<title>Contents | A New Instrument for Microbial Epidemiology</title>
<metaname="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."/>
<metaname="generator"content="bookdown 0.22 and GitBook 2.6.7"/>
<metaproperty="og:title"content="Contents | A New Instrument for Microbial Epidemiology"/>
<metaproperty="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."/>
<metaname="twitter:title"content="Contents | A New Instrument for Microbial Epidemiology"/>
<metaname="twitter: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."/>
<liclass="chapter"data-level="1"data-path="ch01-introduction.html"><ahref="ch01-introduction.html"><iclass="fa fa-check"></i><b>1</b> General Introduction</a>
<liclass="chapter"data-level="1.2.2"data-path="ch01-introduction.html"><ahref="ch01-introduction.html#interpretation-of-raw-results"><iclass="fa fa-check"></i><b>1.2.2</b> Interpretation of raw results</a></li>
<liclass="chapter"data-level="1.3"data-path="ch01-introduction.html"><ahref="ch01-introduction.html#data-analysis-using-r"><iclass="fa fa-check"></i><b>1.3</b> Data analysis using R</a></li>
<liclass="chapter"data-level="1.4"data-path="ch01-introduction.html"><ahref="ch01-introduction.html#setting-for-this-thesis"><iclass="fa fa-check"></i><b>1.4</b> Setting for this thesis</a></li>
<liclass="chapter"data-level="1.5"data-path="ch01-introduction.html"><ahref="ch01-introduction.html#aim-of-this-thesis-and-introduction-to-its-chapters"><iclass="fa fa-check"></i><b>1.5</b> Aim of this thesis and introduction to its chapters</a></li>
<liclass="chapter"data-level="2"data-path="ch02-diagnostic-stewardship.html"><ahref="ch02-diagnostic-stewardship.html"><iclass="fa fa-check"></i><b>2</b> Diagnostic Stewardship: Sense or Nonsense?!</a>
<liclass="chapter"data-level="2.1.1"data-path="ch02-diagnostic-stewardship.html"><ahref="ch02-diagnostic-stewardship.html#case-1"><iclass="fa fa-check"></i><b>2.1.1</b> Case 1</a></li>
<liclass="chapter"data-level="2.1.2"data-path="ch02-diagnostic-stewardship.html"><ahref="ch02-diagnostic-stewardship.html#case-2"><iclass="fa fa-check"></i><b>2.1.2</b> Case 2</a></li>
<liclass="chapter"data-level="2.2"data-path="ch02-diagnostic-stewardship.html"><ahref="ch02-diagnostic-stewardship.html#the-general-concept"><iclass="fa fa-check"></i><b>2.2</b> The general concept</a>
<liclass="chapter"data-level="2.2.2"data-path="ch02-diagnostic-stewardship.html"><ahref="ch02-diagnostic-stewardship.html#dsp-in-the-microbiological-laboratory"><iclass="fa fa-check"></i><b>2.2.2</b> DSP in the microbiological laboratory</a></li>
<liclass="chapter"data-level="2.2.3"data-path="ch02-diagnostic-stewardship.html"><ahref="ch02-diagnostic-stewardship.html#dsp-as-process-optimisation"><iclass="fa fa-check"></i><b>2.2.3</b> DSP as process optimisation</a></li>
<liclass="chapter"data-level="2.2.4"data-path="ch02-diagnostic-stewardship.html"><ahref="ch02-diagnostic-stewardship.html#multidisciplinary-aspects-of-dsp-and-infection-management"><iclass="fa fa-check"></i><b>2.2.4</b> Multidisciplinary aspects of DSP and infection management</a></li>
<liclass="chapter"data-level="3"data-path="ch03-introducing-new-method.html"><ahref="ch03-introducing-new-method.html"><iclass="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>
<liclass="chapter"data-level="3.2"data-path="ch03-introducing-new-method.html"><ahref="ch03-introducing-new-method.html#standardising-amr-data-analysis"><iclass="fa fa-check"></i><b>3.2</b> Standardising AMR data analysis</a></li>
<liclass="chapter"data-level="3.3"data-path="ch03-introducing-new-method.html"><ahref="ch03-introducing-new-method.html#comparison-with-existing-software-methods"><iclass="fa fa-check"></i><b>3.3</b> Comparison with existing software methods</a></li>
<liclass="chapter"data-level="3.4"data-path="ch03-introducing-new-method.html"><ahref="ch03-introducing-new-method.html#user-feedback"><iclass="fa fa-check"></i><b>3.4</b> User feedback</a></li>
<liclass="chapter"data-level="4"data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html"><iclass="fa fa-check"></i><b>4</b><code>AMR</code> - An <code>R</code> Package for Working with Antimicrobial Resistance Data</a>
<liclass="chapter"data-level="4.3.1"data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html#working-with-taxonomically-valid-microorganism-names"><iclass="fa fa-check"></i><b>4.3.1</b> Working with taxonomically valid microorganism names</a></li>
<liclass="chapter"data-level="4.3.2"data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html#working-with-antimicrobial-names-or-codes"><iclass="fa fa-check"></i><b>4.3.2</b> Working with antimicrobial names or codes</a></li>
<liclass="chapter"data-level="4.3.3"data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html#working-with-antimicrobial-susceptibility-test-results"><iclass="fa fa-check"></i><b>4.3.3</b> Working with antimicrobial susceptibility test results</a></li>
<liclass="chapter"data-level="4.3.4"data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html#interpretative-rules-by-eucast"><iclass="fa fa-check"></i><b>4.3.4</b> Interpretative rules by EUCAST</a></li>
<liclass="chapter"data-level="4.3.5"data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html#working-with-defined-daily-doses-ddd"><iclass="fa fa-check"></i><b>4.3.5</b> Working with defined daily doses (DDD)</a></li>
<liclass="chapter"data-level="4.4.1"data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html#determining-first-isolates"><iclass="fa fa-check"></i><b>4.4.1</b> Determining first isolates</a></li>
<liclass="chapter"data-level=""data-path="ch04-amr-r-package.html"><ahref="ch04-amr-r-package.html#appendix-a-included-data-sets"><iclass="fa fa-check"></i>Appendix A: Included Data Sets</a></li>
</ul></li>
<liclass="chapter"data-level="5"data-path="ch05-radar.html"><ahref="ch05-radar.html"><iclass="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>
<liclass="chapter"data-level="5.3.3"data-path="ch05-radar.html"><ahref="ch05-radar.html#development-process"><iclass="fa fa-check"></i><b>5.3.3</b> Development Process</a></li>
<liclass="chapter"data-level="5.4.1"data-path="ch05-radar.html"><ahref="ch05-radar.html#principal-findings"><iclass="fa fa-check"></i><b>5.4.1</b> Principal Findings</a></li>
<liclass="chapter"data-level=""data-path="ch05-radar.html"><ahref="ch05-radar.html#conflicts-of-interests"><iclass="fa fa-check"></i>Conflicts of interests</a></li>
<liclass="chapter"data-level="6"data-path="ch06-radar2.html"><ahref="ch06-radar2.html"><iclass="fa fa-check"></i><b>6</b> Better Antimicrobial Resistance Data Analysis and Reporting in Less Time</a>
<liclass="chapter"data-level="6.2.1"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#study-setup"><iclass="fa fa-check"></i><b>6.2.1</b> Study setup</a></li>
<liclass="chapter"data-level="6.2.2"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#amr-data"><iclass="fa fa-check"></i><b>6.2.2</b> AMR data</a></li>
<liclass="chapter"data-level="6.2.3"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#amr-data-analysis-and-reporting"><iclass="fa fa-check"></i><b>6.2.3</b> AMR data analysis and reporting</a></li>
<liclass="chapter"data-level="6.2.4"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#study-participants"><iclass="fa fa-check"></i><b>6.2.4</b> Study participants</a></li>
<liclass="chapter"data-level="6.2.5"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#study-execution-and-data"><iclass="fa fa-check"></i><b>6.2.5</b> Study execution and data</a></li>
<liclass="chapter"data-level="6.2.6"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#evaluation-and-study-data-analysis"><iclass="fa fa-check"></i><b>6.2.6</b> Evaluation and study data analysis</a></li>
<liclass="chapter"data-level="6.3.1"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#study-participants-1"><iclass="fa fa-check"></i><b>6.3.1</b> Study participants</a></li>
<liclass="chapter"data-level="6.3.2"data-path="ch06-radar2.html"><ahref="ch06-radar2.html#effectiveness-and-accuracy"><iclass="fa fa-check"></i><b>6.3.2</b> Effectiveness and accuracy</a></li>
<liclass="chapter"data-level=""data-path="ch06-radar2.html"><ahref="ch06-radar2.html#conflict-of-interest"><iclass="fa fa-check"></i>Conflict of interest</a></li>
<liclass="chapter"data-level="7"data-path="ch07-cons.html"><ahref="ch07-cons.html"><iclass="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>
<liclass="chapter"data-level="7.2"data-path="ch07-cons.html"><ahref="ch07-cons.html#materials-methods"><iclass="fa fa-check"></i><b>7.2</b> Materials & methods</a>
<liclass="chapter"data-level="7.2.1"data-path="ch07-cons.html"><ahref="ch07-cons.html#study-setting-and-patient-cohort"><iclass="fa fa-check"></i><b>7.2.1</b> Study setting and patient cohort</a></li>
<liclass="chapter"data-level="7.2.2"data-path="ch07-cons.html"><ahref="ch07-cons.html#microbiological-and-demographic-data"><iclass="fa fa-check"></i><b>7.2.2</b> Microbiological and demographic data</a></li>
<liclass="chapter"data-level="7.2.3"data-path="ch07-cons.html"><ahref="ch07-cons.html#species-determination-and-antibiotic-susceptibility-testing-ast"><iclass="fa fa-check"></i><b>7.2.3</b> Species determination and antibiotic susceptibility testing (AST)</a></li>
<liclass="chapter"data-level="7.2.4"data-path="ch07-cons.html"><ahref="ch07-cons.html#selection-of-bacterial-isolates"><iclass="fa fa-check"></i><b>7.2.4</b> Selection of bacterial isolates</a></li>
<liclass="chapter"data-level="7.2.5"data-path="ch07-cons.html"><ahref="ch07-cons.html#eucast-rules-and-antibiotic-resistance-analysis"><iclass="fa fa-check"></i><b>7.2.5</b> EUCAST rules and antibiotic resistance analysis</a></li>
<liclass="chapter"data-level="7.3.1"data-path="ch07-cons.html"><ahref="ch07-cons.html#patients-and-included-isolates"><iclass="fa fa-check"></i><b>7.3.1</b> Patients and included isolates</a></li>
<liclass="chapter"data-level="7.3.2"data-path="ch07-cons.html"><ahref="ch07-cons.html#occurrence-of-cons-species"><iclass="fa fa-check"></i><b>7.3.2</b> Occurrence of CoNS species</a></li>
<liclass="chapter"data-level="7.3.3"data-path="ch07-cons.html"><ahref="ch07-cons.html#definition-of-cons-persistence"><iclass="fa fa-check"></i><b>7.3.3</b> Definition of CoNS persistence</a></li>
<liclass="chapter"data-level="8"data-path="ch08-defining-mdr.html"><ahref="ch08-defining-mdr.html"><iclass="fa fa-check"></i><b>8</b> Defining Multidrug Resistance of Gram-Negative Bacteria in the Dutch-German Border Region: Impact of National Guidelines</a>
<liclass="chapter"data-level="8.3.1"data-path="ch08-defining-mdr.html"><ahref="ch08-defining-mdr.html#number-of-antibiograms-and-patients"><iclass="fa fa-check"></i><b>8.3.1</b> Number of Antibiograms and Patients</a></li>
<liclass="chapter"data-level="8.3.2"data-path="ch08-defining-mdr.html"><ahref="ch08-defining-mdr.html#results-of-mrgn-and-brmo-classification"><iclass="fa fa-check"></i><b>8.3.2</b> Results of MRGN and BRMO Classification</a></li>
<liclass="chapter"data-level=""data-path="ch08-defining-mdr.html"><ahref="ch08-defining-mdr.html#conflicts-of-interest"><iclass="fa fa-check"></i>Conflicts of interest</a></li>
<liclass="chapter"data-level="9"data-path="ch09-changing-epidemiology.html"><ahref="ch09-changing-epidemiology.html"><iclass="fa fa-check"></i><b>9</b> 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</a>
<liclass="chapter"data-level="9.2.2"data-path="ch09-changing-epidemiology.html"><ahref="ch09-changing-epidemiology.html#guidelines-for-patients-at-risk-for-mrsa-and-infection-prevention-and-control-measures"><iclass="fa fa-check"></i><b>9.2.2</b> Guidelines for patients at risk for MRSA and infection prevention and control measures</a></li>
<liclass="chapter"data-level="9.2.3"data-path="ch09-changing-epidemiology.html"><ahref="ch09-changing-epidemiology.html#data-collection"><iclass="fa fa-check"></i><b>9.2.3</b> Data collection</a></li>
<liclass="chapter"data-level="9.2.5"data-path="ch09-changing-epidemiology.html"><ahref="ch09-changing-epidemiology.html#data-analysis"><iclass="fa fa-check"></i><b>9.2.5</b> Data analysis</a></li>
<liclass="chapter"data-level="9.3.1"data-path="ch09-changing-epidemiology.html"><ahref="ch09-changing-epidemiology.html#trend-and-cross-border-comparison-of-mrsa-rates"><iclass="fa fa-check"></i><b>9.3.1</b> Trend and cross-border comparison of MRSA rates</a></li>
<liclass="chapter"data-level="9.3.2"data-path="ch09-changing-epidemiology.html"><ahref="ch09-changing-epidemiology.html#cross-border-comparison-of-healthcare-utilisation"><iclass="fa fa-check"></i><b>9.3.2</b> Cross-border comparison of healthcare utilisation</a></li>
<liclass="chapter"data-level="10"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html"><iclass="fa fa-check"></i><b>10</b> A Prospective Multicentre MDRO Screening Study on ICUs in the Dutch-German Cross-Border Region (2017-2018): The Importance of Healthcare Structures</a>
<liclass="chapter"data-level="10.2.1"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#study-design"><iclass="fa fa-check"></i><b>10.2.1</b> Study Design</a></li>
<liclass="chapter"data-level="10.2.2"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#statistical-analysis-software"><iclass="fa fa-check"></i><b>10.2.2</b> Statistical Analysis & Software</a></li>
<liclass="chapter"data-level="10.3.1"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#healthcare-structure-of-the-participating-hospitals"><iclass="fa fa-check"></i><b>10.3.1</b> Healthcare structure of the participating hospitals</a></li>
<liclass="chapter"data-level="10.3.2"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#study-population-and-screening-samples-from-icus"><iclass="fa fa-check"></i><b>10.3.2</b> Study population and screening samples from ICUs</a></li>
<liclass="chapter"data-level="10.3.3"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#prevalence-of-gram-positive-mdros-mrsa-and-vre"><iclass="fa fa-check"></i><b>10.3.3</b> Prevalence of Gram-positive MDROs: MRSA and VRE</a></li>
<liclass="chapter"data-level="10.3.4"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#prevalence-of-gram-negative-mdro-3gcre-and-cre"><iclass="fa fa-check"></i><b>10.3.4</b> Prevalence of Gram-negative MDRO: 3GCRE and CRE</a></li>
<liclass="chapter"data-level="10.3.5"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#prevalence-of-gram-negative-mdros-based-on-dutch-and-german-definitions"><iclass="fa fa-check"></i><b>10.3.5</b> Prevalence of Gram-negative MDROs based on Dutch and German definitions</a></li>
<liclass="chapter"data-level="10.3.6"data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#comparison-of-mdro-prevalence-between-nl-br-and-de-br-icus-in-university-and-non-university-hospitals"><iclass="fa fa-check"></i><b>10.3.6</b> Comparison of MDRO prevalence between NL-BR and DE-BR ICUs in university and non-university hospitals</a></li>
<liclass="chapter"data-level=""data-path="ch10-multi-mdro-screening.html"><ahref="ch10-multi-mdro-screening.html#conflict-of-interest-1"><iclass="fa fa-check"></i>Conflict of interest</a></li>
<liclass="chapter"data-level=""data-path="gearfetting-yn-frysk.html"><ahref="gearfetting-yn-frysk.html"><iclass="fa fa-check"></i>Gearfetting yn Frysk</a></li>
<liclass="chapter"data-level=""data-path="samenvatting-in-het-nederlands.html"><ahref="samenvatting-in-het-nederlands.html"><iclass="fa fa-check"></i>Samenvatting in het Nederlands</a></li>
<liclass="chapter"data-level=""data-path="zusammenfassung-auf-deutsch.html"><ahref="zusammenfassung-auf-deutsch.html"><iclass="fa fa-check"></i>Zusammenfassung auf Deutsch</a></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>
<olstart="4"style="list-style-type: decimal">
<li><p><strong>AMR - An R Package for Working with Antimicrobial Resistance Data</strong><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/>
<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/>
<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>
<olstart="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/>
