Targeted Next-Generation Sequencing Analysis of BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia

Targeted Next-Generation Sequencing Analysis of BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia | 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 Article Targeted Next-Generation Sequencing Analysis of BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia Yafei Fan, Yingzheng Ren, Junjie An, Xia Wang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8342132/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: Severe community-acquired pneumonia (SCAP) is associated with high mortality. However, data on the bronchoalveolar lavage fluid (BALF) microbiota in Chinese SCAP patients remain limited. This study aimed to characterize the clinical features and BALF microbiome composition in patients with SCAP compared to non-severe CAP using targeted next-generation sequencing (tNGS). Methods: We conducted a retrospective study involving 224 CAP and 97 SCAP patients from two hospitals in Shanxi, China (January 2023–January 2025). Clinical characteristics and inflammatory cytokines were compared between groups. BALF samples were analyzed via tNGS to evaluate microbial alpha and beta diversity. Differentially abundant taxa were identified using Linear Discriminant Analysis Effect Size (LEfSe). Results: Compared to the CAP group, SCAP patients were significantly older, had a higher prevalence of comorbidities (hypertension, coronary heart disease, diabetes), and exhibited elevated inflammatory indices (CRP, IL-6, PCT, ESR). SCAP patients also demonstrated a higher likelihood of mixed infections, and the number of detected pathogens showed a positive correlation with the length of hospital stay. tNGS analysis revealed significant differences in alpha diversity and distinct beta diversity clustering between the two groups. LEfSe analysis identified Pseudomonas as a potential biomarker enriched in SCAP, whereas Streptococcus was predominant in CAP. Conclusions: In patients with SCAP, the BALF microbiota showed a significant increase in alpha diversity, which appears to mediate inflammatory cytokine production and is associated with disease worsening. There were pronouned differences between SCAP and CAP in both clinical characteristics and microbiome profiles, highlighting the necessity of integrated diagnostic approaches in pneumonia care. Future research should prioritize delineating the dynamic shifts of microbial communities and their influence on pneumonia severity, with the goal of refining and optimizing treatment strategies. Health sciences/Biomarkers Health sciences/Cardiology Health sciences/Diseases Health sciences/Medical research Biological sciences/Microbiology community-acquired pneumonia severe community-acquired pneumonia clinical characteristics targeted next-generation sequencing microbiological profiles Full Text Additional Declarations No competing interests reported. Supplementary Files mergeddatacomplete.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. 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-8342132","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":577768127,"identity":"efc58ca2-2e6f-4933-ba9e-9da0817bcd79","order_by":0,"name":"Yafei Fan","email":"","orcid":"","institution":"Yuncheng Central Hospital, Shanxi Medical University","correspondingAuthor":false,"prefix":"","firstName":"Yafei","middleName":"","lastName":"Fan","suffix":""},{"id":577768128,"identity":"f23f0907-e009-4783-b1de-2806763cde19","order_by":1,"name":"Yingzheng Ren","email":"","orcid":"","institution":"The Second Hospital of Dalian Medical 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BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"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},"keywords":"community-acquired pneumonia, severe community-acquired pneumonia, clinical characteristics, targeted next-generation sequencing, microbiological profiles","lastPublishedDoi":"10.21203/rs.3.rs-8342132/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8342132/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground: \u003c/strong\u003eSevere community-acquired pneumonia (SCAP) is associated with high mortality. However, data on the bronchoalveolar lavage fluid (BALF) microbiota in Chinese SCAP patients remain limited. This study aimed to characterize the clinical features and BALF microbiome composition in patients with SCAP compared to non-severe CAP using targeted next-generation sequencing (tNGS).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods: \u003c/strong\u003eWe conducted a retrospective study involving 224 CAP and 97 SCAP patients from two hospitals in Shanxi, China (January 2023–January 2025). Clinical characteristics and inflammatory cytokines were compared between groups. BALF samples were analyzed via tNGS to evaluate microbial alpha and beta diversity. Differentially abundant taxa were identified using Linear Discriminant Analysis Effect Size (LEfSe).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults: \u003c/strong\u003eCompared to the CAP group, SCAP patients were significantly older, had a higher prevalence of comorbidities (hypertension, coronary heart disease, diabetes), and exhibited elevated inflammatory indices (CRP, IL-6, PCT, ESR). SCAP patients also demonstrated a higher likelihood of mixed infections, and the number of detected pathogens showed a positive correlation with the length of hospital stay. tNGS analysis revealed significant differences in alpha diversity and distinct beta diversity clustering between the two groups. LEfSe analysis identified Pseudomonas as a potential biomarker enriched in SCAP, whereas Streptococcus was predominant in CAP.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions: \u003c/strong\u003eIn patients with SCAP, the BALF microbiota showed a significant increase in alpha diversity, which appears to mediate inflammatory cytokine production and is associated with disease worsening. There were pronouned differences between SCAP and CAP in both clinical characteristics and microbiome profiles, highlighting the necessity of integrated diagnostic approaches in pneumonia care. Future research should prioritize delineating the dynamic shifts of microbial communities and their influence on pneumonia severity, with the goal of refining and optimizing treatment strategies.\u003c/p\u003e","manuscriptTitle":"Targeted Next-Generation Sequencing Analysis of BALF Microbiota and Clinical Characteristics in Severe versus Non-Severe Community-Acquired Pneumonia","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-22 20:03:54","doi":"10.21203/rs.3.rs-8342132/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":"a6103681-5fef-4f3f-991a-aee15e756c25","owner":[],"postedDate":"January 22nd, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":61470056,"name":"Health sciences/Biomarkers"},{"id":61470057,"name":"Health sciences/Cardiology"},{"id":61470058,"name":"Health sciences/Diseases"},{"id":61470059,"name":"Health sciences/Medical research"},{"id":61470060,"name":"Biological sciences/Microbiology"}],"tags":[],"updatedAt":"2026-01-29T05:39:59+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-22 20:03:54","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8342132","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8342132","identity":"rs-8342132","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}