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MO group fixes

This commit is contained in:
dr. M.S. (Matthijs) Berends 2023-07-12 15:04:48 +01:00
parent 9cf054903b
commit 0c46f61260
28 changed files with 1822 additions and 861 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.0.0.9037
Version: 2.0.0.9038
Date: 2023-07-11
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.0.0.9037
# AMR 2.0.0.9038
## New
* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations

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R/mo.R
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@ -482,13 +482,13 @@ as.mo <- function(x,
# group D - all enterococci
out[out %like_case% "^B_ENTRC(_|$)"] <- "B_STRPT_GRPD"
}
# group F - S. anginosus, incl. S. anginosus anginosus and S. anginosus whileyi
out[out %like_case% "^B_STRPT_ANGN(_|$)"] <- "B_STRPT_GRPF"
# group F - Milleri group == S. anginosus group, which incl. S. anginosus, S. constellatus, S. intermedius
out[out %like_case% "^B_STRPT_(ANGN|CNST|INTR)(_|$)"] <- "B_STRPT_GRPF"
# group G - S. dysgalactiae and S. canis (though dysgalactiae is also group C and will be matched there)
out[out %like_case% "^B_STRPT_(DYSG|CANS)(_|$)"] <- "B_STRPT_GRPG"
# group H - S. sanguinis
out[out %like_case% "^B_STRPT_SNGN(_|$)"] <- "B_STRPT_GRPH"
# group K - S. salivarius, incl. S. salivarius salivariuss and S. salivarius thermophilus
# group K - S. salivarius, incl. S. salivarius salivarius and S. salivarius thermophilus
out[out %like_case% "^B_STRPT_SLVR(_|$)"] <- "B_STRPT_GRPK"
# group L - only S. dysgalactiae which is also group C & G, so ignore it here
}

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data-raw/clin_break.md5
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data-raw/microorganisms.groups.txt
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@ -58,6 +58,13 @@
"B_BRKHL_CEPC-C" "B_BRKHL_VTNM" "Burkholderia cepacia complex" "Burkholderia vietnamiensis"
"F_CANDD_ALBC-C" "F_CANDD_AFRC" "Candida albicans complex" "Candida africana"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_ALBC" "Candida albicans complex" "Candida albicans albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_CLSS" "Candida albicans complex" "Candida albicans claussenii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_MTLN" "Candida albicans complex" "Candida albicans metalondinensis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_NNLQ" "Candida albicans complex" "Candida albicans non-liquefaciens"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_STLL" "Candida albicans complex" "Candida albicans stellatoidea"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_TRPC" "Candida albicans complex" "Candida albicans tropicalis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_VLLM" "Candida albicans complex" "Candida albicans vuilleminii"
"F_CANDD_ALBC-C" "F_CANDD_DBLN" "Candida albicans complex" "Candida dubliniensis"
"F_CANDD_GLBR-C" "F_CANDD_BRCR" "Candida glabrata complex" "Candida bracarensis"
"F_CANDD_GLBR-C" "F_CANDD_GLBR" "Candida glabrata complex" "Candida glabrata"
@ -65,6 +72,11 @@
"F_CANDD_PRPS-C" "F_CANDD_MTPS" "Candida parapsilosis complex" "Candida metapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_ORTH" "Candida parapsilosis complex" "Candida orthopsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_HOKK" "Candida parapsilosis complex" "Candida parapsilosis hokkaii"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_INTR" "Candida parapsilosis complex" "Candida parapsilosis intermedia"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_PRPS" "Candida parapsilosis complex" "Candida parapsilosis parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QURC" "Candida parapsilosis complex" "Candida parapsilosis querci"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QRCS" "Candida parapsilosis complex" "Candida parapsilosis quercus"
"P_CHLMS" "F_CANDD_DBSH" "Chilomastix" "Candida duobushaemulonii"
"P_CHLMS" "F_CANDD_HMLN" "Chilomastix" "Candida haemulonii"
"P_CHLMS" "B_CANDD_HMLN-C" "Chilomastix" "Candida haemulonii complex"
@ -137,6 +149,7 @@
"B_STPHY_CONS" "B_STPHY_SPRP_BOVS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus bovis"
"B_STPHY_CONS" "B_STPHY_SPRP_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi"
"B_STPHY_CONS" "B_STPHY_SCHL_CGLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_CONS" "B_STPHY_SCHL_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi schleiferi"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri"
"B_STPHY_CONS" "B_STPHY_SCIR_CRNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri carnaticus"
@ -184,6 +197,8 @@
"B_CORYNF" "B_CRYNB" "Coryneform bacterium" "Corynebacterium"
"B_CORYNF" "B_CRYNB_ACCL" "Coryneform bacterium" "Corynebacterium accolens"
"B_CORYNF" "B_CRYNB_AFRM" "Coryneform bacterium" "Corynebacterium afermentans"
"B_CORYNF" "B_CRYNB_AFRM_AFRM" "Coryneform bacterium" "Corynebacterium afermentans afermentans"
"B_CORYNF" "B_CRYNB_AFRM_LPPH" "Coryneform bacterium" "Corynebacterium afermentans lipophilum"
"B_CORYNF" "B_CRYNB_AMYC" "Coryneform bacterium" "Corynebacterium amycolatum"
"B_CORYNF" "B_CRYNB_ARGN" "Coryneform bacterium" "Corynebacterium argentoratense"
"B_CORYNF" "B_CRYNB_ARMC" "Coryneform bacterium" "Corynebacterium aurimucosum"
@ -192,6 +207,8 @@
"B_CORYNF" "B_CRYNB_COYL" "Coryneform bacterium" "Corynebacterium coyleae"
"B_CORYNF" "B_CRYNB_CYST" "Coryneform bacterium" "Corynebacterium cystitidis"
"B_CORYNF" "B_CRYNB_DPHT" "Coryneform bacterium" "Corynebacterium diphtheriae"
"B_CORYNF" "B_CRYNB_DPHT_DPHT" "Coryneform bacterium" "Corynebacterium diphtheriae diphtheriae"
"B_CORYNF" "B_CRYNB_DPHT_LSNN" "Coryneform bacterium" "Corynebacterium diphtheriae lausannense"
"B_CORYNF" "B_CRYNB_GLCR" "Coryneform bacterium" "Corynebacterium glucuronolyticum"
"B_CORYNF" "B_CRYNB_GLTM" "Coryneform bacterium" "Corynebacterium glutamicum"
"B_CORYNF" "B_CRYNB_JEKM" "Coryneform bacterium" "Corynebacterium jeikeium"
@ -231,8 +248,14 @@
"B_CORYNF" "B_TRCLL_OTTD" "Coryneform bacterium" "Turicella otitidis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_ASBR" "Enterobacter cloacae complex" "Enterobacter asburiae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae cloacae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC_DSSL" "Enterobacter cloacae complex" "Enterobacter cloacae dissolvens"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC" "Enterobacter cloacae complex" "Enterobacter hormaechei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_HFFM" "Enterobacter cloacae complex" "Enterobacter hormaechei hoffmannii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_HRMC" "Enterobacter cloacae complex" "Enterobacter hormaechei hormaechei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_OHAR" "Enterobacter cloacae complex" "Enterobacter hormaechei oharae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_STGR" "Enterobacter cloacae complex" "Enterobacter hormaechei steigerwaltii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_XNGF" "Enterobacter cloacae complex" "Enterobacter hormaechei xiangfangensis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_KOBE" "Enterobacter cloacae complex" "Enterobacter kobei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_LDWG" "Enterobacter cloacae complex" "Enterobacter ludwigii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_NMPR" "Enterobacter cloacae complex" "Enterobacter nimipressuralis"
@ -284,18 +307,30 @@
"F_MYRZY_GLLR-C" "F_MYRZY_CRBB" "Meyerozyma guilliermondii complex" "Meyerozyma caribbica"
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_JPNC" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii japonica"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_MUHR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii muhira"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_PSDG" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii pseudoguilliermondii"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_PRTB" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium paratuberculosis"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_SLVT" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium silvaticum"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_CHMR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare chimaera"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_INTR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_YNGN" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare yongonense"
"B_MYCBC_TBRC-C" "B_MYCBC_AFRC" "Mycobacterium tuberculosis complex" "Mycobacterium africanum"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium bovis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_MCRT" "Mycobacterium tuberculosis complex" "Mycobacterium microti"
"B_MYCBC_TBRC-C" "B_MYCBC_MUNG" "Mycobacterium tuberculosis complex" "Mycobacterium mungi"
"B_MYCBC_TBRC-C" "B_MYCBC_ORYG" "Mycobacterium tuberculosis complex" "Mycobacterium orygis"
"B_MYCBC_TBRC-C" "B_MYCBC_PNNP" "Mycobacterium tuberculosis complex" "Mycobacterium pinnipedii"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis tuberculosis"
"B_PSDMN_FLRS-C" "B_PSDMN_FLRS" "Pseudomonas fluorescens complex" "Pseudomonas fluorescens"
"B_MYCBC_RGM" "B_MYCBC_ABSC_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus abscessus"
"B_MYCBC_RGM" "B_MYCBC_ABSC_BLLT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus bolletii"
@ -318,6 +353,10 @@
"B_MYCBC_RGM" "B_MYCBC_CNRS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium canariasense"
"B_MYCBC_RGM" "B_MYCBC_CLRF" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium celeriflavum"
"B_MYCBC_RGM" "B_MYCBC_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae abscessus"
"B_MYCBC_RGM" "B_MYCBC_CHLN_BOVS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae bovis"
"B_MYCBC_RGM" "B_MYCBC_CHLN_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_GWNK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae gwanakae"
"B_MYCBC_RGM" "B_MYCBC_CHIT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chitae"
"B_MYCBC_RGM" "B_MYCBC_CHLR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chlorophenolicum"
"B_MYCBC_RGM" "B_MYCBC_CHBN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chubuense"
@ -331,6 +370,8 @@
"B_MYCBC_RGM" "B_MYCBC_FLVS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium flavescens"
"B_MYCBC_RGM" "B_MYCBC_VRNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fluoranthenivorans"
"B_MYCBC_RGM" "B_MYCBC_FRTT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fortuitum"
"B_MYCBC_RGM" "B_MYCBC_FRTT_ACTM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fortuitum acetamidolyticum"
"B_MYCBC_RGM" "B_MYCBC_FRTT_FRTT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fortuitum fortuitum"
"B_MYCBC_RGM" "B_MYCBC_FRNK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium franklinii"
"B_MYCBC_RGM" "B_MYCBC_FRDR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium frederiksbergense"
"B_MYCBC_RGM" "B_MYCBC_GADM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium gadium"
@ -391,6 +432,10 @@
"B_MYCBC_SGM" "B_MYCBC_MLMN" "Slowly growing Mycobacterium (SGM)" "Mycobacterium malmoense"
"B_MYCBC_SGM" "B_MYCBC_MRNM" "Slowly growing Mycobacterium (SGM)" "Mycobacterium marinum"
"B_STRPT_GRPA" "B_STRPT_PYGN" "Streptococcus Group A" "Streptococcus pyogenes"
"B_STRPT_ABCG" "B_STRPT_GRPA" "Streptococcus Group A, B, C, G" "Streptococcus Group A"
"B_STRPT_ABCG" "B_STRPT_GRPB" "Streptococcus Group A, B, C, G" "Streptococcus Group B"
"B_STRPT_ABCG" "B_STRPT_GRPC" "Streptococcus Group A, B, C, G" "Streptococcus Group C"
"B_STRPT_ABCG" "B_STRPT_GRPG" "Streptococcus Group A, B, C, G" "Streptococcus Group G"
"B_STRPT_ABCG" "B_STRPT_AGLC" "Streptococcus Group A, B, C, G" "Streptococcus agalactiae"
"B_STRPT_ABCG" "B_STRPT_CANS" "Streptococcus Group A, B, C, G" "Streptococcus canis"
"B_STRPT_ABCG" "B_STRPT_DYSG" "Streptococcus Group A, B, C, G" "Streptococcus dysgalactiae"
@ -412,6 +457,11 @@
"B_STRPT_GRPF" "B_STRPT_ANGN" "Streptococcus Group F" "Streptococcus anginosus"
"B_STRPT_GRPF" "B_STRPT_ANGN_ANGN" "Streptococcus Group F" "Streptococcus anginosus anginosus"
"B_STRPT_GRPF" "B_STRPT_ANGN_WHLY" "Streptococcus Group F" "Streptococcus anginosus whileyi"
"B_STRPT_GRPF" "B_STRPT_CNST" "Streptococcus Group F" "Streptococcus constellatus"
"B_STRPT_GRPF" "B_STRPT_CNST_CNST" "Streptococcus Group F" "Streptococcus constellatus constellatus"
"B_STRPT_GRPF" "B_STRPT_CNST_PHRY" "Streptococcus Group F" "Streptococcus constellatus pharyngis"
"B_STRPT_GRPF" "B_STRPT_CNST_VBRG" "Streptococcus Group F" "Streptococcus constellatus viborgensis"
"B_STRPT_GRPF" "B_STRPT_INTR" "Streptococcus Group F" "Streptococcus intermedius"
"B_STRPT_GRPG" "B_STRPT_CANS" "Streptococcus Group G" "Streptococcus canis"
"B_STRPT_GRPG" "B_STRPT_DYSG" "Streptococcus Group G" "Streptococcus dysgalactiae"
"B_STRPT_GRPG" "B_STRPT_DYSG_DYSG" "Streptococcus Group G" "Streptococcus dysgalactiae dysgalactiae"
@ -420,10 +470,18 @@
"B_STRPT_GRPK" "B_STRPT_SLVR" "Streptococcus Group K" "Streptococcus salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_SLVR" "Streptococcus Group K" "Streptococcus salivarius salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_THRM" "Streptococcus Group K" "Streptococcus salivarius thermophilus"
"B_STRPT_GRPL" "B_STRPT_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_EQSM" "Streptococcus Group L" "Streptococcus dysgalactiae equisimilis"
"B_STRPT_VIRI" "B_STRPT_MILL" "Viridans Group Streptococcus (VGS)" "Milleri Group Streptococcus (MGS)"
"B_STRPT_VIRI" "B_STRPT_ACDM" "Viridans Group Streptococcus (VGS)" "Streptococcus acidominimus"
"B_STRPT_VIRI" "B_STRPT_ANGN" "Viridans Group Streptococcus (VGS)" "Streptococcus anginosus"
"B_STRPT_VIRI" "B_STRPT_ANGN_ANGN" "Viridans Group Streptococcus (VGS)" "Streptococcus anginosus anginosus"
"B_STRPT_VIRI" "B_STRPT_ANGN_WHLY" "Viridans Group Streptococcus (VGS)" "Streptococcus anginosus whileyi"
"B_STRPT_VIRI" "B_STRPT_CNST" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus"
"B_STRPT_VIRI" "B_STRPT_CNST_CNST" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus constellatus"
"B_STRPT_VIRI" "B_STRPT_CNST_PHRY" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus pharyngis"
"B_STRPT_VIRI" "B_STRPT_CNST_VBRG" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus viborgensis"
"B_STRPT_VIRI" "B_STRPT_CRCT" "Viridans Group Streptococcus (VGS)" "Streptococcus criceti"
"B_STRPT_VIRI" "B_STRPT_CRST" "Viridans Group Streptococcus (VGS)" "Streptococcus cristatus"
"B_STRPT_VIRI" "B_STRPT_DOWN" "Viridans Group Streptococcus (VGS)" "Streptococcus downei"
@ -435,9 +493,14 @@
"B_STRPT_VIRI" "B_STRPT_MITS" "Viridans Group Streptococcus (VGS)" "Streptococcus mitis"
"B_STRPT_VIRI" "B_STRPT_MTNS" "Viridans Group Streptococcus (VGS)" "Streptococcus mutans"
"B_STRPT_VIRI" "B_STRPT_ORLS" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis"
"B_STRPT_VIRI" "B_STRPT_ORLS_DNTS" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis dentisani"
"B_STRPT_VIRI" "B_STRPT_ORLS_ORLS" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis oralis"
"B_STRPT_VIRI" "B_STRPT_ORLS_TGRN" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis tigurinus"
"B_STRPT_VIRI" "B_STRPT_PRSN" "Viridans Group Streptococcus (VGS)" "Streptococcus parasanguinis"
"B_STRPT_VIRI" "B_STRPT_RATT" "Viridans Group Streptococcus (VGS)" "Streptococcus ratti"
"B_STRPT_VIRI" "B_STRPT_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_THRM" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius thermophilus"
"B_STRPT_VIRI" "B_STRPT_SNGN" "Viridans Group Streptococcus (VGS)" "Streptococcus sanguinis"
"B_STRPT_VIRI" "B_STRPT_SBRN" "Viridans Group Streptococcus (VGS)" "Streptococcus sobrinus"
"B_STRPT_VIRI" "B_STRPT_SUIS" "Viridans Group Streptococcus (VGS)" "Streptococcus suis"

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data-raw/reproduction_of_clinical_breakpoints.R
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@ -297,8 +297,22 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- 2
breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 512
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G now includes all streptococci:
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STRPT" & clinical_breakpoints$ref_tbl %like% "strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
# 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$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
# Haemophilus same error (must only be H. influenzae)
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_HMPHL" & clinical_breakpoints$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
# EUCAST says that for H. parainfluenzae the H. influenza rules can be used, so add them
clinical_breakpoints <- clinical_breakpoints %>%
bind_rows(
clinical_breakpoints %>%
filter(guideline %like% "EUCAST", mo == "B_HMPHL_INFL") %>%
mutate(mo = as.mo("B_HMPHL_PRNF"))
) %>%
arrange(desc(guideline), mo, ab, type, 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"))
# 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"))
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
# EUCAST 2022 guideline: S <= 8 and R > 8

32
data-raw/reproduction_of_microorganisms.groups.R
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@ -66,7 +66,7 @@ whonet_organisms %>%
group_by(SPECIES_GROUP) %>%
summarise(complex = ORGANISM[ORGANISM %like% " (group|complex)"][1],
organisms = paste0(n(), ": ", paste(sort(unique(ORGANISM)), collapse = ", "))) %>%
filter(!SPECIES_GROUP %in% AMR::microorganisms.codes$code)
filter(!SPECIES_GROUP %in% microorganisms.codes$code)
# create the species group data set ----
microorganisms.groups <- whonet_organisms %>%
@ -98,9 +98,9 @@ microorganisms.groups <- whonet_organisms %>%
# group C - all subspecies within S. dysgalactiae and S. equi (such as S. equi zooepidemicus)
bind_rows(tibble(mo_group = as.mo("Streptococcus Group C"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(DYSG|EQUI)(_|$)")])) %>%
# group F - S. anginosus, incl. S. anginosus anginosus and S. anginosus whileyi
# group F - Milleri group == S. anginosus group, which incl. S. anginosus, S. constellatus, S. intermedius
bind_rows(tibble(mo_group = as.mo("Streptococcus Group F"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_ANGN(_|$)")])) %>%
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(ANGN|CNST|INTR)(_|$)")])) %>%
# group G - S. dysgalactiae and S. canis (though dysgalactiae is also group C and will be matched there)
bind_rows(tibble(mo_group = as.mo("Streptococcus Group G"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(DYSG|CANS)(_|$)")])) %>%
@ -110,6 +110,9 @@ microorganisms.groups <- whonet_organisms %>%
# group K - S. salivarius, incl. S. salivarius salivariuss and S. salivarius thermophilus
bind_rows(tibble(mo_group = as.mo("Streptococcus Group K"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_SLVR(_|$)")])) %>%
# group L - only S. dysgalactiae
bind_rows(tibble(mo_group = as.mo("Streptococcus Group L"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_DYSG(_|$)")])) %>%
# and for EUCAST: Strep group A, B, C, G
bind_rows(tibble(mo_group = as.mo("Streptococcus Group A, B, C, G"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(PYGN|AGLC|DYSG|EQUI|CANS|GRPA|GRPB|GRPC|GRPG)(_|$)")])) %>%
@ -131,8 +134,24 @@ microorganisms.groups <- whonet_organisms %>%
# RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
filter(mo_group != "B_MYCBC_RGM") %>%
bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE))) %>%
# add full names
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE)))
# add subspecies to all species
for (group in unique(microorganisms.groups$mo_group)) {
spp <- microorganisms.groups %>%
filter(mo_group == group & mo_rank(mo, keep_synonyms = TRUE) == "species") %>%
pull(mo) %>%
paste0(collapse = "|") %>%
paste0("^(", ., ")")
mos <- microorganisms %>%
filter(mo %like% spp & rank == "subspecies") %>%
pull(mo)
# add them
microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = group, mo = mos))
}
# add full names, arrange and clean
microorganisms.groups <- microorganisms.groups %>%
mutate(mo_group_name = mo_name(mo_group, keep_synonyms = TRUE, language = NULL),
mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
arrange(mo_group_name, mo_name) %>%
@ -141,6 +160,9 @@ microorganisms.groups <- whonet_organisms %>%
dataset_UTF8_to_ASCII()
mo_uncertainties()
# add subspecies to all species
class(microorganisms.groups$mo_group) <- c("mo", "character")
class(microorganisms.groups$mo) <- c("mo", "character")
usethis::use_data(microorganisms.groups, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)

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2
man/as.sir.Rd
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@ -171,7 +171,7 @@ After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Clinical Breakpoints}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 28 885 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 29 747 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
}
\subsection{Other}{

2
man/clinical_breakpoints.Rd
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@ -5,7 +5,7 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 28 885 observations and 12 variables:
A \link[tibble:tibble]{tibble} with 29 747 observations and 12 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"

4
man/microorganisms.groups.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms.groups}
\alias{microorganisms.groups}
\title{Data Set with 448 Microorganisms In Species Groups}
\title{Data Set with 507 Microorganisms In Species Groups}
\format{
A \link[tibble:tibble]{tibble} with 448 observations and 4 variables:
A \link[tibble:tibble]{tibble} with 507 observations and 4 variables:
\itemize{
\item \code{mo_group}\cr ID of the species group / microbiological complex
\item \code{mo}\cr ID of the microorganism belonging in the species group / microbiological complex