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Antibiotic resistance threats in the United States, 2013. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.cdc.gov\/drugresistance\/pdf\/ar-threats-2013-508.pdf\" xlink:type=\"simple\">http:\/\/www.cdc.gov\/drugresistance\/pdf\/ar-threats-2013-508.pdf<\/ext-link>. Accessed 26 September 2015."},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1001\/jama.2015.11629","article-title":"Measuring carbapenem-resistant Enterobacteriaceae in the United States: a critical step for control","volume":"314","author":"MK Hayden","year":"2015","journal-title":"JAMA"},{"key":"ref3","unstructured":"National Action Plan for Combating Antibiotic-resistant Bacterial. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.whitehouse.gov\/sites\/default\/files\/docs\/national_action_plan_for_combating_antibotic-resistant_bacteria.pdf\" xlink:type=\"simple\">https:\/\/www.whitehouse.gov\/sites\/default\/files\/docs\/national_action_plan_for_combating_antibotic-resistant_bacteria.pdf<\/ext-link>. Accessed 5 November 2015."},{"key":"ref4","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1093\/cid\/civ433","article-title":"Genomic epidemiology: revealing hidden reservoirs for Klebsiella pneumonia","volume":"61","author":"AR Manges","year":"2015","journal-title":"Clin Infect Dis"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1093\/cid\/ciu319","article-title":"The Antimicrobial Resistance Monitoring and Research (ARMoR) Program: the Department of Defense\u2019s response to escalating antimicrobial resistance","volume":"59","author":"E Lesho","year":"2014","journal-title":"Clin Infect Dis"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1017\/ice.2015.133","article-title":"Whole genomic sequencing in real-time investigation and management of a Pseudomonas aeruginosa outbreak on a neonatal intensive car unit","volume":"36","author":"RJ Davis","year":"2015","journal-title":"Infect Control Hosp Epidemiol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/nrg3624","article-title":"Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions","volume":"15","author":"WF Fricke","year":"2014","journal-title":"Nature Rev"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1128\/JCM.02452-13","article-title":"Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples","volume":"52","author":"H Hasman","year":"2014","journal-title":"J Clin Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1038\/nbt.1978","article-title":"Outbreak Genomics","volume":"29","year":"2011","journal-title":"Nature Biotechnology"},{"key":"ref10","article-title":"How next generation sequencing might not transform infectious disease practice","author":"E. Lesho","year":"2016","journal-title":"Clin Infect Dis"},{"key":"ref11","article-title":"Real time application of whole genome sequencing for outbreak investigation\u2014what is an achievable turnaround time?","author":"P McGann","year":"2015","journal-title":"Diag Microbiol Infect Dis"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.ygeno.2011.05.009","article-title":"Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies","volume":"98","author":"Y Kong","year":"2011","journal-title":"Genomics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: Fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"T Magoc","year":"2011","journal-title":"Bioinformatics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"E Zankari","year":"2012","journal-title":"J Antimicrob Chemother"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jmoldx.2015.07.004","article-title":"Next-generation sequencing for infectious disease diagnosis and management","volume":"17","author":"MI Lefterova","year":"2015","journal-title":"J Mol Diag"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tig.2014.07.003","article-title":"Whole-genome sequencing to control antimicrobial resistance","volume":"30","author":"CU Koeser","year":"2014","journal-title":"Trends Genetics"},{"key":"ref19","first-page":"1053","article-title":"Reply to Lesho","volume":"62","author":"TR Pak","year":"2016","journal-title":"Clin Infect Dis"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1001\/jamainternmed.2013.7042","article-title":"The time is now for gene and genome-based bacterial diagnostics","volume":"173","author":"GD Ehrlich","year":"2013","journal-title":"JAMA Intern Med"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nbt.2403","article-title":"Assuring the quality of next-generation sequencing in clinical laboratory practice","volume":"30","author":"AS Gargis","year":"2012","journal-title":"Nature Biotech"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"481","DOI":"10.5858\/arpa.2014-0250-CP","article-title":"College of American Pathologists\u2019 laboratory standards for next-generation sequencing clinical tests","volume":"139","author":"N Aziz","year":"2015","journal-title":"Arch Pathol Lab Med"},{"key":"ref23","unstructured":"Global Microbial Identifier. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.globalmicrobialidentifier.org\/Workgroups\/About-the-GMI-Proficiency-Test-2015\" xlink:type=\"simple\">http:\/\/www.globalmicrobialidentifier.org\/Workgroups\/About-the-GMI-Proficiency-Test-2015<\/ext-link>. Accessed 5 November 2015."},{"key":"ref24","unstructured":"US News &amp; World Report: A Health Hack Wakeup Call. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.usnews.com\/opinion\/blogs\/policy-dose\/articles\/2016-04-01\/ransomware-hacks-are-a-hospital-health-it-wake-up-call\" xlink:type=\"simple\">http:\/\/www.usnews.com\/opinion\/blogs\/policy-dose\/articles\/2016-04-01\/ransomware-hacks-are-a-hospital-health-it-wake-up-call<\/ext-link>. Accessed 3 April 2016."}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0155770","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,20]],"date-time":"2018-10-20T09:12:13Z","timestamp":1540026733000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0155770"}},"subtitle":[],"editor":[{"given":"Yung-Fu","family":"Chang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,5,19]]},"references-count":24,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2016,5,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0155770","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,5,19]]}}}