incorporate Bartlett et al (2022)

data-raw/_pre_commit_hook.R

@@ -168,29 +168,21 @@ MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptoc
   ))]
 MO_FULLNAME_LOWER <- create_MO_fullname_lower()
 MO_PREVALENT_GENERA <- c(
-  "Absidia", "Acanthamoeba", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes", "Alloprevotella",
-  "Alternaria", "Amoeba", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles",
-  "Apophysomyces", "Arachnia", "Aspergillus", "Aureobasidium", "Bacteroides", "Basidiobolus",
-  "Beauveria", "Bergeyella", "Blastocystis", "Blastomyces", "Borrelia", "Brachyspira", "Branhamella",
-  "Butyricimonas", "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cetobacterium", "Chaetomium",
-  "Chlamydia", "Chlamydophila", "Christensenella", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium",
-  "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus", "Demodex",
-  "Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia",
-  "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", "Meyerozyma",
-  "Microsporidium", "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
-  "Nectria", "Ochroconis", "Odoribacter", "Oesophagostomum", "Oidiodendron", "Opisthorchis",
-  "Ornithobacterium", "Parabacteroides", "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola",
-  "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",
-  "Syngamus", "Taenia", "Tannerella", "Tenacibaculum", "Terrimonas", "Toxocara", "Treponema", "Trichinella",
-  "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus",
-  "Trichuris", "Tritirachium", "Trypanosoma", "Trombicula", "Tunga", "Ureaplasma", "Victivallis", "Wautersiella",
-  "Weeksella", "Wuchereria"
+  "Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
+  "Anisakis", "Anopheles", "Apophysomyces", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
+  "Blastocystis", "Blastomyces", "Candida", "Capillaria", "Chaetomium", "Chrysonilia", "Cladophialophora",
+  "Cladosporium", "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex",
+  "Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Echinostoma", "Entamoeba", "Enterobius",
+  "Exophiala", "Exserohilum", "Fasciola", "Fonsecaea", "Fusarium", "Giardia", "Haloarcula", "Halobacterium",
+  "Halococcus", "Hendersonula", "Heterophyes", "Histomonas", "Histoplasma", "Hymenolepis", "Hypomyces",
+  "Hysterothylacium", "Leishmania", "Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma", "Microsporidium",
+  "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Necator", "Nectria", "Ochroconis", "Oesophagostomum",
+  "Oidiodendron", "Opisthorchis", "Pediculus", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces",
+  "Pityrosporum", "Pneumocystis", "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus",
+  "Rhodotorula", "Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra",
+  "Sporobolomyces", "Stachybotrys", "Strongyloides", "Syngamus", "Taenia", "Toxocara", "Trichinella", "Trichobilharzia",
+  "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium",
+  "Trombicula", "Trypanosoma", "Tunga", "Wuchereria"
 )
 
 # antibiotic groups

data-raw/eucast_rules.tsv

@@ -69,9 +69,9 @@ genus_species	is	Moraxella catarrhalis	ERY	S	AZM, CLR, RXT	S	Moraxella catarrhal
 genus_species	is	Moraxella catarrhalis	ERY	I	AZM, CLR, RXT	I	Moraxella catarrhalis	Breakpoints	10	
 genus_species	is	Moraxella catarrhalis	ERY	R	AZM, CLR, RXT	R	Moraxella catarrhalis	Breakpoints	10	
 genus_species	is	Moraxella catarrhalis	TCY	S	DOX, MNO	S	Moraxella catarrhalis	Breakpoints	10	
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	S	AMP, AMX, PIP, TZP, TIC	S	Anaerobic Gram-positives	Breakpoints	10	
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	I	AMP, AMX, PIP, TZP, TIC	I	Anaerobic Gram-positives	Breakpoints	10	
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	R	AMP, AMX, PIP, TZP, TIC	R	Anaerobic Gram-positives	Breakpoints	10	
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	S	AMP, AMX, PIP, TZP, TIC	S	Anaerobic Gram-positives	Breakpoints	10	
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	I	AMP, AMX, PIP, TZP, TIC	I	Anaerobic Gram-positives	Breakpoints	10	
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	R	AMP, AMX, PIP, TZP, TIC	R	Anaerobic Gram-positives	Breakpoints	10	
 genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	S	AMP, AMX, PIP, TZP, TIC	S	Anaerobic Gram-negatives	Breakpoints	10	
 genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	I	AMP, AMX, PIP, TZP, TIC	I	Anaerobic Gram-negatives	Breakpoints	10	
 genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	R	AMP, AMX, PIP, TZP, TIC	R	Anaerobic Gram-negatives	Breakpoints	10	
@@ -175,9 +175,9 @@ genus_species	is	Moraxella catarrhalis	ERY	S	AZM, CLR, RXT	S	Moraxella catarrhal
 genus_species	is	Moraxella catarrhalis	ERY	I	AZM, CLR, RXT	I	Moraxella catarrhalis	Breakpoints	11	
 genus_species	is	Moraxella catarrhalis	ERY	R	AZM, CLR, RXT	R	Moraxella catarrhalis	Breakpoints	11	
 genus_species	is	Moraxella catarrhalis	TCY	S	DOX, MNO	S	Moraxella catarrhalis	Breakpoints	11	
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	S	AMP, AMX, PIP, TIC	S	Anaerobic Gram-positives	Breakpoints	11	
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	I	AMP, AMX, PIP, TIC	I	Anaerobic Gram-positives	Breakpoints	11	
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	R	AMP, AMX, PIP, TIC	R	Anaerobic Gram-positives	Breakpoints	11	
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	S	AMP, AMX, PIP, TIC	S	Anaerobic Gram-positives	Breakpoints	11	
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	I	AMP, AMX, PIP, TIC	I	Anaerobic Gram-positives	Breakpoints	11	
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	R	AMP, AMX, PIP, TIC	R	Anaerobic Gram-positives	Breakpoints	11	
 genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	S	AMP, AMX, PIP, TIC	S	Anaerobic Gram-negatives	Breakpoints	11	
 genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	I	AMP, AMX, PIP, TIC	I	Anaerobic Gram-negatives	Breakpoints	11	
 genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	R	AMP, AMX, PIP, TIC	R	Anaerobic Gram-negatives	Breakpoints	11	

data-raw/microorganisms.md5

@@ -1 +1 @@
-6e6f44705995094be5eddc00e0878308
+9e75112567e7786a6712024730056057

data-raw/reproduction_of_microorganisms.R

@@ -36,20 +36,29 @@
 # 2. Go to https://lpsn.dsmz.de/downloads (register first) and download the latest
 #    CSV file (~12,5 MB) as "taxonomy.csv". Their API unfortunately does
 #    not include the full taxonomy and is currently (2022) pretty worthless.
-# 3. Set this folder_location to the path where these two files are:
+# 3. For data about human pathogens, we use Bartlett et al. (2022),
+#    https://doi.org/10.1099/mic.0.001269. Their latest supplementary material 
+#    can be found here: https://github.com/padpadpadpad/bartlett_et_al_2022_human_pathogens.
+#.   Download their latest xlsx file in the `data` folder and save it to our
+#.   `data-raw` folder.
+# 4. Set this folder_location to the path where these two files are:
 folder_location <- "~/Downloads/backbone/"
 file_gbif <- paste0(folder_location, "Taxon.tsv")
 file_lpsn <- paste0(folder_location, "taxonomy.csv")
 
+file_bartlett <- "data-raw/bartlett_et_al_2022_human_pathogens.xlsx"
+
 # 4. Run the rest of this script line by line and check everything :)
 
 if (!file.exists(file_gbif)) stop("GBIF file not found")
 if (!file.exists(file_lpsn)) stop("LPSN file not found")
+if (!file.exists(file_bartlett)) stop("Bartlett et al. Excel file not found")
 
 library(dplyr)
 library(vroom) # to import files
 library(rvest) # to scape LPSN website
 library(progress) # to show progress bars
+library(readxl) # for reading the Bartlett Excel file
 devtools::load_all(".") # load AMR package
 
 # Helper functions --------------------------------------------------------
@@ -776,32 +785,6 @@ taxonomy$gbif_parent[taxonomy$rank == "subspecies" & !is.na(taxonomy$gbif)] <- t
 all(taxonomy$lpsn_parent %in% taxonomy$lpsn)
 all(taxonomy$gbif_parent %in% taxonomy$gbif)
 
-
-# Add prevalence ----------------------------------------------------------
-
-# update prevalence based on taxonomy (our own JSS paper: Berends MS et al. (2022), DOI 10.18637/jss.v104.i03)
-taxonomy <- taxonomy %>%
-  mutate(prevalence = case_when(
-    class == "Gammaproteobacteria" |
-      genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
-    ~ 1,
-    kingdom %in% c("Archaea", "Bacteria", "Chromista", "Fungi") &
-      (phylum %in% c(
-        "Sarcomastigophora",
-        "Firmicutes", # old, now Bacillota
-        "Bacillota",
-        "Proteobacteria", # old, now Pseudomonadota
-        "Pseudomonadota",
-        "Actinobacteria", # old, now Actinomycetota
-        "Actinomycetota"
-      ) |
-        genus %in% AMR:::MO_PREVALENT_GENERA)
-    ~ 2,
-    TRUE ~ 3
-  ))
-table(taxonomy$prevalence, useNA = "always")
-# (a lot will be removed further below)
-
 # fix rank
 taxonomy <- taxonomy %>%
   mutate(rank = case_when(
@@ -817,6 +800,71 @@ taxonomy <- taxonomy %>%
   ))
 
 
+# Add prevalence ----------------------------------------------------------
+
+pathogens <- read_excel(file_bartlett, sheet = "Tab 6 Full List")
+
+# get all established, both old and current taxonomic names
+established <- pathogens %>% 
+  filter(status == "established") %>% 
+  mutate(fullname = paste(genus, species)) %>%
+  pull(fullname) %>% 
+  c(unlist(mo_current(.)),
+    unlist(mo_synonyms(., keep_synonyms = FALSE))) %>% 
+  strsplit(" ", fixed = TRUE) %>% 
+  sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>% 
+  sort() %>% 
+  unique()
+
+# get all putative, both old and current taxonomic names
+putative <- pathogens %>% 
+  filter(status == "putative") %>% 
+  mutate(fullname = paste(genus, species)) %>%
+  pull(fullname) %>% 
+  c(unlist(mo_current(.)),
+    unlist(mo_synonyms(., keep_synonyms = FALSE))) %>% 
+  strsplit(" ", fixed = TRUE) %>% 
+  sapply(function(x) ifelse(length(x) == 1, x, paste(x[1], x[2]))) %>% 
+  sort() %>% 
+  unique()
+
+established <- established[established %unlike% "unknown"]
+putative <- putative[putative %unlike% "unknown"]
+
+other_bacterial_genera <- c(established, putative) %>% 
+  strsplit(" ", fixed = TRUE) %>% 
+  sapply(function(x) x[1]) %>% 
+  sort() %>% 
+  unique()
+
+other_genera <- AMR:::MO_PREVALENT_GENERA %>% 
+  c(unlist(mo_current(.)),
+    unlist(mo_synonyms(., keep_synonyms = FALSE))) %>% 
+  strsplit(" ", fixed = TRUE) %>% 
+  sapply(function(x) x[1]) %>% 
+  sort() %>% 
+  unique()
+other_genera <- other_genera[other_genera %unlike% "unknown"]
+
+# update prevalence based on taxonomy (following the recent and thorough work of Bartlett et al., 2022)
+# see https://doi.org/10.1099/mic.0.001269
+taxonomy <- taxonomy %>% 
+  mutate(prevalence = case_when(
+    # 'established' gets a 1 and means 'have infected at least three persons in three or more references'
+    paste(genus, species) %in% established & rank %in% c("genus", "species", "subspecies") ~ 1.0,
+    # 'putative' gets a 2 and  means 'fewer than three known cases'
+    paste(genus, species) %in% putative & rank %in% c("genus", "species", "subspecies") ~ 2.0,
+    # other species from a genus in either group get a 2.5
+    genus %in% other_bacterial_genera & rank %in% c("genus", "species", "subspecies") ~ 2.5,
+    # we keep track of prevalent genera too of non-bacterial species
+    genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 2.5,
+    # all others get a 3
+    TRUE ~ 3.0))
+
+table(taxonomy$prevalence, useNA = "always")
+# (a lot will be removed further below)
+
+
 # Save intermediate results (2) -------------------------------------------
 
 saveRDS(taxonomy, "data-raw/taxonomy2.rds")