Front Microbiol.: co-auth.: group Dessimoz

Front Microbiol. 2020 Nov 24;11:591093. 
doi: 10.3389/fmicb.2020.591093. eCollection 2020.

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

David Dylus 1 2 3Trestan Pillonel 4Onya Opota 4Daniel Wüthrich 5 6Helena M B Seth-Smith 5 6Adrian Egli 5 6Stefano Leo 7Vladimir Lazarevic 7Jacques Schrenzel 7Sacha Laurent 4Claire Bertelli 4Dominique S Blanc 8Stefan Neuenschwander 9Alban Ramette 9Laurent Falquet 3 10Frank Imkamp 11Peter M Keller 11Andre Kahles 3 12Simone Oberhaensli 3 13Valérie Barbié 3Christophe Dessimoz 1 2 3 14 15Gilbert Greub 4Aitana Lebrand 3

Free PMC article


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.