{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T05:27:19Z","timestamp":1734672439462,"version":"3.32.0"},"reference-count":18,"publisher":"Akademiai Kiado Zrt.","issue":"4","license":[{"start":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T00:00:00Z","timestamp":1734566400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Medical Research Fund of Guangdong Province","award":["B2024095"],"award-info":[{"award-number":["B2024095"]}]},{"name":"2023 Joint Chinese-Western Medicine \u201cFlagship\u201d Hospital Special In-House","award":["ZXYXTQJ202301"],"award-info":[{"award-number":["ZXYXTQJ202301"]}]},{"name":"Teaching Reform Project of the First Affiliated Hospital (Clinical Medical School) of Guangdong Pharmaceutical University","award":["2021JX09"],"award-info":[{"award-number":["2021JX09"]}]}],"content-domain":{"domain":["akjournals.com"],"crossmark-restriction":true},"short-container-title":["AMicr"],"published-print":{"date-parts":[[2024,12,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The incidence of lower respiratory tract infections (LRTIs) caused by multidrug-resistant organisms (MDRO) has been high in recent years. However, traditional etiological detection methods have not been able to meet the needs for clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for diagnosis and treatment of\u00a0LRTIs. We conducted a retrospective study on 95 patients with lower respiratory tract infections caused by MDRO admitted to our respiratory department from January 2022 to December 2023. These\u00a0patients underwent mNGS testing and conventional culture testing. Additionally, 150 patients without lower respiratory tract infections caused by MDRO during the same period were included as the\u00a0non-MDRO group. General information was collected, and Logistic regression analysis was performed to identify risk factors for MDRO infections in patients with lower respiratory tract infections. Our results show that the time to pathogen detection by mNGS was 50.76 \u00b1 1.730\u2009h, that is significantly shorter than 55.53 \u00b1 2.782\u2009h required for conventional culture testing. The pathogen detection rate by mNGS was 89.47% (85\/95), higher than the 67.37% (64\/95) identified by conventional testing. In terms of pathogen genus distribution, mNGS detected a total of 279 pathogens, while conventional testing detected 121 pathogens. Logistic multivariate regression analysis identified that the use of more than\u00a0two antibiotics, invasive procedures, invasive mechanical ventilation for \u22657 days, and stay in the\u00a0respiratory intensive care unit (RICU) for \u22657 days were the main influencing factors for lower respiratory tract infections caused by MDRO (<jats:italic>P<\/jats:italic> &lt; 0.05).<\/jats:p>","DOI":"10.1556\/030.2024.02463","type":"journal-article","created":{"date-parts":[[2024,12,17]],"date-time":"2024-12-17T11:59:15Z","timestamp":1734436755000},"page":"273-279","update-policy":"https:\/\/doi.org\/10.1556\/policypage.crossmark.crossref.2","source":"Crossref","is-referenced-by-count":0,"title":["Application of metagenomic next-generation sequencing in pathogen detection for patients with lower respiratory tract infections caused by\u00a0multidrug-resistant organisms and analysis of\u00a0related factors"],"prefix":"10.1556","volume":"71","author":[{"given":"Yanqun","family":"Zhao","sequence":"first","affiliation":[{"name":"Infection Management Department, First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Mao","sequence":"additional","affiliation":[{"name":"Respiratory Department, First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanyun","family":"Zhong","sequence":"additional","affiliation":[{"name":"Infection Management Department, First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinghui","family":"Lu","sequence":"additional","affiliation":[{"name":"Infection Management Department, First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Gong","sequence":"additional","affiliation":[{"name":"Infection Management Department, First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenhua","family":"Yi","sequence":"additional","affiliation":[{"name":"Infection Management Department, First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2701-8556","authenticated-orcid":true,"given":"Zhihuan","family":"Zeng","sequence":"additional","affiliation":[{"name":"Cardiology Department, First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"425","reference":[{"issue":"3","key":"B1","series-title":"Int J Antimicrob Agents","first-page":"106886","article-title":"Changes in the prevalence of pathogens causing hospital-acquired bacterial pneumonia and the impact of their antimicrobial resistance patterns on clinical outcomes: a propensity-score-matched study","volume":"62","author":"Choi MH","year":"2023","unstructured":"Choi MH, Kim D, Lee KH, Cho JH, Jeong SH. Changes in the prevalence of pathogens causing hospital-acquired bacterial pneumonia and the impact of their antimicrobial resistance patterns on clinical outcomes: a propensity-score-matched study. Int J Antimicrob Agents 2023; 62(3): 106886. https:\/\/doi.org\/10.1016\/j.ijantimicag.2023.106886."},{"issue":"2","key":"B2","series-title":"Clin Microbiol Infect","first-page":"174","article-title":"Critical factors in the recovery of pathogenic microorganisms in blood","volume":"26","author":"Wilson M","year":"2020","unstructured":"Wilson M. Critical factors in the recovery of pathogenic microorganisms in blood. Clin Microbiol Infect 2020; 26(2): 174\u2013179. https:\/\/doi.org\/10.1016\/j.cmi.2019.07.023."},{"issue":"5","key":"B3","series-title":"Curr Opin Microbiol","first-page":"589","article-title":"Antibiotic resistance in the environment: a link to the clinic?","volume":"13","author":"Wright GD","year":"2010","unstructured":"Wright GD. Antibiotic resistance in the environment: a link to the clinic? Curr Opin Microbiol 2010; 13(5): 589\u2013594. https:\/\/doi.org\/10.1016\/j.mib.2010.08.005."},{"key":"B4","series-title":"PeerJ","first-page":"e11699","article-title":"Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study","volume":"9","author":"Chen H","year":"2021","unstructured":"Chen H, Li J, Yan S, Sun H, Tan C, Liu M, et al. Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study. PeerJ 2021; 9: e11699. https:\/\/doi.org\/10.7717\/peerj.11699."},{"issue":"1","key":"B5","series-title":"Sci Rep","first-page":"24493","article-title":"Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens","volume":"14","author":"Jia X","year":"2024","unstructured":"Jia X, Wang W, Wu M, Pang L, Yang C, Ling Y, et al. Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens. Sci Rep 2024; 14(1): 24493. https:\/\/doi.org\/10.1038\/s41598-024-75120-x."},{"key":"B6","series-title":"Front Cell Infect Microbiol","first-page":"694756","article-title":"The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection","volume":"11","author":"Zheng Y","year":"2021","unstructured":"Zheng Y, Qiu X, Wang T, Zhang J. The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection. Front Cell Infect Microbiol 2021; 11: 694756. https:\/\/doi.org\/10.3389\/fcimb.2021.694756."},{"issue":"4","key":"B7","series-title":"Virulence","first-page":"460","article-title":"The global epidemiology of carbapenemase-producing Enterobacteriaceae","volume":"8","author":"van Duin D","year":"2017","unstructured":"van Duin D, Doi Y. The global epidemiology of carbapenemase-producing Enterobacteriaceae. Virulence 2017; 8(4): 460\u2013469. https:\/\/doi.org\/10.1080\/21505594.2016.1250574."},{"issue":"3","key":"B8","series-title":"Lancet Infect Dis","first-page":"318","article-title":"Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis","volume":"18","author":"Tacconelli E","year":"2018","unstructured":"Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M, Monnet DL, et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis 2018; 18(3): 318\u2013327. https:\/\/doi.org\/10.1016\/S1473-3099(17)30753-3."},{"issue":"25","key":"B9","series-title":"N Engl J Med","first-page":"2408","article-title":"Actionable diagnosis of neuroleptospirosis by next-generation sequencing","volume":"370","author":"Wilson MR","year":"2014","unstructured":"Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 2014; 370(25): 2408\u20132417. https:\/\/doi.org\/10.1056\/NEJMoa1401268."},{"key":"B10","series-title":"Annu Rev Pathol","first-page":"319","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu W","year":"2019","unstructured":"Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol 2019; 14: 319\u2013338. https:\/\/doi.org\/10.1146\/annurev-pathol-020117-043617."},{"issue":"5","key":"B11","series-title":"Clin Infect Dis","first-page":"778","article-title":"Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases","volume":"66","author":"Simner PJ","year":"2018","unstructured":"Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis 2018; 66(5): 778\u2013788. https:\/\/doi.org\/10.1093\/cid\/cix881."},{"issue":"4","key":"B12","series-title":"Nat Microbiol","first-page":"663","article-title":"Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease","volume":"4","author":"Blauwkamp TA","year":"2019","unstructured":"Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vilfan ID, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol 2019; 4(4): 663\u2013674. https:\/\/doi.org\/10.1038\/s41564-018-0349-6."},{"issue":"6","key":"B13","series-title":"Nat Rev Genet","first-page":"341","article-title":"Clinical metagenomics","volume":"20","author":"Chiu CY","year":"2019","unstructured":"Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet 2019; 20(6): 341\u2013355. https:\/\/doi.org\/10.1038\/s41576-019-0113-7."},{"issue":"12","key":"B14","series-title":"Lancet Infect Dis","first-page":"1057","article-title":"Antibiotic resistance\u2014the need for global solutions","volume":"13","author":"Laxminarayan R","year":"2013","unstructured":"Laxminarayan R, Duse A, Wattal C, Zaidi AK, Wertheim HF, Sumpradit N, et al. Antibiotic resistance\u2014the need for global solutions. Lancet Infect Dis 2013; 13(12): 1057\u20131098. https:\/\/doi.org\/10.1016\/S1473-3099(13)70318-9."},{"issue":"5","key":"B15","series-title":"N Engl J Med","first-page":"407","article-title":"Duodenal infusion of donor feces for recurrent Clostridium difficile","volume":"368","author":"van Nood E","year":"2013","unstructured":"van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013; 368(5): 407\u2013415. https:\/\/doi.org\/10.1056\/NEJMoa1205037."},{"issue":"2","key":"B16","series-title":"J Mol Diagn","first-page":"165","article-title":"Metagenomic next-generation sequencing for infectious disease diagnosis: a review of technologies, applications, and challenges","volume":"23","author":"Gu W","year":"2021","unstructured":"Gu W, Miller S, Chiu CY. Metagenomic next-generation sequencing for infectious disease diagnosis: a review of technologies, applications, and challenges. J Mol Diagn 2021; 23(2): 165\u2013182. https:\/\/doi.org\/10.1016\/j.jmoldx.2020.10.004."},{"issue":"3","key":"B17","series-title":"Lancet Infect Dis","first-page":"318","article-title":"Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis","volume":"18","author":"Tacconelli E","year":"2018","unstructured":"Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M, Monnet DL, et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis 2018; 18(3): 318\u2013327. https:\/\/doi.org\/10.1016\/S1473-3099(17)30753-3."},{"issue":"12","key":"B18","series-title":"N Engl J Med","first-page":"1107","article-title":"Neuromuscular blockers in early acute respiratory distress syndrome","volume":"363","author":"Papazian L","year":"2010","unstructured":"Papazian L, Forel JM, Gacouin A, Penot-Ragon C, Perrin G, Loundou A, et al. Neuromuscular blockers in early acute respiratory distress syndrome. N Engl J Med 2010; 363(12): 1107\u20131116. https:\/\/doi.org\/10.1056\/NEJMoa1005372."}],"container-title":["Acta Microbiologica et Immunologica Hungarica"],"original-title":[],"link":[{"URL":"https:\/\/akjournals.com\/view\/journals\/030\/71\/4\/article-p273.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/akjournals.com\/downloadpdf\/journals\/030\/71\/4\/article-p273.xml","content-type":"text\/html","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/akjournals.com\/downloadpdf\/journals\/030\/71\/4\/article-p273.xml","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T13:45:27Z","timestamp":1734615927000},"score":1,"resource":{"primary":{"URL":"https:\/\/akjournals.com\/view\/journals\/030\/71\/4\/article-p273.xml"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,19]]},"references-count":18,"journal-issue":{"issue":"4"},"URL":"https:\/\/doi.org\/10.1556\/030.2024.02463","relation":{},"ISSN":["1217-8950","1588-2640"],"issn-type":[{"type":"print","value":"1217-8950"},{"type":"electronic","value":"1588-2640"}],"subject":[],"published":{"date-parts":[[2024,12,19]]}}}