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CTD patients undergoing bronchoscopy and BALF-tNGS between January 2022 and July 2025 were enrolled, and results were compared with conventional microbiological tests (CMTs). Logistic regression identified risk factors for mono- versus polymicrobial infection. BALF-tNGS showed significantly higher sensitivity and altered treatment in nearly half of patients.",{"@graph":69,"@context":123},[70,84,106],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":35,"@type":76,"position":81},"https://docshare.wps.com/document/healthcare/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/targeted-next-generation-sequencing-of-bronchoalveolar-lavage-fluid-for-pathogen-detection-in-connective-tissue-disease-related-pulmonary-infections/446563/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/targeted-next-generation-sequencing-of-bronchoalveolar-lavage-fluid-for-pathogen-detection-in-connective-tissue-disease-related-pulmonary-infections/446563.png","ImageObject",300,407,{"name":92,"@type":93},"Mabel","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-31","2026-09-29",true,{"@type":102,"interactionType":103,"userInteractionCount":105},"InteractionCounter",{"@type":104},"ViewAction",16,{"@type":107,"mainEntity":108},"FAQPage",[109,115,119],{"name":110,"@type":111,"acceptedAnswer":112},"What is the main objective of BALF-tNGS in this study?","Question",{"text":113,"@type":114},"To assess the clinical value of targeted next-generation sequencing of bronchoalveolar lavage fluid for detecting pathogens in CTD-related pulmonary infections and to characterize infection profiles.","Answer",{"name":116,"@type":111,"acceptedAnswer":117},"How were BALF-tNGS results evaluated against conventional microbiological tests?",{"text":118,"@type":114},"BALF-tNGS detected pathogens in a larger proportion of patients and yielded more isolates across bacteria, viruses, fungi, and Mycoplasma pneumoniae compared with CMTs.",{"name":120,"@type":111,"acceptedAnswer":121},"Which factors were identified as independent risk factors for polymicrobial infection?",{"text":122,"@type":114},"Interstitial lung disease (ILD), chronic kidney disease (CKD), and decreased T-cell count were identified as independent risk factors for polymicrobial infection.","https://schema.org",{"og:url":83,"og:type":125,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":127,"canonical":83},"index,follow",{"doc_id":129,"site_id":62},446563,1791033052,{"code":4,"msg":5,"data":132},{"doc_id":129,"user_id":133,"nickname":92,"user_avatar":134,"doc_module":4,"category_id":34,"category_name":35,"doc_title":65,"doc_description":67,"doc_content":135,"file_id":136,"file_url":137,"file_type":138,"file_size":139,"view_count":105,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":140,"language":141,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":142,"faqs":143,"seo_title":144,"seo_description":67,"update_tm":145,"read_time":146,"preview_page_count":4},7971474920318,"https://ap-avatar.wpscdn.com/avatar/74000ee537e6b0ca360?x-image-process=image/resize,m_fixed,w_180,h_180&k=1788430171632181674","| Open Peer Review | Clinical Microbiology | Research Article  \nTargeted next-generation sequencing of bronchoalveolar lavage fluid for pathogen detection in connective tissue disease-related pulmonary infections  \nXiaoyan Zhong,1,2 Yuheng Xing,1 Yuexi Zhang,1 Zhiheng Luo,3 Wu Xu,3 Xu Chen,1 Meng Liu,1 Guanqun Yi,1 Yukai Huang,1 Shaoling Zheng,1 Weiming Deng,1 Xuechan Huang,1 Tianwang Li,1,4 Zhengping Huang1  \nAUTHOR AFFILIATIONS See affiliation list on p. 12.  \nABSTRACT The study aims to assess the clinical value of targeted next-generation sequencing of bronchoalveolar lavage fluid (BALF-tNGS) in pulmonary infection associated with connective tissue diseases (CTDs) and characterize the infection profilesin these patients. CTD patients undergoing bronchoscopy with BALF-tNGS between January 2022 to July 2025 were enrolled. tNGS results were compared with conventional microbiological tests (CMTs) . Logistic regression identified risk factors for monomicrobial infection and polymicrobial infection. Among 124 CTD patients enrolled, 45 (36.3%) were male with the mean age of 52.6 ± 15.4 years, and the mean disease duration was 4.1 ± 6.1 years. CMTs detected pathogens in 43 patients, yielding 55 isolates: 23 bacteria, 13 viruses, 12 fungi, and 9 Mycoplasma pneumoniae. tNGS identified pathogens in 105 patients, yielding 168 isolates: 70 bacteria, 48 viruses, 43 fungi, and 7 M. pneumoniae. The sensitivity of tNGS was significantly higher than that of CMTs (P = 0.02) . Treatment regimens were adjusted in 54 patients (49.5%) based on tNGS results. Polymicrobial infection was observed in 44 patients (40.37%), whereas 65 patients (59.63%) had monomicrobial infection. Multivariable analysis identified interstitial lung disease (ILD; odds ratio [OR] 3.90, 95% confidence interval [CI] 1.42–10.72), chronic kidney disease (CKD; OR 6. 75, 95% CI 1.09–41.81), and decreased T-cell count (OR 0.30, 95% CI 0.13– 0.69) as independent risk factors for polymicrobial infection. BALF-tNGS substantially increases the sensitivity of pathogen detection in CTD-related pulmonary infection and guides pathogen-directed antimicrobial therapy. Polymicrobial infection is common in CTD patients; ILD, CKD, and reduced T-cell counts are independent risk factors for its development.  \nIMPORTANCE The study delineates the infection landscape of connective tissue disease-related pneumonia and demonstrates that targeted next-generation sequencing of bronchoalveolar lavage fluid (BALF-tNGS) doubles the yield of identified pathogens, frequently revealing polymicrobial disease. This molecular insight prompted a change in antimicrobial therapy in nearly half of the cohort. Patients with concurrent interstitial lung disease, renal impairment, or lymphopenia were particularly susceptible to mixed infections. By enabling pathogen-directed treatment, BALF-tNGS reduces unnecessary antibiotic exposure, shortens recovery, and supports early, precision therapy.  \nKEYWORDS targeted next-generation sequencing, bronchoalveolar lavage fluid, connective tissue disease, pulmonary infections, lupus  \nC onnective tissue diseases (CTDs), including rheumatoid arthritis (RA), systemic lupus  \nerythematosus (SLE), dermatomyositis (DM), and primary Sjögren’s syndrome (pSS), refer to a cluster of autoimmune disorders characterized by chronic inflammation and  \nEditor Benjamin M. Liu, Children's National Hospital, George Washington University, Washington, DC, USA  \nPeer Reviewer Shivaprakash M. Rudramurthy, Postgraduate Institute of Medical Education and Research, Chandigarh, India  \nAddress correspondence to Zhengping Huang, [zhuangrheu@gmail.com](zhuangrheu@gmail.com), or Tianwang Li, litian[wang@163.com](wang@163.com).  \nXiaoyan Zhong, Yuheng Xing, and Yuexi Zhang contributed equally to this article. The author order was determined based on the sequence of their contributions the research  \ndamage to connective tissues, affecting multiple organ systems including the skin, joints, blood vessels, ","cbCaihFhuYL1lfx2","https://ap.wps.com/l/cbCaihFhuYL1lfx2","pdf",507233,13,"English","# Abstract\n## Study design and comparison (BALF-tNGS vs CMTs)\n## Pathogen detection and infection profiles\n## Risk factors for mono- vs polymicrobial infection\n## Clinical impact and treatment guidance","[{\"question\":\"What is the main objective of BALF-tNGS in this study?\",\"answer\":\"To assess the clinical value of targeted next-generation sequencing of bronchoalveolar lavage fluid for detecting pathogens in CTD-related pulmonary infections and to characterize infection profiles.\"},{\"question\":\"How were BALF-tNGS results evaluated against conventional microbiological tests?\",\"answer\":\"BALF-tNGS detected pathogens in a larger proportion of patients and yielded more isolates across bacteria, viruses, fungi, and Mycoplasma pneumoniae compared with CMTs.\"},{\"question\":\"Which factors were identified as independent risk factors for polymicrobial infection?\",\"answer\":\"Interstitial lung disease (ILD), chronic kidney disease (CKD), and decreased T-cell count were identified as independent risk factors for polymicrobial infection.\"}]","Targeted next-generation sequencing of bronchoalveolar lavage fluid for pathogen detection in connective tissue disease-related pulmonary infections | PDF",1790715980,33]