Comparative Genomic Analysis of Hypervirulent and Classical Klebsiella pneumoniae Isolates from Respiratory Samples: A Computational Assessment of Virulence Genes

Comparative Genomic Analysis of Hypervirulent and Classical Klebsiella pneumoniae Isolates from Respiratory Samples: A Computational Assessment of Virulence Genes | 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 Comparative Genomic Analysis of Hypervirulent and Classical Klebsiella pneumoniae Isolates from Respiratory Samples: A Computational Assessment of Virulence Genes Manoj Kumar Thirugnanasambantham, Srimathy Ramachandran, S. Suma Mohan, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8796276/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 28 Apr, 2026 Read the published version in Functional & Integrative Genomics → Version 1 posted 12 You are reading this latest preprint version Abstract Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a major cause of severe respiratory infections worldwide; however, its genomic distinction from classical K. pneumoniae (cKp), particularly within respiratory isolates, remains incompletely understood. In this study, we conducted a large-scale comparative genomic analysis of 1,293 respiratory Kp genomes retrieved from the BV-BRC database, of which 538 were classified as hvKp and 755 as cKp based on established marker genes. Comprehensive profiling of 127 virulence-associated genes revealed that hvKp isolates exhibited a more specialized virulence architecture, with significantly higher prevalence of key iron acquisition systems and capsule-associated loci compared with cKp isolates (p < 0.001). In contrast, cKp isolates demonstrated greater virulence gene diversity, as reflected by higher Shannon diversity indices, despite lower prevalence of individual virulence markers. Notably, classical high-virulence risk lineages, particularly ST11-K64, displayed hybrid virulence profiles with partial acquisition of hvKp-associated determinants, suggesting an evolutionary continuum between classical and hypervirulent pathotypes. Presence–absence–based phylogenetic analysis revealed clustering driven by virulence gene repertoires rather than strict core-genome lineage, indicating functional convergence among genetically distinct isolates. Importantly, virulence gene prevalence did not directly correlate with genetic diversity, underscoring the limitations of single-marker approaches for hypervirulence prediction. Collectively, these findings provide quantitative insights into the pathotype-dependent organization and evolution of virulence determinants in respiratory Kp and highlight the value of integrated genomic frameworks for surveillance and virulence risk assessment of emerging hypervirulent lineages. Klebsiella pneumoniae hypervirulent classical respiratory samples comparative study genomic analysis virulence factors Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementerymaterial.zip Cite Share Download PDF Status: Published Journal Publication published 28 Apr, 2026 Read the published version in Functional & Integrative Genomics → Version 1 posted Editorial decision: Revision requested 02 Mar, 2026 Reviews received at journal 01 Mar, 2026 Reviews received at journal 27 Feb, 2026 Reviewers agreed at journal 19 Feb, 2026 Reviewers agreed at journal 19 Feb, 2026 Reviewers agreed at journal 19 Feb, 2026 Reviewers agreed at journal 17 Feb, 2026 Reviewers agreed at journal 17 Feb, 2026 Reviewers invited by journal 17 Feb, 2026 Editor assigned by journal 12 Feb, 2026 Submission checks completed at journal 12 Feb, 2026 First submitted to journal 05 Feb, 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. 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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-8796276","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":594043542,"identity":"f5dbe65e-a579-4f59-9e86-ee655c12b074","order_by":0,"name":"Manoj Kumar Thirugnanasambantham","email":"","orcid":"","institution":"SASTRA University","correspondingAuthor":false,"prefix":"","firstName":"Manoj","middleName":"Kumar","lastName":"Thirugnanasambantham","suffix":""},{"id":594043543,"identity":"d6a73c8a-4677-4bd2-8d30-536cd88f8f9e","order_by":1,"name":"Srimathy Ramachandran","email":"","orcid":"","institution":"SASTRA University","correspondingAuthor":false,"prefix":"","firstName":"Srimathy","middleName":"","lastName":"Ramachandran","suffix":""},{"id":594043544,"identity":"fbb93d2f-9dc5-44f0-80bb-03f4bb53875d","order_by":2,"name":"S. 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