_MCRSP_FLVM"
"MIPCAN" "F_MCRSP_CANS"
"MIPDIS" "F_MCRSP_DSTR"
"MIPDIS" "F_MCRSP_EQNM"
"MIPFER" "F_MCRSP_FRRG"
"MIPFUL" "F_MCRSP_FLVM"
"MIPGYP" "F_MCRSP_GYPS"
@@ -3108,7 +3108,7 @@
"MIPPRA" "F_MCRSP_PRCX"
"MIPRAC" "F_MCRSP_RCMS"
"MIPSPP" "F_MCRSP"
"MIPVAN" "F_MCRSP_VNBR"
"MIPVAN" "F_MCRSP_GLLN"
"MIR" "B_MCRBC"
"MIRARB" "B_MCRBC_ARBR"
"MIRAUR" "B_MCRBC_AURM"
@@ -3164,7 +3164,7 @@
"MOISPP" "B_MRTLL"
"MOO" "B_MRXLL_OVIS"
"MOR" "B_MRGNL"
"MORANA" "B_MRXLL_TFRA"
"MORANA" "B_RMRLL_TFRA"
"MORATL" "B_MRXLL_ATLN"
"MORBOV" "B_MRXLL_BOVS"
"MORCAN" "B_MRXLL_CANS"
@@ -3243,7 +3243,7 @@
"MUT" "B_MRXLL"
"MUTSPP" "B_MRXLL"
"MVA" "B_MYCBC_VACC"
"MVB" "F_MCRSP_VNBR"
"MVB" "F_MCRSP_GLLN"
"MVI" "B_MRTLL_VSCS"
"MWI" "B_MLLRL_WSCN"
"MXC" "B_MRXLL_CANS"
@@ -3349,7 +3349,7 @@
"MYPSPP" "B_MYCPLS"
"MYR" "B_MYRDS"
"MYRODM" "B_MYRDS_ODRT"
"MYRODO" "B_MYRDS_DRTM"
"MYRODO" "B_MYRDS_DRTS"
"MYRSPE" "B_MYRDS"
"MYRSPP" "B_MYRDS"
"MYS" "B_MYCBC_TBRC"
@@ -3359,7 +3359,7 @@
"MZC" "F_MYRZY_CRBB"
"NAE" "P_NAGLR"
"NAEFOW" "P_NAGLR_FWLR"
"NAM" "AN_NECTR_AMRC"
"NAM" "F_NECATR_AMRC"
"NAS" "B_NOCRD_ASTR"
"NBR" "B_NOCRD_BRSL"
"NCA" "B_NESSR_CANS"
@@ -3376,7 +3376,7 @@
"NDGPR" "B_GRAMP"
"NE-" "B_NESSR"
"NEC" "F_NECATR"
"NECAME" "AN_NECTR_AMRC"
"NECAME" "F_NECATR_AMRC"
"NECSPP" "F_NECATR"
"NEI" "B_NESSR"
"NEICAN" "B_NESSR_CANS"
@@ -3639,7 +3639,7 @@
"PEU" "AN_PDCLS"
"PEX" "F_EXPHL_EXPH"
"PFL" "B_PSDMN_FLRS"
"PFN" "F_PICHI_FRNS"
"PFN" "F_MLLRZ_FRNS"
"PFNSPP" "F_PICHI"
"PFR" "B_PRPNB_FRDN"
"PFX" "B_PSDMN_FLRS-C"
@@ -3734,7 +3734,7 @@
"PPI" "B_RLSTN_PCKT"
"PPL" "B_PSDMN_OLVR"
"PPM" "B_BRKHL_PSDM"
"PPN" "B_RDNTB_PNMTR"
"PPN" "B_RDNTB_PNMT"
"PPNGOR" "B_PPTNP"
"PPNHAR" "B_PPTNP"
"PPNIND" "B_PPTNP_INDL"
@@ -3968,7 +3968,7 @@
"RHDSPP" "F_RHDTR"
"RHI" "F_RHZMC"
"RHIMIC" "F_RHZPS_MCRS"
"RHIORY" "F_RHZPS_ORYZ"
"RHIORY" "F_RHZPS_ARRH"
"RHIRAD" "B_AGRBCT_RDBC"
"RHISPE" "F_RHZPS"
"RHISPP" "F_RHZPS"
@@ -4125,7 +4125,7 @@
"SCOSPP" "F_SCPLR"
"SCP" "B_STPHY_CAPR"
"SCR" "B_LCTCC_CRMR"
"SCS" "F_SCLCB_CNST"
"SCS" "F_OCHRC_CNST"
"SCT" "B_STRPT_CNST"
"SCU" "B_STPHY_CRNS"
"SCY" "F_SCYTL"
@@ -4250,7 +4250,7 @@
"SHO" "B_STPHY_HMNS"
"SHR" "B_SLMNL_ENTR_ENTR"
"SHT" "B_SLMNL_ENTR_HOTN"
"SHU" "F_SCLCB_HMCL"
"SHU" "F_OCHRC_HMCL"
"SHWPUT" "B_SHWNL_PTRF"
"SHY" "B_STPHY_HYCS"
"SIA" "B_STRPT_INFN"
@@ -4663,35 +4663,35 @@
"TCTSPP" "B_TRPNM"
"TDE" "B_TRPNM_DNTC"
"TEN" "B_TRPNM_PRLS"
"TEQ" "F_TRCHP_EQNM"
"TEQ" "F_TRCHP_TNSR"
"TER" "B_TRRBCL"
"TERSPP" "B_TRRBCL"
"TFO" "P_TRTRC_SUIS"
"TGA" "P_THMNS_GLLN"
"TGASPP" "F_TRCHD_NTHS"
"TGO" "P_TXPL_GOND"
"TGO" "C_TXPL_GOND"
"TGU" "B_TRBLS_GMNS"
"THA" "F_CANDD_HMLN"
"THM" "B_SLMNL_ENTR_ENTR"
"THO" "F_TRCHD_NTHS"
"THOSPP" "F_TRCHD_NTHS"
"THS" "F_CANDD_PSDH"
"THX" "B_CANDD_HMLN-C"
"THX" "F_CANDD_HMLN-C"
"TIN" "F_CANDD_INCN"
"TIS" "B_TSSRL"
"TISPRA" "B_TSSRL_PRCT"
"TISSPP" "B_TSSRL"
"TME" "F_TRCHP_MNTG"
"TMG" "F_TRCHP_MGNN"
"TMG" "F_TRCHP_RBRM"
"TMU" "F_TRCHS"
"TMUSPP" "F_TRCHS"
"TNB" "B_TNCBC"
"TNM" "B_TNCBC_MRTM"
"TNS" "B_SLMNL_ENTR_ENTR"
"TOP" "P_TXPL"
"TOP" "C_TXPL"
"TOT" "B_CRYNB_OTTD"
"TOX" "AN_TOXCR"
"TOXGON" "P_TXPL_GOND"
"TOXGON" "C_TXPL_GOND"
"TPA" "B_TRPNM_PRLS"
"TPH" "B_TRPNM_PHGD"
"TPHSPP" "B_TRPNM"
@@ -4734,24 +4734,24 @@
"TRICHO" "F_TRCHP"
"TRICON" "F_TRCHP_CNCN"
"TRICSP" "F_TRCHS"
"TRIEQU" "F_TRCHP_EQNM"
"TRIFIS" "F_TRCHP_FSCH"
"TRIEQU" "F_TRCHP_TNSR"
"TRIFIS" "F_TRCHP_RBRM"
"TRIFLA" "F_TRCHP_FLVS"
"TRIFLU" "F_TRCHP_FLVM"
"TRIFLU" "F_TRCHP_RBRM"
"TRIGEO" "F_TRCHP_GLOR"
"TRIGLO" "F_TRCHP_GLOR"
"TRIGOU" "F_TRCHP_GRVL"
"TRIINT" "F_TRCHP_MNTG"
"TRIKAN" "F_TRCHP_KANE"
"TRILON" "F_TRCHP_LNGF"
"TRIMEG" "F_TRCHP_MGNN"
"TRIKAN" "F_TRCHP_RBRM"
"TRILON" "F_ADRMA_FLVM"
"TRIMEG" "F_TRCHP_RBRM"
"TRIMEN" "F_TRCHP_MNTG"
"TRIPRO" "F_TRCHP_PRLF"
"TRIRAU" "F_TRCHP_RBTS"
"TRIRAU" "F_TRCHP_RBRM"
"TRIRUB" "F_TRCHP_RBRM"
"TRISCH" "F_TRCHP_SCHN"
"TRISIM" "F_TRCHP_SIMI"
"TRISOU" "F_TRCHP_SDNN"
"TRISOU" "F_TRCHP_VLCM"
"TRISPI" "AN_TRCHN_SPRL"
"TRISPP" "F_TRCHP"
"TRITER" "F_TRCHP_TRRS"
@@ -4761,7 +4761,7 @@
"TRIVER" "F_TRCHP_VRRC"
"TRIVIO" "F_TRCHP_VLCM"
"TRIVIR" "F_TRCHD_VIRD"
"TRIYAO" "F_TRCHP_YAND"
"TRIYAO" "F_TRCHP_VLCM"
"TRL" "B_TRPRL"
"TRLSPI" "AN_TRCHN_SPRL"
"TRLSPP" "AN_TRCHN"
@@ -4793,7 +4793,7 @@
"TSO" "AN_TAENI_SOLM"
"TSOSPP" "AN_TAENI"
"TSP" "AN_TRCHN_SPRL"
"TSU" "F_TRCHP_SDNN"
"TSU" "F_TRCHP_VLCM"
"TTC" "P_TRTRC"
"TTE" "F_TRCHP_TRRS"
"TTN" "P_THMNS_TENX"

BIN
data-raw/microorganisms.codes.xlsx
View File

Binary file not shown.

0
data-raw/microorganisms.codes.xpt
View File

BIN
data-raw/microorganisms.dta
View File

Binary file not shown.

BIN
data-raw/microorganisms.feather
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.dta
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.feather
View File

Binary file not shown.

2
data-raw/microorganisms.groups.md5
View File

@@ -1 +1 @@
c296aff21039582a1c2d3c092ccf848c
a16b8db2140952b8a5848989afdccb53

BIN
data-raw/microorganisms.groups.parquet
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.rds
View File

Binary file not shown.

BIN
data-raw/microorganisms.groups.sav
View File

Binary file not shown.

170
data-raw/microorganisms.groups.txt
View File

@@ -1,14 +1,14 @@
"mo_group" "mo" "mo_group_name" "mo_name"
"B_ACNTB_BMNN-C" "B_ACNTB_BMNN" "Acinetobacter baumannii complex" "Acinetobacter baumannii"
"B_ACNTB_BMNN-C" "B_ACNTB_CLCC" "Acinetobacter baumannii complex" "Acinetobacter calcoaceticus"
"B_ACNTB_BMNN-C" "B_ACNTB_DJKS" "Acinetobacter baumannii complex" "Acinetobacter dijkshoorniae"
"B_ACNTB_BMNN-C" "B_ACNTB_LCTC" "Acinetobacter baumannii complex" "Acinetobacter dijkshoorniae"
"B_ACNTB_BMNN-C" "B_ACNTB_NSCM" "Acinetobacter baumannii complex" "Acinetobacter nosocomialis"
"B_ACNTB_BMNN-C" "B_ACNTB_PITT" "Acinetobacter baumannii complex" "Acinetobacter pittii"
"B_ACNTB_BMNN-C" "B_ACNTB_SFRT" "Acinetobacter baumannii complex" "Acinetobacter seifertii"
"B_BCTRD_FRGL-C" "B_BCTRD_FRGL" "Bacteroides fragilis complex" "Bacteroides fragilis"
"B_BCTRD_FRGL-C" "B_BCTRD_OVTS" "Bacteroides fragilis complex" "Bacteroides ovatus"
"B_BCTRD_FRGL-C" "B_BCTRD_THTT" "Bacteroides fragilis complex" "Bacteroides thetaiotaomicron"
"B_BCTRD_FRGL-C" "B_BCTRD_VLGT" "Bacteroides fragilis complex" "Bacteroides vulgatus"
"B_BCTRD_FRGL-C" "B_PHCCL_VLGT" "Bacteroides fragilis complex" "Bacteroides vulgatus"
"B_BCTRD_FRGL-C" "B_PRBCT_DSTS" "Bacteroides fragilis complex" "Parabacteroides distasonis"
"B_STRPT_HAEM" "B_STRPT_GRPA" "Beta-haemolytic Streptococcus" "Streptococcus Group A"
"B_STRPT_HAEM" "B_STRPT_ABCG" "Beta-haemolytic Streptococcus" "Streptococcus Group A, B, C, G"
@@ -43,8 +43,8 @@
"B_STRPT_HAEM" "B_STRPT_PRCN" "Beta-haemolytic Streptococcus" "Streptococcus porcinus"
"B_STRPT_HAEM" "B_STRPT_PYGN" "Beta-haemolytic Streptococcus" "Streptococcus pyogenes"
"B_STRPT_HAEM" "B_STRPT_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius"
"B_STRPT_HAEM" "B_STRPT_SLVR_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius salivarius"
"B_STRPT_HAEM" "B_STRPT_SLVR_THRM" "Beta-haemolytic Streptococcus" "Streptococcus salivarius thermophilus"
"B_STRPT_HAEM" "B_STRPT_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius salivarius"
"B_STRPT_HAEM" "B_STRPT_THRM" "Beta-haemolytic Streptococcus" "Streptococcus salivarius thermophilus"
"B_STRPT_HAEM" "B_STRPT_SNGN" "Beta-haemolytic Streptococcus" "Streptococcus sanguinis"
"B_BRKHL_CEPC-C" "B_BRKHL_AMBF" "Burkholderia cepacia complex" "Burkholderia ambifaria"
"B_BRKHL_CEPC-C" "B_BRKHL_ANTH" "Burkholderia cepacia complex" "Burkholderia anthina"
@@ -56,15 +56,15 @@
"B_BRKHL_CEPC-C" "B_BRKHL_STBL" "Burkholderia cepacia complex" "Burkholderia stabilis"
"B_BRKHL_CEPC-C" "B_BRKHL_UBNN" "Burkholderia cepacia complex" "Burkholderia ubonensis"
"B_BRKHL_CEPC-C" "B_BRKHL_VTNM" "Burkholderia cepacia complex" "Burkholderia vietnamiensis"
"F_CANDD_ALBC-C" "F_CANDD_AFRC" "Candida albicans complex" "Candida africana"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida africana"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_ALBC" "Candida albicans complex" "Candida albicans albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_CLSS" "Candida albicans complex" "Candida albicans claussenii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_MTLN" "Candida albicans complex" "Candida albicans metalondinensis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_NNLQ" "Candida albicans complex" "Candida albicans non-liquefaciens"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_STLL" "Candida albicans complex" "Candida albicans stellatoidea"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_TRPC" "Candida albicans complex" "Candida albicans tropicalis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_VLLM" "Candida albicans complex" "Candida albicans vuilleminii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans claussenii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans metalondinensis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans non-liquefaciens"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans stellatoidea"
"F_CANDD_ALBC-C" "F_CANDD_TRPC" "Candida albicans complex" "Candida albicans tropicalis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans vuilleminii"
"F_CANDD_ALBC-C" "F_CANDD_DBLN" "Candida albicans complex" "Candida dubliniensis"
"F_CANDD_GLBR-C" "F_CANDD_BRCR" "Candida glabrata complex" "Candida bracarensis"
"F_CANDD_GLBR-C" "F_CANDD_GLBR" "Candida glabrata complex" "Candida glabrata"
@@ -72,14 +72,14 @@
"F_CANDD_PRPS-C" "F_CANDD_MTPS" "Candida parapsilosis complex" "Candida metapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_ORTH" "Candida parapsilosis complex" "Candida orthopsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_HOKK" "Candida parapsilosis complex" "Candida parapsilosis hokkaii"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_INTR" "Candida parapsilosis complex" "Candida parapsilosis intermedia"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_PRPS" "Candida parapsilosis complex" "Candida parapsilosis parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QURC" "Candida parapsilosis complex" "Candida parapsilosis querci"
"F_CANDD_PRPS-C" "F_CANDD_MLBS" "Candida parapsilosis complex" "Candida parapsilosis hokkaii"
"F_CANDD_PRPS-C" "F_CANDD_MLBS" "Candida parapsilosis complex" "Candida parapsilosis intermedia"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis querci"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QRCS" "Candida parapsilosis complex" "Candida parapsilosis quercus"
"P_CHLMS" "F_CANDD_DBSH" "Chilomastix" "Candida duobushaemulonii"
"P_CHLMS" "F_CANDD_HMLN" "Chilomastix" "Candida haemulonii"
"P_CHLMS" "B_CANDD_HMLN-C" "Chilomastix" "Candida haemulonii complex"
"P_CHLMS" "F_CANDD_HMLN-C" "Chilomastix" "Candida haemulonii complex"
"B_CTRBC_AMLN-C" "B_CTRBC_AMLN" "Citrobacter amalonaticus complex" "Citrobacter amalonaticus"
"B_CTRBC_AMLN-C" "B_CTRBC_FRMR" "Citrobacter amalonaticus complex" "Citrobacter farmeri"
"B_CTRBC_AMLN-C" "B_CTRBC_SDLK" "Citrobacter amalonaticus complex" "Citrobacter sedlakii"
@@ -101,18 +101,18 @@
"B_STPHY_CONS" "B_STPHY_CPTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis"
"B_STPHY_CONS" "B_STPHY_CPTS_CPTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis capitis"
"B_STPHY_CONS" "B_STPHY_CPTS_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis urealyticus"
"B_STPHY_CONS" "B_STPHY_CPTS_YTCS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis ureolyticus"
"B_STPHY_CONS" "B_STPHY_CPTS_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis ureolyticus"
"B_STPHY_CONS" "B_STPHY_CAPR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caprae"
"B_STPHY_CONS" "B_STPHY_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus"
"B_STPHY_CONS" "B_STPHY_CRNS_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus carnosus"
"B_STPHY_CONS" "B_STPHY_CRNS_UTLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus utilis"
"B_STPHY_CONS" "B_STPHY_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus carnosus"
"B_STPHY_CONS" "B_STPHY_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus utilis"
"B_STPHY_CONS" "B_STPHY_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus casei"
"B_STPHY_CONS" "B_STPHY_CSLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caseolyticus"
"B_STPHY_CONS" "B_MCRCC_CSLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caseolyticus"
"B_STPHY_CONS" "B_STPHY_CHRM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus chromogenes"
"B_STPHY_CONS" "B_STPHY_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii"
"B_STPHY_CONS" "B_STPHY_COHN_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii cohnii"
"B_STPHY_CONS" "B_STPHY_COHN_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticum"
"B_STPHY_CONS" "B_STPHY_COHN_YTCS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticus"
"B_STPHY_CONS" "B_STPHY_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii cohnii"
"B_STPHY_CONS" "B_STPHY_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticum"
"B_STPHY_CONS" "B_STPHY_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticus"
"B_STPHY_CONS" "B_STPHY_CNDM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus condimenti"
"B_STPHY_CONS" "B_STPHY_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus croceilyticus"
"B_STPHY_CONS" "B_STPHY_DBCK" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus debuckii"
@@ -130,7 +130,7 @@
"B_STPHY_CONS" "B_STPHY_HMNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis"
"B_STPHY_CONS" "B_STPHY_HMNS_HMNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis hominis"
"B_STPHY_CONS" "B_STPHY_HMNS_NVBS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis novobiosepticus"
"B_STPHY_CONS" "B_STPHY_JTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus jettensis"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus jettensis"
"B_STPHY_CONS" "B_STPHY_KLOS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus kloosii"
"B_STPHY_CONS" "B_STPHY_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus lentus"
"B_STPHY_CONS" "B_STPHY_LLYD" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus lloydii"
@@ -141,40 +141,40 @@
"B_STPHY_CONS" "B_STPHY_NPLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus nepalensis"
"B_STPHY_CONS" "B_STPHY_PSTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pasteuri"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii"
"B_STPHY_CONS" "B_STPHY_PTRS_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii croceilyticus"
"B_STPHY_CONS" "B_STPHY_PTRS_JTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii jettensis"
"B_STPHY_CONS" "B_STPHY_PTRS_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii petrasii"
"B_STPHY_CONS" "B_STPHY_PTRS_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii pragensis"
"B_STPHY_CONS" "B_STPHY_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii croceilyticus"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii jettensis"
"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii petrasii"
"B_STPHY_CONS" "B_STPHY_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii pragensis"
"B_STPHY_CONS" "B_STPHY_PTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pettenkoferi"
"B_STPHY_CONS" "B_STPHY_PSCF" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus piscifermentans"
"B_STPHY_CONS" "B_STPHY_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pragensis"
"B_STPHY_CONS" "B_STPHY_PSDX" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pseudoxylosus"
"B_STPHY_CONS" "B_STPHY_PLVR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pulvereri"
"B_STPHY_CONS" "B_STPHY_VTLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pulvereri"
"B_STPHY_CONS" "B_STPHY_RATT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus ratti"
"B_STPHY_CONS" "B_STPHY_RSTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus rostri"
"B_STPHY_CONS" "B_STPHY_SCCH" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saccharolyticus"
"B_STPHY_CONS" "B_STPHY_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SPRP_BOVS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus bovis"
"B_STPHY_CONS" "B_STPHY_SPRP_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus bovis"
"B_STPHY_CONS" "B_STPHY_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi"
"B_STPHY_CONS" "B_STPHY_SCHL_CGLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_CONS" "B_STPHY_SCHL_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi schleiferi"
"B_STPHY_CONS" "B_STPHY_CGLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_CONS" "B_STPHY_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi schleiferi"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri"
"B_STPHY_CONS" "B_STPHY_SCIR_CRNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri carnaticus"
"B_STPHY_CONS" "B_STPHY_SCIR_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri lentus"
"B_STPHY_CONS" "B_STPHY_SCIR_RDNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri rodentium"
"B_STPHY_CONS" "B_STPHY_SCIR_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri sciuri"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri carnaticus"
"B_STPHY_CONS" "B_STPHY_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri lentus"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri rodentium"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri sciuri"
"B_STPHY_CONS" "B_STPHY_SMLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus simulans"
"B_STPHY_CONS" "B_STPHY_STPN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus stepanovicii"
"B_STPHY_CONS" "B_STPHY_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus"
"B_STPHY_CONS" "B_STPHY_SCCN_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus casei"
"B_STPHY_CONS" "B_STPHY_SCCN_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus succinus"
"B_STPHY_CONS" "B_STPHY_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus casei"
"B_STPHY_CONS" "B_STPHY_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus succinus"
"B_STPHY_CONS" "B_STPHY_TWNN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus taiwanensis"
"B_STPHY_CONS" "B_STPHY_URLYT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus urealyticus"
"B_STPHY_CONS" "B_STPHY_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus ureilyticus"
"B_STPHY_CONS" "B_STPHY_VRTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus veratri"
"B_STPHY_CONS" "B_STPHY_VTLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulinus"
"B_STPHY_CONS" "B_STPHY_VTLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulus"
"B_STPHY_CONS" "B_STPHY_VTLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulus"
"B_STPHY_CONS" "B_STPHY_WRNR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus warneri"
"B_STPHY_CONS" "B_STPHY_XYLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus xylosus"
"B_STPHY_COPS" "B_STPHY_AGNT" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus agnetis"
@@ -183,13 +183,13 @@
"B_STPHY_COPS" "B_STPHY_CRNB" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus cornubiensis"
"B_STPHY_COPS" "B_STPHY_DLPH" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus delphini"
"B_STPHY_COPS" "B_STPHY_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus"
"B_STPHY_COPS" "B_STPHY_HYCS_CHRM" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus chromogenes"
"B_STPHY_COPS" "B_STPHY_HYCS_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus hyicus"
"B_STPHY_COPS" "B_STPHY_CHRM" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus chromogenes"
"B_STPHY_COPS" "B_STPHY_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus hyicus"
"B_STPHY_COPS" "B_STPHY_INTR" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus intermedius"
"B_STPHY_COPS" "B_STPHY_LUTR" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus lutrae"
"B_STPHY_COPS" "B_STPHY_PSDN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus pseudintermedius"
"B_STPHY_COPS" "B_STPHY_RTRD" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus roterodami"
"B_STPHY_COPS" "B_STPHY_SCHL_CGLN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_COPS" "B_STPHY_CGLN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_COPS" "B_STPHY_SCHW" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schweitzeri"
"B_STPHY_COPS" "B_STPHY_SIMI" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus simiae"
"B_STPHY_COPS" "B_STPHY_SNGP" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus singaporensis"
@@ -252,8 +252,8 @@
"B_CORYNF" "B_TRPRL" "Coryneform bacterium" "Trueperella"
"B_CORYNF" "B_TRPRL_BRNR" "Coryneform bacterium" "Trueperella bernardiae"
"B_CORYNF" "B_TRPRL_PYGN" "Coryneform bacterium" "Trueperella pyogenes"
"B_CORYNF" "B_TRCLL" "Coryneform bacterium" "Turicella"
"B_CORYNF" "B_TRCLL_OTTD" "Coryneform bacterium" "Turicella otitidis"
"B_CORYNF" "B_CRYNB" "Coryneform bacterium" "Turicella"
"B_CORYNF" "B_CRYNB_OTTD" "Coryneform bacterium" "Turicella otitidis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_ASBR" "Enterobacter cloacae complex" "Enterobacter asburiae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae cloacae"
@@ -266,59 +266,59 @@
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_XNGF" "Enterobacter cloacae complex" "Enterobacter hormaechei xiangfangensis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_KOBE" "Enterobacter cloacae complex" "Enterobacter kobei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_LDWG" "Enterobacter cloacae complex" "Enterobacter ludwigii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_NMPR" "Enterobacter cloacae complex" "Enterobacter nimipressuralis"
"B_HACEK" "B_ACTNB_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Actinobacillus actinomycetemcomitans"
"B_ENTRBC_CLOC-C" "B_LLLTT_NMPR" "Enterobacter cloacae complex" "Enterobacter nimipressuralis"
"B_HACEK" "B_AGGRG_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Actinobacillus actinomycetemcomitans"
"B_HACEK" "B_AGGRG" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter"
"B_HACEK" "B_AGGRG_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter actinomycetemcomitans"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter aphrophilus"
"B_HACEK" "B_AGGRG_KILN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter kilianii"
"B_HACEK" "B_AGGRG_PRPH" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter paraphrophilus"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter paraphrophilus"
"B_HACEK" "B_AGGRG_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter segnis"
"B_HACEK" "B_CRDBC_HMNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Cardiobacterium hominis"
"B_HACEK" "B_EKNLL_CRRD" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Eikenella corrodens"
"B_HACEK" "B_HMPHL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus"
"B_HACEK" "B_HMPHL_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus actinomycetemcomitans"
"B_HACEK" "B_AGGRG_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus actinomycetemcomitans"
"B_HACEK" "B_HMPHL_AEGY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aegyptius"
"B_HACEK" "B_HMPHL_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aphrophilus"
"B_HACEK" "B_HMPHL_AVIM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus avium"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aphrophilus"
"B_HACEK" "B_AVBCT_AVIM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus avium"
"B_HACEK" "B_HMPHL_DCRY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus ducreyi"
"B_HACEK" "B_HMPHL_EQGN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus equigenitalis"
"B_HACEK" "B_TYLRL_EQGN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus equigenitalis"
"B_HACEK" "B_HMPHL_FELS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus felis"
"B_HACEK" "B_HMPHL_HMGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemoglobinophilus"
"B_HACEK" "B_CANCL_HMGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemoglobinophilus"
"B_HACEK" "B_HMPHL_HMLY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemolyticus"
"B_HACEK" "B_HMPHL_INFL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus influenzae"
"B_HACEK" "B_HMPHL_MSSL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus massiliensis"
"B_HACEK" "B_HMPHL_PRCN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paracuniculus"
"B_HACEK" "B_HMPHL_PRGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paragallinarum"
"B_HACEK" "B_AVBCT_PRGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paragallinarum"
"B_HACEK" "B_HMPHL_PRHM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parahaemolyticus"
"B_HACEK" "B_HMPHL_PRNF" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parainfluenzae"
"B_HACEK" "B_HMPHL_PRPH" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrohaemolyticus"
"B_HACEK" "B_HMPHL_PHLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrophilus"
"B_HACEK" "B_HMPHL_PRSS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parasuis"
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrophilus"
"B_HACEK" "B_GLSSR_PRSS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parasuis"
"B_HACEK" "B_HMPHL_PSCM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus piscium"
"B_HACEK" "B_HMPHL_PTTM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pittmaniae"
"B_HACEK" "B_HMPHL_PLRP" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pleuropneumoniae"
"B_HACEK" "B_ACTNB_PLRP" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pleuropneumoniae"
"B_HACEK" "B_HMPHL_QNTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus quentini"
"B_HACEK" "B_HMPHL_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus segnis"
"B_HACEK" "B_AGGRG_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus segnis"
"B_HACEK" "B_HMPHL_SMNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus seminalis"
"B_HACEK" "B_HMPHL_SPTR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus sputorum"
"B_HACEK" "B_HMPHL_VGNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus vaginalis"
"B_HACEK" "B_GRDNR_VGNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus vaginalis"
"B_HACEK" "B_KGLLA" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella"
"B_HACEK" "B_KGLLA_DNTR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella denitrificans"
"B_HACEK" "B_KGLLA_INDL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella indologenes"
"B_HACEK" "B_STTNL_INDL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella indologenes"
"B_HACEK" "B_KGLLA_KING" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella kingae"
"B_HACEK" "B_KGLLA_NGVN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella negevensis"
"B_HACEK" "B_KGLLA_ORAL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella orale"
"B_HACEK" "B_KGLLA_ORLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella orale"
"B_HACEK" "B_KGLLA_ORLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella oralis"
"B_HACEK" "B_KGLLA_POTS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella potus"
"F_MYRZY_GLLR-C" "F_CANDD_FRMN" "Meyerozyma guilliermondii complex" "Candida fermentati"
"F_MYRZY_GLLR-C" "F_MYRZY_CRBB" "Meyerozyma guilliermondii complex" "Meyerozyma caribbica"
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_JPNC" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii japonica"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_MUHR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii muhira"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_PSDG" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii pseudoguilliermondii"
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii japonica"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii muhira"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii pseudoguilliermondii"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_PRTB" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium paratuberculosis"
@@ -326,19 +326,19 @@
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_CHMR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare chimaera"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_INTR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_YNGN" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare yongonense"
"B_MYCBC_TBRC-C" "B_MYCBC_AFRC" "Mycobacterium tuberculosis complex" "Mycobacterium africanum"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium bovis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_MCRT" "Mycobacterium tuberculosis complex" "Mycobacterium microti"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_CHMR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare yongonense"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium africanum"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium bovis bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium bovis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium microti"
"B_MYCBC_TBRC-C" "B_MYCBC_MUNG" "Mycobacterium tuberculosis complex" "Mycobacterium mungi"
"B_MYCBC_TBRC-C" "B_MYCBC_ORYG" "Mycobacterium tuberculosis complex" "Mycobacterium orygis"
"B_MYCBC_TBRC-C" "B_MYCBC_PNNP" "Mycobacterium tuberculosis complex" "Mycobacterium pinnipedii"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium pinnipedii"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis tuberculosis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis tuberculosis"
"B_PSDMN_FLRS-C" "B_PSDMN_FLRS" "Pseudomonas fluorescens complex" "Pseudomonas fluorescens"
"B_MYCBC_RGM" "B_MYCBC_ABSC_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus abscessus"
"B_MYCBC_RGM" "B_MYCBC_ABSC_BLLT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus bolletii"
@@ -361,8 +361,8 @@
"B_MYCBC_RGM" "B_MYCBC_CNRS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium canariasense"
"B_MYCBC_RGM" "B_MYCBC_CLRF" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium celeriflavum"
"B_MYCBC_RGM" "B_MYCBC_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae abscessus"
"B_MYCBC_RGM" "B_MYCBC_CHLN_BOVS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae bovis"
"B_MYCBC_RGM" "B_MYCBC_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae abscessus"
"B_MYCBC_RGM" "B_MYCBC_CHLN_BVST" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae bovis"
"B_MYCBC_RGM" "B_MYCBC_CHLN_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_GWNK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae gwanakae"
"B_MYCBC_RGM" "B_MYCBC_CHIT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chitae"
@@ -428,7 +428,7 @@
"B_MYCBC_RGM" "B_MYCBC_THRM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium thermoresistibile"
"B_MYCBC_RGM" "B_MYCBC_TKNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium tokaiense"
"B_MYCBC_RGM" "B_MYCBC_VACC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vaccae"
"B_MYCBC_RGM" "B_MYCBC_VNBL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vanbaalenii"
"B_MYCBC_RGM" "B_MYCBC_ASTR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vanbaalenii"
"B_MYCBC_RGM" "B_MYCBC_WLNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium wolinskyi"
"B_MYCBC_SGM" "B_MYCBC_FRCN" "Slowly growing Mycobacterium (SGM)" "Mycobacterium farcinogenes"
"B_MYCBC_SGM" "B_MYCBC_GSTR" "Slowly growing Mycobacterium (SGM)" "Mycobacterium gastri"
@@ -476,8 +476,8 @@
"B_STRPT_GRPG" "B_STRPT_DYSG_EQSM" "Streptococcus Group G" "Streptococcus dysgalactiae equisimilis"
"B_STRPT_GRPH" "B_STRPT_SNGN" "Streptococcus Group H" "Streptococcus sanguinis"
"B_STRPT_GRPK" "B_STRPT_SLVR" "Streptococcus Group K" "Streptococcus salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_SLVR" "Streptococcus Group K" "Streptococcus salivarius salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_THRM" "Streptococcus Group K" "Streptococcus salivarius thermophilus"
"B_STRPT_GRPK" "B_STRPT_SLVR" "Streptococcus Group K" "Streptococcus salivarius salivarius"
"B_STRPT_GRPK" "B_STRPT_THRM" "Streptococcus Group K" "Streptococcus salivarius thermophilus"
"B_STRPT_GRPL" "B_STRPT_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_EQSM" "Streptococcus Group L" "Streptococcus dysgalactiae equisimilis"
@@ -507,8 +507,8 @@
"B_STRPT_VIRI" "B_STRPT_PRSN" "Viridans Group Streptococcus (VGS)" "Streptococcus parasanguinis"
"B_STRPT_VIRI" "B_STRPT_RATT" "Viridans Group Streptococcus (VGS)" "Streptococcus ratti"
"B_STRPT_VIRI" "B_STRPT_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_THRM" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius thermophilus"
"B_STRPT_VIRI" "B_STRPT_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius salivarius"
"B_STRPT_VIRI" "B_STRPT_THRM" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius thermophilus"
"B_STRPT_VIRI" "B_STRPT_SNGN" "Viridans Group Streptococcus (VGS)" "Streptococcus sanguinis"
"B_STRPT_VIRI" "B_STRPT_SBRN" "Viridans Group Streptococcus (VGS)" "Streptococcus sobrinus"
"B_STRPT_VIRI" "B_STRPT_SUIS" "Viridans Group Streptococcus (VGS)" "Streptococcus suis"
@@ -516,7 +516,7 @@
"B_STRPT_VIRI" "B_STRPT_VSTB" "Viridans Group Streptococcus (VGS)" "Streptococcus vestibularis"
"B_YERSN_PSDT-C" "B_YERSN_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_SMLS" "Yersinia pseudotuberculosis complex" "Yersinia similis"
"B_YERSN_PSDT-C" "B_YERSN_WTRS" "Yersinia pseudotuberculosis complex" "Yersinia wautersii"

BIN
data-raw/microorganisms.groups.xlsx
View File

Binary file not shown.

0
data-raw/microorganisms.groups.xpt
View File

2
data-raw/microorganisms.md5
View File

@@ -1 +1 @@
f6957ab7c3022dfcdb686f70453a9795
f1cbe414851c1eee08ff5440a47af76c

BIN
data-raw/microorganisms.parquet
View File

Binary file not shown.

BIN
data-raw/microorganisms.rds
View File

Binary file not shown.

BIN
data-raw/microorganisms.sav
View File

Binary file not shown.

39589
data-raw/microorganisms.txt
View File

File diff suppressed because it is too large Load Diff

BIN
data-raw/microorganisms.xlsx
View File

Binary file not shown.

BIN
data-raw/microorganisms.xpt
View File

Binary file not shown.

620
data-raw/reproduction_of_microorganisms.R
View File

File diff suppressed because it is too large Load Diff

BIN
data-raw/taxonomy0.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy1.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy0b.rds → data-raw/taxonomy1b.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy1c.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy2.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy2b.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy2c.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy3.rds
View File

Binary file not shown.

BIN
data-raw/taxonomy3b.rds Normal file
View File

Binary file not shown.

BIN
data-raw/taxonomy_gbif.rds
View File

Binary file not shown.