{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T15:05:14Z","timestamp":1790867114838,"version":"4.1.0"},"reference-count":44,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2019,3,27]],"date-time":"2019-03-27T00:00:00Z","timestamp":1553644800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,4,1]],"date-time":"2019-04-01T00:00:00Z","timestamp":1554076800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"European Research Council","award":["309540-EVODRTB"],"award-info":[{"award-number":["309540-EVODRTB"]}]},{"DOI":"10.13039\/501100012390","name":"SystemsX.ch","doi-asserted-by":"crossref","award":["TbX"],"award-info":[{"award-number":["TbX"]}],"id":[{"id":"10.13039\/501100012390","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI096299"],"award-info":[{"award-number":["U01 AI096299"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI069919"],"award-info":[{"award-number":["U01 AI069919"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI069924"],"award-info":[{"award-number":["U01 AI069924"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI069911"],"award-info":[{"award-number":["U01 AI069911"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI069907"],"award-info":[{"award-number":["U01 AI069907"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI096186"],"award-info":[{"award-number":["U01 AI096186"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI069923"],"award-info":[{"award-number":["U01 AI069923"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["IZRJZ3_164171"],"award-info":[{"award-number":["IZRJZ3_164171"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["310030-166687"],"award-info":[{"award-number":["310030-166687"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["IZLSZ3_170834"],"award-info":[{"award-number":["IZLSZ3_170834"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["CRSII5_177163"],"award-info":[{"award-number":["CRSII5_177163"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["31003A_153349"],"award-info":[{"award-number":["31003A_153349"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["320030_153442\/1"],"award-info":[{"award-number":["320030_153442\/1"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Antimicrob Agents Chemother"],"published-print":{"date-parts":[[2019,4]]},"abstract":"<jats:p>\n                    Whole-genome sequencing allows rapid detection of drug-resistant\n                    <jats:named-content content-type=\"genus-species\">Mycobacterium tuberculosis<\/jats:named-content>\n                    isolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited.\n                  <\/jats:p>","DOI":"10.1128\/aac.02175-18","type":"journal-article","created":{"date-parts":[[2019,2,5]],"date-time":"2019-02-05T08:45:10Z","timestamp":1549356310000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":82,"title":["Whole-Genome Sequencing for Drug Resistance Profile Prediction in\n                    <i>Mycobacterium tuberculosis<\/i>"],"prefix":"10.1128","volume":"63","author":[{"given":"Sebastian M.","family":"Gygli","sequence":"first","affiliation":[{"name":"Swiss Tropical and Public Health Institute, Basel, Switzerland"},{"name":"University of Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter M.","family":"Keller","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"Institute for Infectious Diseases, University of Bern, Bern, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Ballif","sequence":"additional","affiliation":[{"name":"Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Bl\u00f6chliger","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rico","family":"H\u00f6mke","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"National Center for Mycobacteria, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"Reinhard","sequence":"additional","affiliation":[{"name":"Swiss Tropical and Public Health Institute, Basel, Switzerland"},{"name":"University of Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chlo\u00e9","family":"Loiseau","sequence":"additional","affiliation":[{"name":"Swiss Tropical and Public Health Institute, Basel, Switzerland"},{"name":"University of Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Ritter","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"National Center for Mycobacteria, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Sander","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"National Center for Mycobacteria, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"Borrell","sequence":"additional","affiliation":[{"name":"Swiss Tropical and Public Health Institute, Basel, Switzerland"},{"name":"University of Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jimena","family":"Collantes Loo","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anchalee","family":"Avihingsanon","sequence":"additional","affiliation":[{"name":"HIV-NAT\/Thai Red Cross AIDS Research Centre, Bangkok, Thailand"},{"name":"TB Research Unit, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joachim","family":"Gnokoro","sequence":"additional","affiliation":[{"name":"Centre de Prise en Charge de Recherche et de Formation, Yopougon, Abidjan, C\u00f4te d'Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcel","family":"Yotebieng","sequence":"additional","affiliation":[{"name":"College of Public Health, Ohio State University, Columbus, Ohio, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Egger","sequence":"additional","affiliation":[{"name":"Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland"},{"name":"Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastien","family":"Gagneux","sequence":"additional","affiliation":[{"name":"Swiss Tropical and Public Health Institute, Basel, Switzerland"},{"name":"University of Basel, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik C.","family":"B\u00f6ttger","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"National Center for Mycobacteria, University of Z\u00fcrich, Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.5588\/ijtld.15.0221"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fux011"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2016.06.016"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00251-16"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02597-13"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.3109\/23744235.2015.1061205"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.05905-11"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-015-0164-0"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(15)00062-6"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1800474"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx506"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00298-17"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00535-16"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2011.03551.x"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciy179"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2016.01.019"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-27962-5"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2016.10.022"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.06460-11"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1261\/rna.057257.116"},{"key":"e_1_3_3_27_2","first-page":"527","volume-title":"Efflux-mediated antimicrobial resistance in bacteria","author":"Pea DS","year":"2016","unstructured":"Pea DS, Machado D, Ramos D, Couto I, Von Groll A, Viveiros M. 2016. Efflux pumps in mycobacteria: antimicrobial resistance, physiological functions, and role in pathogenicity, p 527\u2013559. In Li X-Z, Elkins CA, Zgurskaya HI (ed), Efflux-mediated antimicrobial resistance in bacteria. Springer International Publishing, Cham, Switzerland."},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2743"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/35.3.381"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.3181\/00379727-55-14461"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2001741"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/emph\/eot003"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2878"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001880"},{"key":"e_1_3_3_35_2","volume-title":"The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide","author":"World Health Organization","year":"2018","unstructured":"World Health Organization. 2018. The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide. World Health Organization, Geneva, Switzerland."},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201510-2091OC"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01354-2017"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01209-13"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00344-18"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/civ610"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02501-08"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00126-16"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMc1505196"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/ije\/dyr080"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.2471\/BLT.11.096644"},{"key":"e_1_3_3_46_2","volume-title":"Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis","author":"World Health Organization","year":"2014","unstructured":"World Health Organization. 2014. Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis. World Health Organization, Geneva, Switzerland."},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v064.i04"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(86)90837-8"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-15278-9"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmyco.2015.09.001"}],"container-title":["Antimicrobial Agents and Chemotherapy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AAC.02175-18","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AAC.02175-18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,21]],"date-time":"2022-02-21T16:42:24Z","timestamp":1645461744000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AAC.02175-18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4]]},"references-count":44,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2019,4]]}},"alternative-id":["10.1128\/AAC.02175-18"],"URL":"https:\/\/doi.org\/10.1128\/aac.02175-18","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/401703","asserted-by":"object"}]},"ISSN":["0066-4804","1098-6596"],"issn-type":[{"value":"0066-4804","type":"print"},{"value":"1098-6596","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4]]},"assertion":[{"value":"2018-10-15","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-01-25","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-03-27","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e02175-18"}}