You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

417 lines
19 KiB

<!DOCTYPE html>
<!-- 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=1.0">
<title>How to apply EUCAST rules • 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">
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script><!-- 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">
<!-- 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><!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to apply EUCAST rules">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<meta name="twitter:card" content="summary_large_image">
<meta name="twitter:creator" content="@msberends">
<meta name="twitter:site" content="@univgroningen">
<!-- 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]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
<a href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
Authors
</a>
</li>
<li>
<a href="../news/index.html">
<span class="far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR" class="external-link">
<span class="fab fa-github"></span>
Source Code
</a>
</li>
</ul>
</div>
<!--/.nav-collapse -->
</div>
<!--/.container -->
</div>
<!--/.navbar -->
</header><script src="EUCAST_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to apply EUCAST rules</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div>
</div>
<div id="introduction" class="section level2">
<h2 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h2>
<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">on their website</a>:</p>
<blockquote>
<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
</blockquote>
<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.2, 2020).</p>
<p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
</div>
<div id="examples" class="section level2">
<h2 class="hasAnchor">
<a href="#examples" class="anchor" aria-hidden="true"></a>Examples</h2>
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<span class="st">"Escherichia"</span><span class="op">)</span>,
ampicillin <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
<span class="va">oops</span>
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella S</span>
<span class="co"># 2 Escherichia S</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella R</span>
<span class="co"># 2 Escherichia S</span></code></pre></div>
<p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
<span class="st">"ampicillin"</span><span class="op">)</span>
<span class="co"># [1] TRUE FALSE</span>
<span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
<span class="co"># [1] TRUE FALSE</span></code></pre></div>
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
<span class="st">"Enterococcus faecalis"</span>,
<span class="st">"Escherichia coli"</span>,
<span class="st">"Klebsiella pneumoniae"</span>,
<span class="st">"Pseudomonas aeruginosa"</span><span class="op">)</span>,
VAN <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
AMX <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
COL <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span>
CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylenicillin</span>
FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data</span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
<th align="center">VAN</th>
<th align="center">AMX</th>
<th align="center">COL</th>
<th align="center">CAZ</th>
<th align="center">CXM</th>
<th align="center">PEN</th>
<th align="center">FOX</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Staphylococcus aureus</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Enterococcus faecalis</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left">Escherichia coli</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Klebsiella pneumoniae</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left">Pseudomonas aeruginosa</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
<th align="center">VAN</th>
<th align="center">AMX</th>
<th align="center">COL</th>
<th align="center">CAZ</th>
<th align="center">CXM</th>
<th align="center">PEN</th>
<th align="center">FOX</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Staphylococcus aureus</td>
<td align="center">-</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Enterococcus faecalis</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="left">Escherichia coli</td>
<td align="center">R</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left">Pseudomonas aeruginosa</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">-</td>
<td align="center">-</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer><div class="copyright">
<p></p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
</div>
</footer>
</div>
</body>
</html>