Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?
Published by Elsevier Inc..
Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2016 |
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| Erschienen: |
2016 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:85 |
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| Enthalten in: |
Diagnostic microbiology and infectious disease - 85(2016), 3 vom: 19. Juli, Seite 277-282 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
McGann, Patrick [VerfasserIn] |
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| Links: |
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| Themen: |
Case Reports |
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| Anmerkungen: |
Date Completed 08.02.2017 Date Revised 10.12.2019 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.diagmicrobio.2016.04.020 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM26040604X |
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| 520 | |a Published by Elsevier Inc. | ||
| 520 | |a Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations | ||
| 650 | 4 | |a Case Reports | |
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| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a Turnaround time | |
| 650 | 4 | |a Whole genome sequencing | |
| 700 | 1 | |a Bunin, Jessica L |e verfasserin |4 aut | |
| 700 | 1 | |a Snesrud, Erik |e verfasserin |4 aut | |
| 700 | 1 | |a Singh, Seema |e verfasserin |4 aut | |
| 700 | 1 | |a Maybank, Rosslyn |e verfasserin |4 aut | |
| 700 | 1 | |a Ong, Ana C |e verfasserin |4 aut | |
| 700 | 1 | |a Kwak, Yoon I |e verfasserin |4 aut | |
| 700 | 1 | |a Seronello, Scott |e verfasserin |4 aut | |
| 700 | 1 | |a Clifford, Robert J |e verfasserin |4 aut | |
| 700 | 1 | |a Hinkle, Mary |e verfasserin |4 aut | |
| 700 | 1 | |a Yamada, Stephen |e verfasserin |4 aut | |
| 700 | 1 | |a Barnhill, Jason |e verfasserin |4 aut | |
| 700 | 1 | |a Lesho, Emil |e verfasserin |4 aut | |
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