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<meta property="og:description" content="This is the integral PhD thesis ‘A New Instrument for Microbial Epidemiology’ (DOI 10.33612/diss.177417131) by Matthijs S. Berends, which was defended publicly at the University of Groningen, the Netherlands, on 25 August 2021." />
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<meta name="author" content="Matthijs S. Berends" />
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<ul class="summary">
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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>
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<li class="divider"></li>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preamble</a>
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<ul>
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<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>
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</ul></li>
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<li class="chapter" data-level="" data-path="colophon.html"><a href="colophon.html"><i class="fa fa-check"></i>Colophon</a></li>
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<li class="chapter" data-level="" data-path="contents.html"><a href="contents.html"><i class="fa fa-check"></i>Contents</a></li>
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<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>
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<ul>
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<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>
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<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>
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<ul>
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<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>
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<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>
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<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>
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<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>
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</ul></li>
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<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>
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<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>
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<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>
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<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>
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</ul></li>
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<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>
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<ul>
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<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>
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<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>
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<ul>
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<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>
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<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>
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</ul></li>
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<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>
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<ul>
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<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>
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<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>
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<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>
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<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>
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</ul></li>
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<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>
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<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>
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<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>
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</ul></li>
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<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>
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<ul>
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<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>
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<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>
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||
<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>
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<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>
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<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>
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<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>
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<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>
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</ul></li>
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<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>
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<ul>
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<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>
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||
<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>
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||
<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>
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<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>
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<ul>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
</ul></li>
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||
<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>
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||
<ul>
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||
<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>
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||
</ul></li>
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||
<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>
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<ul>
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||
<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>
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</ul></li>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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||
<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>
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<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>
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</ul></li>
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<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>
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<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>
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<ul>
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<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>
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<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>
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</ul></li>
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<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>
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||
<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>
|
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<ul>
|
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<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>
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<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>
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<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>
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<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>
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<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>
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</ul></li>
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<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>
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<ul>
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<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>
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<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>
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</ul></li>
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<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>
|
||
<li class="chapter" data-level="" data-path="ch05-radar.html"><a href="ch05-radar.html#conflicts-of-interests"><i class="fa fa-check"></i>Conflicts of interests</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>
|
||
</ul></li>
|
||
<li class="chapter" data-level="6" data-path="ch06-radar2.html"><a href="ch06-radar2.html"><i class="fa fa-check"></i><b>6</b> Better Antimicrobial Resistance Data Analysis and Reporting in Less Time</a>
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||
<ul>
|
||
<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#abstract-4"><i class="fa fa-check"></i>Abstract</a></li>
|
||
<li class="chapter" data-level="6.1" data-path="ch06-radar2.html"><a href="ch06-radar2.html#introduction-3"><i class="fa fa-check"></i><b>6.1</b> Introduction</a></li>
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||
<li class="chapter" data-level="6.2" data-path="ch06-radar2.html"><a href="ch06-radar2.html#methods-1"><i class="fa fa-check"></i><b>6.2</b> Methods</a>
|
||
<ul>
|
||
<li class="chapter" data-level="6.2.1" data-path="ch06-radar2.html"><a href="ch06-radar2.html#study-setup"><i class="fa fa-check"></i><b>6.2.1</b> Study setup</a></li>
|
||
<li class="chapter" data-level="6.2.2" data-path="ch06-radar2.html"><a href="ch06-radar2.html#amr-data"><i class="fa fa-check"></i><b>6.2.2</b> AMR data</a></li>
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<li class="chapter" data-level="6.2.3" data-path="ch06-radar2.html"><a href="ch06-radar2.html#amr-data-analysis-and-reporting"><i class="fa fa-check"></i><b>6.2.3</b> AMR data analysis and reporting</a></li>
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<li class="chapter" data-level="6.2.4" data-path="ch06-radar2.html"><a href="ch06-radar2.html#study-participants"><i class="fa fa-check"></i><b>6.2.4</b> Study participants</a></li>
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<li class="chapter" data-level="6.2.5" data-path="ch06-radar2.html"><a href="ch06-radar2.html#study-execution-and-data"><i class="fa fa-check"></i><b>6.2.5</b> Study execution and data</a></li>
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<li class="chapter" data-level="6.2.6" data-path="ch06-radar2.html"><a href="ch06-radar2.html#evaluation-and-study-data-analysis"><i class="fa fa-check"></i><b>6.2.6</b> Evaluation and study data analysis</a></li>
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<li class="chapter" data-level="6.3" data-path="ch06-radar2.html"><a href="ch06-radar2.html#results-1"><i class="fa fa-check"></i><b>6.3</b> Results</a>
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||
<ul>
|
||
<li class="chapter" data-level="6.3.1" data-path="ch06-radar2.html"><a href="ch06-radar2.html#study-participants-1"><i class="fa fa-check"></i><b>6.3.1</b> Study participants</a></li>
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<li class="chapter" data-level="6.3.2" data-path="ch06-radar2.html"><a href="ch06-radar2.html#effectiveness-and-accuracy"><i class="fa fa-check"></i><b>6.3.2</b> Effectiveness and accuracy</a></li>
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||
<li class="chapter" data-level="6.3.3" data-path="ch06-radar2.html"><a href="ch06-radar2.html#efficiency"><i class="fa fa-check"></i><b>6.3.3</b> Efficiency</a></li>
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||
<li class="chapter" data-level="6.3.4" data-path="ch06-radar2.html"><a href="ch06-radar2.html#satisfaction"><i class="fa fa-check"></i><b>6.3.4</b> Satisfaction</a></li>
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</ul></li>
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<li class="chapter" data-level="6.4" data-path="ch06-radar2.html"><a href="ch06-radar2.html#discussion-2"><i class="fa fa-check"></i><b>6.4</b> Discussion</a></li>
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<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#acknowledgements-2"><i class="fa fa-check"></i>Acknowledgements</a></li>
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||
<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#funding"><i class="fa fa-check"></i>Funding</a></li>
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<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#conflict-of-interest"><i class="fa fa-check"></i>Conflict of interest</a></li>
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<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#references-5"><i class="fa fa-check"></i>References</a></li>
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<ul>
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<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#appendix-a1-task-lists-including-correct-results"><i class="fa fa-check"></i>Appendix A1: Task lists including correct results</a></li>
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<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#appendix-a2-system-usability-scale-sus"><i class="fa fa-check"></i>Appendix A2: System Usability Scale (SUS)</a></li>
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<li class="chapter" data-level="" data-path="ch06-radar2.html"><a href="ch06-radar2.html#appendix-a3-task-3-sub-analysis"><i class="fa fa-check"></i>Appendix A3: Task 3 sub-analysis</a></li>
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</ul></li>
|
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</ul></li>
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<li class="chapter" data-level="7" data-path="ch07-cons.html"><a href="ch07-cons.html"><i class="fa fa-check"></i><b>7</b> Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Blood in the Northern Netherlands between 2013 and 2019</a>
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<ul>
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<li class="chapter" data-level="7.1" data-path="ch07-cons.html"><a href="ch07-cons.html#abstract-5"><i class="fa fa-check"></i><b>7.1</b> Abstract</a></li>
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<li class="chapter" data-level="7.2" data-path="ch07-cons.html"><a href="ch07-cons.html#introduction-4"><i class="fa fa-check"></i><b>7.2</b> Introduction</a></li>
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<li class="chapter" data-level="7.3" data-path="ch07-cons.html"><a href="ch07-cons.html#materials-methods"><i class="fa fa-check"></i><b>7.3</b> Materials & methods</a>
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<ul>
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<li class="chapter" data-level="7.3.1" data-path="ch07-cons.html"><a href="ch07-cons.html#study-setting-and-patient-cohort"><i class="fa fa-check"></i><b>7.3.1</b> Study setting and patient cohort</a></li>
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<li class="chapter" data-level="7.3.2" data-path="ch07-cons.html"><a href="ch07-cons.html#microbiological-and-demographic-data"><i class="fa fa-check"></i><b>7.3.2</b> Microbiological and demographic data</a></li>
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<li class="chapter" data-level="7.3.3" data-path="ch07-cons.html"><a href="ch07-cons.html#species-determination-and-antibiotic-susceptibility-testing-ast"><i class="fa fa-check"></i><b>7.3.3</b> Species determination and antibiotic susceptibility testing (AST)</a></li>
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<li class="chapter" data-level="7.3.4" data-path="ch07-cons.html"><a href="ch07-cons.html#selection-of-bacterial-isolates"><i class="fa fa-check"></i><b>7.3.4</b> Selection of bacterial isolates</a></li>
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<li class="chapter" data-level="7.3.5" data-path="ch07-cons.html"><a href="ch07-cons.html#eucast-rules-and-antibiotic-resistance-analysis"><i class="fa fa-check"></i><b>7.3.5</b> EUCAST rules and antibiotic resistance analysis</a></li>
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<li class="chapter" data-level="7.3.6" data-path="ch07-cons.html"><a href="ch07-cons.html#statistical-analysis"><i class="fa fa-check"></i><b>7.3.6</b> Statistical analysis</a></li>
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<li class="chapter" data-level="7.3.7" data-path="ch07-cons.html"><a href="ch07-cons.html#ethical-considerations"><i class="fa fa-check"></i><b>7.3.7</b> Ethical considerations</a></li>
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</ul></li>
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<li class="chapter" data-level="7.4" data-path="ch07-cons.html"><a href="ch07-cons.html#results-2"><i class="fa fa-check"></i><b>7.4</b> Results</a>
|
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<ul>
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<li class="chapter" data-level="7.4.1" data-path="ch07-cons.html"><a href="ch07-cons.html#patients-and-included-isolates"><i class="fa fa-check"></i><b>7.4.1</b> Patients and included isolates</a></li>
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<li class="chapter" data-level="7.4.2" data-path="ch07-cons.html"><a href="ch07-cons.html#occurrence-of-cons-species"><i class="fa fa-check"></i><b>7.4.2</b> Occurrence of CoNS species</a></li>
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<li class="chapter" data-level="7.4.3" data-path="ch07-cons.html"><a href="ch07-cons.html#definition-of-cons-persistence"><i class="fa fa-check"></i><b>7.4.3</b> Definition of CoNS persistence</a></li>
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<li class="chapter" data-level="7.4.4" data-path="ch07-cons.html"><a href="ch07-cons.html#antibiotic-resistance-analysis"><i class="fa fa-check"></i><b>7.4.4</b> Antibiotic resistance analysis</a></li>
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<li class="chapter" data-level="7.5" data-path="ch07-cons.html"><a href="ch07-cons.html#discussion-3"><i class="fa fa-check"></i><b>7.5</b> Discussion</a></li>
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<li class="chapter" data-level="" data-path="ch07-cons.html"><a href="ch07-cons.html#supplementary-tables"><i class="fa fa-check"></i>Supplementary tables</a></li>
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<li class="chapter" data-level="" data-path="ch07-cons.html"><a href="ch07-cons.html#references-6"><i class="fa fa-check"></i>References</a></li>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
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<p>The work described within this thesis was supported by (1) the Certe Medical Diagnostics and Advice Foundation, (2) the INTERREG V A (202085) funded project EurHealth-1Health (<a href="http://www.eurhealth1health.eu" class="uri">http://www.eurhealth1health.eu</a>), part of a Dutch-German cross-border network supported by the European Commission, the Dutch Ministry of Health, Welfare and Sport, the Ministry of Economy, Innovation, Digitalisation and Energy of the German Federal State of North Rhine-Westphalia, and the Ministry for National and European Affairs and Regional Development of the German Federal State of Lower Saxony, (3) the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement 713660 (MSCA-COFUND-2015-DP “Pronkjewail”), and (4) the European Society for Clinical Microbiology and Infectious Diseases (ESCMID) through the ESCMID Study Group for Antimicrobial Stewardship (ESGAP).</p>
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