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Restored Pichia and Meyerozyma

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dr. M.S. (Matthijs) Berends 2022-09-23 13:12:46 +02:00
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commit 6e3c553d0c
25 changed files with 83 additions and 83 deletions
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DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.8.1.9060
Version: 1.8.1.9061
Date: 2022-09-23
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 1.8.1.9060
# AMR 1.8.1.9061
This version will eventually become v2.0! We're happy to reach a new major milestone soon!

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data-raw/_pre_commit_hook.R
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@ -173,11 +173,11 @@ MO_PREVALENT_GENERA <- c(
"Empedobacter", "Entamoeba", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea",
"Fusarium", "Fusobacterium", "Giardia", "Haloarcula", "Halobacterium", "Halococcus", "Hendersonula",
"Heterophyes", "Histomonas", "Histoplasma", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Leishmania", "Lelliottia",
"Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus",
"Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma",
"Microsporidium", "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
"Nectria", "Ochroconis", "Odoribacter", "Oesophagostomum", "Oidiodendron", "Opisthorchis",
"Ornithobacterium", "Parabacteroides", "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola",
"Phocanema", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Pneumocystis", "Porphyromonas", "Prevotella",
"Phocanema", "Phoma", "Pichia", "Piedraia", "Pithomyces", "Pityrosporum", "Pneumocystis", "Porphyromonas", "Prevotella",
"Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula", "Riemerella",
"Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
"Spirometra", "Spiroplasma", "Sporobolomyces", "Stachybotrys", "Streptobacillus", "Strongyloides",

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@ -8,7 +8,7 @@
"EUCAST 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_CRYPT_NFRM" "Cryptococcus neoformans" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2022" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -82,7 +82,7 @@
"EUCAST 2022" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 4 4 FALSE
"EUCAST 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2022" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 18 FALSE
@ -1068,7 +1068,7 @@
"EUCAST 2021" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2021" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -1140,7 +1140,7 @@
"EUCAST 2021" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2021" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 18 FALSE
@ -1957,7 +1957,7 @@
"EUCAST 2020" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2020" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -2027,7 +2027,7 @@
"EUCAST 2020" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2020" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 18 FALSE
@ -2765,7 +2765,7 @@
"EUCAST 2019" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2019" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2019" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2019" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -2824,7 +2824,7 @@
"EUCAST 2019" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2019" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2019" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 18 18 FALSE
@ -3506,7 +3506,7 @@
"EUCAST 2018" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2018" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2018" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2018" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -3562,7 +3562,7 @@
"EUCAST 2018" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2018" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2018" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2018" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -4231,7 +4231,7 @@
"EUCAST 2017" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2017" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2017" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2017" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -4287,7 +4287,7 @@
"EUCAST 2017" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2017" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2017" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 26 21 FALSE
"EUCAST 2017" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2017" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -4946,7 +4946,7 @@
"EUCAST 2016" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2016" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2016" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2016" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -4999,7 +4999,7 @@
"EUCAST 2016" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2016" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2016" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 24 21 FALSE
"EUCAST 2016" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2016" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -5597,7 +5597,7 @@
"EUCAST 2015" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2015" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2015" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2015" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -5650,7 +5650,7 @@
"EUCAST 2015" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2015" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2015" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 24 21 FALSE
"EUCAST 2015" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2015" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -6224,7 +6224,7 @@
"EUCAST 2014" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2014" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 19 19 FALSE
"EUCAST 2014" "DISK" "UTI" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20-10" 16 16 TRUE
"EUCAST 2014" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
@ -6277,7 +6277,7 @@
"EUCAST 2014" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Candida" 0.002 4 FALSE
"EUCAST 2014" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2014" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30" 24 21 FALSE
"EUCAST 2014" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2014" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30" 50 16 FALSE
@ -6846,7 +6846,7 @@
"EUCAST 2013" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pichia" 3 "AMB" "Amphotericin B" "Candida" 1 1 FALSE
"EUCAST 2013" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" "20/10ug" 17 17 FALSE
"EUCAST 2013" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Enterobacteriaceae" 8 8 FALSE
"EUCAST 2013" "MIC" "B_ENTRC" "Enterococcus" 3 "AMC" "Amoxicillin/clavulanic acid" "Enterococcus" 4 8 FALSE
@ -6896,7 +6896,7 @@
"EUCAST 2013" "MIC" "F_CANDD_ALBC" "Candida albicans" 2 "ANI" "Anidulafungin" "Candida" 0.032 0.032 FALSE
"EUCAST 2013" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2013" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 24 21 FALSE
"EUCAST 2013" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2013" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseud" "30ug" 50 16 FALSE
@ -8481,8 +8481,8 @@
"CLSI 2022" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" "30ug" 21 17 FALSE
"CLSI 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" 4 16 FALSE
"CLSI 2022" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
@ -8532,10 +8532,10 @@
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" "10ug" 18 14 FALSE
"CLSI 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" 4 16 FALSE
"CLSI 2022" "DISK" "B_HMPHL_INFL" "Haemophilus influenzae" 2 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
@ -9292,10 +9292,10 @@
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2022" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" "30ug" 16 12 FALSE
"CLSI 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" 4 16 FALSE
"CLSI 2022" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
@ -9679,8 +9679,8 @@
"CLSI 2022" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2022" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2022" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2022" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" "20ug/10ug" 18 13 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" 8 32 FALSE
"CLSI 2021" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
@ -9745,8 +9745,8 @@
"CLSI 2021" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" "30ug" 21 17 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" 4 16 FALSE
"CLSI 2021" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
@ -9792,10 +9792,10 @@
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" "10ug" 18 14 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" 4 16 FALSE
"CLSI 2021" "DISK" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
@ -10488,10 +10488,10 @@
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2021" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" "30ug" 16 12 FALSE
"CLSI 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" 4 16 FALSE
"CLSI 2021" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
@ -10861,8 +10861,8 @@
"CLSI 2021" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2021" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2021" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2021" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" "20ug/10ug" 18 13 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "AMC" "Amoxicillin/clavulanic acid" "Table 2A" 8 32 FALSE
"CLSI 2020" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
@ -10927,8 +10927,8 @@
"CLSI 2020" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" "30ug" 21 17 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Table 2A" 4 16 FALSE
"CLSI 2020" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
@ -10971,10 +10971,10 @@
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" "10ug" 18 14 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "CAT" "Cefetamet" "Table 2A" 4 16 FALSE
"CLSI 2020" "DISK" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
@ -11658,10 +11658,10 @@
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2020" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" "30ug" 16 12 FALSE
"CLSI 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "MNO" "Minocycline" "Table 2A" 4 16 FALSE
"CLSI 2020" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
@ -12038,8 +12038,8 @@
"CLSI 2020" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2020" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2020" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2020" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2019" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
"CLSI 2019" "MIC" "B_AGGRG" "Aggregatibacter" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 9" 4 8 FALSE
"CLSI 2019" "MIC" "B_BRKHL_PSDM" "Burkholderia pseudomallei" 2 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 21" 8 32 FALSE
@ -12098,8 +12098,8 @@
"CLSI 2019" "MIC" "F_CANDD_KRUS" "Candida krusei" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "ANI" "Anidulafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "ANI" "Anidulafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 2" "30ug" 21 17 FALSE
"CLSI 2019" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "M45 Table 3" 4 16 FALSE
"CLSI 2019" "MIC" "B_GRAMN" "(unknown Gram-negatives)" 2 "ATM" "Aztreonam" "Table 2B-5" 8 32 FALSE
@ -12140,10 +12140,10 @@
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 13 10 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "CAS" "Caspofungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "CAS" "Caspofungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" "10ug" 18 14 FALSE
"CLSI 2019" "MIC" "B_HMPHL" "Haemophilus" 3 "CAT" "Cefetamet" "Table 2E" 4 16 FALSE
"CLSI 2019" "DISK" "B_ACNTB" "Acinetobacter" 3 "CAZ" "Ceftazidime" "Table 2B-2" "30ug" 18 14 FALSE
@ -12740,10 +12740,10 @@
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 16 13 FALSE
"CLSI 2019" "MIC" "F_MYRZY_GLLR" "Meyerozyma guilliermondii" 2 "MIF" "Micafungin" "Table 1" 2 8 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 22 19 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "MIF" "Micafungin" "Table 1" 0.25 1 FALSE
"CLSI 2019" "DISK" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" "30ug" 16 12 FALSE
"CLSI 2019" "MIC" "B_ACNTB" "Acinetobacter" 3 "MNO" "Minocycline" "Table 2B-2" 4 16 FALSE
"CLSI 2019" "DISK" "B_BRKHL_CEPC" "Burkholderia cepacia" 2 "MNO" "Minocycline" "Table 2B-3" "30ug" 19 14 FALSE
@ -13074,8 +13074,8 @@
"CLSI 2019" "MIC" "F_CANDD_PRPS" "Candida parapsilosis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2019" "DISK" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 17 14 FALSE
"CLSI 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "VOR" "Voriconazole" "Table 1" 0.125 1 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pithomyces djbhatii" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2019" "DISK" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 15 12 FALSE
"CLSI 2019" "MIC" "F_PICHI" "Pichia" 3 "VOR" "Voriconazole" "Table 1" 0.5 2 FALSE
"CLSI 2018" "DISK" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" "20ug" 18 13 FALSE
"CLSI 2018" "MIC" "B_AERMN" "Aeromonas" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 2" 8 32 FALSE
"CLSI 2018" "MIC" "B_AGGRG" "Aggregatibacter" 3 "AMC" "Amoxicillin/clavulanic acid" "M45 Table 7" 4 8 FALSE

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man/as.mo.Rd
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@ -162,13 +162,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
\section{Reference Data Publicly Available}{

6
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 48,651 Microorganisms}
\title{Data Set with 48,787 Microorganisms}
\format{
A \link[tibble:tibble]{tibble} with 48,651 observations and 22 variables:
A \link[tibble:tibble]{tibble} with 48,787 observations and 22 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.
@ -47,7 +47,7 @@ For example, \emph{Staphylococcus pettenkoferi} was described for the first time
Included taxonomic data are:
\itemize{
\item All ~34,000 (sub)species from the kingdoms of Archaea and Bacteria
\item ~7,200 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histoplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
\item ~7,400 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histoplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
\item ~4,900 (sub)species from the kingdom of Protozoa
\item ~1,500 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item All ~9,400 previously accepted names of all included (sub)species (these were taxonomically renamed)

4
man/mo_matching_score.Rd
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@ -34,13 +34,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
\section{Reference Data Publicly Available}{

4
man/mo_property.Rd
View File

@ -317,13 +317,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
\section{Source}{