Diagnostic Yield of 16S Ribosomal Ribonucleic Acid Gene-Based Targeted Metagenomic Sequencing for Evaluation of Pleural Space Infection: A Prospective Study.

Autor:	Gimenez-Miranda L; Internal Medicine Department, Virgen del Rocío University Hospital and Clinical Epidemiology and Vascular Risk Research Group, Biomedicine Institute of Seville, Spain., Samhouri BF; Division of Pulmonary and Critical Care Medicine, Asante Health System, Medford, OR., Wolf MJ; Division of Clinical Microbiology, Mayo Clinic, Rochester, MN., Anderson DK; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN., Midthun DE; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN., Lim KG; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN., Kern RM; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN., Patel R; Division of Clinical Microbiology, Mayo Clinic, Rochester, MN.; Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, MN., Carmona EM; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN.
Jazyk:	angličtina
Zdroj:	Mayo Clinic proceedings. Innovations, quality & outcomes [Mayo Clin Proc Innov Qual Outcomes] 2023 Aug 26; Vol. 7 (5), pp. 373-381. Date of Electronic Publication: 2023 Aug 26 (Print Publication: 2023).
DOI:	10.1016/j.mayocpiqo.2023.07.010
Abstrakt:	Objective: To better understand the microbial profile of complicated parapneumonic effusions and empyema, and to evaluate whether antimicrobial selection would differ if guided by targeted metagenomic sequencing (tMGS) vs conventional cultures (CCs) alone. Patients and Methods: We analyzed the pleural fluid of a cohort of 47 patients undergoing thoracentesis from January 1, 2017 to August 31, 2019, to characterize their microbial profile. All samples underwent 16S ribosomal ribonucleic acid gene polymerase chain reaction, followed by tMGS. Results: Pleural space infection was deemed clinically present in 20 of the 47 (43%) participants. Of those, n=7 (35%) had positive pleural fluid cultures and n=14 (70%) had positive tMGS results. The organisms identified by tMGS were concordant with CCs; however, tMGS detected additional bacterial species over CCs alone. Streptococcus and Staphylococcus species were the most common organisms identified, with Streptococcus intermedius/constellatus identified in 5 patients . Polymicrobial infections were found in 6 of the 20 patients, with anaerobes being the most common organisms identified in these cases. Conclusion: Streptococci and staphylococci were the most common organisms identified in infected pleural fluid. Anaerobes were common in polymicrobial infections. When compared with CCs, tMGS had higher sensitivity than CCs. Targeted metagenomic sequencing identified additional organisms, not identified by CCs, with associated potential management implications. Competing Interests: Dr Patel reports receiving grants from ContraFect, TenNor Therapeutics Limited, and BioFire. Dr Patel is a consultant for PhAST, Torus Biosystems, Day Zero Diagnostics, Mammoth Biosciences, and HealthTrackRx; monies are paid to Mayo Clinic. Mayo Clinic and Dr Patel have a relationship with Pathogenomix. Dr Patel has research supported by Adaptive Phage Therapeutics. Mayo Clinic has a royalty-bearing know-how agreement and equity in Adaptive Phage Therapeutics. Dr Patel is also a consultant for Netflix, Abbott Laboratories, Oxford Nanopore Technologies, and CARB-X. In addition, Dr Patel has a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, with royalties paid by Samsung to Mayo Clinic, and a patent on an anti-biofilm substance issued. Dr Patel receives honoraria from the NBME, Up-to-Date and the Infectious Diseases Board Review Course. Dr Samhouri reports providing consultation (unpaid) to AI Therapeutics that is unrelated to the submitted work. Dr Carmona reports providing consultation to Boehringer Ingelheim for sarcoidosis that is unrelated to the submitted work. (© 2023 The Authors.)
Databáze:	MEDLINE
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