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    <title language="eng">Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens</title>
    <parentTitle language="eng">Applied and Environmental Microbiology</parentTitle>
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      <firstName>Rafał</firstName>
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      <firstName>Stefan</firstName>
      <lastName>Rödiger</lastName>
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      <firstName>Michał</firstName>
      <lastName>Burdukiewicz</lastName>
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      <firstName>Marcjanna</firstName>
      <lastName>Wimonć</lastName>
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      <firstName>Adrianna</firstName>
      <lastName>Aleksandrowicz</lastName>
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      <firstName>Aamir</firstName>
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      <firstName>Istvan</firstName>
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      <firstName>Karsten</firstName>
      <lastName>Tedin</lastName>
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      <firstName>Scott J.</firstName>
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      <firstName>Derek</firstName>
      <lastName>Pickhard</lastName>
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    <title language="eng">Investigation of Commensal Escherichia coli Populations of Cormorant Hatchlings in the Absence of Anthropogenic Impacts in Remote Areas of West Mongolia</title>
    <parentTitle language="eng">Microorganisms</parentTitle>
    <identifier type="doi">10.3390/microorganisms9020372</identifier>
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    <author>
      <firstName>Muhammad Moman</firstName>
      <lastName>Khan</lastName>
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      <firstName>Stefan</firstName>
      <lastName>Rödiger</lastName>
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      <firstName>Rafał</firstName>
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      <firstName>Peter</firstName>
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      <firstName>Jörg</firstName>
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    <author>
      <firstName>Stefan</firstName>
      <lastName>Rödiger</lastName>
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      <firstName>Jakob</firstName>
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    <author>
      <firstName>Michael</firstName>
      <lastName>Stubbe</lastName>
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    <author>
      <firstName>Davaa</firstName>
      <lastName>Lkhagvasuren</lastName>
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    <author>
      <firstName>Sebastian</firstName>
      <lastName>Guenther</lastName>
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    <author>
      <firstName>Katharina</firstName>
      <lastName>Schaufler</lastName>
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    <title language="eng">Adhesion of Enteropathogenic, Enterotoxigenic, and Commensal Escherichia coli to the Major Zymogen Granule Membrane Glyoprotein 2</title>
    <parentTitle language="eng">Applied abd Environmental Microbiology</parentTitle>
    <identifier type="issn">1098-5536</identifier>
    <identifier type="doi">10.1128/aem.02279-21</identifier>
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    <author>
      <firstName>Christin</firstName>
      <lastName>Bartlitz</lastName>
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    <submitter>
      <firstName>Jörg</firstName>
      <lastName>Weinreich</lastName>
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    <author>
      <firstName>Rafał</firstName>
      <lastName>Kolenda</lastName>
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      <firstName>Jarosław</firstName>
      <lastName>Chilimoniuk</lastName>
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      <firstName>Krzysztof</firstName>
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      <firstName>Stefan</firstName>
      <lastName>Rödiger</lastName>
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    <author>
      <firstName>Rolf</firstName>
      <lastName>Bauerfeind</lastName>
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      <firstName>Aamir</firstName>
      <lastName>Ali</lastName>
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      <firstName>Veronika</firstName>
      <lastName>Tchesnokovag</lastName>
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      <firstName>Dirk</firstName>
      <lastName>Roggenbuck</lastName>
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      <firstName>Peter</firstName>
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    <completedDate>2024-04-17</completedDate>
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    <title language="eng">Characterization of clumpy adhesion of Escherichia coli to human cells and associated factors influencing antibiotic sensitivity</title>
    <abstract language="eng">Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic E. coli, with the pilV and spnT genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes, flgH, ffp, pilV, spnT, and yggT, affected motility, adhesion, or antibiotic stress. ΔflgH exhibited 80% decrease and ΔyggT depicted 184% increase in adhesion, and upon complementation, adhesion was significantly reduced to 13%. ΔflgH lost motility and was regenerated when complemented, whereas Δffp had significantly increased motility, and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by Δffp and ΔspnT were more resistant and protected the bacteria, with ΔspnT showing the best clump formation in terms of ampicillin stress protection. ΔyggT had the lowest tolerance to gentamicin, where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on cell surface adhesion and antimicrobial tolerance, with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics.</abstract>
    <parentTitle language="eng">Microbiology Spectrum</parentTitle>
    <identifier type="doi">10.1128/spectrum.02606-23</identifier>
    <identifier type="issn">2165-0497</identifier>
    <enrichment key="opus_doi_flag">true</enrichment>
    <enrichment key="opus_doi_json">{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T01:56:09Z","timestamp":1711504569155},"reference-count":69,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T00:00:00Z","timestamp":1711411200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T00:00:00Z","timestamp":1711411200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"abstract":"&lt;jats:title&gt;ABSTRACT&lt;\/jats:title&gt;\n          &lt;jats:sec&gt;\n            &lt;jats:title \/&gt;\n            &lt;jats:p&gt;\n              &lt;jats:italic&gt;Escherichia coli&lt;\/jats:italic&gt;\n              intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of\n              &lt;jats:italic&gt;E. coli&lt;\/jats:italic&gt;\n              strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic\n              &lt;jats:italic&gt;E. coli,&lt;\/jats:italic&gt;\n              with the\n              &lt;jats:italic&gt;pilV&lt;\/jats:italic&gt;\n              and\n              &lt;jats:italic&gt;spnT&lt;\/jats:italic&gt;\n              genes being the least frequent or absent from most groups. Deletion (\u0394) of five differentially expressed genes,\n              &lt;jats:italic&gt;flgH&lt;\/jats:italic&gt;\n              ,\n              &lt;jats:italic&gt;ffp&lt;\/jats:italic&gt;\n              ,\n              &lt;jats:italic&gt;pilV&lt;\/jats:italic&gt;\n              ,\n              &lt;jats:italic&gt;spnT,&lt;\/jats:italic&gt;\n              and\n              &lt;jats:italic&gt;yggT,&lt;\/jats:italic&gt;\n              affected motility, adhesion, or antibiotic stress. \u0394\n              &lt;jats:italic&gt;flgH&lt;\/jats:italic&gt;\n              exhibited 80% decrease and \u0394\n              &lt;jats:italic&gt;yggT&lt;\/jats:italic&gt;\n              depicted 184% increase in adhesion, and upon complementation, adhesion was significantly reduced to 13%. \u0394\n              &lt;jats:italic&gt;flgH&lt;\/jats:italic&gt;\n              lost motility and was regenerated when complemented, whereas \u0394\n              &lt;jats:italic&gt;ffp&lt;\/jats:italic&gt;\n              had significantly increased motility, and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by \u0394\n              &lt;jats:italic&gt;ffp&lt;\/jats:italic&gt;\n              and \u0394\n              &lt;jats:italic&gt;spnT&lt;\/jats:italic&gt;\n              were more resistant and protected the bacteria, with \u0394\n              &lt;jats:italic&gt;spnT&lt;\/jats:italic&gt;\n              showing the best clump formation in terms of ampicillin stress protection. \u0394\n              &lt;jats:italic&gt;yggT&lt;\/jats:italic&gt;\n              had the lowest tolerance to gentamicin, where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on cell surface adhesion and antimicrobial tolerance, with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics.\n            &lt;\/jats:p&gt;\n          &lt;\/jats:sec&gt;\n          &lt;jats:sec&gt;\n            &lt;jats:title&gt;IMPORTANCE&lt;\/jats:title&gt;\n            &lt;jats:p&gt;\n              The study explores a biofilm-like clumpy adhesion phenotype in\n              &lt;jats:italic&gt;Escherichia coli,&lt;\/jats:italic&gt;\n              along with various factors and implications for antibiotic susceptibility. The phenotype permitted the bacteria to survive the onslaught of high antibiotic concentrations. Profiles of the transcriptome and proteome allowed the differentiation between adhered bacteria in clumps and planktonic bacteria in the supernatant. The deletion mutants of genes differentially expressed between adhered and planktonic bacteria, i.e.,\n              &lt;jats:italic&gt;flgH&lt;\/jats:italic&gt;\n              ,\n              &lt;jats:italic&gt;ffp&lt;\/jats:italic&gt;\n              ,\n              &lt;jats:italic&gt;pilV&lt;\/jats:italic&gt;\n              ,\n              &lt;jats:italic&gt;spnT&lt;\/jats:italic&gt;\n              , and\n              &lt;jats:italic&gt;yggT,&lt;\/jats:italic&gt;\n              and respective complementations in\n              &lt;jats:italic&gt;trans&lt;\/jats:italic&gt;\n              cemented their roles in multiple capacities.\n              &lt;jats:italic&gt;ffp&lt;\/jats:italic&gt;\n              , an uncharacterized gene, is involved in motility and resistance to ampicillin in a clumpy state. 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      <firstName>Muhammad Moman</firstName>
      <lastName>Khan</lastName>
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      <firstName>Muhammad Moman</firstName>
      <lastName>Khan</lastName>
    </submitter>
    <author>
      <firstName>Katarzyna</firstName>
      <lastName>Sidorczuk</lastName>
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    <author>
      <firstName>Juliane</firstName>
      <lastName>Becker</lastName>
    </author>
    <author>
      <firstName>Adrianna</firstName>
      <lastName>Aleksandrowicz</lastName>
    </author>
    <author>
      <firstName>Karolina</firstName>
      <lastName>Baraniewicz</lastName>
    </author>
    <author>
      <firstName>Christina</firstName>
      <lastName>Ludwig</lastName>
    </author>
    <author>
      <firstName>Aamir</firstName>
      <lastName>Ali</lastName>
    </author>
    <author>
      <firstName>Robert A.</firstName>
      <lastName>Kingsley</lastName>
    </author>
    <author>
      <firstName>Peter</firstName>
      <lastName>Schierack</lastName>
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      <firstName>Rafał</firstName>
      <lastName>Kolenda</lastName>
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      <value>Ecology</value>
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      <language>eng</language>
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    <completedDate>2025-01-15</completedDate>
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    <title language="eng">AdhesiomeR: a tool for Escherichia coli adhesin classification and analysis</title>
    <abstract language="eng">AbstractAdhesins are crucial factors in the virulence of bacterial pathogens such as Escherichia coli. However, to date no resources have been dedicated to the detailed analysis of E. coli adhesins. Here, we provide adhesiomeR software that enables characterization of the complete adhesin repertoire, termed the adhesiome. AdhesiomeR incorporates the most comprehensive database of E. coli adhesins and facilitates an extensive analysis of adhesiome. We demonstrate that adhesiomeR achieves 98% accuracy when compared with experimental analyses. Based on analysis of 15,000 E. coli genomes, we define novel adhesiome profiles and clusters, providing a nomenclature for a unified comparison of E. coli adhesiomes.</abstract>
    <parentTitle language="eng">BMC Genomics</parentTitle>
    <identifier type="doi">10.1186/s12864-024-10525-6</identifier>
    <identifier type="issn">1471-2164</identifier>
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However, to date no resources have been dedicated to the detailed analysis of &lt;jats:italic&gt;E.\u00a0coli&lt;\/jats:italic&gt; adhesins. Here, we provide adhesiomeR software that enables characterization of the complete adhesin repertoire, termed the adhesiome. AdhesiomeR incorporates the most comprehensive database of &lt;jats:italic&gt;E.\u00a0coli&lt;\/jats:italic&gt; adhesins and facilitates an extensive analysis of adhesiome. We demonstrate that adhesiomeR achieves 98% accuracy when compared with experimental analyses. 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