Routine respiratory metagenomics service for intensive care unit patients
Routine respiratory metagenomics service for intensive care unit patients
Abstract BackgroundRespiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into clinical practice. MethodsFeasibility, performance and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service for patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory intensive care units (ICU) at Guy’s & St Thomas NHS foundation Trust, London. ResultsRMg was performed on 128 samples from 87 patients during the first 15-weeks providing same-day results for 110 samples (86%) with median turnaround time of 6.7hrs (IQR 6.1-7.5 hrs). RMg was 92% sensitive and 82% specific for clinically-relevant pathogens compared with routine testing. 48% of RMg results informed antimicrobial prescribing changes (22% escalation; 26% de-escalation) with escalation based on speciation in 20/24 cases and detection of acquired-resistance genes in 4/24 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 bed-side 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. ConclusionsRMg provides frequent diverse benefits for treatment, infection control and public health. The combination of rapid comprehensive results, alongside revealing and characterising a hidden burden of infections makes the case for expediting routine service implementation.
Batra Rahul、Barrett Nicholas A.、Jeyaratnam Dakshika、Tucker Fearghal、Nebbia Gaia、O?ˉGrady Justin、Williams Tom G.S.、Humayun Gul、Meadows Christopher I.S.、Richard Paul、Al-Yaakoubi Noor、Edgeworth Jonathan D.、Newsholme William、Wilks Mark、Charalampous Themoula、Wyncoll Duncan L.A.、Cliff Penelope R.、Hemsley Carolyn J.、Chand Meera、Alcolea-Medina Adela、Snell Luke B.、Tan Mark、Patel Amita、Goldenberg Simon、Alder Christopher
Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College London||Department of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustCritical Care Directorate, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustDepartment of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustInfection SciencesDepartment of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustOxford Nanopore Technologies (ONT)Department of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College LondonCritical Care Directorate, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation Trust||Faculty of Life Sciences and Medicine, King?ˉs CollegeCritical Care Directorate, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College LondonCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College London||Department of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustDepartment of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustQueen Mary UniversityCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College LondonCritical Care Directorate, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustInfection SciencesDepartment of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustThe UK Health Security Agency (UKHSA)Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College London||Infection SciencesCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College London||Department of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College LondonCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College London||Department of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustDepartment of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation TrustCentre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King?ˉs College London||Department of Infectious Diseases, Guy?ˉs and St Thomas?ˉ Hospital NHS Foundation Trust
医学研究方法临床医学微生物学
Batra Rahul,Barrett Nicholas A.,Jeyaratnam Dakshika,Tucker Fearghal,Nebbia Gaia,O?ˉGrady Justin,Williams Tom G.S.,Humayun Gul,Meadows Christopher I.S.,Richard Paul,Al-Yaakoubi Noor,Edgeworth Jonathan D.,Newsholme William,Wilks Mark,Charalampous Themoula,Wyncoll Duncan L.A.,Cliff Penelope R.,Hemsley Carolyn J.,Chand Meera,Alcolea-Medina Adela,Snell Luke B.,Tan Mark,Patel Amita,Goldenberg Simon,Alder Christopher.Routine respiratory metagenomics service for intensive care unit patients[EB/OL].(2025-03-28)[2025-04-29].https://www.medrxiv.org/content/10.1101/2023.05.15.23289731.点此复制
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