{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T12:02:23Z","timestamp":1781092943571,"version":"3.54.1"},"reference-count":43,"publisher":"SAGE Publications","issue":"7","license":[{"start":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T00:00:00Z","timestamp":1747353600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Foodborne Pathogens and Disease"],"published-print":{"date-parts":[[2026,7,1]]},"abstract":"\n Antimicrobial-resistant\n Salmonella<\/jats:italic>\n has posed a huge threat to food safety and public health, and tetracycline is the commonly used antibiotic for treating salmonellosis. In this study, eight\n Salmonella<\/jats:italic>\n Typhimurium isolates from diarrhea patients (\n n<\/jats:italic>\n = 7) and clam (\n n<\/jats:italic>\n = 1) exhibited high-level tetracycline resistance (minimum inhibitory concentration = 128 \u03bcg\/mL), and these isolates were further resistant to ampicillin and sulfonamides, formatting the R-type ASuT (ampicillin, sulfonamides, and tetracycline). Then, these eight isolates were sequenced using PacBio platform, revealing the presence of tetracycline resistance gene\n tet<\/jats:italic>\n (B), along with sulfonamide-resistance gene\n sul<\/jats:italic>\n 2, extended-spectrum-\u03b2-lactamase gene\n bla<\/jats:italic>\n TEM-1B<\/jats:sub>\n , and aminoglycoside resistance genes\n aph(3\u2033)<\/jats:italic>\n -Ib and\n aph(6)<\/jats:italic>\n -Id on the chromosome, which was associated with R-type ASuT. Four types (A, B1, B2, and C) of genetic arrangement for chromosomally encoding\n tet<\/jats:italic>\n (B) were found, inserted into\n flj<\/jats:italic>\n BA operon. Type C (\n flj<\/jats:italic>\n BA operon-\n tet<\/jats:italic>\n (B)-\n sul<\/jats:italic>\n 2-\n bla<\/jats:italic>\n TEM-1B<\/jats:sub>\n -\n aph(3\u2033)<\/jats:italic>\n -Ib-\n aph(6)<\/jats:italic>\n -Id-\n mer<\/jats:italic>\n ACDEPTR) was the most common type and was accompanied by various insertion sequences (ISs) (IS\n 26<\/jats:italic>\n , IS\n 1<\/jats:italic>\n , and IS\n Vsa5<\/jats:italic>\n ) and recombinases. Pairwise sequence alignment showed that type C arrangement likely resulted from stepwise acquisitions and rearrangements facilitated by the actions of ISs, followed by integration into the chromosome by prophages. Phylogenomic analysis showed that all eight\n Salmonella<\/jats:italic>\n Typhimurium isolates from China in this study, along with a human-borne\n Salmonella<\/jats:italic>\n Typhimurium isolate (DA34821) from Germany and a foodborne\n Salmonella<\/jats:italic>\n Typhimurium isolate (CFSA629) from China, clustered into a single clade, sharing \u226467 SNPs, which suggested that clone spread occurred. These findings underline the emergence of R-type ASuT in\n Salmonella<\/jats:italic>\n Typhimurium, which is attributed to the presence of an antimicrobial resistance gene cluster (\n tet<\/jats:italic>\n (B),\n sul<\/jats:italic>\n 2,\n bla<\/jats:italic>\n TEM-1B<\/jats:sub>\n ,\n aph(3\u2033)<\/jats:italic>\n -Ib, and\n aph(6)<\/jats:italic>\n -Id) encoded on the chromosome.\n <\/jats:p>","DOI":"10.1089\/fpd.2024.0172","type":"journal-article","created":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T04:33:59Z","timestamp":1747370039000},"page":"441-450","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":1,"title":["Genomics Revealed Novel Chromosomal Integration of Antimicrobial Resistance Cluster\n tet<\/i>\n (B),\n sul<\/i>\n 2,\n bla<\/i>\n TEM-1B<\/sub>\n ,\n aph(3\u2033)<\/i>\n -Ib, and\n aph(6)<\/i>\n -Id in\n Salmonella<\/i>\n Typhimurium"],"prefix":"10.1177","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7062-7613","authenticated-orcid":false,"given":"Zengfeng","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Food Science & Technology, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengjun","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Food Science & Technology, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kannappan","family":"Arunachalam","sequence":"additional","affiliation":[{"name":"Department of Food Science & Technology, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunlei","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Food Science & Technology, School of Agriculture and Biology, State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2025,5,16]]},"reference":[{"key":"e_1_3_3_2_1","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2013.1714"},{"key":"e_1_3_3_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.12.2607"},{"key":"e_1_3_3_4_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00270-15"},{"key":"e_1_3_3_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkaa345"},{"key":"e_1_3_3_6_1","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"e_1_3_3_7_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.65.2.232-260.2001"},{"key":"e_1_3_3_8_1","volume-title":"Performance standards for antimicrobial susceptibility testing","author":"CLSI (Clinical and Laboratory Standards Institute)","year":"2019","unstructured":"CLSI (Clinical and Laboratory Standards Institute). 2019. Performance standards for antimicrobial susceptibility testing. Wayne, PA: Clinical and Laboratory Standards Institute."},{"key":"e_1_3_3_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"e_1_3_3_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm009"},{"key":"e_1_3_3_11_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-020-05203-3"},{"key":"e_1_3_3_12_1","unstructured":"EUCAST. The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0 2019."},{"key":"e_1_3_3_13_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1007888"},{"key":"e_1_3_3_14_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2022.27.3.2100071"},{"key":"e_1_3_3_15_1","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2010.0189"},{"key":"e_1_3_3_16_1","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.46.9.2977-2981.2002"},{"key":"e_1_3_3_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dki400"},{"key":"e_1_3_3_18_1","doi-asserted-by":"publisher","DOI":"10.15212\/ZOONOSES-2023-0001"},{"key":"e_1_3_3_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2019.01.046"},{"key":"e_1_3_3_20_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11033-022-07997-8"},{"key":"e_1_3_3_21_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"e_1_3_3_22_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2022.27.15.2200314"},{"key":"e_1_3_3_23_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.06094-11"},{"key":"e_1_3_3_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"e_1_3_3_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2018.10.012"},{"key":"e_1_3_3_26_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01523"},{"key":"e_1_3_3_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.eng.2022.05.006"},{"key":"e_1_3_3_28_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11274-009-0004-8"},{"key":"e_1_3_3_29_1","unstructured":"O\u2019NeillJ Review on Antimicrobial Resistance Antimicrobial Resistance: Tackling a crisis for the health and wealth of nations. London: Review on Antimicrobial Resistance. 2014. Available from https:\/\/amr-review.org\/sites\/default\/files\/AMR%20Review%20Paper%20-%20Tackling%20a%20crisis%20for%20the%20health%20and%20wealth%20of%20nations_1.pdf"},{"key":"e_1_3_3_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1226"},{"key":"e_1_3_3_31_1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00088-17"},{"key":"e_1_3_3_32_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsle.2005.02.034"},{"key":"e_1_3_3_33_1","doi-asserted-by":"publisher","DOI":"10.3390\/foods11192966"},{"key":"e_1_3_3_34_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1608858113"},{"key":"e_1_3_3_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodcont.2020.107810"},{"key":"e_1_3_3_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_3_37_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(20)30925-9"},{"key":"e_1_3_3_38_1","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00334-19"},{"key":"e_1_3_3_39_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963"},{"key":"e_1_3_3_40_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00510"},{"key":"e_1_3_3_41_1","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2018.2557"},{"key":"e_1_3_3_42_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2501.180835"},{"key":"e_1_3_3_43_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.fbio.2024.105248"},{"key":"e_1_3_3_44_1","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00262-24"}],"container-title":["Foodborne Pathogens and Disease"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1089\/fpd.2024.0172","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/fpd.2024.0172","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/fpd.2024.0172","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T11:19:12Z","timestamp":1781090352000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1089\/fpd.2024.0172"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,16]]},"references-count":43,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,7,1]]}},"alternative-id":["10.1089\/fpd.2024.0172"],"URL":"https:\/\/doi.org\/10.1089\/fpd.2024.0172","relation":{},"ISSN":["1535-3141","1556-7125"],"issn-type":[{"value":"1535-3141","type":"print"},{"value":"1556-7125","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,16]]}}}