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<!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, shrink-to-fit=no"><title>Determine Multidrug-Resistant Organisms (MDRO) — mdro • 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-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Determine Multidrug-Resistant Organisms (MDRO) — mdro"><meta name="description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines."><meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
<!-- 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"><title>Determine Multidrug-Resistant Organisms (MDRO) — mdro • 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-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Determine Multidrug-Resistant Organisms (MDRO) — mdro"><meta name="description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines."><meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -48,7 +48,7 @@
</div>
<div class="ref-description section level2">
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.</p>
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.</p>
</div>
<div class="section level2">
@@ -163,8 +163,11 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<li><p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; <a href="https://doi.org/10.1186/s13756-015-0047-6" class="external-link">doi:10.1186/s13756-015-0047-6</a></p></li>
<li><p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p></li>
</ul><p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link">https://github.com/msberends/AMR/issues/new</a>.</p>
<p>The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" (<a href="https://www.sri-richtlijnen.nl/brmo" class="external-link">link</a>)</p>
<p>Also:</p><ul><li><p><code>guideline = "BRMO 2017"</code></p>
<p>The former Dutch national guideline - Werkgroep Infectiepreventie (WIP), RIVM, last revision as of 2017: "Bijzonder Resistente Micro-Organismen (BRMO)"</p></li>
</ul></li>
</ul><p>Please suggest to implement guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link">https://github.com/msberends/AMR/issues/new</a>.</p>
</div>
<div class="section level2">
<h2 id="using-custom-guidelines">Using Custom Guidelines<a class="anchor" aria-label="anchor" href="#using-custom-guidelines"></a></h2>
@@ -229,7 +232,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> out</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Positive, unconfirmed Positive </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1978 0 6 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1994 0 6 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu">custom_mdro_guideline</span><span class="op">(</span></span></span>
@@ -263,7 +266,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with pct_required_classes)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Multi-drug-resistant (MDR) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1601 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1617 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Extensively drug-resistant (XDR) Pandrug-resistant (PDR) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 </span>
<span class="r-in"><span><span class="co"># }</span></span></span>