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cli-147-2091

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2024-06-16 19:00:31 +00:00
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@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<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="">2.1.1.9051</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9052</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">
@ -630,9 +630,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
@ -648,20 +646,20 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 15</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo method</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-16 <span style="color: #949494;">09:32:52</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-16 <span style="color: #949494;">09:32:48</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-06-16 <span style="color: #949494;">09:32:47</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-16 <span style="color: #949494;">18:58:30</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-16 <span style="color: #949494;">18:58:30</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-16 <span style="color: #949494;">18:58:30</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-16 <span style="color: #949494;">18:58:30</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-16 <span style="color: #949494;">18:58:26</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-16 <span style="color: #949494;">18:58:26</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-16 <span style="color: #949494;">18:58:26</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-16 <span style="color: #949494;">18:58:26</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-16 <span style="color: #949494;">18:58:26</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-16 <span style="color: #949494;">18:58:25</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-06-16 <span style="color: #949494;">18:58:25</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-06-16 <span style="color: #949494;">18:58:25</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-06-16 <span style="color: #949494;">18:58:25</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN DISK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 8 more variables: input &lt;dbl&gt;, outcome &lt;sir&gt;, host &lt;chr&gt;, notes &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;, breakpoint_S_R &lt;chr&gt;</span></span>
<span class="r-in"><span></span></span>
@ -677,9 +675,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>