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(v2.1.1.9079) fix for uti in as.sir()

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dr. M.S. (Matthijs) Berends
2024-09-24 15:34:12 +02:00
parent 127892430d
commit 1ca40e8d67
32 changed files with 98 additions and 109 deletions
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@@ -4,7 +4,7 @@
* Used in over 175 countries, available in 20 languages
* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs and disk zones
* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs, disk zones and ECOFFs
* Corrects for duplicate isolates, **calculates** and **predicts** AMR per antibiotic class
* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
* 100% free of costs and dependencies, highly suitable for places with **limited resources**
@@ -98,18 +98,18 @@ antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
```
|Pathogen (N min-max) | AMK| GEN| IPM| KAN| MEM| TOB|
|:------------------------|---:|---:|---:|---:|---:|---:|
|CoNS (43-309) | 0| 86| 52| 0| 52| 22|
|*E. coli* (0-462) | 100| 98| 100| | 100| 97|
|*E. faecalis* (0-39) | 0| 0| 100| 0| | 0|
|*K. pneumoniae* (0-58) | | 90| 100| | 100| 90|
|*P. aeruginosa* (17-30) | | 100| | 0| | 100|
|*P. mirabilis* (0-34) | | 94| 94| | | 94|
|*S. aureus* (2-233) | | 99| | | | 98|
|*S. epidermidis* (8-163) | 0| 79| | 0| | 51|
|*S. hominis* (3-80) | | 92| | | | 85|
|*S. pneumoniae* (11-117) | 0| 0| | 0| | 0|
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
|:------------------------|:----------------:|:---------------:|:----------------:|:----------------:|:----------------:|:----------------:|
| CoNS | 0% (0/43) | 86% (267/309) | 52% (25/48) | 0% (0/43) | 52% (25/48) | 22% (12/55) |
| *E. coli* | 100% (171/171) | 98% (451/460) | 100% (422/422) | | 100% (418/418) | 97% (450/462) |
| *E. faecalis* | 0% (0/39) | 0% (0/39) | 100% (38/38) | 0% (0/39) | | 0% (0/39) |
| *K. pneumoniae* | | 90% (52/58) | 100% (51/51) | | 100% (53/53) | 90% (52/58) |
| *P. aeruginosa* | | 100% (30/30) | | 0% (0/30) | | 100% (30/30) |
| *P. mirabilis* | | 94% (32/34) | 94% (30/32) | | | 94% (32/34) |
| *S. aureus* | | 99% (231/233) | | | | 98% (84/86) |
| *S. epidermidis* | 0% (0/44) | 79% (128/163) | | 0% (0/44) | | 51% (45/89) |
| *S. hominis* | | 92% (74/80) | | | | 85% (53/62) |
| *S. pneumoniae* | 0% (0/117) | 0% (0/117) | | 0% (0/117) | | 0% (0/117) |
In combination antibiograms, it is clear that combined antibiotics yield higher empiric coverage:
@@ -119,10 +119,10 @@ antibiogram(example_isolates,
mo_transform = "gramstain")
```
|Pathogen (N min-max) | TZP| TZP + GEN| TZP + TOB|
|:------------------------|---:|---------:|---------:|
|Gram-negative (641-693) | 88| 99| 98|
|Gram-positive (345-1044) | 86| 98| 95|
| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:--------------|:-----------------------:|:-------------------------------------:|:------------------------------------:|
| Gram-negative | 88% (565/641) | 99% (681/691) | 98% (679/693) |
| Gram-positive | 86% (296/345) | 98% (1018/1044) | 95% (524/550) |
Like many other functions in this package, `antibiogram()` comes with support for 20 languages that are often detected automatically based on system language:
@@ -134,11 +134,10 @@ antibiogram(example_isolates,
language = "uk") # Ukrainian
```
|Збудник (N min-max) | Гентаміцин| Тобраміцин| Ципрофлоксацин|
|:------------------------|----------:|----------:|--------------:|
|Грамнегативні (684-686) | 96| 96| 91|
|Грампозитивні (665-1170) | 63| 34| 77|
| Збудник | Гентаміцин | Тобраміцин | Ципрофлоксацин |
|:---------------|:--------------------:|:-------------------:|:------------------:|
| Грамнегативні | 96% (659/684) | 96% (658/686) | 91% (621/684) |
| Грампозитивні | 63% (740/1170) | 34% (228/665) | 77% (560/724) |
#### Calculating resistance per group