@ -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 >
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@ -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 < / 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 > < / code > < / pre >
< p > But clinicians don’ < 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 × < / 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 × < / 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\times 0.7) = 0.82< / annotation > < / semantics > < / math > < / >
< 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 < / code > n
= (n₁, …, nₖ) be the observed counts per species.< / p >
< p > Then the posterior incidence follows:< / p >
< p > ``` incidence ∼ α < / p >
< p > In simulations, we draw from this posterior using:< / p >
< p > ``` xᵢ ∼ < / 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– : - < code > prior: Beta(1, 1) - < / code >
data: S susceptible out of N tested< / p >
< p > Then:< / p >
< p > ``` susceptibility ∼ < / p >
< p > In each simulation, we draw random susceptibility per species from
this Beta distribution.< / p >
< hr >
< p > Each pathogen– 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 ∼
susceptibility ∼ < / p >
< p > We repeat this (e.g. × < str ong > 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}< / annotati on> < / 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. × < / 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" > S imulate 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 s imulate 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 > < spanclass = "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 × < / 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 < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < 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%)< / t d>
< 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 = "tab le" >
< 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 > < / thea d >
< 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%;" = "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 = "1 2%" >
< 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" > Amp icillin< / th >
< th align = "left" > Azithromy cin< / 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" > Amox icillin/clavulanic acid + Ciprofloxacin < / th >
< th align = "left" > Amoxicillin/clavulanic acid + Gentami cin< / 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" > 8 7.1% (85.3-88.7 %)< / td >
< / tr >
< tr class = "even" >
< td align = "left" > UTI< / td >
< td align = "left" > 91.5% (88.8-9 3.5 %)< / td >
< td align = "left" > 50 % (4 5.5-54.6 %)< / td >
< td align = "left" > 8 0.9% (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% (77.7-8 3.8 %)< / td >
< td align = "left" > 88.2 % (8 5.7-90.5 %)< / td >
< td align = "left" > 9 0.9% (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 = "1 2%" >
< col width = "21 %" >
< col width = "34 %" >
< col width = "3 1%" >
< / colgroup >
< thead > < tr class = "header" >
< th align = "left" > Amoxicillin/clavulanic acid < / th >
< th align = "left" > Amoxicill in/ clavula nic 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 clavulá nico < / 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" > 8 0.9% (77.7-83.9%) < / td >
< td align = "left" > 88.2% (85.5-90.6%) < / td >
< td align = "left" > 9 0.9% (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 = 3 0< / code > : exclude regimens with < 30 isolates
tested.< / li >
< code > simulations = 100 0< / 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. < br > < em > Weighted-incidence syndromic combination antibiograms to guide
empir ic t reat ment in pediatric bloodstream infections.< / em > < br > < strong > J Antimicrob Chemother< / strong > , 71(2):529– < 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. < em > Selecting appropriate empirical
antibiot ic regi mens for pa ediatric 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 >
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