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<title>Contents | A New Instrument for Microbial Epidemiology</title>
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<li><a href="https://doi.org/10.33612/diss.177417131" target="blank"><img src="images/cover.jpg" style="width:90%; margin-left:5%;"></a></li>
<li class="divider"></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preamble</a>
<ul>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html#short-summary-250-words"><i class="fa fa-check"></i>Short summary (250 words)</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="colophon.html"><a href="colophon.html"><i class="fa fa-check"></i>Colophon</a></li>
<li class="chapter" data-level="" data-path="contents.html"><a href="contents.html"><i class="fa fa-check"></i>Contents</a></li>
<li class="chapter" data-level="1" data-path="ch01-introduction.html"><a href="ch01-introduction.html"><i class="fa fa-check"></i><b>1</b> General Introduction</a>
<ul>
<li class="chapter" data-level="1.1" data-path="ch01-introduction.html"><a href="ch01-introduction.html#microbial-epidemiology"><i class="fa fa-check"></i><b>1.1</b> Microbial epidemiology</a></li>
<li class="chapter" data-level="1.2" data-path="ch01-introduction.html"><a href="ch01-introduction.html#antimicrobial-resistance-in-microorganisms"><i class="fa fa-check"></i><b>1.2</b> Antimicrobial resistance in microorganisms</a>
<ul>
<li class="chapter" data-level="1.2.1" data-path="ch01-introduction.html"><a href="ch01-introduction.html#laboratory-diagnostics"><i class="fa fa-check"></i><b>1.2.1</b> Laboratory diagnostics</a></li>
<li class="chapter" data-level="1.2.2" data-path="ch01-introduction.html"><a href="ch01-introduction.html#interpretation-of-raw-results"><i class="fa fa-check"></i><b>1.2.2</b> Interpretation of raw results</a></li>
<li class="chapter" data-level="1.2.3" data-path="ch01-introduction.html"><a href="ch01-introduction.html#multi-drug-resistant-organisms"><i class="fa fa-check"></i><b>1.2.3</b> Multi-drug resistant organisms</a></li>
<li class="chapter" data-level="1.2.4" data-path="ch01-introduction.html"><a href="ch01-introduction.html#surveillance-programs"><i class="fa fa-check"></i><b>1.2.4</b> Surveillance programs</a></li>
</ul></li>
<li class="chapter" data-level="1.3" data-path="ch01-introduction.html"><a href="ch01-introduction.html#data-analysis-using-r"><i class="fa fa-check"></i><b>1.3</b> Data analysis using R</a></li>
<li class="chapter" data-level="1.4" data-path="ch01-introduction.html"><a href="ch01-introduction.html#setting-for-this-thesis"><i class="fa fa-check"></i><b>1.4</b> Setting for this thesis</a></li>
<li class="chapter" data-level="1.5" data-path="ch01-introduction.html"><a href="ch01-introduction.html#aim-of-this-thesis-and-introduction-to-its-chapters"><i class="fa fa-check"></i><b>1.5</b> Aim of this thesis and introduction to its chapters</a></li>
<li class="chapter" data-level="" data-path="ch01-introduction.html"><a href="ch01-introduction.html#references"><i class="fa fa-check"></i>References</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html"><i class="fa fa-check"></i><b>2</b> Diagnostic Stewardship: Sense or Nonsense?!</a>
<ul>
<li class="chapter" data-level="" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#abstract"><i class="fa fa-check"></i>Abstract</a></li>
<li class="chapter" data-level="2.1" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#introduction"><i class="fa fa-check"></i><b>2.1</b> Introduction</a>
<ul>
<li class="chapter" data-level="2.1.1" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#case-1"><i class="fa fa-check"></i><b>2.1.1</b> Case 1</a></li>
<li class="chapter" data-level="2.1.2" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#case-2"><i class="fa fa-check"></i><b>2.1.2</b> Case 2</a></li>
</ul></li>
<li class="chapter" data-level="2.2" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#the-general-concept"><i class="fa fa-check"></i><b>2.2</b> The general concept</a>
<ul>
<li class="chapter" data-level="2.2.1" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#diagnostics"><i class="fa fa-check"></i><b>2.2.1</b> ‘Diagnostics’</a></li>
<li class="chapter" data-level="2.2.2" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#dsp-in-the-microbiological-laboratory"><i class="fa fa-check"></i><b>2.2.2</b> DSP in the microbiological laboratory</a></li>
<li class="chapter" data-level="2.2.3" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#dsp-as-process-optimisation"><i class="fa fa-check"></i><b>2.2.3</b> DSP as process optimisation</a></li>
<li class="chapter" data-level="2.2.4" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#multidisciplinary-aspects-of-dsp-and-infection-management"><i class="fa fa-check"></i><b>2.2.4</b> Multidisciplinary aspects of DSP and infection management</a></li>
</ul></li>
<li class="chapter" data-level="2.3" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#conclusion"><i class="fa fa-check"></i><b>2.3</b> Conclusion</a></li>
<li class="chapter" data-level="" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#financing"><i class="fa fa-check"></i>Financing</a></li>
<li class="chapter" data-level="" data-path="ch02-diagnostic-stewardship.html"><a href="ch02-diagnostic-stewardship.html#references-1"><i class="fa fa-check"></i>References</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html"><i class="fa fa-check"></i><b>3</b> Introducing a New, Free, and Independent Method for Standardised, Reproducible and Reliable Analyses of Antimicrobial Resistance Data</a>
<ul>
<li class="chapter" data-level="" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html#abstract-1"><i class="fa fa-check"></i>Abstract</a></li>
<li class="chapter" data-level="3.1" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html#background"><i class="fa fa-check"></i><b>3.1</b> Background</a></li>
<li class="chapter" data-level="3.2" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html#standardising-amr-data-analysis"><i class="fa fa-check"></i><b>3.2</b> Standardising AMR data analysis</a></li>
<li class="chapter" data-level="3.3" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html#comparison-with-existing-software-methods"><i class="fa fa-check"></i><b>3.3</b> Comparison with existing software methods</a></li>
<li class="chapter" data-level="3.4" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html#user-feedback"><i class="fa fa-check"></i><b>3.4</b> User feedback</a></li>
<li class="chapter" data-level="3.5" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html#conclusion-1"><i class="fa fa-check"></i><b>3.5</b> Conclusion</a></li>
<li class="chapter" data-level="" data-path="ch03-introducing-new-method.html"><a href="ch03-introducing-new-method.html#references-2"><i class="fa fa-check"></i>References</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html"><i class="fa fa-check"></i><b>4</b> <code>AMR</code> - An <code>R</code> Package for Working with Antimicrobial Resistance Data</a>
<ul>
<li class="chapter" data-level="" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#abstract-2"><i class="fa fa-check"></i>Abstract</a></li>
<li class="chapter" data-level="4.1" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#introduction-1"><i class="fa fa-check"></i><b>4.1</b> Introduction</a></li>
<li class="chapter" data-level="4.2" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#antimicrobial-resistance-data"><i class="fa fa-check"></i><b>4.2</b> Antimicrobial resistance data</a></li>
<li class="chapter" data-level="4.3" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#antimicrobial-resistance-data-transformation"><i class="fa fa-check"></i><b>4.3</b> Antimicrobial resistance data transformation</a>
<ul>
<li class="chapter" data-level="4.3.1" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#working-with-taxonomically-valid-microorganism-names"><i class="fa fa-check"></i><b>4.3.1</b> Working with taxonomically valid microorganism names</a></li>
<li class="chapter" data-level="4.3.2" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#working-with-antimicrobial-names-or-codes"><i class="fa fa-check"></i><b>4.3.2</b> Working with antimicrobial names or codes</a></li>
<li class="chapter" data-level="4.3.3" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#working-with-antimicrobial-susceptibility-test-results"><i class="fa fa-check"></i><b>4.3.3</b> Working with antimicrobial susceptibility test results</a></li>
<li class="chapter" data-level="4.3.4" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#interpretative-rules-by-eucast"><i class="fa fa-check"></i><b>4.3.4</b> Interpretative rules by EUCAST</a></li>
<li class="chapter" data-level="4.3.5" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#working-with-defined-daily-doses-ddd"><i class="fa fa-check"></i><b>4.3.5</b> Working with defined daily doses (DDD)</a></li>
</ul></li>
<li class="chapter" data-level="4.4" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#enhancing-antimicrobial-resistance-data"><i class="fa fa-check"></i><b>4.4</b> Enhancing antimicrobial resistance data</a>
<ul>
<li class="chapter" data-level="4.4.1" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#determining-first-isolates"><i class="fa fa-check"></i><b>4.4.1</b> Determining first isolates</a></li>
<li class="chapter" data-level="4.4.2" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#determining-multi-drug-resistant-organisms-mdro"><i class="fa fa-check"></i><b>4.4.2</b> Determining multi-drug resistant organisms (MDRO)</a></li>
</ul></li>
<li class="chapter" data-level="4.5" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#analysing-antimicrobial-resistance-data"><i class="fa fa-check"></i><b>4.5</b> Analysing antimicrobial resistance data</a>
<ul>
<li class="chapter" data-level="4.5.1" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#calculation-of-antimicrobial-resistance"><i class="fa fa-check"></i><b>4.5.1</b> Calculation of antimicrobial resistance</a></li>
</ul></li>
<li class="chapter" data-level="4.6" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#design-decisions"><i class="fa fa-check"></i><b>4.6</b> Design decisions</a></li>
<li class="chapter" data-level="4.7" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#reproducible-example"><i class="fa fa-check"></i><b>4.7</b> Reproducible example</a></li>
<li class="chapter" data-level="4.8" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#discussion"><i class="fa fa-check"></i><b>4.8</b> Discussion</a></li>
<li class="chapter" data-level="" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#computational-details"><i class="fa fa-check"></i>Computational Details</a></li>
<li class="chapter" data-level="" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#acknowledgements"><i class="fa fa-check"></i>Acknowledgements</a></li>
<li class="chapter" data-level="" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#references-3"><i class="fa fa-check"></i>References</a></li>
<li class="chapter" data-level="" data-path="ch04-amr-r-package.html"><a href="ch04-amr-r-package.html#appendix-a-included-data-sets"><i class="fa fa-check"></i>Appendix A: Included Data Sets</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="ch05-radar.html"><a href="ch05-radar.html"><i class="fa fa-check"></i><b>5</b> Rapid Analysis of Diagnostic and Antimicrobial Patterns in R (RadaR): Interactive Open-Source Software App for Infection Management and Antimicrobial Stewardship</a>
<ul>
<li class="chapter" data-level="" data-path="ch05-radar.html"><a href="ch05-radar.html#abstract-3"><i class="fa fa-check"></i>Abstract</a></li>
<li class="chapter" data-level="5.1" data-path="ch05-radar.html"><a href="ch05-radar.html#introduction-2"><i class="fa fa-check"></i><b>5.1</b> Introduction</a>
<ul>
<li class="chapter" data-level="5.1.1" data-path="ch05-radar.html"><a href="ch05-radar.html#background-1"><i class="fa fa-check"></i><b>5.1.1</b> Background</a></li>
<li class="chapter" data-level="5.1.2" data-path="ch05-radar.html"><a href="ch05-radar.html#objectives"><i class="fa fa-check"></i><b>5.1.2</b> Objectives</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="ch05-radar.html"><a href="ch05-radar.html#methods"><i class="fa fa-check"></i><b>5.2</b> Methods</a></li>
<li class="chapter" data-level="5.3" data-path="ch05-radar.html"><a href="ch05-radar.html#results"><i class="fa fa-check"></i><b>5.3</b> Results</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="ch05-radar.html"><a href="ch05-radar.html#overview"><i class="fa fa-check"></i><b>5.3.1</b> Overview</a></li>
<li class="chapter" data-level="5.3.2" data-path="ch05-radar.html"><a href="ch05-radar.html#application-design"><i class="fa fa-check"></i><b>5.3.2</b> Application Design</a></li>
<li class="chapter" data-level="5.3.3" data-path="ch05-radar.html"><a href="ch05-radar.html#development-process"><i class="fa fa-check"></i><b>5.3.3</b> Development Process</a></li>
<li class="chapter" data-level="5.3.4" data-path="ch05-radar.html"><a href="ch05-radar.html#workflow"><i class="fa fa-check"></i><b>5.3.4</b> Workflow</a></li>
<li class="chapter" data-level="5.3.5" data-path="ch05-radar.html"><a href="ch05-radar.html#customisation"><i class="fa fa-check"></i><b>5.3.5</b> Customisation</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="ch05-radar.html"><a href="ch05-radar.html#discussion-1"><i class="fa fa-check"></i><b>5.4</b> Discussion</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="ch05-radar.html"><a href="ch05-radar.html#principal-findings"><i class="fa fa-check"></i><b>5.4.1</b> Principal Findings</a></li>
<li class="chapter" data-level="5.4.2" data-path="ch05-radar.html"><a href="ch05-radar.html#conclusions"><i class="fa fa-check"></i><b>5.4.2</b> Conclusions</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="ch05-radar.html"><a href="ch05-radar.html#acknowledgements-1"><i class="fa fa-check"></i>Acknowledgements</a></li>
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<li class="chapter" data-level="" data-path="ch05-radar.html"><a href="ch05-radar.html#references-4"><i class="fa fa-check"></i>References</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
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<section class="normal" id="section-">
<div id="contents" class="section level1 unnumbered">
<h1>Contents</h1>
<p><strong>Section I</strong></p>
<ol style="list-style-type: decimal">
<li><p><strong>General Introduction</strong></p></li>
<li><p><strong>Diagnostic Stewardship: Sense or Nonsense?!</strong><br />
Berends MS*, Luz CF*, Wouthuyzen-Bakker M, Märtson AG, Alffenaar JW, Dik JWH, Glasner C, Sinha BNM<br />
<em>Dutch Journal of Clinical Microbiology (2018) 26;3</em></p></li>
<li><p><strong>Introducing a New, Free, and Independent Method for Standardised, Reproducible and Reliable Analyses of Antimicrobial Resistance Data</strong><br />
Berends MS, Luz CF, Sinha BNM, Glasner C<sup>‡</sup>, Friedrich AW<sup>‡</sup><br />
<em>In preparation</em></p></li>
</ol>
<p><strong>Section II</strong></p>
<ol start="4" style="list-style-type: decimal">
<li><p><strong>AMR - An R Package for Working with Antimicrobial Resistance Data</strong><br />
Berends MS*, Luz CF*, Friedrich AW, Sinha BNM, Albers CJ, Glasner C<br />
<em>Journal of Statistical Software (2021), ahead of print</em></p></li>
<li><p><strong>Rapid Analysis of Diagnostic and Antimicrobial Patterns in R (RadaR): Interactive Open-Source Software App for Infection Management and Antimicrobial Stewardship</strong><br />
Luz CF, Berends MS, Dik JWH, Lokate M, Pulcini C, Glasner C, Sinha BNM<br />
<em>Journal of Medical Internet Research (2019) 21;6, e12843</em></p></li>
<li><p><strong>Better Antimicrobial Resistance Data Analysis and Reporting in Less Time</strong><br />
Berends MS*, Luz CF*, Zhou X, Friedrich AW, Lokate ML, Sinha BNM<sup>‡</sup>, Glasner C<sup>‡</sup><br />
<em>medRxiv [preprint] (2021), 21257599</em></p></li>
</ol>
<p><strong>Section III</strong></p>
<ol start="7" style="list-style-type: decimal">
<li><p><strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Blood in the Northern Netherlands between 2013 and 2019</strong><br />
Berends MS, Luz CF, Ott A, Andriesse GI, Becker K, Glasner C<sup>‡</sup>, Friedrich AW<sup>‡</sup><br />
<em>In preparation</em></p></li>
<li><p><strong>Defining Multidrug Resistance of Gram-Negative Bacteria in the Dutch-German Border Region-Impact of National Guidelines</strong><br />
Köck R, Siemer P, Esser J, Kampmeier S, Berends MS, Glasner C, Arends JP, Becker K, Friedrich AW<br />
<em>Microorganisms (2018) 6;1</em></p></li>
<li><p><strong>Changing Epidemiology of Methicillin-Resistant <em>Staphylococcus aureus</em> in 42 Hospitals in the Dutch-German Border Region, 2012 to 2016: Results of the Search-and-Follow-Policy</strong><br />
Jurke A, Daniels-Haardt I, Silvis W, Berends MS, Glasner C, Becker K, Köck R, Friedrich AW<br />
<em>Eurosurveillance (2019) 24;15</em></p></li>
<li><p><strong>A Prospective Multicentre MDRO Screening Study on ICUs in the Dutch-German Cross-Border Region (2017-2018): The Importance of Healthcare Structures</strong><br />
Berends MS*, Glasner C*, Becker K, Esser J, Gieffers J, Jurke A, Kampinga G, Kampmeier S, Klont R, Köck R, Al Naemi N, Ott A, Ruis G, Saris K, Tami A, Van Zeijl J, Von Müller L, Voss A, Waar K, Friedrich AW<br />
<em>Eurosurveillance (2021), ahead of print</em></p></li>
</ol>
<p><strong>Section IV</strong></p>
<ol start="11" style="list-style-type: decimal">
<li><strong>Summary and Future Perspectives</strong></li>
</ol>
<p><strong>Gearfetting</strong> yn Frysk<br />
<strong>Samenvatting</strong> in het Nederlands<br />
<strong>Zusammenfassung</strong> auf Deutsch<br />
<strong>Alphabetical list of published work</strong><br />
<strong>Alphabetical list of related presentations</strong><br />
<strong>Acknowledgements</strong> / Tankwurd / Dankwoord / Danksagung<br />
<strong>Curriculum Vitae</strong></p>
<hr />
<p>* Equal contribution<br />
<sup>‡</sup> Equal contribution</p>
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