{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T00:45:49Z","timestamp":1784335549697,"version":"3.55.0"},"reference-count":49,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T00:00:00Z","timestamp":1762560000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["773830"],"award-info":[{"award-number":["773830"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003407","name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["00000033"],"award-info":[{"award-number":["00000033"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["1034"],"award-info":[{"award-number":["1034"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Science of The Total Environment"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1016\/j.scitotenv.2025.180930","type":"journal-article","created":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T11:37:15Z","timestamp":1763379435000},"page":"180930","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"special_numbering":"C","title":["Bathing seawater and sand as reservoirs of clinically relevant and antimicrobial resistant Klebsiella pneumoniae strains"],"prefix":"10.1016","volume":"1006","author":[{"given":"Alessandra","family":"Cornacchia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Di Cesare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gianluca","family":"Corno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasa","family":"Sbaffi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriella","family":"Centorotola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Chiaverini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Antonietta","family":"Saletti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciano","family":"Ricchiuti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cesare","family":"Camm\u00e0","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierpaolo","family":"Piccone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofia Chiatamone","family":"Ranieri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola","family":"D'Alterio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Pomilio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.scitotenv.2025.180930_bb0005","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.scitotenv.2025.180930_bb0010","series-title":"Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data","author":"Andrews","year":"2010"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0015","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.983294","article-title":"Resistance and virulence features of hypermucoviscous Klebsiella pneumoniae from bloodstream infections: Results of a nationwide Italian surveillance study","volume":"13","author":"Arena","year":"2022","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0020","doi-asserted-by":"crossref","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":"10.1016\/j.scitotenv.2025.180930_bb0025","doi-asserted-by":"crossref","first-page":"e02711","DOI":"10.1128\/AEM.02711-19","article-title":"The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples","volume":"86","author":"Barbier","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0030","doi-asserted-by":"crossref","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":"10.1016\/j.scitotenv.2025.180930_bb0035","doi-asserted-by":"crossref","DOI":"10.1128\/aem.00991-22","article-title":"mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements","volume":"88","author":"Brown","year":"2022","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0040","doi-asserted-by":"crossref","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":"10.1016\/j.scitotenv.2025.180930_bb0045","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0050","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0250525","article-title":"Multidrug-resistant Klebsiella pneumoniae harboring extended spectrum \u03b2-lactamase encoding genes isolated from human septicemias","volume":"16","author":"Carvalho","year":"2021","journal-title":"PLoS One"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0055","doi-asserted-by":"crossref","DOI":"10.1128\/mra.00140-22","article-title":"Whole-Genome Sequences of Two Klebsiella pneumoniae Strains (Sequence Types 23 and 35) from Wildlife","volume":"11","author":"Cornacchia","year":"2022","journal-title":"Microbiol Resour Announc"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0060","doi-asserted-by":"crossref","DOI":"10.7717\/peerj-cs.20","article-title":"CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data","volume":"1","author":"Davis","year":"2015","journal-title":"PeerJ Comput. Sci."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0065","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2024.124598","article-title":"Treated wastewater: A hotspot for multidrug- and colistin-resistant Klebsiella pneumoniae","volume":"359","author":"Di Cesare","year":"2024","journal-title":"Environ. Pollut."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0070","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1111\/1758-2229.12125","article-title":"The marine environment as a reservoir of enterococci carrying resistance and virulence genes strongly associated with clinical strains","volume":"6","author":"Di Cesare","year":"2014","journal-title":"Environ. Microbiol. Rep."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0075","doi-asserted-by":"crossref","DOI":"10.1093\/jambio\/lxaf017","article-title":"Making sense of sentinels: wildlife as the One Health bridge for environmental antimicrobial resistance surveillance","volume":"136","author":"Doyle","year":"2025","journal-title":"J. Appl. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0080","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1186\/s12879-019-4565-3","article-title":"Co-existence of virulence factors and antibiotic resistance in new Klebsiella pneumoniae clones emerging in south of Italy","volume":"19","author":"Fasciana","year":"2019","journal-title":"BMC Infect. Dis."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0085","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"Felsenstein","year":"1981","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0090","first-page":"eads4355","article-title":"Anthropogenic activity and climate change exacerbate the spread of pathogenic bacteria in the environment. Science","volume":"11","author":"Geng","year":"2025","journal-title":"Advances"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0095","doi-asserted-by":"crossref","first-page":"W484","DOI":"10.1093\/nar\/gkad326","article-title":"Proksee: in-depth characterization and visualization of bacterial genomes","volume":"51","author":"Grant","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0100","doi-asserted-by":"crossref","first-page":"D491","DOI":"10.1093\/nar\/gkw975","article-title":"Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation","volume":"45","author":"Grazziotin","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0105","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","article-title":"VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses","volume":"9","author":"Guo","year":"2021","journal-title":"Microbiome"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0110","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0115","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijantimicag.2024.107275","article-title":"Clinical and laboratory insights into the threat of hypervirulent Klebsiella pneumoniae","volume":"64","author":"Han","year":"2024","journal-title":"Int. J. Antimicrob. Agents"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0120","doi-asserted-by":"crossref","first-page":"7593","DOI":"10.1128\/AEM.00736-15","article-title":"The ocean as a global reservoir of antibiotic resistance genes","volume":"81","author":"Hatosy","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0125","first-page":"mgen001005","article-title":"Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17","volume":"9","author":"Hetland","year":"2023","journal-title":"Microb Genom"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0130","doi-asserted-by":"crossref","DOI":"10.1016\/j.envint.2021.106466","article-title":"A Point Prevalence Survey of Antibiotic Resistance in the Irish Environment, 2018-2019","volume":"152","author":"Hooban","year":"2021","journal-title":"Environ. Int."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0135","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/molbev\/msw046","article-title":"ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data","volume":"33","author":"Huerta-Cepas","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0140","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1016\/S0140-6736(22)02185-7","article-title":"Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019","volume":"400","author":"Ikuta","year":"2022","journal-title":"Lancet"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0145","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0104984","article-title":"Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms","volume":"9","author":"Kaas","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0150","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.ijheh.2019.09.008","article-title":"Thinking outside the box: Association of antimicrobial resistance with climate warming in Europe \u2013 A 30 country observational study","volume":"223","author":"Kaba","year":"2020","journal-title":"Int. J. Hyg. Environ. Health"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0155","doi-asserted-by":"crossref","first-page":"4188","DOI":"10.1038\/s41467-021-24448-3","article-title":"A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex","volume":"12","author":"Lam","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0160","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1016\/j.envint.2017.11.003","article-title":"Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: Environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey)","volume":"114","author":"Leonard","year":"2018","journal-title":"Environ. Int."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0165","article-title":"Association between antibiotic resistance and increasing ambient temperature in China: An ecological study with nationwide panel data","volume":"30","author":"Li","year":"2023","journal-title":"Lancet Reg Health West Pac"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0170","article-title":"cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis","volume":"10","author":"Liu","year":"2019","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0175","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. Infect."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0180","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2017.22.15.30513","article-title":"Indistinguishable NDM-producing Escherichia coli isolated from recreational waters, sewage, and a clinical specimen in Ireland, 2016 to 2017","volume":"22","author":"Mahon","year":"2017","journal-title":"Euro Surveill."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0185","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/s41579-024-01054-w","article-title":"ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics","volume":"22","author":"Miller","year":"2024","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0190","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1093\/femsre\/fux013","article-title":"Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance","volume":"41","author":"Navon-Venezia","year":"2017","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0195","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0200","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00821-19","article-title":"Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis","volume":"5","author":"Pan","year":"2020","journal-title":"mSystems"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0205","doi-asserted-by":"crossref","first-page":"3659","DOI":"10.2147\/IDR.S318717","article-title":"Importance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy","volume":"14","author":"Spaziante","year":"2021","journal-title":"Infect Drug Resist"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0210","doi-asserted-by":"crossref","first-page":"3882","DOI":"10.1093\/bioinformatics\/btaa250","article-title":"Phigaro: high-throughput prophage sequence annotation","volume":"36","author":"Starikova","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0215","doi-asserted-by":"crossref","DOI":"10.1093\/eep\/dvad008","article-title":"Inheritance of environment-induced phenotypic changes through epigenetic mechanisms","volume":"9","author":"Tando","year":"2023","journal-title":"Environ Epigenet"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0220","doi-asserted-by":"crossref","first-page":"2054","DOI":"10.1038\/s41564-022-01263-0","article-title":"A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings","volume":"7","author":"Thorpe","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0225","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1093\/bioinformatics\/btl369","article-title":"Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands","volume":"22","author":"Vernikos","year":"2006","journal-title":"Bioinformatics"},{"key":"10.1016\/j.scitotenv.2025.180930_bb0230","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.mib.2018.04.004","article-title":"Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria","volume":"45","author":"Wyres","year":"2018","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0235","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/s41579-019-0315-1","article-title":"Population genomics of Klebsiella pneumoniae","volume":"18","author":"Wyres","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0240","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00138-20","article-title":"The Genotype-to-Phenotype Dilemma: How Should Laboratories Approach Discordant Susceptibility Results?","volume":"59","author":"Yee","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.180930_bb0245","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2020.115200","article-title":"High levels of antibiotic resistance genes and opportunistic pathogenic bacteria indicators in urban wild bird feces","volume":"266","author":"Zhao","year":"2020","journal-title":"Environ. Pollut."}],"container-title":["Science of The Total Environment"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969725025707?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969725025707?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T19:36:55Z","timestamp":1766086615000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0048969725025707"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":49,"alternative-id":["S0048969725025707"],"URL":"https:\/\/doi.org\/10.1016\/j.scitotenv.2025.180930","relation":{},"ISSN":["0048-9697"],"issn-type":[{"value":"0048-9697","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Bathing seawater and sand as reservoirs of clinically relevant and antimicrobial resistant Klebsiella pneumoniae strains","name":"articletitle","label":"Article Title"},{"value":"Science of The Total Environment","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.scitotenv.2025.180930","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"180930"}}