Challenge in identifying S, I,R for Vancomycin in Staphylococcus aureus isolates in my daatset

[sengeruan]

Hi all,
I am doing data analysis using AMR Package Version 2.1.1. I have successfully executed the function as.mo() for bacterial identification, as.ab() for antibacterial identification and as.disk () for converting the diameters to disks in my dataset. However, when I executed as.sir() across the antibacterial columns with respective to bacterial names, only Staphylococcus aureus and CONS antibiotic susceptibility tests results returned "NA" instead of "S", or "I" or "R" as I need. Where did I went wrong? Anyone to help on this will be appreciated.

[msberends]

Hi, thanks for using this package! Can you provide a small example of how the data looks? At least the columns with the staphylococcal species and the antibiotics? Then I’m better able to help you.

Many thanks!

[sengeruan]

Here is the file.
staphy_vanco.xlsx

[msberends]

I also only get NAs:

staph |> 
  mutate(VA = as.disk(VA),
         VA_SIR = as.sir(VA, ab = "vancomycin", mo = organism))
#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with all the details of the breakpoint interpretations. Note that
#>   some microorganisms might not have breakpoints for each antimicrobial drug in EUCAST 2023.
#> 
#> Interpreting disk diffusion zones: 'vancomycin' (VAN), EUCAST 2023... OK 
#> # A data.frame: 15 × 4
#>      No_ organism                 VA VA_SIR
#>    <int> <chr>                 <dsk> <sir> 
#>  1     1 Staphylococcus aureus    17   NA  
#>  2     2 Staphylococcus aureus    30   NA  
#>  3     3 Staphylococcus aureus    16   NA  
#>  4     4 CNS                      NA   NA  
#>  5     5 Staphylococcus aureus    12   NA  
#>  6     6 Staphylococcus aureus     6   NA  
#>  7     7 Staphylococcus aureus    15   NA  
#>  8     8 Staphylococcus aureus    NA   NA  
#>  9     9 Staphylococcus aureus    22   NA  
#> 10    10 CNS                      18   NA  
#> 11    11 Staphylococcus aureus    18   NA  
#> 12    12 Staphylococcus aureus    NA   NA  
#> 13    13 CNS                      16   NA  
#> 14    14 CNS                       6   NA  
#> 15    15 Staphylococcus aureus    17   NA  ,

This is because vancomycin breakpoints are not available for disk diffusion zones. Not in EUCAST, and also not CLSI. You will have to use MIC to get interpretations.

[sengeruan]

Thanks Berends for your feedback. So, it means breakpoints for some microorganisms are not available, and alternatively we can use MIC values? Regards, Lameck Pashet.

…

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On Sat, Apr 6, 2024 at 3:13 PM Matthijs Berends ***@***.***> wrote: I also only get NAs: staph |> mutate(VA = as.disk(VA), VA_SIR = as.sir(VA, ab = "vancomycin", mo = organism))#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with all the details of the breakpoint interpretations. Note that#> some microorganisms might not have breakpoints for each antimicrobial drug in EUCAST 2023.#> #> Interpreting disk diffusion zones: 'vancomycin' (VAN), EUCAST 2023... OK #> # A data.frame: 15 × 4#> No_ organism VA VA_SIR#> <int> <chr> <dsk> <sir> #> 1 1 Staphylococcus aureus 17 NA #> 2 2 Staphylococcus aureus 30 NA #> 3 3 Staphylococcus aureus 16 NA #> 4 4 CNS NA NA #> 5 5 Staphylococcus aureus 12 NA #> 6 6 Staphylococcus aureus 6 NA #> 7 7 Staphylococcus aureus 15 NA #> 8 8 Staphylococcus aureus NA NA #> 9 9 Staphylococcus aureus 22 NA #> 10 10 CNS 18 NA #> 11 11 Staphylococcus aureus 18 NA #> 12 12 Staphylococcus aureus NA NA #> 13 13 CNS 16 NA #> 14 14 CNS 6 NA #> 15 15 Staphylococcus aureus 17 NA , This is because vancomycin breakpoints are not available for disk diffusion zones. Not in EUCAST, and also not CLSI. You will have to use MIC to get interpretations. — Reply to this email directly, view it on GitHub <#139 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARFT75QOADV2SW2UGGVXQDDY37RGDAVCNFSM6AAAAABENYWQOCVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TAMRZGIZTG> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[msberends]

Exactly. There is not much of a choice...