mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 11:48:00 +02:00
Built site for AMR@2.1.1.9268: 2461631
This commit is contained in:
github-actions
@ -30,7 +30,7 @@
|
||||
|
||||
<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="">2.1.1.9267</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
|
||||
@ -87,6 +87,11 @@
|
||||
|
||||
|
||||
|
||||
<blockquote>
|
||||
<p>This explainer was largely written by our <a href="https://chat.amr-for-r.org" class="external-link">AMR for R Assistant</a>, a ChatGPT
|
||||
manually-trained model able to answer any question about the
|
||||
<code>AMR</code> package.</p>
|
||||
</blockquote>
|
||||
<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h2>
|
||||
@ -94,33 +99,40 @@
|
||||
<em>probabilistic reasoning</em>: what is the chance that a regimen will
|
||||
cover the likely infecting organisms, before culture results are
|
||||
available?</p>
|
||||
<p>This is the purpose of <strong>WISCA</strong>, or:</p>
|
||||
<blockquote>
|
||||
<p><strong>Weighted-Incidence Syndromic Combination
|
||||
Antibiogram</strong></p>
|
||||
</blockquote>
|
||||
<p>WISCA is a Bayesian approach that integrates: - <strong>Pathogen
|
||||
prevalence</strong> (how often each species causes the syndrome), -
|
||||
<p>This is the purpose of <strong>WISCA</strong>, or
|
||||
<strong>Weighted-Incidence Syndromic Combination
|
||||
Antibiogram</strong>.</p>
|
||||
<p>WISCA is a Bayesian approach that integrates:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>Pathogen prevalence</strong> (how often each species causes
|
||||
the syndrome),</li>
|
||||
<li>
|
||||
<strong>Regimen susceptibility</strong> (how often a regimen works
|
||||
<em>if</em> the pathogen is known),</p>
|
||||
<em>if</em> the pathogen is known),</li>
|
||||
</ul>
|
||||
<p>to estimate the <strong>overall empirical coverage</strong> of
|
||||
antimicrobial regimens — with quantified uncertainty.</p>
|
||||
antimicrobial regimens, with quantified uncertainty.</p>
|
||||
<p>This vignette explains how WISCA works, why it is useful, and how to
|
||||
apply it in <strong>AMR</strong>.</p>
|
||||
<hr>
|
||||
apply it using the <code>AMR</code> package.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="why-traditional-antibiograms-fall-short">Why traditional antibiograms fall short<a class="anchor" aria-label="anchor" href="#why-traditional-antibiograms-fall-short"></a>
|
||||
</h2>
|
||||
<p>A standard antibiogram gives you:</p>
|
||||
<p>``` Species → Antibiotic → Susceptibility %</p>
|
||||
<pre><code>Species → Antibiotic → Susceptibility %</code></pre>
|
||||
<p>But clinicians don’t know the species <em>a priori</em>. They need to
|
||||
choose a regimen that covers the <strong>likely pathogens</strong> —
|
||||
choose a regimen that covers the <strong>likely pathogens</strong>,
|
||||
without knowing which one is present.</p>
|
||||
<p>Traditional antibiograms: - Fragment information by organism, - Do
|
||||
not weight by real-world prevalence, - Do not account for combination
|
||||
therapy or sample size, - Do not provide uncertainty.</p>
|
||||
<hr>
|
||||
<p>Traditional antibiograms calculate the susceptibility % as just the
|
||||
number of resistant isolates divided by the total number of tested
|
||||
isolates. Therefore, traditional antibiograms:</p>
|
||||
<ul>
|
||||
<li>Fragment information by organism,</li>
|
||||
<li>Do not weight by real-world prevalence,</li>
|
||||
<li>Do not account for combination therapy or sample size,</li>
|
||||
<li>Do not provide uncertainty.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="the-idea-of-wisca">The idea of WISCA<a class="anchor" aria-label="anchor" href="#the-idea-of-wisca"></a>
|
||||
@ -130,21 +142,31 @@ therapy or sample size, - Do not provide uncertainty.</p>
|
||||
<p>“What is the <strong>probability</strong> that this regimen
|
||||
<strong>will cover</strong> the pathogen, given the syndrome?”</p>
|
||||
</blockquote>
|
||||
<p>This means combining two things: - <strong>Incidence</strong> of each
|
||||
pathogen in the syndrome, - <strong>Susceptibility</strong> of each
|
||||
pathogen to the regimen.</p>
|
||||
<p>This means combining two things:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>Incidence</strong> of each pathogen in the syndrome,</li>
|
||||
<li>
|
||||
<strong>Susceptibility</strong> of each pathogen to the
|
||||
regimen.</li>
|
||||
</ul>
|
||||
<p>We can write this as:</p>
|
||||
<p>``` coverage = ∑ (pathogen incidence × susceptibility)</p>
|
||||
<p>For example, suppose: - E. coli causes 60% of cases, and 90% of
|
||||
<em>E. coli</em> are susceptible to a drug. - Klebsiella causes 40% of
|
||||
cases, and 70% of <em>Klebsiella</em> are susceptible.</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munder><mo>∑</mo><mi>i</mi></munder><mrow><mo stretchy="true" form="prefix">(</mo><msub><mtext mathvariant="normal">Incidence</mtext><mi>i</mi></msub><mo>×</mo><msub><mtext mathvariant="normal">Susceptibility</mtext><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_i (\text{Incidence}_i \times \text{Susceptibility}_i)</annotation></semantics></math></p>
|
||||
<p>For example, suppose:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<em>E. coli</em> causes 60% of cases, and 90% of <em>E. coli</em>
|
||||
are susceptible to a drug.</li>
|
||||
<li>
|
||||
<em>Klebsiella</em> causes 40% of cases, and 70% of
|
||||
<em>Klebsiella</em> are susceptible.</li>
|
||||
</ul>
|
||||
<p>Then:</p>
|
||||
<p>``` coverage = (0.6 × 0.9) + (0.4 × 0.7) = 0.82</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.6</mn><mo>×</mo><mn>0.9</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>+</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.4</mn><mo>×</mo><mn>0.7</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>0.82</mn></mrow><annotation encoding="application/x-tex">\text{Coverage} = (0.6 \times 0.9) + (0.4 \times 0.7) = 0.82</annotation></semantics></math></p>
|
||||
<p>But in real data, incidence and susceptibility are <strong>estimated
|
||||
from samples</strong> — so they carry uncertainty. WISCA models this
|
||||
from samples</strong>, so they carry uncertainty. WISCA models this
|
||||
<strong>probabilistically</strong>, using conjugate Bayesian
|
||||
distributions.</p>
|
||||
<hr>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="the-bayesian-engine-behind-wisca">The Bayesian engine behind WISCA<a class="anchor" aria-label="anchor" href="#the-bayesian-engine-behind-wisca"></a>
|
||||
@ -152,486 +174,270 @@ distributions.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="pathogen-incidence">Pathogen incidence<a class="anchor" aria-label="anchor" href="#pathogen-incidence"></a>
|
||||
</h3>
|
||||
<p>Let: - K be the number of pathogens, -
|
||||
<code>α = (1, 1, ..., 1) be a **Dirichlet** prior (uniform), -</code> n
|
||||
= (n₁, …, nₖ) be the observed counts per species.</p>
|
||||
<p>Then the posterior incidence follows:</p>
|
||||
<p>``` incidence ∼ Dirichlet(α + n)</p>
|
||||
<p>In simulations, we draw from this posterior using:</p>
|
||||
<p>``` xᵢ ∼ Gamma(αᵢ + nᵢ, 1)</p>
|
||||
<p>``` incidenceᵢ = xᵢ / ∑ xⱼ</p>
|
||||
<hr>
|
||||
<p>Let:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>K</mi><annotation encoding="application/x-tex">K</annotation></semantics></math>
|
||||
be the number of pathogens,</li>
|
||||
<li>
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>α</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>,</mo><mn>1</mn><mo>,</mo><mi>…</mi><mo>,</mo><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\alpha = (1, 1, \ldots, 1)</annotation></semantics></math>
|
||||
be a <strong>Dirichlet</strong> prior (uniform),</li>
|
||||
<li>
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>n</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">n = (n_1, \ldots, n_K)</annotation></semantics></math>
|
||||
be the observed counts per species.</li>
|
||||
</ul>
|
||||
<p>Then the posterior incidence is:</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>p</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>1</mn></msub><mo>+</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>α</mi><mi>K</mi></msub><mo>+</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">p \sim \text{Dirichlet}(\alpha_1 + n_1, \ldots, \alpha_K + n_K)</annotation></semantics></math></p>
|
||||
<p>To simulate from this, we use:</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>x</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Gamma</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mi>i</mi></msub><mo>+</mo><msub><mi>n</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>,</mo><mspace width="1.0em"></mspace><msub><mi>p</mi><mi>i</mi></msub><mo>=</mo><mfrac><msub><mi>x</mi><mi>i</mi></msub><mrow><munderover><mo>∑</mo><mrow><mi>j</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>x</mi><mi>j</mi></msub></mrow></mfrac></mrow><annotation encoding="application/x-tex">x_i \sim \text{Gamma}(\alpha_i + n_i,\ 1), \quad p_i = \frac{x_i}{\sum_{j=1}^{K} x_j}</annotation></semantics></math></p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="susceptibility">Susceptibility<a class="anchor" aria-label="anchor" href="#susceptibility"></a>
|
||||
</h3>
|
||||
<p>Each pathogen–regimen pair has: - <code>prior: Beta(1, 1) -</code>
|
||||
data: S susceptible out of N tested</p>
|
||||
<p>Then:</p>
|
||||
<p>``` susceptibility ∼ Beta(1 + S, 1 + (N - S))</p>
|
||||
<p>In each simulation, we draw random susceptibility per species from
|
||||
this Beta distribution.</p>
|
||||
<hr>
|
||||
<p>Each pathogen–regimen pair has a prior and data:</p>
|
||||
<ul>
|
||||
<li>Prior:
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>,</mo><msub><mi>β</mi><mn>0</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Beta}(\alpha_0, \beta_0)</annotation></semantics></math>,
|
||||
with default
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>α</mi><mn>0</mn></msub><mo>=</mo><msub><mi>β</mi><mn>0</mn></msub><mo>=</mo><mn>1</mn></mrow><annotation encoding="application/x-tex">\alpha_0 = \beta_0 = 1</annotation></semantics></math>
|
||||
</li>
|
||||
<li>Data:
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
|
||||
susceptible out of
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>N</mi><annotation encoding="application/x-tex">N</annotation></semantics></math>
|
||||
tested</li>
|
||||
</ul>
|
||||
<p>The
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
|
||||
category could also include values SDD (susceptible, dose-dependent) and
|
||||
I (intermediate [CLSI], or susceptible, increased exposure
|
||||
[EUCAST]).</p>
|
||||
<p>Then the posterior is:</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>θ</mi><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>+</mo><mi>S</mi><mo>,</mo><mspace width="0.222em"></mspace><msub><mi>β</mi><mn>0</mn></msub><mo>+</mo><mi>N</mi><mo>−</mo><mi>S</mi><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta \sim \text{Beta}(\alpha_0 + S,\ \beta_0 + N - S)</annotation></semantics></math></p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="final-coverage-estimate">Final coverage estimate<a class="anchor" aria-label="anchor" href="#final-coverage-estimate"></a>
|
||||
</h3>
|
||||
<p>Putting it together:</p>
|
||||
<p>``` For each simulation: - Draw incidence ∼ Dirichlet - Draw
|
||||
susceptibility ∼ Beta - Multiply → coverage estimate</p>
|
||||
<p>We repeat this (e.g. 1000×) and summarise: - <strong>Mean</strong>:
|
||||
expected coverage - <strong>Quantiles</strong>: credible interval
|
||||
(default 95%)</p>
|
||||
<hr>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>Simulate pathogen incidence:
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>𝐩</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext></mrow><annotation encoding="application/x-tex">\boldsymbol{p} \sim \text{Dirichlet}</annotation></semantics></math>
|
||||
</li>
|
||||
<li>Simulate susceptibility:
|
||||
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>θ</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>+</mo><msub><mi>S</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo>+</mo><msub><mi>R</mi><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta_i \sim \text{Beta}(1 + S_i,\ 1 + R_i)</annotation></semantics></math>
|
||||
</li>
|
||||
<li>Combine:</li>
|
||||
</ol>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munderover><mo>∑</mo><mrow><mi>i</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>p</mi><mi>i</mi></msub><mo>⋅</mo><msub><mi>θ</mi><mi>i</mi></msub></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_{i=1}^{K} p_i \cdot \theta_i</annotation></semantics></math></p>
|
||||
<p>Repeat this simulation (e.g. 1000×) and summarise:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>Mean</strong> = expected coverage</li>
|
||||
<li>
|
||||
<strong>Quantiles</strong> = credible interval</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="practical-use-in-amr">Practical use in AMR<a class="anchor" aria-label="anchor" href="#practical-use-in-amr"></a>
|
||||
<h2 id="practical-use-in-the-amr-package">Practical use in the <code>AMR</code> package<a class="anchor" aria-label="anchor" href="#practical-use-in-the-amr-package"></a>
|
||||
</h2>
|
||||
<div class="section level3">
|
||||
<h3 id="simulate-a-synthetic-syndrome">Simulate a synthetic syndrome<a class="anchor" aria-label="anchor" href="#simulate-a-synthetic-syndrome"></a>
|
||||
<h3 id="prepare-data-and-simulate-synthetic-syndrome">Prepare data and simulate synthetic syndrome<a class="anchor" aria-label="anchor" href="#prepare-data-and-simulate-synthetic-syndrome"></a>
|
||||
</h3>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
|
||||
<span><span class="va">data</span> <span class="op"><-</span> <span class="va">example_isolates</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Add a fake syndrome column for stratification</span></span>
|
||||
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"Other"</span><span class="op">)</span></span></code></pre></div>
|
||||
<span><span class="co"># Structure of our data</span></span>
|
||||
<span><span class="va">data</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
|
||||
<span><span class="co">#> date patient age gender ward mo PEN OXA FLC AMX </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># Add a fake syndrome column</span></span>
|
||||
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"No UTI"</span><span class="op">)</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="basic-wisca-antibiogram">Basic WISCA antibiogram<a class="anchor" aria-label="anchor" href="#basic-wisca-antibiogram"></a>
|
||||
</h3>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||||
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||||
<span> antimicrobials <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">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="1%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="left">Amikacin</th>
|
||||
<th align="left">Amoxicillin</th>
|
||||
<th align="left">Amoxicillin/clavulanic acid</th>
|
||||
<th align="left">Ampicillin</th>
|
||||
<th align="left">Azithromycin</th>
|
||||
<th align="left">Benzylpenicillin</th>
|
||||
<th align="left">Cefazolin</th>
|
||||
<th align="left">Cefepime</th>
|
||||
<th align="left">Cefotaxime</th>
|
||||
<th align="left">Cefoxitin</th>
|
||||
<th align="left">Ceftazidime</th>
|
||||
<th align="left">Ceftriaxone</th>
|
||||
<th align="left">Cefuroxime</th>
|
||||
<th align="left">Chloramphenicol</th>
|
||||
<th align="left">Ciprofloxacin</th>
|
||||
<th align="left">Clindamycin</th>
|
||||
<th align="left">Colistin</th>
|
||||
<th align="left">Doxycycline</th>
|
||||
<th align="left">Erythromycin</th>
|
||||
<th align="left">Flucloxacillin</th>
|
||||
<th align="left">Fosfomycin</th>
|
||||
<th align="left">Gentamicin</th>
|
||||
<th align="left">Imipenem</th>
|
||||
<th align="left">Kanamycin</th>
|
||||
<th align="left">Linezolid</th>
|
||||
<th align="left">Meropenem</th>
|
||||
<th align="left">Metronidazole</th>
|
||||
<th align="left">Moxifloxacin</th>
|
||||
<th align="left">Mupirocin</th>
|
||||
<th align="left">Nitrofurantoin</th>
|
||||
<th align="left">Oxacillin</th>
|
||||
<th align="left">Piperacillin/tazobactam</th>
|
||||
<th align="left">Rifampicin</th>
|
||||
<th align="left">Teicoplanin</th>
|
||||
<th align="left">Tetracycline</th>
|
||||
<th align="left">Tigecycline</th>
|
||||
<th align="left">Tobramycin</th>
|
||||
<th align="left">Trimethoprim</th>
|
||||
<th align="left">Trimethoprim/sulfamethoxazole</th>
|
||||
<th align="left">Vancomycin</th>
|
||||
</tr></thead>
|
||||
<tbody><tr class="odd">
|
||||
<td align="left">41.7% (37.2-47.5%)</td>
|
||||
<td align="left">35.7% (33.3-38.2%)</td>
|
||||
<td align="left">73.7% (71.7-75.8%)</td>
|
||||
<td align="left">35.8% (33.6-38.1%)</td>
|
||||
<td align="left">43.8% (41.5-46%)</td>
|
||||
<td align="left">28.2% (25.8-30.8%)</td>
|
||||
<td align="left">69.3% (64.9-73.8%)</td>
|
||||
<td align="left">74.8% (70.5-78.8%)</td>
|
||||
<td align="left">73.3% (69.2-77.3%)</td>
|
||||
<td align="left">69.6% (65.5-73.7%)</td>
|
||||
<td align="left">35.9% (33.6-38.2%)</td>
|
||||
<td align="left">73.3% (68.9-77.2%)</td>
|
||||
<td align="left">71.9% (69.8-74%)</td>
|
||||
<td align="left">64.9% (51.7-78.5%)</td>
|
||||
<td align="left">77% (74.5-79.6%)</td>
|
||||
<td align="left">47.3% (44.7-49.6%)</td>
|
||||
<td align="left">33% (30.8-35.1%)</td>
|
||||
<td align="left">63.6% (52.1-74.9%)</td>
|
||||
<td align="left">43.7% (41.6-46%)</td>
|
||||
<td align="left">59.3% (47-71%)</td>
|
||||
<td align="left">60.5% (55.5-65.8%)</td>
|
||||
<td align="left">72.7% (70.7-74.8%)</td>
|
||||
<td align="left">78.2% (74-82.2%)</td>
|
||||
<td align="left">25.6% (13.5-37.7%)</td>
|
||||
<td align="left">54.9% (50.4-59%)</td>
|
||||
<td align="left">77.1% (72.8-81.2%)</td>
|
||||
<td align="left">56.1% (39.5-70.7%)</td>
|
||||
<td align="left">49.6% (43.6-55.6%)</td>
|
||||
<td align="left">65.2% (52.7-78.1%)</td>
|
||||
<td align="left">76.5% (69.4-82.3%)</td>
|
||||
<td align="left">57.8% (45.4-69.6%)</td>
|
||||
<td align="left">69.4% (64.2-74.2%)</td>
|
||||
<td align="left">52.4% (47.6-56.8%)</td>
|
||||
<td align="left">48.1% (43.4-52.9%)</td>
|
||||
<td align="left">61.4% (53.6-70.5%)</td>
|
||||
<td align="left">81.9% (78.1-85.5%)</td>
|
||||
<td align="left">60.7% (57.8-63.5%)</td>
|
||||
<td align="left">61% (58.8-63.5%)</td>
|
||||
<td align="left">76.5% (74.5-78.5%)</td>
|
||||
<td align="left">61.9% (59.8-64.2%)</td>
|
||||
<td align="left">77% (74.3-79.4%)</td>
|
||||
<td align="left">72.8% (70.7-74.8%)</td>
|
||||
</tr></tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="use-combination-regimens">Use combination regimens<a class="anchor" aria-label="anchor" href="#use-combination-regimens"></a>
|
||||
</h3>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||||
<span> antimicrobials <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">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="24%">
|
||||
<col width="38%">
|
||||
<col width="36%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="left">Amoxicillin/clavulanic acid</th>
|
||||
<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
|
||||
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
|
||||
</tr></thead>
|
||||
<tbody><tr class="odd">
|
||||
<td align="left">73.8% (71.8-75.7%)</td>
|
||||
<td align="left">87.5% (85.9-89%)</td>
|
||||
<td align="left">89.7% (88.2-91.1%)</td>
|
||||
</tr></tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="stratify-by-syndrome">Stratify by syndrome<a class="anchor" aria-label="anchor" href="#stratify-by-syndrome"></a>
|
||||
</h3>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||||
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span>,</span>
|
||||
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||||
<table style="width:100%;" class="table">
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||||
<span> antimicrobials <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">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
|
||||
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="2%">
|
||||
<col width="3%">
|
||||
<col width="2%">
|
||||
<col width="12%">
|
||||
<col width="21%">
|
||||
<col width="34%">
|
||||
<col width="31%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="left">Syndromic Group</th>
|
||||
<th align="left">Amikacin</th>
|
||||
<th align="left">Amoxicillin</th>
|
||||
<th align="left">Amoxicillin/clavulanic acid</th>
|
||||
<th align="left">Ampicillin</th>
|
||||
<th align="left">Azithromycin</th>
|
||||
<th align="left">Benzylpenicillin</th>
|
||||
<th align="left">Cefazolin</th>
|
||||
<th align="left">Cefepime</th>
|
||||
<th align="left">Cefotaxime</th>
|
||||
<th align="left">Cefoxitin</th>
|
||||
<th align="left">Ceftazidime</th>
|
||||
<th align="left">Ceftriaxone</th>
|
||||
<th align="left">Cefuroxime</th>
|
||||
<th align="left">Chloramphenicol</th>
|
||||
<th align="left">Ciprofloxacin</th>
|
||||
<th align="left">Clindamycin</th>
|
||||
<th align="left">Colistin</th>
|
||||
<th align="left">Doxycycline</th>
|
||||
<th align="left">Erythromycin</th>
|
||||
<th align="left">Flucloxacillin</th>
|
||||
<th align="left">Fosfomycin</th>
|
||||
<th align="left">Gentamicin</th>
|
||||
<th align="left">Imipenem</th>
|
||||
<th align="left">Kanamycin</th>
|
||||
<th align="left">Linezolid</th>
|
||||
<th align="left">Meropenem</th>
|
||||
<th align="left">Metronidazole</th>
|
||||
<th align="left">Moxifloxacin</th>
|
||||
<th align="left">Mupirocin</th>
|
||||
<th align="left">Nitrofurantoin</th>
|
||||
<th align="left">Oxacillin</th>
|
||||
<th align="left">Piperacillin/tazobactam</th>
|
||||
<th align="left">Rifampicin</th>
|
||||
<th align="left">Teicoplanin</th>
|
||||
<th align="left">Tetracycline</th>
|
||||
<th align="left">Tigecycline</th>
|
||||
<th align="left">Tobramycin</th>
|
||||
<th align="left">Trimethoprim</th>
|
||||
<th align="left">Trimethoprim/sulfamethoxazole</th>
|
||||
<th align="left">Vancomycin</th>
|
||||
<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
|
||||
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Other</td>
|
||||
<td align="left">25% (20.2-31.7%)</td>
|
||||
<td align="left">31.6% (28.7-34%)</td>
|
||||
<td align="left">70.1% (67.7-72.4%)</td>
|
||||
<td align="left">31.6% (29.1-34.1%)</td>
|
||||
<td align="left">56.4% (53.8-58.8%)</td>
|
||||
<td align="left">36.3% (33.1-39.4%)</td>
|
||||
<td align="left">61.5% (55.7-66.5%)</td>
|
||||
<td align="left">68.5% (63.4-73.8%)</td>
|
||||
<td align="left">66.7% (61.4-71.9%)</td>
|
||||
<td align="left">63% (57.7-68.6%)</td>
|
||||
<td align="left">18.3% (15.9-20.8%)</td>
|
||||
<td align="left">66.6% (61.4-71.5%)</td>
|
||||
<td align="left">65.5% (62.7-68%)</td>
|
||||
<td align="left">69.6% (60-77.2%)</td>
|
||||
<td align="left">74% (70.8-77.2%)</td>
|
||||
<td align="left">60.9% (58.1-63.6%)</td>
|
||||
<td align="left">13.9% (11.8-15.8%)</td>
|
||||
<td align="left">67.4% (63.7-70.9%)</td>
|
||||
<td align="left">56.4% (54-58.9%)</td>
|
||||
<td align="left">61.4% (56-67.6%)</td>
|
||||
<td align="left">49.6% (43.2-56.3%)</td>
|
||||
<td align="left">65.6% (62.8-68.1%)</td>
|
||||
<td align="left">71.8% (66.7-77%)</td>
|
||||
<td align="left">18.6% (13.1-25.9%)</td>
|
||||
<td align="left">70.8% (65.1-75.8%)</td>
|
||||
<td align="left">70.6% (65.1-75.7%)</td>
|
||||
<td align="left">49.8% (34.2-66.6%)</td>
|
||||
<td align="left">63.3% (56.2-70.3%)</td>
|
||||
<td align="left">69.8% (62.6-76.4%)</td>
|
||||
<td align="left">70.5% (61.2-77.5%)</td>
|
||||
<td align="left">60% (54.4-65.4%)</td>
|
||||
<td align="left">62.4% (56.4-68.6%)</td>
|
||||
<td align="left">67.6% (61.9-73.2%)</td>
|
||||
<td align="left">61.9% (55.4-67.6%)</td>
|
||||
<td align="left">67.8% (64.8-70.6%)</td>
|
||||
<td align="left">77% (72.3-81.8%)</td>
|
||||
<td align="left">50.1% (46.7-53.6%)</td>
|
||||
<td align="left">61.1% (58.4-64%)</td>
|
||||
<td align="left">78.8% (76.4-80.9%)</td>
|
||||
<td align="left">79.6% (77.4-81.8%)</td>
|
||||
<td align="left">No UTI</td>
|
||||
<td align="left">70.1% (67.8-72.3%)</td>
|
||||
<td align="left">85.2% (83.1-87.2%)</td>
|
||||
<td align="left">87.1% (85.3-88.7%)</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">UTI</td>
|
||||
<td align="left">91.5% (88.8-93.5%)</td>
|
||||
<td align="left">50% (45.5-54.6%)</td>
|
||||
<td align="left">80.9% (77.8-84%)</td>
|
||||
<td align="left">49.9% (45.6-54.3%)</td>
|
||||
<td align="left">8.2% (6.4-10.5%)</td>
|
||||
<td align="left">8.2% (6.3-10.3%)</td>
|
||||
<td align="left">88.9% (84.2-92.3%)</td>
|
||||
<td align="left">89.4% (86.5-91.8%)</td>
|
||||
<td align="left">89.9% (87.4-92.1%)</td>
|
||||
<td align="left">86.1% (82.9-88.9%)</td>
|
||||
<td align="left">89.8% (87.2-91.9%)</td>
|
||||
<td align="left">89.8% (87.1-92.1%)</td>
|
||||
<td align="left">87.4% (84.5-89.8%)</td>
|
||||
<td align="left">NA</td>
|
||||
<td align="left">81.4% (78.3-84.3%)</td>
|
||||
<td align="left">8.2% (6.3-10.4%)</td>
|
||||
<td align="left">91.7% (89.6-93.8%)</td>
|
||||
<td align="left">NA</td>
|
||||
<td align="left">8.1% (6.3-10.4%)</td>
|
||||
<td align="left">NA</td>
|
||||
<td align="left">90.6% (86.5-93.3%)</td>
|
||||
<td align="left">90.2% (87.9-92.2%)</td>
|
||||
<td align="left">91.8% (89.7-93.8%)</td>
|
||||
<td align="left">NA</td>
|
||||
<td align="left">8.1% (6.1-10.2%)</td>
|
||||
<td align="left">91.8% (89.6-93.8%)</td>
|
||||
<td align="left">71.4% (31.8-91.6%)</td>
|
||||
<td align="left">9.3% (6.7-13.3%)</td>
|
||||
<td align="left">NA</td>
|
||||
<td align="left">89.4% (86.9-91.7%)</td>
|
||||
<td align="left">NA</td>
|
||||
<td align="left">87.2% (84.4-89.6%)</td>
|
||||
<td align="left">8.2% (6.3-10.4%)</td>
|
||||
<td align="left">8.2% (6.3-10.3%)</td>
|
||||
<td align="left">41.2% (14.3-74.4%)</td>
|
||||
<td align="left">90.9% (87.7-93.3%)</td>
|
||||
<td align="left">89.6% (87.1-91.8%)</td>
|
||||
<td align="left">59.1% (54.7-63.4%)</td>
|
||||
<td align="left">65.3% (61.3-69.2%)</td>
|
||||
<td align="left">8.2% (6.2-10.3%)</td>
|
||||
<td align="left">80.9% (77.7-83.8%)</td>
|
||||
<td align="left">88.2% (85.7-90.5%)</td>
|
||||
<td align="left">90.9% (88.7-93%)</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="use-combination-regimens">Use combination regimens<a class="anchor" aria-label="anchor" href="#use-combination-regimens"></a>
|
||||
</h3>
|
||||
<p>The <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function supports combination
|
||||
regimens:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||||
<span> antimicrobials <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">"AMC"</span>, <span class="st">"GEN"</span>, <span class="st">"AMC + GEN"</span>, <span class="st">"CIP"</span><span class="op">)</span>,</span>
|
||||
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>The <code>AMR</code> package is available in 20 languages, which can
|
||||
all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></code> function too:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||||
<span> antimicrobials <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">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
|
||||
<span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"UTI"</span>, <span class="st">"UCI"</span>, <span class="va">data</span><span class="op">$</span><span class="va">syndrome</span><span class="op">)</span>,</span>
|
||||
<span> language <span class="op">=</span> <span class="st">"Spanish"</span><span class="op">)</span></span></code></pre></div>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="26%">
|
||||
<col width="39%">
|
||||
<col width="16%">
|
||||
<col width="18%">
|
||||
<col width="12%">
|
||||
<col width="21%">
|
||||
<col width="34%">
|
||||
<col width="31%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="left">Amoxicillin/clavulanic acid</th>
|
||||
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
|
||||
<th align="left">Ciprofloxacin</th>
|
||||
<th align="left">Gentamicin</th>
|
||||
</tr></thead>
|
||||
<tbody><tr class="odd">
|
||||
<td align="left">73.8% (71.7-75.8%)</td>
|
||||
<td align="left">89.7% (88.2-91.2%)</td>
|
||||
<td align="left">77% (74.3-79.6%)</td>
|
||||
<td align="left">72.8% (70.6-74.9%)</td>
|
||||
</tr></tbody>
|
||||
</table>
|
||||
<hr>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="interpretation">Interpretation<a class="anchor" aria-label="anchor" href="#interpretation"></a>
|
||||
</h2>
|
||||
<p>Suppose you get this output:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th>Regimen</th>
|
||||
<th>Coverage</th>
|
||||
<th>Lower_CI</th>
|
||||
<th>Upper_CI</th>
|
||||
<th align="left">Grupo sindrómico</th>
|
||||
<th align="left">Amoxicilina/ácido clavulánico</th>
|
||||
<th align="left">Amoxicilina/ácido clavulánico + Ciprofloxacina</th>
|
||||
<th align="left">Amoxicilina/ácido clavulánico + Gentamicina</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>AMC</td>
|
||||
<td>0.72</td>
|
||||
<td>0.65</td>
|
||||
<td>0.78</td>
|
||||
<td align="left">No UCI</td>
|
||||
<td align="left">70% (67.8-72.4%)</td>
|
||||
<td align="left">85.3% (83.3-87.2%)</td>
|
||||
<td align="left">87% (85.3-88.8%)</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>AMC + GEN</td>
|
||||
<td>0.88</td>
|
||||
<td>0.83</td>
|
||||
<td>0.93</td>
|
||||
<td align="left">UCI</td>
|
||||
<td align="left">80.9% (77.7-83.9%)</td>
|
||||
<td align="left">88.2% (85.5-90.6%)</td>
|
||||
<td align="left">90.9% (88.7-93%)</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Interpretation:</p>
|
||||
<blockquote>
|
||||
<p><em>“AMC + GEN covers 88% of expected pathogens for this syndrome,
|
||||
with 95% certainty that the true coverage lies between 83% and
|
||||
93%.”</em></p>
|
||||
</blockquote>
|
||||
<p>Regimens with few tested isolates will show <strong>wider
|
||||
intervals</strong>.</p>
|
||||
<hr>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="sensible-defaults-but-you-can-customise">Sensible defaults, but you can customise<a class="anchor" aria-label="anchor" href="#sensible-defaults-but-you-can-customise"></a>
|
||||
<h2 id="sensible-defaults-which-can-be-customised">Sensible defaults, which can be customised<a class="anchor" aria-label="anchor" href="#sensible-defaults-which-can-be-customised"></a>
|
||||
</h2>
|
||||
<ul>
|
||||
<li>
|
||||
<code>minimum = 30</code>: exclude regimens with <30 isolates
|
||||
tested.</li>
|
||||
<code>simulations = 1000</code>: number of Monte Carlo draws</li>
|
||||
<li>
|
||||
<code>simulations = 1000</code>: number of Monte Carlo samples.</li>
|
||||
<code>conf_interval = 0.95</code>: coverage interval width</li>
|
||||
<li>
|
||||
<code>conf_interval = 0.95</code>: coverage interval width.</li>
|
||||
<li>
|
||||
<code>combine_SI = TRUE</code>: count “I”/“SDD” as susceptible.</li>
|
||||
<code>combine_SI = TRUE</code>: count “I” and “SDD” as
|
||||
susceptible</li>
|
||||
</ul>
|
||||
<hr>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="limitations">Limitations<a class="anchor" aria-label="anchor" href="#limitations"></a>
|
||||
</h2>
|
||||
<ul>
|
||||
<li>WISCA does not model time trends or temporal resistance shifts.</li>
|
||||
<li>It assumes data are representative of current clinical
|
||||
practice.</li>
|
||||
<li>It does not account for patient-level covariates (yet).</li>
|
||||
<li>Species-specific data are abstracted into syndrome-level
|
||||
estimates.</li>
|
||||
<li>It assumes your data are representative</li>
|
||||
<li>No adjustment for patient-level covariates, although these could be
|
||||
passed onto the <code>syndromic_group</code> argument</li>
|
||||
<li>WISCA does not model resistance over time, you might want to use
|
||||
<code>tidymodels</code> for that, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a
|
||||
basic introduction</a>
|
||||
</li>
|
||||
</ul>
|
||||
<hr>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
|
||||
</h2>
|
||||
<p>WISCA enables:</p>
|
||||
<ul>
|
||||
<li>Empirical regimen comparison,</li>
|
||||
<li>Syndrome-specific coverage estimation,</li>
|
||||
<li>Fully probabilistic interpretation.</li>
|
||||
</ul>
|
||||
<p>It is available in the <code>AMR</code> package via either:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">...</span>, wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference">Reference<a class="anchor" aria-label="anchor" href="#reference"></a>
|
||||
</h2>
|
||||
<p>Bielicki JA et al. (2016).<br><em>Weighted-incidence syndromic combination antibiograms to guide
|
||||
empiric treatment in pediatric bloodstream infections.</em><br><strong>J Antimicrob Chemother</strong>, 71(2):529–536. <a href="doi:10.1093/jac/dkv397" class="uri">doi:10.1093/jac/dkv397</a></p>
|
||||
<hr>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
|
||||
</h2>
|
||||
<p>WISCA shifts empirical therapy from simple percent susceptible toward
|
||||
<strong>probabilistic, syndrome-based decision support</strong>. It is a
|
||||
statistically principled, clinically intuitive method to guide regimen
|
||||
selection — and easy to use via the <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function
|
||||
in the <strong>AMR</strong> package.</p>
|
||||
<p>For antimicrobial stewardship teams, it enables
|
||||
<strong>disease-specific, reproducible, and data-driven
|
||||
guidance</strong> — even in the face of sparse data.</p>
|
||||
<p>Bielicki, JA, et al. (2016). <em>Selecting appropriate empirical
|
||||
antibiotic regimens for paediatric bloodstream infections: application
|
||||
of a Bayesian decision model to local and pooled antimicrobial
|
||||
resistance surveillance data.</em> <strong>J Antimicrob
|
||||
Chemother</strong>. 71(3):794-802. <a href="https://doi.org/10.1093/jac/dkv397" class="external-link uri">https://doi.org/10.1093/jac/dkv397</a></p>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
</nav></aside>
|
||||
|
||||
Reference in New Issue
Block a user