Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units
© 2021. The Author(s)..
BACKGROUND: Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity.
METHODS: CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave.
RESULTS: An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs.
CONCLUSION: CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:13 |
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| Enthalten in: |
Genome medicine - 13(2021), 1 vom: 17. Nov., Seite 182 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Charalampous, Themoula [VerfasserIn] |
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| Links: |
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| Themen: |
Anti-Bacterial Agents |
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| Anmerkungen: |
Date Completed 24.11.2021 Date Revised 06.03.2024 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1186/s13073-021-00991-y |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM333226666 |
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| 100 | 1 | |a Charalampous, Themoula |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units |
| 264 | 1 | |c 2021 | |
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| 500 | |a Date Completed 24.11.2021 | ||
| 500 | |a Date Revised 06.03.2024 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2021. The Author(s). | ||
| 520 | |a BACKGROUND: Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity | ||
| 520 | |a METHODS: CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave | ||
| 520 | |a RESULTS: An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs | ||
| 520 | |a CONCLUSION: CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 7 | |a Anti-Bacterial Agents |2 NLM | |
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| 700 | 1 | |a Snell, Luke B |e verfasserin |4 aut | |
| 700 | 1 | |a Williams, Tom G S |e verfasserin |4 aut | |
| 700 | 1 | |a Batra, Rahul |e verfasserin |4 aut | |
| 700 | 1 | |a Alder, Christopher |e verfasserin |4 aut | |
| 700 | 1 | |a Telatin, Andrea |e verfasserin |4 aut | |
| 700 | 1 | |a Camporota, Luigi |e verfasserin |4 aut | |
| 700 | 1 | |a Meadows, Christopher I S |e verfasserin |4 aut | |
| 700 | 1 | |a Wyncoll, Duncan |e verfasserin |4 aut | |
| 700 | 1 | |a Barrett, Nicholas A |e verfasserin |4 aut | |
| 700 | 1 | |a Hemsley, Carolyn J |e verfasserin |4 aut | |
| 700 | 1 | |a Bryan, Lisa |e verfasserin |4 aut | |
| 700 | 1 | |a Newsholme, William |e verfasserin |4 aut | |
| 700 | 1 | |a Boyd, Sara E |e verfasserin |4 aut | |
| 700 | 1 | |a Green, Anna |e verfasserin |4 aut | |
| 700 | 1 | |a Mahadeva, Ula |e verfasserin |4 aut | |
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| 700 | 1 | |a O'Grady, Justin |e verfasserin |4 aut | |
| 700 | 1 | |a Edgeworth, Jonathan D |e verfasserin |4 aut | |
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