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support veterinary MIC/disk translation

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dr. M.S. (Matthijs) Berends
2024-02-24 15:16:52 +01:00
parent 74ea6c8c60
commit 7be4dabbc0
69 changed files with 34521 additions and 30207 deletions
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---
title: "AMR Goes Vet"
author: "Jason, Matthew, Javier, Matthijs"
date: "2024-02-20"
format:
html:
embed-resources: true
---
## Import WHONET data set
```{r, message=FALSE, warning=FALSE}
library(dplyr)
library(readr)
library(tidyr)
library(janitor)
# WHONET version of 16th Feb 2024
whonet_breakpoints <- read_tsv("WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
show_col_types = FALSE, guess_max = Inf) %>%
filter(GUIDELINES %in% c("CLSI", "EUCAST"))
dim(whonet_breakpoints)
```
# EDA of Animal Breakpoints
```{r}
whonet_breakpoints |>
filter(BREAKPOINT_TYPE != "Human")
whonet_breakpoints |>
filter(BREAKPOINT_TYPE != "Human") |>
count(BREAKPOINT_TYPE)
whonet_breakpoints |>
filter(BREAKPOINT_TYPE == "Animal")
```
### Count of all animal breakpoints
```{r}
whonet_breakpoints |>
filter(BREAKPOINT_TYPE == "Animal") |>
count(YEAR, HOST, REFERENCE_TABLE = gsub("VET[0-9]+ ", "", REFERENCE_TABLE)) |>
pivot_wider(names_from = YEAR, values_from = n, values_fill = list(n = 0)) |>
arrange(HOST, REFERENCE_TABLE) |>
adorn_totals(name = "TOTAL")
```
### Cats only
```{r}
whonet_breakpoints |>
filter(HOST == "Cats", YEAR >= 2021) |>
select(GUIDELINES, YEAR, TEST_METHOD, ORGANISM_CODE, R, S) |>
mutate(MO_NAME = AMR::mo_shortname(ORGANISM_CODE), .before = R) |>
as.data.frame()
```
### Site of infection in cats (2023)
```{r}
whonet_breakpoints |>
filter(HOST == "Cats", YEAR == 2023) |>
mutate(MO = AMR::mo_shortname(ORGANISM_CODE),
AB = AMR::ab_name(WHONET_ABX_CODE),
SITE_OF_INFECTION = substr(SITE_OF_INFECTION, 1, 25)) |>
arrange(MO, AB) |>
select(MO, AB, SITE_OF_INFECTION) |>
as.data.frame()
```

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@@ -157,20 +157,21 @@ MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms$genus == "Stre
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(_|$))")]
MO_PREVALENT_GENERA <- c(
"Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
"Anisakis", "Anopheles", "Apophysomyces", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
"Blastocystis", "Blastomyces", "Candida", "Capillaria", "Chaetomium", "Chrysonilia", "Cladophialophora",
"Anisakis", "Anopheles", "Apophysomyces", "Arthroderma", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
"Blastocystis", "Blastomyces", "Candida", "Capillaria", "Chaetomium", "Chrysonilia", "Chrysosporium", "Cladophialophora",
"Cladosporium", "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex",
"Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Echinostoma", "Entamoeba", "Enterobius",
"Exophiala", "Exserohilum", "Fasciola", "Fonsecaea", "Fusarium", "Giardia", "Haloarcula", "Halobacterium",
"Exophiala", "Exserohilum", "Fasciola", "Fonsecaea", "Fusarium", "Geotrichum", "Giardia", "Haloarcula", "Halobacterium",
"Halococcus", "Hendersonula", "Heterophyes", "Histomonas", "Histoplasma", "Hymenolepis", "Hypomyces",
"Hysterothylacium", "Leishmania", "Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma", "Microsporidium",
"Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Necator", "Nectria", "Ochroconis", "Oesophagostomum",
"Oidiodendron", "Opisthorchis", "Pediculus", "Penicillium", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces",
"Hysterothylacium", "Kloeckera", "Kodamaea", "Leishmania", "Lichtheimia", "Lodderomyces",
"Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma", "Microsporidium",
"Microsporum", "Millerozyma", "Mortierella", "Mucor", "Mycocentrospora", "Necator", "Nectria", "Ochroconis", "Oesophagostomum",
"Oidiodendron", "Opisthorchis", "Paecilomyces", "Pediculus", "Penicillium", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces",
"Pityrosporum", "Pneumocystis", "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus",
"Rhodotorula", "Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra",
"Sporobolomyces", "Stachybotrys", "Strongyloides", "Syngamus", "Taenia", "Talaromyces", "Toxocara", "Trichinella",
"Rhodotorula", "Saccharomyces", "Saprochaete", "Sarcoptes", "Scedosporium", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra",
"Sporobolomyces", "Sporotrichum", "Stachybotrys", "Strongyloides", "Syngamus", "Taenia", "Talaromyces", "Toxocara", "Trichinella",
"Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris",
"Tritirachium", "Trombicula", "Trypanosoma", "Tunga", "Wuchereria"
"Tritirachium", "Trombicula", "Trypanosoma", "Tunga", "Verticillium", "Wuchereria"
)
# antibiotic groups

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"AMX" 33613 "Amoxicillin" "Beta-lactams/penicillins" "J01CA04" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "ac,amox,amx" "actimoxi,amoclen,amolin,amopen,amopenixin,amoxibiotic,amoxicaps,amoxicilina,amoxicillin,amoxicillin hydrate,amoxicilline,amoxicillinum,amoxiden,amoxil,amoxivet,amoxy,amoxycillin,amoxyke,anemolin,aspenil,atoksilin,biomox,bristamox,cemoxin,clamoxyl,damoxy,delacillin,demoksil,dispermox,efpenix,flemoxin,hiconcil,histocillin,hydroxyampicillin,ibiamox,imacillin,lamoxy,largopen,metafarma capsules,metifarma capsules,moksilin,moxacin,moxatag,ospamox,pamoxicillin,piramox,promoxil,remoxil,robamox,sawamox pm,tolodina,topramoxin,unicillin,utimox,vetramox" 1.5 "g" 3 "g" "101498-4,15-8,16-6,16365-9,17-4,18-2,18861-5,18862-3,19-0,20-8,21-6,22-4,25274-2,25310-4,3344-9,55614-2,55615-9,55616-7,6976-5,6977-3,80133-2"
"AMC" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "J01CR02" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/c,amcl,aml,aug,xl" "amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,augmentan,augmentin,augmentin xr,augmentine,auspilic,clamentin,clamobit,clavamox,clavinex,clavoxilin plus,clavulin,clavumox,coamoxiclav,eumetinex,kmoxilin,spectramox,spektramox,synulox,viaclav,xiclav" 1.5 "g" 3 "g" ""
"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "NA" "" "" "55614-2,55615-9,55616-7"
"AMB" 5280965 "Amphotericin B" "Antifungals/antimycotics" "A01AB04,A07AA07,G01AA03,J02AA01" "Antimycotics for systemic use" "Antibiotics" "amf,amfb,amph" "abelcet,abelecet,ambisome,amfotericina b,amphocin,amphomoronal,amphortericin b,amphotec,amphotericin,amphotericin b,amphotericine b,amphotericinum b,amphozone,anfotericine b,fungilin,fungisome,fungisone,fungizone,halizon" 40 "mg" 35 "mg" "16370-9,18863-1,23-2,24-0,25-7,26-5,3353-0,3354-8,40707-2,40757-7,49859-2,6978-1"
"AMB" 5280965 "Amphotericin B" "Antifungals/antimycotics" "A01AB04,A07AA07,G01AA03,J02AA01" "Antimycotics for systemic use" "Antibiotics" "amf,amfb,amph" "abelcet,abelecet,ambisome,amfotericina b,amphocin,amphomoronal,amphortericin b,amphotec,amphotericin,amphotericin b,amphotericine b,amphotericinum b,amphozone,anfotericine b,fungilin,fungisome,fungisone,fungizone,halizon" 40 "mg" 210 "mg" "16370-9,18863-1,23-2,24-0,25-7,26-5,3353-0,3354-8,40707-2,40757-7,49859-2,6978-1"
"AMH" "Amphotericin B-high" "Aminoglycosides" "NA" "amfo b high,amhl,ampho b high,amphotericin high" "" ""
"AMP" 6249 "Ampicillin" "Beta-lactams/penicillins" "J01CA01,S01AA19" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "am,amp,ampi" "acillin,adobacillin,amblosin,amcill,amfipen,amfipen v,amipenix s,ampichel,ampicil,ampicilina,ampicillin,ampicillin a,ampicillin acid,ampicillin anhydrate,ampicillin anhydrous,ampicillin base,ampicillin hydrate,ampicillin sodium,ampicillina,ampicilline,ampicillinum,ampicin,ampifarm,ampikel,ampimed,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,anhydrous ampicillin,austrapen,binotal,bonapicillin,britacil,campicillin,copharcilin,delcillin,deripen,divercillin,doktacillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,olin kid,omnipen,orbicilina,pen a oral,pen ampil,penbristol,penbritin,penbritin paediatric,penbritin syrup,penbrock,penicline,penimic,pensyn,pentrex,pentrexl,pentrexyl,pentritin,pfizerpen a,polycillin,polyflex,ponecil,princillin,principen,qidamp,racenacillin,redicilin,rosampline,roscillin,semicillin,semicillin r,servicillin,sumipanto,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,viccillin s,vidocillin,wypicil" 2 "g" 6 "g" "101477-8,101478-6,18864-9,18865-6,20374-5,21066-6,23618-2,27-3,28-1,29-9,30-7,31-5,32-3,33-1,3355-5,33562-0,33919-2,34-9,43883-8,43884-6,6979-9,6980-7,87604-5"
"SAM" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "J01CR01" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/s,ab,ams,amsu,apsu,sam" "sulacillin" 6 "g" "101478-6,18865-6,20374-5,23618-2,31-5,32-3,33-1,34-9,6980-7"
"AMR" 73341 "Amprolium" "Other antibacterials" "NA" "" "amprocidum,amprol,amprolio,amprolium,amprolium chloride,amprovine,thiacoccid" ""
"AMR" 73341 "Amprolium" "Other antibacterials" "QP51BX02" "" "amprocidum,amprol,amprolio,amprolium,amprolium chloride,amprovine,thiacoccid" ""
"ANI" 166548 "Anidulafungin" "Antifungals/antimycotics" "J02AX06" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid" "anidulafungin,anidulafungina,anidulafungine,anidulafunginum,ecalta,eraxis" 0.1 "g" "55343-8,57095-2,58420-1,77162-6"
"APL" 6602341 "Apalcillin" "Beta-lactams/penicillins" "NA" "" "apalcilina,apalcillin,apalcilline,apalcillinum" ""
"APR" 3081545 "Apramycin" "Aminoglycosides" "NA" "" "ambylan,apralan,apramicina,apramycin,apramycine,apramycinum,nebramycin ii" "23659-6,73652-0,73653-8"
"APR" 3081545 "Apramycin" "Aminoglycosides" "QA07AA92,QJ01GB90,QJ51GB90" "" "ambylan,apralan,apramicina,apramycin,apramycine,apramycinum,nebramycin ii" "23659-6,73652-0,73653-8"
"ARB" 68682 "Arbekacin" "Aminoglycosides" "J01GB12" "" "arbekacin,arbekacina,arbekacine,arbekacini sulfas,arbekacinum,habekacin,haberacin" 0.2 "g" "32373-3,53818-1,54173-0"
"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "J01CA19" "" "aspoxicilina,aspoxicillan,aspoxicillin,aspoxicilline,aspoxicillinum" 4 "g" ""
"AST" 5284517 "Astromicin" "Aminoglycosides" "NA" "" "astromicin,astromicin a,astromicina,astromicine,astromicinum,fortimicin,fortimicin a" ""
"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "NA" "" "avibactam,avibactam free acid,avibactamfreeacid" ""
"AVI" 71674 "Avilamycin" "Other antibacterials" "NA" "" "avilamycin,avilamycina,avilamycine,avilamycinum,surmax" "35754-1,35755-8,35756-6,55619-1"
"AVI" 71674 "Avilamycin" "Other antibacterials" "QA07AA95" "" "avilamycin,avilamycina,avilamycine,avilamycinum,surmax" "35754-1,35755-8,35756-6,55619-1"
"AVO" 16131159 "Avoparcin" "Glycopeptides" "NA" "" "avoparcin,avoparcina,avoparcine,avoparcinum,avotan" ""
"AZD" 15574941 "Azidocillin" "Beta-lactams/penicillins" "J01CE04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "azidocilina,azidocillin,azidocillina,azidocilline,azidocillinum" 1.5 "g" ""
"AZM" 447043 "Azithromycin" "Macrolides/lincosamides" "J01FA10,S01AA26" "Macrolides, lincosamides and streptogramins" "Macrolides" "az,azi,azit,azm" "aritromicina,aruzilina,azasite,azenil,azifast,azigram,azimakrol,azithramycine,azithrocin,azithromycin,azithromycine,azithromycinum,azitrocin,azitromax,azitromicina,azitromicine,azitromin,aziwin,aziwok,aztrin,azyter,azythromycin,durasite,hemomycin,macrozit,misultina,mixoterin,setron,sumamed,toraseptol,tromix,trozocina,trulimax,xithrone,zentavion,zithrax,zithromac,zithromax,zithromax iv,zithromycin,zitrim,zitromax,zitrotek,zmax sr,zythromax" 0.3 "g" 0.5 "g" "100043-9,16420-2,16421-0,18866-4,23612-5,25233-8,35-6,36-4,37-2,38-0,6981-5,89480-8"
@@ -30,7 +30,7 @@
"AZA" "Aztreonam/avibactam" "Beta-lactams/penicillins" "NA" "" "" ""
"ANC" "Aztreonam/nacubactam" "Beta-lactams/penicillins" "NA" "" "" ""
"BAM" 441397 "Bacampicillin" "Beta-lactams/penicillins" "J01CA06" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "bacampicilina,bacampicillin,bacampicilline,bacampicillinum,penglobe" 1.2 "g" "18869-8,47-1,48-9,49-7,50-5,55620-9"
"BAC" 78358334 "Bacitracin" "Other antibacterials" "R02AB04,J01XX10" "baci" "fortracin,md bacitracin" "10868-8,16428-5,18870-6,6827-0,6983-1,87603-7"
"BAC" 78358334 "Bacitracin" "Other antibacterials" "D06AX05,J01XX10,R02AB04,S01AA32" "baci" "fortracin,md bacitracin" "10868-8,16428-5,18870-6,6827-0,6983-1,87603-7"
"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "J04AK05" "" "bedaquiline,sirturo" 86 "mg" "80637-2,88703-4,88704-2,94274-8,96107-8"
"BEK" 439318 "Bekanamycin" "Aminoglycosides" "J01GB13" "" "aminodeoxykanamycin,becanamicina,bekanamycin,bekanamycine,bekanamycinum,kanamycin b,klebcil,nebramycin v" 0.6 "g" ""
"BNB" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "J01CE08" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "beacillin,cepacilina,extencilline,lentopenil,penidural,tardocillin" 3.6 "g" ""
@@ -75,10 +75,10 @@
"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" "95767-0,99280-0,99503-5"
"FDC" 77843966 "Cefiderocol" "Other antibacterials" "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" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "bestron,cefmax,cefmenoxima,cefmenoxime,cefmenoximum" 2 "g" "32375-8,54174-8,54203-5,55641-5"
"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"
"CMZ" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "J01DC09" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "cefmetazole,cefmetazolesodium,cefmetazolo,cefmetazolum" 4 "g" "11575-8,18881-3,25222-1,87-7,88-5,89-3,90-1"
"CNX" 71141 "Cefminox" "Other antibacterials" "J01DC12" "" "cefminox,cefminoxum" 4 "g" "54908-9"
"DIZ" 5361871 "Cefodizime" "Cephalosporins (3rd gen.)" "J01DD09" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "cefodizima,cefodizime,cefodizime acid,cefodizime disodium,cefodizimum,cefodizme,diezime,modivid,neucef,timecef" 2 "g" "18882-1,6988-0,91-9,92-7,93-5,94-3"
@@ -93,7 +93,7 @@
"CTT" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "J01DC05" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cftt,cn,cte,ctn,ctt,tans" "apacef,cefotan,cefotetan,cefotetan acid,cefotetan free acid,cefotetanum" 4 "g" "111-5,112-3,113-1,114-9,18887-0,25239-5,3447-0,41672-7,41673-5,41674-3,41729-5,6990-6"
"CTF" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "J01DC07" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "" "cefotiam,cefotiam?,cefotiamum,ceradolan,ceradon,haloapor" 1.2 "g" 4 "g" "32374-1,35772-3,35773-1,55645-6,55737-1,55738-9,55739-7,55740-5"
"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "NA" "" "cefotiam cilexetil,pansporin t" "55737-1,55738-9,55739-7,55740-5"
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "NA" "" "cefovecin" "76147-8,87792-8"
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "QJ01DD91" "" "cefovecin" "76147-8,87792-8"
"FOX" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "J01DC01" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cfox,cfx,cfxt,cx,fox,fx" "cefoxitin,cefoxitina,cefoxitine,cefoxitinum,cefoxotin,cenomycin,cephoxitin,mefoxin,mefoxitin,rephoxitin" 6 "g" "101492-7,115-6,116-4,117-2,118-0,18888-8,25220-5,25240-3,25366-6,3448-8,41675-0,41676-8,41677-6,41730-3,6991-4"
"FOX1" "Cefoxitin screening" "Cephalosporins (2nd gen.)" "NA" "cfsc" "" ""
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "J01DE03" "" "cefozopran" 4 "g" "100045-4,53820-7"
@@ -104,7 +104,7 @@
"CPX" 6526396 "Cefpodoxime proxetil" "Cephalosporins (3rd gen.)" "NA" "" "cefodox,cefoprox,cefpodoxime proxetil,cepodem,orelox,orelox paed,otreon,podomexef,simplicef,vantin" ""
"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "NA" "cecl" "" ""
"CPR" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "J01DC10" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cpr,cpz,fp" "arzimol,brisoral,cefprozil,cefprozil anhydrous,cefprozil hydrate,cefprozilo,cefprozilum,cefzil,cronocef,procef,serozil" 1 "g" "123-0,124-8,125-5,126-3,18891-2,6994-8"
"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "NA" "" "cefquinoma,cefquinome,cefquinomum,cobactan" "100046-2,76150-2"
"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)" "QG51AA07,QJ01DE90,QJ51DE90" "" "cefquinoma,cefquinome,cefquinomum,cobactan" "100046-2,76150-2"
"CRD" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "J01DB11" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "cefroxadin,cefroxadine,cefroxadino,cefroxadinum,oraspor" 2.1 "g" ""
"CFS" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "J01DD03" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cfsl,cfsu" "cefonomil,cefsulodin,cefsulodine,cefsulodino,cefsulodinum" 4 "g" "127-1,128-9,129-7,130-5,131-3,18892-0,25242-9,55647-2"
"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "NA" "" "cefsulmid,cefsumide,cefsumido,cefsumidum" ""
@@ -117,12 +117,12 @@
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "NA" "" "cefteram pivoxil,cefterampivoxil,tomiron" ""
"CTL" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "J01DB12" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "ceftezol,ceftezole,ceftezolo,ceftezolum,demethylcefazolin" 3 "g" ""
"CTB" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "J01DD14" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cb,cfbu,ctb,tib" "ceftem,ceftibuten,ceftibuten dihydrate,ceftibuten hydrate,ceftibutene,ceftibuteno,ceftibutenum,ceftibutin,cephem,ceprifran,isocef,keimax" 0.4 "g" "35777-2,35778-0,35779-8,6996-3"
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "NA" "" "ceftiofur,ceftiofurum,excede,excenel,naxcel" "23709-9,35780-6,35781-4,55652-2"
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "QJ01DD90,QJ51DD90" "" "ceftiofur,ceftiofurum,excede,excenel,naxcel" "23709-9,35780-6,35781-4,55652-2"
"CZX" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "J01DD07" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cfzx,ctz,cz,czx,tiz,zox" "cefizox,ceftisomin,ceftix,ceftizoxima,ceftizoxime,ceftizoximum,epocelin,eposerin" 4 "g" "136-2,137-0,138-8,139-6,18894-6,20378-6,23622-4,25243-7,3450-4,6997-1"
"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "NA" "" "" ""
"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "NA" "" "ceftobiprole" "43269-0,43270-8,43271-6,43272-4,85052-9"
"CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "J01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "" 1.5 "g" ""
"CZT" 86291594 "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "CEI" "zerbaxa" 3 "g" "101484-4,73602-5,73624-9,73647-0,87735-7"
"CZT" 86291594 "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "J01DI54" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "cei" "zerbaxa" 3 "g" "101484-4,73602-5,73624-9,73647-0,87735-7"
"CRO" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "J01DD04" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "axo,cax,cftr,cro,ctr,frx,tx" "biotrakson,cefatriaxone,cefatriaxone hydrate,ceftriaxon,ceftriaxona,ceftriaxone,ceftriaxone sodium,ceftriaxonum,ceftriazone,cephtriaxone,longacef,rocefin,rocephalin,rocephin,rocephine,rophex" 2 "g" "101485-1,140-4,141-2,142-0,143-8,18895-3,25244-5,25367-4,31140-7,31141-5,3451-2,41681-8,41682-6,41683-4,41732-9,50633-7,55190-3,6998-9,80957-4"
"CEB" "Ceftriaxone/beta-lactamase inhibitor" "Cephalosporins (3rd gen.)" "J01DD63" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" "" 2 "g" ""
"CXM" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "J01DC02,S01AA27" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cfrx,cfur,cfx,crm,cxm,fur,rox,xm" "biofuroksym,cefuril,cefuroxim,cefuroxima,cefuroxime,cefuroxime acid,cefuroximine,cefuroximo,cefuroximum,cephuroxime,kefurox,sharox,zinacef,zinacef danmark" 0.5 "g" 3 "g" "101503-1,144-6,145-3,146-1,147-9,18896-1,20460-2,25245-2,3452-0,35782-2,35783-0,51724-3,51774-8,55653-0,55654-8,6999-7,74699-0,80608-3,80617-4"
@@ -154,32 +154,32 @@
"COP" "Colistin/polysorbate" "Other antibacterials" "NA" "" "" ""
"CYC" 6234 "Cycloserine" "Oxazolidinones" "J04AB01" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "cicloserina,closerin,closina,cyclorin,cycloserin,cycloserine,cycloserinum,farmiserina,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,tisomycin,wasserina" 0.75 "g" "16702-3,18914-2,212-1,213-9,214-7,215-4,23608-3,25207-2,25208-0,25209-8,25251-0,3519-6,55667-0"
"DAL" 23724878 "Dalbavancin" "Glycopeptides" "J01XA04" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "dalbavancin,dalvance" 1.5 "g" "41688-3,41689-1,41690-9,41734-5"
"DAN" 71335 "Danofloxacin" "Quinolones" "NA" "" "advocin,danofloxacin,danofloxacine,danofloxacino,danofloxacinum" "73601-7,73623-1,73646-2"
"DAN" 71335 "Danofloxacin" "Quinolones" "QJ01MA92" "" "advocin,danofloxacin,danofloxacine,danofloxacino,danofloxacinum" "73601-7,73623-1,73646-2"
"DPS" 2955 "Dapsone" "Other antibacterials" "D10AX05,J04BA02" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "aczone,araldite ht,atrisone,avlosulfon,avlosulfone,avlosulphone,avsulfor,bis sulfone,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsone,dapsonum,di sulfone,diaphenyl sulfone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,dimitone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dubronaz,dumitone,eporal,metabolite c,novophone,protogen,servidapson,slphadione,sulfadione,sulfona,sulfone ucb,sulfonyldianiline,sulphadione,sulphonyldianiline,sumicure s,tarimyl,udolac" 50 "mg" "51698-9,9747-7"
"DAP" 16134395 "Daptomycin" "Other antibacterials" "J01XX09" "Other antibacterials" "Other antibacterials" "dap,dapt" "cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum" 0.28 "g" "35787-1,35788-9,35789-7,41691-7"
"DFX" 487101 "Delafloxacin" "Quinolones" "J01MA23" "" "baxdela,delafloxacin,delafloxacinum,quofenix" 0.9 "g" 0.6 "g" "88885-9,90447-4,93790-4"
"DLM" 6480466 "Delamanid" "Antimycobacterials" "J04AK06" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "dela" "delamanid,deltyba" 0.2 "g" "93851-4,96109-4"
"DEM" 54680690 "Demeclocycline" "Tetracyclines" "D06AA01,J01AA01" "Tetracyclines" "Tetracyclines" "" "bioterciclin,clortetrin,declomycin,deganol,demeclociclina,demeclocycline,demeclocyclinum,demeclor,demetraclin,diuciclin,elkamicina,ledermycin,mexocine,novotriclina,perciclina,sumaclina" 0.6 "g" "10982-7,18915-9,216-2,217-0,218-8,219-6,29494-2,7006-0"
"DKB" 470999 "Dibekacin" "Aminoglycosides" "J01GB09" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "debecacin,dibekacin,dibekacin sulfate,dibekacina,dibekacine,dibekacinum,dideoxykanamycin b,kappati,orbicin,panamicin" 0.14 "g" "55669-6,55670-4,55671-2,55672-0"
"DKB" 470999 "Dibekacin" "Aminoglycosides" "J01GB09,S01AA29" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "debecacin,dibekacin,dibekacin sulfate,dibekacina,dibekacine,dibekacinum,dideoxykanamycin b,kappati,orbicin,panamicin" 0.14 "g" "55669-6,55670-4,55671-2,55672-0"
"DIC" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "J01CF01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "dicl" "dichloroxacillin,diclossacillina,dicloxaciclin,dicloxacilin,dicloxacilina,dicloxacillin,dicloxacillin sodium,dicloxacillina,dicloxacilline,dicloxacillinum,dicloxacycline,dycill,dynapen,maclicine,nm|| dicloxacillin,pathocil" 2 "g" 2 "g" "10984-3,16769-2,18916-7,220-4,221-2,222-0,223-8,25252-8,32380-8,55668-8"
"DIF" 56206 "Difloxacin" "Quinolones" "NA" "" "dicural,difloxacin,pulsaflox" "35790-5,35791-3,35792-1"
"DIF" 56206 "Difloxacin" "Quinolones" "QJ01MA94" "" "dicural,difloxacin,pulsaflox" "35790-5,35791-3,35792-1"
"DIR" 6473883 "Dirithromycin" "Macrolides/lincosamides" "J01FA13" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "dirithromycin,dirithromycine,dirithromycinum,diritromicina,divitross,dynabac,noriclan,valodin" 0.5 "g" "35793-9,35794-7,35795-4,7007-8"
"DOR" 73303 "Doripenem" "Carbapenems" "J01DH04" "Other beta-lactam antibacterials" "Carbapenems" "dori" "doribax,doripenem,doripenem hydrate,finibax" 1.5 "g" "56031-8,58711-3,60535-2,72893-1"
"DOX" 54671203 "Doxycycline" "Tetracyclines" "A01AB22,J01AA02" "Tetracyclines" "Tetracyclines" "dox,doxy" "atridox,azudoxat,deoxymykoin,dossiciclina,doxcycline anhydrous,doxiciclina,doxirobe,doxitard,doxivetin,doxycen,doxychel,doxycin,doxycyclin,doxycycline,doxycycline calcium,doxycycline hyclate,doxycyclinum,doxylin,doxysol,doxytec,doxytetracycline,hydramycin,investin,jenacyclin,liviatin,monodox,oracea,periostat,ronaxan,spanor,supracyclin,vibramycin,vibramycin novum,vibramycine,vibravenos,zenavod" 0.1 "g" 0.1 "g" "10986-8,18917-5,20379-4,21250-6,224-6,225-3,226-1,227-9,23623-2,25223-9,26902-7,7008-6"
"ECO" 3198 "Econazole" "Antifungals/antimycotics" "D01AC03,G01AF05" "Antifungals for topical use" "Imidazole and triazole derivatives" "econ" "econazol,econazole,econazolum,ecostatin,ecostatin cream,palavale,pevaryl,spectazole,spectazole cream" "25595-0,25637-0,54178-9,55673-8"
"ENX" 3229 "Enoxacin" "Quinolones" "J01MA04" "Quinolone antibacterials" "Fluoroquinolones" "enox" "almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,enoxacin,enoxacina,enoxacine,enoxacino,enoxacinum,enoxen,enoxin,enoxor,flumark,penetrex" 0.8 "g" "16816-1,18918-3,228-7,229-5,230-3,231-1,3590-7,41692-5"
"ENR" 71188 "Enrofloxacin" "Quinolones" "NA" "" "baytril,enrofloxacin,enrofloxacine,enrofloxacino,enrofloxacinum,enroxil" "23712-3,35796-2,35797-0,35798-8"
"ENV" 135565326 "Enviomycin" "Antimycobacterials" "J04AB06" "tuberactinomycin" "enviomicina,enviomycin,enviomycina,enviomycinum,tuberactin" ""
"ENR" 71188 "Enrofloxacin" "Quinolones" "QJ01MA90" "" "baytril,enrofloxacin,enrofloxacine,enrofloxacino,enrofloxacinum,enroxil" "23712-3,35796-2,35797-0,35798-8"
"ENV" 135565326 "Enviomycin" "Antimycobacterials" "J04AB06" "tuberactinomycin" "enviomicina,enviomycin,enviomycina,enviomycinum,tuberactin" 1 "g" ""
"EPE" "Eperozolid" "Other antibacterials" "NA" "" "" ""
"EPC" 71392 "Epicillin" "Beta-lactams/penicillins" "J01CA07" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "dexacillin,dihydroampicillin,epicilina,epicillin,epicilline,epicillinum" 2 "g" 2 "g" ""
"EPP" 68916 "Epiroprim" "Other antibacterials" "NA" "" "epiroprim,epiroprima,epiroprime,epiroprimum" ""
"ERV" 54726192 "Eravacycline" "Tetracyclines" "J01AA13" "Tetracyclines" "Tetracyclines" "erav" "eravacycline,xerava" "100049-6,85423-2,93767-2"
"ERV" 54726192 "Eravacycline" "Tetracyclines" "J01AA13" "Tetracyclines" "Tetracyclines" "erav" "eravacycline,xerava" 0.14 "g" "100049-6,85423-2,93767-2"
"ETP" 150610 "Ertapenem" "Carbapenems" "J01DH03" "Other beta-lactam antibacterials" "Carbapenems" "erta,etp" "ertapenem,invanz" 1 "g" "101486-9,35799-6,35800-2,35801-0,35802-8"
"ERY" 12560 "Erythromycin" "Macrolides/lincosamides" "D10AF02,J01FA01,S01AA17" "Macrolides, lincosamides and streptogramins" "Macrolides" "e,em,ery,eryt" "abboticin,abomacetin,acneryne,acnesol,akne cordes losung,aknederm ery gel,aknemycin,austrias,benzamycin,bristamycin,derimer,deripil,dotycin,dumotrycin,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,eryc sprinkles,erycen,erycette,erycin,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erypar,erysafe,erytab,erythrocin,erythrocin stearate,erythroderm,erythrogran,erythroguent,erythromid,erythromycin,erythromycin a,erythromycin base,erythromycin lactate,erythromycine,erythromycines,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,ilotycin gluceptate,ilotycin t.s.,inderm,inderm gel,indermretcin,latotryd,lederpax,mephamycin,mercina,oftamolets,paediathrocin,pantoderm,pantodrin,pantomicina,pce dispertab,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,romycin,sansac,skid gel e,staticin,stiemicyn,stiemycin,theramycin z,tiloryth,tiprocin,torlamicina,udima ery gel,wyamycin s" 2 "g" 1 "g" "100050-4,11576-6,12298-6,16829-4,16830-2,18919-1,18920-9,20380-2,232-9,233-7,234-5,235-2,236-0,23633-1,237-8,238-6,239-4,25224-7,25275-9,3597-2,7009-4"
"ETH" 14052 "Ethambutol" "Antimycobacterials" "J04AK02" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "etha" "aethambutolum,diambutol,ebutol,etambutol,etambutolo,etapiam,ethambutol,ethambutolum,myambutol,mycobutol,purderal,servambutol,tibutol" 1.2 "g" 1.2 "g" "100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
"ETI" 456476 "Ethambutol/isoniazid" "Antimycobacterials" "J04AM03" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
"ETI1" 2761171 "Ethionamide" "Antimycobacterials" "J04AD03" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "ethi" "aethionamidum,aetina,aetiva,amidazin,amidazine,ethatyl,ethimide,ethina,ethinamide,ethionamide,ethionamidum,ethioniamide,ethylisothiamide,ethyonomide,etimid,etiocidan,etionamid,etionamida,etionamide,etioniamid,etionid,etionizin,etionizina,etionizine,fatoliamid,iridocin,iridocin bayer,iridozin,isothin,isotiamida,itiocide,nicotion,nisotin,nizotin,rigenicid,sertinon,teberus,thianid,thianide,thioamide,thiodine,thiomid,thioniden,tianid,tiomid,trecator,trecator sc,trekator,trescatyl,trescazide,tubenamide,tubermin,tuberoid,tuberoson" 0.75 "g" "16099-4,16845-0,18922-5,20382-8,23617-4,25183-5,25196-7,25198-3,25231-2,41693-3,42647-8,42648-6,7011-0,96110-2"
"ETO" 6034 "Ethopabate" "Other antibacterials" "NA" "" "amprol plus,ethopabat,ethopabate,ethyl pabate" ""
"ETO" 6034 "Ethopabate" "Other antibacterials" "QP51AX17" "" "amprol plus,ethopabat,ethopabate,ethyl pabate" ""
"EXE" "Exebacase" "NA" "" "" ""
"FAR" 65894 "Faropenem" "Other antibacterials" "J01DI03" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "" "faropenem,faropenem sodium,fropenem,fropenum sodium" 0.75 "g" "73600-9,73622-3,73645-4"
"FDX" 10034073 "Fidaxomicin" "Other antibacterials" "A07AA12" "" "dificid,dificlir,difimicin,fidaxomicin,lipiarmicin,lipiarmycin,lipiarrmycin,tiacumicin b" 0.4 "g" "73599-3,73621-5,73644-7"
@@ -187,23 +187,23 @@
"FLA" 46783781 "Flavomycin" "Other antibacterials" "NA" "" "flavophospholipol,moenomycin complex" ""
"FLE" 3357 "Fleroxacin" "Quinolones" "J01MA08" "Quinolone antibacterials" "Fluoroquinolones" "fler" "fleroxacin,fleroxacine,fleroxacino,fleroxacinum,fleroxicin,megalocin,megalone,megalosin,quinodis" 0.4 "g" 0.4 "g" "25411-0,32372-5,35806-9,7012-8"
"FLO" 65864 "Flomoxef" "Other antibacterials" "J01DC14" "" "flomoxef,flomoxefo,flomoxefum" 2 "g" "100052-0,53822-3"
"FLR" 114811 "Florfenicol" "Other antibacterials" "NA" "" "aquafen,florfenicol,nuflor,nuflor gold" "23740-4,35807-7,35808-5,87599-7"
"FLR" 114811 "Florfenicol" "Other antibacterials" "QJ01BA90,QJ51BA90" "" "aquafen,florfenicol,nuflor,nuflor gold" "23740-4,35807-7,35808-5,87599-7"
"FLC" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "J01CF05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "clox,flux" "culpen,floxacillin,floxacillin sodium,floxapen,floxapen sodium salt,fluclox,flucloxacilina,flucloxacillin,flucloxacilline,flucloxacillinum,fluorochloroxacillin,staphylex" 2 "g" 2 "g" ""
"FLU" 3365 "Fluconazole" "Antifungals/antimycotics" "D01AC15,J02AC01" "Antimycotics for systemic use" "Triazole derivatives" "fluc,fluz,flz" "alflucoz,alfumet,alkanazole,biocanol,biozole,biozolene,canzol,cryptal,diflazon,diflucan,dimycon,elazor,flucazol,fluconazol,fluconazole,fluconazole capsules,fluconazoli,fluconazolum,flucoral,flucostat,flukezol,flunazol,flunizol,flusol,fluzon,fluzone,forcan,fuconal,fungata,loitin,oxifugol,pritenzol,syscan,trican,triconal,triflucan,zoltec" 0.2 "g" 0.2 "g" "10987-6,16870-8,18924-1,248-5,249-3,250-1,251-9,25255-1,7013-6,80530-9"
"FCT" 3366 "Flucytosine" "Antifungals/antimycotics" "D01AE21,J02AX01" "Antifungals for topical use" "Other antifungals for topical use" "5flc,fcu,fluo,fluy" "alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucystine,flucytosin,flucytosine,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine" ""
"FCT" 3366 "Flucytosine" "Antifungals/antimycotics" "D01AE21,J02AX01" "Antifungals for topical use" "Other antifungals for topical use" "5flc,fcu,fluo,fluy" "alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucystine,flucytosin,flucytosine,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine" 10 "g" 10 "g" ""
"FLM" 3374 "Flumequine" "Quinolones" "J01MB07" "Quinolone antibacterials" "Other quinolones" "" "apurone,fantacin,flumequine,flumequino,flumequinum,flumigal,flumiquil,flumisol,flumix,imequyl" 1.2 "g" "55675-3,55676-1,55677-9,55678-7"
"FLR1" 71260 "Flurithromycin" "Macrolides/lincosamides" "J01FA14" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "flurithromicina,flurithromycime,flurithromycin,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic" 0.75 "g" ""
"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "NA" "" "fosfluconazole,phosfluconazole,procif,prodif" ""
"FOS" 446987 "Fosfomycin" "Other antibacterials" "J01XX01" "Other antibacterials" "Other antibacterials" "ff,fm,fo,fof,fos,fosf" "calcium fosfomycin,fosfocina,fosfomicin,fosfomicina,fosfomycin,fosfomycin sodium,fosfomycine,fosfomycinum,fosfonomycin,infectophos,monuril,monurol,phosphonemycin,phosphonomycin,veramina" 3 "g" 8 "g" "25596-8,25653-7,35809-3,35810-1"
"FOS" 446987 "Fosfomycin" "Other antibacterials" "J01XX01,S02AA17" "Other antibacterials" "Other antibacterials" "ff,fm,fo,fof,fos,fosf" "calcium fosfomycin,fosfocina,fosfomicin,fosfomicina,fosfomycin,fosfomycin sodium,fosfomycine,fosfomycinum,fosfonomycin,infectophos,monuril,monurol,phosphonemycin,phosphonomycin,veramina" 3 "g" 8 "g" "25596-8,25653-7,35809-3,35810-1"
"FMD" 572 "Fosmidomycin" "Other antibacterials" "NA" "" "fosmidomycin,fosmidomycina,fosmidomycine,fosmidomycinum" ""
"FRM" 8378 "Framycetin" "Aminoglycosides" "D09AA01,R01AX08,S01AA07" "fram" "actilin,actiline,antibiotique,bycomycin,dekamycin iii,endomixin,enterfram,fradiomycin,fradiomycin b,fradiomycinum,framicetina,framidal,framycetin,framycetin sulfate,framycetine,framycetinum,framycin,framygen,francetin,fraquinol,jernadex,myacine,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycin,neomycin b,neomycin b sulfate,neomycin solution,neomycin sulfate,neomycin sulphate,neomycinb,neomycine,neomycinum,nivemycin,pimavecort,soframycin,soframycine,tuttomycin,vonamycin,vonamycin powder v" "18926-6,257-6,258-4,259-2,260-0,55679-5"
"FUR" 6870646 "Furazidin" "Other antibacterials" "J01XE03" "Other antibacterials" "Nitrofuran derivatives" "" "akritoin,furagin,furaginum,furamag,furazidin,furazidine" 0.3 "g" ""
"FRZ" 5323714 "Furazolidone" "Other antibacterials" "G01AX06" "" "bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furaxon,furaxone,furazol,furazolidine,furazolidon,furazolidona,furazolidone,furazolidonum,furazolum,furazon,furidon,furovag,furox aerosol powder,furoxal,furoxane,furoxon,furoxone,furoxone liquid,furoxone swine mix,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofurazolidone,nitrofurazolidonum,nitrofuroxon,optazol,ortazol,puradin,roptazol,sclaventerol,tikofuran,topazone,trichofuron,tricofuron,tricoron,trifurox,viofuragyn" "69574-2,87794-4"
"FUS" 3000226 "Fusidic acid" "Other antibacterials" "D06AX01,D09AA02,J01XC01,S01AA13" "Other antibacterials" "Steroid antibacterials" "fa,fusi" "acide fusidique,acido fusidico,acidum fusidicum,flucidin,fucidate,fucidate sodium,fucidic acid,fucidin,fucidin acid,fucithalmic,fusidate,fusidate acid,fusidic acid,fusidicacid,fusidine,fusidinic acid,ramycin,taksta" 1.5 "g" 1.5 "g" ""
"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "NA" "" "gamithromycin" "100054-6,88376-9,88378-5"
"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "QJ01FA95" "" "gamithromycin" "100054-6,88376-9,88378-5"
"GRN" 124093 "Garenoxacin" "Quinolones" "J01MA19" "" "ganefloxacin,garenfloxacin,garenoxacin" 0.4 "g" "35811-9,35812-7,35813-5"
"GAT" 5379 "Gatifloxacin" "Quinolones" "J01MA16,S01AE06" "Quinolone antibacterials" "Fluoroquinolones" "gati" "gatiflo,gatifloxacin,gatifloxacin hydrate,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,tequin,tequin and zymar,zymaxid" 0.4 "g" 0.4 "g" "31036-7,31038-3,31040-9,31042-5,41494-6"
"GEM" 9571107 "Gemifloxacin" "Quinolones" "J01MA15" "Quinolone antibacterials" "Fluoroquinolones" "" "factiv,factive,gemifioxacin,gemifloxacin,gemifloxacine,gemifloxacino,gemifloxacinum" 0.32 "g" "35814-3,35815-0,35816-8,41697-4"
"GEM" 9571107 "Gemifloxacin" "Quinolones" "J01MA15" "Quinolone antibacterials" "Fluoroquinolones" "" "factiv,factive,gemifioxacin,gemifloxacin,gemifloxacine,gemifloxacino,gemifloxacinum" 0.32 "g" 0.2 "g" "35814-3,35815-0,35816-8,41697-4"
"GEN" 3467 "Gentamicin" "Aminoglycosides" "D06AX07,J01GB03,S01AA11,S02AA14,S03AA06" "Aminoglycoside antibacterials" "Other aminoglycosides" "cn,gen,gent,gm" "apogen,centicin,cidomycin,garamycin,garasol,genoptic liquifilm,genoptic s.o.p.,gentacycol,gentafair,gentak,gentamar,gentamcin sulfate,gentamicin,gentamicina,gentamicine,gentamicins,gentamicinum,gentamycin,gentamycins,gentamycinum,gentavet,gentocin,jenamicin,lyramycin,oksitselanim,refobacin,refobacin tm,septigen,uromycine" 0.24 "g" "101494-3,13561-6,13562-4,15106-8,18928-2,18929-0,22746-2,22747-0,266-7,267-5,268-3,269-1,31091-2,31092-0,31093-8,35668-3,35817-6,3663-2,3664-0,3665-7,39082-3,47109-4,50630-3,59379-8,7016-9,7017-7,7018-5,80971-5,88111-0,89481-6"
"GEH" "Gentamicin-high" "Aminoglycosides" "NA" "gehi,gehl,genta high,gentamicin high" "" "18929-0,35817-6,7017-7,7018-5"
"GEP" 25101874 "Gepotidacin" "Other antibacterials" "NA" "" "gepotidacin" ""
@@ -213,11 +213,11 @@
"HCH" 11979956 "Hachimycin" "Antifungals/antimycotics" "D01AA03,G01AA06,J02AA02" "Antimycotics for systemic use" "Antibiotics" "" "cabimicina,hachimicina,hachimycin,hachimycine,hachimycinum,trichomycinum,trichonat" ""
"HET" 443387 "Hetacillin" "Beta-lactams/penicillins" "J01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "etacillina,hetacilina,hetacillin,hetacillin acid,hetacilline,hetacillinum,phenazacillin,versapen" 2 "g" "18931-6,274-1,275-8,276-6,277-4"
"HYG" 56928061 "Hygromycin" "Aminoglycosides" "NA" "" "antihelmycin,hydromycin b,hygrovetine" ""
"IBX" "Ibrexafungerp" "Antifungals" "NA" "" "ibrexafungerp" ""
"IBX" "Ibrexafungerp" "Antifungals" "J02AX07" "" "ibrexafungerp" ""
"ICL" 213043 "Iclaprim" "Other antibacterials" "J01EA03" "" "iclaprim,mersarex" "73597-7,73619-9,73642-1"
"IPM" 104838 "Imipenem" "Carbapenems" "J01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imp" "imipemide,imipenem,imipenem anhydrous,imipenem hydrate,imipenem/cilastatin,imipenemum,imipenen,primaxin,recarbrio .,tienamycin" 2 "g" "101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8"
"IPE" "Imipenem/EDTA" "Carbapenems" "NA" "" "" "35819-2,54170-6,54171-4,54172-2"
"IMR" "Imipenem/relebactam" "Carbapenems" "NA,J01DH56" "" "" "85424-0,93232-7,96372-8"
"IMR" "Imipenem/relebactam" "Carbapenems" "NA,J01DH56" "" "" 2 "g" "85424-0,93232-7,96372-8"
"ISV" 6918485 "Isavuconazole" "Antifungals/antimycotics" "J02AC05" "isav" "isavuconazole" 0.2 "g" 0.2 "g" "85381-2,88887-5"
"ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "isepacin,isepalline,isepamicin,isepamicina,isepamicine,isepamicinsulphate,isepamicinum" 0.4 "g" "32381-6,35820-0,35821-8,55680-3"
"ISO" 3760 "Isoconazole" "Antifungals/antimycotics" "D01AC05,G01AF07" "Antimycotics for topic use" "Triazole derivatives" "" "isoconazol,isoconazole,isoconazolum,travogen" "55681-1,55682-9,55683-7,55684-5"
@@ -229,8 +229,8 @@
"KAH" "Kanamycin-high" "Aminoglycosides" "NA" "k_h,kahl" "" "18936-5,7023-5,7024-3"
"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "NA" "" "" ""
"KET" 456201 "Ketoconazole" "Antifungals/antimycotics" "D01AC08,G01AF11,H02CA03,J02AB02" "Antimycotics for systemic use" "Imidazole derivatives" "keto,ktc" "extina,fungarest,fungoral,ketocanazole,ketoconazol,ketoconazole,ketoconazolum,ketoderm,nizoral,xolegel" 0.6 "g" "10990-0,12393-5,18937-3,25259-3,294-9,295-6,296-4,297-2,60091-6,60092-4,7025-0"
"KIT" "Kitasamycin" "Macrolides/lincosamides" "NA" "leucomycin" "jomybel,josacine,josamicina,josamycin,josamycine,josamycinum" ""
"LAS" 5360807 "Lasalocid" "Other antibacterials" "NA" "" "avatec,lasalocid,lasalocid a,lasalocide,lasalocide a,lasalocido,lasalocidum" "87598-9"
"KIT" "Kitasamycin" "Macrolides/lincosamides" "QJ01FA93" "leucomycin" "jomybel,josacine,josamicina,josamycin,josamycine,josamycinum" ""
"LAS" 5360807 "Lasalocid" "Other antibacterials" "QP51BB02" "" "avatec,lasalocid,lasalocid a,lasalocide,lasalocide a,lasalocido,lasalocidum" "87598-9"
"LSC" 71528768 "Lascufloxacin" "Quinolones" "J01MA25" "Quinolone antibacterials" "Fluoroquinolones" "" "lascufloxacin" 75 "mg" ""
"LTM" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "J01DD06" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "mox,moxa,moxalactam" "disodium moxalactam,festamoxin,lamoxactam,latamoxef,latamoxefum,moxalactamsupplement,shiomarin" 4 "g" ""
"LMU" 25185057 "Lefamulin" "Other antibacterials" "J01XX12" "" "lefamulin,xenleta" "85425-7,99281-8"
@@ -247,7 +247,7 @@
"LYM" 54707177 "Lymecycline" "Tetracyclines" "J01AA04" "Tetracyclines" "Tetracyclines" "" "biovetin,chlortetracyclin,ciclisin,ciclolysal,ciclolysine,infaciclina,limeciclina,lisinbiotic,lymecyclin,lymecycline,lymecyclinum,mucomycin,ntetracycline,tetralisal,tetralysal,vebicyclysal" 0.6 "g" 0.6 "g" "18941-5,310-3,311-1,312-9,313-7"
"MNA" 1292 "Mandelic acid" "Other antibacterials" "B05CA06,J01XX06" "Other antibacterials" "Other antibacterials" "" "acido mandelico,almond acid,ammonium mandelate,amygdalic acid,benzoglycolic acid,hydroxyacetic acid,kyselina mandlova,mandelic acid,paramandelic acid,phenylglycolic acid,uromaline" 12 "g" ""
"MGX" "Manogepix" "Antifungals" "NA" "" "manogepix" ""
"MAR" 60651 "Marbofloxacin" "Quinolones" "NA" "" "marbocyl,marbofloxacin,marbofloxacine,marbofloxacino,marbofloxacinum,zeniquin" "73596-9,73618-1,73641-3"
"MAR" 60651 "Marbofloxacin" "Quinolones" "QJ01MA93" "" "marbocyl,marbofloxacin,marbofloxacine,marbofloxacino,marbofloxacinum,zeniquin" "73596-9,73618-1,73641-3"
"MEC" 36273 "Mecillinam" "Beta-lactams/penicillins" "J01CA11" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "amdinocillin" "amdinocillin,coactin,hexacillin,mecilinamo,mecillinam,mecillinamum,micillinam,penicillin hx,selexidin" 1.2 "g" ""
"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "NA" "" "" ""
"MEM" 441130 "Meropenem" "Carbapenems" "J01DH02" "Other beta-lactam antibacterials" "Carbapenems" "mem,mer,mero,mp,mrp" "meronem,meropen,meropenem,meropenem anhydrous,meropenem hydrate,meropenem trihydrate,meropenemum,merrem,merrem i.v.,merrem iv" 3 "g" "101222-8,101488-5,101489-3,18943-1,41406-0,6651-4,6652-2,6653-0,6654-8,7029-2,85426-5,85427-3,88892-5,90980-4"
@@ -279,9 +279,9 @@
"NAF" 8982 "Nafcillin" "Beta-lactams/penicillins" "J01CF06" "" "nafcilina,nafcillin,nafcillin sodium,nafcilline,nafcillinum,nallpen,naphcillin,unipen" 3 "g" "10993-4,18951-4,25232-0,346-7,347-5,348-3,349-1,41704-8"
"ZWK" 117587595 "Nafithromycin" "Macrolides/lincosamides" "NA" "" "nafithromycin" ""
"NAL" 4421 "Nalidixic acid" "Quinolones" "J01MB02" "Quinolone antibacterials" "Other quinolones" "na,nal,nali" "acide nalidixico,acide nalidixique,acido nalidissico,acido nalidixico,acidum nalidixicum,betaxina,dixiben,dixinal,eucisten,eucistin,innoxalomn,innoxalon,jicsron,kusnarin,naldixic acid,nalidic acid,nalidicron,nalidixan,nalidixane,nalidixate,nalidixate sodium,nalidixic,nalidixic acid,nalidixicacid,nalidixin,nalidixinic acid,nalidixinsaure,nalitucsan,nalurin,narigix,naxuril,neggram,negram,nevigramon,nicelate,nogram,poleon,sicmylon,specifen,specifin,unaserus,uralgin,uriben,uriclar,urisal,urodixin,uroman,uroneg,uronidix,uropan,wintomylon,wintron" 4 "g" ""
"NAR" 65452 "Narasin" "Other antibacterials" "NA" "" "monteban,narasin,narasin a,narasine,narasino,narasinum,narasul" "87570-8"
"NAR" 65452 "Narasin" "Other antibacterials" "QP51BB04" "" "monteban,narasin,narasin a,narasine,narasino,narasinum,narasul" "87570-8"
"NEM" 11993740 "Nemonoxacin" "Quinolones" "J01MB08" "Quinolone antibacterials" "Other quinolones" "" "nemonoxacin" ""
"NEO" 8378 "Neomycin" "Aminoglycosides" "A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,R02AB01,S01AA03,S02AA07,S03AA01" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom" "actilin,actiline,antibiotique,bycomycin,dekamycin iii,endomixin,enterfram,fradiomycin,fradiomycin b,fradiomycinum,framicetina,framidal,framycetin,framycetin sulfate,framycetine,framycetinum,framycin,framygen,francetin,fraquinol,jernadex,myacine,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycin,neomycin b,neomycin b sulfate,neomycin solution,neomycin sulfate,neomycin sulphate,neomycinb,neomycine,neomycinum,nivemycin,pimavecort,soframycin,soframycine,tuttomycin,vonamycin,vonamycin powder v" 5 "g" "10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
"NEO" 8378 "Neomycin" "Aminoglycosides" "A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,R02AB01,S01AA03,S02AA07,S03AA01" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom" "actilin,actiline,antibiotique,bycomycin,dekamycin iii,endomixin,enterfram,fradiomycin,fradiomycin b,fradiomycinum,framicetina,framidal,framycetin,framycetin sulfate,framycetine,framycetinum,framycin,framygen,francetin,fraquinol,jernadex,myacine,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycin,neomycin b,neomycin b sulfate,neomycin solution,neomycin sulfate,neomycin sulphate,neomycinb,neomycine,neomycinum,nivemycin,pimavecort,soframycin,soframycine,tuttomycin,vonamycin,vonamycin powder v" 5 "g" 1 "g" "10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
"NET" 441306 "Netilmicin" "Aminoglycosides" "J01GB07,S01AA23" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti" "netillin,netilmicin,netilmicin sulfate,netilmicina,netilmicine,netilmicinum,netilyn,netira,nettacin,vectacin" 0.35 "g" 0.35 "g" "18954-8,25263-5,358-2,359-0,360-8,361-6,3848-9,3849-7,3850-5,47385-0,59565-2,59566-0,59567-8,7035-9"
"NIC" 9507 "Nicarbazin" "Other antibacterials" "NA" "" "nicarb,nicarbasin,nicarbazin,nicarbazine,nicoxin,nicrazin,nicrazine,nirazin" ""
"NIF" 71946 "Nifuroquine" "Quinolones" "NA" "" "abimasten,nifuroquina,nifuroquine,nifuroquinum,quinaldofur" ""
@@ -294,24 +294,24 @@
"NME" "Norfloxacin/metronidazole" "Other antibacterials" "J01RA14" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
"NTI" "Norfloxacin/tinidazole" "Other antibacterials" "J01RA13" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
"NVA" 10419027 "Norvancomycin" "Glycopeptides" "NA" "" "norvancomycin" ""
"NOV" 54675769 "Novobiocin" "Other antibacterials" "NA" "novo" "albamix,albamycin,cardelmycin,cathocin,cathomycin,crystallinic acid,inamycin,novobiocin,novobiocina,novobiocine,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin" "17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
"NOV" 54675769 "Novobiocin" "Other antibacterials" "QJ01XX95" "novo" "albamix,albamycin,cardelmycin,cathocin,cathomycin,crystallinic acid,inamycin,novobiocin,novobiocina,novobiocine,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin" "17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
"NYS" 6433272 "Nystatin" "Antifungals/antimycotics" "A07AA02,D01AA01,G01AA01" "nyst" "biofanal,candex lotion,comycin,diastatin,herniocid,moronal,myconystatin,mycostatin,mycostatin pastilles,mykinac,mykostatyna,nilstat,nistatin,nistatina,nyamyc,nyotran,nyotrantrade mark,nystaform,nystan,nystatin,nystatin a,nystatin g,nystatin hydrate,nystatin lf,nystatine,nystatinum,nystatyna,nystavescent,nystex,nystop,stamycin,terrastatin,zydin e" 1.5 "MU" "10697-1,10698-9,18958-9,35824-2,55689-4"
"OFX" 4583 "Ofloxacin" "Quinolones" "J01MA01,S01AE01,S02AA16" "Quinolone antibacterials" "Fluoroquinolones" "of,ofl,oflo,ofx" "bactocin,danoflox,dextrofloxacin,effexin,exocin,exocine,flobacin,flodemex,flotavid,flovid,floxal,floxil,floxin,floxin otic,floxstat,fugacin,inoflox,kinflocin,kinoxacin,levofloxacin hcl,liflox,loxinter,marfloxacin,medofloxine,mergexin,monoflocet,novecin,nufafloqo,occidal,ocuflox,oflocee,oflocet,oflocin,oflodal,oflodex,oflodura,ofloxacin,ofloxacin otic,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxin,onexacin,operan,orocin,otonil,oxaldin,pharflox,praxin,puiritol,qinolon,quinolon,quotavil,sinflo,tabrin,taravid,tariflox,tarivid,telbit,tructum,uro tarivid,viotisone,visiren,zanocin" 0.4 "g" 0.4 "g" "18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
"OOR" "Ofloxacin/ornidazole" "Other antibacterials" "J01RA09" "Combinations of antibacterials" "Combinations of antibacterials" "" "" ""
"OLE" 72493 "Oleandomycin" "Macrolides/lincosamides" "J01FA05" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "amimycin,landomycin,matromycin,oleandomicina,oleandomycin,oleandomycin a,oleandomycine,oleandomycinum,romicil" 1 "g" "18960-5,378-0,379-8,380-6,381-4,55690-2"
"OMC" 54697325 "Omadacycline" "Tetracyclines" "J01AA15" "" "amadacycline,omadacycline" 0.3 "g" 0.1 "g" "73594-4,73616-5,73639-7"
"OPT" 87880 "Optochin" "Other antibacterials" "NA" "" "numoquin,optochin,optoquine" "100055-3,73665-2"
"ORB" 60605 "Orbifloxacin" "Quinolones" "NA" "" "orbifloxacin" "35825-9,35826-7,35827-5"
"ORB" 60605 "Orbifloxacin" "Quinolones" "QJ01MA95" "" "orbifloxacin" "35825-9,35826-7,35827-5"
"ORI" 16136912 "Oritavancin" "Glycopeptides" "J01XA05" "Other antibacterials" "Glycopeptide antibacterials" "orit" "kimyrsa,oritavancin" "41707-1,41708-9,41709-7,41736-0"
"ORS" "Ormetroprim/sulfamethoxazole" "Other antibacterials" "NA" "" "" "73593-6,73615-7,73638-9"
"ORN" 28061 "Ornidazole" "Other antibacterials" "G01AF06,J01XD03,P01AB03" "Other antibacterials" "Imidazole derivatives" "" "madelen,ornidal,ornidazol,ornidazole,ornidazolum,tiberal" 1.5 "g" 1 "g" "55691-0,55692-8,55693-6,55694-4"
"OTE" 77050711 "Oteseconazole" "Antifungals/antimycotics" "J02AC06" "Antimycotics for systemic use" "Triazole derivatives" "" "oteseconazole" ""
"OTE" 77050711 "Oteseconazole" "Antifungals/antimycotics" "J02AC06" "Antimycotics for systemic use" "Triazole derivatives" "" "oteseconazole" 21 "mg" ""
"OXA" 6196 "Oxacillin" "Beta-lactams/penicillins" "J01CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "ox,oxa,oxac,oxal,oxs" "bactocill,ossacillina,oxacilina,oxacillin,oxacillin sodium,oxacilline,oxacillinum,oxazocillin,oxazocilline,prostaphlin,prostaphlyn,sodium oxacillin" 2 "g" 2 "g" "18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1"
"OXO" 4628 "Oxolinic acid" "Quinolones" "J01MB05" "Quinolone antibacterials" "Other quinolones" "" "acide oxolinique,acido ossolico,acido oxolinico,acidum oxolinicum,aqualinic,cistopax,dioxacin,emyrenil,gramurin,inoxyl,nidantin,oksaren,orthurine,ossian,oxoboi,oxolinic,oxolinic acid,pietil,prodoxal,prodoxol,starner,tiurasin,ultibid,urinox,uritrate,urotrate,uroxol,utibid" 1 "g" ""
"OXY" 54675779 "Oxytetracycline" "Tetracyclines" "D06AA03,G01AA07,J01AA06,S01AA04" "Tetracyclines" "Tetracyclines" "" "adamycin,berkmycen,biostat,biostat pa,bisolvomycin,dabicycline,dalimycin,embryostat,fanterrin,galsenomycin,geomycin,geotilin,hydroxytetracyclinum,imperacin,lenocycline,macocyn,medamycin,mepatar,oksisyklin,ossitetraciclina,oxacycline,oxitetraciclina,oxitetracyclin,oxitetracycline,oxitetracyclinum,oxydon,oxymycin,oxymykoin,oxypam,oxysteclin,oxyterracin,oxyterracine,oxyterracyne,oxytetracid,oxytetracyclin,oxytetracycline,oxytetracycline base,oxytetracyclinum,proteroxyna,riomitsin,ryomycin,solkaciclina,stecsolin,stevacin,tarocyn,tarosin,teravit,terrafungine,terramitsin,terramycin,terramycin im,terramycine,tetran,unimycin,ursocyclin,ursocycline,vendarcin" 1 "g" 1 "g" "17396-3,18962-1,25266-8,386-3,387-1,388-9,389-7,55699-3,87595-5"
"OXY" 54675779 "Oxytetracycline" "Tetracyclines" "A01AB25,D06AA03,G01AA07,J01AA06,S01AA04" "Tetracyclines" "Tetracyclines" "" "adamycin,berkmycen,biostat,biostat pa,bisolvomycin,dabicycline,dalimycin,embryostat,fanterrin,galsenomycin,geomycin,geotilin,hydroxytetracyclinum,imperacin,lenocycline,macocyn,medamycin,mepatar,oksisyklin,ossitetraciclina,oxacycline,oxitetraciclina,oxitetracyclin,oxitetracycline,oxitetracyclinum,oxydon,oxymycin,oxymykoin,oxypam,oxysteclin,oxyterracin,oxyterracine,oxyterracyne,oxytetracid,oxytetracyclin,oxytetracycline,oxytetracycline base,oxytetracyclinum,proteroxyna,riomitsin,ryomycin,solkaciclina,stecsolin,stevacin,tarocyn,tarosin,teravit,terrafungine,terramitsin,terramycin,terramycin im,terramycine,tetran,unimycin,ursocyclin,ursocycline,vendarcin" 1 "g" 1 "g" "17396-3,18962-1,25266-8,386-3,387-1,388-9,389-7,55699-3,87595-5"
"OZN" "Ozenoxacin" "D06AX14" "" "ozadub,ozenoxacin,ozenoxacin cream" ""
"PAS" 4649 "P-aminosalicylic acid" "Antimycobacterials" "NA" "" "aminopar,aminosalicylic,aminosalicylic acid,aminosalyl,aminox,apacil,deapasil,entepas,ferrosan,gabbropas,granupas,helipidyl,hellipidyl,neopasalate,osacyl,pamacyl,pamisyl,paramycin,parasal,parasalicil,parasalindon,pasalon,pasara,pascorbic,pasdium,paser granules,paskalium,pasmed,pasnodia,pasolac,propasa,rezipas,teebacin" ""
"PAN" 72015 "Panipenem" "Carbapenems" "NA,J01DH55" "" "panipenem,panipenem/betamipron,panipenemum,penipanem" "100056-1,53823-1"
"PAN" 72015 "Panipenem" "Carbapenems" "NA,J01DH55" "" "panipenem,panipenem/betamipron,panipenemum,penipanem" 2 "g" "100056-1,53823-1"
"PAR" 165580 "Paromomycin" "Other antibacterials" "A07AA06" "" "aminosidin,aminosidine,aminosidine i,aminosidine sulfate,amminosidin,crestomycin,estomycin,gabbromicina,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,hydroxymycin sulfate,monomycin,monomycin a,neomycin e,paramomycin,paramomycin sulfate,paromomicina,paromomycin,paromomycin i,paromomycine,paromomycinum,paucimycin,paucimycinum,quintomycin c" 3 "g" "51719-3,53824-9,55700-9,55701-7,55702-5"
"PAZ" 65957 "Pazufloxacin" "Quinolones" "J01MA18" "Quinolone antibacterials" "Fluoroquinolones" "" "pazufloxacin,pazufloxacine,pazufloxacino,pazufloxacinum" 1 "g" ""
"PEF" 51081 "Pefloxacin" "Quinolones" "J01MA03" "Quinolone antibacterials" "Fluoroquinolones" "pefl" "abactal,labocton,pefloxacin,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,perfloxacin,silver pefloxacin" 0.8 "g" 0.8 "g" "18963-9,35828-3,390-5,3906-5,7040-9"
@@ -330,7 +330,7 @@
"PIS" "Piperacillin/sulbactam" "Beta-lactams/penicillins" "NA" "" "" "54197-9,54198-7,54199-5,55704-1"
"TZP" 461573 "Piperacillin/tazobactam" "Beta-lactams/penicillins" "J01CR05" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp" "tazocel,tazocillin,tazocin,zosyn" 14 "g" "101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
"PRC" 71978 "Piridicillin" "Beta-lactams/penicillins" "NA" "" "piridicillin" ""
"PRL" 157385 "Pirlimycin" "Macrolides/lincosamides" "NA" "" "pirlimycin,pirlimycina,pirlimycine,pirlimycinum,pirsue" "35829-1,35830-9,35831-7"
"PRL" 157385 "Pirlimycin" "Macrolides/lincosamides" "QJ51FF90" "" "pirlimycin,pirlimycina,pirlimycine,pirlimycinum,pirsue" "35829-1,35830-9,35831-7"
"PIR" 4855 "Piromidic acid" "Quinolones" "J01MB03" "Quinolone antibacterials" "Other quinolones" "" "acide piromidique,acido piromidico,acidum piromidicum,actrun c,bactramyl,enterol,gastrurol,panacid,pirodal,piromidate,piromidic acid,piromidicacid,pyrido,reelon,septural,urisept,uropir,zaomeal" 2 "g" ""
"PVM" 33478 "Pivampicillin" "Beta-lactams/penicillins" "J01CA02" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "berocillin,pivaloylampicillin,pivampicilina,pivampicillin,pivampicilline,pivampicillinum,pondocillin" 1.05 "g" "18971-2,415-0,416-8,417-6,418-4"
"PME" 115163 "Pivmecillinam" "Beta-lactams/penicillins" "J01CA08" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "amdinocillin pivoxil,coactabs,hydroxymethyl,pivmecilinamo,pivmecillinam,pivmecillinam hcl,pivmecillinamum" 0.6 "g" ""
@@ -338,9 +338,9 @@
"PLB" 49800004 "Polymyxin B" "Polymyxins" "A07AA05,J01XB02,S01AA18,S02AA11,S03AA03" "Other antibacterials" "Polymyxins" "pb,pol,polb,poly,poly b,polymixin,polymixin b" "polimixina b,polumyxin b,polymixin b,polymyxine b" 3 "MU" 0.15 "g" "17473-0,18972-0,25269-2,35832-5,419-2,420-0,421-8,422-6"
"POP" "Polymyxin B/polysorbate 80" "Polymyxins" "NA" "" "" ""
"POS" 468595 "Posaconazole" "Antifungals/antimycotics" "J02AC04" "Antimycotics for systemic use" "Triazole derivatives" "posa" "noxafil,posaconazole,posaconazole sp,posconazole" 0.3 "g" 0.3 "g" "53731-6,54186-2,54187-0,54188-8,54189-6,80545-7"
"PRA" 9802884 "Pradofloxacin" "Quinolones" "NA" "" "pradofloxacin,pudofloxacin,veraflox" "76148-6,87800-9"
"PRA" 9802884 "Pradofloxacin" "Quinolones" "QJ01MA97" "" "pradofloxacin,pudofloxacin,veraflox" "76148-6,87800-9"
"PRX" 71455 "Premafloxacin" "Quinolones" "NA" "" "premafloxacin,remafloxacin" "73591-0,73613-2,73636-3"
"PMD" 456199 "Pretomanid" "Antimycobacterials" "J04AK08" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "oxazine,pretomanid" "93850-6"
"PMD" 456199 "Pretomanid" "Antimycobacterials" "J04AK08" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "oxazine,pretomanid" 0.2 "g" "93850-6"
"PRM" 6446787 "Primycin" "Macrolides/lincosamides" "NA" "" "primycin" ""
"PRI" 11979535 "Pristinamycin" "Macrolides/lincosamides" "J01FG01" "Macrolides, lincosamides and streptogramins" "Streptogramins" "pris" "eskalin v,mikamycin,mikamycine,mikamycinum,ostreogrycinum,pristinamycine,pristinamycinum,stafac,stafytracine,staphylomycin,starfac,streptogramin,vernamycin,virgimycin,virgimycine,virginiamycin,virginiamycina,virginiamycine,virginiamycinum" 2 "g" "32383-2,35833-3,35834-1,55709-0"
"PRB" 5903 "Procaine benzylpenicillin" "Beta-lactams/penicillins" "J01CE09" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "depocillin,duphapen,hostacillin,hydracillin,jenacillin o,nopcaine,penicillin procaine,retardillin,vetspen,vitablend" 0.6 "g" ""
@@ -349,13 +349,13 @@
"PTH" 666418 "Protionamide" "Antimycobacterials" "J04AD01" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "prot" "ektebin,peteha,prothionamide,prothionamidum,protion,protionamid,protionamida,protionamide,protionamidum,protionizina,tebeform,trevintix,tuberex" 0.75 "g" ""
"PRU" 65947 "Prulifloxacin" "Quinolones" "J01MA17" "Quinolone antibacterials" "Fluoroquinolones" "" "prulifloxacin,pruvel,pufloxacin dioxolil,quisnon" 0.6 "g" "100058-7,76145-2"
"PZA" 1046 "Pyrazinamide" "Antimycobacterials" "J04AK01" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "pyra" "aldinamid,aldinamide,braccopiral,corsazinmid,dipimide,eprazin,farmizina,isopas,lynamide,novamid,p ezetamid,pezetamid,pharozinamide,piraldina,pirazimida,pirazinamid,pirazinamida,pirazinamide,prazina,pyrafat,pyramide,pyrazide,pyrazinamdie,pyrazinamid,pyrazinamide,pyrazinamidum,pyrazine carboxamide,pyrazineamide,pyrizinamide,rifafour,rozide,tebrazid,tebrazio,tisamid,unipyranamide,zinamide,zinastat" 1.5 "g" "11001-5,18973-8,20461-0,23632-3,25186-8,25229-6,25270-0,423-4,424-2,425-9,426-7,42935-7,55710-8,55711-6,56026-8,92242-7"
"QDA" 11979418 "Quinupristin/dalfopristin" "Macrolides/lincosamides" "J01FG02" "Macrolides, lincosamides and streptogramins" "Streptogramins" "q/d,qda,qida,quda,rp,syn" "" 1.5 "g" "23640-6,23641-4,33334-4,35835-8,58712-1"
"QDA" 11979418 "Quinupristin/dalfopristin" "Macrolides/lincosamides" "QJ01FG02" "Macrolides, lincosamides and streptogramins" "Streptogramins" "q/d,qda,qida,quda,rp,syn" "" "23640-6,23641-4,33334-4,35835-8,58712-1"
"RAC" 56052 "Ractopamine" "Other antibacterials" "NA" "" "optaflexx,paylean,ractopamina,ractopamine,ractopaminum" ""
"RAM" 16132338 "Ramoplanin" "Glycopeptides" "NA" "" "ramoplanin" "41710-5,41711-3,41712-1,41737-8"
"RZM" 10993211 "Razupenem" "Carbapenems" "NA" "" "razupenem" "73590-2,73612-4,73635-5"
"RTP" 6918462 "Retapamulin" "Other antibacterials" "D06AX13" "Antibiotics for topical use" "Other antibiotics for topical use" "ret" "altabax,altargo,retapamulin" ""
"RZF" "Rezafungin" "Antifungals" "NA" "" "biafungin,rezafungin cation,rezafungin ion" ""
"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali,ribociclib" 0.45 ""
"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali,ribociclib" 0.45 "g" ""
"RST" 33042 "Ribostamycin" "Aminoglycosides" "J01GB10" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "dekamycin iv,hetangmycin,ribastamin,ribostamicina,ribostamycin,ribostamycine,ribostamycinum,vistamycin,xylostatin" 1 "g" ""
"RID1" 16659285 "Ridinilazole" "Other antibacterials" "NA" "" "ridinilazole" ""
"RIB" 135398743 "Rifabutin" "Antimycobacterials" "J04AB04" "Drugs for treatment of tuberculosis" "Antibiotics" "rifb" "alfacid,ansamicin,ansamycin,ansatipin,ansatipine,assatipin,mycobutin,rifabutin,rifabutina,rifabutine,rifabutinum" 0.15 "g" "100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
@@ -364,7 +364,7 @@
"RFI" "Rifampicin/isoniazid" "Antimycobacterials" "J04AM02" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "rifinah,rimactazid" ""
"RPEI" "Rifampicin/pyrazinamide/ethambutol/isoniazid" "Antimycobacterials" "J04AM06" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
"RPI" "Rifampicin/pyrazinamide/isoniazid" "Antimycobacterials" "J04AM05" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
"RFM" 6324616 "Rifamycin" "Antimycobacterials" "A07AA13,D06AX15,J04AB03,S01AA16,S02AA12" "Drugs for treatment of tuberculosis" "Antibiotics" "" "aemcolo,rifacin,rifamicina,rifamicine sv,rifamycin,rifamycine,rifamycinum,rifocin,rifocyn,rifomycin,rifomycin sv,tuborin" 0.6 "g" ""
"RFM" 6324616 "Rifamycin" "Antimycobacterials" "A07AA13,D06AX15,J04AB03,S01AA16,S02AA12" "Drugs for treatment of tuberculosis" "Antibiotics" "" "aemcolo,rifacin,rifamicina,rifamicine sv,rifamycin,rifamycine,rifamycinum,rifocin,rifocyn,rifomycin,rifomycin sv,tuborin" 0.8 "g" 0.6 "g" ""
"RFP" 135403821 "Rifapentine" "Antimycobacterials" "J04AB05" "Drugs for treatment of tuberculosis" "Antibiotics" "rifp,rpt" "cyclopentyl rifampin,prifitin,priftin,rifapentin,rifapentina,rifapentine,rifapentinum" 0.11 "g" "100059-5,76627-9"
"RFX" 6436173 "Rifaximin" "Other antibacterials" "A07AA11,D06AX11" "Intestinal antiinfectives" "Antibiotics" "" "fatroximin,flonorm,lormyx,lumenax,normix,redactiv,rifacol,rifamixin,rifaxidin,rifaximin,rifaximina,rifaximine,rifaximinum,rifaxin,ritacol,spiraxin,xifaxan,xifaxsan" 0.6 "g" "73589-4,73611-6,73634-8"
"RIT" 65633 "Ritipenem" "Carbapenems" "NA" "" "ritipenem" ""
@@ -374,8 +374,8 @@
"ROS" 287180 "Rosoxacin" "Quinolones" "J01MB01" "Quinolone antibacterials" "Other quinolones" "" "acrosoxacin,eracine,eradacil,eradacin,eradicin,rosoxacin,rosoxacine,rosoxacino,rosoxacinum,roxadyl,winoxacin,winuron" 0.3 "g" "18977-9,439-0,440-8,441-6,442-4,55713-2"
"RXT" "Roxithromycin" "Macrolides/lincosamides" "J01FA06" "Macrolides, lincosamides and streptogramins" "Macrolides" "roxi" "roxithromycin,roxithromycine,roxithromycinum,roxitromicina,rulide" 0.3 "g" "18978-7,443-2,444-0,445-7,446-5,7046-6"
"RFL" 58258 "Rufloxacin" "Quinolones" "J01MA10" "Quinolone antibacterials" "Fluoroquinolones" "" "rufloxacin,rufloxacin hcl,rufloxacine,rufloxacino,rufloxacinum" 0.2 "g" ""
"SAL" 3085092 "Salinomycin" "Other antibacterials" "NA" "" "coxistac,procoxacin,salinomicina,salinomycin,salinomycine,salinomycinum" "35836-6,35837-4,35838-2,87593-0"
"SAR" 56208 "Sarafloxacin" "Quinolones" "NA" "" "difloxacine,difloxacino,difloxacinum,quinolone der.,saraflox,sarafloxacin,sarafloxacine,sarafloxacino,sarafloxacinum" "73588-6,73610-8,73633-0"
"SAL" 3085092 "Salinomycin" "Other antibacterials" "QP51BB01" "" "coxistac,procoxacin,salinomicina,salinomycin,salinomycine,salinomycinum" "35836-6,35837-4,35838-2,87593-0"
"SAR" 56208 "Sarafloxacin" "Quinolones" "QJ01MA98" "" "difloxacine,difloxacino,difloxacinum,quinolone der.,saraflox,sarafloxacin,sarafloxacine,sarafloxacino,sarafloxacinum" "73588-6,73610-8,73633-0"
"SRC" 54681908 "Sarecycline" "Tetracyclines" "J01AA14" "Tetracyclines" "Tetracyclines" "" "sarecycline,seysara" 0.1 "g" ""
"SRX" 9933415 "Sarmoxicillin" "Beta-lactams/penicillins" "NA" "" "sarmoxicillin" ""
"SEC" 71815 "Secnidazole" "Other antibacterials" "P01AB07" "" "flagentyl,secnidal,secnidazol,secnidazole,secnidazolum,secnil,sindose,solosec" 2 "g" ""
@@ -395,7 +395,7 @@
"SUL" 130313 "Sulbactam" "Beta-lactams/penicillins" "J01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "" "betamaze,sulbactam,sulbactam acid,sulbactam free acid,sulbactamum" 1 "g" "41716-2,41717-0,41718-8,41739-4"
"SBC" 20055036 "Sulbenicillin" "Beta-lactams/penicillins" "J01CA16" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "kedacillina,sulbenicilina,sulbenicillin,sulbenicilline,sulbenicillinum" 15 "g" ""
"SUC" 5318 "Sulconazole" "Antifungals/antimycotics" "D01AC09" "" "sulconazol,sulconazole,sulconazolum" ""
"SUP" 6634 "Sulfachlorpyridazine" "Other antibacterials" "NA" "" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone vet,prinzone vet.,solfaclorpiridazina,sonilyn,sulfachlorpyridazine,sulfacloropiridazina,vetisulid" ""
"SUP" 6634 "Sulfachlorpyridazine" "Other antibacterials" "QJ01EQ12" "" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone vet,prinzone vet.,solfaclorpiridazina,sonilyn,sulfachlorpyridazine,sulfacloropiridazina,vetisulid" ""
"SDI" 5215 "Sulfadiazine" "Trimethoprims" "J01EC02" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "" "adiazin,adiazine,cocodiazine,codiazine,cremodiazine,cremotres,debenal,deltazina,diazin,diazolone,diazovit,diazyl,eskadiazine,honey diazine,liquadiazine,microsulfon,neazine,neotrizine,nsulfanilamide,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,sildaflo,silvadene,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazine,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonamides duplex,sulfonsol,sulfose,sulphadiazine,sulphadiazine e,terfonyl,theradiazine,thermazene,trifonamide,triple sulfa,triple sulfas,trisem,truozine,zinc sulfadiazine" 0.6 "g" "18984-5,27216-1,463-0,464-8,465-5,466-3,59742-7,6907-0,7050-8"
"SLT" 122284 "Sulfadiazine/tetroxoprim" "Trimethoprims" "J01EE06" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "cotetroxazine" ""
"SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims" "J01EE02" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "" "antastmon,cotrimazine,diaziprim forte,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim" ""
@@ -432,7 +432,7 @@
"TAL" 71447 "Talampicillin" "Beta-lactams/penicillins" "J01CA15" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "talampicilina,talampicillin,talampicilline,talampicillinum" 2 "g" "18988-6,479-6,480-4,481-2,482-0"
"TLP" 163307 "Talmetoprim" "Other antibacterials" "NA" "" "talmetoprim" ""
"TAZ" 123630 "Tazobactam" "Beta-lactams/penicillins" "J01CG02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo" "tazobactam,tazobactam acid,tazobactamum,tazobactum" "41719-6,41720-4,41721-2,41740-2"
"TBP" 9800194 "Tebipenem" "Carbapenems" "NA,J01DH06" "" "tebipenem pivoxil" ""
"TBP" 9800194 "Tebipenem" "Carbapenems" "NA,J01DH06" "" "tebipenem pivoxil" 0.56 "g" ""
"TZD" 11234049 "Tedizolid" "Oxazolidinones" "J01XX11" "Other antibacterials" "Other antibacterials" "tedi" "sivextro,tedizolid,torezolid" 0.2 "g" 0.2 "g" "73586-0,73608-2,73631-4"
"TEC" 16131923 "Teicoplanin" "Glycopeptides" "J01XA02" "Other antibacterials" "Glycopeptide antibacterials" "tec,tei,teic,tp,tpl,tpn" "targocid,tecoplanina,tecoplanine,tecoplaninum,teichomycin,teicoplanin,teicoplanina,teicoplanine,teicoplaninum" 0.4 "g" "18989-4,25534-9,25535-6,34378-0,34379-8,4043-6,483-8,484-6,485-3,486-1,7051-6,80968-1"
"TCM" "Teicoplanin-macromethod" "Glycopeptides" "NA" "" "" ""
@@ -450,29 +450,29 @@
"THI" 27200 "Thiamphenicol" "Amphenicols" "J01BA02" "Amphenicols" "Amphenicols" "" "descocin,dexawin,dextrosulfenidol,dextrosulphenidol,efnicol,hyrazin,igralin,macphenicol,masatirin,neomyson,racefenicol,racefenicolo,racefenicolum,raceophenidol,racephenicol,rincrol,thiamcol,thiamphenicol,thiamphenicolum,thiocymetin,thiomycetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamicina,urfamycine,vicemycetin" 1.5 "g" 1.5 "g" "41723-8,41724-6,41725-3,54169-8"
"TAT" 9568512 "Thioacetazone" "Antimycobacterials" "J04AK07" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "aktivan,ambathizon,amithiozone,amitiozon,benthiozone,benzothiozane,benzothiozon,berculon a,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mirizone neustab,mivizon,myvizone,neotibil,neustab,novakol,nuclon argentinian,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebesone i,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazone,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal" ""
"THI1" "Thioacetazone/isoniazid" "Antimycobacterials" "J04AM04" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""
"TIA" 656958 "Tiamulin" "Other antibacterials" "NA" "" "denagard,thiamutilin,tiamulin,tiamulin pamoate,tiamulina,tiamuline,tiamulinum,tiavet p" "35846-5,35847-3,35848-1,87589-8"
"TIA" 656958 "Tiamulin" "Other antibacterials" "QJ01XQ01" "" "denagard,thiamutilin,tiamulin,tiamulin pamoate,tiamulina,tiamuline,tiamulinum,tiavet p" "35846-5,35847-3,35848-1,87589-8"
"TIC" 36921 "Ticarcillin" "Beta-lactams/penicillins" "J01CA13" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "tc,ti,tic,tica" "ticarcilina,ticarcillin,ticarcilline,ticarcillinum,ticillin,timentin" 15 "g" "18994-4,18995-1,25254-4,4054-3,4055-0,499-4,500-9,501-7,502-5,503-3,504-1,505-8,506-6,55716-5,55717-3,55718-1,55719-9,7053-2,7054-0"
"TCC" 6437075 "Ticarcillin/clavulanic acid" "Beta-lactams/penicillins" "J01CR03" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "t/c,tcc,ticl,tim,tlc" "timentin" 15 "g" ""
"TGC" 54686904 "Tigecycline" "Tetracyclines" "J01AA12" "Tetracyclines" "Tetracyclines" "tgc,tig,tige" "haizheng li xing,tigeciclina,tigecyclin,tigecycline,tigecycline hydrate,tigecyclinum,tigilcycline,tygacil" 0.1 "g" "101499-2,42354-1,42355-8,42356-6,42357-4,55158-0"
"TBQ" 65592 "Tilbroquinol" "Quinolones" "P01AA05" "" "tilbroquinol,tilbroquinolum" ""
"TIP" 24860548 "Tildipirosin" "Macrolides/lincosamides" "NA" "" "tildipirosin,zuprevo" "100060-3,88375-1,88377-7"
"TIL" 5282521 "Tilmicosin" "Macrolides/lincosamides" "NA" "" "micotil,pulmotil,tilmicosin,tilmicosina,tilmicosine,tilmicosinum" "35849-9,35850-7,35851-5,87588-0"
"TIN" 5479 "Tinidazole" "Other antibacterials" "J01XD02,P01AB02" "Other antibacterials" "Imidazole derivatives" "tini" "amtiba,bioshik,ethyl sulfone,fasigin,fasigyn,fasigyntrade mark,fasygin,glongyn,haisigyn,pletil,simplotan,simplotantrade mark,sorquetan,symplotan,tindamax,tindamaxtrade mark,tinidazol,tinidazole,tinidazolum,tricolam,trimonase" 2 "g" 1.5 "g" "54928-7,55720-7,55721-5,55722-3"
"TIP" 24860548 "Tildipirosin" "Macrolides/lincosamides" "QJ01FA96" "" "tildipirosin,zuprevo" "100060-3,88375-1,88377-7"
"TIL" 5282521 "Tilmicosin" "Macrolides/lincosamides" "QJ01FA91" "" "micotil,pulmotil,tilmicosin,tilmicosina,tilmicosine,tilmicosinum" "35849-9,35850-7,35851-5,87588-0"
"TIN" 5479 "Tinidazole" "Other antibacterials" "G01AF21,J01XD02,P01AB02" "Other antibacterials" "Imidazole derivatives" "tini" "amtiba,bioshik,ethyl sulfone,fasigin,fasigyn,fasigyntrade mark,fasygin,glongyn,haisigyn,pletil,simplotan,simplotantrade mark,sorquetan,symplotan,tindamax,tindamaxtrade mark,tinidazol,tinidazole,tinidazolum,tricolam,trimonase" 2 "g" 1.5 "g" "54928-7,55720-7,55721-5,55722-3"
"TCR" 3001386 "Tiocarlide" "Antimycobacterials" "J04AD02" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "" "amixyl,datanil,disocarban,disoxyl,isoxyl,thiocarlide,tiocarlid,tiocarlida,tiocarlide,tiocarlidum" 7 "g" ""
"TDC" 10247721 "Tiodonium chloride" "Other antibacterials" "NA" "" "cloruro de tiodonio,tiodonii chloridum,tiodonium chloride" ""
"TXC" 65788 "Tioxacin" "Quinolones" "NA" "" "tioxacin,tioxacine,tioxacino,tioxacinum,tioxic acid" ""
"TIZ" 394397 "Tizoxanide" "Other antibacterials" "NA" "" "ntzdes" "73585-2,73607-4,73629-8"
"TOB" 36294 "Tobramycin" "Aminoglycosides" "J01GB01,S01AA12" "Aminoglycoside antibacterials" "Other aminoglycosides" "nn,tm,to,tob,tobr" "bethkis,brulamycin,deoxykanamycin b,distobram,gernebcin,gotabiotic,kitabis,kitabis pak,nebcin,nebicin,nebramycin,nebramycin vi,obramycin,sybryx,tenebrimycin,tenemycin,tobacin,tobi podhaler,tobracin,tobradex,tobradistin,tobralex,tobramaxin,tobramicin,tobramicina,tobramitsetin,tobramycetin,tobramycin,tobramycin base,tobramycin sulfate,tobramycine,tobramycinum,tobrased,tobrasone,tobrex" 0.24 "g" "101496-8,13584-8,17808-7,18996-9,22750-4,22751-2,22752-0,25227-0,25800-4,31094-6,31095-3,31096-1,35239-3,35670-9,4057-6,4058-4,4059-2,507-4,508-2,509-0,50927-3,510-8,52962-8,59380-6,7055-7,80966-5"
"TOH" "Tobramycin-high" "Aminoglycosides" "NA" "tobra high,tobramycin high,tohl" "" ""
"TFX" 5517 "Tosufloxacin" "Quinolones" "J01MA22" "" "tosufloxacin" 0.45 "g" "100061-1,76146-0"
"TFX" 5517 "Tosufloxacin" "Quinolones" "J01MA22,S01AE09" "" "tosufloxacin" 0.45 "g" "100061-1,76146-0"
"TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "t,tmp,tr,tri,trim,w" "abaprim,alprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacterial,bacticel,bactifor,bactin,bactoprim,bactramin,bactrim,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,colizole ds,conprim,cotrimel,cotrimoxizole,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,idotrim,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lagatrim forte,lastrim,lescot,methoprim,metoprim,monoprim,monotrim,monotrimin,novotrimel,omstat,oraprim,pancidim,polytrim,priloprim,primosept,primsol,proloprim,protrin,purbal,resprim,resprim forte,roubac,roubal,salvatrim,septrin ds,septrin forte,septrin s,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfamethoprim,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,tmp smx,toprim,trimanyl,trimethioprim,trimethopim,trimethoprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexazole,trimexol,trimezol,trimogal,trimono,trimopan,trimpex,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim" 0.4 "g" 0.4 "g" "101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1"
"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bacterial forte,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrim ds,bactrim forte,bactrim pediatric,bactrimel,bactrizol,bactromin,bactropin,baktar,belcomycine,berlocid,bibacrim,biseptol,chemitrim,chemotrim,ciplin,colimycin,colimycin sulphate,colisticin,colistimethate,colistimethate sodium,colistin sulfate,colistin sulphate,colomycin,coly-mycin,cotribene,cotrim d.s.,cotrim eu rho,cotrim holsen,cotrim.l.u.t.,cotrimaxazol,cotrimazole,cotrimhexal,cotrimoxazol,cotrimoxazol al,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,esteprim,eusaprim,fectrim,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,jenamoxazol,kemoprim,kepinol,kepinol forte,laratrim,linaris,maxtrim,microtrim,microtrim forte,mikrosid,momentol,oecotrim,oriprim,oxaprim,pantoprim,polymyxin e,polymyxin e. sulfate,primazole,promixin,septra,septra ds,septra grape,septrim,septrin,servitrim,sigaprim,sigaprin,sulfatrim pediatric,sulfotrim,sulfotrimin,sulmeprim pediatric,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,totazina,tribakin,trifen,trigonyl,trimesulf,trimetho comp,trimethoprimsulfa,trimetoger,trimexazol,trimforte,trimosulfa,uroplus,uroplus ds,uroplus ss" "101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3"
"TRL" 202225 "Troleandomycin" "Macrolides/lincosamides" "J01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "acetyloleandomycin,aovine,cyclamycin,evramicina,matromicina,matromycin t,micotil,oleandocetine,oleandomycin,t.a.o.,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycin,troleandomycine,troleandomycinum,viamicina,wytrion" 1 "g" "18999-3,519-9,520-7,521-5,522-3"
"TRO" 55886 "Trospectomycin" "Other antibacterials" "NA" "" "rubidiumnitrate,trospectinomycin,trospectomicina,trospectomycin,trospectomycine,trospectomycinum" ""
"TVA" 62959 "Trovafloxacin" "Quinolones" "J01MA13" "Quinolone antibacterials" "Fluoroquinolones" "trov" "trovafloxacin,trovan" 0.2 "g" 0.2 "g" "23642-2,23643-0,35855-6,7058-1"
"TUL" 9832301 "Tulathromycin" "Macrolides/lincosamides" "NA" "" "draxxin,tulathrmycin a,tulathromycin,tulathromycin a" "76149-4,87798-5"
"TYL" 5280440 "Tylosin" "Macrolides/lincosamides" "NA" "" "fradizine,tilosina,tylocine,tylosin,tylosin a,tylosine,tylosinum" "35856-4,35857-2,35858-0,87587-2"
"TYL1" 6441094 "Tylvalosin" "Macrolides/lincosamides" "NA" "tvn" "tylvalosin" "101526-2,87586-4"
"TUL" 9832301 "Tulathromycin" "Macrolides/lincosamides" "QJ01FA94" "" "draxxin,tulathrmycin a,tulathromycin,tulathromycin a" "76149-4,87798-5"
"TYL" 5280440 "Tylosin" "Macrolides/lincosamides" "QJ01FA90,QJ51FA90" "" "fradizine,tilosina,tylocine,tylosin,tylosin a,tylosine,tylosinum" "35856-4,35857-2,35858-0,87587-2"
"TYL1" 6441094 "Tylvalosin" "Macrolides/lincosamides" "QJ01FA92" "tvn" "tylvalosin" "101526-2,87586-4"
"PRU1" 124225 "Ulifloxacin (Prulifloxacin)" "Other antibacterials" "NA" "" "ulifloxacin" ""
"VAN" 14969 "Vancomycin" "Glycopeptides" "A07AA09,J01XA01,S01AA28" "Other antibacterials" "Glycopeptide antibacterials" "va,van,vanc" "vancocin,vancocin hcl,vancoled,vancomicina,vancomycin,vancomycin hcl,vancomycine,vancomycinum,vancor,viomycin derivative" 2 "g" 2 "g" "13586-3,13587-1,19000-9,20578-1,23615-8,25228-8,31012-8,39092-2,39796-8,39797-6,4089-9,4090-7,4091-5,4092-3,50938-0,523-1,524-9,525-6,526-4,59381-4,7059-9,92241-9,97657-1"
"VAM" "Vancomycin-macromethod" "Glycopeptides" "NA" "" "" ""

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data-raw/reproduction_of_antibiotics.R
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@@ -754,12 +754,20 @@ antibiotics <- antibiotics %>%
# update ATC codes from WHOCC website -------------------------------------
# last time checked: 2022-10-29
# last time checked: 2024-02-22
library(rvest)
updated_atc <- as.list(antibiotics$atc)
get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
get_atcs <- function(ab_name, type = "human") {
if (type == "human") {
url <- "https://www.whocc.no/atc_ddd_index/"
} else if (type == "veterinary") {
url <- "https://www.whocc.no/atcvet/atcvet_index/"
} else {
stop("invalid type")
}
ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE)
# we will do a search on their website, which means:
@@ -780,6 +788,7 @@ get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
html_node("table") %>%
# transform it to an R data set
html_table(header = FALSE)
# and get the ATCs (first column) of only exact hits
unique(as.character(atc_tbl[which(tolower(atc_tbl[, 2, drop = TRUE]) == ab_name), 1, drop = TRUE]))
}
@@ -790,7 +799,10 @@ for (i in seq_len(nrow(antibiotics))) {
" - Downloading ", antibiotics$name[i],
appendLF = FALSE
)
atcs <- get_atcs(antibiotics$name[i])
atcs <- get_atcs(antibiotics$name[i], type = "human")
if (all(is.na(atcs))) {
atcs <- get_atcs(antibiotics$name[i], type = "veterinary")
}
if (length(atcs) > 0) {
updated_atc[[i]] <- atcs
message(" (", length(atcs), " results)")
@@ -805,7 +817,7 @@ antibiotics$atc <- updated_atc
# update DDDs from WHOCC website ------------------------------------------
# last time checked: 2022-10-29
# last time checked: 2024-02-22
ddd_oral <- rep(NA_real_, nrow(antibiotics))
ddd_oral_units <- rep(NA_character_, nrow(antibiotics))
ddd_iv <- rep(NA_real_, nrow(antibiotics))

42
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -213,7 +213,10 @@ unknown <- breakpoints %>%
breakpoints %>%
filter(code %in% unknown) %>%
count(GUIDELINES, YEAR, ORGANISM_CODE, BREAKPOINT_TYPE, sort = TRUE)
# these codes are currently (2023-07-08): clu, kma. No clue (are not in MO list of WHONET), so remove them:
# 2024-02-22: clu and kma are know (see below), fix the PBI one
breakpoints$mo[breakpoints$ORGANISM_CODE == "PBI"] <- as.mo("Parabacteroides")
breakpoints$ORGANISM_CODE[breakpoints$ORGANISM_CODE == "PBI"] <- "Parabacteroides"
# 2023-07-08: these codes are currently: clu, kma. No clue (are not in MO list of WHONET), so remove them:
breakpoints <- breakpoints %>%
filter(!is.na(mo))
@@ -236,6 +239,7 @@ breakpoints_new <- breakpoints %>%
transmute(
guideline = paste(GUIDELINES, YEAR),
type = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(BREAKPOINT_TYPE)),
host = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(HOST)),
method = TEST_METHOD,
site = SITE_OF_INFECTION,
mo,
@@ -263,15 +267,15 @@ breakpoints_new <- breakpoints %>%
gsub("–", "-", ., fixed = TRUE)) %>%
arrange(desc(guideline), mo, ab, type, method) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
distinct(guideline, type, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
# check the strange duplicates
breakpoints_new %>%
mutate(id = paste(guideline, type, ab, mo, method, site)) %>%
mutate(id = paste(guideline, type, host, ab, mo, method, site)) %>%
filter(id %in% .$id[which(duplicated(id))])
# remove duplicates
breakpoints_new <- breakpoints_new %>%
distinct(guideline, type, ab, mo, method, site, .keep_all = TRUE)
distinct(guideline, type, host, ab, mo, method, site, .keep_all = TRUE)
# fix reference table names
breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl)) %>% View()
@@ -284,6 +288,10 @@ breakpoints_new <- breakpoints_new %>%
breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S", drop = TRUE]))
breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R", drop = TRUE]))
# regarding animal breakpoints, CLSI has adults and foals for horses, but only for amikacin - remove them
breakpoints_new <- breakpoints_new |>
filter(host %unlike% "foal") |>
mutate(host = ifelse(host %like% "horse", "horse", host))
# FIXES FOR WHONET ERRORS ----
@@ -301,27 +309,29 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 5
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STRPT" & clinical_breakpoints$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
breakpoints_new$mo[breakpoints_new$mo == "B_STRPT" & breakpoints_new$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
# Haemophilus same error (must only be H. influenzae)
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_HMPHL" & clinical_breakpoints$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
breakpoints_new$mo[breakpoints_new$mo == "B_HMPHL" & breakpoints_new$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
# EUCAST says that for H. parainfluenzae the H. influenza rules can be used, so add them
clinical_breakpoints <- clinical_breakpoints %>%
breakpoints_new <- breakpoints_new %>%
bind_rows(
clinical_breakpoints %>%
breakpoints_new %>%
filter(guideline %like% "EUCAST", mo == "B_HMPHL_INFL") %>%
mutate(mo = as.mo("B_HMPHL_PRNF"))
) %>%
arrange(desc(guideline), mo, ab, type, method)
arrange(desc(guideline), mo, ab, type, host, method)
# Achromobacter denitrificans is in WHONET included in their A. xylosoxidans table, must be removed
clinical_breakpoints <- clinical_breakpoints %>% filter(mo != as.mo("Achromobacter denitrificans"))
breakpoints_new <- breakpoints_new %>% filter(mo != as.mo("Achromobacter denitrificans"))
# WHONET contains gentamicin breakpoints for viridans streptocci, which are intrinsic R - they meant genta-high, which is ALSO in their table, so we just remove gentamicin in viridans streptococci
clinical_breakpoints <- clinical_breakpoints %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
breakpoints_new <- breakpoints_new %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
# Nitrofurantoin in Staph (EUCAST) only applies to S. saprophyticus, while WHONET has the DISK correct but the MIC on genus level
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STPHY" & clinical_breakpoints$ab == "NIT" & clinical_breakpoints$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
breakpoints_new$mo[breakpoints_new$mo == "B_STPHY" & breakpoints_new$ab == "NIT" & breakpoints_new$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
# WHONET sets the 2023 breakpoints for SAM to MIC of 16/32 for Enterobacterales, should be MIC 8/32 like AMC (see issue #123 on github.com/msberends/AMR)
clinical_breakpoints$breakpoint_S[clinical_breakpoints$mo == "B_[ORD]_ENTRBCTR" & clinical_breakpoints$ab == "SAM" & clinical_breakpoints$guideline %like% "CLSI 2023" & clinical_breakpoints$method == "MIC"] <- 8
# UPDATE 2024-02-22: fixed now
# breakpoints_new$breakpoint_S[breakpoints_new$mo == "B_[ORD]_ENTRBCTR" & breakpoints_new$ab == "SAM" & breakpoints_new$guideline %like% "CLSI 2023" & breakpoints_new$method == "MIC"] <- 8
# determine rank again now that some changes were made on taxonomic level (genus -> species)
clinical_breakpoints <- clinical_breakpoints %>%
breakpoints_new <- breakpoints_new %>%
mutate(rank_index = case_when(
is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
@@ -337,7 +347,7 @@ clinical_breakpoints <- clinical_breakpoints %>%
# EUCAST 2022 guideline: S <= 8 and R > 8
# WHONET file: S <= 8 and R >= 16
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
# this will make an MIC of 12 I, which should be R, so:
# this will make an MIC of 12 I, which should be R according to EUCAST, so:
breakpoints_new <- breakpoints_new %>%
mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "MIC" & log2(breakpoint_R) - log2(breakpoint_S) != 0,
pmax(breakpoint_S, breakpoint_R / 2),
@@ -350,7 +360,7 @@ breakpoints_new <- breakpoints_new %>%
breakpoint_R + 1,
breakpoint_R
))
# fix missing R breakpoint where there is an S breakpoint
# fill missing R breakpoint where there is an S breakpoint
breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]

426
data-raw/reproduction_of_microorganisms.R
View File

@@ -150,12 +150,14 @@ df_remove_nonASCII <- function(df) {
# to retrieve LPSN and authors from LPSN website
get_lpsn_and_author <- function(rank, name) {
name <- gsub("^Candidatus ", "", name)
url <- paste0("https://lpsn.dsmz.de/", tolower(rank), "/", tolower(name))
page_txt <- tryCatch(read_html(url), error = function(e) NULL)
if (is.null(page_txt)) {
warning("No LPSN found for ", tolower(rank), " '", name, "'")
lpsn <- NA_character_
ref <- NA_character_
status <- "unknown"
} else {
page_txt <- page_txt %>%
html_element("#detail-page") %>%
@@ -164,9 +166,33 @@ get_lpsn_and_author <- function(rank, name) {
ref <- page_txt %>%
gsub(".*?Name: (.*[0-9]{4}?).*", "\\1", ., perl = FALSE) %>%
gsub(name, "", ., fixed = TRUE) %>%
gsub("^\"?Candidatus ?\"?", "", .) %>%
trimws()
status <- trimws(gsub(".*Nomenclatural status:[\r\n\t ]*([a-zA-Z, ]+)[\r\n\t].*", "\\1", page_txt, perl = FALSE))
if ((status %like% "validly published" & status %unlike% "not valid") | status %like% "[\r\n\t]") {
# we used to take "accepted" for every LPSN record, also candidates. Now only for missing values and explicit accepted ones.
status <- "accepted"
} else {
status <- "not validly published"
}
}
c("lpsn" = lpsn, "ref" = ref, "status" = status)
}
# this will e.g. take the family from the root genus record, and gives all species that family
get_top_lvl <- function(current, rank, rank_target) {
if (!rank_target %in% rank) {
current[1]
} else {
out <- current[rank == rank_target][1]
if (out %in% c("", NA)) {
out <- names(sort(table(current[which(!current %in% c("", NA))]), decreasing = TRUE)[1])
if (is.null(out)) {
out <- ""
}
}
out
}
c("lpsn" = lpsn, "ref" = ref)
}
# MB/ August 2022: useless, does not contain full taxonomy, e.g. LPSN::request(cred, category = "family") is empty.
@@ -208,11 +234,12 @@ include_fungal_orders_ids <- taxonomy_gbif.bak %>%
include_fungal_orders <- taxonomy_gbif.bak %>%
filter(taxonID %in% c(include_fungal_orders_ids$taxonID, include_fungal_orders_ids$acceptedNameUsageID)) %>%
distinct(order) %>%
pull(order)
pull(order) |>
sort()
# check some columns to validate below filters
sort(table(taxonomy_gbif.bak$taxonomicStatus))
sort(table(taxonomy_gbif.bak$taxonRank))
taxonomy_gbif.bak$taxonomicStatus |> table() |> sort() |> as.data.frame()
taxonomy_gbif.bak$taxonRank |> table() |> sort() |> as.data.frame()
taxonomy_gbif <- taxonomy_gbif.bak %>%
# immediately filter rows we really never want
@@ -223,10 +250,7 @@ taxonomy_gbif <- taxonomy_gbif.bak %>%
# include these kingdoms (no Chromista)
kingdom %in% c("Archaea", "Bacteria", "Protozoa") |
# include all of these fungal orders
order %in% c(
"Eurotiales", "Microascales", "Mucorales", "Saccharomycetales",
"Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"
) |
order %in% include_fungal_orders |
# and all of these important genera (see "data-raw/_pre_commit_hook.R")
# (they also contain bacteria and protozoa, but these will get prevalence = 2 later on)
genus %in% AMR:::MO_PREVALENT_GENERA
@@ -289,9 +313,6 @@ taxonomy_gbif
taxonomy_lpsn.bak <- vroom(file_lpsn)
# check some columns to validate below filters
sort(table(is.na(taxonomy_lpsn.bak$record_lnk))) # accepted = TRUE
taxonomy_lpsn <- taxonomy_lpsn.bak %>%
transmute(
genus = genus_name,
@@ -309,6 +330,10 @@ taxonomy_lpsn <- taxonomy_lpsn.bak %>%
lpsn_renamed_to = as.character(record_lnk)
) %>%
mutate(source = "LPSN")
# integrity tests
sort(table(taxonomy_lpsn$rank))
sort(table(taxonomy_lpsn$status))
taxonomy_lpsn
# download additional taxonomy to the domain/kingdom level (their API is not sufficient...)
@@ -322,17 +347,22 @@ taxonomy_lpsn_missing <- tibble(
)
for (page in LETTERS) {
# this will not alter `taxonomy_lpsn` yet
message("Downloading page ", page, "...", appendLF = FALSE)
message("Downloading page ", page, "...", appendLF = TRUE)
url <- paste0("https://lpsn.dsmz.de/genus?page=", page)
x <- read_html(url) %>%
x <- tryCatch(read_html(url),
error = function(e) {
message("Waiting 10 seconds because of error: ", e$message)
Sys.sleep(10)
read_html(url)
})
x <- x %>%
# class "main-list" is the main table
html_element(".main-list") %>%
# get every list element with a set <id> attribute
html_elements("li[id]")
pb <- progress_bar$new(total = length(x), format = "[:bar] :current/:total :eta")
for (i in seq_len(length(x))) {
if (i %% 25 == 0) {
message(".", appendLF = FALSE)
}
pb$tick()
elements <- x[[i]] %>% html_elements("a")
hrefs <- elements %>% html_attr("href")
ranks <- hrefs %>% gsub(".*/(.*?)/.*", "\\1", .)
@@ -344,21 +374,26 @@ for (page in LETTERS) {
names <- names[ranks != "species"]
ranks <- ranks[ranks != "species"]
ranks[ranks == "domain"] <- "kingdom"
df <- names %>%
tibble() %>%
t() %>%
as_tibble(.name_repair = "unique") %>%
setNames(ranks) %>%
# no candidates please
filter(genus %unlike% "^(Candidatus|\\[)")
suppressMessages(
df <- names %>%
tibble() %>%
t() %>%
as_tibble(.name_repair = "unique") %>%
setNames(ranks) %>%
# no candidates please
filter(genus %unlike% "^(Candidatus|\\[)")
)
taxonomy_lpsn_missing <- taxonomy_lpsn_missing %>%
bind_rows(df)
}
message(length(x), " entries incl. candidates (cleaned total: ", nrow(taxonomy_lpsn_missing), ")")
message(" => ", length(x), " entries incl. candidates (cleaned total: ", nrow(taxonomy_lpsn_missing), ")")
}
taxonomy_lpsn_missing
taxonomy_lpsn_missing <- taxonomy_lpsn_missing |> distinct()
# had to pick the right genus/family combination here:
taxonomy_lpsn_missing <- taxonomy_lpsn_missing |> filter(!(genus == "Pusillimonas" & family == "Oscillospiraceae"))
taxonomy_lpsn.bak2 <- taxonomy_lpsn.bak
taxonomy_lpsn <- taxonomy_lpsn %>%
left_join(taxonomy_lpsn_missing, by = "genus") %>%
@@ -367,8 +402,10 @@ taxonomy_lpsn <- taxonomy_lpsn %>%
mutate_all(function(x) ifelse(x %like_case% " no ", NA_character_, x))
taxonomy_lpsn.bak2 <- taxonomy_lpsn
# download family directly from LPSN website using scraping
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$family)))
# download family directly from LPSN website using scraping, by using get_lpsn_and_author()
# try it first:
# get_lpsn_and_author("genus", "Escherichia")
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$family)), format = "[:bar] :current/:total :eta")
for (f in unique(taxonomy_lpsn$family)) {
pb$tick()
if (is.na(f)) next
@@ -381,14 +418,14 @@ for (f in unique(taxonomy_lpsn$family)) {
order = taxonomy_lpsn$order[which(taxonomy_lpsn$family == f)[1]],
family = f,
rank = "family",
status = "accepted",
status = unname(tax_info["status"]),
source = "LPSN",
lpsn = unname(tax_info["lpsn"]),
ref = unname(tax_info["ref"])
))
}
# download order directly from LPSN website using scraping
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$order)))
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$order)), format = "[:bar] :current/:total :eta")
for (o in unique(taxonomy_lpsn$order)) {
pb$tick()
if (is.na(o)) next
@@ -400,14 +437,14 @@ for (o in unique(taxonomy_lpsn$order)) {
class = taxonomy_lpsn$class[which(taxonomy_lpsn$order == o)[1]],
order = o,
rank = "order",
status = "accepted",
status = unname(tax_info["status"]),
source = "LPSN",
lpsn = unname(tax_info["lpsn"]),
ref = unname(tax_info["ref"])
))
}
# download class directly from LPSN website using scraping
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$class)))
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$class)), format = "[:bar] :current/:total :eta")
for (cc in unique(taxonomy_lpsn$class)) {
pb$tick()
if (is.na(cc)) next
@@ -418,14 +455,14 @@ for (cc in unique(taxonomy_lpsn$class)) {
phylum = taxonomy_lpsn$phylum[which(taxonomy_lpsn$class == cc)[1]],
class = cc,
rank = "class",
status = "accepted",
status = unname(tax_info["status"]),
source = "LPSN",
lpsn = unname(tax_info["lpsn"]),
ref = unname(tax_info["ref"])
))
}
# download phylum directly from LPSN website using scraping
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$phylum)))
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$phylum)), format = "[:bar] :current/:total :eta")
for (p in unique(taxonomy_lpsn$phylum)) {
pb$tick()
if (is.na(p)) next
@@ -435,14 +472,14 @@ for (p in unique(taxonomy_lpsn$phylum)) {
kingdom = taxonomy_lpsn$kingdom[which(taxonomy_lpsn$phylum == p)[1]],
phylum = p,
rank = "phylum",
status = "accepted",
status = unname(tax_info["status"]),
source = "LPSN",
lpsn = unname(tax_info["lpsn"]),
ref = unname(tax_info["ref"])
))
}
# download kingdom directly from LPSN website using scraping
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$kingdom)))
pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$kingdom)), format = "[:bar] :current/:total :eta")
for (k in unique(taxonomy_lpsn$kingdom)) {
pb$tick()
if (is.na(k)) next
@@ -451,7 +488,7 @@ for (k in unique(taxonomy_lpsn$kingdom)) {
bind_rows(tibble(
kingdom = k,
rank = "kingdom",
status = "accepted",
status = unname(tax_info["status"]),
source = "LPSN",
lpsn = unname(tax_info["lpsn"]),
ref = unname(tax_info["ref"])
@@ -469,6 +506,7 @@ saveRDS(taxonomy_gbif, "data-raw/taxonomy_gbif.rds", version = 2)
saveRDS(taxonomy_lpsn, "data-raw/taxonomy_lpsn.rds", version = 2)
# this allows to always get back to this point by simply loading the files from data-raw/.
# Add full names ----------------------------------------------------------
taxonomy_gbif <- taxonomy_gbif %>%
@@ -515,29 +553,28 @@ taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "subspecies"] <- taxonomy_lpsn$l
# Combine the datasets ----------------------------------------------------
# basis must be LPSN as it's most recent
taxonomy <- taxonomy_lpsn %>%
# join GBIF identifiers to them
left_join(taxonomy_gbif %>% select(kingdom, fullname, starts_with("gbif")),
by = c("kingdom", "fullname")
)
# for everything else, add the GBIF data
taxonomy <- taxonomy %>%
bind_rows(taxonomy_gbif %>%
filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname))) %>%
arrange(fullname) %>%
filter(fullname != "")
taxonomy <- taxonomy_lpsn |>
# start by adding GBIF to the bottom
bind_rows(taxonomy_gbif) |>
# group on unique species
group_by(kingdom, fullname) |>
# fill the NAs in LPSN/GBIF fields and ref with the other source (so LPSN: 123 and GBIF: NA will become LPSN: 123 and GBIF: 123)
mutate(across(matches("^(lpsn|gbif|ref)"), function(x) rep(x[!is.na(x)][1], length(x)))) |>
# ungroup again
ungroup() |>
# only keep unique species per kingdom
distinct(kingdom, fullname, .keep_all = TRUE) |>
arrange(fullname)
# get missing entries from existing microorganisms data set
taxonomy <- taxonomy %>%
bind_rows(AMR::microorganisms %>%
taxonomy.old <- AMR::microorganisms %>%
select(all_of(colnames(taxonomy))) %>%
filter(
!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
# these will be added later:
source != "manually added"
)) %>%
source != "manually added")
taxonomy <- taxonomy %>%
bind_rows(taxonomy.old) %>%
arrange(fullname) %>%
filter(fullname != "")
@@ -557,6 +594,29 @@ taxonomy <- taxonomy %>%
))
table(taxonomy$rank, useNA = "always")
# at this point, it happens that some genera within kingdoms have multiple families / orders, etc., see here:
taxonomy |> filter(genus != "") |> group_by(kingdom, genus) |> filter(n_distinct(family) > 1) |> View()
# so make this universal
taxonomy <- taxonomy |>
group_by(kingdom, genus) |>
mutate(family = get_top_lvl(family, rank, "genus")) |>
group_by(kingdom, family) |>
mutate(order = get_top_lvl(order, rank, "family")) |>
group_by(kingdom, order) |>
mutate(class = get_top_lvl(class, rank, "order")) |>
group_by(kingdom, class) |>
mutate(phylum = get_top_lvl(phylum, rank, "class")) |>
ungroup()
# and remove the taxonomy where it must remain empty
taxonomy <- taxonomy |>
mutate(phylum = ifelse(rank %in% c("kingdom"), "", phylum),
class = ifelse(rank %in% c("kingdom", "phylum"), "", class),
order = ifelse(rank %in% c("kingdom", "phylum", "class"), "", order),
family = ifelse(rank %in% c("kingdom", "phylum", "class", "order"), "", family),
genus = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family"), "", genus),
species = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family", "genus"), "", species),
subspecies = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family", "genus", "species"), "", subspecies))
# Save intermediate results (0) -------------------------------------------
@@ -575,28 +635,23 @@ current_gbif <- taxonomy_gbif.bak %>%
)
# add missing kingdoms
taxonomy <- taxonomy %>%
bind_rows(
taxonomy %>%
filter(kingdom != "") %>%
distinct(kingdom) %>%
mutate(
fullname = kingdom,
rank = "kingdom",
status = "accepted",
source = "manually added"
) %>%
filter(!paste(kingdom, rank) %in% paste(taxonomy$kingdom, taxonomy$rank)) %>%
left_join(
current_gbif %>%
select(kingdom, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
by = c("kingdom", "rank")
) %>%
mutate(source = ifelse(!is.na(gbif), "GBIF", source))
)
taxonomy_all_missing <- taxonomy %>%
filter(kingdom != "") %>%
distinct(kingdom) %>%
mutate(
fullname = kingdom,
rank = "kingdom"
) %>%
filter(!paste(kingdom, rank) %in% paste(taxonomy$kingdom, taxonomy$rank)) %>%
left_join(
current_gbif %>%
select(kingdom, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
by = c("kingdom", "rank")
) %>%
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
status = ifelse(!is.na(gbif), "accepted", "unknown"))
# 2 = phylum ... 6 = genus
taxonomy_all_missing <- NULL
for (i in 2:6) {
i_name <- colnames(taxonomy)[i + 1]
message("Adding missing: ", i_name, "... ", appendLF = FALSE)
@@ -606,25 +661,20 @@ for (i in 2:6) {
select(kingdom:(i + 1)) %>%
mutate(
fullname = .[[ncol(.)]],
rank = i_name,
status = "accepted",
source = "manually added"
rank = i_name
) %>%
filter(!paste(kingdom, .[[ncol(.) - 4]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
filter(!paste(kingdom, .[[ncol(.) - 2]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
# get GBIF identifier where available
left_join(
current_gbif %>%
select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
by = c("kingdom", "rank", i_name)
) %>%
mutate(source = ifelse(!is.na(gbif), "GBIF", source))
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
status = ifelse(!is.na(gbif), "accepted", "unknown"))
message("n = ", nrow(to_add))
if (is.null(taxonomy_all_missing)) {
taxonomy_all_missing <- to_add
} else {
taxonomy_all_missing <- taxonomy_all_missing %>%
bind_rows(to_add)
}
taxonomy_all_missing <- taxonomy_all_missing %>%
bind_rows(to_add)
}
taxonomy_all_missing %>% View()
@@ -652,7 +702,7 @@ taxonomy <- taxonomy %>%
select(-fullname_rank, -rank_index) %>%
arrange(fullname)
# now also add missing species (requires combination with genus)
# now also add missing species that have subspecies (requires combination with genus)
taxonomy <- taxonomy %>%
bind_rows(
taxonomy %>%
@@ -661,9 +711,7 @@ taxonomy <- taxonomy %>%
select(kingdom:species) %>%
mutate(
fullname = paste(genus, species),
rank = "species",
status = "accepted",
source = "manually added"
rank = "species"
) %>%
filter(!paste(kingdom, genus, species, rank) %in% paste(taxonomy$kingdom, taxonomy$genus, taxonomy$species, taxonomy$rank)) %>%
# get GBIF identifier where available
@@ -672,13 +720,15 @@ taxonomy <- taxonomy %>%
select(kingdom, genus, species = specificEpithet, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
by = c("kingdom", "rank", "genus", "species")
) %>%
mutate(source = ifelse(!is.na(gbif), "GBIF", source))
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
status = ifelse(!is.na(gbif), "accepted", "unknown"))
)
# remove NAs from taxonomy again, and keep unique full names
taxonomy <- taxonomy %>%
mutate(across(kingdom:subspecies, function(x) ifelse(is.na(x), "", x))) %>%
arrange(kingdom, fullname, ref) |>
distinct(kingdom, fullname, .keep_all = TRUE) %>%
filter(kingdom != "")
@@ -691,12 +741,11 @@ saveRDS(taxonomy, "data-raw/taxonomy1.rds")
# Get previously manually added entries -----------------------------------
manually_added <- AMR::microorganisms %>%
filter(source == "manually added", !paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname)) %>%
filter(source == "manually added",
!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
!rank %in% c("kingdom", "phylum", "class", "order", "family")) %>%
select(fullname:subspecies, ref, source, rank)
manually_added <- manually_added %>%
bind_rows(salmonellae)
# get latest taxonomy for those entries
for (g in unique(manually_added$genus[manually_added$genus != "" & manually_added$genus %in% taxonomy$genus])) {
manually_added$family[which(manually_added$genus == g)] <- taxonomy$family[which(taxonomy$genus == g & is.na(taxonomy$lpsn))][1]
@@ -716,11 +765,14 @@ for (p in unique(manually_added$phylum[manually_added$phylum != "" & manually_ad
manually_added <- manually_added %>%
mutate(
status = "accepted",
status = "unknown",
rank = ifelse(fullname %like% "unknown", "(unknown rank)", rank)
)
manually_added
# these are now included in the new taxonomy, check them
manually_added |> filter(fullname %in% taxonomy$fullname)
taxonomy <- taxonomy %>%
# here also the 'unknowns' are added, such as "(unknown fungus)"
bind_rows(manually_added) %>%
@@ -728,6 +780,31 @@ taxonomy <- taxonomy %>%
table(taxonomy$rank, useNA = "always")
# Get LPSN data for records missing from `taxonomy_lpsn` ------------------
# Weirdly enough, some LPSN records were lacking from `taxonomy_lpsn`,
# such as family Thiotrichaceae and its order Thiotrichales. When running
# get_lpsn_and_author("family", "Thiotrichaceae") you do get a result.
# So check every non-LPSN records from the kingdom of Bacteria and add it
gbif_bacteria <- which(taxonomy$kingdom == "Bacteria" & taxonomy$source == "GBIF" & taxonomy$rank %in% c("phylum", "class", "order", "family"))
added <- 0
pb <- progress_bar$new(total = length(gbif_bacteria), format = "[:bar] :current/:total :eta")
for (record in gbif_bacteria) {
pb$tick()
lpsn <- get_lpsn_and_author(rank = taxonomy$rank[record],
name = taxonomy$fullname[record])
if (is.na(lpsn["lpsn"])) {
next
} else {
added <- added + 1
taxonomy$source[record] <- "LPSN"
taxonomy$lpsn[record] <- unname(lpsn["lpsn"])
taxonomy$ref[record] <- unname(lpsn["ref"])
taxonomy$status[record] <- unname(lpsn["status"])
}
}
message(added, " GBIF records altered to latest LPSN")
taxbak <- taxonomy
# Clean scientific reference ----------------------------------------------
@@ -737,7 +814,7 @@ taxonomy <- taxonomy %>%
# Get the latest upper taxonomy from LPSN for non-LPSN data ---------------
# (e.g., phylum above class "Bacilli" was still "Firmicutes", should be "Bacillota" in 2022)
# (e.g., phylum above class "Bacilli" was still "Firmicutes" in 2023, should be "Bacillota")
for (k in unique(taxonomy$kingdom[taxonomy$kingdom != ""])) {
message("Fixing GBIF taxonomy for kingdom ", k, ".", appendLF = FALSE)
i <- 0
@@ -765,17 +842,25 @@ for (k in unique(taxonomy$kingdom[taxonomy$kingdom != ""])) {
}
# we need to fix parent GBIF identifiers
taxonomy$gbif_parent[taxonomy$rank == "phylum" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "class" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "order" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "family" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "genus" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "species" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "subspecies" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies" & !is.na(taxonomy$gbif)], taxonomy$species[taxonomy$rank == "subspecies" & !is.na(taxonomy$gbif)]), taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "phylum"] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "class"] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "order"] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "family"] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "genus"] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "species"] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "subspecies"] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
# and LPSN parents
taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
# these still have no record in our data set:
all(taxonomy$lpsn_parent %in% taxonomy$lpsn)
all(taxonomy$gbif_parent %in% taxonomy$gbif)
which(!taxonomy$lpsn_parent %in% taxonomy$lpsn)
which(!taxonomy$gbif_parent %in% taxonomy$gbif)
# fix rank
taxonomy <- taxonomy %>%
@@ -794,6 +879,7 @@ taxonomy <- taxonomy %>%
# Add prevalence ----------------------------------------------------------
taxonomy_lpsn.bak3 <- taxonomy
pathogens <- read_excel(file_bartlett, sheet = "Tab 6 Full List")
# get all established, both old and current taxonomic names
@@ -902,6 +988,7 @@ mo_kingdom <- taxonomy %>%
kingdom == "Protozoa" ~ "P",
TRUE ~ ""
))
# phylum until family are abbreviated with 8 characters and prefixed with their rank
# Phylum - keep old and fill up for new ones
@@ -1196,58 +1283,120 @@ taxonomy <- taxonomy %>%
taxonomy %>%
filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE]) %>%
View()
# fullnames must be unique, we'll keep the most relevant ones only
taxonomy <- taxonomy %>%
mutate(rank_index = case_when(
kingdom == "Bacteria" ~ 1,
kingdom == "Fungi" ~ 2,
kingdom == "Protozoa" ~ 3,
kingdom == "Archaea" ~ 4,
TRUE ~ 5
kingdom == "Animalia" ~ 5,
TRUE ~ 6
)) %>%
arrange(fullname, rank_index) %>%
distinct(fullname, .keep_all = TRUE) %>%
select(-rank_index) %>%
filter(mo != "")
# keep the codes from manually added ones
manual_mos <- as.character(AMR::microorganisms$mo)[match(taxonomy$fullname[taxonomy$source == "manually added"], AMR::microorganisms$fullname)]
taxonomy$mo[taxonomy$source == "manually added"][!is.na(manual_mos)] <- manual_mos[!is.na(manual_mos)]
# this must not exist:
taxonomy %>%
filter(mo %like% "__") %>%
View()
taxonomy <- taxonomy %>% filter(mo %unlike% "__")
taxonomy_lpsn.bak4 <- taxonomy
# Some integrity checks ---------------------------------------------------
# are mo codes unique?
taxonomy %>% filter(mo %in% .[duplicated(mo), "mo", drop = TRUE])
taxonomy <- taxonomy %>% distinct(mo, .keep_all = TRUE)
taxonomy %>% filter(mo %in% .[duplicated(mo), "mo", drop = TRUE]) |> arrange(mo) |> View()
# no, there are not, so sort on MO and keep the first
taxonomy <- taxonomy %>% arrange(mo) |> distinct(mo, .keep_all = TRUE)
taxonomy <- taxonomy |>
mutate(fullname = case_match(rank,
"phylum" ~ phylum,
"class" ~ class,
"order" ~ order,
"family" ~ family,
.default = fullname))
# are fullnames unique?
taxonomy %>% filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE])
# are all GBIFs available?
taxonomy %>%
filter(!gbif_parent %in% gbif) %>%
count(rank)
# try to find the right gbif IDs
taxonomy$gbif_parent[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "species")] <- taxonomy$gbif[match(taxonomy$genus[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "species")], taxonomy$genus)]
taxonomy$gbif_parent[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "class")] <- taxonomy$gbif[match(taxonomy$phylum[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "class")], taxonomy$phylum)]
taxonomy %>%
filter(!gbif_parent %in% gbif) %>%
count(rank)
filter((!gbif_parent %in% gbif) | (!lpsn_parent %in% lpsn)) %>%
count(source = ifelse(!gbif_parent %in% gbif, "GBIF", "LPSN"),
rank)
# are all LPSNs available?
# so fix again all parent GBIF identifiers
taxonomy$gbif_parent[taxonomy$rank == "phylum"] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "class"] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "order"] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "family"] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "genus"] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "species"] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
taxonomy$gbif_parent[taxonomy$rank == "subspecies"] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
# and LPSN identifiers
taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
# check again
taxonomy %>%
filter(!lpsn_parent %in% lpsn) %>%
count(rank)
# make GBIF refer to newest renaming according to LPSN
taxonomy$gbif_renamed_to[which(!is.na(taxonomy$gbif_renamed_to) & !is.na(taxonomy$lpsn_renamed_to))] <- taxonomy$gbif[match(taxonomy$lpsn_renamed_to[which(!is.na(taxonomy$gbif_renamed_to) & !is.na(taxonomy$lpsn_renamed_to))], taxonomy$lpsn)]
filter((!gbif_parent %in% gbif) | (!lpsn_parent %in% lpsn)) %>%
count(source = ifelse(!gbif_parent %in% gbif, "GBIF", "LPSN"),
rank)
# Save intermediate results (3) -------------------------------------------
saveRDS(taxonomy, "data-raw/taxonomy3.rds")
# Redo LPSN missings and parents ------------------------------------------
gbif_bacteria_second_run <- which(taxonomy$kingdom == "Bacteria" & taxonomy$source == "GBIF" & taxonomy$rank %in% c("phylum", "class", "order", "family"))
gbif_bacteria_second_run <- gbif_bacteria_second_run[!gbif_bacteria_second_run %in% gbif_bacteria]
added <- 0
pb <- progress_bar$new(total = length(gbif_bacteria_second_run), format = "[:bar] :current/:total :eta")
for (record in gbif_bacteria_second_run) {
pb$tick()
lpsn <- get_lpsn_and_author(rank = taxonomy$rank[record],
name = taxonomy$fullname[record])
if (is.na(lpsn["lpsn"])) {
next
} else {
added <- added + 1
taxonomy$source[record] <- "LPSN"
taxonomy$lpsn[record] <- unname(lpsn["lpsn"])
taxonomy$ref[record] <- unname(lpsn["ref"])
taxonomy$status[record] <- unname(lpsn["status"])
}
}
message(added, " GBIF records altered to latest LPSN")
taxbak <- taxonomy
taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
# TODO: there is no order Eggerthellales anymore
# Remove unwanted taxonomic entries from Protoza/Fungi --------------------
# this must be done after the microbial ID generation, since it will otherwise generate a lot of different IDs
@@ -1256,12 +1405,12 @@ taxonomy <- taxonomy %>%
# Protozoa:
!(phylum %in% c("Choanozoa", "Mycetozoa") & prevalence == 3),
# Fungi:
!(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 3),
!(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 3 & rank %in% c("genus", "species", "subspecies")),
!(genus %in% c("Phoma", "Leptosphaeria", "Physarum") & rank %in% c("species", "subspecies")), # only genus of this rare fungus, with resp. 1300 and 800 species
# (leave Alternaria in there, part of human mycobiome and opportunistic pathogen)
# Animalia:
!genus %in% c("Lucilia", "Lumbricus"),
!(class == "Insecta" & rank %in% c("species", "subspecies")), # keep only genus of insects
!(class == "Insecta" & rank %in% c("species", "subspecies")), # keep only genus of insects, not all of their (sub)species
!(genus == "Amoeba" & kingdom == "Animalia"),
!(genus %in% c("Aedes", "Anopheles") & rank %in% c("species", "subspecies")), # only genus of the many hundreds of mosquitoes species
kingdom != "Plantae"
@@ -1270,7 +1419,8 @@ taxonomy <- taxonomy %>%
# no ghost families, orders classes, phyla
taxonomy <- taxonomy %>%
group_by(kingdom, family) %>%
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
# (but keep the ghost families of bacteria)
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom" | kingdom == "Bacteria") %>%
group_by(kingdom, order) %>%
filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
group_by(kingdom, class) %>%
@@ -1280,6 +1430,34 @@ taxonomy <- taxonomy %>%
ungroup()
for (i in which(colnames(taxonomy) %in% c("phylum", "class", "order", "family")) - 1) {
i_name <- colnames(taxonomy)[i + 1]
message("Adding missing: ", i_name, "... ", appendLF = FALSE)
to_add <- taxonomy %>%
filter(.[[i + 1]] != "") %>%
distinct(kingdom, .[[i + 1]], .keep_all = TRUE) %>%
select(kingdom:(i + 1)) %>%
mutate(
fullname = .[[ncol(.)]],
rank = i_name
) %>%
filter(!paste(kingdom, .[[ncol(.) - 2]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
# get GBIF identifier where available
left_join(
current_gbif %>%
select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
by = c("kingdom", "rank", i_name)
) %>%
mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
status = ifelse(!is.na(gbif), "accepted", "unknown"))
message("n = ", nrow(to_add))
# taxonomy_all_missing <- taxonomy_all_missing %>%
# bind_rows(to_add)
}
message(
"\nCongratulations! The new taxonomic table will contain ", format(nrow(taxonomy), big.mark = " "), " rows.\n",
"This was ", format(nrow(AMR::microorganisms), big.mark = " "), " rows.\n"

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7
data-raw/translations.tsv
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@@ -278,3 +278,10 @@ Macrolides/lincosamides FALSE TRUE TRUE FALSE 大环内酯类/林可酰胺类 Ma
Other antibacterials FALSE TRUE TRUE FALSE 其他抗菌剂 Ostatní antibakteriální látky Andre antibakterielle stoffer Overige antibiotica Muut antibakteeriset aineet Autres antibactériens Andere Antibiotika Άλλα αντιβακτηριακά Altri antibatterici その他の抗菌薬 Andre antibakterielle midler Inne środki przeciwbakteryjne Outros antibacterianos Alte antibacteriene Другие антибактериальные препараты Otros antibacterianos Andra antibakteriella medel Diğer antibakteriyeller Інші антибактеріальні засоби
Polymyxins FALSE TRUE TRUE FALSE 多粘菌素类 Polymyxiny Polymyxiner Polymyxines Polymysiinit Polymyxines Polymyxine Πολυμυξίνες Polimixine ポリミキシン Polymyxiner Polimyksyny Polimixinas Polimixine Полимиксины Polimixinas Polymyxiner Polimiksinler Поліміксини
Quinolones FALSE TRUE TRUE FALSE 喹诺酮类 Chinolony Kinoloner Quinolonen Kinolonit Quinolones Quinolone Κινολόνες Chinoloni キノロン Kinoloner Quinolony Quinolones Quinolone Хинолоны Quinolonas Kinoloner Kinolonlar Хінолони
aquatic|fish FALSE FALSE FALSE FALSE 水生|条鱼|鱼 vodní|ryba|ryby akvatisk|fisk aquatisch|vis|vissen vesieliö|kala|kalaa aquatique|poisson|poissons wasser|fisch|fische υδρόβια|ψάρι|ψάρια acquatico|pesce|pesci アクアティック|1匹|魚 akvatisk|fisk wodny|ryba|ryby aquático|peixe|peixes acvatic|pește|pești водные|рыба|рыбы acuático|pez|peces vattenlevande|fisk|fiskar sucul|balık водний|риба|рибки
cattle|bovine FALSE FALSE FALSE FALSE 牛|牛 skot kvæg vee|rund karja|nauta bovins|bovin rinder βοοειδή bovini|bovino 牛|ウシ storfe|storfe bydło|bydło bovinos|bovino bovine|bovine крупный рогатый скот|крупный рогатый скот bovino|bovino nötkreatur|nötkreatur sığır|büyükbaş hayvan велика рогата худоба|бичачий
cat|cats|feline FALSE FALSE FALSE FALSE 猫|猫|猫科动物 kočka|kočky|kočky kat|katte|kat kat|katten|katachtig kissa|kissat|kissa chat|chats|félin katze|katzen γάτα|γάτες|αιλουροειδή gatto|gatti|felino 猫|猫|ネコ katt kot|koty gato|gatos|felino pisică|pisici|felină кошка|кошки|кошка gato|gatos|felino katt|katter|kattdjur kedi|kediler|kedi кіт|коти|котячий
dog|dogs|canine FALSE FALSE FALSE FALSE 狗|狗|犬类 pes|psi|psí hund|hunde hond|honden koira|koirat|koira chien|canine hund|hunde|hund σκύλος|σκύλοι|σκύλος cane|cani|canino 犬|犬|イヌ hund pies|psy|pies cão|cães|canino câine|câini|canin собака|собаки|собака perro|perros|canino hund|hundar köpek|köpekler пес|собаки|собачий
horse|horses|equine FALSE FALSE FALSE FALSE 马|马|马 kůň|koně|koně hest|heste paard|paarden hevonen|hevoset|hevoset cheval|chevaux|équine pferd|pferde άλογο|άλογα|ιπποειδή cavallo|cavalli|equino 馬|馬|馬 hest koń|konie|koń cavalo|cavalos|equinos cal|cai|ecvideu лошадь|лошади|лошадь caballo|caballos|equino häst|hästar|häst at|atlar|atçılık кінь|коні|конячий
bird|birds|poultry FALSE FALSE FALSE FALSE 鸟类|鸟类|家禽 ptáci|ptáci|drůbež fugl|fugle|fjerkræ vogel|vogels|pluimvee lintu|linnut|siipikarja oiseaux|oiseaux|volaille vogel|vögel|geflügel πουλιά|πουλιά|πουλερικά uccello|uccelli|pollame 鳥|鳥|家禽 fugl|fugler|fjørfe ptak|ptaki|drób aves|aves|aves de capoeira pasăre|păsări|păsări de curte птица|птицы|домашняя птица aves|aves|aves de corral fågel|fåglar|fjäderfä kuş|kuşlar|kümes hayvanları птах|птахів|птиця
swine|swines FALSE FALSE FALSE FALSE 猪|猪 prasata|prasata svin varken|varkens sika|sikaa porcine|porcs schwein|schweine χοίροι|χοίροι suino|suini 豚|豚|頭 svin trzoda chlewna|świnie suínos porc|porcine свинья|свиньи porcino|porcinos svin domuz|domuz свиня|свині
1 pattern regular_expr case_sensitive affect_ab_name affect_mo_name zh cs da nl fi fr de el it ja no pl pt ro ru es sv tr uk
278 Other antibacterials FALSE TRUE TRUE FALSE 其他抗菌剂 Ostatní antibakteriální látky Andre antibakterielle stoffer Overige antibiotica Muut antibakteeriset aineet Autres antibactériens Andere Antibiotika Άλλα αντιβακτηριακά Altri antibatterici その他の抗菌薬 Andre antibakterielle midler Inne środki przeciwbakteryjne Outros antibacterianos Alte antibacteriene Другие антибактериальные препараты Otros antibacterianos Andra antibakteriella medel Diğer antibakteriyeller Інші антибактеріальні засоби
279 Polymyxins FALSE TRUE TRUE FALSE 多粘菌素类 Polymyxiny Polymyxiner Polymyxines Polymysiinit Polymyxines Polymyxine Πολυμυξίνες Polimixine ポリミキシン Polymyxiner Polimyksyny Polimixinas Polimixine Полимиксины Polimixinas Polymyxiner Polimiksinler Поліміксини
280 Quinolones FALSE TRUE TRUE FALSE 喹诺酮类 Chinolony Kinoloner Quinolonen Kinolonit Quinolones Quinolone Κινολόνες Chinoloni キノロン Kinoloner Quinolony Quinolones Quinolone Хинолоны Quinolonas Kinoloner Kinolonlar Хінолони
281 aquatic|fish FALSE FALSE FALSE FALSE 水生|条鱼|鱼 vodní|ryba|ryby akvatisk|fisk aquatisch|vis|vissen vesieliö|kala|kalaa aquatique|poisson|poissons wasser|fisch|fische υδρόβια|ψάρι|ψάρια acquatico|pesce|pesci アクアティック|1匹|魚 akvatisk|fisk wodny|ryba|ryby aquático|peixe|peixes acvatic|pește|pești водные|рыба|рыбы acuático|pez|peces vattenlevande|fisk|fiskar sucul|balık водний|риба|рибки
282 cattle|bovine FALSE FALSE FALSE FALSE 牛|牛 skot kvæg vee|rund karja|nauta bovins|bovin rinder βοοειδή bovini|bovino 牛|ウシ storfe|storfe bydło|bydło bovinos|bovino bovine|bovine крупный рогатый скот|крупный рогатый скот bovino|bovino nötkreatur|nötkreatur sığır|büyükbaş hayvan велика рогата худоба|бичачий
283 cat|cats|feline FALSE FALSE FALSE FALSE 猫|猫|猫科动物 kočka|kočky|kočky kat|katte|kat kat|katten|katachtig kissa|kissat|kissa chat|chats|félin katze|katzen γάτα|γάτες|αιλουροειδή gatto|gatti|felino 猫|猫|ネコ katt kot|koty gato|gatos|felino pisică|pisici|felină кошка|кошки|кошка gato|gatos|felino katt|katter|kattdjur kedi|kediler|kedi кіт|коти|котячий
284 dog|dogs|canine FALSE FALSE FALSE FALSE 狗|狗|犬类 pes|psi|psí hund|hunde hond|honden koira|koirat|koira chien|canine hund|hunde|hund σκύλος|σκύλοι|σκύλος cane|cani|canino 犬|犬|イヌ hund pies|psy|pies cão|cães|canino câine|câini|canin собака|собаки|собака perro|perros|canino hund|hundar köpek|köpekler пес|собаки|собачий
285 horse|horses|equine FALSE FALSE FALSE FALSE 马|马|马 kůň|koně|koně hest|heste paard|paarden hevonen|hevoset|hevoset cheval|chevaux|équine pferd|pferde άλογο|άλογα|ιπποειδή cavallo|cavalli|equino 馬|馬|馬 hest koń|konie|koń cavalo|cavalos|equinos cal|cai|ecvideu лошадь|лошади|лошадь caballo|caballos|equino häst|hästar|häst at|atlar|atçılık кінь|коні|конячий
286 bird|birds|poultry FALSE FALSE FALSE FALSE 鸟类|鸟类|家禽 ptáci|ptáci|drůbež fugl|fugle|fjerkræ vogel|vogels|pluimvee lintu|linnut|siipikarja oiseaux|oiseaux|volaille vogel|vögel|geflügel πουλιά|πουλιά|πουλερικά uccello|uccelli|pollame 鳥|鳥|家禽 fugl|fugler|fjørfe ptak|ptaki|drób aves|aves|aves de capoeira pasăre|păsări|păsări de curte птица|птицы|домашняя птица aves|aves|aves de corral fågel|fåglar|fjäderfä kuş|kuşlar|kümes hayvanları птах|птахів|птиця
287 swine|swines FALSE FALSE FALSE FALSE 猪|猪 prasata|prasata svin varken|varkens sika|sikaa porcine|porcs schwein|schweine χοίροι|χοίροι suino|suini 豚|豚|頭 svin trzoda chlewna|świnie suínos porc|porcine свинья|свиньи porcino|porcinos svin domuz|domuz свиня|свині