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(v2.1.1.9198) support eucast expert rules 14 and 13.1
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@ -235,152 +235,554 @@ genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Br
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genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 12
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genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 12
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genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 12 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
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genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 12
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genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 12
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genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
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genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
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genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
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genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 12
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genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
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genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
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genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 12 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
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genus_species is Staphylococcus aureus "PEN, FOX-S" "S, S" penicillins S Staphylococcus Breakpoints 12
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genus_species is Staphylococcus aureus "PEN, FOX-S" "R, S" "betalactams_with_inhibitor, isoxazolylpenicillins, NAF" S Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX-S R "PEN, PHN, AMP, AMX, PIP, TIC" R Staphylococcus Breakpoints 12
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genus_species is Staphylococcus saprophyticus AMP S "AMP, SAM, AMX, AMC, PIP, TZP" S Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX-S S "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" S Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
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genus is Staphylococcus FOX-S I "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" I Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
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genus is Staphylococcus FOX-S R "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" R Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
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genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R "PEN, PHN, AMP, AMX, PIP, TIC" R Staphylococcus Breakpoints 12
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genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S S "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" S Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
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genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S I "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" I Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
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genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R "BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP" R Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))"
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genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 12
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genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 12
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genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 12 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
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genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 12 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
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genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 12 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
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genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S S carbapenems S Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method"
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genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S I carbapenems I Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method"
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genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R carbapenems R Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method"
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genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 12
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genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 12
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genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 12
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genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 12 MRSA isolates are in this file safely denoted as FOX resistant
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genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 12
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genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 12
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genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 12
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genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 12
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genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 12
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genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 12
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genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 12
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genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S Streptococcus groups A, B, C, G Breakpoints 12 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
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genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I Streptococcus groups A, B, C, G Breakpoints 12 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
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genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R Streptococcus groups A, B, C, G Breakpoints 12 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 12 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
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genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 12 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
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genus is Staphylococcus NOR-S S "CIP, LVX" I Staphylococcus Breakpoints 12
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genus_species is Staphylococcus aureus VAN S "DAL, ORI" S Staphylococcus Breakpoints 12
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genus_species is Staphylococcus aureus "FOX-S, VAN" "R, S" TLV S Staphylococcus Breakpoints 12 MRSA isolates are in this file safely denoted as FOX resistant
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genus is Staphylococcus ERY S "AZM, CLR, RXT" S Staphylococcus Breakpoints 12
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genus is Staphylococcus TCY-S S "DOX, MNO" S Staphylococcus Breakpoints 12
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genus is Enterococcus AMP S "AMP, SAM, AMX, AMC, PIP, TZP" S Enterococcus Breakpoints 12
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genus is Enterococcus AMP I "AMP, SAM, AMX, AMC, PIP, TZP" I Enterococcus Breakpoints 12
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genus is Enterococcus AMP R "AMP, SAM, AMX, AMC, PIP, TZP" R Enterococcus Breakpoints 12
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genus is Enterococcus NOR-S S "CIP, LVX" S Enterococcus Breakpoints 12
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genus is Enterococcus NOR-S I "CIP, LVX" I Enterococcus Breakpoints 12
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genus is Enterococcus NOR-S R "CIP, LVX" R Enterococcus Breakpoints 12
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genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN S penicillins S "Streptococcus groups A, B, C, G" Breakpoints 12
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genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN I penicillins I "Streptococcus groups A, B, C, G" Breakpoints 12
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genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN R penicillins R "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species is Streptococcus Group B PEN S "AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP" S "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]"
|
||||
genus_species is Streptococcus Group B PEN I "AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP" I "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]"
|
||||
genus_species is Streptococcus Group B PEN R "AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP" R "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]"
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN S cephalosporins S "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN I cephalosporins I "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN R cephalosporins R "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN S carbapenems S "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN I carbapenems I "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN R carbapenems R "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S S MFX S "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S S LVX I "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S R "MFX, LVX" R "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" VAN S "DAL, ORI" S "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" ERY S "AZM, CLR, RXT" S "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" ERY R "AZM, CLR, RXT" R "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" TCY-S S "DOX, MNO" S "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" TCY-S R "DOX, MNO" R "Streptococcus groups A, B, C, G" Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae OXA-S S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP" S Streptococcus pneumoniae Breakpoints 12 "x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2022"" & clinical_breakpoints$mo == as.mo(""S. pneumoniae"") & clinical_breakpoints$ab != as.ab(""cefaclor""))]); sort(c(x[x %in% betalactams()], ""SAM"", ""PIP"", ""TZP"", ""PHN"", ""IMR"", ""MEV""))"
|
||||
genus_species is Streptococcus pneumoniae PEN S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP" S Streptococcus pneumoniae Breakpoints 12 "x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2022"" & clinical_breakpoints$mo == as.mo(""S. pneumoniae"") & clinical_breakpoints$ab != as.ab(""cefaclor""))]); sort(c(x[x %in% betalactams()], ""SAM"", ""PIP"", ""TZP"", ""PHN"", ""IMR"", ""MEV""))"
|
||||
genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06
|
||||
genus_species is Streptococcus pneumoniae OXA-S R "PEN, PHN" R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06
|
||||
genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06
|
||||
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP S "AMX, AMC, SAM, PIP, TZP" S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP I "AMX, AMC, SAM, PIP, TZP" I Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP R "AMX, AMC, SAM, PIP, TZP" R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 12
|
||||
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 Milleri Group Streptococcus (MGS), 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 Milleri Group Streptococcus (MGS), 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 Milleri Group Streptococcus (MGS), 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 Milleri Group Streptococcus (MGS), 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 Milleri Group Streptococcus (MGS), 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 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$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
|
||||
genus_species is Haemophilus influenzae PEN-S, BTL-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae NOR-S R "MFX, LVX" R Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae ERY S "AZM, CLR, RXT" S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae ERY R "AZM, CLR, RXT" R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae TCY-S S "DOX, MNO" S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae TCY-S R "DOX, MNO" R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" PEN-S S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$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$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species is Haemophilus influenzae PEN-S S "AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP" S Haemophilus influenzae Breakpoints 12 "x <- c(unique(clinical_breakpoints$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, BTL-S" "R, R" "AMP, AMX, PIP" R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis BTL-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R Moraxella catarrhalis Breakpoints 12 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
|
||||
genus_species is Haemophilus influenzae NAL-S S "CIP, LVX, MFX, OFX" S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae NAL-S I "CIP, LVX, MFX, OFX" I Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae NAL-S R "CIP, LVX, MFX, OFX" R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae TCY S "DOX, MNO" S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae TCY R "DOX, MNO" R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis BTL-S R "AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC" R Moraxella catarrhalis Breakpoints 12 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
|
||||
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae BTL-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis NAL-S S "CIP, LVX, MFX, OFX" S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis NAL-S R "CIP, LVX, MFX, OFX" R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY S "AZM, CLR, RXT" S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY R "AZM, CLR, RXT" R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis TCY S "DOX, MNO" S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis TCY R "DOX, MNO" R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae BTL-S R "AMP, AMX" R Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae "BTL-S, PEN" "S, S" "AMP, AMX" S Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae "BTL-S, PEN" "S, I" "AMP, AMX" I Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Neisseria gonorrhoeae "BTL-S, PEN" "S, R" "AMP, AMX" R Neisseria gonorrhoeae Breakpoints 12
|
||||
genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 12
|
||||
genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 12
|
||||
genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 12
|
||||
genus is Prevotella PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & mo_genus(clinical_breakpoints$mo) == ""Prevotella"")]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM""); sort(x[x %in% betalactams()])"
|
||||
genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints
|
||||
genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints
|
||||
genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints
|
||||
genus_species is Fusobacterium necrophorum PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & clinical_breakpoints$mo == as.mo(""Fusobacterium necrophorum""))]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM""); sort(x[x %in% betalactams()])"
|
||||
genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints
|
||||
genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints
|
||||
genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints
|
||||
genus_species is Clostridium perfringens PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & clinical_breakpoints$mo == as.mo(""Fusobacterium necrophorum""))]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM""); sort(x[x %in% betalactams()])"
|
||||
genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints
|
||||
genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints
|
||||
genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints
|
||||
genus_species is Cutibacterium acnes PEN S "AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & clinical_breakpoints$mo == as.mo(""Cutibacterium acnes""))]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM"", ""TZP"", ""CTX"", ""CRO""); sort(x[x %in% betalactams()])"
|
||||
genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints
|
||||
genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints
|
||||
genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints
|
||||
genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints
|
||||
genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints
|
||||
genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints
|
||||
genus_species is Pasteurella multocida PEN S "AMP, AMX" S Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN I "AMP, AMX" I Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN R "AMP, AMX" R Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida NAL-S S "CIP, LVX" S Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida NAL-S R "CIP, LVX" R Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 12
|
||||
genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 12
|
||||
genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 12
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Kingella kingae BTL-S R PEN, AMP, AMX R Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 12
|
||||
genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY S "AZM, CLR" S Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY I "AZM, CLR" I Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY R "AZM, CLR" R Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY S DOX S Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY I DOX I Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY R DOX R Campylobacter coli/jejuni Breakpoints 12
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN S CTX S Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY I DOX I Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 12
|
||||
genus_species is Kingella kingae BTL-S R "PEN, AMP, AMX" R Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN S "AMP, AMX" S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN I "AMP, AMX" I Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN R "AMP, AMX" R Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY S "AZM, CLR" S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY I "AZM, CLR" I Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY R "AZM, CLR" R Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 12
|
||||
genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio PEF-S S "CIP, LVX" S Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio PEF-S I "CIP, LVX" I Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio PEF-S R "CIP, LVX" R Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 12
|
||||
genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 12
|
||||
genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 12
|
||||
genus is Bacillus NOR-S S "CIP, LVX" I Bacillus Breakpoints 12
|
||||
genus is Bacillus NOR-S R "CIP, LVX" R Bacillus Breakpoints 12
|
||||
genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 12
|
||||
genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 12
|
||||
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 13.1
|
||||
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 13.1
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 13.1
|
||||
order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 13.1
|
||||
order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 13.1
|
||||
genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 13.1
|
||||
genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 13.1
|
||||
genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 13.1
|
||||
genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 13.1
|
||||
genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 13.1
|
||||
genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 13.1
|
||||
genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 13.1 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
|
||||
genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 13.1
|
||||
genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 13.1
|
||||
genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 13.1
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 13.1
|
||||
genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 13.1
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 13.1
|
||||
genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 13.1
|
||||
genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 13.1
|
||||
genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 13.1
|
||||
genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 13.1
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
|
||||
genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 13.1
|
||||
genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 13.1
|
||||
genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 13.1
|
||||
genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 13.1 MRSA isolates are in this file safely denoted as FOX resistant
|
||||
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 13.1
|
||||
genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 13.1
|
||||
genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 13.1
|
||||
genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 13.1
|
||||
genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 13.1
|
||||
genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 13.1
|
||||
genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 13.1
|
||||
genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
|
||||
genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
|
||||
genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 13.1 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
|
||||
genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 13.1 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
|
||||
genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 13.1 from flowchart: when OXA < 20 or PEN > 0.06
|
||||
genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 13.1 from flowchart: when OXA < 20 or PEN > 0.06
|
||||
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 13.1
|
||||
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 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, BTL-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
|
||||
genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis BTL-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R Moraxella catarrhalis Breakpoints 13.1 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
|
||||
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 13.1
|
||||
genus_species is Neisseria gonorrhoeae BTL-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 13.1
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 13.1
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 13.1
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 13.1
|
||||
genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 13.1
|
||||
genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 13.1
|
||||
genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 13.1
|
||||
genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints 13.1
|
||||
genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints 13.1
|
||||
genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
|
||||
genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 13.1
|
||||
genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 13.1
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 13.1
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 13.1
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 13.1
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 13.1
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 13.1
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY I DOX I Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 13.1
|
||||
genus_species is Kingella kingae BTL-S R PEN, AMP, AMX R Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 13.1
|
||||
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 13.1
|
||||
genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 13.1
|
||||
genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 13.1
|
||||
genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 13.1
|
||||
genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 13.1
|
||||
genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 13.1
|
||||
genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 13.1
|
||||
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 14
|
||||
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 14
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 14
|
||||
order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 14
|
||||
order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 14
|
||||
genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 14
|
||||
genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 14
|
||||
genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 14
|
||||
genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 14
|
||||
genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 14
|
||||
genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 14
|
||||
genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 14 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
|
||||
genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 14
|
||||
genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 14
|
||||
genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 14
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 14
|
||||
genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 14
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))]))
|
||||
genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 14
|
||||
genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 14
|
||||
genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 14
|
||||
genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 14
|
||||
genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 14
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
|
||||
genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
|
||||
genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 14
|
||||
genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 14
|
||||
genus_species is Staphylococcus coagulase-negative VAN, TEC S, S DAL S Staphylococcus Breakpoints 14
|
||||
genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 14
|
||||
genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 14 MRSA isolates are in this file safely denoted as FOX resistant
|
||||
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 14
|
||||
genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 14
|
||||
genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 14
|
||||
genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 14
|
||||
genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 14
|
||||
genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 14
|
||||
genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 14
|
||||
genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
|
||||
genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
|
||||
genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())]
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 14 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
|
||||
genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 14 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
|
||||
genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 14 from flowchart: when OXA < 20 or PEN > 0.06
|
||||
genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 14 from flowchart: when OXA < 20 or PEN > 0.06
|
||||
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones
|
||||
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 14
|
||||
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$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S Haemophilus influenzae Breakpoints 14 x <- c(unique(clinical_breakpoints$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, BTL-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis BTL-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R Moraxella catarrhalis Breakpoints 14 penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
|
||||
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 14
|
||||
genus_species is Neisseria gonorrhoeae BTL-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 14
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 14
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 14
|
||||
genus_species is Neisseria gonorrhoeae BTL-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 14
|
||||
genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 14
|
||||
genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 14
|
||||
genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 14
|
||||
genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints 14
|
||||
genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints 14
|
||||
genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
|
||||
genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints 14
|
||||
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 14
|
||||
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 14
|
||||
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 14
|
||||
genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 14
|
||||
genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 14
|
||||
genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 14
|
||||
genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 14
|
||||
genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 14
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 14
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 14
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 14
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 14
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 14
|
||||
genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 14
|
||||
genus_species is Kingella kingae BTL-S R PEN, AMP, AMX R Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 14
|
||||
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 14
|
||||
genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 14
|
||||
genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 14
|
||||
genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 14
|
||||
genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 14
|
||||
genus_species is Bacillus anthracis PEN I AMX S Bacillus anthracis Breakpoints 14
|
||||
genus_species is Bacillus anthracis PEN R AMX R Bacillus anthracis Breakpoints 14
|
||||
genus_species is Bacillus anthracis TCY-S S DOX S Bacillus anthracis Breakpoints 14
|
||||
genus_species is Bacillus anthracis TCY-S R DOX R Bacillus anthracis Breakpoints 14
|
||||
genus_species is Brucella melitensis TCY-S S DOX S Brucella melitensis Breakpoints 14
|
||||
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
|
||||
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
|
||||
|
||||
|
Can't render this file because it has a wrong number of fields in line 9.
|
Reference in New Issue
Block a user