{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T14:54:56Z","timestamp":1770821696745,"version":"3.50.1"},"reference-count":101,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T00:00:00Z","timestamp":1753920000000},"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:p>Interconnected reservoirs contribute to the global spread of antimicrobial resistance (AMR), including carbapenem- and colistin-resistant <jats:italic>Enterobacterales<\/jats:italic>, highlighting the need for a One Health approach. We assessed the genomic epidemiology, diversity and AMR mechanisms of <jats:italic>Enterobacter<\/jats:italic> spp. across interconnected human, animal, plant, and environmental reservoirs in a Portuguese Open Air Laboratory. Over a one year monitoring period, samples from 12 different compartments were collected and processed using selective media to isolate <jats:italic>Enterobacter<\/jats:italic> spp., which were subjected to antibiotic susceptibility testing, whole-genome sequencing and subsequent analyses to identify AMR determinants, characterize plasmids and phylogenetic relationships. We established a collection of 61 <jats:italic>Enterobacter<\/jats:italic> isolates spanning nine species and 32 sequence types, including 16 novel ones, across nine compartments (river water, wastewater, soil, manure, feed, air, farmers, pigs, wild animals), reflecting the diversity and ubiquity of <jats:italic>Enterobacter<\/jats:italic> species. Core-genome analysis revealed eight genetic clusters, suggesting clonal transmission across compartments. In total, 29 antibiotic resistance genes were detected across all isolates. Notably, this is the first documentation of <jats:italic>bla<\/jats:italic><jats:sub>FRI<\/jats:sub>-harbouring <jats:italic>Enterobacterales<\/jats:italic> in European environmental settings and the first to describe <jats:italic>bla<\/jats:italic><jats:sub>FRI<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>IMI<\/jats:sub> and <jats:italic>mcr-10<\/jats:italic> genes in Portugal. <jats:italic>bla<\/jats:italic><jats:sub>FRI-8<\/jats:sub> was detected in all <jats:italic>E. vonholyi<\/jats:italic> isolates (<jats:italic>n<\/jats:italic> = 17), located on four different IncFII(Yp) plasmids, and <jats:italic>bla<\/jats:italic><jats:sub>IMI-6<\/jats:sub> in an <jats:italic>E. asburiae<\/jats:italic> isolate, flanked by IS3 family transposases. <jats:italic>E. vonholyi<\/jats:italic> and the <jats:italic>bla<\/jats:italic><jats:sub>IMI-6<\/jats:sub>-harbouring <jats:italic>E. asburiae<\/jats:italic> isolate were resistant to carbapenems. A <jats:italic>mcr-10.1<\/jats:italic> gene was identified in an <jats:italic>E. roggenkampii<\/jats:italic> isolate on an IncFII(pECLA) plasmid. These plasmids exhibited high sequence similarity with global counterparts, indicating potential for horizontal gene transfer. Other antimicrobial resistance genes included <jats:italic>qnrE1<\/jats:italic>, <jats:italic>sul1<\/jats:italic>, and <jats:italic>aadA2<\/jats:italic>. Our findings underscore the importance of <jats:italic>Enterobacter<\/jats:italic> as vectors for AMR and the critical role of environmental compartments in its dissemination, reinforcing the importance of adopting a One Health approach to fully understand AMR dynamics.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1593872","type":"journal-article","created":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T05:39:16Z","timestamp":1753940356000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Genomic epidemiology and resistome dynamics of Enterobacter species in a Portuguese Open Air Laboratory: the emergence of the FRI-8 carbapenemase"],"prefix":"10.3389","volume":"16","author":[{"given":"Pedro","family":"Teixeira","sequence":"first","affiliation":[]},{"given":"Miguel","family":"Ramos","sequence":"additional","affiliation":[]},{"given":"Rani","family":"Rivi\u00e8re","sequence":"additional","affiliation":[]},{"given":"M\u00f3nica","family":"Azevedo","sequence":"additional","affiliation":[]},{"given":"M\u00e1rio","family":"Ferreira","sequence":"additional","affiliation":[]},{"given":"Maria Manuela","family":"Cano","sequence":"additional","affiliation":[]},{"given":"Patr\u00edcia","family":"Vieira","sequence":"additional","affiliation":[]},{"given":"L\u00edgia","family":"Reis","sequence":"additional","affiliation":[]},{"given":"Rui","family":"Matias","sequence":"additional","affiliation":[]},{"given":"Jo\u00e3o","family":"Rodrigues","sequence":"additional","affiliation":[]},{"given":"Carina","family":"Menezes","sequence":"additional","affiliation":[]},{"given":"T\u00e2nia","family":"Rosado","sequence":"additional","affiliation":[]},{"given":"Ant\u00f3nio","family":"Sequeira","sequence":"additional","affiliation":[]},{"given":"Olga","family":"Moreira","sequence":"additional","affiliation":[]},{"given":"Werner","family":"Ruppitsch","sequence":"additional","affiliation":[]},{"given":"Adriana","family":"Cabal-Rosel","sequence":"additional","affiliation":[]},{"given":"Solveig S\u00f8lver\u00f8d","family":"Mo","sequence":"additional","affiliation":[]},{"given":"Elsa","family":"Dias","sequence":"additional","affiliation":[]},{"given":"Markus","family":"Woegerbauer","sequence":"additional","affiliation":[]},{"given":"Manuela","family":"Cani\u00e7a","sequence":"additional","affiliation":[]},{"given":"Vera","family":"Manageiro","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2025,7,31]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"3061","DOI":"10.1093\/jac\/dkab284","article-title":"Characterization of FRI carbapenemase-producing Enterobacter spp. isolated from a hospital and the environment in Osaka, Japan","volume":"76","author":"Adachi","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1111\/1758-2229.12779","article-title":"Early emergence of mcr-1-positive Enterobacteriaceae in gulls from Spain and Portugal","volume":"11","author":"Ahlstrom","year":"2019","journal-title":"Environ. Microbiol. Rep."},{"key":"ref3","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":"ref4","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST ring image generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1089\/mdr.2022.0228","article-title":"Plasmid-mediated Colistin resistance genes mcr-1 and mcr-4 in multidrug-resistant Escherichia coli strains isolated from a healthy pig in Portugal","volume":"29","author":"Amaro","year":"2023","journal-title":"Microb. Drug Resist."},{"key":"ref6","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":"ref7","doi-asserted-by":"publisher","first-page":"272","DOI":"10.3390\/antibiotics11020272","article-title":"Low level of Colistin resistance and mcr genes presence in Salmonella spp.: evaluation of isolates collected between 2000 and 2020 from animals and environment","volume":"11","author":"Bertelloni","year":"2022","journal-title":"Antibiotics"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e02540-16","DOI":"10.1128\/AAC.02540-16","article-title":"MCR-1 and OXA-48 in vivo acquisition in KPC-producing Escherichia coli after colistin treatment","volume":"61","author":"Beyrouthy","year":"2017","journal-title":"Antimicrob. 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Rev."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1128\/spectrum.04620-22","article-title":"Phenotypic and molecular characterization of an Enterobacter ludwigii clinical isolate carrying a plasmid-mediated blaIMI-6 gene","volume":"11","author":"Blanco-Mart\u00edn","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmed.2020.616490","article-title":"Genetic diversity, biochemical properties, and detection methods of minor carbapenemases in Enterobacterales","volume":"7","author":"Bonnin","year":"2021","journal-title":"Front. 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Agents Chemother."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e02338-18","DOI":"10.1128\/AAC.02338-18","article-title":"Novel carbapenemases FLC-1 and IMI-2 encoded by an Enterobacter cloacae complex isolated from food products","volume":"63","author":"Brouwer","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e00047-19","DOI":"10.1128\/CMR.00047-19","article-title":"Epidemiology of \u03b2-lactamase-producing pathogens","volume":"33","author":"Bush","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. 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Food Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/spectrum.01245-22","article-title":"Worldwide disseminated IncX4 plasmid carrying mcr-1 arrives to wild mammal in Portugal","volume":"10","author":"Dantas Palmeira","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e00002","DOI":"10.1128\/CMR.00002-19","article-title":"Enterobacter spp.: update on taxonomy, clinical aspects, and emerging antimicrobial resistance","volume":"32","author":"Davin-Regli","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/CMR.00181-19","article-title":"Antimicrobial resistance in ESKAPE pathogens","volume":"33","author":"De Oliveira","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"7420","DOI":"10.1128\/AAC.01636-15","article-title":"Genetic and biochemical characterization of FRI-1, a Carbapenem-hydrolyzing class Beta-lactamase from Enterobacter cloacae","volume":"59","author":"Dortet","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.3201\/eid3006.231525","article-title":"IMI-type Carbapenemase-producing Enterobacter cloacae Complex, France and overseas regions, 2012\u20132022","volume":"30","author":"Emeraud","year":"2024","journal-title":"Emerg. Infect. Dis."},{"key":"ref28","volume-title":"A European one health action plan against antimicrobial resistance (AMR)","year":"2017"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"105802","DOI":"10.1016\/j.ijantimicag.2019.09.006","article-title":"Occurrence of CTX-M-15- and MCR-1-producing Enterobacterales in pigs in Portugal: evidence of direct links with antibiotic selective pressure","volume":"55","author":"Fournier","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1038\/s41586-024-07960-6","article-title":"Commensal consortia decolonize Enterobacteriaceae via ecological control","volume":"633","author":"Furuichi","year":"2024","journal-title":"Nature"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e02501","DOI":"10.1128\/AAC.02501-17","article-title":"Characteristics of carbapenemase-producing Enterobacteriaceae in wastewater revealed by genomic analysis","volume":"62","author":"Gomi","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1093\/jac\/dkac029","article-title":"Emergence of rare carbapenemases (FRI, GES-5, IMI, SFC and SFH-1) in Enterobacterales isolated from surface waters in Japan","volume":"77","author":"Gomi","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"105625","DOI":"10.1016\/j.envint.2020.105625","article-title":"Characteristics of and variation in airborne ARGs among urban hospitals and adjacent urban and suburban communities: a metagenomic approach","volume":"139","author":"He","year":"2020","journal-title":"Environ. Int."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"dlab046","DOI":"10.1093\/jacamr\/dlab046","article-title":"A genetic cluster of MDR Enterobacter cloacae complex ST78 harbouring a plasmid containing blaVIM-1 and mcr-9 in the Netherlands","volume":"3","author":"Hendrickx","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"164179","DOI":"10.1016\/j.scitotenv.2023.164179","article-title":"Carbapenemase-producing gram-negative bacteria in hospital wastewater, wastewater treatment plants and surface waters in a metropolitan area in Germany, 2020","volume":"890","author":"Hoffmann","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"115880","DOI":"10.1016\/j.watres.2020.115880","article-title":"The role of the natural aquatic environment in the dissemination of extended spectrum beta-lactamase and carbapenemase encoding genes: a scoping review","volume":"180","author":"Hooban","year":"2020","journal-title":"Water Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"163600","DOI":"10.1016\/j.scitotenv.2023.163600","article-title":"Genomic epidemiology and transmission characteristics of mcr1-positive colistin-resistant Escherichia coli strains circulating at natural environment","volume":"882","author":"Hu","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"3670","DOI":"10.1128\/JB.01920-07","article-title":"Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-\u03b2-1,6-N-acetyl-D-glucosamine","volume":"190","author":"Itoh","year":"2008","journal-title":"J. Bacteriol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"2023","DOI":"10.3201\/eid2312.170883","article-title":"High rate of MCR-1\u2013producing Escherichia coli and Klebsiella pneumoniae among pigs, Portugal","volume":"23","author":"Kieffer","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"2919","DOI":"10.1128\/JCM.01648-16","article-title":"Whole-genome multilocus sequence typing of extended-Spectrum- Beta-lactamase-producing Enterobacteriaceae","volume":"54","author":"Kluytmans-van den Bergh","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"2969","DOI":"10.1093\/jac\/dky291","article-title":"FRI-4 carbapenemase-producing Enterobacter cloacae complex isolated in Tokyo, Japan","volume":"73","author":"Kubota","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.envint.2018.04.041","article-title":"Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance","volume":"117","author":"Larsson","year":"2018","journal-title":"Environ. Int."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1038\/s41579-021-00649-x","article-title":"Antibiotic resistance in the environment","volume":"20","author":"Larsson","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.jgar.2018.06.022","article-title":"Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human","volume":"15","author":"Laurens","year":"2018","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"3885","DOI":"10.1016\/j.csbj.2023.08.004","article-title":"Molecular epidemiology and genomic characterization of a plasmid-mediated mcr-10 and blaNDM-1 co-harboring multidrug-resistant Enterobacter asburiae","volume":"21","author":"Li","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"106573","DOI":"10.1016\/j.ijantimicag.2022.106573","article-title":"High prevalence of colistin resistance and mcr-9\/10 genes in Enterobacter spp. in a tertiary hospital over a decade","volume":"59","author":"Liao","year":"2022","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2020.1842992","article-title":"Contribution of biofilm formation genetic locus, pgaABCD, to antibiotic resistance development in gut microbiome","volume":"12","author":"Lin","year":"2020","journal-title":"Gut Microbes"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"3087","DOI":"10.1093\/jac\/dkaa205","article-title":"Epidemiology of mobile colistin resistance genes mcr-1 to mcr-9","volume":"75","author":"Ling","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1186\/s12866-021-02250-x","article-title":"Characterization of resistance mechanisms of Enterobacter cloacae Complex co-resistant to carbapenem and colistin","volume":"21","author":"Liu","year":"2021","journal-title":"BMC Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.jgar.2017.12.017","article-title":"First detection of OXA-48-producing Klebsiella pneumoniae in community-acquired urinary tract infection in Algeria","volume":"12","author":"Loucif","year":"2018","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"367","DOI":"10.3389\/fmicb.2019.00367","article-title":"IncX4 plasmid carrying the new mcr-1.9 gene variant in a CTX-M-8-producing Escherichia coli isolate recovered from swine","volume":"10","author":"Manageiro","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1111\/1574-6968.12340","article-title":"GES-5 among the \u03b2-lactamases detected in ubiquitous bacteria isolated from aquatic environment samples","volume":"351","author":"Manageiro","year":"2014","journal-title":"FEMS Microbiol. Lett."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"4","DOI":"10.3390\/microorganisms8030429","article-title":"Plasmid-mediated colistin resistance (mcr-1) in Escherichia coli from non-imported fresh vegetables for human consumption in Portugal","volume":"8","author":"Manageiro","year":"2020","journal-title":"Microorganisms"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.3390\/antibiotics11091232","article-title":"Genomic analysis of a mcr-9.1-Harbouring IncHI2-ST1 plasmid from Enterobacter ludwigii isolated in fish farming","volume":"11","author":"Manageiro","year":"2022","journal-title":"Antibiotics"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1089\/mdr.2022.0123","article-title":"Genetic and phenotypic characterization of the first Canadian case of ambler class A Carbapenemase FRI-8","volume":"29","author":"Mataseje","year":"2023","journal-title":"Microb. Drug Resist."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"2478","DOI":"10.1093\/jac\/dkx173","article-title":"FRI-2 carbapenemase-producing Enterobacter cloacae complex in the UK","volume":"72","author":"Meunier","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"113143","DOI":"10.1016\/j.envpol.2019.113143","article-title":"The threat of carbapenem-resistant bacteria in the environment: evidence of widespread contamination of reservoirs at a global scale","volume":"255","author":"Mills","year":"2019","journal-title":"Environ. 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