<metaproperty="og:description"content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables."/>
<p>Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <ahref='http://eucast.org'>http://eucast.org</a>), see <em>Source</em>. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.</p>
<td><p>column name of the unique IDs of the microorganisms (see <code><ahref='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><ahref='as.mo.html'>as.mo</a></code>.</p></td>
<td><p>a character vector that specifies which rules should be applied - one or more of <code><ahref='https://www.rdocumentation.org/packages/base/topics/c'>c("breakpoints", "expert", "other", "all")</a></code></p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected</p></td>
<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with verbose info.</p>
<p>To define antibiotics column names, input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<preclass="examples"><divclass='input'><spanclass='no'>a</span><spanclass='kw'><-</span><spanclass='fu'>eucast_rules</span>(<spanclass='no'>septic_patients</span>)</div><divclass='output co'>#><spanclass='message'><spanstyle='color: #0000BB;'>NOTE: Using column `</span><spanstyle='color: #0000BB;font-weight: bold;'>mo</span><spanstyle='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><divclass='output co'>#><spanclass='warning'>Warning: These columns do not exist and will be ignored: azlo, aztr, cefa, cfra, clar, dapt, erta, fusi, levo, linc, mezl, mino, nali, neom, neti, novo, norf, oflo, pipe, poly, pris, qida, roxi, siso, tica.</span>
#><spanclass='warning'>THIS MAY STRONGLY INFLUENCE THE OUTCOME.</span></div><divclass='output co'>#>
#> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
#></span><spanstyle='font-weight: bold;'>
#> EUCAST Clinical Breakpoints (v8.1, 2018)
#></span><span>Enterobacteriales (Order)</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Staphylococcus</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Enterococcus</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Streptococcus</span><span> groups A, B, C, G</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Streptococcus pneumoniae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Viridans group streptococci</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Haemophilus influenzae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Moraxella catarrhalis</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Anaerobic Gram positives</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Anaerobic Gram negatives</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Pasteurella multocida</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Campylobacter jejuni</span><span> and </span><spanstyle='font-style: italic;'>C. coli</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Aerococcus sanguinicola</span><span> and </span><spanstyle='font-style: italic;'>A. urinae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Kingella kingae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 1: Intrinsic resistance in </span><spanstyle='font-style: italic;'>Enterobacteriaceae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 3: Intrinsic resistance in other Gram-negative bacteria</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 4: Intrinsic resistance in Gram-positive bacteria</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 9: Interpretive rules for B-lactam agents and Gram-negative rods</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 12: Interpretive rules for aminoglycosides</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Table 13: Interpretive rules for quinolones</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-weight: bold;'>
#> Other rules
#></span><span>Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-weight: bold;'>
#> => EUCAST rules affected 1,980 out of 2,000 rows -></span><spanstyle='color: #00BB00;font-weight: bold;'>changed 0 test results.
<spanclass='no'>b</span><spanclass='kw'><-</span><spanclass='fu'>eucast_rules</span>(<spanclass='no'>a</span>, <spanclass='st'>"mo"</span>) <spanclass='co'># 18 results are forced as R or S</span></div><divclass='output co'>#><spanclass='warning'>Warning: These columns do not exist and will be ignored: amcl, amik, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot, cftr, chlo, cipr, clar, clin, clox, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, oxac, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu.</span>
#><spanclass='warning'>THIS MAY STRONGLY INFLUENCE THE OUTCOME.</span></div><divclass='output co'>#>
#> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</div><divclass='output co'>#><spanclass='message'></span><spanstyle='color: #0000BB;'>NOTE: Using column `</span><spanstyle='color: #0000BB;font-weight: bold;'>amox</span><spanstyle='color: #0000BB;'>` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.</span><span></span></div><divclass='output co'>#></span><spanstyle='font-weight: bold;'>
#> EUCAST Clinical Breakpoints (v8.1, 2018)
#></span><span>Enterobacteriales (Order)</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Enterococcus</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Streptococcus</span><span> groups A, B, C, G</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Streptococcus pneumoniae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Viridans group streptococci</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Haemophilus influenzae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Moraxella catarrhalis</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Anaerobic Gram positives</span><spanstyle='color: #00BB00;'> (no changes)
#></span><span>Anaerobic Gram negatives</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Pasteurella multocida</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Campylobacter jejuni</span><span> and </span><spanstyle='font-style: italic;'>C. coli</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Aerococcus sanguinicola</span><span> and </span><spanstyle='font-style: italic;'>A. urinae</span><spanstyle='color: #00BB00;'> (no changes)
#></span><spanstyle='font-style: italic;'>Kingella kingae</span><spanstyle='color: #00BB00;'> (no changes)
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
