{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T05:01:16Z","timestamp":1780290076924,"version":"3.54.0"},"reference-count":41,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"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. Cell. Infect. Microbiol."],"abstract":"\n Introduction<\/jats:title>\n \n Acinetobacter baumannii<\/jats:italic>\n is a major healthcare-associated opportunistic pathogen with exceptional environmental persistence. However, its ecological distribution and potential transmission pathways in veterinary hospital environments remain poorly characterized.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Samples were collected from multiple departments and surface types across eight veterinary hospitals in Beijing from September to December 2020.\u00a0A\n . baumannii<\/jats:italic>\n isolates were recovered and subjected to antimicrobial susceptibility testing and whole-genome sequencing. Environmental risk factors were assessed using generalized linear mixed-effects models (GLMMs) with a binomial distribution and logit link, with hospital included as a random intercept and sampling site and department as fixed effects. Genomic analyses included profiling of antimicrobial resistance genes, virulence factors, and biocide\/metal resistance genes, as well as Bayesian population structure and cgMLST to infer potential transmission patterns.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Among 1,136 environmental samples collected across eight veterinary hospitals in Beijing, 64\u00a0A\n . baumannii<\/jats:italic>\n isolates were recovered, with an overall isolation rate of 5.63% and hospital-level rates ranging from 0.54% to 15.33%. The X-ray room showed the highest observed department-level isolation rate (16.36%, 9\/55) and was significantly associated with increased\n A. baumannii<\/jats:italic>\n recovery compared with the clinic room reference category in the multivariable GLMM. Floors (12.40%, 31\/250), sinks (9.80%, 10\/102), and staff uniforms (9.73%, 11\/113) showed the highest surface-level isolation rates and were significantly associated with increased recovery compared with the door reference category (all\n P<\/jats:italic>\n \u00a0&lt;\u00a00.05). Most isolates were susceptible to the tested antimicrobial agents, while ceftriaxone showed the highest non-susceptibility rate (43.8% intermediate, 4.7% resistant). Two isolates were multidrug-resistant, including one carrying a 7,561-bp resistance region with a class 1 integron cassette array (\n aadA1\u2013cmlA\u2013aadA2\u2013bla<\/jats:italic>\n PSE-1<\/jats:sub>\n ). Whole-genome analysis revealed a conserved baseline resistome, core virulence determinants related to adhesion, biofilm formation, nutrient acquisition, regulation, and secretion systems, as well as broadly distributed metal tolerance and oxidative-stress defense genes. In contrast, accessory ARGs, VFs, and disinfectant- or metal-associated resistance determinants showed lineage- or isolate-specific variability. Bayesian population structure analysis resolved nine BAPS lineages with distinct spatial distribution patterns, including hospital-restricted, locally shared, and spatially dispersed lineages. cgMLST further identified hospital-specific near-clonal subclusters within these lineages, defined by \u22648 allelic differences and 0\u20133 core-genome SNPs. These subclusters were detected across multiple departments and environmental surfaces within the same hospital, indicating broad within-hospital environmental distribution of highly related isolates.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n \n This study demonstrates heterogeneous environmental contamination of\n A. baumannii<\/jats:italic>\n in veterinary hospitals, with higher recovery from X-ray rooms, wet sites, staff uniforms, floors, and other shared or frequently contacted surfaces. Although most isolates were not multidrug-resistant, they carried conserved resistance-, virulence-, and environmental survival-associated genomic determinants, suggesting that their ecological risk may be related to surface survival, stress tolerance, and redistribution within hospital environments rather than widespread MDR clone dissemination. Population structure and cgMLST analyses revealed both inter-hospital lineage sharing and hospital-specific near-clonal subclusters, indicating the presence of highly related\n A. baumannii<\/jats:italic>\n isolates across multiple departments and environmental surfaces within individual hospitals. These findings highlight the need to incorporate environmental opportunistic bacteria such as\n A. baumannii<\/jats:italic>\n into veterinary hospital surveillance and infection prevention and control planning, particularly in high-use functional areas, wet zones, staff uniforms, shared equipment, and high-touch surfaces.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1824342","type":"journal-article","created":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T04:19:21Z","timestamp":1780287561000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Multicenter genomic analysis reveals environmental hotspots and near-clonal subclusters of Acinetobacter baumannii in veterinary hospitals in Beijing, China"],"prefix":"10.3389","volume":"16","author":[{"given":"Yu","family":"Song","sequence":"first","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyu","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]},{"name":"Veterinary Teaching Hospital, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rina","family":"Bai","sequence":"additional","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]},{"name":"Veterinary Teaching Hospital, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"An","sequence":"additional","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gege","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Veterinary Public Health Safety, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]},{"name":"Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Veterinary Public Health Safety, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]},{"name":"Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaofei","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]},{"name":"Veterinary Teaching Hospital, China Agricultural University","place":["Beijing, China"]},{"name":"National Key Laboratory of Veterinary Public Health Safety, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]},{"name":"Key Laboratory of Animal Antimicrobial Resistance Surveillance, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,1]]},"reference":[{"key":"B1","article-title":"Infection prevention and control best practices for small animal veterinary clinics","author":"Anderson","year":"2008"},{"key":"B2","doi-asserted-by":"publisher","first-page":"3740","DOI":"10.1128\/JB.00389-11","article-title":"Acinetobacter baumannii RecA protein in repair of DNA damage, antimicrobial resistance, general stress response, and virulence","volume":"193","author":"Aranda","year":"2011","journal-title":"J. Bacteriol."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1429443","article-title":"Environmental contamination with carbapenem resistant Acinetobacter baumannii in healthcare settings in Fiji: a potential source of infection","volume":"14","author":"Baleivanualala","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B4","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":"B5","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00478-15","article-title":"Reinforcing lipid A acylation on the cell surface of Acinetobacter baumannii promotes cationic antimicrobial peptide resistance and desiccation survival","volume":"6","author":"Boll","year":"2015","journal-title":"mBio"},{"key":"B6","doi-asserted-by":"publisher","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1224","DOI":"10.1093\/molbev\/mst028","article-title":"Hierarchical and spatially explicit clustering of DNA sequences with BAPS software","volume":"30","author":"Cheng","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B8","volume-title":"Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically (M07)","year":"2018"},{"key":"B9","volume-title":"Performance standards for antimicrobial susceptibility testing","year":"2020"},{"key":"B10","volume-title":"Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals","year":"2021"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanwpc.2023.100780","article-title":"Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit","volume":"37","author":"Doughty","year":"2023","journal-title":"Lancet Reg. Health West. Pac."},{"key":"B12","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.jhin.2011.08.013","article-title":"Effect of biofilm formation on the survival of Acinetobacter baumannii on dry surfaces","volume":"80","author":"Espinal","year":"2012","journal-title":"J. Hosp. Infect."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"B14","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1021\/pr400603f","article-title":"Molecular mechanisms involved in the response to desiccation stress and persistence in Acinetobacter baumannii","volume":"13","author":"Gayoso","year":"2014","journal-title":"J. Proteome Res."},{"key":"B15","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1038\/nrmicro.2017.148","article-title":"Uncovering the mechanisms of Acinetobacter baumannii virulence","volume":"16","author":"Harding","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"20254","DOI":"10.1073\/pnas.1317052110","article-title":"Transcriptomic and biochemical analyses identify a family of chlorhexidine efflux proteins","volume":"110","author":"Hassan","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0179228","article-title":"Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii","volume":"12","author":"Higgins","year":"2017","journal-title":"PloS One"},{"key":"B18","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1016\/j.jgar.2021.05.003","article-title":"First report of NDM-1 in an Acinetobacter baumannii strain from a pet animal in Europe","volume":"26","author":"Jacobmeyer","year":"2021","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01475-16","article-title":"Acinetobacter baumannii coordinates urea metabolism with metal import to resist host-mediated metal limitation","volume":"7","author":"Juttukonda","year":"2016","journal-title":"mBio"},{"key":"B20","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1111\/mmi.12300","article-title":"A common pathway for O-linked protein-glycosylation and synthesis of capsule in Acinetobacter baumannii","volume":"89","author":"Lees-Miller","year":"2013","journal-title":"Mol. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"9483","DOI":"10.1038\/s41467-024-53817-x","article-title":"Longitudinal genomics reveals carbapenem-resistant Acinetobacter baumannii population changes with emergence of highly resistant ST164 clone","volume":"15","author":"Liu","year":"2024","journal-title":"Nat. Commun."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-014-0052-7","article-title":"The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites","volume":"3","author":"Misic","year":"2015","journal-title":"Microbiome"},{"key":"B23","doi-asserted-by":"publisher","first-page":"123","DOI":"10.3390\/pathogens11020123","article-title":"Genomic investigation of two Acinetobacter baumannii outbreaks in a veterinary intensive care unit in The Netherlands","volume":"11","author":"Naing","year":"2022","journal-title":"Pathogens"},{"key":"B24","doi-asserted-by":"publisher","first-page":"127","DOI":"10.3390\/pathogens10020127","article-title":"Acinetobacter baumannii: its clinical significance in human and veterinary medicine","volume":"10","author":"Nocera","year":"2021","journal-title":"Pathogens"},{"key":"B25","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1128\/JB.02176-12","article-title":"Antibiotic resistance acquired through a DNA damage-inducible response in Acinetobacter baumannii","volume":"195","author":"Norton","year":"2013","journal-title":"J. Bacteriol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J."},{"key":"B27","doi-asserted-by":"publisher","first-page":"D737","DOI":"10.1093\/nar\/gkt1252","article-title":"BacMet: antibacterial biocide and metal resistance genes database","volume":"42","author":"Pal","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B28","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1093\/jac\/dkw481","article-title":"Public health risk of antimicrobial resistance transfer from companion animals","volume":"72","author":"Pomba","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"B29","doi-asserted-by":"publisher","first-page":"3993","DOI":"10.1128\/IAI.00366-10","article-title":"The K1 capsular polysaccharide of Acinetobacter baumannii strain 307\u20130294 is a major virulence factor","volume":"78","author":"Russo","year":"2010","journal-title":"Infect. Immun."},{"key":"B30","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1016\/j.cmi.2017.12.016","article-title":"Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches","volume":"24","author":"Schurch","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"B31","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":"B32","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000166","article-title":"chewBBACA: a complete suite for gene-by-gene schema creation and strain identification","volume":"4","author":"Silva","year":"2018","journal-title":"Microb. Genom."},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"Todd","year":"2014","journal-title":"Genome Biol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"93","DOI":"10.12688\/wellcomeopenres.14694.1","article-title":"RhierBAPS: an R implementation of the population clustering algorithm hierBAPS","volume":"3","author":"Tonkin-Hill","year":"2018","journal-title":"Wellcome Open Res."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1016\/j.ajic.2015.06.016","article-title":"Outbreak of drug-resistant Acinetobacter baumannii ST219 caused by oral care using tap water from contaminated hand hygiene sinks as a reservoir","volume":"43","author":"Umezawa","year":"2015","journal-title":"Am. J. Infect. Control"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0035197","article-title":"Sharing more than friendship--nasal colonization with coagulase-positive staphylococci (CPS) and co-habitation aspects of dogs and their owners","volume":"7","author":"Walther","year":"2012","journal-title":"PloS One"},{"key":"B37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s11259-018-9742-0","article-title":"Acinetobacter baumannii - a neglected pathogen in veterinary and environmental health in Germany","volume":"43","author":"Wareth","year":"2019","journal-title":"Vet. Res. Commun."},{"key":"B38","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1016\/j.tim.2017.01.005","article-title":"The secrets of Acinetobacter secretion","volume":"25","author":"Weber","year":"2017","journal-title":"Trends Microbiol."},{"key":"B39","volume-title":"Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics","year":"2017"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PloS Comput. Biol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.jhin.2015.09.020","article-title":"Characterization of NDM-1- and OXA-23-producing Acinetobacter baumannii isolates from inanimate surfaces in a hospital environment in Algeria","volume":"92","author":"Zenati","year":"2016","journal-title":"J. Hosp. Infect."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1824342\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T04:19:23Z","timestamp":1780287563000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1824342\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,1]]},"references-count":41,"alternative-id":["10.3389\/fcimb.2026.1824342"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2026.1824342","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,1]]},"article-number":"1824342"}}