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

Frontiers in Microbiology

Laurent Falquet¹  Frank Imkamp²  Peter M. Keller²  Andre Kahles³  Simone Oberhaensli⁴  Christophe Dessimoz⁶  Helena M. B. Seth-Smith⁷  Daniel Wüthrich⁷  Adrian Egli⁷  Jacques Schrenzel⁸  Vladimir Lazarevic⁸  Stefano Leo⁸  Alban Ramette^1,12  Stefan Neuenschwander^1,12  Onya Opota^1,13  Trestan Pillonel^1,13  Gilbert Greub^1,13  Sacha Laurent^1,13  Claire Bertelli^1,13  Valérie Barbié^1,14  Aitana Lebrand^1,14  David Dylus^1,14  Dominique S. Blanc^1,15 

[1] 0Department of Biology, University of Fribourg, Fribourg, Switzerland;1Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland;2Biomedical Informatics, Swiss Federal Institute of Technology (ETH Zürich), ETH Zürich, Zurich, Switzerland;3Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland;4Department of Genetics, Evolution and Environment, University College London, London, United Kingdom;5Department of Computer Science, University College London, London, United Kingdom;Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland;Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland;Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland;Department of Computational Biology, University of Lausanne, Lausanne, Switzerland;Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland;Institute for Infectious Diseases, University of Bern, Bern, Switzerland;Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland;SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland;Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland;

关键词: next generation sequencing;    NGS;    bacterial typing;    SNP;    ring trial;    external quality assessment;   

DOI  :  10.3389/fmicb.2020.591093

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown