Freshwater beach sandy sediments harbour latent β-lactamases with deep phylogenetic roots in Chitinophagaceae

Freshwater beach sandy sediments harbour latent β-lactamases with deep phylogenetic roots in Chitinophagaceae | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Freshwater beach sandy sediments harbour latent β-lactamases with deep phylogenetic roots in Chitinophagaceae Davide Corso, Sven Iburg, Manuela Coci, Angelina Cordone, Andrea Di Cesare, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8368209/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background : Antibiotic resistance genes (ARGs) of environmental origin represent an underexplored but potentially important source of future clinical resistance. Here, we characterized the resistome of wet beach sandy sediments from Lake Maggiore using a metagenomic approach to assess the diversity, origin, and potential horizontal mobility of ARGs in this transitional environment. Results : Despite significant spatial variation in resistome β-diversity between beaches and sampling depths, the dominant resistance classes were consistent across sites, with aminoglycoside, polyketide, quinolone, and tetracycline resistance genes prevailing. In contrast, at the metagenome-assembled genome (MAG) level, β-lactamases were the most abundant ARGs, primarily associated with members of the family Chitinophagaceae (phylum Bacteroidetes). Within this group, the genera Ferruginibacter and Lacibacter carried the majority of β-lactamase genes, belonging to classes A, B1, and D. None of the detected ARGs were associated with mobile genetic elements, and all β-lactamase genes were chromosomal. Phylogenetic analyses of our MAGs and all deposited Chitinophagaceae β-lactamase gene sequences revealed that this family contributed substantial novel diversity to β-lactamase phylogenies, with strong phylogenetic clustering at the genus level indicating lineage-specific conservation. The presence of multiple β-lactamase classes within single strains further suggests convergent evolution and potential functional roles beyond antibiotic resistance. Conclusions : Collectively, these findings identify Chitinophagaceae as a major environmental reservoir of chromosomal β-lactamases and point to freshwater sandy sediments as overlooked hotspots of latent resistance diversity. These results highlight the need to consider the environment not as a passive reservoir for ARGs, but as potentially active sources of their development and evolution. Antibiotic resistance cycle Freshwater beach sand Resistance evolution β-lactamases Natural resistance Chitinophagaceae Ferruginibacter Full Text Additional Declarations No competing interests reported. Supplementary Files Suppmaterialchitinophaga.pdf SupplementaryTable3MGEs.xlsx Supptabel4GenesfoundinChitinophaga1.xlsx SuppementaryTable5Activesites.xlsx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8368209","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":598489556,"identity":"6c4b2beb-fb2a-475f-aec1-32379ec58da8","order_by":0,"name":"Davide Corso","email":"","orcid":"","institution":"National Research Council","correspondingAuthor":false,"prefix":"","firstName":"Davide","middleName":"","lastName":"Corso","suffix":""},{"id":598489557,"identity":"dfabf021-26da-487e-9d66-942fc2fe3d87","order_by":1,"name":"Sven Iburg","email":"","orcid":"","institution":"National Research Council","correspondingAuthor":false,"prefix":"","firstName":"Sven","middleName":"","lastName":"Iburg","suffix":""},{"id":598489558,"identity":"a3aa5a27-1762-4536-9074-d3e20712acc0","order_by":2,"name":"Manuela Coci","email":"","orcid":"","institution":"National Research Council","correspondingAuthor":false,"prefix":"","firstName":"Manuela","middleName":"","lastName":"Coci","suffix":""},{"id":598489559,"identity":"52b708db-4f89-4cfb-9fbd-2e1e38fef8f4","order_by":3,"name":"Angelina Cordone","email":"","orcid":"","institution":"University of Naples Federico II","correspondingAuthor":false,"prefix":"","firstName":"Angelina","middleName":"","lastName":"Cordone","suffix":""},{"id":598489560,"identity":"7212c7c2-2fd9-47da-85fa-0b72f74f20fd","order_by":4,"name":"Andrea Di Cesare","email":"","orcid":"","institution":"National Research Council","correspondingAuthor":false,"prefix":"","firstName":"Andrea","middleName":"Di","lastName":"Cesare","suffix":""},{"id":598489561,"identity":"ade3e00c-3cad-4a35-9839-e2d1a53f62a6","order_by":5,"name":"Donato Giovannelli","email":"","orcid":"","institution":"University of Naples Federico II","correspondingAuthor":false,"prefix":"","firstName":"Donato","middleName":"","lastName":"Giovannelli","suffix":""},{"id":598489562,"identity":"9882abd5-ac4e-4354-ab04-ac2f3948c2d3","order_by":6,"name":"Tomasa Sbaffi","email":"","orcid":"","institution":"National Research Council","correspondingAuthor":false,"prefix":"","firstName":"Tomasa","middleName":"","lastName":"Sbaffi","suffix":""},{"id":598489563,"identity":"e74e980c-785b-4939-b02b-8cd6cc9f61e4","order_by":7,"name":"Alejandro Martínez","email":"","orcid":"","institution":"National Research Council","correspondingAuthor":false,"prefix":"","firstName":"Alejandro","middleName":"","lastName":"Martínez","suffix":""},{"id":598489564,"identity":"7d4c413e-5d03-4085-8cdf-bcc4c3c7cfd9","order_by":8,"name":"Ester M. 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Here, we characterized the resistome of wet beach sandy sediments from Lake Maggiore using a metagenomic approach to assess the diversity, origin, and potential horizontal mobility of ARGs in this transitional environment.\u0026nbsp;\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e: Despite significant spatial variation in resistome β-diversity between beaches and sampling depths, the dominant resistance classes were consistent across sites, with aminoglycoside, polyketide, quinolone, and tetracycline resistance genes prevailing. In contrast, at the metagenome-assembled genome (MAG) level, β-lactamases were the most abundant ARGs, primarily associated with members of the family Chitinophagaceae (phylum Bacteroidetes). Within this group, the genera Ferruginibacter and Lacibacter carried the majority of β-lactamase genes, belonging to classes A, B1, and D. None of the detected ARGs were associated with mobile genetic elements, and all β-lactamase genes were chromosomal. Phylogenetic analyses of our MAGs and all deposited Chitinophagaceae β-lactamase gene sequences revealed that this family contributed substantial novel diversity to β-lactamase phylogenies, with strong phylogenetic clustering at the genus level indicating lineage-specific conservation. The presence of multiple β-lactamase classes within single strains further suggests convergent evolution and potential functional roles beyond antibiotic resistance.\u0026nbsp;\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e: Collectively, these findings identify Chitinophagaceae as a major environmental reservoir of chromosomal β-lactamases and point to freshwater sandy sediments as overlooked hotspots of latent resistance diversity. These results highlight the need to consider the environment not as a passive reservoir for ARGs, but as potentially active sources of their development and evolution.\u003c/p\u003e","manuscriptTitle":"Freshwater beach sandy sediments harbour latent β-lactamases with deep phylogenetic roots in Chitinophagaceae","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-03 07:13:01","doi":"10.21203/rs.3.rs-8368209/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"eaf2a071-9fb5-432b-9506-2705e8fa344e","owner":[],"postedDate":"March 3rd, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-03-26T07:41:36+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-03 07:13:01","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8368209","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8368209","identity":"rs-8368209","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}