Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study.
Infection control
SARS-CoV-2
Sequencing
Turnaround time
Journal
The Journal of hospital infection
ISSN: 1532-2939
Titre abrégé: J Hosp Infect
Pays: England
ID NLM: 8007166
Informations de publication
Date de publication:
Jan 2023
Jan 2023
Historique:
received:
21
06
2022
revised:
13
09
2022
accepted:
22
09
2022
pubmed:
14
10
2022
medline:
18
1
2023
entrez:
13
10
2022
Statut:
ppublish
Résumé
Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis. The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT. Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.
Sections du résumé
BACKGROUND
BACKGROUND
Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions.
AIM
OBJECTIVE
To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study.
METHODS
METHODS
For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis.
FINDINGS
RESULTS
The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT.
CONCLUSION
CONCLUSIONS
Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.
Identifiants
pubmed: 36228768
pii: S0195-6701(22)00318-8
doi: 10.1016/j.jhin.2022.09.022
pmc: PMC9550290
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
34-42Subventions
Organisme : Medical Research Council
ID : MC_PC_19027
Pays : United Kingdom
Informations de copyright
Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.
Références
Lancet Microbe. 2020 Jul;1(3):e99-e100
pubmed: 32835336
Clin Chem. 2021 Dec 30;68(1):153-162
pubmed: 34633030
Elife. 2022 Sep 13;11:
pubmed: 36098502
BMJ Open. 2012 Jun 06;2(3):
pubmed: 22674929
BMJ Open. 2022 Apr 19;12(4):e052514
pubmed: 35440446
J Infect Dis. 2022 Jan 5;225(1):10-18
pubmed: 34555152
Elife. 2021 Jun 29;10:
pubmed: 34184637
Front Genet. 2021 Nov 02;12:774846
pubmed: 34795698
J Mol Diagn. 2017 Mar;19(2):303-312
pubmed: 28041870
Clin Infect Dis. 2021 Dec 1;73(Suppl_4):S258-S266
pubmed: 34850836
Clin Infect Dis. 2022 Mar 23;74(6):1039-1046
pubmed: 34181711
Diagn Microbiol Infect Dis. 2016 Jul;85(3):277-282
pubmed: 27185645
BMC Bioinformatics. 2018 Dec 18;19(1):532
pubmed: 30563445