{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T06:09:33Z","timestamp":1792130973473,"version":"4.4.0"},"reference-count":26,"publisher":"Centers for Disease Control and Prevention (CDC)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Emerg. Infect. Dis."],"published-print":{"date-parts":[[2025]]},"DOI":"10.3201\/eid3113.241227","type":"journal-article","created":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T15:19:50Z","timestamp":1746544790000},"source":"Crossref","is-referenced-by-count":11,"title":["Integrating Genomic Data into Public Health Surveillance for Multidrug-Resistant Organisms, Washington, USA"],"prefix":"10.3201","volume":"31","author":[{"given":"Laura Marcela","family":"Torres","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jared","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Valentine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Brezak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily C.","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marisa","family":"D\u2019Angeli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Morgan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Brostrom-Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi N.","family":"Hua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Tran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Darren","family":"Lucas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joenice Gonzalez","family":"De Leon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Drew","family":"MacKellar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Dykema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly J.","family":"Kauber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allison","family":"Black","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1822","reference":[{"key":"key-10.3201\/eid3113.241227-202504241055-R1","unstructured":"Centers for Disease Control and Prevention. Antibiotic resistance threats in the United States, 2019. 2019 Nov [cited 2024 Apr 8]. https:\/\/stacks.cdc.gov\/view\/cdc\/82532"},{"key":"key-10.3201\/eid3113.241227-202504241055-R2","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1093\/cid\/cix893","article-title":"Carbapenemase-producing organisms: a global scourge.","volume":"66","author":"Bonomo","year":"2018","journal-title":"Clin Infect Dis"},{"key":"key-10.3201\/eid3113.241227-202504241055-R3","doi-asserted-by":"publisher","first-page":"4910","DOI":"10.1128\/AAC.00014-16","article-title":"Horizontal transfer of carbapenemase-encoding plasmids and comparison with hospital epidemiology data.","volume":"60","author":"Hardiman","year":"2016","journal-title":"Antimicrob Agents Chemother"},{"key":"key-10.3201\/eid3113.241227-202504241055-R4","doi-asserted-by":"publisher","first-page":"e00204","DOI":"10.1128\/mBio.00204-11","article-title":"Molecular dissection of an outbreak of carbapenem-resistant enterobacteriaceae reveals Intergenus KPC carbapenemase transmission through a promiscuous plasmid.","volume":"2","author":"Mathers","year":"2011","journal-title":"MBio"},{"key":"key-10.3201\/eid3113.241227-202504241055-R5","doi-asserted-by":"crossref","unstructured":"Siegel JD, Rhinehart E, Jackson M, Chiarello L. Management of multidrug-resistant organisms in healthcare settings, 2006. 2006 [cited 2024 Jul 17]. https:\/\/www.cdc.gov\/infection-control\/media\/pdfs\/Guideline-MDRO-H.pdf","DOI":"10.1016\/j.ajic.2007.10.006"},{"key":"key-10.3201\/eid3113.241227-202504241055-R6","doi-asserted-by":"publisher","first-page":"e99","DOI":"10.1016\/S1473-3099(17)30485-1","article-title":"Surveillance for control of antimicrobial resistance.","volume":"18","author":"Tacconelli","year":"2018","journal-title":"Lancet Infect Dis"},{"key":"key-10.3201\/eid3113.241227-202504241055-R7","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13073-022-01020-2","article-title":"Exploiting genomics to mitigate the public health impact of antimicrobial resistance.","volume":"14","author":"Waddington","year":"2022","journal-title":"Genome Med"},{"key":"key-10.3201\/eid3113.241227-202504241055-R8","unstructured":"World Health Organization. Global antimicrobial resistance and use surveillance system (GLASS) report 2022. 2022 [cited 2024 Jul 17]. https:\/\/iris.who.int\/bitstream\/handle\/10665\/364996\/9789240062702-eng.pdf"},{"key":"key-10.3201\/eid3113.241227-202504241055-R9","doi-asserted-by":"publisher","first-page":"e26","DOI":"10.1017\/ash.2022.333","article-title":"The future of automated infection detection: Innovation to transform practice (Part III\/III).","volume":"3","author":"Branch-Elliman","year":"2023","journal-title":"Antimicrob Steward Healthc Epidemiol"},{"key":"key-10.3201\/eid3113.241227-202504241055-R10","doi-asserted-by":"crossref","unstructured":"Black A, Dudas G. The applied genomic epidemiology handbook: a practical guide to leveraging pathogen genomic data in public health. 1st edition. Boca Raton (FL): Chapman & Hall\/CRC Press; 2024.","DOI":"10.1201\/9781003409809-1"},{"key":"key-10.3201\/eid3113.241227-202504241055-R11","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1099\/mic.0.000700","article-title":"Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.","volume":"164","author":"Peacock","year":"2018","journal-title":"Microbiology (Reading)"},{"key":"key-10.3201\/eid3113.241227-202504241055-R12","doi-asserted-by":"publisher","first-page":"100446","DOI":"10.1016\/j.lanwpc.2022.100446","article-title":"Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis.","volume":"23","author":"Sherry","year":"2022","journal-title":"Lancet Reg Health West Pac"},{"key":"key-10.3201\/eid3113.241227-202504241055-R13","doi-asserted-by":"publisher","first-page":"e1035","DOI":"10.1016\/S2666-5247(23)00281-1","article-title":"Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group.","volume":"4","author":"Baker","year":"2023","journal-title":"Lancet Microbe"},{"key":"key-10.3201\/eid3113.241227-202504241055-R14","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1186\/s12866-021-02270-7","article-title":"WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective.","volume":"21","author":"Wareth","year":"2021","journal-title":"BMC Microbiol"},{"key":"key-10.3201\/eid3113.241227-202504241055-R15","unstructured":"Centers for Disease Control and Prevention. Antimicrobial Resistance Laboratory Network testing. 2024 [cited 2024 Jul 17]. https:\/\/www.cdc.gov\/antimicrobial-resistance-laboratory-networks\/php\/about\/testing-services.html"},{"key":"key-10.3201\/eid3113.241227-202504241055-R16","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1101\/gr.241455.118","article-title":"Fast and flexible bacterial genomic epidemiology with PopPUNK.","volume":"29","author":"Lees","year":"2019","journal-title":"Genome Res"},{"key":"key-10.3201\/eid3113.241227-202504241055-R17","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"key-10.3201\/eid3113.241227-202504241055-R18","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"key-10.3201\/eid3113.241227-202504241055-R19","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution.","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"key-10.3201\/eid3113.241227-202504241055-R20","doi-asserted-by":"publisher","first-page":"e000093","DOI":"10.1099\/mgen.0.000093","article-title":"Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.","volume":"2","author":"Argim\u00f3n","year":"2016","journal-title":"Microb Genom"},{"key":"key-10.3201\/eid3113.241227-202504241055-R21","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol Evol"},{"key":"key-10.3201\/eid3113.241227-202504241055-R22","doi-asserted-by":"publisher","first-page":"e0020923","DOI":"10.1128\/spectrum.00209-23","article-title":"Genomic Characterization of carbapenem-resistant Acinetobacter baumannii (CRAB) in mechanically ventilated COVID-19 patients and impact of infection control measures on reducing CRAB circulation during the second wave of the SARS-CoV-2 pandemic in Milan, Italy.","volume":"11","author":"Mangioni","year":"2023","journal-title":"Microbiol Spectr"},{"key":"key-10.3201\/eid3113.241227-202504241055-R23","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1128\/JCM.01818-15","article-title":"Utility of whole-genome sequencing in characterizing Acinetobacter epidemiology and analyzing hospital outbreaks.","volume":"54","author":"Fitzpatrick","year":"2016","journal-title":"J Clin Microbiol"},{"key":"key-10.3201\/eid3113.241227-202504241055-R24","unstructured":"Centers for Disease Control and Prevention. Implementing whole genome sequencing for foodborne disease surveillance. PulseNet. 2024 [cited 2024 Dec 4]. https:\/\/www.cdc.gov\/pulsenet\/php\/wgs\/wgs-vision.html"},{"key":"key-10.3201\/eid3113.241227-202504241055-R25","unstructured":"Centers for Disease Control and Prevention. Tuberculosis whole-genome sequencing. 2024 [cited 2024 Dec 4]. https:\/\/www.cdc.gov\/tb\/php\/genotyping\/whole-genome-sequencing.html"},{"key":"key-10.3201\/eid3113.241227-202504241055-R26","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1089\/fpd.2019.2637","article-title":"An overview of PulseNet USA databases.","volume":"16","author":"Tolar","year":"2019","journal-title":"Foodborne Pathog Dis"}],"container-title":["Emerging Infectious Diseases"],"original-title":[],"deposited":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T15:19:52Z","timestamp":1746544792000},"score":1,"resource":{"primary":{"URL":"https:\/\/wwwnc.cdc.gov\/eid\/article\/31\/13\/24-1227_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":26,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2025]]}},"URL":"https:\/\/doi.org\/10.3201\/eid3113.241227","relation":{},"ISSN":["1080-6040","1080-6059"],"issn-type":[{"value":"1080-6040","type":"print"},{"value":"1080-6059","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025]]}}}