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(v1.4.0.9048) AmpC de-repressed cephalo-resistant mutants

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dr. M.S. (Matthijs) Berends
2020-12-27 14:23:11 +01:00
parent 8b52f9b1be
commit ed198916bf
24 changed files with 93 additions and 41 deletions
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7
docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.4.0.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span>
</span>
</div>
@ -252,6 +252,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
version_breakpoints <span class='op'>=</span> <span class='fl'>10</span>,
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
@ -286,6 +287,10 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<th>version_expertrules</th>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: 3.1, 3.2.</p></td>
</tr>
<tr>
<th>ampc_cephalosporin_resistance</th>
<td><p>a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of <code>NA</code> for this argument will remove results for these agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Enterobacter</em>, <em>Klebsiella aerogenes</em>, <em>Citrobacter freundii</em>, <em>Hafnia alvei</em>, <em>Serratia</em>, <em>Morganella morganii</em>, <em>Providencia</em>.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>column name of an antibiotic, please see section <em>Antibiotics</em> below</p></td>