Autor: |
Penelope R. Cliff, Carolyn J Hemsley, Lisa Bryan, Rahul Batra, Luke B Snell, Justin O'Grady, Christopher I S Meadows, Luigi Camporota, Ula Mahadeva, Themoula Charalampous, Andrew J. Page, Nicholas A Barrett, Tom G. S. Williams, Jonathan D. Edgeworth, Amita Patel, Anna Green, Duncan Wyncoll, Adela Alcolea-Medina, Sara E Boyd, William Newsholme |
Rok vydání: |
2020 |
Předmět: |
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Popis: |
BackgroundClinical metagenomics (CMg) is being evaluated for translation from a research tool into routine diagnostic service, but its potential to significantly improve management of acutely unwell patients has not been demonstrated. The SARS-CoV-2 pandemic provides impetus to determine that benefit given increased risk of secondary infection and nosocomial transmission by multi-drug resistant (MDR) pathogens linked with expansion of critical care capacity.MethodsProspective evaluation of CMg using nanopore sequencing was performed on 43 respiratory samples over 14 weeks from a cohort of 274 intubated patients across seven COVID-19 intensive care units.ResultsBacteria or fungi were cultured from 200 (73%) patients, with a predominance of Klebsiella spp. (31%) and C. striatum (7%) amongst other common respiratory pathogens. An 8 hour CMg workflow was 93% sensitive and 81% specific for bacterial identification compared to culture, and reported presence or absence of β-lactam resistance genes carried by Enterobacterales that would modify initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus (4 positive and 39 negative samples). Single nucleotide polymorphism (SNP)-typing using 24 hour sequence data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak potentially involving 14 patients across three ICUs.ConclusionCMg testing for ICU patients provides same-day pathogen detection and antibiotic resistance prediction that significantly improves initial treatment of nosocomial pneumonia and rapidly detects unsuspected outbreaks of MDR-pathogens. |
Databáze: |
OpenAIRE |
Externí odkaz: |
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