Shotgun Metagenomic Profiling of Non-cpe Clostridium perfringens Reveals Mucinolytic and Cytolytic Genes in Pediatric Adenovirus Gastroenteritis

Shotgun Metagenomic Profiling of Non-cpe Clostridium perfringens Reveals Mucinolytic and Cytolytic Genes in Pediatric Adenovirus Gastroenteritis | 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 Shotgun Metagenomic Profiling of Non-cpe Clostridium perfringens Reveals Mucinolytic and Cytolytic Genes in Pediatric Adenovirus Gastroenteritis Samar M. El-Shahidy, Amira M. Zakaria, Mohanad A. Ibrahim, Atef M. Diab This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8633709/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 6 You are reading this latest preprint version Abstract Background Viral–bacterial co-infections contribute to disease severity in pediatric acute gastroenteritis but are frequently underdiagnosed using routine methods. Enteric viruses, including human adenoviruses (HAdVs), may coexist with bacterial pathogens that influence intestinal pathology through virulence and antimicrobial resistance determinants. This study applied shotgun metagenomic sequencing to characterize concurrent viral and bacterial pathogens in a pediatric prolonged diarrhea. Methods Shotgun metagenomic sequencing was performed on a pediatric diarrheic stool sample, followed by quality filtering, de novo assembly, taxonomic classification, phylogenetic reconstruction, and integrated virulome-resistome profiling, including plasmid-associated resistance elements. Results Routine diagnostics identified adenovirus as the sole pathogen. Metagenomic analysis confirmed human adenovirus F40, showing close phylogenetic relatedness to globally distributed HAdV-F40 reference strains and a clear distinction from HAdV-F41. In addition, metagenomics uniquely detected a co-occurring Clostridium perfringens strain (SAM_A8, ST-5) that was not recovered by culture. The strain lacked the classical enterotoxin gene ( cpe ) but harbored a conserved histotoxic virulence profile, including plc , pfoA , colA , hyaluronidases, and sialidases. Plasmid-associated tetracycline resistance genes ( tetA(P) and tetB(P) ) were also identified. Conclusion Shotgun metagenomic sequencing enabled genomic characterization of a viral–bacterial co-infection missed by conventional diagnostics, highlighting its value for pathogen identification and resistance surveillance. Adenovirus F40 Clostridium perfringens metagenomics gastroenteritis co-infection virulence genes mucin degradation antimicrobial resistance Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryTables.docx SupplementaryFigures.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviewers agreed at journal 14 May, 2026 Reviewers invited by journal 02 Feb, 2026 Editor invited by journal 21 Jan, 2026 Editor assigned by journal 20 Jan, 2026 Submission checks completed at journal 20 Jan, 2026 First submitted to journal 18 Jan, 2026 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-8633709","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":584529218,"identity":"3744b596-b0f1-45fd-9be9-b37759a4c390","order_by":0,"name":"Samar M. 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Enteric viruses, including human adenoviruses (HAdVs), may coexist with bacterial pathogens that influence intestinal pathology through virulence and antimicrobial resistance determinants. This study applied shotgun metagenomic sequencing to characterize concurrent viral and bacterial pathogens in a pediatric prolonged diarrhea.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eShotgun metagenomic sequencing was performed on a pediatric diarrheic stool sample, followed by quality filtering, de novo assembly, taxonomic classification, phylogenetic reconstruction, and integrated virulome-resistome profiling, including plasmid-associated resistance elements.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eRoutine diagnostics identified adenovirus as the sole pathogen. Metagenomic analysis confirmed human adenovirus F40, showing close phylogenetic relatedness to globally distributed HAdV-F40 reference strains and a clear distinction from HAdV-F41. In addition, metagenomics uniquely detected a co-occurring \u003cem\u003eClostridium perfringens\u003c/em\u003e strain (SAM_A8, ST-5) that was not recovered by culture. The strain lacked the classical enterotoxin gene (\u003cem\u003ecpe\u003c/em\u003e) but harbored a conserved histotoxic virulence profile, including \u003cem\u003eplc\u003c/em\u003e, \u003cem\u003epfoA\u003c/em\u003e, \u003cem\u003ecolA\u003c/em\u003e, hyaluronidases, and sialidases. Plasmid-associated tetracycline resistance genes (\u003cem\u003etetA(P)\u003c/em\u003e and \u003cem\u003etetB(P)\u003c/em\u003e) were also identified.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eShotgun metagenomic sequencing enabled genomic characterization of a viral\u0026ndash;bacterial co-infection missed by conventional diagnostics, highlighting its value for pathogen identification and resistance surveillance.\u003c/p\u003e","manuscriptTitle":"Shotgun Metagenomic Profiling of Non-cpe Clostridium perfringens Reveals Mucinolytic and Cytolytic Genes in Pediatric Adenovirus Gastroenteritis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-02-04 09:06:41","doi":"10.21203/rs.3.rs-8633709/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"reviewerAgreed","content":"128695868568810507787334183594020923745","date":"2026-05-14T15:18:01+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-02-02T16:46:59+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-01-21T06:53:28+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-01-20T14:27:10+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-01-20T14:24:18+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Microbiology","date":"2026-01-18T22:00:22+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-microbiology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"mcro","sideBox":"Learn more about [BMC Microbiology](http://bmcmicrobiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/mcro","title":"BMC Microbiology","twitterHandle":"#bmcmicrobiology","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"564d6908-bbc4-4c23-a463-5449376ce9d4","owner":[],"postedDate":"February 4th, 2026","published":true,"recentEditorialEvents":[{"type":"reviewerAgreed","content":"128695868568810507787334183594020923745","date":"2026-05-14T15:18:01+00:00","index":78,"fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-02-04T09:06:41+00:00","versionOfRecord":[],"versionCreatedAt":"2026-02-04 09:06:41","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8633709","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8633709","identity":"rs-8633709","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}