NGS-based S. aureus typing and outbreak analysis in clinical microbiology laboratories

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

doi:10.3389/fmicb.2020.591093

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NGS-based S. aureus typing and outbreak analysis in clinical microbiology laboratories : Lessons learned from a Swiss-wide proficiency test

Dylus, David Department of Computational Biology, University of Lausanne, Lausanne, Switzerland - Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland - SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Pillonel, Trestan Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
Opota, Onya Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
Wüthrich, Daniel Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland - Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
Seth-Smith, Helena M. B. Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland - Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
Egli, Adrian Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland - Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
Leo, Stefano Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
Lazarevic, Vladimir Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
Schrenzel, Jacques Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
Laurent, Sacha Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
Bertelli, Claire Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
Blanc, Dominique S. Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
Neuenschwander, Stefan Institute for Infectious Diseases, University of Bern, Bern, Switzerland
Ramette, Alban Institute for Infectious Diseases, University of Bern, Bern, Switzerland
Falquet, Laurent SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland - Department of Biology, University of Fribourg, Fribourg, Switzerland
Imkamp, Frank Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
Keller, Peter M. Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
Kahles, Andre SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland - Biomedical Informatics, Swiss Federal Institute of Technology (ETH Zürich), ETH Zürich, Zurich, Switzerland
Oberhaensli, Simone SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland - Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
Barbié, Valérie SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Dessimoz, Christophe Department of Computational Biology, University of Lausanne, Lausanne, Switzerland - Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland - SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland - Department of Genetics, Evolution and Environment, University College London, London, United Kingdom - Department of Computer Science, University College London, London, United Kingdom
Greub, Gilbert Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
Lebrand, Aitana SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland

24.11.2020

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Frontiers in Microbiology. - 2020, vol. 11, p. 591093

English 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.

Faculty

Faculté des sciences et de médecine

Department

Département de Biologie

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