基于16S核糖体核糖核酸基因的靶向宏基因组测序评估胸膜间隙感染的诊断率:一项前瞻性研究

Luis Gimenez-Miranda MD , Bilal F. Samhouri MD , Matthew J. Wolf MS , Dagny K. Anderson MD , David E. Midthun MD , Kaiser G. Lim MD , Ryan M. Kern MD , Robin Patel MD , Eva M. Carmona MD, PhD
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The organisms identified by tMGS were concordant with CCs; however, tMGS detected additional bacterial species over CCs alone. <em>Streptococcus</em> and <em>Staphylococcus species</em> were the most common organisms identified, with <em>Streptococcus intermedius/constellatus</em> identified in 5 patients<em>.</em> Polymicrobial infections were found in 6 of the 20 patients, with anaerobes being the most common organisms identified in these cases.</p></div><div><h3>Conclusion</h3><p><em>Streptococci</em> and <em>staphylococci</em> 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.</p></div>\",\"PeriodicalId\":94132,\"journal\":{\"name\":\"Mayo Clinic proceedings. 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引用次数: 0

摘要

目的更好地了解复杂肺旁积液和脓胸的微生物特征,并评估靶向宏基因组测序(targeted metagenomics sequencing, tMGS)与常规培养(conventional cultures, CCs)在抗菌药物选择上的差异。患者和方法我们分析了2017年1月1日至2019年8月31日47例胸腔穿刺患者的胸腔液,以表征其微生物谱。所有样品均进行16S核糖体核糖核酸基因聚合酶链反应,然后进行tMGS。结果47例参与者中有20例(43%)被认为临床存在胸膜间隙感染。其中,n=7(35%)胸膜液培养阳性,n=14 (70%) tMGS结果阳性。tMGS鉴定的生物与CCs一致;然而,tMGS在单独的CCs上检测到额外的细菌种类。链球菌和葡萄球菌是最常见的微生物,其中5例患者检出中间/星座链球菌。20例患者中有6例发现多微生物感染,厌氧菌是这些病例中最常见的微生物。结论链球菌和葡萄球菌是感染胸膜液中最常见的细菌。厌氧菌在多微生物感染中很常见。与CCs相比,tMGS的敏感性高于CCs。靶向宏基因组测序鉴定了其他未被CCs鉴定的生物体,具有相关的潜在管理意义。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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

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

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.

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来源期刊
Mayo Clinic proceedings. Innovations, quality & outcomes
Mayo Clinic proceedings. Innovations, quality & outcomes Surgery, Critical Care and Intensive Care Medicine, Public Health and Health Policy
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