clinical_breakpoints
A data set with 34 382 rows and 14 columns, containing the following +
A data set with 34 376 rows and 14 columns, containing the following column names:guideline, type, host, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti, and is_SDD.
This data set is in R available as clinical_breakpoints, after you load the AMR package.
AMR
It was last updated on 13 March 2025 13:30:14 UTC. Find more info +
It was last updated on 13 March 2025 14:38:39 UTC. Find more info about the structure of this data set here.
Direct download links:
(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using the instructions here.)
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island’s Atlantic Veterinary College, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
antibiotics
antimicrobials
rsi
sir
as.sir()
breakpoint_type = "animal"
host
ab
mo
uti
as.sir(..., ab = "column1", mo = "column2", uti = "column3")
vctrs
dplyr
bind_rows()
rowwise()
c_across()
mic
.xpt
This changelog only contains changes from AMR v3.0 (March 2025) and later.
Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
S
SDD
I
R
NI
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
All breakpoints used for interpretation are available in our clinical_breakpoints data set.
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 2011-2024, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.
CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing, 2011-2024, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m100/.
CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals, 2019-2024, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/veterinary-medicine/documents/vet01/.
CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings, 2019-2024, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/veterinary-medicine/documents/vet09/.
EUCAST Breakpoint tables for interpretation of MICs and zone diameters, 2011-2024, European Committee on Antimicrobial Susceptibility Testing (EUCAST). https://www.eucast.org/clinical_breakpoints.
WHONET as a source for machine-reading the clinical breakpoints (read more here), 1989-2024, WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. https://whonet.org/.
For veterinary guidelines, these might be the best options:
options(AMR_guideline = "CLSI") options(AMR_breakpoint_type = "animal")
When applying veterinary breakpoints (by setting host or by setting breakpoint_type = "animal"), the CLSI VET09 guideline will be applied to cope with missing animal species-specific breakpoints.
The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 34 382 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. This allows for easy implementation of these rules in laboratory information systems (LIS). Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 34 376 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. This allows for easy implementation of these rules in laboratory information systems (LIS). Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
Use as.sir() to transform MICs or disks measurements to SIR values.
A tibble with 34 382 observations and 14 variables:
guideline Name of the guideline
guideline
A tibble with 34 376 observations and 14 variables:
type Breakpoint type, either "ECOFF", "animal", or "human"
type
host Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"
method Testing method, either "DISK" or "MIC"
method
clinical_breakpoints -#> # A tibble: 34,382 × 14 +#> # A tibble: 34,376 × 14 #> guideline type host method site mo rank_index ab ref_tbl #> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr> #> 1 EUCAST 2024 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo… @@ -147,7 +147,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values.">#> 8 EUCAST 2024 human human DISK Uncomp… B_ACNTB 3 AMK Acineto… #> 9 EUCAST 2024 human human MIC NA B_ACNTB 3 AMK Acineto… #> 10 EUCAST 2024 human human MIC Uncomp… B_ACNTB 3 AMK Acineto… -#> # ℹ 34,372 more rows +#> # ℹ 34,366 more rows #> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>, #> # uti <lgl>, is_SDD <lgl>