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

David Dylus; Trestan Pillonel; Onya Opota; Daniel Wüthrich; Helena M B Seth-Smith; Adrian Egli; Stefano Leo; Vladimir Lazarevic; Jacques Schrenzel; Sacha Laurent; Claire Bertelli; Dominique S Blanc; Stefan Neuenschwander; Alban Ramette; Laurent Falquet; Frank Imkamp; Peter M Keller; Andre Kahles; Simone Oberhaensli; Valérie Barbié; Christophe Dessimoz; Gilbert Greub; Aitana Lebrand

doi:10.3389/fmicb.2020.591093

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

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

Authors

David Dylus^{1

2

3}, Trestan Pillonel⁴, Onya Opota⁴, Daniel Wüthrich^{5

6}, Helena M B Seth-Smith^{5

6}, Adrian Egli^{5

6}, Stefano Leo⁷, Vladimir Lazarevic⁷, Jacques Schrenzel⁷, Sacha Laurent⁴, Claire Bertelli⁴, Dominique S Blanc⁸, Stefan Neuenschwander⁹, Alban Ramette⁹, Laurent Falquet^{3

10}, Frank Imkamp¹¹, Peter M Keller¹¹, Andre Kahles^{3

12}, Simone Oberhaensli^{3

13}, Valérie Barbié³, Christophe Dessimoz^{1

2

3

14

15}, Gilbert Greub⁴, Aitana Lebrand³

Affiliations

¹ Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
² Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
³ SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
⁴ Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.
⁵ Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.
⁶ Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
⁷ Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland.
⁸ Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.
⁹ Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
¹⁰ Department of Biology, University of Fribourg, Fribourg, Switzerland.
¹¹ Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
¹² Biomedical Informatics, Swiss Federal Institute of Technology (ETH Zürich), ETH Zürich, Zurich, Switzerland.
¹³ Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland.
¹⁴ Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
¹⁵ Department of Computer Science, University College London, London, United Kingdom.

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: EQA; NGS; SNP; bacterial typing; external quality assessment; next generation sequencing; quality control; ring trial.

Copyright © 2020 Dylus, Pillonel, Opota, Wüthrich, Seth-Smith, Egli, Leo, Lazarevic, Schrenzel, Laurent, Bertelli, Blanc, Neuenschwander, Ramette, Falquet, Imkamp, Keller, Kahles, Oberhaensli, Barbié, Dessimoz, Greub and Lebrand.