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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 --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.3.1/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><linkhref="../deps/Lato-0.4.9/font.css"rel="stylesheet"><linkhref="../deps/Fira_Code-0.4.9/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="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 --><scriptsrc="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 --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js"integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw=="crossorigin="anonymous"referrerpolicy="no-referrer"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><metaproperty="og:description"content="DatasetcontainingclinicalbreakpointstointerpretMICanddiskdiffusiontoSIRvalues,accordingtointernationalguidelines.Thisdatasetcontainbreakpointsforhumans,7differentanimalgroups,andECOFFs.
Use as.sir() to transform MICs or disks measurements to SIR values."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@msberends"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="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]>
<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>
<p>A <ahref="https://tibble.tidyverse.org/reference/tibble.html"class="external-link">tibble</a> with 34 085 observations and 13 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<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>
<li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li>
<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
<li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
<li><p><code>uti</code><br> A <ahref="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>
<h3id="different-types-of-breakpoints">Different types of breakpoints<aclass="anchor"aria-label="anchor"href="#different-types-of-breakpoints"></a></h3>
<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>
<p>The default is <code>"human"</code>, which can also be set with the <ahref="AMR-options.html">package option</a><code><ahref="AMR-options.html">AMR_breakpoint_type</a></code>. Use <code><ahref="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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<divclass="section">
<h3id="imported-from-whonet">Imported from WHONET<aclass="anchor"aria-label="anchor"href="#imported-from-whonet"></a></h3>
<p>Clinical breakpoints in this package were validated through and imported from <ahref="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 <ahref="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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<divclass="section">
<h3id="response-from-clsi-and-eucast">Response from CLSI and EUCAST<aclass="anchor"aria-label="anchor"href="#response-from-clsi-and-eucast"></a></h3>
<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>
<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 <ahref="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <ahref="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>
<p><strong>NOTE:</strong> this <code>AMR</code> package (and the WHONET software as well) contains rather complex internal methods to apply the guidelines. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the <ahref="microorganisms.groups.html">microorganisms.groups</a> data set). It is important that this is considered when using the breakpoints for own use.</p>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 1</span> EUCAST 2024 human human DISK <spanstyle="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 2</span> EUCAST 2024 human human MIC <spanstyle="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 3</span> EUCAST 2024 human human DISK <spanstyle="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 4</span> EUCAST 2024 human human MIC <spanstyle="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 5</span> EUCAST 2024 human human DISK <spanstyle="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 6</span> EUCAST 2024 human human MIC <spanstyle="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 7</span> EUCAST 2024 human human DISK <spanstyle="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 8</span> EUCAST 2024 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;"> 9</span> EUCAST 2024 human human MIC <spanstyle="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #BCBCBC;">10</span> EUCAST 2024 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…</span>
<spanclass="r-out co"><spanclass="r-pr">#></span><spanstyle="color: #949494;"># ℹ 34,075 more rows</span></span>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_blank"href="https://github.com/msberends/AMR/blob/main/LICENSE"class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
