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

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 bioinforma...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793906/
https://www.ncbi.nlm.nih.gov/pubmed/33424794
http://dx.doi.org/10.3389/fmicb.2020.591093
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author 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
author_facet 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
author_sort Dylus, David
collection PubMed
description 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.
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spelling pubmed-77939062021-01-09 NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test 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 Front Microbiol Microbiology 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. Frontiers Media S.A. 2020-11-24 /pmc/articles/PMC7793906/ /pubmed/33424794 http://dx.doi.org/10.3389/fmicb.2020.591093 Text en 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. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
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
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
title NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
title_full NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
title_fullStr NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
title_full_unstemmed NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
title_short NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
title_sort ngs-based s. aureus typing and outbreak analysis in clinical microbiology laboratories: lessons learned from a swiss-wide proficiency test
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793906/
https://www.ncbi.nlm.nih.gov/pubmed/33424794
http://dx.doi.org/10.3389/fmicb.2020.591093
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