{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T09:43:20Z","timestamp":1780047800970,"version":"3.53.1"},"reference-count":106,"publisher":"Oxford University Press (OUP)","issue":"6","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["75N93019C00076"],"award-info":[{"award-number":["75N93019C00076"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HR0011150042"],"award-info":[{"award-number":["HR0011150042"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. Funding agencies worldwide and the global research community have expended considerable capital and effort tracking the evolution and spread of AMR by isolating and sequencing bacterial strains and performing antimicrobial susceptibility testing (AST). For the last several years, we have been capturing these efforts by curating data from the literature and data resources and building a set of assembled bacterial genome sequences that are paired with laboratory-derived AST data. This collection currently contains AST data for over 67\u00a0000 genomes encompassing approximately 40 genera and over 100 species. In this paper, we describe the characteristics of this collection, highlighting areas where sampling is comparatively deep or shallow, and showing areas where attention is needed from the research community to improve sampling and tracking efforts. In addition to using the data to track the evolution and spread of AMR, it also serves as a useful starting point for building machine learning models for predicting AMR phenotypes. We demonstrate this by describing two machine learning models that are built from the entire dataset to show where the predictive power is comparatively high or low. This AMR metadata collection is freely available and maintained on the Bacterial and Viral Bioinformatics Center (BV-BRC) FTP site ftp:\/\/ftp.bvbrc.org\/RELEASE_NOTES\/PATRIC_genomes_AMR.txt.<\/jats:p>","DOI":"10.1093\/bib\/bbab313","type":"journal-article","created":{"date-parts":[[2021,7,27]],"date-time":"2021-07-27T19:10:34Z","timestamp":1627413034000},"source":"Crossref","is-referenced-by-count":34,"title":["A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes"],"prefix":"10.1093","volume":"22","author":[{"given":"Margo","family":"VanOeffelen","sequence":"first","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus","family":"Nguyen","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA"},{"name":"Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derya","family":"Aytan-Aktug","sequence":"additional","affiliation":[{"name":"National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Brettin","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA"},{"name":"Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily M","family":"Dietrich","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA"},{"name":"Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald W","family":"Kenyon","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dustin","family":"Machi","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunhong","family":"Mao","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Olson","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA"},{"name":"Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon D","family":"Pusch","sequence":"additional","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maulik","family":"Shukla","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA"},{"name":"Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4268-4020","authenticated-orcid":false,"given":"Rick","family":"Stevens","sequence":"additional","affiliation":[{"name":"Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA"},{"name":"Department of Computer Science, University of Chicago, Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronika","family":"Vonstein","sequence":"additional","affiliation":[{"name":"Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew S","family":"Warren","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice R","family":"Wattam","sequence":"additional","affiliation":[{"name":"Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA"},{"name":"Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyunseung","family":"Yoo","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA"},{"name":"Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0435-6891","authenticated-orcid":false,"given":"James J","family":"Davis","sequence":"additional","affiliation":[{"name":"University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA"},{"name":"Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA"},{"name":"Northwestern Argonne Institute for Science and Engineering, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,11]]},"reference":[{"key":"2021110815085839400_ref1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.3389\/fpubh.2014.00145","article-title":"The antimicrobial resistance crisis: causes, consequences, and management","volume":"2","author":"Michael","year":"2014","journal-title":"Front Public 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