search

markusrt / NRZMyk

The National Reference Center for Invasive Fungal Infections (NRZMyk) is the central contact point for diagnostics and management of invasive fungal infections.
https://www.nrz-myk.de
MIT License
0 stars 1 forks source link

read points of gradient tests #85

Open joheli opened 3 years ago

joheli commented 3 years ago

Please note that read points of gradient tests (Etests) are 0.002, 0.003, 0.004, 0.006 etc. (see bioMérieux package insert), corresponding to a series where each value equals the previous value multiplied by the squareroot of 2.

E.g. in R:

etest_readpoints <- function(start = 0.002, steps = 20) start * (sqrt(2) ^ (0:steps))
markusrt commented 3 years ago

@joheli Thanks for the input. I will take a look. @MaxAldejohann also today mentioned some issues regarding the breakpoints. Maybe this is related.

So you are referring to this, correct? image

Meaning the steps on the list should follow the formula above.

joheli commented 3 years ago

Exactly. Please compare entries in above drop-down field with actual read points from gradient tests used in the Würzburg lab. I only use Fluconazol and Anidulafungin in my lab - if you wish I can send you some pictures from those.

markusrt commented 3 years ago

Thanks for finding out. You can attach the pictures here. This would be really helpful.

I will update the config accordingly https://github.com/markusrt/NRZMyk/blob/dea9a16998cdc8d53aaa7a53c0b38161bba2446d/NRZMyk.Client/wwwroot/appsettings.json#L462-L476

https://github.com/markusrt/NRZMyk/blob/dea9a16998cdc8d53aaa7a53c0b38161bba2446d/NRZMyk.Client/wwwroot/appsettings.json#L568-L582

@MaxAldejohann will provide steps for the other antimycotics.

Issue will be fixed with next release and I would take care to fix existing database entries

joheli commented 3 years ago

Ok - please see the images attached (we´re using bioMérieux etests for fluconazole and anidulafungin).

fluconazole_etest_label fluconazole_etest_readpoints anidulafungin_etest_label anidulafungin_etest_readpoints

markusrt commented 3 years ago

@joheli Update for fluconazole and anidulafungin is realeased with v.1.0.2106.2220

Some production data records required an update but mostly trivial, i.e.

However for two of the latter this affected the evaluation as they are now treated as resistant due to break point Anidulafungin - Candida albicans - v10.0. Is this expected? Breakpoints as of the initial specification is set to R >0.3

joheli commented 3 years ago

@markusrt marginal disagreement around cutoff values is to be expected and it's not always straightforward to iron those out.

Let me elaborate: in bacteria it is common to find cutoff values derived from the reference broth microdilution method, for ciprofloxacin in Enterobacterales it says e.g. '<= 0.25' -> 'S' and '> 0.5' -> 'R'). When you then get an etest MIC of 0.38 you actually wouldn't expect the strain to grow at 0.5 in the reference broth microdilution method (which should in theory prompt you to choose category 'S') - but then 0.38 is bigger than 0.25, therefore some prefer to err on the safe side categorizing the result as 'I'.

Be it as it may, I would suggest you discuss margin cases with the NRZMyk folks, as they are the experts in the field!

markusrt commented 2 years ago

Assigned to @MaxAldejohann as he will provide breakpoints for additional antifungal agents. Additionally he will take a look on the comment regarding margin cases.

MaxAldejohann commented 2 years ago

@joheli thx for bringing up this issue. @markusrt I can additionally provide MIC values for -micafungin, caspofungin, voriconazole, posaconzole, ampho B MIC-ranges are equal to that of anidulafungin, so overall i would suggest amending the scale accordingly for all E-tests. -concerning the marginal disagreement around cutoff values I would recomend to choose S category in such are cases.