{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T03:18:13Z","timestamp":1792811893101,"version":"4.5.0"},"reference-count":34,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T00:00:00Z","timestamp":1472688000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Antimicrob Agents Chemother"],"published-print":{"date-parts":[[2016,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Laboratory-based\n                    <jats:italic>in vitro<\/jats:italic>\n                    antimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidal\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Salmonella<\/jats:named-content>\n                    and correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred forty\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Salmonella<\/jats:named-content>\n                    of 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (\n                    <jats:italic>n =<\/jats:italic>\n                    59) in the 104 human isolates than in the 536 retail meat isolates (\n                    <jats:italic>n =<\/jats:italic>\n                    36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum \u03b2-lactamases (ESBLs) (\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M1<\/jats:sub>\n                    and\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV2a<\/jats:sub>\n                    ) in retail meat isolates of\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Salmonella<\/jats:named-content>\n                    in the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidal\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Salmonella<\/jats:named-content>\n                    , although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.\n                  <\/jats:p>","DOI":"10.1128\/aac.01030-16","type":"journal-article","created":{"date-parts":[[2016,7,5]],"date-time":"2016-07-05T22:58:59Z","timestamp":1467759539000},"page":"5515-5520","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":344,"title":["Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella"],"prefix":"10.1128","volume":"60","author":[{"given":"Patrick F.","family":"McDermott","sequence":"first","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory H.","family":"Tyson","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudine","family":"Kabera","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuansha","family":"Chen","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong","family":"Li","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason P.","family":"Folster","sequence":"additional","affiliation":[{"name":"Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sherry L.","family":"Ayers","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Lam","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather P.","family":"Tate","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaohua","family":"Zhao","sequence":"additional","affiliation":[{"name":"Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1086\/647952"},{"key":"e_1_3_3_3_2","volume-title":"Performance standards for antimicrobial susceptibility testing; twenty-fifth informational supplement","author":"CLSI","year":"2015","unstructured":"CLSI. 2015. Performance standards for antimicrobial susceptibility testing; twenty-fifth informational supplement. Clinical and Laboratory Standards Institute, Wayne, PA."},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.3109\/03009734.2014.901446"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.2217\/17460913.2.5.493"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00745-06"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40246-015-0037-z"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.03117-13"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkt180"},{"key":"e_1_3_3_10_2","volume-title":"National Antimicrobial Resistance Monitoring System (NARMS): 2012 retail meat report","author":"FDA","year":"2015","unstructured":"FDA. 2015. National Antimicrobial Resistance Monitoring System (NARMS): 2012 retail meat report. US Department of Health and Human Services, Food and Drug Administration, Rockville, MD."},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkv186"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1089\/omi.2008.0017"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst197"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1515\/hsz-2013-0292"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cimid.2012.08.004"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkg168"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01093-07"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.35.8.1647"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1402.070573"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/41.6.635"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01144-12"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2010.0028"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3226"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2109.150570"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00323-15"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-32"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evu079"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2008.131399"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiv297"},{"key":"e_1_3_3_30_2","volume-title":"Multistate outbreak of Salmonella Braenderup infections linked to nut butter manufactured by nSpired Natural Foods, Inc","author":"CDC","year":"2014","unstructured":"CDC. 16 October 2014, posting date. Multistate outbreak of Salmonella Braenderup infections linked to nut butter manufactured by nSpired Natural Foods, Inc. CDC, Atlanta, GA. http:\/\/www.cdc.gov\/salmonella\/braenderup-08-14\/index.html."},{"key":"e_1_3_3_31_2","doi-asserted-by":"crossref","first-page":"pii:fnw009","DOI":"10.1093\/femsle\/fnw009","article-title":"Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli","volume":"363","author":"Tyson GH","year":"2016","unstructured":"Tyson GH, Li C, Ayers S, McDermott PF, Zhao S. 2016. Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli. FEMS Microbiol Lett 363:pii:fnw009.","journal-title":"FEMS Microbiol Lett"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2011.0064"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1412.080494"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks496"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02873-15"}],"container-title":["Antimicrobial Agents and Chemotherapy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AAC.01030-16","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AAC.01030-16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,21]],"date-time":"2022-02-21T15:33:19Z","timestamp":1645457599000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AAC.01030-16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9]]},"references-count":34,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2016,9]]}},"alternative-id":["10.1128\/AAC.01030-16"],"URL":"https:\/\/doi.org\/10.1128\/aac.01030-16","relation":{},"ISSN":["0066-4804","1098-6596"],"issn-type":[{"value":"0066-4804","type":"print"},{"value":"1098-6596","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9]]},"assertion":[{"value":"2016-05-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-06-27","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-08-22","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}