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Added C. freundii complex and Y. pseudotuberculosis complex

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dr. M.S. (Matthijs) Berends
2023-07-14 10:49:06 +02:00
parent fd480d1a9a
commit 7a4628b73f
26 changed files with 52 additions and 18 deletions
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"B_CTRBC_AMLN-C" "B_CTRBC_AMLN" "Citrobacter amalonaticus complex" "Citrobacter amalonaticus"
"B_CTRBC_AMLN-C" "B_CTRBC_FRMR" "Citrobacter amalonaticus complex" "Citrobacter farmeri"
"B_CTRBC_AMLN-C" "B_CTRBC_SDLK" "Citrobacter amalonaticus complex" "Citrobacter sedlakii"
"B_CTRBC_FRND-C" "B_CTRBC_BRAK" "Citrobacter freundii complex" "Citrobacter braakii"
"B_CTRBC_FRND-C" "B_CTRBC_FRND" "Citrobacter freundii complex" "Citrobacter freundii"
"B_CTRBC_FRND-C" "B_CTRBC_GLLN" "Citrobacter freundii complex" "Citrobacter gillenii"
"B_CTRBC_FRND-C" "B_CTRBC_MRLN" "Citrobacter freundii complex" "Citrobacter murliniae"
"B_CTRBC_FRND-C" "B_CTRBC_PRTC" "Citrobacter freundii complex" "Citrobacter portucalensis"
"B_CTRBC_FRND-C" "B_CTRBC_SDLK" "Citrobacter freundii complex" "Citrobacter sedlakii"
"B_CTRBC_FRND-C" "B_CTRBC_WRKM" "Citrobacter freundii complex" "Citrobacter werkmanii"
"B_CTRBC_FRND-C" "B_CTRBC_YONG" "Citrobacter freundii complex" "Citrobacter youngae"
"B_STPHY_CONS" "B_STPHY_ARGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus argensis"
"B_STPHY_CONS" "B_STPHY_ARLT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus arlettae"
"B_STPHY_CONS" "B_STPHY_ARCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus auricularis"
@@ -506,3 +514,9 @@
"B_STRPT_VIRI" "B_STRPT_SUIS" "Viridans Group Streptococcus (VGS)" "Streptococcus suis"
"B_STRPT_VIRI" "B_STRPT_UBRS" "Viridans Group Streptococcus (VGS)" "Streptococcus uberis"
"B_STRPT_VIRI" "B_STRPT_VSTB" "Viridans Group Streptococcus (VGS)" "Streptococcus vestibularis"
"B_YERSN_PSDT-C" "B_YERSN_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT_PSTS" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pestis"
"B_YERSN_PSDT-C" "B_YERSN_PSDT_PSDT" "Yersinia pseudotuberculosis complex" "Yersinia pseudotuberculosis pseudotuberculosis"
"B_YERSN_PSDT-C" "B_YERSN_SMLS" "Yersinia pseudotuberculosis complex" "Yersinia similis"
"B_YERSN_PSDT-C" "B_YERSN_WTRS" "Yersinia pseudotuberculosis complex" "Yersinia wautersii"

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@@ -11206,6 +11206,7 @@
"B_CTRBC_ERPS" "Citrobacter europaeus" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "europaeus" "" "species" "Ribeiro et al., 2017" "facultative anaerobe" "LPSN" "795042" "515376" "9554238" "11150190" 1.5 ""
"B_CTRBC_FRMR" "Citrobacter farmeri" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "farmeri" "" "species" "Brenner et al., 1993" "aerobe" "LPSN" "774746" "515376" "3221799" "11150190" 1 "1089701000112106,114263005"
"B_CTRBC_FRND" "Citrobacter freundii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "freundii" "" "species" "Werkman et al., 1932" "aerobe" "LPSN" "774747" "515376" "10732598" "11150190" 1 "1089901000112108,6265002,721909006,715206000"
"B_CTRBC_FRND-C" "Citrobacter freundii complex" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "freundii complex" "" "species group" "aerobe" "manually added" "515376" "11150190" 1 ""
"B_CTRBC_GLLN" "Citrobacter gillenii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "gillenii" "" "species" "Brenner et al., 2000" "aerobe" "LPSN" "774750" "515376" "3221794" "11150190" 1.5 "416990006"
"B_CTRBC_KOSR" "Citrobacter koseri" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "koseri" "" "species" "Frederiksen, 1970" "aerobe" "LPSN" "774752" "515376" "3221790" "11150190" 1 "1090401000112109,114264004"
"B_CTRBC_MLNT" "Citrobacter malonatica" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "malonatica" "" "species" "Young et al., 1971" "aerobe" "GBIF" "5427569" "11150190" "3221790" 1 ""
@@ -38966,6 +38967,7 @@
"B_RPHDP_SBRC" "Raphidiopsis subrecta" "synonym" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Nostocaceae" "Raphidiopsis" "subrecta" "" "species" "Fremy et al." "GBIF" "7555557" "3219380" "4306613" 2 ""
"B_RPDTH" "Rapidithrix" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Flammeovirgaceae" "Rapidithrix" "" "" "genus" "Srisukchayakul et al., 2007" "aerobe" "LPSN" "517677" "522" "4903792" 2 ""
"B_RPDTH_THLN" "Rapidithrix thailandica" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Flammeovirgaceae" "Rapidithrix" "thailandica" "" "species" "Srisukchayakul et al., 2007" "aerobe" "LPSN" "786823" "517677" "5917946" "4903792" 2 ""
"B_MYCBC_RGM" "Rapidly growing Mycobacterium (RGM)" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "rapidly growing" "" "species group" "facultative anaerobe" "manually added" "912" "8084" 1 ""
"B_RPPPR" "Rappaport" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Cardiobacteriales" "Cardiobacteriaceae" "Rappaport" "" "" "genus" "GBIF" "10714677" "8970" 2 ""
"B_RPPPR_ISRL" "Rappaport israeli" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Cardiobacteriales" "Cardiobacteriaceae" "Rappaport" "israeli" "" "species" "GBIF" "10890221" "10714677" 2 ""
"B_RRGLB" "Rariglobus" "accepted" "Bacteria" "Verrucomicrobiota" "Opitutae" "Opitutales" "Opitutaceae" "Rariglobus" "" "" "genus" "Pitt et al., 2020" "LPSN" "4967" "993" "11151485" 2 ""
@@ -51989,6 +51991,7 @@
"B_YERSN_PHLM" "Yersinia philomiragia" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Yersiniaceae" "Yersinia" "philomiragia" "" "species" "Jensen et al., 1969" "microaerophile" "LPSN" "783201" "516947" "776319" 1 ""
"B_YERSN_PRXM" "Yersinia proxima" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Yersiniaceae" "Yersinia" "proxima" "" "species" "Le Guern et al., 2020" "likely facultative anaerobe" "LPSN" "14095" "516947" 1.5 ""
"B_YERSN_PSDT" "Yersinia pseudotuberculosis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Yersiniaceae" "Yersinia" "pseudotuberculosis" "" "species" "Smith et al., 1965" "likely facultative anaerobe" "LPSN" "783202" "516947" "5427620" "3221889" "5427631" 1 "90530002"
"B_YERSN_PSDT-C" "Yersinia pseudotuberculosis complex" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Yersiniaceae" "Yersinia" "pseudotuberculosis complex" "" "species group" "likely facultative anaerobe" "manually added" "516947" "3221889" 1 ""
"B_YERSN_PSDT_PSTS" "Yersinia pseudotuberculosis pestis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Yersiniaceae" "Yersinia" "pseudotuberculosis" "pestis" "subspecies" "Bercovier et al., 1981" "aerobe" "LPSN" "798529" "783202" "785226" 1 ""
"B_YERSN_PSDT_PSDT" "Yersinia pseudotuberculosis pseudotuberculosis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Yersiniaceae" "Yersinia" "pseudotuberculosis" "pseudotuberculosis" "subspecies" "Bercovier et al., 1981" "aerobe" "LPSN" "798530" "783202" "783202" 1 ""
"B_YERSN_RCHS" "Yersinia rochesterensis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Yersiniaceae" "Yersinia" "rochesterensis" "" "species" "Nguyen et al., 2021" "likely facultative anaerobe" "LPSN" "17336" "516947" "11652009" "3221889" 1.5 ""
@@ -52167,4 +52170,3 @@
"B_ZYMPH" "Zymophilus" "synonym" "Bacteria" "Bacillota" "Negativicutes" "Selenomonadales" "Selenomonadaceae" "Zymophilus" "" "" "genus" "Schleifer et al., 1990" "anaerobe" "LPSN" "516961" "2042" "516396" 2 "438883001"
"B_ZYMPH_PCVR" "Zymophilus paucivorans" "synonym" "Bacteria" "Bacillota" "Negativicutes" "Selenomonadales" "Selenomonadaceae" "Zymophilus" "paucivorans" "" "species" "Schleifer et al., 1990" "anaerobe" "LPSN" "783229" "516961" "792213" 2 "440843008"
"B_ZYMPH_RFFN" "Zymophilus raffinosivorans" "synonym" "Bacteria" "Bacillota" "Negativicutes" "Selenomonadales" "Selenomonadaceae" "Zymophilus" "raffinosivorans" "" "species" "Schleifer et al., 1990" "anaerobe" "LPSN" "783230" "516961" "792212" 2 "440844002"
"B_MYCBC_RGM" "Rapidly growing Mycobacterium (RGM)" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "rapidly growing" "" "species group" "facultative anaerobe" "manually added" "912" "8084" 1 ""

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data-raw/reproduction_of_microorganisms.groups.R
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@@ -38,6 +38,13 @@ devtools::load_all()
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
# BACTERIAL COMPLEXES
# find all bacterial complex in the NCBI Taxonomy Browser here:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=6&lin=f&keep=1&srchmode=1&unlock
# and search the page for 'complex', then follow the link and add the missing ones in this R file
# READ DATA ----
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
@@ -131,6 +138,16 @@ microorganisms.groups <- whonet_organisms %>%
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = as.mo("Eikenella corrodens", keep_synonyms = TRUE))) %>%
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = microorganisms %>% filter(genus == "Kingella") %>% pull(mo))) %>%
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = as.mo("Actinobacillus actinomycetemcomitans", keep_synonyms = TRUE))) %>%
# Citrobacter freundii complex in the NCBI Taxonomy Browser:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1344959
filter(mo_group != "B_CTRBC_FRND-C") %>%
bind_rows(tibble(mo_group = as.mo("B_CTRBC_FRND-C"),
mo = paste("Citrobacter", c("freundii", "braakii", "gillenii", "murliniae", "portucalensis", "sedlakii", "werkmanii", "youngae")) %>% as.mo(keep_synonyms = TRUE))) %>%
# Yersinia pseudotuberculosis complex in the NCBI Taxonomy Browser:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1649845
filter(mo_group != "B_YERSN_PSDT-C") %>%
bind_rows(tibble(mo_group = as.mo("B_YERSN_PSDT-C"),
mo = paste("Yersinia", c("pseudotuberculosis", "pestis", "similis", "wautersii")) %>% as.mo(keep_synonyms = TRUE))) %>%
# RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
filter(mo_group != "B_MYCBC_RGM") %>%
bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),