{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T19:14:24Z","timestamp":1784229264830,"version":"3.55.0"},"reference-count":31,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T00:00:00Z","timestamp":1661990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Diagnostics"],"abstract":"<jats:p>Objective: The purpose of this study was to explore the clinical applications of high-throughput sequencing (HTS) in the identification of pathogens in patients with urinary tract infection (UTI), peritoneal dialysis-associated peritonitis (PDAP), central venous catheter related blood infections (CRBIs), and lung infections in the nephrology department. Methods: Midstream urine samples from 112 patients with UTI, peritoneal fluid samples from 67 patients with PDAP, blood samples from 15 patients with CRBI, and sputum specimens from 53 patients with lung infection were collected. The HTS and ordinary culture methods were carried out in parallel to identify the pathogens in each sample. Pathogen detection positive rate and efficacy were compared between the two methods. Results: The pathogen positive detection rates of HTS in UTI, PDAP, CRBI, and lung infection were strikingly higher than those of the culture method (84.8% vs. 35.7, 71.6% vs. 23.9%, 75% vs. 46.7%, 84.9% vs. 5.7%, p &lt; 0.05, respectively). HTS was superior to the culture method in the sensitivity of detecting bacteria, fungi, atypical pathogens, and mixed microorganisms in those infections. In patients who had empirically used antibiotics before the test being conducted, HTS still exhibited a considerably higher positive rate than the culture method (81.6% vs. 39.0%, 68.1% vs. 14.9%, 72.7% vs. 36.4%, 83.3% vs. 4.2%, p &lt; 0.05, respectively). Conclusions: HTS is remarkably more efficient than the culture method in detecting pathogens in diverse infectious diseases in nephrology, and is particularly potential in identifying the pathogens that are unable to be identified by the common culture method, such as in cases of complex infection with specific pathogens or subclinical infection due to preemptive use of antibiotics.<\/jats:p>","DOI":"10.3390\/diagnostics12092128","type":"journal-article","created":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T21:27:17Z","timestamp":1662067637000},"page":"2128","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Application of High-Throughput Sequencing Technology in the Pathogen Identification of Diverse Infectious Diseases in Nephrology Departments"],"prefix":"10.3390","volume":"12","author":[{"given":"Yujuan","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyi","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianhua","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyun","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongqing","family":"Tong","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2836-1217","authenticated-orcid":false,"given":"Ming","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1706-2342","authenticated-orcid":false,"given":"Huiming","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Cohen, G. (2020). Immune Dysfunction in Uremia 2020. Toxins, 12.","DOI":"10.3390\/toxins12070439"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1111\/ijcp.12672","article-title":"Chronic kidney disease and end-stage renal disease are risk factors for poor outcomes of Clostridium difficile infection: A systematic review and meta-analysis","volume":"69","author":"Thongprayoon","year":"2015","journal-title":"Int. J. Clin. Pract."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/599376","article-title":"Clinical practice guidelines for the diagnosis and management of intravascular catheter-related infection: 2009 Update by the Infectious Diseases Society of America","volume":"49","author":"Mermel","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"ref_4","first-page":"822","article-title":"New Microbiological Techniques in the Diagnosis of Bloodstream Infections","volume":"115","author":"Idelevich","year":"2018","journal-title":"Dtsch. Arztebl. Int."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.cmi.2019.11.017","article-title":"Bloodstream infections\u2014Standard and progress in pathogen diagnostics","volume":"26","author":"Lamy","year":"2020","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"7143","DOI":"10.1111\/jcmm.14624","article-title":"Applications of sequencing technology in clinical microbial infection","volume":"23","author":"Yu","year":"2019","journal-title":"J. Cell. Mol. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/j.jinf.2019.08.012","article-title":"Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults","volume":"79","author":"Zhang","year":"2019","journal-title":"J. Infect."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.3389\/fmicb.2019.01993","article-title":"The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid","volume":"10","author":"Wang","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1847","DOI":"10.1093\/cid\/ciy802","article-title":"Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children","volume":"68","author":"Zinter","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1177\/0896860820970834","article-title":"ISPD guidelines for peritoneal dialysis in acute kidney injury: 2020 update (adults)","volume":"41","author":"Cullis","year":"2021","journal-title":"Perit. Dial. Int."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1007\/s10156-010-0069-1","article-title":"Blood cultures: Key elements for best practices and future directions","volume":"16","author":"Riedel","year":"2010","journal-title":"J. Infect. Chemother."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e27022","DOI":"10.1128\/spectrum.00270-22","article-title":"Clinical Performance of Nanopore Targeted Sequencing for Diagnosing Infectious Diseases","volume":"10","author":"Fu","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1093\/clinchem\/hvab061","article-title":"Clinical Evaluation of an Improved Metagenomic Next-Generation Sequencing Test for the Diagnosis of Bloodstream Infections","volume":"67","author":"Jing","year":"2021","journal-title":"Clin. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/s41564-018-0349-6","article-title":"Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease","volume":"4","author":"Blauwkamp","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu. Rev. Pathol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1097\/APO.0000000000000366","article-title":"The Next Generation of Ocular Pathogen Detection","volume":"10","author":"Sabapathypillai","year":"2021","journal-title":"Asia. Pac. J. Ophthalmol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"S231","DOI":"10.1093\/cid\/ciy693","article-title":"Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice","volume":"67","author":"Miao","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.cmi.2017.10.013","article-title":"Next-generation sequencing technologies and their application to the study and control of bacterial infections","volume":"24","author":"Besser","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Wang, H., Lu, Z., Bao, Y., Yang, Y., De Groot, R., Dai, W., De Jonge, M.I., and Zheng, Y. (2020). Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0232610"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1001\/jamaneurol.2018.0463","article-title":"Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing","volume":"75","author":"Wilson","year":"2018","journal-title":"JAMA Neurol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e00827-19","DOI":"10.1128\/JCM.00827-19","article-title":"Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo","volume":"57","author":"Li","year":"2019","journal-title":"J. Clin. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.2147\/IDR.S250654","article-title":"A Systematic Review on Drug Resistant Urinary Tract Infection Among Pregnant Women in Developing Countries in Africa and Asia; 2005\u20132016","volume":"13","author":"Belete","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref_23","first-page":"270","article-title":"Demographic characteristics and outcomes of continuous ambulatory peritoneal dialysis related peritonitis in Miri General Hospital, Malaysia","volume":"74","author":"Tang","year":"2019","journal-title":"Med. J. Malays."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"162","DOI":"10.3747\/pdi.2013.00275","article-title":"32 years\u2019 experience of peritoneal dialysis-related peritonitis in a university hospital","volume":"34","author":"Krediet","year":"2014","journal-title":"Perit. Dial. Int."},{"key":"ref_25","first-page":"561","article-title":"Central venous catheters and infections","volume":"71","author":"David","year":"2005","journal-title":"Minerva Anestesiol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ruiz-Giardin, J.M., Ochoa Chamorro, I., Vel\u00e1zquez R\u00edos, L., Jaqueti Aroca, J., Garc\u00eda Arata, M.I., SanMart\u00edn L\u00f3pez, J.V., and Guerrero Santill\u00e1n, M. (2019). Blood stream infections associated with central and peripheral venous catheters. BMC Infect. Dis., 19.","DOI":"10.1186\/s12879-019-4505-2"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/j.jiph.2016.06.008","article-title":"Hemodialysis catheter-related infection: Rates, risk factors and pathogens","volume":"10","author":"Sahli","year":"2017","journal-title":"J. Infect. Public Health"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"196","DOI":"10.2174\/1871526511313030008","article-title":"Infection and hemodialysis access: An updated review","volume":"13","author":"Gupta","year":"2013","journal-title":"Infect. Disord. Drug Targets"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2299","DOI":"10.1007\/s10096-019-03675-z","article-title":"Predicting factors for chronic colonization of Pseudomonas aeruginosa in bronchiectasis","volume":"38","author":"Pieters","year":"2019","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1093\/cid\/civ1214","article-title":"Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia","volume":"62","author":"Gadsby","year":"2016","journal-title":"Clin. Infect. Dis."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1080\/1040841X.2019.1681933","article-title":"mNGS in clinical microbiology laboratories: On the road to maturity","volume":"45","author":"Han","year":"2019","journal-title":"Crit. Rev. Microbiol."}],"container-title":["Diagnostics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-4418\/12\/9\/2128\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:21:52Z","timestamp":1760142112000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-4418\/12\/9\/2128"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,1]]},"references-count":31,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,9]]}},"alternative-id":["diagnostics12092128"],"URL":"https:\/\/doi.org\/10.3390\/diagnostics12092128","relation":{},"ISSN":["2075-4418"],"issn-type":[{"value":"2075-4418","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,1]]}}}