{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T15:47:18Z","timestamp":1780674438376,"version":"3.54.1"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,10,6]],"date-time":"2021-10-06T00:00:00Z","timestamp":1633478400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["031L0209B"],"award-info":[{"award-number":["031L0209B"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid and accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) is time-consuming, low throughput and viable only for cultivable bacteria. Machine learning methods may pave the way for automated AMR prediction based on genomic data of the bacteria. However, comparing different machine learning methods for the prediction of AMR based on different encodings and whole-genome sequencing data without previously known knowledge remains to be done.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we evaluated logistic regression (LR), support vector machine (SVM), random forest (RF) and convolutional neural network (CNN) for the prediction of AMR for the antibiotics ciprofloxacin, cefotaxime, ceftazidime and gentamicin. We could demonstrate that these models can effectively predict AMR with label encoding, one-hot encoding and frequency matrix chaos game representation (FCGR encoding) on whole-genome sequencing data. We trained these models on a large AMR dataset and evaluated them on an independent public dataset. Generally, RFs and CNNs perform better than LR and SVM with AUCs up to 0.96. Furthermore, we were able to identify mutations that are associated with AMR for each antibiotic.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code in data preparation and model training are provided at GitHub website (https:\/\/github.com\/YunxiaoRen\/ML-iAMR).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab681","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T20:54:33Z","timestamp":1633035273000},"page":"325-334","source":"Crossref","is-referenced-by-count":186,"title":["Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning"],"prefix":"10.1093","volume":"38","author":[{"given":"Yunxiao","family":"Ren","sequence":"first","affiliation":[{"name":"Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg , Marburg 35032, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trinad","family":"Chakraborty","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, Justus Liebig University Giessen , Giessen 35392, Germany"},{"name":"German Center for Infection Research, Partner site Giessen-Marburg-Langen , Giessen 35392, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Swapnil","family":"Doijad","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, Justus Liebig University Giessen , Giessen 35392, Germany"},{"name":"German Center for Infection Research, Partner site Giessen-Marburg-Langen , Giessen 35392, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Falgenhauer","sequence":"additional","affiliation":[{"name":"German Center for Infection Research, Partner site Giessen-Marburg-Langen , Giessen 35392, Germany"},{"name":"Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen , Giessen 35392, Germany"},{"name":"Hessisches universit\u00e4res Kompetenzzentrum Krankenhaushygiene , Giessen 35392, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Falgenhauer","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, Justus Liebig University Giessen , Giessen 35392, Germany"},{"name":"German Center for Infection Research, Partner site Giessen-Marburg-Langen , Giessen 35392, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Goesmann","sequence":"additional","affiliation":[{"name":"German Center for Infection Research, Partner site Giessen-Marburg-Langen , Giessen 35392, Germany"},{"name":"Department of Bioinformatics and Systems Biology, Justus Liebig University Giessen , Giessen 35392, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Christin","family":"Hauschild","sequence":"additional","affiliation":[{"name":"Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg , Marburg 35032, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Schwengers","sequence":"additional","affiliation":[{"name":"German Center for Infection Research, Partner site Giessen-Marburg-Langen , Giessen 35392, Germany"},{"name":"Department of Bioinformatics and Systems Biology, Justus Liebig University Giessen , Giessen 35392, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3108-8311","authenticated-orcid":false,"given":"Dominik","family":"Heider","sequence":"additional","affiliation":[{"name":"Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg , Marburg 35032, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,10,6]]},"reference":[{"key":"2023020108461528400_btab681-B1","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s13756-019-0505-7","article-title":"Phenotypic and genotypic characterization of antibiotic resistance in the methicillin-resistant Staphylococcus aureus strains isolated from hospital cockroaches","volume":"8","author":"Abdolmaleki","year":"2019","journal-title":"Antimicrob. 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