{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T02:43:56Z","timestamp":1790131436433,"version":"4.0.1"},"reference-count":56,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001343","name":"University of Pretoria","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001343","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010753","name":"National Health Laboratory Service","doi-asserted-by":"publisher","award":["004_94917"],"award-info":[{"award-number":["004_94917"]}],"id":[{"id":"10.13039\/501100010753","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Environmental Pollution"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.envpol.2026.128450","type":"journal-article","created":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T07:01:36Z","timestamp":1779951696000},"page":"128450","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Wild birds as reservoirs of antimicrobial-resistant enterococci: Genomic surveillance in Gauteng, South Africa, during the migratory season"],"prefix":"10.1016","volume":"404","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3605-9357","authenticated-orcid":false,"given":"Theevasha","family":"Govender","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronica","family":"Ueckermann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thabo","family":"Hamiwe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerbrand A.","family":"van der Zel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John Paul","family":"Makumbi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1877-4317","authenticated-orcid":false,"given":"Hlambani","family":"Shirinda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marthie M.","family":"Ehlers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.envpol.2026.128450_bib1","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1007\/s10096-023-04579-9","article-title":"Nasotracheal enterococcal carriage and resistomes: detection of optrA-, poxtA- and cfrD-carrying strains in migratory birds, livestock, pets, and in-contact humans in Spain","volume":"42","author":"Abdullahi","year":"2023","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"10.1016\/j.envpol.2026.128450_bib2","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.jgar.2022.12.006","article-title":"optrA-mediated linezolid resistance in an Enterococcus faecalis isolate recovered from a wild raptor (Falco peregrinus peregrinus), central Italy","volume":"32","author":"Albini","year":"2023","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"10.1016\/j.envpol.2026.128450_bib3","doi-asserted-by":"crossref","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":"10.1016\/j.envpol.2026.128450_bib4","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-77696-6","article-title":"Prevalence of vancomycin-resistant enterococcus in Africa in one health approach: a systematic review and meta-analysis","volume":"10","author":"Alemayehu","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.envpol.2026.128450_bib5","series-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"10.1016\/j.envpol.2026.128450_bib6","doi-asserted-by":"crossref","first-page":"852","DOI":"10.3390\/antibiotics11070852","article-title":"Antimicrobial-resistant enterococcus spp. in wild avifauna from Central Italy","volume":"11","author":"Cagnoli","year":"2022","journal-title":"Antibiotics"},{"key":"10.1016\/j.envpol.2026.128450_bib7","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.envpol.2026.128450_bib8","doi-asserted-by":"crossref","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. Agents Chemother."},{"key":"10.1016\/j.envpol.2026.128450_bib9","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.3390\/biomedicines12071625","article-title":"CRISPR-cas system, antimicrobial resistance, and enterococcus genus-A complicated relationship","volume":"12","author":"Costache","year":"2024","journal-title":"Biomedicines"},{"key":"10.1016\/j.envpol.2026.128450_bib10","doi-asserted-by":"crossref","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":"10.1016\/j.envpol.2026.128450_bib11","doi-asserted-by":"crossref","DOI":"10.3389\/fmed.2021.720647","article-title":"The global prevalence of daptomycin, tigecycline, and Linezolid-resistant Enterococcus faecalis and Enterococcus faecium strains from human clinical samples: a systematic review and meta-analysis","volume":"8","author":"Dadashi","year":"2021","journal-title":"Front. Med."},{"key":"10.1016\/j.envpol.2026.128450_bib13","doi-asserted-by":"crossref","first-page":"857","DOI":"10.3390\/antibiotics11070857","article-title":"Enterococcus virulence and resistant traits associated with its permanence in the hospital environment","volume":"11","author":"Geraldes","year":"2022","journal-title":"Antibiotics"},{"key":"10.1016\/j.envpol.2026.128450_bib14","doi-asserted-by":"crossref","first-page":"3190","DOI":"10.3390\/foods11203190","article-title":"Emergence and genomic characterization of the first reported optrA-carrying linezolid-resistant enterococci isolated from retail broiler meat in the United Arab Emirates","volume":"11","author":"Habib","year":"2022","journal-title":"Foods"},{"key":"10.1016\/j.envpol.2026.128450_bib15","author":"Hawkins"},{"key":"10.1016\/j.envpol.2026.128450_bib16","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1111\/j.1469-0691.2010.03226.x","article-title":"Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium","volume":"16","author":"Hegstad","year":"2010","journal-title":"Clin. Microbiol. Infection"},{"key":"10.1016\/j.envpol.2026.128450_bib17","doi-asserted-by":"crossref","first-page":"421","DOI":"10.4161\/viru.21282","article-title":"Intrinsic and acquired resistance mechanisms in enterococcus","volume":"3","author":"Hollenbeck","year":"2012","journal-title":"Virulence"},{"key":"10.1016\/j.envpol.2026.128450_bib18","first-page":"55","article-title":"Comparison of three different methods of genomic DNA extraction from gram positive and gram negative bacteria","volume":"2","author":"Hossain Ripon","year":"2011","journal-title":"Journal of Experimental Biosciences"},{"key":"10.1016\/j.envpol.2026.128450_bib20","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: mobileelementfinder","volume":"76","author":"Johansson","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.envpol.2026.128450_bib21","doi-asserted-by":"crossref","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":"10.1016\/j.envpol.2026.128450_bib22","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1128\/JCM.01704-06","article-title":"Clonal structure of Enterococcus faecalis isolated from Polish hospitals: characterization of epidemic clones","volume":"45","author":"Kawalec","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.envpol.2026.128450_bib23","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/s13104-020-05018-0","article-title":"Improved detection of esp, hyl, asa1, gelE, cylA virulence genes among clinical isolates of enterococci","volume":"13","author":"Kiruthiga","year":"2020","journal-title":"BMC Res. Notes"},{"key":"10.1016\/j.envpol.2026.128450_bib24","series-title":"Enterococci: from Commensals to Leading Causes of Drug Resistant Infection","article-title":"Enterococcal infection\u2014Treatment and antibiotic resistance","author":"Kristich","year":"2014"},{"key":"10.1016\/j.envpol.2026.128450_bib25","series-title":"FelixKrueger\/TrimGalore: V0.6.10 - Add Default Decompression Path (0.6.10)","author":"Krueger","year":"2023"},{"key":"10.1016\/j.envpol.2026.128450_bib26","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1186\/s12917-019-2221-1","article-title":"Methicillin-resistant Staphylococcus aureus and glycopeptide-resistant enterococci in fecal samples of birds from South-Eastern Poland","volume":"15","author":"Kutkowska","year":"2019","journal-title":"BMC Vet. Res."},{"key":"10.1016\/j.envpol.2026.128450_bib27","series-title":"Jekesa: an automated easy-to-use pipeline for bacterial whole genome typing","author":"Kwenda","year":"2020"},{"key":"10.1016\/j.envpol.2026.128450_bib28","doi-asserted-by":"crossref","first-page":"836","DOI":"10.3390\/pathogens12060836","article-title":"Prevalence of enterococcus spp. and the whole-genome characteristics of Enterococcus faecium and Enterococcus faecalis strains isolated from free-living birds in Poland","volume":"12","author":"Kwit","year":"2023","journal-title":"Pathogens"},{"key":"10.1016\/j.envpol.2026.128450_bib29","doi-asserted-by":"crossref","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":"10.1016\/j.envpol.2026.128450_bib30","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijantimicag.2024.107251","article-title":"Antimicrobial resistance among clinically significant bacteria in wildlife: an overlooked one health concern","volume":"64","author":"Li","year":"2024","journal-title":"Int. J. Antimicrob. Agents"},{"key":"10.1016\/j.envpol.2026.128450_bib31","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infection"},{"key":"10.1016\/j.envpol.2026.128450_bib32","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.3390\/antibiotics12071140","article-title":"Dissemination of enterococcal genetic lineages: a one health perspective","volume":"12","author":"Marques","year":"2023","journal-title":"Antibiotics"},{"key":"10.1016\/j.envpol.2026.128450_bib33","doi-asserted-by":"crossref","DOI":"10.1128\/cmr.00121-23","article-title":"Non-faecium non-faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance","volume":"37","author":"Mullally","year":"2024","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.envpol.2026.128450_bib34","doi-asserted-by":"crossref","first-page":"1839","DOI":"10.3390\/microorganisms8111839","article-title":"Detection of the phenicol\u2013oxazolidinone resistance gene poxtA in Enterococcus faecium and Enterococcus faecalis from food-producing animals during 2008\u20132018 in Korea","volume":"8","author":"Na","year":"2020","journal-title":"Microorganisms"},{"key":"10.1016\/j.envpol.2026.128450_bib36","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.envpol.2026.128450_bib37","doi-asserted-by":"crossref","first-page":"740","DOI":"10.4315\/JFP-21-431","article-title":"Fattening pigs are a reservoir of florfenicol-resistant enterococci harboring oxazolidinone resistance genes","volume":"85","author":"N\u00fcesch-Inderbinen","year":"2022","journal-title":"J. Food Protect."},{"key":"10.1016\/j.envpol.2026.128450_bib38","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.envpol.2026.128450_bib39","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00088-17","article-title":"Mobile genetic elements associated with antimicrobial resistance","volume":"31","author":"Partridge","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.envpol.2026.128450_bib40","doi-asserted-by":"crossref","first-page":"8207","DOI":"10.3390\/ijms26178207","article-title":"Linezolid in the focus of antimicrobial resistance of enterococcus species: a global overview of genomic studies","volume":"26","author":"Peykov","year":"2025","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.envpol.2026.128450_bib41","series-title":"R: a Language and Environment for Statistical Computing","year":"2025"},{"key":"10.1016\/j.envpol.2026.128450_bib42","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13620-020-0156-2","article-title":"A pilot study using environmental screening to determine the prevalence of Mycobacterium avium subspecies paratuberculosis (MAP) and antimicrobial resistance (AMR) in Irish cattle herds","volume":"73","author":"Ramovic","year":"2020","journal-title":"Ir. Vet. J."},{"key":"10.1016\/j.envpol.2026.128450_bib43","doi-asserted-by":"crossref","first-page":"2220","DOI":"10.1128\/JCM.02596-05","article-title":"Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination","volume":"44","author":"Ruiz-Garbajosa","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.envpol.2026.128450_bib44","doi-asserted-by":"crossref","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":"10.1016\/j.envpol.2026.128450_bib45","series-title":"Shovill","author":"Seemann","year":"2016"},{"key":"10.1016\/j.envpol.2026.128450_bib46","doi-asserted-by":"crossref","DOI":"10.1155\/2024\/6462849","article-title":"Wild birds as drivers of salmonella braenderup and multidrug resistant bacteria in wetlands of Northern Italy","volume":"2024","author":"Smoglica","year":"2024","journal-title":"Transbound. Emerg. Dis."},{"key":"10.1016\/j.envpol.2026.128450_bib47","doi-asserted-by":"crossref","first-page":"219","DOI":"10.7589\/2017-05-118","article-title":"Wild birds as a potential source of known and novel multilocus sequence types of antibiotic-resistant Enterococcus faecalis","volume":"54","author":"St\u0119pie\u0144-Py\u015bniak","year":"2018","journal-title":"J. Wildl. Dis."},{"key":"10.1016\/j.envpol.2026.128450_bib48","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1008310","article-title":"Competent but complex communication: the phenomena of pheromone-responsive plasmids","volume":"16","author":"Sterling","year":"2020","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.envpol.2026.128450_bib50","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.ARBA-0032-2018","article-title":"Antimicrobial resistance in enterococcus spp. of animal origin","volume":"6","author":"Torres","year":"2018","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.envpol.2026.128450_bib51","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1111\/nyas.12948","article-title":"Mechanisms of drug resistance: Daptomycin resistance","volume":"1354","author":"Tran","year":"2015","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"10.1016\/j.envpol.2026.128450_bib52","doi-asserted-by":"crossref","first-page":"396","DOI":"10.3390\/ani10030396","article-title":"A preliminary study: antibiotic resistance patterns of Escherichia coli and enterococcus species from wildlife species subjected to supplementary feeding on various South African farms","volume":"10","author":"van den Honert","year":"2020","journal-title":"Animals"},{"key":"10.1016\/j.envpol.2026.128450_bib53","first-page":"1083","article-title":"Antibiotic resistance to critically important antimicrobials and virulence genes in Enterococcus faecalis strains isolated from Eurasian Griffon Vultures (Gyps fulvus) and their association with mobile genetic elements","volume":"12","author":"Vela","year":"2025","journal-title":"Vet. Sci."},{"key":"10.1016\/j.envpol.2026.128450_bib54","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1007\/s00284-011-9880-x","article-title":"Multidrug-resistant enterococci in animal meat and faeces and co-transfer of resistance from an Enterococcus durans to a human Enterococcus faecium","volume":"62","author":"Vignaroli","year":"2011","journal-title":"Curr. Microbiol."},{"key":"10.1016\/j.envpol.2026.128450_bib55","doi-asserted-by":"crossref","DOI":"10.1016\/j.microb.2024.100041","article-title":"Global occurrence of linezolid-resistant enterococcus (LRE): the first systematic review and meta-analysis","volume":"2","author":"Wada","year":"2024","journal-title":"Microbe"},{"key":"10.1016\/j.envpol.2026.128450_bib56","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2022.119603","article-title":"Role of environmental stresses in elevating resistance mutations in bacteria: phenomena and mechanisms","volume":"307","author":"Wang","year":"2022","journal-title":"Environ. Pollut."},{"key":"10.1016\/j.envpol.2026.128450_bib57","series-title":"WHO bacterial priority pathogens list, 2024: bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance","year":"2024"},{"key":"10.1016\/j.envpol.2026.128450_bib58","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1016\/j.ijantimicag.2018.05.005","article-title":"Antimicrobial resistance and genetic lineages of faecal enterococci of wild birds: emergence of vanA and vanB2 harbouring Enterococcus faecalis","volume":"52","author":"Yahia","year":"2018","journal-title":"Int. J. Antimicrob. Agents"},{"key":"10.1016\/j.envpol.2026.128450_bib59","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1139\/cjm-2024-0024","article-title":"Enterococci as a one health indicator of antimicrobial resistance","volume":"70","author":"Zaidi","year":"2024","journal-title":"Can. J. Microbiol."},{"key":"10.1016\/j.envpol.2026.128450_bib60","doi-asserted-by":"crossref","first-page":"D871","DOI":"10.1093\/nar\/gkae968","article-title":"Vfdb 2025: an integrated resource for exploring anti-virulence compounds","volume":"53","author":"Zhou","year":"2025","journal-title":"Nucleic Acids Res."}],"container-title":["Environmental Pollution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0269749126008201?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0269749126008201?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T23:09:13Z","timestamp":1783120153000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0269749126008201"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":56,"alternative-id":["S0269749126008201"],"URL":"https:\/\/doi.org\/10.1016\/j.envpol.2026.128450","relation":{},"ISSN":["0269-7491"],"issn-type":[{"value":"0269-7491","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Wild birds as reservoirs of antimicrobial-resistant enterococci: Genomic surveillance in Gauteng, South Africa, during the migratory season","name":"articletitle","label":"Article Title"},{"value":"Environmental Pollution","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.envpol.2026.128450","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"128450"}}