Candida auris mapped to only Candida by as.mo()

[remcv]

Hello Matthijs,

Thank you for continuing to maintain and update this great package.

The problem is that as.mo("Candida auris") is wrongly identified as just Candida and is treated as an uncertain result.

> mo_uncertainties() "Candida auris" -> Candida (F_CANDD, 0.143)

I checked the library's microorganism dataset and Candida auris is present there.

AMR package version 1.8.2

[remcv]

I can see there is a workaround described by you in a different issue https://github.com/msberends/AMR/issues/54#issuecomment-1120890522

[msberends]

Thanks, and you’re welcome!

Yes, it seems the current release shows some problems with translating user input. Not sure why this didn’t come up in the past three years. Especially for C. auris it’s rather painful that it doesn’t work right.

The good news is that the new algorithm fixes this, which is now available as beta version.

as.mo("Candida auris") 
#> Class 'mo'
#> [1] F_CANDD_AURS

# full info:
mo_info("Candida auris")
#> $kingdom
#> [1] "Fungi"
#>
#> $phylum
#> [1] "Ascomycota"
#>
#> $class
#> [1] "Saccharomycetes"
#> 
#> $order
#> [1] "Saccharomycetales"
#> 
#> $family
#> [1] "Debaryomycetaceae"
#> 
#> $genus
#> [1] "Candida"
#> 
#> $species
#> [1] "auris"
#> 
#> $subspecies
#> [1] ""
#> 
#> $status
#> [1] "accepted"
#> 
#> $synonyms
#> NULL
#> 
#> $gramstain
#> [1] NA
#> 
#> $url
#> [1] "https://www.gbif.org/species/3479791"
#> 
#> $ref
#> [1] "Satoh et al., 2009"
#> 
#> $snomed
#> [1] "3491000146109"

You can install the beta version with:

remotes::install_github("msberends/AMR")

We’re curious for feedback, so please let us know :)

[remcv]

I've installed the beta version and used it. The good news is that the Candida auris problem is solved. The bad news is that now there are more mo uncertainties, including microbes that had a name change and were previously (in 1.8.2) detected as such.

Below is the list of germs I'm trying to map to MOs.

> unique(urinary_isolates$microb)
 [1] Enterobacter cloacae                          Candida tropicalis                           
 [3] Escherichia coli                              Citrobacter koseri                           
 [5] Proteus mirabilis                             Klebsiella pneumoniae                        
 [7] Streptococcus agalactiae                      Enterococcus faecalis                        
 [9] Candida parapsilosis                          Candida albicans                             
[11] Pseudomonas aeruginosa                        Enterococcus faecium                         
[13] Cronobacter sakazakii                         Serratia marcescens                          
[15] Citrobacter freundii                          Enterococcus spp                             
[17] Candida non-albicans                          Klebsiella aerogenes                         
[19] Klebsiella oxytoca                            Morganella morganii                          
[21] Kluyveromyces marxianus                       Proteus vulgaris                             
[23] Staphylococcus aureus                         Acinetobacter baumannii                      
[25] Providencia stuartii                          Acinetobacter calcoaceticus/baumannii complex
[27] Candida rugosa                                Pseudomonas spp                              
[29] Enterobacter hormaechei                       Providencia rettgeri                         
[31] Proteus penneri                               Candida glabrata                             
[33] Enterococcus gallinarum                       Pantoea agglomerans                          
[35] Stenotrophomonas maltophilia                  Candida norvegensis                          
[37] Candida krusei                                Candida guilliermondii                       
[39] Citrobacter spp                               Atelosaccharomyces hudeloi                   
[41] Citrobacter braakii                           Candida auris                                
[43] Cryptococcus laurentii                        Acinetobacter pittii                         
[45] Burkholderia cepacia                          Serratia spp                                 
[47] Enterobacter asburiae                         Salmonella enterica                          
[49] Raoultella ornithinolytica                    Acinetobacter lwoffii                        
[51] Alcaligenes faecalis                          Pseudomonas putida                           
[53] Achromobacter xylosoxidans                    Serratia odorifera                           
[55] Candida dubliniensis                          Citrobacter farmeri                          
[57] Candida ciferrii                              Staphylococcus hominis                       
[59] Citrobacter youngae                           Enterobacter kobei                           
[61] Staphylococcus saprophyticus                  Achromobacter denitrificans                  
[63] Saprochaete capitata                          Acinetobacter spp                            
[65] Proteus hauseri                               Pantoea dispersa                             
[67] Klebsiella variicola                          Sphingomonas paucimobilis                    
[69] Serratia liquefaciens                         Candida lusitaniae                           
[71] Hafnia alvei                                  Enterococcus hirae                           
[73] Streptococcus gallolyticus                    Serratia ficaria                             
[75] Burkholderia contaminans                      Serratia fonticola                           
[77] Proteus spp                                   Enterobacter spp                             
[79] Myroides spp                                  Pseudomonas luteola

[msberends]

That’s right, AMR now supports former taxonomic names with an own ID, for users who do not want to transform old names to currently used names.

For this reason, we added the ‘keepsynonyms’ argument to as.mo() and all `mo*()` functions. This value defaults to FALSE to reflect the old behaviour (so not much should change for users).

I should check your whole list, but a lot of your microorganisms never had a name change, such as E. cloacae (first on your list). I’ll get back to you!

[remcv]

Thanks, I was not aware of the keep synonyms addition. Indeed, the problems with the old naming appear only for some Candida species. This means that the Candida auris issue is solved by using the beta version 🥳 and the naming by using the keep synonyms.

[msberends]

👍🏼