NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test

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State: Public
Version: author
License: CC BY 4.0
Serval ID
serval:BIB_347E9A7AF57F
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
Journal
Frontiers in Microbiology
Author(s)
Dylus David, Pillonel Trestan, Opota Onya, Wüthrich Daniel, Seth-Smith Helena M. B., Egli Adrian, Leo Stefano, Lazarevic Vladimir, Schrenzel Jacques, Laurent Sacha, Bertelli Claire, Blanc Dominique S., Neuenschwander Stefan, Ramette Alban, Falquet Laurent, Imkamp Frank, Keller Peter M., Kahles Andre, Oberhaensli Simone, Barbié Valérie, Dessimoz Christophe, Greub Gilbert, Lebrand Aitana
ISSN
1664-302X (Print)
ISSN-L
1664-302X
Publication state
Published
Issued date
24/11/2020
Peer-reviewed
Oui
Volume
11
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain relatedness from WGS and epidemiological data. The RT was designed to disentangle the variability arising from differences in sample preparation, SNP calling and phylogenetic methods. Nine laboratories participated. The resulting phylogenetic tree and cluster identification were highly reproducible across the laboratories. Cluster interpretation was, however, more laboratory dependent, suggesting that an increased sharing of expertise across laboratories would contribute to further harmonization of practices. More detailed bioinformatic analyses unveiled that while similar clusters were found across laboratories, these were actually based on different sets of SNPs, differentially retained after sample preparation and SNP calling procedures. Despite this, the observed number of SNP differences between pairs of strains, an important criterion to determine strain relatedness given epidemiological information, was similar across pipelines for closely related strains when restricting SNP calls to a common core genome defined by S. aureus cgMLST schema. The lessons learned from this pilot study will serve the implementation of larger-scale RT, as a mean to have regular external quality assessments for laboratories performing WGS analyses in a clinical setting.
Keywords
Microbiology (medical), Microbiology
Pubmed
Web of science
Open Access
Yes
Create date
17/12/2020 17:56
Last modification date
25/03/2021 7:36
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