{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:21Z","timestamp":1772138061860,"version":"3.50.1"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T00:00:00Z","timestamp":1687392000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013281","name":"Joint Programming Initiative on Antimicrobial Resistance","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013281","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Danish Innovation Foundation","award":["7044-00004B"],"award-info":[{"award-number":["7044-00004B"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44\u20130.55], 0.43 for pKJK5 (0.95% CI: 0.41\u20130.49), and 0.53 for RP4 (0.95% CI: 0.48\u20130.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The predictive tool is available as an application at https:\/\/github.com\/DaneshMoradigaravand\/PlasmidPerm.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad400","type":"journal-article","created":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T21:25:52Z","timestamp":1687469152000},"source":"Crossref","is-referenced-by-count":2,"title":["Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6652-5617","authenticated-orcid":false,"given":"Danesh","family":"Moradigaravand","sequence":"first","affiliation":[{"name":"Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia"},{"name":"KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4349-0532","authenticated-orcid":false,"given":"Liguan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Environmental Engineering, Technical University of Denmark , 2800 Kgs Lyngby, Denmark"},{"name":"Department of Civil Engineering, The University of Hong Kong , Hong Kong, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6638-2158","authenticated-orcid":false,"given":"Arnaud","family":"Dechesne","sequence":"additional","affiliation":[{"name":"Department of Environmental Engineering, Technical University of Denmark , 2800 Kgs Lyngby, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1929-5040","authenticated-orcid":false,"given":"Joseph","family":"Nesme","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Copenhagen , 2100 Copenhagen, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5669-4302","authenticated-orcid":false,"given":"Roberto","family":"de la Cruz","sequence":"additional","affiliation":[{"name":"Center for Computational Biology, University of Birmingham , Birmingham, B15 2TT, United Kingdom"},{"name":"Institute of Microbiology and Infection, University of Birmingham , Birmingham, B15 2TT, United Kingdom"},{"name":"School of Biosciences, University of Birmingham , Birmingham, B15 2TT, United Kingdom"}]},{"given":"Huda","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia"},{"name":"KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia"},{"name":"Center for Computational Biology, University of Birmingham , Birmingham, B15 2TT, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4682-1037","authenticated-orcid":false,"given":"Manuel","family":"Banzhaf","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Infection, University of Birmingham , Birmingham, B15 2TT, United Kingdom"},{"name":"School of Biosciences, University of Birmingham , Birmingham, B15 2TT, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6227-9906","authenticated-orcid":false,"given":"S\u00f8ren J","family":"S\u00f8rensen","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Copenhagen , 2100 Copenhagen, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4119-6292","authenticated-orcid":false,"given":"Barth F","family":"Smets","sequence":"additional","affiliation":[{"name":"Department of Environmental Engineering, Technical University of Denmark , 2800 Kgs Lyngby, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2351-224X","authenticated-orcid":false,"given":"Jan-Ulrich","family":"Kreft","sequence":"additional","affiliation":[{"name":"Center for Computational Biology, University of Birmingham , Birmingham, B15 2TT, United Kingdom"},{"name":"Institute of Microbiology and Infection, University of Birmingham , Birmingham, B15 2TT, United Kingdom"},{"name":"School of Biosciences, University of Birmingham , Birmingham, B15 2TT, United 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