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Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit
We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of M...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7021795/ https://www.ncbi.nlm.nih.gov/pubmed/32060342 http://dx.doi.org/10.1038/s41598-020-59015-1 |
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author | Cremers, A. J. H. Coolen, J. P. M. Bleeker-Rovers, C. P. van der Geest-Blankert, A. D. J. Haverkate, D. Hendriks, H. Henriet, S. S. V. Huynen, M. A. Kolwijck, E. Liem, D. Melchers, W. J. G. Rossen, J. W. Zoll, J. van Heijst, A. Hopman, J. Wertheim, H. F. L. |
author_facet | Cremers, A. J. H. Coolen, J. P. M. Bleeker-Rovers, C. P. van der Geest-Blankert, A. D. J. Haverkate, D. Hendriks, H. Henriet, S. S. V. Huynen, M. A. Kolwijck, E. Liem, D. Melchers, W. J. G. Rossen, J. W. Zoll, J. van Heijst, A. Hopman, J. Wertheim, H. F. L. |
author_sort | Cremers, A. J. H. |
collection | PubMed |
description | We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference. |
format | Online Article Text |
id | pubmed-7021795 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-70217952020-02-24 Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit Cremers, A. J. H. Coolen, J. P. M. Bleeker-Rovers, C. P. van der Geest-Blankert, A. D. J. Haverkate, D. Hendriks, H. Henriet, S. S. V. Huynen, M. A. Kolwijck, E. Liem, D. Melchers, W. J. G. Rossen, J. W. Zoll, J. van Heijst, A. Hopman, J. Wertheim, H. F. L. Sci Rep Article We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference. Nature Publishing Group UK 2020-02-14 /pmc/articles/PMC7021795/ /pubmed/32060342 http://dx.doi.org/10.1038/s41598-020-59015-1 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Cremers, A. J. H. Coolen, J. P. M. Bleeker-Rovers, C. P. van der Geest-Blankert, A. D. J. Haverkate, D. Hendriks, H. Henriet, S. S. V. Huynen, M. A. Kolwijck, E. Liem, D. Melchers, W. J. G. Rossen, J. W. Zoll, J. van Heijst, A. Hopman, J. Wertheim, H. F. L. Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit |
title | Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit |
title_full | Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit |
title_fullStr | Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit |
title_full_unstemmed | Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit |
title_short | Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit |
title_sort | surveillance-embedded genomic outbreak resolution of methicillin-susceptible staphylococcus aureus in a neonatal intensive care unit |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7021795/ https://www.ncbi.nlm.nih.gov/pubmed/32060342 http://dx.doi.org/10.1038/s41598-020-59015-1 |
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