Routine respiratory metagenomics service for intensive care unit patients
Abstract Background Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into clinical practice.Methods Feasibility, 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.Results RMg 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 andLegionella pneumophilaST1326, which was subsequently isolated from the bed-side water outlet. Application to consecutive severe community-acquired LRTI cases identifiedStaphylococcus aureus(two withSCCmecand three withlukF/S virulence determinants),Streptococcus pyogenes(emm1-M1uk clone),S. dysgalactiaesubspecies equisimilis (STG62647A) andAspergillus fumigatuswith multiple treatments and public-health impacts.Conclusions RMg 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..
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Preprint| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
bioRxiv.org - (2023) vom: 18. Mai Zur Gesamtaufnahme - year:2023 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Charalampous, Themoula [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| doi: |
10.1101/2023.05.15.23289731 |
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| PPN (Katalog-ID): |
XBI039572099 |
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| 520 | |a Abstract Background Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into clinical practice.Methods Feasibility, 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.Results RMg 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 andLegionella pneumophilaST1326, which was subsequently isolated from the bed-side water outlet. Application to consecutive severe community-acquired LRTI cases identifiedStaphylococcus aureus(two withSCCmecand three withlukF/S virulence determinants),Streptococcus pyogenes(emm1-M1uk clone),S. dysgalactiaesubspecies equisimilis (STG62647A) andAspergillus fumigatuswith multiple treatments and public-health impacts.Conclusions RMg 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. | ||
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| 700 | 1 | |a Tan, Mark |4 aut | |
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