Abstract
Rationale: Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into routine clinical practice.
Objectives: Feasibility, performance and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service.
Methods: RMg was performed on 128 samples from 87 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.
Measurements and main results: During the first 15-weeks RMg provided same-day results for 110 samples (86%) with median turnaround time of 6.7hrs (IQR 6.1-7.5 hrs). RMg was 93% sensitive and 81% 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.
Conclusions: 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. Multi-centre studies are now required to inform future translation into routine service.
Objectives: Feasibility, performance and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service.
Methods: RMg was performed on 128 samples from 87 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.
Measurements and main results: During the first 15-weeks RMg provided same-day results for 110 samples (86%) with median turnaround time of 6.7hrs (IQR 6.1-7.5 hrs). RMg was 93% sensitive and 81% 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.
Conclusions: 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. Multi-centre studies are now required to inform future translation into routine service.
| Original language | English |
|---|---|
| Journal | American Journal of Respiratory and Critical Care Medicine |
| DOIs | |
| Publication status | Published - 8 Nov 2023 |
