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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -92,7 +92,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ul><li><p>Bielicki JA <em>et al.</em> (2016). <strong>Selecting appropriate empirical antibiotic regimens for paediatric bloodstream infections: application of a Bayesian decision model to local and pooled antimicrobial resistance surveillance data</strong> <em>Journal of Antimicrobial Chemotherapy</em> 71(3); <a href="https://doi.org/10.1093/jac/dkv397" class="external-link">doi:10.1093/jac/dkv397</a></p></li>
<li><p>Bielicki JA <em>et al.</em> (2020). <strong>Evaluation of the coverage of 3 antibiotic regimens for neonatal sepsis in the hospital setting across Asian countries</strong> <em>JAMA Netw Open.</em> 3(2):e1921124; <a href="https://doi.org/10.1001.jamanetworkopen.2019.21124" class="external-link">doi:10.1001.jamanetworkopen.2019.21124</a></p></li>
<li><p>Bielicki JA <em>et al.</em> (2020). <strong>Evaluation of the coverage of 3 antibiotic regimens for neonatal sepsis in the hospital setting across Asian countries</strong> <em>JAMA Netw Open.</em> 3(2):e1921124; <a href="https://doi.org/10.1001/jamanetworkopen.2019.21124" class="external-link">doi:10.1001/jamanetworkopen.2019.21124</a></p></li>
<li><p>Klinker KP <em>et al.</em> (2021). <strong>Antimicrobial stewardship and antibiograms: importance of moving beyond traditional antibiograms</strong>. <em>Therapeutic Advances in Infectious Disease</em>, May 5;8:20499361211011373; <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a></p></li>
<li><p>Barbieri E <em>et al.</em> (2021). <strong>Development of a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) to guide the choice of the empiric antibiotic treatment for urinary tract infection in paediatric patients: a Bayesian approach</strong> <em>Antimicrobial Resistance &amp; Infection Control</em> May 1;10(1):74; <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">doi:10.1186/s13756-021-00939-2</a></p></li>
<li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
@ -254,7 +254,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<p>There are various antibiogram types, as summarised by Klinker <em>et al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a>
), and they are all supported by <code>antibiogram()</code>.</p>
<p>For clinical coverage estimations, <strong>use WISCA whenever possible</strong>, since it provides more precise coverage estimates by accounting for pathogen incidence and antimicrobial susceptibility, as has been shown by Bielicki <em>et al.</em> (2020, <a href="https://doi.org/10.1001.jamanetworkopen.2019.21124" class="external-link">doi:10.1001.jamanetworkopen.2019.21124</a>
<p>For clinical coverage estimations, <strong>use WISCA whenever possible</strong>, since it provides more precise coverage estimates by accounting for pathogen incidence and antimicrobial susceptibility, as has been shown by Bielicki <em>et al.</em> (2020, <a href="https://doi.org/10.1001/jamanetworkopen.2019.21124" class="external-link">doi:10.1001/jamanetworkopen.2019.21124</a>
). See the section <em>Explaining WISCA</em> on this page. Do note that WISCA is pathogen-agnostic, meaning that the outcome is not stratied by pathogen, but rather by syndrome.</p><ol><li><p><strong>Traditional Antibiogram</strong></p>
<p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to piperacillin/tazobactam (TZP)</p>
<p>Code example:</p>