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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
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Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
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Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
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Use as.sir() to transform MICs or disks measurements to SIR values."><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.8/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
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Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
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Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
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Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with Clinical Breakpoints for SIR Interpretation</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>clinical_breakpoints.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.</p>
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<p>Currently available breakpoint guidelines for <strong>clinical microbiology</strong> are EUCAST 2011-2023 and CLSI 2011-2023.</p>
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<p>Currently available breakpoint guidelines for <strong>veterinary microbiology</strong> are EUCAST 2021-2023 and CLSI 2019-2023.</p>
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<p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">clinical_breakpoints</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 29 883 observations and 13 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
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<li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
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<li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"</p></li>
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<li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
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<li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li>
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<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
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<li><p><code>rank_index</code><br> Taxonomic rank index of <code>mo</code> from 1 (subspecies/infraspecies) to 5 (unknown microorganism)</p></li>
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<li><p><code>ab</code><br> Antibiotic code as used by this package, EARS-Net and WHONET, see <code><a href="as.ab.html">as.ab()</a></code></p></li>
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<li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li>
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<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
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<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
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<li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
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<li><p><code>uti</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<div class="section">
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<h3 id="different-types-of-breakpoints">Different types of breakpoints<a class="anchor" aria-label="anchor" href="#different-types-of-breakpoints"></a></h3>
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<p>Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.</p>
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<p>The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. Use <code><a href="as.sir.html">as.sir(..., breakpoint_type = ...)</a></code> to interpret raw data using a specific breakpoint type, e.g. <code>as.sir(..., breakpoint_type = "ECOFF")</code> to use ECOFFs.</p>
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</div>
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<div class="section">
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<h3 id="imported-from-whonet">Imported from WHONET<a class="anchor" aria-label="anchor" href="#imported-from-whonet"></a></h3>
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<p>Clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their development on the WHONET software.</p>
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</div>
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<div class="section">
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<h3 id="response-from-clsi-and-eucast">Response from CLSI and EUCAST<a class="anchor" aria-label="anchor" href="#response-from-clsi-and-eucast"></a></h3>
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<p>The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this <code>AMR</code> package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the <code>AMR</code> package.</p>
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</div>
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<div class="section">
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<h3 id="download">Download<a class="anchor" aria-label="anchor" href="#download"></a></h3>
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<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>. They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.</p>
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<p><strong>NOTE:</strong> this <code>AMR</code> package (and the WHONET software as well) contains internal methods to apply the guidelines, which is rather complex. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the <a href="microorganisms.groups.html">microorganisms.groups</a> data set). It is important that this is considered when using the breakpoints for own use.</p>
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</div>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p><a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 29,883 × 13</span></span>
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<span class="r-out co"><span class="r-pr">#></span> guideline type host method site mo rank_index ab ref_tbl </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2023 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2023 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 29,873 more rows</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 4 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># uti <lgl></span></span>
|
||
</code></pre></div>
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