{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T17:06:22Z","timestamp":1778605582914,"version":"3.51.4"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:00:00Z","timestamp":1760140800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:00:00Z","timestamp":1760140800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Curr Microbiol"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1007\/s00284-025-04548-9","type":"journal-article","created":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:58:59Z","timestamp":1760187539000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genomic and Pan-Genomic Characterization of\u00a0Elizabethkingia meningoseptica\u00a0Reveals Resistance Gene Profiles, Phylogenetic Clusters, and Functional Landscape"],"prefix":"10.1007","volume":"82","author":[{"given":"Zheng","family":"Zhou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenqing","family":"Xiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao","family":"Fang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongqiang","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,10,11]]},"reference":[{"key":"4548_CR1","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01338-22","volume":"10","author":"JN Lin","year":"2022","unstructured":"Lin JN, Lai CH, Lin SY, Lee CC, Lee NY, Liu PY, Yang CH, Huang YH (2022) Effect of intragenomic sequence heterogeneity among multiple 16S rRNA genes on species identification of Elizabethkingia. Microbiol Spectr 10:e0133822. https:\/\/doi.org\/10.1128\/spectrum.01338-22","journal-title":"Microbiol Spectr"},{"key":"4548_CR2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02454-24","volume":"13","author":"S Takei","year":"2025","unstructured":"Takei S, Teramoto K, Sekiguchi Y, Miida T, Kirikae T, Tada T, Tabe Y (2025) Identification of Elizabethkingia species by MALDI-TOF MS proteotyping. Microbiol Spectr 13:e0245424. https:\/\/doi.org\/10.1128\/spectrum.02454-24","journal-title":"Microbiol Spectr"},{"key":"4548_CR3","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1089\/mdr.2022.0179","volume":"29","author":"AG Stewart","year":"2023","unstructured":"Stewart AG, Roberts JA, Forde BM, Bergh H, Kidd TJ, Wright H, Harris PNA (2023) Treatment failure due to adaptive resistance mechanisms in a severe and complicated bloodstream infection due to Elizabethkingia meningoseptica. Microb Drug Resist 29:145\u2013149. https:\/\/doi.org\/10.1089\/mdr.2022.0179","journal-title":"Microb Drug Resist"},{"key":"4548_CR4","doi-asserted-by":"publisher","first-page":"256","DOI":"10.4266\/acc.2020.01158","volume":"36","author":"A Umair","year":"2021","unstructured":"Umair A, Nasir N (2021) Clinical features and outcomes of critically ill patients with Elizabethkingia meningoseptica: an emerging pathogen. Acute Crit Care 36:256\u2013261. https:\/\/doi.org\/10.4266\/acc.2020.01158","journal-title":"Acute Crit Care"},{"key":"4548_CR5","doi-asserted-by":"publisher","first-page":"531","DOI":"10.2147\/idr.S397051","volume":"16","author":"S Ma","year":"2023","unstructured":"Ma S, Gong Y, Luo X, Peng Y, Zhang C, Zhang X, Hu X, Tang P, Yuan Z, Luo G, Li H (2023) Emerging prevalence and clinical features of Elizabethkingia meningoseptica infection in southwest China: a 9-year retrospective study and systematic review. Infect Drug Resist 16:531\u2013543. https:\/\/doi.org\/10.2147\/idr.S397051","journal-title":"Infect Drug Resist"},{"key":"4548_CR6","doi-asserted-by":"publisher","first-page":"2174","DOI":"10.3201\/eid3010.240917","volume":"30","author":"DA Holcomb","year":"2024","unstructured":"Holcomb DA, Riner D, Cowan B, Salah Z, Jennings WC, Mattioli MC, Murphy JL (2024) Chlorine inactivation of Elizabethkingia spp. in water. Emerg Infect Dis 30:2174\u20132177. https:\/\/doi.org\/10.3201\/eid3010.240917","journal-title":"Emerg Infect Dis"},{"key":"4548_CR7","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1093\/jac\/dkae137","volume":"79","author":"PJ Chen","year":"2024","unstructured":"Chen PJ, Tan MC, Huang WC, Hsu SY, Chen TL, Yang CY, Kuo SC (2024) The individual contributions of blaB, blaGOB and blaCME on MICs of \u03b2-lactams in Elizabethkingia anophelis. J Antimicrob Chemother 79:1577\u20131580. https:\/\/doi.org\/10.1093\/jac\/dkae137","journal-title":"J Antimicrob Chemother"},{"key":"4548_CR8","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1097\/inf.0000000000001368","volume":"36","author":"BA Kwambana-Adams","year":"2017","unstructured":"Kwambana-Adams BA, Laxton CS, Foster-Nyarko E, Laxton CS, Weinstock G, Antonio M (2017) Isolation of Methicillin-resistant Staphylococcus aureus and Multidrug-resistant Elizabethkingia meningoseptica from neonates within minutes of birth. Pediatr Infect Dis J 36:123\u2013124. https:\/\/doi.org\/10.1097\/inf.0000000000001368","journal-title":"Pediatr Infect Dis J"},{"key":"4548_CR9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0222648","author":"HC Scholz","year":"2019","unstructured":"Scholz HC, Chen S, Soehnlen M, Blom J, Terrapon N, Henrissat B, Walker ED (2019) Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica\u00a0strains. Plos One. https:\/\/doi.org\/10.1371\/journal.pone.0222648","journal-title":"Plos One"},{"key":"4548_CR10","doi-asserted-by":"publisher","DOI":"10.1186\/s13099-016-0130-4","author":"T Wang","year":"2016","unstructured":"Wang T, Jiang X, Feng C, Li A, Dong H, Wu S, Zheng B (2016) Whole genome sequencing uncovers a novel IND-16 metallo-\u03b2-lactamase from an extensively drug-resistant Chryseobacterium indologenes strain J31. Gut Pathog. https:\/\/doi.org\/10.1186\/s13099-016-0130-4","journal-title":"Gut Pathog"},{"key":"4548_CR11","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.1007\/s10096-017-2942-7","volume":"36","author":"YC Huang","year":"2017","unstructured":"Huang YC, Huang YW, Lin YT, Wang FD, Chan YJ, Yang TC (2017) Risk factors and outcome of levofloxacin-resistant Elizabethkingia meningoseptica bacteraemia in adult patients in Taiwan. Eur J Clin Microbiol Infect Dis 36:1373\u20131380. https:\/\/doi.org\/10.1007\/s10096-017-2942-7","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"4548_CR12","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/j.ijantimicag.2017.05.018","volume":"51","author":"Y-C Huang","year":"2018","unstructured":"Huang Y-C, Lin Y-T, Wang F-D (2018) Comparison of the therapeutic efficacy of fluoroquinolone and non-fluoroquinolone treatment in patients with Elizabethkingia meningoseptica bacteraemia. Int J Antimicrob Agents 51:47\u201351. https:\/\/doi.org\/10.1016\/j.ijantimicag.2017.05.018","journal-title":"Int J Antimicrob Agents"},{"key":"4548_CR13","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00730-20","author":"D Burnard","year":"2020","unstructured":"Burnard D, Gore L, Henderson A, Ranasinghe A, Bergh H, Cottrell K, Sarovich DS, Price EP, Paterson DL, Harris PNA, Dekker JP (2020) Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveal nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines, and trimethoprim-sulfamethoxazole. J Clin Microbiol. https:\/\/doi.org\/10.1128\/jcm.00730-20","journal-title":"J Clin Microbiol"},{"key":"4548_CR14","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-57564-3","author":"F Commans","year":"2024","unstructured":"Commans F, Hayer J, Do BN, Tran TTT, Le TTH, Bui TT, Le HS, Ba\u00f1uls A-L, Bui TS, Nguyen QH (2024) Whole-genome sequence and resistance determinants of four Elizabethkingia anophelis clinical isolates collected in Hanoi, Vietnam. Sci Rep. https:\/\/doi.org\/10.1038\/s41598-024-57564-3","journal-title":"Sci Rep"},{"key":"4548_CR15","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-55795-3","author":"C-Y Liang","year":"2019","unstructured":"Liang C-Y, Yang C-H, Lai C-H, Huang Y-H, Lin J-N (2019) Comparative genomics of 86 whole-genome sequences in the six species of the Elizabethkingia genus reveals intraspecific and interspecific divergence. Sci Rep. https:\/\/doi.org\/10.1038\/s41598-019-55795-3","journal-title":"Sci Rep"},{"key":"4548_CR16","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms7090295","author":"J-N Lin","year":"2019","unstructured":"Lin J-N, Lai C-H, Yang C-H, Huang Y-H (2019) Elizabethkingia infections in humans: from genomics to clinics. Microorganisms. https:\/\/doi.org\/10.3390\/microorganisms7090295","journal-title":"Microorganisms"},{"key":"4548_CR17","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068\u20132069. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153","journal-title":"Bioinformatics"},{"key":"4548_CR18","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00483-19","author":"M Feldgarden","year":"2019","unstructured":"Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W (2019) Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother. https:\/\/doi.org\/10.1128\/aac.00483-19","journal-title":"Antimicrob Agents Chemother"},{"key":"4548_CR19","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1186\/s13059-014-0524-x","volume":"15","author":"TJ Treangen","year":"2014","unstructured":"Treangen TJ, Ondov BD, Koren S, Phillippy AM (2014) The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15:524. https:\/\/doi.org\/10.1186\/s13059-014-0524-x","journal-title":"Genome Biol"},{"key":"4548_CR20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price MN, Dehal PS, Arkin AP (2010) FastTree 2\u2013approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490. https:\/\/doi.org\/10.1371\/journal.pone.0009490","journal-title":"PLoS ONE"},{"key":"4548_CR21","doi-asserted-by":"publisher","first-page":"W242","DOI":"10.1093\/nar\/gkw290","volume":"44","author":"I Letunic","year":"2016","unstructured":"Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242-245. https:\/\/doi.org\/10.1093\/nar\/gkw290","journal-title":"Nucleic Acids Res"},{"key":"4548_CR22","doi-asserted-by":"publisher","first-page":"24373","DOI":"10.1038\/srep24373","volume":"6","author":"NM Chaudhari","year":"2016","unstructured":"Chaudhari NM, Gupta VK, Dutta C (2016) BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 6:24373. https:\/\/doi.org\/10.1038\/srep24373","journal-title":"Sci Rep"},{"key":"4548_CR23","unstructured":"Kolde R (2019) pheatmap: Pretty Heatmaps. R package version 1012 https:\/\/CRAN.R-project.org\/package=pheatmap"},{"key":"4548_CR24","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1186\/s12864-024-10921-y","volume":"25","author":"P Andriyanov","year":"2024","unstructured":"Andriyanov P, Zhurilov P, Menshikova A, Tutrina A, Yashin I, Kashina D (2024) Large-scale genomic analysis of Elizabethkingia anophelis. BMC Genomics 25:1015. https:\/\/doi.org\/10.1186\/s12864-024-10921-y","journal-title":"BMC Genomics"}],"container-title":["Current Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00284-025-04548-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00284-025-04548-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00284-025-04548-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T16:04:07Z","timestamp":1763222647000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00284-025-04548-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,11]]},"references-count":24,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["4548"],"URL":"https:\/\/doi.org\/10.1007\/s00284-025-04548-9","relation":{},"ISSN":["0343-8651","1432-0991"],"issn-type":[{"value":"0343-8651","type":"print"},{"value":"1432-0991","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,11]]},"assertion":[{"value":"5 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}},{"value":"This study was approved by the ethics committee of the Children\u2019s Hospital, Zhejiang University School of Medicine, China. (2025-IRB-0264-P-01).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical Approval"}}],"article-number":"546"}}