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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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-11-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2020.591093/full |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
David Dylus David Dylus David Dylus Trestan Pillonel Onya Opota Daniel Wüthrich Daniel Wüthrich Helena M. B. Seth-Smith Helena M. B. Seth-Smith Adrian Egli Adrian Egli Stefano Leo Vladimir Lazarevic Jacques Schrenzel Sacha Laurent Claire Bertelli Dominique S. Blanc Stefan Neuenschwander Alban Ramette Laurent Falquet Laurent Falquet Frank Imkamp Peter M. Keller Andre Kahles Andre Kahles Simone Oberhaensli Simone Oberhaensli Valérie Barbié Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Gilbert Greub Aitana Lebrand |
| spellingShingle |
David Dylus David Dylus David Dylus Trestan Pillonel Onya Opota Daniel Wüthrich Daniel Wüthrich Helena M. B. Seth-Smith Helena M. B. Seth-Smith Adrian Egli Adrian Egli Stefano Leo Vladimir Lazarevic Jacques Schrenzel Sacha Laurent Claire Bertelli Dominique S. Blanc Stefan Neuenschwander Alban Ramette Laurent Falquet Laurent Falquet Frank Imkamp Peter M. Keller Andre Kahles Andre Kahles Simone Oberhaensli Simone Oberhaensli Valérie Barbié Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Gilbert Greub Aitana Lebrand NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test Frontiers in Microbiology next generation sequencing NGS bacterial typing SNP ring trial external quality assessment |
| author_facet |
David Dylus David Dylus David Dylus Trestan Pillonel Onya Opota Daniel Wüthrich Daniel Wüthrich Helena M. B. Seth-Smith Helena M. B. Seth-Smith Adrian Egli Adrian Egli Stefano Leo Vladimir Lazarevic Jacques Schrenzel Sacha Laurent Claire Bertelli Dominique S. Blanc Stefan Neuenschwander Alban Ramette Laurent Falquet Laurent Falquet Frank Imkamp Peter M. Keller Andre Kahles Andre Kahles Simone Oberhaensli Simone Oberhaensli Valérie Barbié Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Christophe Dessimoz Gilbert Greub Aitana Lebrand |
| author_sort |
David Dylus |
| title |
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_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_sort |
ngs-based s. aureus typing and outbreak analysis in clinical microbiology laboratories: lessons learned from a swiss-wide proficiency test |
| publisher |
Frontiers Media S.A. |
| series |
Frontiers in Microbiology |
| issn |
1664-302X |
| publishDate |
2020-11-01 |
| 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. |
| topic |
next generation sequencing NGS bacterial typing SNP ring trial external quality assessment |
| url |
https://www.frontiersin.org/articles/10.3389/fmicb.2020.591093/full |
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doaj-c20aa348c6e94d02a156f6cbe0b957852020-11-25T04:10:47ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-11-011110.3389/fmicb.2020.591093591093NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency TestDavid Dylus0David Dylus1David Dylus2Trestan Pillonel3Onya Opota4Daniel Wüthrich5Daniel Wüthrich6Helena M. B. Seth-Smith7Helena M. B. Seth-Smith8Adrian Egli9Adrian Egli10Stefano Leo11Vladimir Lazarevic12Jacques Schrenzel13Sacha Laurent14Claire Bertelli15Dominique S. Blanc16Stefan Neuenschwander17Alban Ramette18Laurent Falquet19Laurent Falquet20Frank Imkamp21Peter M. Keller22Andre Kahles23Andre Kahles24Simone Oberhaensli25Simone Oberhaensli26Valérie Barbié27Christophe Dessimoz28Christophe Dessimoz29Christophe Dessimoz30Christophe Dessimoz31Christophe Dessimoz32Gilbert Greub33Aitana Lebrand34Department of Computational Biology, University of Lausanne, Lausanne, SwitzerlandCenter for Integrative Genomics, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandInstitute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, SwitzerlandInstitute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, SwitzerlandDivision of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, SwitzerlandApplied Microbiology Research, Department of Biomedicine, University of Basel, Basel, SwitzerlandDivision of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, SwitzerlandApplied Microbiology Research, Department of Biomedicine, University of Basel, Basel, SwitzerlandDivision of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, SwitzerlandApplied Microbiology Research, Department of Biomedicine, University of Basel, Basel, SwitzerlandBacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, SwitzerlandBacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, SwitzerlandBacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, SwitzerlandInstitute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, SwitzerlandInstitute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, SwitzerlandService of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, SwitzerlandInstitute for Infectious Diseases, University of Bern, Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Bern, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland0Department of Biology, University of Fribourg, Fribourg, Switzerland1Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland1Institute of Medical Microbiology, University of Zurich, Zurich, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland2Biomedical Informatics, Swiss Federal Institute of Technology (ETH Zürich), ETH Zürich, Zurich, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland3Interfaculty Bioinformatics Unit, University of Bern, Bern, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandDepartment of Computational Biology, University of Lausanne, Lausanne, SwitzerlandCenter for Integrative Genomics, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland4Department of Genetics, Evolution and Environment, University College London, London, United Kingdom5Department of Computer Science, University College London, London, United KingdomInstitute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandWhole 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.https://www.frontiersin.org/articles/10.3389/fmicb.2020.591093/fullnext generation sequencingNGSbacterial typingSNPring trialexternal quality assessment |