Routine Metagenomics Service for ICU Patients with Respiratory Infection.
Routine Metagenomics Service for ICU Patients with Respiratory Infection.
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用于ICU呼吸道感染的ICU患者的常规宏基因组学服务。
DOI：
10.1164/rccm.202305-0901oc
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发表时间：
2024-01-15
影响因子：
24.7
通讯作者：
Edgeworth, Jonathan D.
中科院分区：
文献类型：
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作者：
Charalampous, Themoula;Alcolea-Medina, Adela;Snell, Luke B.;Alder, Christopher;Tan, Mark;Williams, Tom G. S.;Al-Yaakoubi, Noor;Humayun, Gul;Meadows, Christopher I. S.;Wyncoll, Duncan L. A.;Paul, Richard;Hemsley, Carolyn J.;Jeyaratnam, Dakshika;Newsholme, William;Goldenberg, Simon;Patel, Amita;Tucker, Fearghal;Nebbia, Gaia;Wilks, Mark;Chand, Meera;Cliff, Penelope R.;Batra, Rahul;O'Grady, Justin;Barrett, Nicholas A.;Edgeworth, Jonathan D.
呼吸元基因组学(RMG)需要在试点服务环境中进行评估，以确定实用性并将其应用到常规临床实践中。在RMG试点服务期间，记录了抗菌药物处方和感染控制的可行性、性能和临床影响。在伦敦盖伊和圣托马斯NHS基金会信托基金的两个普通呼吸ICU和一个专科呼吸ICU中，对87名疑似下呼吸道感染(LRTI)患者的128份样本进行了RMG检查。在最初的15个 周内，RMG提供了110个样本(86%)的当天结果，中位数周转时间为6.7 小时(四分位数范围 = 6.1-7.5 h)。与常规检测相比，RMG对临床相关病原体的敏感度为93%，特异度为81%。48%的RMG结果通知了抗菌药物处方的变化(22%升级；26%降级)，24例中有20例基于物种形成的升级，24例中4例检测到获得性耐药基因。在21个样本中报告了挑剔或意想不到的微生物，包括厌氧菌(n = 12)、结核分枝杆菌、斜纹夜蛾、巨细胞病毒和嗜肺军团菌ST1326，随后从床边排水口分离出该菌。应用于连续的严重社区获得性下呼吸道感染病例，发现了多种治疗方法和公共卫生影响的金黄色葡萄球菌(2例具有SCCmec和3例具有Luk F/S毒力决定簇)、化脓性链球菌(emm1-M1uk克隆)、等同半乳链球菌亚种(STG62647A)和烟曲霉菌。这项初步研究表明，RMG检测在现实世界的重症监护环境中提供时，有可能为抗菌治疗、感染控制和公共卫生提供好处。现在需要进行多中心研究，以便为未来的翻译提供常规服务。
Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into routine clinical practice. Feasibility, performance, and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service. RMg was performed on 128 samples from 87 patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory ICUs at Guy’s and St Thomas’ NHS Foundation Trust, London. During the first 15 weeks, RMg provided same-day results for 110 samples (86%), with a median turnaround time of 6.7 hours (interquartile range = 6.1–7.5 h). RMg was 93% sensitive and 81% specific for clinically relevant pathogens compared with routine testing. Forty-eight percent of RMg results informed antimicrobial prescribing changes (22% escalation; 26% deescalation) with escalation based on speciation in 20 out of 24 cases and detection of acquired-resistance genes in 4 out of 24 cases. Fastidious or unexpected organisms were reported in 21 samples, including anaerobes (n = 12), Mycobacterium tuberculosis, Tropheryma whipplei, cytomegalovirus, and Legionella pneumophila ST1326, which was subsequently isolated from the bedside water outlet. Application to consecutive severe community-acquired LRTI cases identified Staphylococcus aureus (two with SCCmec and three with luk F/S virulence determinants), Streptococcus pyogenes (emm1-M1uk clone), S. dysgalactiae subspecies equisimilis (STG62647A), and Aspergillus fumigatus with multiple treatments and public health impacts. This pilot study illustrates the potential of RMg testing to provide benefits for antimicrobial treatment, infection control, and public health when provided in a real-world critical care setting. Multicenter studies are now required to inform future translation into routine service.