{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T20:56:54Z","timestamp":1784581014854,"version":"3.55.0"},"reference-count":35,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T00:00:00Z","timestamp":1768521600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Elizabethkingia anophelis<\/jats:italic>\n                      (\n                      <jats:italic>E. anophelis<\/jats:italic>\n                      ) has emerged as a multidrug-resistant pathogen with limited therapeutic options. This study aimed to characterize antimicrobial resistance mechanisms and virulence determinants in six clinical isolates from Shanghai, China, to inform evidence-based treatment strategies.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Six strains were isolated from hospitalized patients (five community-acquired, one healthcare-associated) between September\u2013November 2023. Antimicrobial susceptibility testing followed CLSI M100 guidelines. Whole-genome sequencing employed hybrid Illumina\/PacBio approaches. Phylogenetic relationships were determined through 16S rRNA gene sequence analysis using the Neighbor-Joining method. Antimicrobial resistance genes and virulence factors were annotated using the Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factor Database (VFDB), with relative gene abundance quantified via a TPM-like (transcripts per million-like) method.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      All isolates exhibited resistance to\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactams, fluoroquinolones, carbapenems, and aminoglycosides, but retained minocycline susceptibility (MIC \u22641\u202f\u03bcg\/mL). Phylogenetic analysis revealed two distinct clusters: Cluster I (EA1, EA3, EA6) aligning with East\/Southeast Asian isolates, and Cluster II (EA2, EA4, EA5) showing diverse geographic affinities. Five core resistance mechanisms were identified: antibiotic efflux, antibiotic target alteration, antibiotic inactivation, antibiotic target replacement, and reduced permeability to antibiotics. Virulence determinants included bacterial movement, exotoxin production, biofilm formation, immune regulation, and effector delivery systems. Strain EA5 exhibited unique signatures, including absence of\n                      <jats:italic>cesH<\/jats:italic>\n                      , unique\n                      <jats:italic>sigE<\/jats:italic>\n                      expression, elevated\n                      <jats:italic>AAC(6\u2032)-Iad\/aadS<\/jats:italic>\n                      and reduced\n                      <jats:italic>qacL\/OmpA<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      This study reveals phylogenetically divergent\n                      <jats:italic>E. anophelis<\/jats:italic>\n                      lineages in Shanghai with extensive multidrug resistance but preserved minocycline susceptibility. Findings support minocycline-based therapy, enhanced diagnostics, and regional surveillance networks for strain monitoring.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2025.1751256","type":"journal-article","created":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T06:32:37Z","timestamp":1768545157000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Genomic profiling of Elizabethkingia anophelis clinical isolates from a Shanghai hospital: phylogenetic divergence coexists with heterogeneous antibiotic resistance and virulence determinants"],"prefix":"10.3389","volume":"16","author":[{"given":"Jiasheng","family":"Xiong","sequence":"first","affiliation":[{"name":"Department of Hospital Infection Control, Tongji Hospital, School of Medicine, Tongji University","place":["Shanghai, China"]},{"name":"Shanghai Municipal Center for Disease Control and Prevention","place":["Shanghai, China"]},{"name":"Department of Epidemiology, School of Public Health, Fudan University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiantian","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Hospital Infection Control, Tongji Hospital, School of Medicine, Tongji University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingjing","family":"Hu","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Infectious Disease and Biosecurity, Fudan University","place":["Shanghai, China"]},{"name":"Innostellar Biotherapeutics Co. Ltd","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yitian","family":"Wu","sequence":"additional","affiliation":[{"name":"Shanghai Municipal Center for Disease Control and Prevention","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyan","family":"Huang","sequence":"additional","affiliation":[{"name":"Shanghai Municipal Center for Disease Control and Prevention","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dianyu","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Tongji Hospital, School of Medicine, Tongji University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Hou","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Tongji Hospital, School of Medicine, Tongji University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Hospital Infection Control, Tongji Hospital, School of Medicine, Tongji University","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1039\/c7np00009j","article-title":"Symbiosis-inspired approaches to antibiotic discovery","volume":"34","author":"Adnani","year":"2017","journal-title":"Nat. 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Infect."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e0026222","DOI":"10.1128\/spectrum.00262-22","article-title":"Proteomic network of antibiotic-induced outer membrane vesicles released by extensively drug-resistant Elizabethkingia anophelis","volume":"10","author":"Chiang","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1038\/s41579-022-00820-y","article-title":"Molecular mechanisms of antibiotic resistance revisited","volume":"21","author":"Darby","year":"2023","journal-title":"Nat. Rev. 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Drug Resist."},{"key":"ref32","year":"2024"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"e0178024","DOI":"10.1128\/spectrum.01780-24","article-title":"Comparative genomic analysis of ten Elizabethkingia anophelis isolated from clinical patients in China","volume":"13","author":"Wu","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/s12941-024-00691-6","article-title":"Clinical manifestations, antimicrobial resistance and genomic feature analysis of multidrug-resistant Elizabethkingia strains","volume":"23","author":"Wu","year":"2024","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"882","DOI":"10.3390\/microorganisms10050882","article-title":"Epidemiology and characteristics of Elizabethkingia spp. infections in Southeast Asia","volume":"10","author":"Zajmi","year":"2022","journal-title":"Microorganisms"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1751256\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T06:32:39Z","timestamp":1768545159000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1751256\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,16]]},"references-count":35,"alternative-id":["10.3389\/fmicb.2025.1751256"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1751256","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,16]]},"article-number":"1751256"}}