{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T12:08:42Z","timestamp":1780142922629,"version":"3.54.0"},"reference-count":37,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2019,4,20]],"date-time":"2019-04-20T00:00:00Z","timestamp":1555718400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["MOST 105-2314-B-214-008"],"award-info":[{"award-number":["MOST 105-2314-B-214-008"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["MOST 106-2314-B-214-009-MY2"],"award-info":[{"award-number":["MOST 106-2314-B-214-009-MY2"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004738","name":"E-Da Hospital","doi-asserted-by":"publisher","award":["EDAHP105018"],"award-info":[{"award-number":["EDAHP105018"]}],"id":[{"id":"10.13039\/501100004738","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Bacteria belonging to the genus Chryseobacterium are ubiquitously distributed in natural environments, plants, and animals. Except C. indologenes and C. gleum, other Chryseobacterium species rarely cause human diseases. This study reported the whole-genome features, comparative genomic analysis, and antimicrobial susceptibility patterns of C. arthrosphaerae ED882-96 isolated in Taiwan. Strain ED882-96 was collected from the blood of a patient who had alcoholic liver cirrhosis and was an intravenous drug abuser. This isolate was initially identified as C. indologenes by using matrix-assisted laser desorption ionization\u2013time of flight mass spectrometry. The analysis of 16S ribosomal RNA gene sequence revealed that ED882-96 shared 100% sequence identity with C. arthrosphaerae type strain CC-VM-7T. The results of whole-genome sequencing of ED882-96 showed two chromosome contigs and one plasmid. The total lengths of the draft genomes of chromosome and plasmid were 4,249,864 bp and 435,667 bp, respectively. The findings of both in silico DNA\u2013DNA hybridization and average nucleotide identity analyses clearly demonstrated that strain ED882-96 was a species of C. arthrosphaerae. A total of 83 potential virulence factor homologs were predicted in the whole-genome sequencing of strain ED882-96. This isolate was resistant to all tested antibiotics, including \u03b2-lactams, \u03b2-lactam\/\u03b2-lactamase inhibitor combinations, aminoglycosides, fluoroquinolones, tetracycline, glycylcycline, and trimethoprim-sulfamethoxazole. Only one antibiotic resistance gene was recognized in the plasmid. By contrast, many antibiotic resistance genes were identified in the chromosome. The findings of this study suggest that strain ED882-96 is a highly virulent and multidrug-resistant pathogen. Knowledge regarding genomic characteristics and antimicrobial susceptibility patterns provides valuable insights into this uncommon species.<\/jats:p>","DOI":"10.3390\/genes10040309","type":"journal-article","created":{"date-parts":[[2019,4,22]],"date-time":"2019-04-22T11:02:53Z","timestamp":1555930973000},"page":"309","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Genomic Features, Comparative Genomic Analysis, and Antimicrobial Susceptibility Patterns of Chryseobacterium arthrosphaerae Strain ED882-96 Isolated in Taiwan"],"prefix":"10.3390","volume":"10","author":[{"given":"Chih-Yu","family":"Liang","sequence":"first","affiliation":[{"name":"Department of Information Engineering, I-Shou University, Kaohsiung 824, Taiwan"},{"name":"Department of Emergency Medicine, E-Da Cancer Hospital, Kaohsiung 824, Taiwan"},{"name":"Department of Medical Imaging and Radiological Science, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih-Hui","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Biological Science and Technology, Meiho University, Pingtung 912, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chung-Hsu","family":"Lai","sequence":"additional","affiliation":[{"name":"School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan"},{"name":"Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, Kaohsiung 824, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Han","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan"},{"name":"Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, Kaohsiung 824, Taiwan"},{"name":"Department of Critical Care Medicine, E-Da Hospital, Kaohsiung 824, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4417-5350","authenticated-orcid":false,"given":"Jiun-Nong","family":"Lin","sequence":"additional","affiliation":[{"name":"School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan"},{"name":"Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, Kaohsiung 824, Taiwan"},{"name":"Department of Critical Care Medicine, E-Da Hospital, Kaohsiung 824, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,4,20]]},"reference":[{"key":"ref_1","first-page":"827","article-title":"New perspectives in the classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev","volume":"44","author":"Vandamme","year":"1994","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1099\/ijs.0.016840-0","article-title":"Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems","volume":"60","author":"Arun","year":"2010","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1099\/ijsem.0.001670","article-title":"Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae","volume":"67","author":"Jeong","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_4","unstructured":"(2017, November 30). Chryseobacterium. Available online: http:\/\/www.bacterio.net\/chryseobacterium.html."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"13824","DOI":"10.1038\/s41598-017-14244-9","article-title":"Comparison of four automated microbiology systems with 16S rRNA gene sequencing for identification of Chryseobacterium and Elizabethkingia species","volume":"7","author":"Lin","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e00712-18","DOI":"10.1128\/JCM.00712-18","article-title":"Comparison of the Vitek MS and Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for identification of Chryseobacterium isolated from clinical specimens and report of uncommon Chryseobacterium infections in humans","volume":"56","author":"Lin","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Letunic, I., and Bork, P. (2019). Interactive Tree Of Life (iTOL) v4: Recent updates and new developments. Nucleic Acids Res.","DOI":"10.1093\/nar\/gkz239"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/978-1-4939-3167-5_13","article-title":"Short read alignment using SOAP2","volume":"1374","author":"Hurgobin","year":"2016","journal-title":"Methods Mol. Biol. Clifton NJ"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Non-hybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","author":"Chin","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1101\/gr.132480.111","article-title":"SOAPindel: Efficient identification of indels from short paired reads","volume":"23","author":"Li","year":"2013","journal-title":"Genome Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","article-title":"OrthoANI: An improved algorithm and software for calculating average nucleotide identity","volume":"66","author":"Lee","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and G\u00f6ker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-60"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., and Kubal, M. (2008). The RAST Server: Rapid annotations using subsystems technology. BMC Genom., 9.","DOI":"10.1186\/1471-2164-9-75"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gku1223","article-title":"Expanded microbial genome coverage and improved protein family annotation in the COG database","volume":"43","author":"Galperin","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"D286","DOI":"10.1093\/nar\/gkv1248","article-title":"eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences","volume":"44","author":"Szklarczyk","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Gene Ontology Consortium (2008). The gene ontology project in 2008. Nucleic Acids Res., 36, D440\u2013D444.","DOI":"10.1093\/nar\/gkm883"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gky962","article-title":"New approach for understanding genome variations in KEGG","volume":"47","author":"Kanehisa","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: Hierarchical and refined dataset for big data analysis\u201410 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"W181","DOI":"10.1093\/nar\/gkn179","article-title":"The CGView Server: A comparative genomics tool for circular genomes","volume":"36","author":"Grant","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_25","unstructured":"Clinical and Laboratory Standards Institute (2017). Performance Standards for Antimicrobial Susceptibility Testing, CLSI."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1093\/jac\/dkn311","article-title":"Tigecycline for the treatment of multidrug-resistant Enterobacteriaceae: A systematic review of the evidence from microbiological and clinical studies","volume":"62","author":"Kelesidis","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_27","first-page":"AAC-02256","article-title":"Differences in clinical manifestations, antimicrobial susceptibility patterns and mutations of fluoroquinolone target genes between Chryseobacterium gleum and Chryseobacterium indologenes","volume":"18","author":"Lin","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"D443","DOI":"10.1093\/nar\/gkn656","article-title":"ARDB\u2014antibiotic resistance genes database","volume":"37","author":"Liu","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"W78","DOI":"10.1093\/nar\/gkv487","article-title":"OrthoVenn: A web server for genome wide comparison and annotation of orthologous clusters across multiple species","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"24373","DOI":"10.1038\/srep24373","article-title":"BPGA\u2014An ultra-fast pan-genome analysis pipeline","volume":"6","author":"Chaudhari","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"240","DOI":"10.3389\/fmicb.2015.00240","article-title":"Unravelling the genome of long chain N-acylhomoserine lactone-producing Acinetobacter sp. strain GG2 and identification of its quorum sensing synthase gene","volume":"6","author":"How","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., and Nikolskaya, A.N. (2003). The COG database: An updated version includes eukaryotes. BMC Bioinform., 4.","DOI":"10.1186\/1471-2105-4-41"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1007\/BF02447918","article-title":"Increasing incidence of nosocomial Chryseobacterium indologenes infections in Taiwan","volume":"16","author":"Hsueh","year":"1997","journal-title":"Eur. J. Clin. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1128\/JCM.42.1.445-448.2004","article-title":"Antimicrobial susceptibility and epidemiology of a worldwide collection of Chryseobacterium spp: Report from the SENTRY antimicrobial surveillance program (1997\u20132001)","volume":"42","author":"Kirby","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/j.jmii.2012.08.007","article-title":"Clinical and epidemiological features of Chryseobacterium indologenes infections: Analysis of 215 cases","volume":"46","author":"Chen","year":"2013","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"S120","DOI":"10.1086\/428052","article-title":"Mechanisms of resistance to quinolones","volume":"41","author":"Jacoby","year":"2005","journal-title":"Clin. Infect. Dis."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/10\/4\/309\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:46:59Z","timestamp":1760186819000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/10\/4\/309"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4,20]]},"references-count":37,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,4]]}},"alternative-id":["genes10040309"],"URL":"https:\/\/doi.org\/10.3390\/genes10040309","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,20]]}}}