{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T06:10:54Z","timestamp":1790143854439,"version":"4.0.1"},"reference-count":52,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"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":"\n Introduction<\/jats:title>\n \n Aeromonas<\/jats:italic>\n spp. are increasingly recognized opportunistic pathogens of humans, yet integrated genomic and phenotypic data from clinical, extra-intestinal isolates remain limited. We characterized 74 non-duplicate\n Aeromonas<\/jats:italic>\n isolates recovered from extra-intestinal clinical specimens at a tertiary hospital in Ningbo, China, between 2020 and 2025, combining whole-genome sequencing (WGS)-based taxonomy, antimicrobial susceptibility testing, and resistome and putative virulence factor (VF) prediction.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n Species were identified by average nucleotide identity (ANI) analysis and sequence types (STs) by multilocus sequence typing (MLST). Susceptibility to 11 agents was interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guideline M45. Resistance genes were predicted against the Comprehensive Antibiotic Resistance Database (CARD) and VFs against the Virulence Factors of Pathogenic Bacteria database (VFDB); genotype\u2013phenotype concordance was quantified with Cohen\u2019s \u03ba, and VF profiles were analyzed by principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA).<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Six species were identified, dominated by\n Aeromonas caviae<\/jats:italic>\n (32.4%),\n Aeromonas veronii<\/jats:italic>\n (25.7%) and\n Aeromonas dhakensis<\/jats:italic>\n (24.3%). Bile was the leading source of isolation (51.4%), and species were significantly associated with isolation site (Fisher\u2019s exact test,\n p<\/jats:italic>\n \u202f&lt;\u202f0.001). The population was genetically diverse (71 STs, 39 novel). Resistance was highest to piperacillin\/tazobactam (29.7%), whereas only one isolate was resistant to amikacin. Eighty-five resistance genes were detected, with a ubiquitous intrinsic \u03b2-lactamase background (\n OXA-12-like<\/jats:italic>\n ,\n cphA\/imiH<\/jats:italic>\n and\n MOX-type<\/jats:italic>\n genes in 63.5, 58.1 and 41.9% of isolates, respectively) and the acquired carbapenemase gene\n \n bla\n NDM-1<\/jats:sub>\n <\/jats:italic>\n in three isolates. Genotype\u2013phenotype agreement was substantial for trimethoprim\/sulfamethoxazole (\u03ba\u202f=\u202f0.773\u20130.856) and fluoroquinolones (\n \u03ba<\/jats:italic>\n \u202f=\u202f0.706) but poor for \u03b2-lactams. Fifty-six VFs were detected, comprising a conserved 26-VF core virulome and accessory determinants structured by species (PERMANOVA\n R<\/jats:italic>\n 2<\/jats:sup>\n \u202f=\u202f0.797,\n p<\/jats:italic>\n \u202f=\u202f0.001).\n A. dhakensis<\/jats:italic>\n and\n A. hydrophila<\/jats:italic>\n carried the heaviest VF loads and were enriched for aerolysin, ExoA, MARTX\/RtxA and T6SS, whereas\n A. caviae<\/jats:italic>\n lacked aerolysin and had the sparsest virulome.\n <\/jats:p>\n <\/jats:sec>\n \n Discussion<\/jats:title>\n \n Species identity was the dominant correlate of clinical distribution and virulence potential, supporting genome-based species identification as the basis for risk assessment of clinical\n Aeromonas<\/jats:italic>\n isolates.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1952096","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T05:50:30Z","timestamp":1790142630000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Species distribution, antimicrobial resistance, and putative virulence factor profiles of Aeromonas isolates from extra-intestinal clinical specimens: a whole-genome sequencing study"],"prefix":"10.3389","volume":"17","author":[{"given":"Qifeng","family":"Jiang","sequence":"first","affiliation":[{"name":"Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University","place":["Ningbo, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingbei","family":"Weng","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University","place":["Ningbo, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"7712","DOI":"10.1038\/s41598-023-34887-1","article-title":"Whole spectrum of Aeromonas hydrophila virulence determinants and the identification of novel SNPs using comparative pathogenomics","volume":"13","author":"Abdella","year":"2023","journal-title":"Sci. Rep."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"354","DOI":"10.3390\/antibiotics10040354","article-title":"Taxonomic identification of different species of the genus Aeromonas by whole-genome sequencing and use of their species-specific \u03b2-lactamases as phylogenetic markers","volume":"10","author":"Bertran","year":"2021","journal-title":"Antibiotics"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"117384","DOI":"10.1016\/j.diagmicrobio.2026.117384","article-title":"Epidemiology and antimicrobial resistance patterns of Aeromonas species in Europe, 2020-2024 (AEuROMONAS)","volume":"115","author":"Boattini","year":"2026","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1053\/jinf.1999.0594","article-title":"Aeromonas infection in acute suppurative cholangitis: review of 30 cases","volume":"40","author":"Chan","year":"2000","journal-title":"J. Infect."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/s10096-012-1736-1","article-title":"Biliary tract infections caused by Aeromonas species","volume":"32","author":"Chao","year":"2013","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1401802","DOI":"10.3389\/fmicb.2024.1401802","article-title":"Two colistin resistance-producing Aeromonas strains, isolated from coastal waters in Zhejiang, China: characteristics, multi-drug resistance and pathogenicity","volume":"15","author":"Chen","year":"2024","journal-title":"Front. Microbiol."},{"key":"ref11","doi-asserted-by":"crossref","first-page":"793","DOI":"10.3389\/fmicb.2016.00793","article-title":"Aeromonas dhakensis, an increasingly recognized human pathogen","volume":"7","author":"Chen","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"2625","DOI":"10.1128\/JCM.01025-14","article-title":"Matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry can accurately differentiate Aeromonas dhakensis from A. hydrophila, A. caviae, and A. veronii","volume":"52","author":"Chen","year":"","journal-title":"J. Clin. Microbiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1089\/mdr.2024.0212","article-title":"Comprehensive genomic analysis of antimicrobial resistance in Aeromonas dhakensis","volume":"31","author":"Chen","year":"2025","journal-title":"Microb. Drug Resist."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"O428","DOI":"10.1111\/1469-0691.12456","article-title":"A comparative study of clinical Aeromonas dhakensis and Aeromonas hydrophila isolates in southern Taiwan: A. Dhakensis is more predominant and virulent","volume":"20","author":"Chen","year":"","journal-title":"Clin. Microbiol. Infect."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref16","volume-title":"Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria","year":"2016"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1177\/001316446002000104","article-title":"A coefficient of agreement for nominal scales","volume":"20","author":"Cohen","year":"1960","journal-title":"Educ. Psychol. Meas."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"129","DOI":"10.3390\/microorganisms8010129","article-title":"An update on the genus Aeromonas: taxonomy, epidemiology, and pathogenicity","volume":"8","author":"Fern\u00e1ndez-Bravo","year":"2020","journal-title":"Microorganisms"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"101088","DOI":"10.1016\/j.drup.2024.101088","article-title":"Characterization of NMCR-3, NMCR-4 and NMCR-5, three novel non-mobile colistin resistance determinants: implications for MCR-3, MCR-7, and MCR-5 progenitors, respectively","volume":"75","author":"Guo","year":"2024","journal-title":"Drug Resist. Updat."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1177\/10962964251389150","article-title":"Experience with invasive Aeromonas infections at a rural hospital in the United States of America","volume":"27","author":"Henrichs","year":"2026","journal-title":"Surg. Infect."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1055654","DOI":"10.3389\/fmicb.2022.1055654","article-title":"Genetic characterization and virulence determinants of multidrug-resistant NDM-1-producing Aeromonas caviae","volume":"13","author":"Hu","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1128\/CMR.00039-09","article-title":"The genus Aeromonas: taxonomy, pathogenicity, and infection","volume":"23","author":"Janda","year":"2010","journal-title":"Clin. Microbiol. Rev."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: scalable analysis of bacterial genome variation at the population level","volume":"11","author":"Jolley","year":"2010","journal-title":"BMC Bioinformat."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e11585","DOI":"10.1016\/j.heliyon.2022.e11585","article-title":"Comparison of MALDI-TOF mass spectrometry and rpoB gene sequencing for the identification of clinical isolates of Aeromonas spp","volume":"8","author":"Kitagawa","year":"2022","journal-title":"Heliyon"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1473150","DOI":"10.3389\/fmicb.2025.1473150","article-title":"Whole-genome sequencing-based species classification, multilocus sequence typing, and antibiotic resistance mechanisms of the clinical Aeromonas complex","volume":"16","author":"Lu","year":"2025","journal-title":"Front. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"825389","DOI":"10.3389\/fmicb.2022.825389","article-title":"Emergence of blaNDM-1-carrying Aeromonas caviae K433 isolated from patient with community-acquired pneumonia","volume":"13","author":"Luo","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1131059","DOI":"10.3389\/fcimb.2023.1131059","article-title":"Genomic analysis of chromosomal cointegrated blaNDM-1-carrying ICE and blaRSA-1-carrying IME from clinical multidrug resistant Aeromonas caviae","volume":"13","author":"Luo","year":"2023","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"4986","DOI":"10.1128\/AEM.00708-11","article-title":"Determination of microbial diversity of Aeromonas strains on the basis of multilocus sequence typing, phenotype, and presence of putative virulence genes","volume":"77","author":"Martino","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.jinf.2010.12.003","article-title":"Aeromonas spp. clinical microbiology and disease","volume":"62","author":"Parker","year":"2011","journal-title":"J. Infect."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1111\/j.1574-6976.2009.00175.x","article-title":"Gene cassettes and cassette arrays in mobile resistance integrons","volume":"33","author":"Partridge","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1144","DOI":"10.1093\/cid\/ciae272","article-title":"Clinical presentation, antimicrobial resistance, and treatment outcomes of Aeromonas human infections: a 14-year retrospective study and comparative genomics of 2 isolates from fatal cases","volume":"79","author":"Pineda-Reyes","year":"2024","journal-title":"Clin. Infect. Dis."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"833","DOI":"10.3390\/pathogens11080833","article-title":"Aeromonas dhakensis: clinical isolates with high carbapenem resistance","volume":"11","author":"Puah","year":"2022","journal-title":"Pathogens"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1093\/bioinformatics\/btv681","article-title":"JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison","volume":"32","author":"Richter","year":"2016","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1089\/mdr.1996.2.245","article-title":"The Aeromonas metallo-\u03b2-lactamases: genetics, enzymology, and contribution to drug resistance","volume":"2","author":"Rossolini","year":"1996","journal-title":"Microb. Drug Resist."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"ofad587","DOI":"10.1093\/ofid\/ofad587","article-title":"Clinical features, genome epidemiology, and antimicrobial resistance profiles of Aeromonas spp. causing human infections: a multicenter prospective cohort study","volume":"10","author":"Sakurai","year":"2023","journal-title":"Open Forum Infect. Dis."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref41","author":"Seemann","year":"2015"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"2214","DOI":"10.1038\/s41467-026-68712-w","article-title":"Aeromonas in South Asia: genomic insights into an environmental pathogen and reservoir of antimicrobial resistance","volume":"17","author":"Singh","year":"2026","journal-title":"Nat. Commun."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"256261","DOI":"10.5402\/2012\/256261","article-title":"The main Aeromonas pathogenic factors","volume":"2012","author":"Tom\u00e1s","year":"2012","journal-title":"ISRN Microbiol."},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-026-05573-7","article-title":"Aeromonas dhakensis as an emerging invasive pathogen: a case series highlighting distinct carbapenem resistance and diagnostic challenge","author":"Verma","year":"2026","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1708292","DOI":"10.3389\/fbrio.2025.1708292","article-title":"Genomic and proteomic identification of Aeromonas isolates from diverse sources: comparative performance of WGS and MALDI-TOF MS in species-level resolution","volume":"4","author":"Vieira","year":"2025","journal-title":"Front. Bacteriol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1093\/jac\/40.2.171","article-title":"Distribution and expression of beta-lactamase genes among Aeromonas spp","volume":"40","author":"Walsh","year":"1997","journal-title":"J. Antimicrob. Chemother."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1099\/jmm.0.038323-0","article-title":"Distribution and phenotypic and genotypic detection of a metallo-\u03b2-lactamase, CphA, among bacteraemic Aeromonas isolates","volume":"61","author":"Wu","year":"2012","journal-title":"J. Med. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"100925","DOI":"10.1016\/j.drup.2023.100925","article-title":"Aeromonas spp. from hospital sewage act as a reservoir of genes resistant to last-line antibiotics","volume":"67","author":"Wu","year":"2023","journal-title":"Drug Resist. Updat."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"2835","DOI":"10.2147\/IDR.S360353","article-title":"Detection of NDM-1-positive Aeromonas caviae from bacteremia by using whole-genome sequencing","volume":"15","author":"Xu","year":"2022","journal-title":"Infect. Drug Resist."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"101006","DOI":"10.1016\/j.drup.2023.101006","article-title":"The definition and global epidemiology of nonmobile colistin resistance (NMCR-3) determinants in Aeromonas from 1968 to 2022","volume":"71","author":"Yu","year":"2023","journal-title":"Drug Resist. Updat."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"e00252-19","DOI":"10.1128\/mSystems.00252-19","article-title":"Comprehensive analysis reveals the evolution and pathogenicity of Aeromonas, viewed from both single isolated species and microbial communities","volume":"4","author":"Zhong","year":"2019","journal-title":"mSystems"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s12879-019-3766-0","article-title":"Taxonomy, virulence genes and antimicrobial resistance of Aeromonas isolated from extra-intestinal and intestinal infections","volume":"19","author":"Zhou","year":"2019","journal-title":"BMC Infect. Dis."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1952096\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T05:50:32Z","timestamp":1790142632000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1952096\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,23]]},"references-count":52,"alternative-id":["10.3389\/fmicb.2026.1952096"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1952096","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,23]]},"article-number":"1952096"}}