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Fix some WHONET codes

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dr. M.S. (Matthijs) Berends 2023-04-14 11:12:26 +02:00
parent 549790c2a6
commit 147f9112e9
21 changed files with 109 additions and 60 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 2.0.0.9004
Date: 2023-03-20
Version: 2.0.0.9005
Date: 2023-04-14
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

3
NEWS.md
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@ -1,7 +1,8 @@
# AMR 2.0.0.9004
# AMR 2.0.0.9005
## Changed
* formatting fix for `sir_interpretation_history()`
* Fixed some WHONET codes for microorganisms
# AMR 2.0.0

5
R/aa_helper_functions.R
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@ -644,10 +644,13 @@ format_included_data_number <- function(data) {
rounder <- -3 # round on thousands
} else if (n > 1000) {
rounder <- -2 # round on hundreds
} else if (n < 50) {
# do not round
rounder <- 0
} else {
rounder <- -1 # round on tens
}
paste0("~", format(round(n, rounder), decimal.mark = ".", big.mark = " "))
paste0(ifelse(rounder == 0, "", "~"), format(round(n, rounder), decimal.mark = ".", big.mark = " "))
}
# for eucast_rules() and mdro(), creates markdown output with URLs and names

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R/data.R
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@ -120,8 +120,8 @@
#' ### Manual additions
#' For convenience, some entries were added manually:
#'
#' - `r format_included_data_number(which(microorganisms$genus == "Salmonella" & microorganisms$species == "enterica" & microorganisms$source == "manually added"))` entries for the city-like serovars of *Salmonellae*
#' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
#' - `r format_included_data_number(microorganisms[which(microorganisms$source == "manually added" & microorganisms$genus == "Salmonella"), , drop = FALSE])` entries of *Salmonella*, such as the city-like serovars and groups A to H
#' - `r format_included_data_number(microorganisms[which(microorganisms$source == "manually added" & microorganisms$genus == "Streptococcus"), , drop = FALSE])` entries of *Streptococcus*, such as the beta-haemolytic groups A to K, viridans, and milleri
#' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
#' - 1 entry of *Blastocystis* (*B. hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
#' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology

2
R/mo.R
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@ -547,7 +547,7 @@ mo_cleaning_regex <- function() {
"|",
"([({]|\\[).+([})]|\\])",
"|",
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species)[.]*( |$|(complex|group)$))"
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|var|serogr.?up|e?species)[.]*( |$|(complex|group)$))"
)
}

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data-raw/microorganisms.dta
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data-raw/microorganisms.md5
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7846247d4113c4e8f550cfd2cb87467f
cf8b0db59dbfe8b42fbd0a6c51a7e9b0

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data-raw/microorganisms.parquet
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data-raw/microorganisms.rds
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data-raw/microorganisms.txt
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@ -1,8 +1,8 @@
"mo" "fullname" "status" "kingdom" "phylum" "class" "order" "family" "genus" "species" "subspecies" "rank" "ref" "source" "lpsn" "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" "gbif_renamed_to" "prevalence" "snomed"
"B_GRAMN" "(unknown Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMP" "(unknown Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-positives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_ANAER" "(unknown anaerobic bacteria)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"F_FUNGUS" "(unknown fungus)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMN" "(unknown Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMP" "(unknown Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-positives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"UNKNOWN" "(unknown name)" "accepted" "(unknown kingdom)" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"F_YEAST" "(unknown yeast)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_[FAM]_ABDTBCTR" "Abditibacteriaceae" "accepted" "Bacteria" "Abditibacteriota" "Abditibacteriia" "Abditibacteriales" "Abditibacteriaceae" "" "" "" "family" "Tahon et al., 2018" "LPSN" "4812" "4982" "10678443" "10853930" 2 ""
@ -6477,7 +6477,6 @@
"B_AZYRT" "Azyrtalia" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Azyrtalia" "" "" "genus" "Vologdin et al., 1969" "GBIF" "3237706" "4306626" 2 ""
"B_AZYRT_ZNLT" "Azyrtalia zonulata" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Azyrtalia" "zonulata" "" "species" "Vologdin et al., 1969" "GBIF" "11176322" "3237706" 2 ""
"A_B-DKE" "B-DKE" "accepted" "Archaea" "Euryarchaeota" "Thermoplasmata" "Thermoplasmatales" "Thermoplasmataceae" "B-DKE" "" "" "genus" "GBIF" "11214677" "3810" 2 ""
"A_BE-D" "BE-D" "accepted" "Archaea" "Thermoproteota" "Thermoproteia" "Marsarchaeales" "Marsarchaeaceae" "BE-D" "" "" "genus" "GBIF" "11119914" "10885120" 2 ""
"B_BABEL" "Babela" "accepted" "Bacteria" "Dependentiae" "Babeliae" "Babeliales" "Babeliaceae" "Babela" "" "" "genus" "GBIF" "10699249" "10857700" 2 ""
"B_BABEL_MSSL" "Babela massiliensis" "accepted" "Bacteria" "Dependentiae" "Babeliae" "Babeliales" "Babeliaceae" "Babela" "massiliensis" "" "species" "GBIF" "10816215" "10699249" 2 ""
"B_[FAM]_BABELIAC" "Babeliaceae" "accepted" "Bacteria" "Dependentiae" "Babeliae" "Babeliales" "Babeliaceae" "" "" "" "family" "GBIF" "10857700" "10791973" 2 ""
@ -7289,6 +7288,7 @@
"B_BDLLV_STLP" "Bdellovibrio stolpii" "synonym" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "Bdellovibrio" "stolpii" "" "species" "Seidler et al., 1972" "LPSN" "773991" "516977" "773917" 2 "9752009"
"B_[FAM]_BDLLVBRN" "Bdellovibrionaceae" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "" "" "" "family" "Garrity et al., 2006" "LPSN" "203" "5078" "8932" "652" 2 "427516001"
"B_[ORD]_BDLLVBRN" "Bdellovibrionales" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "" "" "" "" "order" "Garrity et al., 2006" "LPSN" "5078" "111" "652" "10808561" 2 "426331002"
"A_BE-D" "BE-D" "accepted" "Archaea" "Thermoproteota" "Thermoproteia" "Marsarchaeales" "Marsarchaeaceae" "BE-D" "" "" "genus" "GBIF" "11119914" "10885120" 2 ""
"F_BEAVR" "Beauveria" "accepted" "Fungi" "Ascomycota" "Sordariomycetes" "Hypocreales" "Cordycipitaceae" "Beauveria" "" "" "genus" "Vuill, 1912" "GBIF" "2560584" "8418" 1.5 "66193005"
"F_BEAVR_ACRD" "Beauveria acridophila" "accepted" "Fungi" "Ascomycota" "Sordariomycetes" "Hypocreales" "Cordycipitaceae" "Beauveria" "acridophila" "" "species" "Sanjuan et al." "GBIF" "10753468" "2560584" 1.5 ""
"F_BEAVR_AMRP" "Beauveria amorpha" "accepted" "Fungi" "Ascomycota" "Sordariomycetes" "Hypocreales" "Cordycipitaceae" "Beauveria" "amorpha" "" "species" "Minnis et al." "GBIF" "7417312" "2560584" 1.5 ""
@ -19169,7 +19169,6 @@
"B_FSBCTR_VARM" "Fusobacterium varium" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Fusobacteriaceae" "Fusobacterium" "varium" "" "species" "Moore et al., 1969" "LPSN" "783893" "515666" "3225872" "4903731" 1 "1972005"
"B_FSBCTR_VNCN" "Fusobacterium vincentii" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Fusobacteriaceae" "Fusobacterium" "vincentii" "" "species" "Kook et al., 2022" "LPSN" "28103" "515666" "10808231" "4903731" 1.5 ""
"B_FSBCTR_WTNB" "Fusobacterium watanabei" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Fusobacteriaceae" "Fusobacterium" "watanabei" "" "species" "Tomida et al., 2021" "LPSN" "17647" "515666" 1.5 ""
"B_GBCHB" "GBChlB" "accepted" "Bacteria" "Chlorobiota" "Chlorobiia" "Chlorobiales" "Chloroherpetonaceae" "GBChlB" "" "" "genus" "GBIF" "11171983" "10775177" 2 ""
"B_GBNBC" "Gabonibacter" "accepted" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Odoribacteraceae" "Gabonibacter" "" "" "genus" "Mourembou et al., 2017" "LPSN" "519111" "2047" "9240178" 2 "785729002"
"B_GBNBC_JSTS" "Gabonibacter justesenii" "synonym" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Odoribacteraceae" "Gabonibacter" "justesenii" "" "species" "GBIF" "11090238" "9240178" "9415109" 2 ""
"B_GBNBC_MSSL" "Gabonibacter massiliensis" "accepted" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Odoribacteraceae" "Gabonibacter" "massiliensis" "" "species" "Mourembou et al., 2017" "LPSN" "795002" "519111" "9415109" "9240178" 2 ""
@ -19283,6 +19282,7 @@
"B_GSTRN_PHSC" "Gastranaerophilus phascolarctosicola" "accepted" "Bacteria" "Cyanobacteria" "Vampirovibrionia" "Gastranaerophilales" "Gastranaerophilaceae" "Gastranaerophilus" "phascolarctosicola" "" "species" "GBIF" "10876363" "10700903" 2 ""
"P_GDRYN" "Gaudryina" "accepted" "Protozoa" "Sarcomastigophora" "" "" "Verneulidae" "Gaudryina" "" "" "genus" "GBIF" "10167887" "6123475" 2 ""
"P_GDRYN_KKSN" "Gaudryina kokuseiensis" "accepted" "Protozoa" "Sarcomastigophora" "" "" "Verneulidae" "Gaudryina" "kokuseiensis" "" "species" "Ishizaki" "GBIF" "6123479" "10167887" 2 ""
"B_GBCHB" "GBChlB" "accepted" "Bacteria" "Chlorobiota" "Chlorobiia" "Chlorobiales" "Chloroherpetonaceae" "GBChlB" "" "" "genus" "GBIF" "11171983" "10775177" 2 ""
"P_GMPHR" "Geamphorella" "accepted" "Protozoa" "Amoebozoa" "Lobosa" "Arcellinida" "Nebelidae" "Geamphorella" "" "" "genus" "Bonnet, 1959" "GBIF" "4888795" "2170" 2 ""
"P_GMPHR_LUCD" "Geamphorella lucida" "accepted" "Protozoa" "Amoebozoa" "Lobosa" "Arcellinida" "Nebelidae" "Geamphorella" "lucida" "" "species" "Bonnet, 1959" "GBIF" "10677162" "4888795" 2 ""
"B_GEHNG" "Gehongia" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Christensenellaceae" "Gehongia" "" "" "genus" "Liu et al., 2022" "LPSN" "28816" "1935" 2 ""
@ -22583,7 +22583,6 @@
"B_HYNSN_UDNS" "Hyunsoonleella udoensis" "synonym" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Hyunsoonleella" "udoensis" "" "species" "Kim et al., 2016" "LPSN" "793695" "517944" "793694" 2 ""
"B_HYNSN_UDNN" "Hyunsoonleella udonensis" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Hyunsoonleella" "udonensis" "" "species" "Kim et al., 2016" "LPSN" "793694" "517944" "8797340" "7660455" 2 ""
"B_HYNSN_ULVA" "Hyunsoonleella ulvae" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Hyunsoonleella" "ulvae" "" "species" "Wang et al., 2022" "LPSN" "28379" "517944" 2 ""
"B_ISDG" "ISDg" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Lachnospiraceae" "ISDg" "" "" "genus" "GBIF" "11121283" "4713" 2 ""
"A_[FAM]_IAINRCHC" "Iainarchaeaceae" "accepted" "Archaea" "Iainarchaeota" "Iainarchaeia" "Iainarchaeales" "Iainarchaeaceae" "" "" "" "family" "GBIF" "10843220" "10672343" 2 ""
"A_[ORD]_IANRCHLS" "Iainarchaeales" "accepted" "Archaea" "Iainarchaeota" "Iainarchaeia" "Iainarchaeales" "" "" "" "" "order" "GBIF" "10672343" "10847779" 2 ""
"A_[CLS]_IAINARCH" "Iainarchaeia" "accepted" "Archaea" "Iainarchaeota" "Iainarchaeia" "" "" "" "" "" "class" "GBIF" "10847779" "10776132" 2 ""
@ -22793,6 +22792,7 @@
"B_ISCHN_ALKL" "Isachenkonia alkalipeptolytica" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Clostridiaceae" "Isachenkonia" "alkalipeptolytica" "" "species" "Zavarzina et al., 2020" "LPSN" "8748" "8742" 2 ""
"B_ISCTS" "Isactis" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Isactis" "" "" "genus" "Thuret et al., 1886" "GBIF" "3219609" "4306626" 2 ""
"B_ISCTS_PLAN" "Isactis plana" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Isactis" "plana" "" "species" "Thur et al." "GBIF" "3219610" "3219609" 2 ""
"B_ISDG" "ISDg" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Lachnospiraceae" "ISDg" "" "" "genus" "GBIF" "11121283" "4713" 2 ""
"B_ISHKW" "Ishikawaella" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Ishikawaella" "" "" "genus" "GBIF" "10797324" "11158430" 2 ""
"B_ISHKW_CPSL" "Ishikawaella capsulata" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Ishikawaella" "capsulata" "" "species" "GBIF" "10718144" "10797324" 2 ""
"B_ISBCL" "Isobaculum" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Carnobacteriaceae" "Isobaculum" "" "" "genus" "Collins et al., 2002" "LPSN" "515857" "279" "3227154" 2 "432998006"
@ -23653,7 +23653,6 @@
"B_KYTCC_AERL" "Kytococcus aerolatus" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Kytococcaceae" "Kytococcus" "aerolatus" "" "species" "Nouioui et al., 2018" "LPSN" "788155" "515905" "7687887" "3225662" 1.5 ""
"B_KYTCC_SCHR" "Kytococcus schroeteri" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Kytococcaceae" "Kytococcus" "schroeteri" "" "species" "Becker et al., 2002" "LPSN" "777226" "515905" "3225663" "3225662" 1 "428721003"
"B_KYTCC_SDNT" "Kytococcus sedentarius" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Kytococcaceae" "Kytococcus" "sedentarius" "" "species" "Nouioui et al., 2018" "LPSN" "777227" "515905" "3225664" "3225662" 1 "113775009"
"B_LS-NO" "LS-NOB" "accepted" "Bacteria" "Nitrospinota" "Nitrospinia" "Nitrospinales" "Nitrospinaceae" "LS-NOB" "" "" "genus" "GBIF" "11159629" "5444" 2 ""
"B_LABED" "Labedaea" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Labedaea" "" "" "genus" "2012" "LPSN" "518231" "1137" "7668340" "3841" 2 ""
"B_LABED_RHZS" "Labedaea rhizosphaerae" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Labedaea" "rhizosphaerae" "" "species" "2012" "LPSN" "790047" "518231" "7830525" "7668340" 2 ""
"B_LBDLL" "Labedella" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Microbacteriaceae" "Labedella" "" "" "genus" "Li et al., 2019" "LPSN" "517689" "875" "4899919" 2 ""
@ -25498,6 +25497,7 @@
"B_LTTDB" "Lottiidibacillus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Bacillaceae" "Lottiidibacillus" "" "" "genus" "Liu et al., 2020" "LPSN" "9035" "191" 2 ""
"B_LTTDB_PTLL" "Lottiidibacillus patelloidae" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Bacillaceae" "Lottiidibacillus" "patelloidae" "" "species" "Liu et al., 2020" "LPSN" "15262" "9035" 2 ""
"P_[PHL]_LOUKOZOA" "Loukozoa" "accepted" "Protozoa" "Loukozoa" "" "" "" "" "" "" "phylum" "GBIF" "7872314" "7" 2 ""
"B_LS-NO" "LS-NOB" "accepted" "Bacteria" "Nitrospinota" "Nitrospinia" "Nitrospinales" "Nitrospinaceae" "LS-NOB" "" "" "genus" "GBIF" "11159629" "5444" 2 ""
"B_LUCBCTRM" "Lucibacterium" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Lucibacterium" "" "" "genus" "Hendrie et al., 1970" "LPSN" "515980" "1543" "517157" 1 ""
"B_LUCBCTRM_HRVY" "Lucibacterium harveyi" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Lucibacterium" "harveyi" "" "species" "Hendrie et al., 1970" "LPSN" "777606" "515980" "783009" 1 ""
"B_LUCFR" "Lucifera" "accepted" "Bacteria" "Bacillota" "Negativicutes" "Selenomonadales" "Sporomusaceae" "Lucifera" "" "" "genus" "Sanchez-Andrea et al., 2019" "LPSN" "521634" "2041" 2 ""
@ -25850,9 +25850,6 @@
"B_LYTCM" "Lyticum" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rickettsiales" "Ehrlichiaceae" "Lyticum" "" "" "genus" "Preer et al., 1982" "LPSN" "517271" "473" "3221463" "4901684" 2 "433004006"
"B_LYTCM_FLGL" "Lyticum flagellatum" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rickettsiales" "Ehrlichiaceae" "Lyticum" "flagellatum" "" "species" "Preer et al., 1982" "LPSN" "784168" "517271" "3221464" "3221463" 2 "433754005"
"B_LYTCM_SNSM" "Lyticum sinuosum" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rickettsiales" "Ehrlichiaceae" "Lyticum" "sinuosum" "" "species" "Preer et al., 1982" "LPSN" "784169" "517271" "3221465" "3221463" 2 "434353007"
"A_MGII-" "MGIIa-I" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Poseidoniaceae" "MGIIa-I" "" "" "genus" "GBIF" "11196009" "10685831" 2 ""
"A_GII-P" "MGIIb-P" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Thalassarchaeaceae" "MGIIb-P" "" "" "genus" "GBIF" "11123790" "10752789" 2 ""
"B_MZ-XQ" "MZ-XQ" "accepted" "Bacteria" "Mycoplasmatota" "Mollicutes" "Acholeplasmatales" "Acholeplasmataceae" "MZ-XQ" "" "" "genus" "GBIF" "11137212" 2 ""
"B_MBKBC" "Mabikibacter" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Hyphomicrobiales" "Notoacmeibacteraceae" "Mabikibacter" "" "" "genus" "Choi et al., 2017" "LPSN" "519257" "2084" "519233" 2 ""
"B_MBKBC_RUBR" "Mabikibacter ruber" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Hyphomicrobiales" "Notoacmeibacteraceae" "Mabikibacter" "ruber" "" "species" "Choi et al., 2017" "LPSN" "795890" "519257" "795709" "9791970" 2 ""
"B_MCLLB" "Macellibacteroides" "accepted" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Porphyromonadaceae" "Macellibacteroides" "" "" "genus" "Jabari et al., 2012" "LPSN" "518264" "1100" "8021701" 2 ""
@ -27859,6 +27856,8 @@
"F_MYRZY_PRPS_TXTL" "Meyerozyma parapsilosis tuxtlensis" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Meyerozyma" "parapsilosis" "tuxtlensis" "subspecies" "Herrera et al." "GBIF" "3479713" "5893383" 1.5 ""
"F_MYRZY_PSDG" "Meyerozyma pseudoguilliermondii" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Meyerozyma" "pseudoguilliermondii" "" "species" "GBIF" "3556778" "5893380" "5893383" 1.5 ""
"F_MYRZY_SMTH" "Meyerozyma smithsonii" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Meyerozyma" "smithsonii" "" "species" "Yurkov et al." "GBIF" "10712206" "5893380" 1.5 ""
"A_MGII-" "MGIIa-I" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Poseidoniaceae" "MGIIa-I" "" "" "genus" "GBIF" "11196009" "10685831" 2 ""
"A_GII-P" "MGIIb-P" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Thalassarchaeaceae" "MGIIb-P" "" "" "genus" "GBIF" "11123790" "10752789" 2 ""
"B_MCVBR" "Micavibrio" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "Micavibrio" "" "" "genus" "Lambina et al., 1989" "LPSN" "517285" "203" "11199699" "8932" 2 "429897008"
"B_MCVBR_ADMR" "Micavibrio admirandus" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "Micavibrio" "admirandus" "" "species" "Lambina et al., 1989" "LPSN" "784260" "517285" 2 "433368001"
"A_[FAM]_MICRRCHC" "Micrarchaeaceae" "accepted" "Archaea" "Micrarchaeota" "Micrarchaeia" "Micrarchaeales" "Micrarchaeaceae" "" "" "" "family" "GBIF" "10878041" "10702512" 2 ""
@ -30317,6 +30316,7 @@
"B_MYXSR_BRMN" "Myxosarcina burmensis" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Xenococcaceae" "Myxosarcina" "burmensis" "" "species" "Skuja" "GBIF" "3216275" "7729673" 2 ""
"B_MYXSR_CNCN" "Myxosarcina concinna" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Xenococcaceae" "Myxosarcina" "concinna" "" "species" "GBIF" "3217367" "7729673" 2 ""
"B_MYXSR_GLCP" "Myxosarcina gloeocapsoides" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Xenococcaceae" "Myxosarcina" "gloeocapsoides" "" "species" "Komarek et al." "GBIF" "3217365" "7729673" 2 ""
"B_MZ-XQ" "MZ-XQ" "accepted" "Bacteria" "Mycoplasmatota" "Mollicutes" "Acholeplasmatales" "Acholeplasmataceae" "MZ-XQ" "" "" "genus" "GBIF" "11137212" 2 ""
"B_MZBMY" "Mzabimyces" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Mzabimyces" "" "" "genus" "Saker et al., 2015" "LPSN" "518817" "1137" "518590" 2 ""
"B_MZBMY_ALGR" "Mzabimyces algeriensis" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Mzabimyces" "algeriensis" "" "species" "Saker et al., 2015" "LPSN" "793403" "518817" "795677" 2 ""
"B_NAASI" "Naasia" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Microbacteriaceae" "Naasia" "" "" "genus" "Weon et al., 2013" "LPSN" "518394" "875" "8305219" 2 ""
@ -41270,6 +41270,7 @@
"B_SLMNL_ARPH" "Salmonella Arapahoe" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Arapahoe" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARCH" "Salmonella Arechavaleta" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Arechavaleta" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARGN" "Salmonella Argenteuil" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Argenteuil" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARZN" "Salmonella arizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "arizonae" "" "species" "Kauffmann, 1964" "LPSN" "780744" "516547" "780755" "5427588" "3221815" 1.5 ""
"B_SLMNL_ARSH" "Salmonella Arusha" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Arusha" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ASCH" "Salmonella Aschersleben" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Aschersleben" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ASHN" "Salmonella Ashanti" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Ashanti" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41378,6 +41379,7 @@
"B_SLMNL_BLTN" "Salmonella Bolton" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bolton" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BNMS" "Salmonella Bonames" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bonames" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BNRN" "Salmonella Bonariensis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bonariensis" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BNGR" "Salmonella bongori" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "bongori" "" "species" "Reeves et al., 1989" "LPSN" "780745" "516547" "5427596" "3221815" 1 "398393000"
"B_SLMNL_BONN" "Salmonella Bonn" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bonn" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BOTL" "Salmonella Bootle" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bootle" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BRBC" "Salmonella Borbeck" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Borbeck" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41480,6 +41482,14 @@
"B_SLMNL_CHNG" "Salmonella Chingola" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chingola" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHRD" "Salmonella Chiredzi" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chiredzi" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHTT" "Salmonella Chittagong" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chittagong" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHLR" "Salmonella choleraesuis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "" "species" "Weldin, 1927" "LPSN" "780746" "516547" "784857" "7515106" "3221815" "9701185" 1 ""
"B_SLMNL_CHLR_ARZN" "Salmonella choleraesuis arizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "arizonae" "subspecies" "Le Minor et al., 1985" "LPSN" "780747" "780746" "780755" "5427587" "7515106" "5427586" 1 ""
"B_SLMNL_CHLR_BNGR" "Salmonella choleraesuis bongori" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "bongori" "subspecies" "Le Minor et al., 1985" "LPSN" "780748" "780746" "780745" "5427597" "7515106" "5427596" 1 ""
"B_SLMNL_CHLR_CHLR" "Salmonella choleraesuis choleraesuis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "choleraesuis" "subspecies" "Le Minor et al., 1985" "LPSN" "780749" "780746" "780758" "5427590" "7515106" "5427589" 1 ""
"B_SLMNL_CHLR_DRZN" "Salmonella choleraesuis diarizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "diarizonae" "subspecies" "Le Minor et al., 1985" "LPSN" "780750" "780746" "780757" "5427579" "7515106" "5427578" 1 ""
"B_SLMNL_CHLR_HOTN" "Salmonella choleraesuis houtenae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "houtenae" "subspecies" "Le Minor et al., 1985" "LPSN" "780751" "780746" "780759" "5427581" "7515106" "5427580" 1 ""
"B_SLMNL_CHLR_INDC" "Salmonella choleraesuis indica" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "indica" "subspecies" "Le Minor et al., 1987" "LPSN" "780752" "780746" "780760" "5427583" "7515106" "5427582" 1 ""
"B_SLMNL_CHLR_SALM" "Salmonella choleraesuis salamae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "salamae" "subspecies" "Le Minor et al., 1985" "LPSN" "780753" "780746" "780761" "5427585" "7515106" "5427584" 1 ""
"B_SLMNL_CHMD" "Salmonella Chomedey" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chomedey" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHRS" "Salmonella Christiansborg" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Christiansborg" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CLCK" "Salmonella Clackamas" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Clackamas" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41542,6 +41552,7 @@
"B_SLMNL_DESS" "Salmonella Dessau" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dessau" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DTML" "Salmonella Detmold" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Detmold" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DVRS" "Salmonella Deversoir" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Deversoir" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DRZN" "Salmonella diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "diarizonae" "" "species" "GBIF" "516547" "10672082" "3221815" 1.5 ""
"B_SLMNL_DIBR" "Salmonella Dibra" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dibra" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DTRC" "Salmonella Dietrichsdorf" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dietrichsdorf" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DPPL" "Salmonella Dieuppeul" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dieuppeul" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41603,6 +41614,15 @@
"B_SLMNL_ENCN" "Salmonella Encino" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Encino" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ENSC" "Salmonella Enschede" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Enschede" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ENTB" "Salmonella Entebbe" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Entebbe" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ENTR" "Salmonella enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "" "species" "Le Minor et al., 1987" "LPSN" "784857" "516547" "9701185" "3221815" 1 "110378009,397502001,398428002,398508004,398371005,398620001,398488004"
"B_SLMNL_ENTR_ARZN" "Salmonella enterica arizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "arizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780755" "784857" "5427586" "9701185" 1 ""
"B_SLMNL_ENTR_BNGR" "Salmonella enterica bongori" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "bongori" "subspecies" "Le Minor et al., 1987" "LPSN" "780756" "784857" "780745" "5427598" "9701185" "5427596" 1 ""
"B_SLMNL_ENTR_DRZN" "Salmonella enterica diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "diarizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780757" "784857" "5427578" "9701185" 1 ""
"B_SLMNL_ENTR_ENTR" "Salmonella enterica enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "enterica" "subspecies" "Le Minor et al., 1987" "LPSN" "780758" "784857" "5427589" "9701185" 1 ""
"B_SLMNL_ENTR_HOTN" "Salmonella enterica houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "houtenae" "subspecies" "Le Minor et al., 1987" "LPSN" "780759" "784857" "5427580" "9701185" 1 ""
"B_SLMNL_ENTR_INDC" "Salmonella enterica indica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "indica" "subspecies" "Le Minor et al., 1987" "LPSN" "780760" "784857" "5427582" "9701185" 1 ""
"B_SLMNL_ENTR_SALM" "Salmonella enterica salamae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "salamae" "subspecies" "Le Minor et al., 1987" "LPSN" "780761" "784857" "5427584" "9701185" 1 ""
"B_SLMNL_RTDS" "Salmonella enteritidis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enteritidis" "" "species" "Castellani et al., 1919" "LPSN" "780762" "516547" "784857" "5427592" "3221815" "9701185" 1 ""
"B_SLMNL_ENUG" "Salmonella Enugu" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Enugu" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_EPLN" "Salmonella Epalinges" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Epalinges" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_EPCR" "Salmonella Epicrates" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Epicrates" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41725,6 +41745,10 @@
"B_SLMNL_GRPB" "Salmonella Group B" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group B" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPC" "Salmonella Group C" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group C" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPD" "Salmonella Group D" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group D" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPE" "Salmonella Group E" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group E" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPF" "Salmonella Group F" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group F" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPG" "Salmonella Group G" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group G" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPH" "Salmonella Group H" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group H" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GNSS" "Salmonella Grumpensis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Grumpensis" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_GRPR" "Salmonella Guarapiranga" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Guarapiranga" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_GURN" "Salmonella Guerin" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Guerin" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41788,6 +41812,7 @@
"B_SLMNL_HNGK" "Salmonella Hongkong" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Hongkong" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HRSH" "Salmonella Horsham" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Horsham" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HSTN" "Salmonella Houston" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Houston" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HOTN" "Salmonella houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "houtenae" "" "species" "GBIF" "516547" "7617321" "3221815" 1.5 ""
"B_SLMNL_HDDN" "Salmonella Huddinge" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Huddinge" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HTTW" "Salmonella Huettwilen" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Huettwilen" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HULL" "Salmonella Hull" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Hull" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -42257,6 +42282,7 @@
"B_SLMNL_PKST" "Salmonella Pakistan" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Pakistan" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PLMN" "Salmonella Palamaner" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Palamaner" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PALM" "Salmonella Palime" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Palime" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PANM" "Salmonella panama" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "panama" "" "species" "Kauffmann, 1934" "GBIF" "516547" "9407232" "3221815" 1.5 ""
"B_SLMNL_PAPN" "Salmonella Papuana" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Papuana" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PARK" "Salmonella Parakou" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Parakou" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PRTY" "Salmonella Paratyphi" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Paratyphi" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -42459,6 +42485,7 @@
"B_SLMNL_STVN" "Salmonella Stuivenberg" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Stuivenberg" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_STTT" "Salmonella Stuttgart" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Stuttgart" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SUBR" "Salmonella Suberu" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Suberu" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SBTR" "Salmonella subterranea" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "subterranea" "" "species" "Shelobolina et al., 2005" "LPSN" "780769" "516547" "5427595" "3221815" 1.5 ""
"B_SLMNL_SUDN" "Salmonella Sudan" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Sudan" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SLLD" "Salmonella Suelldorf" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Suelldorf" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SNDS" "Salmonella Sundsvall" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Sundsvall" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -42696,29 +42723,6 @@
"B_SLMNL_ZONG" "Salmonella Zongo" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Zongo" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ZULN" "Salmonella Zuilen" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Zuilen" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ZWCK" "Salmonella Zwickau" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Zwickau" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARZN" "Salmonella arizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "arizonae" "" "species" "Kauffmann, 1964" "LPSN" "780744" "516547" "780755" "5427588" "3221815" 1.5 ""
"B_SLMNL_BNGR" "Salmonella bongori" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "bongori" "" "species" "Reeves et al., 1989" "LPSN" "780745" "516547" "5427596" "3221815" 1 "398393000"
"B_SLMNL_CHLR" "Salmonella choleraesuis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "" "species" "Weldin, 1927" "LPSN" "780746" "516547" "784857" "7515106" "3221815" "9701185" 1 ""
"B_SLMNL_CHLR_ARZN" "Salmonella choleraesuis arizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "arizonae" "subspecies" "Le Minor et al., 1985" "LPSN" "780747" "780746" "780755" "5427587" "7515106" "5427586" 1 ""
"B_SLMNL_CHLR_BNGR" "Salmonella choleraesuis bongori" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "bongori" "subspecies" "Le Minor et al., 1985" "LPSN" "780748" "780746" "780745" "5427597" "7515106" "5427596" 1 ""
"B_SLMNL_CHLR_CHLR" "Salmonella choleraesuis choleraesuis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "choleraesuis" "subspecies" "Le Minor et al., 1985" "LPSN" "780749" "780746" "780758" "5427590" "7515106" "5427589" 1 ""
"B_SLMNL_CHLR_DRZN" "Salmonella choleraesuis diarizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "diarizonae" "subspecies" "Le Minor et al., 1985" "LPSN" "780750" "780746" "780757" "5427579" "7515106" "5427578" 1 ""
"B_SLMNL_CHLR_HOTN" "Salmonella choleraesuis houtenae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "houtenae" "subspecies" "Le Minor et al., 1985" "LPSN" "780751" "780746" "780759" "5427581" "7515106" "5427580" 1 ""
"B_SLMNL_CHLR_INDC" "Salmonella choleraesuis indica" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "indica" "subspecies" "Le Minor et al., 1987" "LPSN" "780752" "780746" "780760" "5427583" "7515106" "5427582" 1 ""
"B_SLMNL_CHLR_SALM" "Salmonella choleraesuis salamae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "salamae" "subspecies" "Le Minor et al., 1985" "LPSN" "780753" "780746" "780761" "5427585" "7515106" "5427584" 1 ""
"B_SLMNL_DRZN" "Salmonella diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "diarizonae" "" "species" "GBIF" "516547" "10672082" "3221815" 1.5 ""
"B_SLMNL_ENTR" "Salmonella enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "" "species" "Le Minor et al., 1987" "LPSN" "784857" "516547" "9701185" "3221815" 1 "110378009,397502001,398428002,398508004,398371005,398620001,398488004"
"B_SLMNL_ENTR_ARZN" "Salmonella enterica arizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "arizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780755" "784857" "5427586" "9701185" 1 ""
"B_SLMNL_ENTR_BNGR" "Salmonella enterica bongori" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "bongori" "subspecies" "Le Minor et al., 1987" "LPSN" "780756" "784857" "780745" "5427598" "9701185" "5427596" 1 ""
"B_SLMNL_ENTR_DRZN" "Salmonella enterica diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "diarizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780757" "784857" "5427578" "9701185" 1 ""
"B_SLMNL_ENTR_ENTR" "Salmonella enterica enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "enterica" "subspecies" "Le Minor et al., 1987" "LPSN" "780758" "784857" "5427589" "9701185" 1 ""
"B_SLMNL_ENTR_HOTN" "Salmonella enterica houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "houtenae" "subspecies" "Le Minor et al., 1987" "LPSN" "780759" "784857" "5427580" "9701185" 1 ""
"B_SLMNL_ENTR_INDC" "Salmonella enterica indica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "indica" "subspecies" "Le Minor et al., 1987" "LPSN" "780760" "784857" "5427582" "9701185" 1 ""
"B_SLMNL_ENTR_SALM" "Salmonella enterica salamae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "salamae" "subspecies" "Le Minor et al., 1987" "LPSN" "780761" "784857" "5427584" "9701185" 1 ""
"B_SLMNL_RTDS" "Salmonella enteritidis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enteritidis" "" "species" "Castellani et al., 1919" "LPSN" "780762" "516547" "784857" "5427592" "3221815" "9701185" 1 ""
"B_SLMNL_HOTN" "Salmonella houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "houtenae" "" "species" "GBIF" "516547" "7617321" "3221815" 1.5 ""
"B_SLMNL_PANM" "Salmonella panama" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "panama" "" "species" "Kauffmann, 1934" "GBIF" "516547" "9407232" "3221815" 1.5 ""
"B_SLMNL_SBTR" "Salmonella subterranea" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "subterranea" "" "species" "Shelobolina et al., 2005" "LPSN" "780769" "516547" "5427595" "3221815" 1.5 ""
"B_SLSPL" "Salsipaludibacter" "accepted" "Bacteria" "Actinomycetota" "Nitriliruptoria" "Salsipaludibacterales" "Salsipaludibacteraceae" "Salsipaludibacter" "" "" "genus" "Almeida et al., 2022" "LPSN" "25963" "25953" 2 ""
"B_SLSPL_ALBS" "Salsipaludibacter albus" "accepted" "Bacteria" "Actinomycetota" "Nitriliruptoria" "Salsipaludibacterales" "Salsipaludibacteraceae" "Salsipaludibacter" "albus" "" "species" "Almeida et al., 2022" "LPSN" "25977" "25963" 2 ""
"B_[FAM]_SLSPLDBC" "Salsipaludibacteraceae" "accepted" "Bacteria" "Actinomycetota" "Nitriliruptoria" "Salsipaludibacterales" "Salsipaludibacteraceae" "" "" "" "family" "Almeida et al., 2022" "LPSN" "25953" "25966" 2 ""
@ -45428,15 +45432,6 @@
"B_STRPTB_RATT" "Streptobacillus ratti" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Leptotrichiaceae" "Streptobacillus" "ratti" "" "species" "Eisenberg et al., 2016" "LPSN" "794063" "516688" "9144099" "3225903" 1.5 ""
"B_[FAM]_STRPTCCC" "Streptococcaceae" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "" "" "" "family" "Deibel et al., 1974" "LPSN" "1344" "5123" "4899829" "577" "7798" 2 "115107007"
"B_STRPT" "Streptococcus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "" "" "genus" "Rosenbach, 1884" "LPSN" "517118" "1344" "3223465" "4899829" 1 "58800005,414871004,70160008"
"B_STRPT_GRPA" "Streptococcus Group A" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group A" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPB" "Streptococcus Group B" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group B" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPC" "Streptococcus Group C" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group C" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPD" "Streptococcus Group D" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group D" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPF" "Streptococcus Group F" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group F" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPG" "Streptococcus Group G" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group G" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPH" "Streptococcus Group H" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group H" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPK" "Streptococcus Group K" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group K" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPL" "Streptococcus Group L" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group L" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_ACDM" "Streptococcus acidominimus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "acidominimus" "" "species" "Ayers et al., 1922" "LPSN" "781295" "517118" 1 "51182006"
"B_STRPT_ADJC" "Streptococcus adjacens" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "adjacens" "" "species" "Bouvet et al., 1989" "LPSN" "781296" "517118" "776611" 1.5 ""
"B_STRPT_AGLC" "Streptococcus agalactiae" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "agalactiae" "" "species" "Lehmann et al., 1896" "LPSN" "781297" "517118" 1 "713924007,43492007"
@ -45506,6 +45501,18 @@
"B_STRPT_GLLL_PSTR" "Streptococcus gallolyticus pasteurianus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "gallolyticus" "pasteurianus" "subspecies" "Beck et al., 2008" "LPSN" "781340" "781337" "3227070" 1.25 ""
"B_STRPT_GARV" "Streptococcus garvieae" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "garvieae" "" "species" "Collins et al., 1984" "LPSN" "781341" "517118" "777418" 1 ""
"B_STRPT_GRDN" "Streptococcus gordonii" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "gordonii" "" "species" "Kilian et al., 1989" "LPSN" "781342" "517118" 1 "113986004"
"B_STRPT_GRPA" "Streptococcus Group A" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group A" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPB" "Streptococcus Group B" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group B" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPC" "Streptococcus Group C" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group C" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPD" "Streptococcus Group D" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group D" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPE" "Streptococcus Group E" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group E" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPF" "Streptococcus Group F" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group F" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPG" "Streptococcus Group G" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group G" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPH" "Streptococcus Group H" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group H" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPI" "Streptococcus Group I" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group I" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPJ" "Streptococcus Group J" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group J" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPK" "Streptococcus Group K" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group K" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPL" "Streptococcus Group L" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group L" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GWNG" "Streptococcus gwangjuense" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "gwangjuense" "" "species" "GBIF" "11190550" "3223465" 1.5 ""
"B_STRPT_HLCH" "Streptococcus halichoeri" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "halichoeri" "" "species" "Shewmaker et al., 2016" "LPSN" "781344" "517118" 1.25 "438161002"
"B_STRPT_HLTS" "Streptococcus halitosis" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "halitosis" "" "species" "GBIF" "10822581" "3223465" 1.5 ""
@ -51722,7 +51729,6 @@
"A_WKNGR_YPNS" "Wukongarchaeum yapensis" "accepted" "Archaea" "Asgardarchaeota" "Wukongarchaeia" "Wukongarchaeales" "Wukongarchaeaceae" "Wukongarchaeum" "yapensis" "" "species" "GBIF" "11649514" "11817462" 2 ""
"B_WKNGB" "Wukongibacter" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Peptostreptococcaceae" "Wukongibacter" "" "" "genus" "Li et al., 2016" "LPSN" "519079" "1053" "9506110" "7800" 2 ""
"B_WKNGB_BDNS" "Wukongibacter baidiensis" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Peptostreptococcaceae" "Wukongibacter" "baidiensis" "" "species" "Li et al., 2016" "LPSN" "794822" "519079" "9479445" "9506110" 2 ""
"B_XYC" "XYC" "accepted" "Bacteria" "Nitrospirota" "Thermodesulfovibrionia" "Thermodesulfovibrionales" "Magnetobacteriaceae" "XYC" "" "" "genus" "GBIF" "11695901" "10718264" 2 ""
"P_XNTHS" "Xanthiosphaera" "accepted" "Protozoa" "Sarcomastigophora" "" "" "" "Xanthiosphaera" "" "" "genus" "GBIF" "9472186" 2 ""
"P_XNTHS_LPPC" "Xanthiosphaera lappacea" "accepted" "Protozoa" "Sarcomastigophora" "" "" "" "Xanthiosphaera" "lappacea" "" "species" "Haeckel" "GBIF" "6123506" "9472186" 2 ""
"B_XNTHB" "Xanthobacter" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Hyphomicrobiales" "Xanthobacteraceae" "Xanthobacter" "" "" "genus" "Wiegel et al., 1978" "LPSN" "516929" "1568" 2 "439120008"
@ -51892,6 +51898,7 @@
"B_[FAM]_XPHNMTBC" "Xiphinematobacteraceae" "accepted" "Bacteria" "Verrucomicrobiota" "Verrucomicrobiae" "Chthoniobacterales" "Xiphinematobacteraceae" "" "" "" "family" "GBIF" "10770063" "10733345" 2 ""
"B_XUHSH" "Xuhuaishuia" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Rhodobacteraceae" "Xuhuaishuia" "" "" "genus" "Wang et al., 2016" "LPSN" "518921" "1175" "518801" 2 ""
"B_XUHSH_MNGN" "Xuhuaishuia manganoxidans" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Rhodobacteraceae" "Xuhuaishuia" "manganoxidans" "" "species" "Wang et al., 2016" "LPSN" "793971" "518921" "793304" 2 ""
"B_XYC" "XYC" "accepted" "Bacteria" "Nitrospirota" "Thermodesulfovibrionia" "Thermodesulfovibrionales" "Magnetobacteriaceae" "XYC" "" "" "genus" "GBIF" "11695901" "10718264" 2 ""
"B_XYLNB" "Xylanibacillus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Paenibacillaceae" "Xylanibacillus" "" "" "genus" "Kukolya et al., 2018" "LPSN" "520351" "1013" 2 ""
"B_XYLNB_CMPS" "Xylanibacillus composti" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Paenibacillaceae" "Xylanibacillus" "composti" "" "species" "Kukolya et al., 2018" "LPSN" "797542" "520351" 2 ""
"B_XBCTR" "Xylanibacter" "synonym" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Prevotellaceae" "Xylanibacter" "" "" "genus" "Hitch et al., 2022" "LPSN" "516940" "1105" "516385" 2 ""

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data-raw/reproduction_of_clinical_breakpoints.R
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@ -44,10 +44,18 @@ whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("
# remove old taxonomic names
filter(TAXONOMIC_STATUS == "C") %>%
transmute(ORGANISM_CODE = tolower(WHONET_ORG_CODE), ORGANISM) %>%
# what's wrong here? 'sau' is both S. areus and S. aureus sp. aureus
mutate(
# what's wrong here? all these are only in the table on subspecies level (where species == subspecies), not on species level
ORGANISM = if_else(ORGANISM_CODE == "sau", "Staphylococcus aureus", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "pam", "Pasteurella multocida", ORGANISM)
ORGANISM = if_else(ORGANISM_CODE == "pam", "Pasteurella multocida", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "kpn", "Klebsiella pneumoniae", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "caj", "Campylobacter jejuni", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "mmo", "Morganella morganii", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "sap", "Staphylococcus saprophyticus", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "fne", "Fusobacterium necrophorum", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "fnu", "Fusobacterium nucleatum", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "sdy", "Streptococcus dysgalactiae", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "axy", "Achromobacter xylosoxidans", ORGANISM)
)
whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
filter(BREAKPOINT_TYPE == "Human", GUIDELINES %in% c("CLSI", "EUCAST"))
@ -64,6 +72,36 @@ whonet_organisms <- whonet_organisms %>%
ORGANISM = c("Enterobacterales", "Campylobacter")
))
mo_reset_session()
whonet_organisms.bak <- whonet_organisms
whonet_organisms <- whonet_organisms.bak %>%
mutate(mo = as.mo(gsub("(sero[a-z]*| complex| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
keep_synonyms = TRUE,
language = "en"),
mo = as.mo(ifelse(ORGANISM %like% "Anaerobic", "B_ANAER", mo)),
mo_name = mo_name(mo,
keep_synonyms = TRUE,
language = "en"))
# update microorganisms.codes with the latest WHONET codes
new_mo_codes <- whonet_organisms %>%
mutate(
first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other")
microorganisms.codes <- microorganisms.codes %>%
# remove all old WHONET codes, whether we (in the end) keep them or not
filter(!toupper(code) %in% toupper(new_mo_codes$ORGANISM_CODE)) %>%
bind_rows(new_mo_codes %>%
filter(keep == TRUE) %>%
transmute(code = toupper(ORGANISM_CODE),
mo = mo)) %>%
arrange(code)
# save to package
usethis::use_data(microorganisms.codes, overwrite = TRUE, compress = "xz", version = 2)
rm(microorganisms.codes)
devtools::load_all()
breakpoints <- whonet_breakpoints %>%
mutate(ORGANISM_CODE = tolower(ORGANISM_CODE)) %>%
left_join(whonet_organisms) %>%

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2
man/AMR.Rd
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@ -32,7 +32,7 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated December 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated december 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}

10
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 52 142 Microorganisms}
\title{Data Set with 52 149 Microorganisms}
\format{
A \link[tibble:tibble]{tibble} with 52 142 observations and 22 variables:
A \link[tibble:tibble]{tibble} with 52 149 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.
@ -51,7 +51,7 @@ Included taxonomic data are:
\item All ~36 000 (sub)species from the kingdoms of Archaea and Bacteria
\item ~7 900 (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 ~5 100 (sub)species from the kingdom of Protozoa
\item ~1 400 (sub)species from ~40 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item ~1 400 (sub)species from 43 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item All ~9 800 previously accepted names of all included (sub)species (these were taxonomically renamed)
\item The complete taxonomic tree of all included (sub)species: from kingdom to subspecies
\item The identifier of the parent taxons
@ -61,8 +61,8 @@ Included taxonomic data are:
For convenience, some entries were added manually:
\itemize{
\item ~1 500 entries for the city-like serovars of \emph{Salmonellae}
\item 11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
\item ~1 500 entries of \emph{Salmonella}, such as the city-like serovars and groups A to H
\item 15 entries of \emph{Streptococcus}, such as the beta-haemolytic groups A to K, viridans, and milleri
\item 2 entries of \emph{Staphylococcus} (coagulase-negative (CoNS) and coagulase-positive (CoPS))
\item 1 entry of \emph{Blastocystis} (\emph{B. hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
\item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology

4
man/microorganisms.codes.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Data Set with 5 910 Common Microorganism Codes}
\title{Data Set with 5 751 Common Microorganism Codes}
\format{
A \link[tibble:tibble]{tibble} with 5 910 observations and 2 variables:
A \link[tibble:tibble]{tibble} with 5 751 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set