Description
Currently, when you run as.mo("Staphylococcus argenteus", Becker=T), the output is B_STPHY_COPS as set in microorganisms.groups.txt. By default, S. aureus is excluded from the COPS group with Becker == True. It's only grouped into COPS with Becker == "all".
As S. argenteus (as well as S. schweitzeri) are currently also categorised under the S. aureus complex in the Dutch SRI MRSA guideline[1], it might be helpful to also include S. argenteus (as well as S. schweitzeri) under the B_STPHY_AURS output of as.mo().
It might be a good idea to perhaps add a B_STPHY_AURS-C to the code as the "S. aureus complex" to distinguish the actual S. aureus species from the complex. A quick search using Github didn't show any such complex currently. E.g.:
> mo_group_members("Staphylococcus aureus complex")
[1] "Staphylococcus aureus" "Staphylococcus argenteus" "Staphylococcus schweitzeri"
NB: might also consider S. singaporensis and S. roterodami in this process, see Yan et al.[2]
NB2: perhaps I just can't find it, but is there an easy way to go from m.o. to m.o. complex? Eg. "Citrobacter braakii" as input and "Citrobacter freundii complex" as output? E.g., as the "inverse" of mo_group_members()?
1: https://www.sri-richtlijnen.nl/mrsa/module-1
2: https://pmc.ncbi.nlm.nih.gov/articles/PMC12239731/
Use Case (optional)
No response
Description
Currently, when you run
as.mo("Staphylococcus argenteus", Becker=T), the output isB_STPHY_COPSas set inmicroorganisms.groups.txt. By default, S. aureus is excluded from the COPS group with Becker == True. It's only grouped into COPS with Becker == "all".As S. argenteus (as well as S. schweitzeri) are currently also categorised under the S. aureus complex in the Dutch SRI MRSA guideline[1], it might be helpful to also include S. argenteus (as well as S. schweitzeri) under the
B_STPHY_AURSoutput ofas.mo().It might be a good idea to perhaps add a
B_STPHY_AURS-Cto the code as the "S. aureus complex" to distinguish the actual S. aureus species from the complex. A quick search using Github didn't show any such complex currently. E.g.:NB: might also consider S. singaporensis and S. roterodami in this process, see Yan et al.[2]
NB2: perhaps I just can't find it, but is there an easy way to go from m.o. to m.o. complex? Eg. "Citrobacter braakii" as input and "Citrobacter freundii complex" as output? E.g., as the "inverse" of
mo_group_members()?1: https://www.sri-richtlijnen.nl/mrsa/module-1
2: https://pmc.ncbi.nlm.nih.gov/articles/PMC12239731/
Use Case (optional)
No response