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<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">PLoS Pathog</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plospath</journal-id>
<journal-title-group>
<journal-title>PLOS Pathogens</journal-title>
</journal-title-group>
<issn pub-type="ppub">1553-7366</issn>
<issn pub-type="epub">1553-7374</issn>
<publisher>
<publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, CA USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.1371/journal.ppat.1008905</article-id>
<article-id pub-id-type="publisher-id">PPATHOGENS-D-20-01113</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Opinion</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial control</subject><subj-group><subject>Antimicrobial resistance</subject><subj-group><subject>Antibiotic resistance</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Medicine and health sciences</subject><subj-group><subject>Pharmacology</subject><subj-group><subject>Antimicrobial resistance</subject><subj-group><subject>Antibiotic resistance</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Medicine and health sciences</subject><subj-group><subject>Pharmacology</subject><subj-group><subject>Drugs</subject><subj-group><subject>Antimicrobials</subject><subj-group><subject>Antifungals</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial control</subject><subj-group><subject>Antimicrobials</subject><subj-group><subject>Antifungals</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Mycology</subject><subj-group><subject>Antifungals</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Medicine and health sciences</subject><subj-group><subject>Pharmacology</subject><subj-group><subject>Drugs</subject><subj-group><subject>Antimicrobials</subject><subj-group><subject>Antibiotics</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial control</subject><subj-group><subject>Antimicrobials</subject><subj-group><subject>Antibiotics</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Mycology</subject><subj-group><subject>Fungal evolution</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial evolution</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Evolutionary biology</subject><subj-group><subject>Organismal evolution</subject><subj-group><subject>Microbial evolution</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial control</subject><subj-group><subject>Antimicrobial resistance</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Medicine and health sciences</subject><subj-group><subject>Pharmacology</subject><subj-group><subject>Antimicrobial resistance</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Evolutionary biology</subject><subj-group><subject>Evolutionary genetics</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Medicine and health sciences</subject><subj-group><subject>Pharmacology</subject><subj-group><subject>Drugs</subject><subj-group><subject>Antimicrobials</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3">
<subject>Biology and life sciences</subject><subj-group><subject>Microbiology</subject><subj-group><subject>Microbial control</subject><subj-group><subject>Antimicrobials</subject></subj-group></subj-group></subj-group></subj-group></article-categories>
<title-group>
<article-title>Is antimicrobial resistance evolution accelerating?</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" xlink:type="simple">
<name name-style="western">
<surname>Witzany</surname>
<given-names>Christopher</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author" xlink:type="simple">
<contrib-id authenticated="true" contrib-id-type="orcid">http://orcid.org/0000-0001-8052-3925</contrib-id>
<name name-style="western">
<surname>Bonhoeffer</surname>
<given-names>Sebastian</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes" xlink:type="simple">
<contrib-id authenticated="true" contrib-id-type="orcid">http://orcid.org/0000-0002-1529-5409</contrib-id>
<name name-style="western">
<surname>Rolff</surname>
<given-names>Jens</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff003"><sup>3</sup></xref>
<xref ref-type="corresp" rid="cor001">*</xref>
</contrib>
</contrib-group>
<aff id="aff001"><label>1</label> <addr-line>Freie Universität Berlin, Institut für Biologie, Evolutionary Biology, Berlin, Germany</addr-line></aff>
<aff id="aff002"><label>2</label> <addr-line>Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland</addr-line></aff>
<aff id="aff003"><label>3</label> <addr-line>Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany</addr-line></aff>
<contrib-group>
<contrib contrib-type="editor" xlink:type="simple">
<name name-style="western">
<surname>Round</surname>
<given-names>June L.</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"/>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>University of Utah, UNITED STATES</addr-line></aff>
<author-notes>
<fn fn-type="conflict" id="coi001">
<p>The authors have declared that no competing interests exist.</p>
</fn>
<corresp id="cor001">* E-mail: <email xlink:type="simple">jens.rolff@fu-berlin.de</email></corresp>
</author-notes>
<pub-date pub-type="epub">
<day>22</day>
<month>10</month>
<year>2020</year>
</pub-date>
<pub-date pub-type="collection">
<month>10</month>
<year>2020</year>
</pub-date>
<volume>16</volume>
<issue>10</issue>
<elocation-id>e1008905</elocation-id>
<permissions>
<copyright-year>2020</copyright-year>
<copyright-holder>Witzany et al</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/" xlink:type="simple">
<license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/" xlink:type="simple">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:href="info:doi/10.1371/journal.ppat.1008905"/>
<funding-group>
<funding-statement>JR acknowledges funding from the Volkswagen Foundation (Grant number 96 517, <ext-link ext-link-type="uri" xlink:href="https://www.volkswagenstiftung.de/en/funding" xlink:type="simple">https://www.volkswagenstiftung.de/en/funding</ext-link>). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts>
<fig-count count="2"/>
<table-count count="0"/>
<page-count count="5"/>
</counts>
</article-meta>
</front>
<body>
<p>Globally, antimicrobials are a main pillar of medical, veterinary, and agriculture interventions [<xref ref-type="bibr" rid="ppat.1008905.ref001">1</xref>,<xref ref-type="bibr" rid="ppat.1008905.ref002">2</xref>]. In all cases, resistance of microbes against antimicrobials is prevalent. The problem is exacerbated by the drying up of the antibiotic pipeline, as economic incentives to develop new drugs are very limited. In antifungals, the range of available compounds is also low with only 4 main classes of drugs available to treat fungal infections in humans and 6 main classes used in agriculture, with 1 class, the azoles, used in both [<xref ref-type="bibr" rid="ppat.1008905.ref001">1</xref>].</p>
<p>The problem of drug resistance evolution has been observed early on in the antibiotic era [<xref ref-type="bibr" rid="ppat.1008905.ref003">3</xref>,<xref ref-type="bibr" rid="ppat.1008905.ref004">4</xref>]. Ultimately, however, the introduction of each antimicrobial resulted in resistance evolution in target and nontarget microbes. In realization of this problem, some antibiotics such as daptomycin were even developed with avoiding resistance evolution in mind, yet it took only 2 years from the introduction of daptomycin until resistance was recorded [<xref ref-type="bibr" rid="ppat.1008905.ref004">4</xref>]. But how fast is resistance evolving?</p>
<p>Here, we want to discuss how fast resistance emerges after the introduction of antimicrobials. We base this on widely cited data in the literature for antibiotics ([<xref ref-type="bibr" rid="ppat.1008905.ref004">4</xref>–<xref ref-type="bibr" rid="ppat.1008905.ref007">7</xref>]; see also <xref ref-type="fig" rid="ppat.1008905.g001">Fig 1A</xref>, based on [<xref ref-type="bibr" rid="ppat.1008905.ref008">8</xref>]) and compared this to data on antifungal resistance [<xref ref-type="bibr" rid="ppat.1008905.ref009">9</xref>,<xref ref-type="bibr" rid="ppat.1008905.ref010">10</xref>]. Replotting the antibiotic data (<xref ref-type="fig" rid="ppat.1008905.g001">Fig 1B</xref>), by displaying the time from introduction to resistance emergence over the year of introduction, suggests that the evolution of antibiotic resistance is accelerating over time. The same trend can be observed for antifungals (<xref ref-type="fig" rid="ppat.1008905.g001">Fig 1C and 1D</xref>). In the following, we focus on (1) the quality of the underlying data and (2) possible explanations for this pattern of accelerating resistance.</p>
<fig id="ppat.1008905.g001" position="float">
<object-id pub-id-type="doi">10.1371/journal.ppat.1008905.g001</object-id>
<label>Fig 1</label>
<caption>
<title/>
<p>Timeline of antibiotic (a) and antifungal (c) introduction and detection of surmised evolved resistance depicted by the ends of the bars. In antibiotics (b) and antifungals (d), the time to resistance decreases with the year of introduction: for newer antimicrobials, resistance is described earlier after introduction (linear regression for antibiotics (b) F<sub>1,16</sub> = 6.47, <italic>p</italic> &lt; 0.05*, R<sup>2</sup> = 0.29 and antifungals (d) F<sub>1,13</sub> = 19.57, <italic>p</italic> &lt; 0.001***, R<sup>2</sup> = 0.60).</p>
</caption>
<graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.ppat.1008905.g001" xlink:type="simple"/>
</fig>
<p>We first want to ask how reliable these commonly presented data on resistance emergence are. For this, we tried to trace the original papers from which the aggregated data for antibiotics (using [<xref ref-type="bibr" rid="ppat.1008905.ref007">7</xref>] as a starting point) and antifungals [<xref ref-type="bibr" rid="ppat.1008905.ref009">9</xref>,<xref ref-type="bibr" rid="ppat.1008905.ref010">10</xref>] were obtained. To our great surprise, finding the original data for the antibiotics was very difficult, and many of the original sources could not be verified (see <xref ref-type="supplementary-material" rid="ppat.1008905.s001">S1 Fig</xref> and <xref ref-type="supplementary-material" rid="ppat.1008905.s003">S1 Appendix</xref> for more details). While the pattern of accelerating resistance in antibiotics might be true, it certainly cannot be supported given the data currently available. By contrast, for the antifungal data, it is possible to identify the original publications in most cases (see <xref ref-type="supplementary-material" rid="ppat.1008905.s002">S2 Fig</xref>, <xref ref-type="supplementary-material" rid="ppat.1008905.s004">S2 Appendix</xref>, and <xref ref-type="supplementary-material" rid="ppat.1008905.s005">S1 Table</xref>). Replotting the suspected relation with the data that can be traced shows that the pattern of accelerating resistance evolution still holds for antifungals (<xref ref-type="fig" rid="ppat.1008905.g002">Fig 2</xref>). Given that the antifungal data with traceable sources show a clearly accelerating trend, this should certainly be investigated for antibiotics.</p>
<fig id="ppat.1008905.g002" position="float">
<object-id pub-id-type="doi">10.1371/journal.ppat.1008905.g002</object-id>
<label>Fig 2</label>
<caption>
<title/>
<p>Timeline of antifungal (a) introduction and detection of evolved resistance for antifungals where the source could be traced (unambiguous and reliable sources of data points are shown in blue; untraceable data are shown in red and excluded from analysis) (b). The time to resistance decreases with the year of introduction (linear regression F<sub>1,12</sub> = 8.10, <italic>p</italic> &lt; 0.05*, R<sup>2</sup> = 0.40).</p>
</caption>
<graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.ppat.1008905.g002" xlink:type="simple"/>
</fig>
<p>If we take the data for both antibiotics and antifungals at face value, we see a clear trend of accelerating resistance evolution. We briefly want to propose 3—mutually not exclusive—testable hypotheses: (1) increase in usage; (2) increase in surveillance; and (3) evolutionary dynamics: cross-resistance, concurrent selection, and environmental enrichment of resistance genes.</p>
<sec id="sec001">
<title>Increase in usage</title>
<p>Since the introduction of both antibiotics and antifungals, their use has steadily increased. This results in higher amounts of antibiotics, antifungals, and their residues in the environment, and this problem is exacerbated by the projected increase in global usage (e.g., [<xref ref-type="bibr" rid="ppat.1008905.ref011">11</xref>]). That usage per se is correlated with prevalence of resistance is well established [<xref ref-type="bibr" rid="ppat.1008905.ref012">12</xref>]. However, the hypothesis would predict more specifically that antibiotics and antifungals that have been introduced later are used more, because the pattern we observe is that resistance emerges faster for later introductions. Notably, some of the antibiotics concerned are reserve antibiotics, for which we expect that the usage is limited. Therefore, while testable, we think that this hypothesis may not be the most likely explanation for the timing of resistance emergence.</p>
</sec>
<sec id="sec002">
<title>Increase in surveillance</title>
<p>At the same time when the use of antibiotics and antifungals intensified, a parallel increase in surveilling infections and infection outcomes, and equally pest control measures, can arguably result in a higher probability of resistance detection. If this were true, it might well be sufficient to explain the pattern of accelerating resistance. In fact, if this was the sole explanation, it would be reassuring. It would mean that the older the data, the higher the probability that resistance was not detected when it evolved. In support of this notion, the number of publications on antibiotic resistance is increasing year to year [<xref ref-type="bibr" rid="ppat.1008905.ref013">13</xref>].</p>
</sec>
<sec id="sec003">
<title>Evolutionary dynamics: Cross-resistance, concurrent selection, and environmental enrichment of resistance genes</title>
<p>Many newer antibiotics and antifungals are variations on older substances. Moreover, almost all of the antibiotics are derived from natural antibiotics. Therefore, resistance evolution might become faster, because growing reservoirs of resistance genes and resistant microorganisms in the environment can cause cross-resistance [<xref ref-type="bibr" rid="ppat.1008905.ref014">14</xref>,<xref ref-type="bibr" rid="ppat.1008905.ref015">15</xref>]. Also, some mutations conferring resistance reduce the fitness costs of genes providing resistance against other antibiotics [<xref ref-type="bibr" rid="ppat.1008905.ref016">16</xref>]. Moreover, antibiotic resistance, despite often being costly, can persist in the environment in the absence of the selective agents [<xref ref-type="bibr" rid="ppat.1008905.ref017">17</xref>,<xref ref-type="bibr" rid="ppat.1008905.ref018">18</xref>]. This applies both to the persistence of resistant bacteria as well as the persistence of antibiotic resistance genes and can be caused by several mechanisms that mitigate the costs [<xref ref-type="bibr" rid="ppat.1008905.ref017">17</xref>] or concurrent selection, for example, by heavy metals [<xref ref-type="bibr" rid="ppat.1008905.ref014">14</xref>] or by pesticides [<xref ref-type="bibr" rid="ppat.1008905.ref019">19</xref>]. Finally, as resistance mechanisms against different antibiotics might be under co-selection mediated by genetic linkage [<xref ref-type="bibr" rid="ppat.1008905.ref020">20</xref>], the increase in resistance genes, resistant microbes, and antibiotic residues will facilitate faster resistance evolution. Many of the mechanisms mentioned for antibiotics and possibly others such as increase in mutagenesis or evolution of bet-hedging almost certainly apply to antifungals as well and can be seen as combining to reduce the available genomic resistance space. The risk of emergence of resistant nontarget species of agricultural fungicides is illustrated by potential cross-resistance of <italic>Cryptococcus gattii</italic> against agriculturally used benomyl and clinically used azoles [<xref ref-type="bibr" rid="ppat.1008905.ref021">21</xref>].</p>
<p>We think that each of these hypotheses, especially (2) and (3), warrants further investigation. Resistance evolution is an important challenge to healthcare and food security alike. The pattern of accelerating resistance evolution we identified here for antifungals is certainly of enough significance to motivate studies to investigate how this pattern arises and should inform ways of reversing the trend. For antibiotics, the question of whether resistance evolution is accelerating needs to be urgently addressed. Even though the original data used in several references [<xref ref-type="bibr" rid="ppat.1008905.ref004">4</xref>–<xref ref-type="bibr" rid="ppat.1008905.ref007">7</xref>] could not be identified for antibiotics, it is possible that the trend observed in antifungals also applies to antibiotics. We have to assume that the estimates are based on expert knowledge. And almost certainly, data must exist and await being collated to investigate this pattern. The fact that antifungals show a pattern of accelerating resistance is of high importance itself because of their critical role in food production but should also serve as a sentinel for the study of antibiotic resistance evolution.</p>
</sec>
<sec id="sec004">
<title>Supporting information</title>
<supplementary-material id="ppat.1008905.s001" mimetype="image/tiff" position="float" xlink:href="info:doi/10.1371/journal.ppat.1008905.s001" xlink:type="simple">
<label>S1 Fig</label>
<caption>
<title>The citation network behind the antibiotic introduction and resistance data.</title>
<p>Sources that we could not acquire are indicated with *.</p>
<p>(TIF)</p>
</caption>
</supplementary-material>
<supplementary-material id="ppat.1008905.s002" mimetype="image/tiff" position="float" xlink:href="info:doi/10.1371/journal.ppat.1008905.s002" xlink:type="simple">
<label>S2 Fig</label>
<caption>
<title>The citation network behind the antifungal introduction and resistance data.</title>
<p>Sources that we could not acquire are indicated with *.</p>
<p>(TIF)</p>
</caption>
</supplementary-material>
<supplementary-material id="ppat.1008905.s003" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" position="float" xlink:href="info:doi/10.1371/journal.ppat.1008905.s003" xlink:type="simple">
<label>S1 Appendix</label>
<caption>
<title>Supplemental references for <xref ref-type="supplementary-material" rid="ppat.1008905.s001">S1 Fig</xref>.</title>
<p>(DOCX)</p>
</caption>
</supplementary-material>
<supplementary-material id="ppat.1008905.s004" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" position="float" xlink:href="info:doi/10.1371/journal.ppat.1008905.s004" xlink:type="simple">
<label>S2 Appendix</label>
<caption>
<title>Supplemental references for <xref ref-type="supplementary-material" rid="ppat.1008905.s002">S2 Fig</xref>.</title>
<p>(DOCX)</p>
</caption>
</supplementary-material>
<supplementary-material id="ppat.1008905.s005" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" position="float" xlink:href="info:doi/10.1371/journal.ppat.1008905.s005" xlink:type="simple">
<label>S1 Table</label>
<caption>
<title>Traced and complemented references for introduction and resistance emergence data for antifungals.</title>
<p>(DOCX)</p>
</caption>
</supplementary-material>
</sec>
</body>
<back>
<ack>
<p>We would like to thank Hinrich Schulenburg for feedback.</p>
</ack>
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