{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:10:36Z","timestamp":1790208636271,"version":"4.1.0"},"reference-count":37,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100008903","name":"Ministry of Health and Welfare","doi-asserted-by":"publisher","award":["MOHW113-CDC-C-315-114110, MOHW114-CDC-C-315-124112, MOHW115-CDC-C-305-134118"],"award-info":[{"award-number":["MOHW113-CDC-C-315-114110, MOHW114-CDC-C-315-124112, MOHW115-CDC-C-305-134118"]}],"id":[{"id":"10.13039\/100008903","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008903","name":"Ministry of Health and Welfare","doi-asserted-by":"publisher","award":["MOHW115-CDC-C-305-114304"],"award-info":[{"award-number":["MOHW115-CDC-C-305-114304"]}],"id":[{"id":"10.13039\/100008903","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      is a major zoonotic foodborne pathogen, and antimicrobial resistance (AMR) in\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      presents a significant public health challenge. Compared with conventional antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS) provides a more rapid and comprehensive approach to AMR characterization, thereby informing antimicrobial selection and supporting public health surveillance. In this study, Oxford Nanopore Technology (ONT)-based WGS was performed on 1,490\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      isolates collected through nationwide surveillance in Taiwan in 2025. Genotypic resistance inferred from WGS data was compared with phenotypic AST results to assess the performance of ONT-WGS. Overall, WGS-inferred resistance showed high concordance with phenotypic resistance for most antimicrobials. However, major genotype\u2013phenotype discordance was observed, attributed to four categories: (i) breakpoint-dependent classification, (ii) reduced or absent phenotypic expression of resistance genes, (iii) minimum inhibitory concentration (MIC) modulation by\n                      <jats:italic toggle=\"yes\">ramAp<\/jats:italic>\n                      , and (iv) absence of known AMR determinants. Notable discrepancies included tigecycline resistance without known genetic determinants, nalidixic acid resistance linked to\n                      <jats:italic toggle=\"yes\">ramAp<\/jats:italic>\n                      -mediated MIC elevation, and a high prevalence of colistin resistance (35.7%) in\n                      <jats:italic toggle=\"yes\">S.<\/jats:italic>\n                      Enteritidis, with most resistant isolates lacking identifiable AMR determinants. Additionally, a significant proportion of ESBL- and AmpC-producing isolates were classified as susceptible or intermediate to cefotaxime and ceftazidime under CLSI criteria, highlighting the potential for misclassification and treatment failure. These findings demonstrate that ONT-WGS enables accurate and comprehensive AMR characterization by directly identifying resistance determinants and avoiding potential misclassification associated with breakpoint-based AST interpretations. When interpreted appropriately, WGS can support better antimicrobial selection and serve as a valuable alternative to conventional susceptibility testing.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Accurate prediction of antimicrobial resistance is essential for appropriate therapy and effective surveillance of\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      . However, discordance between genotype-based predictions and phenotypic antimicrobial susceptibility testing (AST) can complicate clinical interpretation. In this nationwide study of 1,490 Salmonella isolates, we show that Oxford Nanopore Technology-based whole-genome sequencing (ONT-WGS) provides rapid and comprehensive detection of antimicrobial resistance determinants with high concordance to phenotypic AST. We further identify four major mechanisms underlying genotype\u2013phenotype discordance, including breakpoint-dependent classification, reduced or absent phenotypic expression of resistance genes, minimum inhibitory concentration (MIC) modulation by\n                      <jats:italic toggle=\"yes\">ramAp<\/jats:italic>\n                      , and the absence of known AMR determinants. These findings demonstrate how WGS can complement conventional AST, improve interpretation of challenging susceptibility results, and strengthen genomic surveillance of emerging antimicrobial-resistant\n                      <jats:italic toggle=\"yes\">Salmonella<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01797-26","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T13:01:09Z","timestamp":1786539669000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Evaluation of Oxford nanopore sequencing for antimicrobial resistance surveillance in\n                    <i>Salmonella<\/i>\n                    : comparison with phenotypic antimicrobial susceptibility in a large-scale study"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2249-7364","authenticated-orcid":true,"given":"Yu-Ping","family":"Hong","sequence":"first","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying-Shu","family":"Liao","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2104-0872","authenticated-orcid":true,"given":"You-Wun","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shao-Chun","family":"Kuo","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ru-Hsiou","family":"Teng","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiu-Yun","family":"Liang","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jui-Hsien","family":"Chang","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsiao Lun","family":"Wei","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3674-1030","authenticated-orcid":true,"given":"Chien-Shun","family":"Chiou","sequence":"additional","affiliation":[{"name":"Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare","place":["Taichung, Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1086\/650733"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001921"},{"key":"e_1_3_4_4_2","volume-title":"WHO bacterial priority pathogens list, 2024: bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance","author":"WHO","year":"2024","unstructured":"WHO. 2024. WHO bacterial priority pathogens list, 2024: bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance. World Health Organization, Geneva. https:\/\/www.who.int\/publications\/i\/item\/9789240093461."},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijregi.2024.100372"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01122-19"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2501.181103"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01334-25"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02979-24"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2908.230472"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2026.1832575"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1752"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2023.0075"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00509-24"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01746-19"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00592"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01030-16"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-023-05605-4"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.64898\/2026.03.20.713089"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1669089"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0072-8"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.21105\/joss.05968"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0147101"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0"},{"key":"e_1_3_4_26_2","volume-title":"Performance standards for antimicrobial susceptibility testing","author":"CLSI","year":"2025","unstructured":"CLSI. 2025. CLSI supplement M100. In Performance standards for antimicrobial susceptibility testing. Clinical and Laboratory Standards Institute, Wayne (PA). https:\/\/clsi.org\/shop\/standards\/m100."},{"key":"e_1_3_4_27_2","unstructured":"European Committee on Antimicrobial Susceptibility Testing. 2026. Breakpoint tables for interpretation of MICs and zone diameters. Version 16.0. https:\/\/www.eucast.org."},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01152-21"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02634-20"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.39.6.2206-2212.2001"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2005.01265.x"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0445-2"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.969769"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2023.07.030"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00391-17"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.592146"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2011.1015"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02831-19"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01797-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01797-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T13:11:56Z","timestamp":1788268316000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01797-26"}},"subtitle":[],"editor":[{"given":"Yosef Daniel","family":"Huberman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":37,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,1]]}},"alternative-id":["10.1128\/spectrum.01797-26"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01797-26","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,1]]},"assertion":[{"value":"2026-05-25","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-12","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01797-26"}}