(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex

data-raw/_pre_commit_checks.R

@@ -448,6 +448,9 @@ pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pr
 pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>%
   filter(group %like% "trimethoprim") %>%
   pull(ab)
+pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>%
+  filter(group %like% "trimethoprim" & name %unlike% "trimethoprim") %>%
+  pull(ab)
 pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
 pre_commit_lst$AB_BETALACTAMS <- sort(c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS, pre_commit_lst$AB_MONOBACTAMS))
 pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%

data-raw/eucast_rules.tsv

@@ -2,7 +2,7 @@
 # For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
 # aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, betalactams_with_inhibitor, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
 # and all separate EARS-Net letter codes such as AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
-# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or 'genus_species' or 'gramstain'.
+# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or 'genus_species' or 'gramstain'. If 'this_value' exists in AMR::microorganisms.groups$mo_group_name it will be expanded in eucast_rules() to all relevant species occuring in microorganisms.groups$mo_name before further processing of the line in this file.
 # The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
 # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 and later
 # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 9 LINES SKIPPED <<<<<
@@ -302,11 +302,11 @@ genus_species	is	Streptococcus pneumoniae	ERY	S	"AZM, CLR, RXT"	S	Streptococcus
 genus_species	is	Streptococcus pneumoniae	ERY	R	"AZM, CLR, RXT"	R	Streptococcus pneumoniae	Breakpoints	12	
 genus_species	is	Streptococcus pneumoniae	TCY-S	S	"DOX, MNO"	S	Streptococcus pneumoniae	Breakpoints	12	
 genus_species	is	Streptococcus pneumoniae	TCY-S	R	"DOX, MNO"	R	Streptococcus pneumoniae	Breakpoints	12	
-genus_species	one_of	"Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis"	PEN-S	S	"AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP"	S	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
-genus_species	one_of	"Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis"	PEN-S	R	"AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP"	R	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
-genus_species	one_of	"Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis"	AMP	S	"AMX, AMC, SAM, PIP, TZP"	S	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
-genus_species	one_of	"Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis"	AMP	I	"AMX, AMC, SAM, PIP, TZP"	I	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
-genus_species	one_of	"Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis"	AMP	R	"AMX, AMC, SAM, PIP, TZP"	R	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
+genus_species	one_of	"Viridans Group Streptococcus (VGS)"	PEN-S	S	"AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP"	S	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
+genus_species	one_of	"Viridans Group Streptococcus (VGS)"	PEN-S	R	"AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP"	R	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
+genus_species	one_of	"Viridans Group Streptococcus (VGS)"	AMP	S	"AMX, AMC, SAM, PIP, TZP"	S	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
+genus_species	one_of	"Viridans Group Streptococcus (VGS)"	AMP	I	"AMX, AMC, SAM, PIP, TZP"	I	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
+genus_species	one_of	"Viridans Group Streptococcus (VGS)"	AMP	R	"AMX, AMC, SAM, PIP, TZP"	R	Viridans group streptococci	Breakpoints	12	"paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
 genus_species	is	Haemophilus influenzae	PEN-S	S	"AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP"	S	Haemophilus influenzae	Breakpoints	12	"x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2022"" & clinical_breakpoints$mo == as.mo(""H. influenzae""))]), ""IMR"", ""MEV""); sort(x[x %in% betalactams()])"
 genus_species	is	Haemophilus influenzae	"PEN-S, BLA-S"	"R, R"	"AMP, AMX, PIP"	R	Haemophilus influenzae	Breakpoints	12	
 genus_species	is	Haemophilus influenzae	AMC	S	SAM	S	Haemophilus influenzae	Breakpoints	12	
@@ -487,11 +487,11 @@ genus_species	is	Streptococcus pneumoniae	ERY	S	AZM, CLR, RXT	S	Streptococcus pn
 genus_species	is	Streptococcus pneumoniae	ERY	R	AZM, CLR, RXT	R	Streptococcus pneumoniae	Breakpoints	13.1	
 genus_species	is	Streptococcus pneumoniae	TCY-S	S	DOX, MNO	S	Streptococcus pneumoniae	Breakpoints	13.1	
 genus_species	is	Streptococcus pneumoniae	TCY-S	R	DOX, MNO	R	Streptococcus pneumoniae	Breakpoints	13.1	
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	PEN-S	S	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	S	Viridans group streptococci	Breakpoints	13.1	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	PEN-S	R	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	R	Viridans group streptococci	Breakpoints	13.1	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	AMP	S	AMX, AMC, SAM, PIP, TZP	S	Viridans group streptococci	Breakpoints	13.1	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	AMP	I	AMX, AMC, SAM, PIP, TZP	I	Viridans group streptococci	Breakpoints	13.1	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	AMP	R	AMX, AMC, SAM, PIP, TZP	R	Viridans group streptococci	Breakpoints	13.1	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
+genus_species	one_of	Viridans Group Streptococcus (VGS)	PEN-S	S	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	S	Viridans group streptococci	Breakpoints	13.1	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	PEN-S	R	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	R	Viridans group streptococci	Breakpoints	13.1	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	AMP	S	AMX, AMC, SAM, PIP, TZP	S	Viridans group streptococci	Breakpoints	13.1	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	AMP	I	AMX, AMC, SAM, PIP, TZP	I	Viridans group streptococci	Breakpoints	13.1	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	AMP	R	AMX, AMC, SAM, PIP, TZP	R	Viridans group streptococci	Breakpoints	13.1	will be expanded in eucast_rules()
 genus_species	is	Haemophilus influenzae	PEN-S	S	AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP	S	Haemophilus influenzae	Breakpoints	13.1	x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
 genus_species	is	Haemophilus influenzae	PEN-S, BLA-S	R, R	AMP, AMX, PIP	R	Haemophilus influenzae	Breakpoints	13.1	
 genus_species	is	Haemophilus influenzae	AMC	S	SAM	S	Haemophilus influenzae	Breakpoints	13.1	
@@ -673,11 +673,11 @@ genus_species	is	Streptococcus pneumoniae	ERY	S	AZM, CLR, RXT	S	Streptococcus pn
 genus_species	is	Streptococcus pneumoniae	ERY	R	AZM, CLR, RXT	R	Streptococcus pneumoniae	Breakpoints	14	
 genus_species	is	Streptococcus pneumoniae	TCY-S	S	DOX, MNO	S	Streptococcus pneumoniae	Breakpoints	14	
 genus_species	is	Streptococcus pneumoniae	TCY-S	R	DOX, MNO	R	Streptococcus pneumoniae	Breakpoints	14	
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	PEN-S	S	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	S	Viridans group streptococci	Breakpoints	14	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	PEN-S	R	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	R	Viridans group streptococci	Breakpoints	14	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	AMP	S	AMX, AMC, SAM, PIP, TZP	S	Viridans group streptococci	Breakpoints	14	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	AMP	I	AMX, AMC, SAM, PIP, TZP	I	Viridans group streptococci	Breakpoints	14	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
-genus_species	one_of	Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis	AMP	R	AMX, AMC, SAM, PIP, TZP	R	Viridans group streptococci	Breakpoints	14	paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
+genus_species	one_of	Viridans Group Streptococcus (VGS)	PEN-S	S	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	S	Viridans group streptococci	Breakpoints	14	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	PEN-S	R	AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP	R	Viridans group streptococci	Breakpoints	14	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	AMP	S	AMX, AMC, SAM, PIP, TZP	S	Viridans group streptococci	Breakpoints	14	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	AMP	I	AMX, AMC, SAM, PIP, TZP	I	Viridans group streptococci	Breakpoints	14	will be expanded in eucast_rules()
+genus_species	one_of	Viridans Group Streptococcus (VGS)	AMP	R	AMX, AMC, SAM, PIP, TZP	R	Viridans group streptococci	Breakpoints	14	will be expanded in eucast_rules()
 genus_species	is	Haemophilus influenzae	PEN-S	S	AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP	S	Haemophilus influenzae	Breakpoints	14	x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
 genus_species	is	Haemophilus influenzae	PEN-S, BLA-S	R, R	AMP, AMX, PIP	R	Haemophilus influenzae	Breakpoints	14	
 genus_species	is	Haemophilus influenzae	AMC	S	SAM	S	Haemophilus influenzae	Breakpoints	14	
@@ -783,6 +783,92 @@ genus_species	is	Brucella melitensis	TCY-S	S	DOX	S	Brucella melitensis	Breakpoin
 genus_species	is	Brucella melitensis	TCY-S	R	DOX	R	Brucella melitensis	Breakpoints	14	
 genus_species	is	Burkholderia pseudomallei	TCY-S	S	DOX	I	Burkholderia pseudomallei	Breakpoints	14	
 genus_species	is	Burkholderia pseudomallei	TCY-S	R	DOX	R	Burkholderia pseudomallei	Breakpoints	14	
+
+
+
+
+
+genus_species	one_of	Citrobacter koseri, Citrobacter amalonaticus			AMP, AMX, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Citrobacter freundii			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	one_of	Enterobacter cloacae complex 			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Escherichia hermannii 			AMP, AMX, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Hafnia alvei 			AMP, AMX, PLB, COL	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Klebsiella aerogenes 			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	one_of	Klebsiella pneumoniae complex			AMX, AMP, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Klebsiella oxytoca			AMX, AMP, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Leclercia adecarboxylata			FOS	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Morganella morganii 			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Plesiomonas shigelloides 			AMX, AMP, SAM	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Proteus mirabilis 			tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Proteus penneri 			AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Proteus vulgaris 			AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Providencia rettgeri 			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Providencia stuartii			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus	is	Raoultella			AMP, AMX, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Serratia marcescens			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Yersinia enterocolitica			AMP, AMX, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Yersinia pseudotuberculosis			PLB, COL	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas hydrophila			AMP, AMX, SAM	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas veronii			AMP, AMX, SAM, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas dhakensis			AMP, AMX, SAM, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas caviae			AMP, AMX, SAM	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas jandaei			AMP, AMX, SAM, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+order	is	Enterobacterales			PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	one_of	Citrobacter koseri, Citrobacter amalonaticus			AMP, AMX, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Citrobacter freundii			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	one_of	Enterobacter cloacae complex			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Escherichia hermannii			AMP, AMX, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Hafnia alvei			AMP, AMX, PLB, COL	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Klebsiella aerogenes 			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	one_of	Klebsiella pneumoniae complex			AMX, AMP, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Klebsiella oxytoca			AMX, AMP, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Leclercia adecarboxylata			FOS	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Morganella morganii 			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Plesiomonas shigelloides 			AMX, AMP, SAM	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Proteus mirabilis 			tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Proteus penneri 			AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Proteus vulgaris 			AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Providencia rettgeri 			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Providencia stuartii			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus	is	Raoultella			AMP, AMX, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Serratia marcescens			AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, PLB, COL, NIT	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Yersinia enterocolitica			AMP, AMX, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Yersinia pseudotuberculosis			PLB, COL	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas hydrophila			AMP, AMX, SAM	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas veronii			AMP, AMX, SAM, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas dhakensis			AMP, AMX, SAM, FOX	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas caviae			AMP, AMX, SAM	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus_species	is	Aeromonas jandaei			AMP, AMX, SAM, TIC	R	Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp.	Expected phenotypes	1.2	
+genus	one_of	Acinetobacter, Achromobacter, Burkholderia, Elizabethkingia, Elizabethkingia, Ochrobactrum, Pseudomonas, Stenotrophomonas, Chryseobacterium			PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	one_of	Acinetobacter baumannii, Acinetobacter pittii, Acinetobacter nosocomialis			AMP, AMX, AMC, CTX, CRO, ATM, ETP, TMP, FOS, TCY, DOX	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Achromobacter xylosoxidans			AMP, AMX, CTX, CRO, ATM, ETP	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	one_of	Burkholderia cepacia complex			AMP, AMX, AMC, SAM, TIC, TCC, PIP, TZP, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, PLB, COL	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Elizabethkingia meningoseptica			AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, PLB, COL	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Elizabethkingia anophelis			AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Ochrobactrum anthropi			AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Pseudomonas aeruginosa			AMP, AMX, AMC, SAM, CTX, CRO, ETP, CHL, TMP, KAN, NEO, tetracyclines, TGC	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Stenotrophomonas maltophilia			AMP, AMX, AMC, SAM, TIC, PIP, TZP, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus	is	Chryseobacterium			AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, PLB, COL	R	Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Haemophilus influenzae			FUS, streptogramins	R	Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Moraxella catarrhalis R			TMP	R	Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus	is	Neisseria			TMP	R	Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Campylobacter fetus			FUS, streptogramins, TMP, NAL	R	Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	one_of	Campylobacter jejuni, Campylobacter coli 			FUS, streptogramins, TMP	R	Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria	Expected phenotypes	1.2	
+genus_species	is	Staphylococcus saprophyticus			FUS, CAZ, FOS, NOV	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	is	Staphylococcus cohnii			CAZ, NOV	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	is	Staphylococcus xylosus			CAZ, NOV	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	is	Staphylococcus capitis			CAZ, FOS	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	one_of	Coagulase-negative Staphylococcus (CoNS), Staphylococcus aureus			CAZ	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus	is	Streptococcus			FUS, CAZ, aminoglycosides	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	is	Enterococcus faecalis			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, sulfonamides	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	one_of	Enterococcus gallinarum, Enterococcus casseliflavus			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, sulfonamides	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	is	Enterococcus faecium			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, sulfonamides	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus	is	Corynebacterium			FOS	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	is	Listeria monocytogenes			CAZ, cephalosporins_except_CAZ	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus	one_of	Leuconostoc, Pediococcus			VAN, FOS	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	is	Lactobacillus casei			VAN, FOS	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+fullname	is	Lactobacillus casei rhamnosus			VAN, FOS	R	Table 4: Expected resistant phenotype in gram-positive bacteria	Expected phenotypes	1.2	
+genus_species	one_of	Clostridium ramosum, Clostridium innocuum			VAN	R	Table 5: Expected resistant phenotype in anaerobes	Expected phenotypes	1.2	
 order	is	Enterobacterales			PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ	R	Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae)	Expert Rules	3.1	
 fullname	like	^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)			aminopenicillins, TIC	R	Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae)	Expert Rules	3.1	
 fullname	like	^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)			aminopenicillins, AMC, CZO, FOX	R	Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae)	Expert Rules	3.1	
@@ -958,7 +1044,7 @@ genus_species	is	Streptococcus pneumoniae	MFX	R	fluoroquinolones	R	Expert Rules
 genus_species	is	Streptococcus pneumoniae	TCY	S	DOX, MNO	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.2	
 genus_species	is	Streptococcus pneumoniae	TCY	R	DOX, MNO	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.2	
 genus_species	is	Streptococcus pneumoniae	VAN	S	lipoglycopeptides	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.2	
-fullname	like	^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$	PEN	S	aminopenicillins, CTX, CRO	S	Expert Rules on Viridans Group Streptococci	Expert Rules	3.2	
+genus_species	one_of	Viridans Group Streptococcus (VGS)	PEN	S	aminopenicillins, CTX, CRO	S	Expert Rules on Viridans Group Streptococci	Expert Rules	3.2	
 genus_species	is	Haemophilus influenzae	PEN	S	betalactams	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.2	
 genus_species	is	Haemophilus influenzae	NAL	S	fluoroquinolones	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.2	
 genus_species	is	Haemophilus influenzae	NAL	R	CIP, LVX, MFX	R	Expert Rules on Haemophilus influenzae	Expert Rules	3.2	
@@ -1076,7 +1162,7 @@ genus_species	is	Streptococcus pneumoniae	MFX	R	fluoroquinolones	R	Expert Rules
 genus_species	is	Streptococcus pneumoniae	TCY	S	DOX, MNO	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
 genus_species	is	Streptococcus pneumoniae	TCY	R	DOX, MNO	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
 genus_species	is	Streptococcus pneumoniae	VAN	S	lipoglycopeptides	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
-fullname	like	^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$	PEN	S	aminopenicillins, CTX, CRO	S	Expert Rules on Viridans Group Streptococci	Expert Rules	3.3	
+genus_species	one_of	Viridans Group Streptococcus (VGS)	PEN	S	aminopenicillins, CTX, CRO	S	Expert Rules on Viridans Group Streptococci	Expert Rules	3.3	
 genus_species	is	Haemophilus influenzae	PEN	S	betalactams	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
 genus_species	is	Haemophilus influenzae	NAL	S	fluoroquinolones	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
 genus_species	is	Haemophilus influenzae	NAL	R	CIP, LVX, MFX	R	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	

data-raw/intrinsicR.md5

@@ -1 +1 @@
-930e15623071edb2196fcf8b2a259380
+cb89a8b02473f40365a46e62fce5ec93

data-raw/intrinsic_resistant.txt

@@ -12182,21 +12182,21 @@
 "Aestuariimicrobium"	"Nalidixic acid"
 "Aestuariimicrobium"	"Polymyxin B"
 "Aestuariimicrobium"	"Temocillin"
-"Aestuariimicrobium ganziense"	"Aztreonam"
-"Aestuariimicrobium ganziense"	"Colistin"
-"Aestuariimicrobium ganziense"	"Nalidixic acid"
-"Aestuariimicrobium ganziense"	"Polymyxin B"
-"Aestuariimicrobium ganziense"	"Temocillin"
-"Aestuariimicrobium kwangyangense"	"Aztreonam"
-"Aestuariimicrobium kwangyangense"	"Colistin"
-"Aestuariimicrobium kwangyangense"	"Nalidixic acid"
-"Aestuariimicrobium kwangyangense"	"Polymyxin B"
-"Aestuariimicrobium kwangyangense"	"Temocillin"
-"Aestuariimicrobium soli"	"Aztreonam"
-"Aestuariimicrobium soli"	"Colistin"
-"Aestuariimicrobium soli"	"Nalidixic acid"
-"Aestuariimicrobium soli"	"Polymyxin B"
-"Aestuariimicrobium soli"	"Temocillin"
+	"Aztreonam"
+	"Colistin"
+	"Nalidixic acid"
+	"Polymyxin B"
+	"Temocillin"
+	"Aztreonam"
+	"Colistin"
+	"Nalidixic acid"
+	"Polymyxin B"
+	"Temocillin"
+	"Aztreonam"
+	"Colistin"
+	"Nalidixic acid"
+	"Polymyxin B"
+	"Temocillin"
 "Affinibrenneria"	"Acetylmidecamycin"
 "Affinibrenneria"	"Acetylspiramycin"
 "Affinibrenneria"	"Avoparcin"
@@ -89868,20 +89868,20 @@
 "Liquorilactobacillus capillatus"	"Nalidixic acid"
 "Liquorilactobacillus capillatus"	"Polymyxin B"
 "Liquorilactobacillus capillatus"	"Temocillin"
-"Lactobacillus casei pseudoplantarum"	"Aztreonam"
-"Lactobacillus casei pseudoplantarum"	"Colistin"
-"Lactobacillus casei pseudoplantarum"	"Nalidixic acid"
-"Lactobacillus casei pseudoplantarum"	"Polymyxin B"
-"Lactobacillus casei pseudoplantarum"	"Teicoplanin"
-"Lactobacillus casei pseudoplantarum"	"Temocillin"
-"Lactobacillus casei pseudoplantarum"	"Vancomycin"
-"Lactobacillus casei casei"	"Aztreonam"
-"Lactobacillus casei casei"	"Colistin"
-"Lactobacillus casei casei"	"Nalidixic acid"
-"Lactobacillus casei casei"	"Polymyxin B"
-"Lactobacillus casei casei"	"Teicoplanin"
-"Lactobacillus casei casei"	"Temocillin"
-"Lactobacillus casei casei"	"Vancomycin"
+	"Aztreonam"
+	"Colistin"
+	"Nalidixic acid"
+	"Polymyxin B"
+	"Teicoplanin"
+	"Temocillin"
+	"Vancomycin"
+	"Aztreonam"
+	"Colistin"
+	"Nalidixic acid"
+	"Polymyxin B"
+	"Teicoplanin"
+	"Temocillin"
+	"Vancomycin"
 "Limosilactobacillus caviae"	"Aztreonam"
 "Limosilactobacillus caviae"	"Colistin"
 "Limosilactobacillus caviae"	"Nalidixic acid"
@@ -293754,16 +293754,16 @@
 "Streptosporangium yunnanense"	"Nalidixic acid"
 "Streptosporangium yunnanense"	"Polymyxin B"
 "Streptosporangium yunnanense"	"Temocillin"
-"Streptoverticillium cinnamoneum lanosum"	"Aztreonam"
-"Streptoverticillium cinnamoneum lanosum"	"Colistin"
-"Streptoverticillium cinnamoneum lanosum"	"Nalidixic acid"
-"Streptoverticillium cinnamoneum lanosum"	"Polymyxin B"
-"Streptoverticillium cinnamoneum lanosum"	"Temocillin"
-"Streptoverticillium cinnamoneum sparsum"	"Aztreonam"
-"Streptoverticillium cinnamoneum sparsum"	"Colistin"
-"Streptoverticillium cinnamoneum sparsum"	"Nalidixic acid"
-"Streptoverticillium cinnamoneum sparsum"	"Polymyxin B"
-"Streptoverticillium cinnamoneum sparsum"	"Temocillin"
+	"Aztreonam"
+	"Colistin"
+	"Nalidixic acid"
+	"Polymyxin B"
+	"Temocillin"
+	"Aztreonam"
+	"Colistin"
+	"Nalidixic acid"
+	"Polymyxin B"
+	"Temocillin"
 "Streptoverticillium olivoreticuli olivoreticuli"	"Aztreonam"
 "Streptoverticillium olivoreticuli olivoreticuli"	"Colistin"
 "Streptoverticillium olivoreticuli olivoreticuli"	"Nalidixic acid"

data-raw/microorganisms.groups.md5

@@ -1 +1 @@
-a16b8db2140952b8a5848989afdccb53
+dfdbbebfe1a542270d63b94c12889860

data-raw/microorganisms.groups.txt

@@ -311,6 +311,19 @@
 "B_HACEK"	"B_KGLLA_ORLS"	"Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)"	"Kingella orale"
 "B_HACEK"	"B_KGLLA_ORLS"	"Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)"	"Kingella oralis"
 "B_HACEK"	"B_KGLLA_POTS"	"Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)"	"Kingella potus"
+"B_KLBSL_PNMN-C"	"B_KLBSL_AFRC"	"Klebsiella pneumoniae complex"	"Klebsiella africana"
+"B_KLBSL_PNMN-C"	"B_KLBSL_PNMN"	"Klebsiella pneumoniae complex"	"Klebsiella pneumoniae"
+"B_KLBSL_PNMN-C"	"B_KLBSL_PNMN_OZAN"	"Klebsiella pneumoniae complex"	"Klebsiella pneumoniae ozaenae"
+"B_KLBSL_PNMN-C"	"B_KLBSL_PNMN_PNMN"	"Klebsiella pneumoniae complex"	"Klebsiella pneumoniae pneumoniae"
+"B_KLBSL_PNMN-C"	"B_KLBSL_PNMN_RHNS"	"Klebsiella pneumoniae complex"	"Klebsiella pneumoniae rhinoscleromatis"
+"B_KLBSL_PNMN-C"	"B_KLBSL_QSPN"	"Klebsiella pneumoniae complex"	"Klebsiella quasipneumoniae"
+"B_KLBSL_PNMN-C"	"B_KLBSL_QSPN_QSPN"	"Klebsiella pneumoniae complex"	"Klebsiella quasipneumoniae quasipneumoniae"
+"B_KLBSL_PNMN-C"	"B_KLBSL_QSPN_SMLP"	"Klebsiella pneumoniae complex"	"Klebsiella quasipneumoniae similipneumoniae"
+"B_KLBSL_PNMN-C"	"B_KLBSL_QSVR"	"Klebsiella pneumoniae complex"	"Klebsiella quasivariicola"
+"B_KLBSL_PNMN-C"	"B_KLBSL_VRCL"	"Klebsiella pneumoniae complex"	"Klebsiella variicola"
+"B_KLBSL_PNMN-C"	"B_KLBSL_VRCL_TRPC"	"Klebsiella pneumoniae complex"	"Klebsiella variicola tropica"
+"B_KLBSL_PNMN-C"	"B_KLBSL_VRCL_LNSS"	"Klebsiella pneumoniae complex"	"Klebsiella variicola tropicalensis"
+"B_KLBSL_PNMN-C"	"B_KLBSL_VRCL_VRCL"	"Klebsiella pneumoniae complex"	"Klebsiella variicola variicola"
 "F_MYRZY_GLLR-C"	"F_CANDD_FRMN"	"Meyerozyma guilliermondii complex"	"Candida fermentati"
 "F_MYRZY_GLLR-C"	"F_MYRZY_CRBB"	"Meyerozyma guilliermondii complex"	"Meyerozyma caribbica"
 "F_MYRZY_GLLR-C"	"F_MYRZY_CRPP"	"Meyerozyma guilliermondii complex"	"Meyerozyma carpophila"

data-raw/microorganisms.md5

@@ -1 +1 @@
-9c53db03dcf9c98ef571fcc6c16d0a68
+5908f9e6e7687dfb8301d27fb26d1790

data-raw/microorganisms.txt

@@ -1831,11 +1831,11 @@
 "B_AESTR_LTRL"	"Aestuariibacter litoralis"	"synonym"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Alteromonadales"	"Alteromonadaceae"	"Aestuariibacter"	"litoralis"	""	"species"	"Tanaka et al., 2010"	"aerobe"	"LPSN"	"788348"	"515053"	"791011"					"3222678"		2	""
 "B_AESTR_SLXG"	"Aestuariibacter salexigens"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Alteromonadales"	"Alteromonadaceae"	"Aestuariibacter"	"salexigens"	""	"species"	"Yi et al., 2004"	"aerobe"	"LPSN"	"772927"	"515053"						"3222678"		2	"426337003"
 "B_RBCLM1"	"Aestuariibaculum"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	""	""	"genus"	"Hameed et al., 2014"	"aerobe"	"LPSN"	"518286"	"524"					"8124539"	"4898201"		2	""
-"B_RBCLM1_B_RBCLM1_LTLN"	"Aestuariibaculum lutulentum"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"lutulentum"	""	"species"	"Gao et al., 2024"	"aerobe"	"LPSN"	"43727"	"518286"						"8124539"		2	""
-"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_MRNM"	"Aestuariibaculum marinum"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"marinum"	""	"species"	"Choi et al., 2019"	"aerobe"	"LPSN"	"798029"	"518286"					"11167655"	"8124539"		2	""
-"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_SCPM"	"Aestuariibaculum scopimerae"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"scopimerae"	""	"species"	"Lee et al., 2021"	"aerobe"	"LPSN"	"18922"	"518286"						"8124539"		2	""
-"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_SDMN"	"Aestuariibaculum sediminum"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"sediminum"	""	"species"	"Wu et al., 2022"	"aerobe"	"LPSN"	"28837"	"518286"					"11894177"	"8124539"		2	""
-"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_SNCH"	"Aestuariibaculum suncheonense"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"suncheonense"	""	"species"	"Jeong et al., 2013"	"aerobe"	"LPSN"	"790362"	"518286"					"7885799"	"8124539"		2	""
+"B_RBCLM1_LTLN"	"Aestuariibaculum lutulentum"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"lutulentum"	""	"species"	"Gao et al., 2024"	"aerobe"	"LPSN"	"43727"	"518286"						"8124539"		2	""
+"B_RBCLM1_MRNM"	"Aestuariibaculum marinum"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"marinum"	""	"species"	"Choi et al., 2019"	"aerobe"	"LPSN"	"798029"	"518286"					"11167655"	"8124539"		2	""
+"B_RBCLM1_SCPM"	"Aestuariibaculum scopimerae"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"scopimerae"	""	"species"	"Lee et al., 2021"	"aerobe"	"LPSN"	"18922"	"518286"						"8124539"		2	""
+"B_RBCLM1_SDMN"	"Aestuariibaculum sediminum"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"sediminum"	""	"species"	"Wu et al., 2022"	"aerobe"	"LPSN"	"28837"	"518286"					"11894177"	"8124539"		2	""
+"B_RBCLM1_SNCH"	"Aestuariibaculum suncheonense"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariibaculum"	"suncheonense"	""	"species"	"Jeong et al., 2013"	"aerobe"	"LPSN"	"790362"	"518286"					"7885799"	"8124539"		2	""
 "B_STRBS"	"Aestuariibius"	"accepted"	"Bacteria"	"Pseudomonadota"	"Alphaproteobacteria"	"Rhodobacterales"	"Roseobacteraceae"	"Aestuariibius"	""	""	"genus"	"Park et al., 2018"		"LPSN"	"520366"	"11172"								2	""
 "B_STRBS_INSL"	"Aestuariibius insulae"	"accepted"	"Bacteria"	"Pseudomonadota"	"Alphaproteobacteria"	"Rhodobacterales"	"Roseobacteraceae"	"Aestuariibius"	"insulae"	""	"species"	"Park et al., 2018"		"LPSN"	"797657"	"520366"								2	""
 "B_AESTRC"	"Aestuariicella"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Alteromonadales"	""	"Aestuariicella"	""	""	"genus"	"Xue et al., 2022"		"LPSN"	"518743"	"5070"					"7614213"			2	""
@@ -1848,9 +1848,9 @@
 "B_HBTNS"	"Aestuariihabitans"	"accepted"	"Bacteria"	"Pseudomonadota"	"Alphaproteobacteria"	"Rhodobacterales"	"Roseobacteraceae"	"Aestuariihabitans"	""	""	"genus"	"Yoon et al., 2014"	"aerobe"	"LPSN"	"518472"	"11172"					"7574420"			2	""
 "B_HBTNS_BLGY"	"Aestuariihabitans beolgyonensis"	"accepted"	"Bacteria"	"Pseudomonadota"	"Alphaproteobacteria"	"Rhodobacterales"	"Roseobacteraceae"	"Aestuariihabitans"	"beolgyonensis"	""	"species"	"Yoon et al., 2014"	"aerobe"	"LPSN"	"791419"	"518472"						"7574420"		2	""
 "B_MCRBM1"	"Aestuariimicrobium"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Propionibacteriales"	"Propionibacteriaceae"	"Aestuariimicrobium"	""	""	"genus"	"Chen et al., 2018"	"facultative anaerobe"	"LPSN"	"517663"	"1114"					"4884973"	"8088"		2	""
-"B_MCRBM1_B_MCRBM1_B_MCRBM1_GNZN"	"Aestuariimicrobium ganziense"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Propionibacteriales"	"Propionibacteriaceae"	"Aestuariimicrobium"	"ganziense"	""	"species"		"likely facultative anaerobe"	"GBIF"		"517663"					"11500818"	"4884973"		2	""
-"B_MCRBM1_B_MCRBM1_B_MCRBM1_B_MCRBM1_KWNG"	"Aestuariimicrobium kwangyangense"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Propionibacteriales"	"Propionibacteriaceae"	"Aestuariimicrobium"	"kwangyangense"	""	"species"	"Jung et al., 2007"	"aerobe"	"LPSN"	"786691"	"517663"					"5905030"	"4884973"		2	""
-"B_MCRBM1_B_MCRBM1_B_MCRBM1_B_MCRBM1_SOLI"	"Aestuariimicrobium soli"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Propionibacteriales"	"Propionibacteriaceae"	"Aestuariimicrobium"	"soli"	""	"species"	"Chen et al., 2018"	"facultative anaerobe"	"LPSN"	"797883"	"517663"						"4884973"		2	""
+"B_MCRBM1_GNZN"	"Aestuariimicrobium ganziense"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Propionibacteriales"	"Propionibacteriaceae"	"Aestuariimicrobium"	"ganziense"	""	"species"		"likely facultative anaerobe"	"GBIF"		"517663"					"11500818"	"4884973"		2	""
+"B_MCRBM1_KWNG"	"Aestuariimicrobium kwangyangense"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Propionibacteriales"	"Propionibacteriaceae"	"Aestuariimicrobium"	"kwangyangense"	""	"species"	"Jung et al., 2007"	"aerobe"	"LPSN"	"786691"	"517663"					"5905030"	"4884973"		2	""
+"B_MCRBM1_SOLI"	"Aestuariimicrobium soli"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Propionibacteriales"	"Propionibacteriaceae"	"Aestuariimicrobium"	"soli"	""	"species"	"Chen et al., 2018"	"facultative anaerobe"	"LPSN"	"797883"	"517663"						"4884973"		2	""
 "B_TRMNS"	"Aestuariimonas"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariimonas"	""	""	"genus"	"Park et al., 2018"	"aerobe"	"LPSN"	"519333"	"524"						"4898201"		2	""
 "B_TRMNS_INSL"	"Aestuariimonas insulae"	"accepted"	"Bacteria"	"Bacteroidota"	"Flavobacteriia"	"Flavobacteriales"	"Flavobacteriaceae"	"Aestuariimonas"	"insulae"	""	"species"	"Park et al., 2018"	"aerobe"	"LPSN"	"796399"	"519333"								2	""
 "B_[FAM]_ASTRRHBD"	"Aestuariirhabdaceae"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Oceanospirillales"	"Aestuariirhabdaceae"	""	""	""	"family"	"Khan et al., 2020"		"LPSN"	"4854"	"5074"					"11127023"			2	""
@@ -33646,6 +33646,7 @@
 "B_KLBSL_PSTR"	"Klebsiella pasteurii"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Klebsiella"	"pasteurii"	""	"species"	"Merla et al., 2020"	"likely facultative anaerobe"	"LPSN"	"5622"	"515890"					"12165548"	"3221927"	"11145273"	1	""
 "B_KLBSL_PLNT"	"Klebsiella planticola"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Klebsiella"	"planticola"	""	"species"	"Bagley et al., 1982"	"facultative anaerobe"	"LPSN"	"777150"	"515890"					"5427566"	"3221927"		1	""
 "B_KLBSL_PNMN"	"Klebsiella pneumoniae"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Klebsiella"	"pneumoniae"	""	"species"	"Trevisan, 1887"	"facultative anaerobe"	"LPSN"	"777151"	"515890"					"3221874"	"3221927"		1	"1098101000112102,446870005,1098201000112108,409801009,56415008,714315002,713926009"
+"B_KLBSL_PNMN-C"	"Klebsiella pneumoniae complex"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Klebsiella"	"pneumoniae complex"	""	"species group"		"facultative anaerobe"	"Manually added"		"515890"						"3221927"		1	""
 "B_KLBSL_PNMN_OZAN"	"Klebsiella pneumoniae ozaenae"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Klebsiella"	"pneumoniae"	"ozaenae"	"subspecies"	"Orskov, 1984"		"LPSN"	"777152"	"777151"					"5427614"	"3221874"		1	"65186004"
 "B_KLBSL_PNMN_PNMN"	"Klebsiella pneumoniae pneumoniae"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Klebsiella"	"pneumoniae"	"pneumoniae"	"subspecies"	"Orskov, 1984"		"LPSN"	"777153"	"777151"					"7234532"	"3221874"		1	"18400002"
 "B_KLBSL_PNMN_RHNS"	"Klebsiella pneumoniae rhinoscleromatis"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Enterobacterales"	"Enterobacteriaceae"	"Klebsiella"	"pneumoniae"	"rhinoscleromatis"	"subspecies"	"Orskov, 1984"		"LPSN"	"777154"	"777151"					"5427616"	"3221874"		1	"17688001"
@@ -34472,12 +34473,12 @@
 "B_LCTBC_CMLL"	"Lactobacillus camelliae"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"camelliae"	""	"species"	"Tanasupawat et al., 2007"	"likely facultative anaerobe"	"LPSN"	"786434"	"517058"	"10738"				"8081695"	"3223445"		1.5	""
 "B_LCTBC_CPLL"	"Lactobacillus capillatus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"capillatus"	""	"species"	"Chao et al., 2008"	"likely facultative anaerobe"	"LPSN"	"787617"	"517058"	"10739"				"7603537"	"3223445"		1.5	""
 "B_LCTBC_CRNS"	"Lactobacillus carnis"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"carnis"	""	"species"	"Shaw et al., 1986"	"likely facultative anaerobe"	"LPSN"	"777267"	"517058"	"774486"					"3223445"		1.5	""
-"B_LCTBC_CASE_PSDP"	"Lactobacillus casei"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	""	"species"	"Hansen et al., 1971"	"likely facultative anaerobe"	"LPSN"	"777268"	"517058"	"10711"				"3227248"	"3223445"		1.15	"1017006,113779003"
-"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_ALCT"	"Lactobacillus casei alactosus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"alactosus"	"subspecies"	"Mills et al., 1973"		"LPSN"	"777269"	"777268"	"777272"				"3227250"	"3227248"	"3227330"	1.15	""
-"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_CASE"	"Lactobacillus casei casei"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"casei"	"subspecies"	"Abo-Elnaga et al., 1965"		"LPSN"	"777270"	"777268"					"7234596"	"3227248"	"3227248"	1.15	"28315003"
-"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_PSDP"	"Lactobacillus casei pseudoplantarum"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"pseudoplantarum"	"subspecies"	"Abo-Elnaga et al., 1965"		"LPSN"	"777272"	"777268"					"3227251"	"3227248"	"3227330"	1.15	"58249006"
-"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_RHMN"	"Lactobacillus casei rhamnosus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"rhamnosus"	"subspecies"	"Hansen, 1968"		"LPSN"	"777273"	"777268"	"10740"				"3227212"	"3227248"	"3227211"	1.15	""
-"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_TLRN"	"Lactobacillus casei tolerans"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"tolerans"	"subspecies"	"Abo-Elnaga et al., 1965"		"LPSN"	"777274"	"777268"	"10878"				"3227332"	"3227248"	"3227331"	1.15	"5234000"
+"B_LCTBC_CASE"	"Lactobacillus casei"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	""	"species"	"Hansen et al., 1971"	"likely facultative anaerobe"	"LPSN"	"777268"	"517058"	"10711"				"3227248"	"3223445"		1.15	"1017006,113779003"
+"B_LCTBC_CASE_ALCT"	"Lactobacillus casei alactosus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"alactosus"	"subspecies"	"Mills et al., 1973"		"LPSN"	"777269"	"777268"	"777272"				"3227250"	"3227248"	"3227330"	1.15	""
+"B_LCTBC_CASE_CASE"	"Lactobacillus casei casei"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"casei"	"subspecies"	"Abo-Elnaga et al., 1965"		"LPSN"	"777270"	"777268"					"7234596"	"3227248"	"3227248"	1.15	"28315003"
+"B_LCTBC_CASE_PSDP"	"Lactobacillus casei pseudoplantarum"	"accepted"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"pseudoplantarum"	"subspecies"	"Abo-Elnaga et al., 1965"		"LPSN"	"777272"	"777268"					"3227251"	"3227248"	"3227330"	1.15	"58249006"
+"B_LCTBC_CASE_RHMN"	"Lactobacillus casei rhamnosus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"rhamnosus"	"subspecies"	"Hansen, 1968"		"LPSN"	"777273"	"777268"	"10740"				"3227212"	"3227248"	"3227211"	1.15	""
+"B_LCTBC_CASE_TLRN"	"Lactobacillus casei tolerans"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"casei"	"tolerans"	"subspecies"	"Abo-Elnaga et al., 1965"		"LPSN"	"777274"	"777268"	"10878"				"3227332"	"3227248"	"3227331"	1.15	"5234000"
 "B_LCTBC_CTNF"	"Lactobacillus catenaforme"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"catenaforme"	""	"species"	"Moore et al., 1970"	"likely facultative anaerobe"	"LPSN"	"798354"	"517058"	"777275"					"3223445"		1.5	""
 "B_LCTBC_CTNFR"	"Lactobacillus catenaformis"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"catenaformis"	""	"species"	"Moore et al., 1970"	"likely facultative anaerobe"	"LPSN"	"777275"	"517058"	"789495"					"3223445"		1.15	""
 "B_LCTBC_CAVI"	"Lactobacillus caviae"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"caviae"	""	"species"	"Killer et al., 2017"	"likely facultative anaerobe"	"LPSN"	"795698"	"517058"	"10866"				"9674251"	"3223445"		1.5	""
@@ -34701,9 +34702,9 @@
 "B_LCTBC_SAKE"	"Lactobacillus sake"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sake"	""	"species"	"Torriani et al., 1996"	"likely facultative anaerobe"	"LPSN"	"784069"	"517058"	"777388"					"3223445"		1.5	""
 "B_LCTBC_SAKE_CRNS"	"Lactobacillus sake carnosus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sake"	"carnosus"	"subspecies"	"Torriani et al., 1996"		"LPSN"	"784070"	"784069"	"777389"							1.5	""
 "B_LCTBC_SAKE_SAKE"	"Lactobacillus sake sake"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sake"	"sake"	"subspecies"	"Torriani et al., 1996"		"LPSN"	"784071"	"784069"	"777390"							1.5	""
-"B_LCTBC_SKEI_SAKE"	"Lactobacillus sakei"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	""	"species"	"Klein et al., 1996"	"likely facultative anaerobe"	"LPSN"	"777388"	"517058"	"10710"				"3227207"	"3223445"		1.5	"39861009,113799009,113800008"
-"B_LCTBC_SKEI_SAKE_SAKE_SAKE_SAKE_CRNS"	"Lactobacillus sakei carnosus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	"carnosus"	"subspecies"	"Torriani et al., 1996"		"LPSN"	"777389"	"777388"	"10881"					"3227207"		1.5	""
-"B_LCTBC_SKEI_SAKE_SAKE_SAKE_SAKE_SAKE"	"Lactobacillus sakei sakei"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	"sakei"	"subspecies"	"Torriani et al., 1996"		"LPSN"	"777390"	"777388"	"10877"					"3227207"		1.5	""
+"B_LCTBC_SKEI"	"Lactobacillus sakei"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	""	"species"	"Klein et al., 1996"	"likely facultative anaerobe"	"LPSN"	"777388"	"517058"	"10710"				"3227207"	"3223445"		1.5	"39861009,113799009,113800008"
+"B_LCTBC_SKEI_CRNS"	"Lactobacillus sakei carnosus"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	"carnosus"	"subspecies"	"Torriani et al., 1996"		"LPSN"	"777389"	"777388"	"10881"					"3227207"		1.5	""
+"B_LCTBC_SKEI_SAKE"	"Lactobacillus sakei sakei"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"sakei"	"sakei"	"subspecies"	"Torriani et al., 1996"		"LPSN"	"777390"	"777388"	"10877"					"3227207"		1.5	""
 "B_LCTBC_SLTL"	"Lactobacillus salitolerans"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"salitolerans"	""	"species"	"Tohno et al., 2019"	"likely facultative anaerobe"	"LPSN"	"800710"	"517058"	"10660"					"3223445"		1.5	""
 "B_LCTBC_SLVR"	"Lactobacillus salivarius"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"salivarius"	""	"species"	"Li et al., 2006"	"likely facultative anaerobe"	"LPSN"	"784072"	"517058"	"10714"				"3227229"	"3223445"		1.5	"37809002"
 "B_LCTBC_SLVR_SLCN"	"Lactobacillus salivarius salicinius"	"synonym"	"Bacteria"	"Bacillota"	"Bacilli"	"Lactobacillales"	"Lactobacillaceae"	"Lactobacillus"	"salivarius"	"salicinius"	"subspecies"	"Rogosa et al., 1953"		"LPSN"	"777391"	"784072"	"10714"				"3227230"	"3227229"	"3227229"	1.5	"86840000"
@@ -61351,9 +61352,9 @@
 "B_RSVRG_MRTM"	"Roseivirga maritima"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"maritima"	""	"species"	"Jung et al., 2016"	"aerobe"	"LPSN"	"794295"	"517334"								2	""
 "B_RSVRG_MSKN"	"Roseivirga misakiensis"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"misakiensis"	""	"species"	"Garcia-Lopez et al., 2020"	"aerobe"	"LPSN"	"7880"	"517334"								2	""
 "B_RSVRG_PCFC"	"Roseivirga pacifica"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"pacifica"	""	"species"	"Garcia-Lopez et al., 2020"	"aerobe"	"LPSN"	"7873"	"517334"								2	""
-"B_RSVRG_SHNS_AQPN"	"Roseivirga seohaensis"	"synonym"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"seohaensis"	""	"species"	"Garcia-Lopez et al., 2019"	"aerobe"	"LPSN"	"784819"	"517334"	"784818"				"7234517"		"9629563"	2	""
-"B_RSVRG_SHNS_AQPN_AQPN_AQPN_AQPN_AQPN"	"Roseivirga seohaensis aquiponti"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"seohaensis"	"aquiponti"	"subspecies"	"Selvaratnam et al., 2016"		"LPSN"	"794907"	"784819"					"9507856"	"7234517"		2	""
-"B_RSVRG_SHNS_AQPN_AQPN_AQPN_AQPN_SHNS"	"Roseivirga seohaensis seohaensis"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"seohaensis"	"seohaensis"	"subspecies"	"Selvaratnam et al., 2016"		"LPSN"	"794906"	"784819"					"9629563"	"7234517"		2	""
+"B_RSVRG_SHNS"	"Roseivirga seohaensis"	"synonym"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"seohaensis"	""	"species"	"Garcia-Lopez et al., 2019"	"aerobe"	"LPSN"	"784819"	"517334"	"784818"				"7234517"		"9629563"	2	""
+"B_RSVRG_SHNS_AQPN"	"Roseivirga seohaensis aquiponti"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"seohaensis"	"aquiponti"	"subspecies"	"Selvaratnam et al., 2016"		"LPSN"	"794907"	"784819"					"9507856"	"7234517"		2	""
+"B_RSVRG_SHNS_SHNS"	"Roseivirga seohaensis seohaensis"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"seohaensis"	"seohaensis"	"subspecies"	"Selvaratnam et al., 2016"		"LPSN"	"794906"	"784819"					"9629563"	"7234517"		2	""
 "B_RSVRG_SPNG"	"Roseivirga spongicola"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"spongicola"	""	"species"	"Hahnke et al., 2016"	"aerobe"	"LPSN"	"784820"	"517334"								2	""
 "B_RSVRG_THRM"	"Roseivirga thermotolerans"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	"Roseivirga"	"thermotolerans"	""	"species"	"Garcia-Lopez et al., 2020"	"aerobe"	"LPSN"	"7881"	"517334"								2	""
 "B_[FAM]_ROSEVRGC"	"Roseivirgaceae"	"accepted"	"Bacteria"	"Bacteroidota"	"Cytophagia"	"Cytophagales"	"Roseivirgaceae"	""	""	""	"family"	"Garcia-Lopez et al., 2020"		"LPSN"	"7785"	"5018"						"7571564"		2	""
@@ -68974,8 +68975,8 @@
 "B_SMYCS_CVRN"	"Streptomyces cavernae"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cavernae"	""	"species"	"Fang et al., 2020"	"aerobe"	"LPSN"	"5701"	"517119"					"11121506"	"3223560"		1.5	""
 "B_SMYCS_CVSC"	"Streptomyces caviscabies"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"caviscabies"	""	"species"	"Goyer et al., 1996"	"likely facultative anaerobe"	"LPSN"	"781532"	"517119"	"781730"				"3224180"	"3223560"	"3224177"	1.25	""
 "B_SMYCS_CVRN1"	"Streptomyces cavourensis"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cavourensis"	""	"species"	"Skarbek et al., 1978"	"likely facultative anaerobe"	"LPSN"	"785000"	"517119"					"3223903"	"3223560"	"3224107"	1.5	"439655009"
-"B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_CVRN"	"Streptomyces cavourensis cavourensis"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cavourensis"	"cavourensis"	"subspecies"	"Skarbek et al., 1978"		"LPSN"	"781533"	"785000"	"785000"				"7073676"	"3223903"	"3224107"	1.5	""
-"B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_WSHN"	"Streptomyces cavourensis washingtonensis"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cavourensis"	"washingtonensis"	"subspecies"	"Skarbek et al., 1978"		"LPSN"	"781534"	"785000"	"781600"				"3223905"	"3223903"	"3223678"	1.5	""
+"B_SMYCS_CVRN1_CVRN"	"Streptomyces cavourensis cavourensis"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cavourensis"	"cavourensis"	"subspecies"	"Skarbek et al., 1978"		"LPSN"	"781533"	"785000"	"785000"				"7073676"	"3223903"	"3224107"	1.5	""
+"B_SMYCS_CVRN1_WSHN"	"Streptomyces cavourensis washingtonensis"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cavourensis"	"washingtonensis"	"subspecies"	"Skarbek et al., 1978"		"LPSN"	"781534"	"785000"	"781600"				"3223905"	"3223903"	"3223678"	1.5	""
 "B_SMYCS_CLLS"	"Streptomyces cellostaticus"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cellostaticus"	""	"species"	"Nouioui et al., 2018"	"likely facultative anaerobe"	"LPSN"	"781536"	"517119"					"3223772"	"3223560"		1.5	"441384008"
 "B_SMYCS_CLLL"	"Streptomyces celluloflavus"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"celluloflavus"	""	"species"	"Madhaiyan et al., 2020"	"likely facultative anaerobe"	"LPSN"	"781537"	"517119"					"3223631"	"3223560"		1.5	"439645005"
 "B_SMYCS_YTCS"	"Streptomyces cellulolyticus"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptomyces"	"cellulolyticus"	""	"species"	"1997"	"likely facultative anaerobe"	"LPSN"	"785001"	"517119"					"3224135"	"3223560"		1.5	"439191003"
@@ -69924,11 +69925,11 @@
 "B_SCLLM_BLDC"	"Streptoverticillium baldaccii"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"baldaccii"	""	"species"	"Farina et al., 1966"		"LPSN"	"782192"	"516693"	"781490"							2	""
 "B_SCLLM_BVRT"	"Streptoverticillium biverticillatum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"biverticillatum"	""	"species"	"Farina et al., 1966"		"LPSN"	"782193"	"516693"	"781748"							2	""
 "B_SCLLM_BLST"	"Streptoverticillium blastmyceticum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"blastmyceticum"	""	"species"	"Locci et al., 1969"		"LPSN"	"782194"	"516693"	"781498"							2	""
-"B_SCLLM_CNNM_LNSM"	"Streptoverticillium cinnamoneum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	""	"species"	"Baldacci et al., 1966"		"LPSN"	"782196"	"516693"	"781561"							2	""
-"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_ALBS"	"Streptoverticillium cinnamoneum albosporum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"albosporum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782197"	"782196"	"781562"							2	""
-"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_CNNM"	"Streptoverticillium cinnamoneum cinnamoneum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"cinnamoneum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782199"	"782196"	"781563"							2	""
-"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_LNSM"	"Streptoverticillium cinnamoneum lanosum"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"lanosum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782200"	"782196"								2	""
-"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_SPRS"	"Streptoverticillium cinnamoneum sparsum"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"sparsum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782201"	"782196"								2	""
+"B_SCLLM_CNNM"	"Streptoverticillium cinnamoneum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	""	"species"	"Baldacci et al., 1966"		"LPSN"	"782196"	"516693"	"781561"							2	""
+"B_SCLLM_CNNM_ALBS"	"Streptoverticillium cinnamoneum albosporum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"albosporum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782197"	"782196"	"781562"							2	""
+"B_SCLLM_CNNM_CNNM"	"Streptoverticillium cinnamoneum cinnamoneum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"cinnamoneum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782199"	"782196"	"781563"							2	""
+"B_SCLLM_CNNM_LNSM"	"Streptoverticillium cinnamoneum lanosum"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"lanosum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782200"	"782196"								2	""
+"B_SCLLM_CNNM_SPRS"	"Streptoverticillium cinnamoneum sparsum"	"accepted"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"cinnamoneum"	"sparsum"	"subspecies"	"Thirumalachar, 1968"		"LPSN"	"782201"	"782196"								2	""
 "B_SCLLM_DSTL"	"Streptoverticillium distallicum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"distallicum"	""	"species"	"Locci et al., 1969"		"LPSN"	"782202"	"516693"	"781875"							2	""
 "B_SCLLM_EHMN"	"Streptoverticillium ehimense"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"ehimense"	""	"species"	"Locci et al., 1969"		"LPSN"	"782203"	"516693"	"781400"							2	""
 "B_SCLLM_ERCD"	"Streptoverticillium eurocidicum"	"synonym"	"Bacteria"	"Actinomycetota"	"Actinomycetes"	"Kitasatosporales"	"Streptomycetaceae"	"Streptoverticillium"	"eurocidicum"	""	"species"	"Locci et al., 1969"		"LPSN"	"782204"	"516693"	"781631"							2	""
@@ -72428,8 +72429,8 @@
 "B_[FAM]_THRMSLFD"	"Thermosulfidibacteraceae"	"accepted"	"Bacteria"	"Aquificota"	"Aquificia"	"Thermosulfidibacterales"	"Thermosulfidibacteraceae"	""	""	""	"family"	"Chuvochina et al., 2024"		"LPSN"	"43615"	"43708"					"10786899"			2	""
 "B_[ORD]_THRMSLFD"	"Thermosulfidibacterales"	"accepted"	"Bacteria"	"Aquificota"	"Aquificia"	"Thermosulfidibacterales"	""	""	""	""	"order"	"Chuvochina et al., 2024"		"LPSN"	"43708"	"37120"								2	""
 "B_TRMNS1"	"Thermosulfurimonas"	"accepted"	"Bacteria"	"Thermodesulfobacteriota"	"Thermodesulfobacteria"	"Thermodesulfobacteriales"	"Thermodesulfobacteriaceae"	"Thermosulfurimonas"	""	""	"genus"	"Slobodkin et al., 2012"	"anaerobe"	"LPSN"	"518269"	"1440"					"11114975"	"9543"		2	""
-"B_TRMNS1_B_TRMNS1_B_TRMNS1_B_TRMNS1_DSMT"	"Thermosulfurimonas dismutans"	"accepted"	"Bacteria"	"Thermodesulfobacteriota"	"Thermodesulfobacteria"	"Thermodesulfobacteriales"	"Thermodesulfobacteriaceae"	"Thermosulfurimonas"	"dismutans"	""	"species"	"Slobodkin et al., 2012"	"anaerobe"	"LPSN"	"790271"	"518269"					"7901824"	"11114975"		2	""
-"B_TRMNS1_B_TRMNS1_B_TRMNS1_B_TRMNS1_B_TRMNS1_MARN"	"Thermosulfurimonas marina"	"accepted"	"Bacteria"	"Thermodesulfobacteriota"	"Thermodesulfobacteria"	"Thermodesulfobacteriales"	"Thermodesulfobacteriaceae"	"Thermosulfurimonas"	"marina"	""	"species"	"Frolova et al., 2019"	"anaerobe"	"LPSN"	"5307"	"518269"						"11114975"		2	""
+"B_TRMNS1_DSMT"	"Thermosulfurimonas dismutans"	"accepted"	"Bacteria"	"Thermodesulfobacteriota"	"Thermodesulfobacteria"	"Thermodesulfobacteriales"	"Thermodesulfobacteriaceae"	"Thermosulfurimonas"	"dismutans"	""	"species"	"Slobodkin et al., 2012"	"anaerobe"	"LPSN"	"790271"	"518269"					"7901824"	"11114975"		2	""
+"B_TRMNS1_MARN"	"Thermosulfurimonas marina"	"accepted"	"Bacteria"	"Thermodesulfobacteriota"	"Thermodesulfobacteria"	"Thermodesulfobacteriales"	"Thermodesulfobacteriaceae"	"Thermosulfurimonas"	"marina"	""	"species"	"Frolova et al., 2019"	"anaerobe"	"LPSN"	"5307"	"518269"						"11114975"		2	""
 "B_TPHLS"	"Thermosulfuriphilus"	"accepted"	"Bacteria"	"Thermodesulfobacteriota"	""	""	""	"Thermosulfuriphilus"	""	""	"genus"	"Slobodkina et al., 2017"		"LPSN"	"519252"	"25893"								2	""
 "B_TPHLS_AMMN"	"Thermosulfuriphilus ammonigenes"	"accepted"	"Bacteria"	"Thermodesulfobacteriota"	""	""	""	"Thermosulfuriphilus"	"ammonigenes"	""	"species"	"Slobodkina et al., 2017"		"LPSN"	"795868"	"519252"								2	""
 "B_[FAM]_THRMSYNC"	"Thermosynechococcaceae"	"accepted"	"Bacteria"	"Cyanobacteria"	"Cyanobacteriia"	"Thermosynechococcales"	"Thermosynechococcaceae"	""	""	""	"family"	"Komarek et al., 2020"		"LPSN"	"39015"						"10683622"	"10831881"		2	""

data-raw/reproduction_of_microorganisms.R

@@ -2107,6 +2107,11 @@ taxonomy$rank[which(taxonomy$fullname %like% "unknown")] <- "(unknown rank)"
 
 # Some final checks -------------------------------------------------------------------------------
 
+# this happened in early 2025, check that MO codes do not have repeated elements
+# fixed it then like this: microorganisms$mo <- gsub("B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM", "B_SCLLM_CNNM", microorganisms$mo)
+taxonomy |> filter(mo %like% "_.*_.*_.*_") |> View()
+
+
 fix_old_mos <- function(dataset) {
   df <- dataset %>% mutate(mo = as.character(mo))
   df$mo[which(!df$mo %in% taxonomy$mo)] <- df %>% filter(!mo %in% taxonomy$mo) %>% mutate(name = mo_name(mo, keep_synonyms = TRUE), new_mo = taxonomy$mo[match(name, taxonomy$fullname)]) %>% pull(new_mo)

data-raw/reproduction_of_microorganisms.groups.R

@@ -27,8 +27,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-# this data set is being used in the clinical_breakpoints data set, and thus by as.sir().
-# it prevents the breakpoints table from being extremely long for species that are part of a species group.
+# This data set is being used in the clinical_breakpoints data set, and thus by as.sir().
+# It prevents the breakpoints table from being extremely long for species that are part of a species group.
+# Also used by eucast_rules() to expand group names.
 
 library(dplyr)
 library(readr)
@@ -143,6 +144,10 @@ microorganisms.groups <- whonet_organisms %>%
   filter(mo_group != "B_CTRBC_FRND-C") %>% 
   bind_rows(tibble(mo_group = as.mo("B_CTRBC_FRND-C"),
                    mo = paste("Citrobacter", c("freundii", "braakii", "gillenii", "murliniae", "portucalensis", "sedlakii", "werkmanii", "youngae")) %>% as.mo(keep_synonyms = TRUE))) %>% 
+  # Klebsiella pneumoniae complex
+  filter(mo_group != "B_KLBSL_PNMN-C") %>% 
+  bind_rows(tibble(mo_group = as.mo("B_KLBSL_PNMN-C"),
+                   mo = paste("Klebsiella", c("africana", "pneumoniae", "quasipneumoniae", "quasivariicola", "variicola")) %>% as.mo(keep_synonyms = TRUE))) %>% 
   # Yersinia pseudotuberculosis complex in the NCBI Taxonomy Browser:
   # https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1649845
   filter(mo_group != "B_YERSN_PSDT-C") %>% 
@@ -164,22 +169,19 @@ for (group in unique(microorganisms.groups$mo_group)) {
     filter(mo %like% spp & rank == "subspecies") %>%
     pull(mo)
   # add them
-  microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = group, mo = mos))
+  microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = as.mo(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)) %>% 
+         mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
   arrange(mo_group_name, mo_name) %>% 
-  filter(mo_group != mo) %>% 
-  distinct() %>% 
+  filter(mo_group != mo) %>%
+  distinct() %>%
   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)