Cargando…

Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany

Despite extensive monitoring programs and preventative measures, Salmonella spp. continue to cause tens of thousands human infections per year, as well as many regional and international food-borne outbreaks, that are of great importance for public health and cause significant socio-economic costs....

Descripción completa

Detalles Bibliográficos
Autores principales: Uelze, Laura, Becker, Natalie, Borowiak, Maria, Busch, Ulrich, Dangel, Alexandra, Deneke, Carlus, Fischer, Jennie, Flieger, Antje, Hepner, Sabrina, Huber, Ingrid, Methner, Ulrich, Linde, Jörg, Pietsch, Michael, Simon, Sandra, Sing, Andreas, Tausch, Simon H., Szabo, Istvan, Malorny, Burkhard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902525/
https://www.ncbi.nlm.nih.gov/pubmed/33643254
http://dx.doi.org/10.3389/fmicb.2021.626941
_version_ 1783654542933491712
author Uelze, Laura
Becker, Natalie
Borowiak, Maria
Busch, Ulrich
Dangel, Alexandra
Deneke, Carlus
Fischer, Jennie
Flieger, Antje
Hepner, Sabrina
Huber, Ingrid
Methner, Ulrich
Linde, Jörg
Pietsch, Michael
Simon, Sandra
Sing, Andreas
Tausch, Simon H.
Szabo, Istvan
Malorny, Burkhard
author_facet Uelze, Laura
Becker, Natalie
Borowiak, Maria
Busch, Ulrich
Dangel, Alexandra
Deneke, Carlus
Fischer, Jennie
Flieger, Antje
Hepner, Sabrina
Huber, Ingrid
Methner, Ulrich
Linde, Jörg
Pietsch, Michael
Simon, Sandra
Sing, Andreas
Tausch, Simon H.
Szabo, Istvan
Malorny, Burkhard
author_sort Uelze, Laura
collection PubMed
description Despite extensive monitoring programs and preventative measures, Salmonella spp. continue to cause tens of thousands human infections per year, as well as many regional and international food-borne outbreaks, that are of great importance for public health and cause significant socio-economic costs. In Germany, salmonellosis is the second most common cause of bacterial diarrhea in humans and is associated with high hospitalization rates. Whole-genome sequencing (WGS) combined with data analysis is a high throughput technology with an unprecedented discriminatory power, which is particularly well suited for targeted pathogen monitoring, rapid cluster detection and assignment of possible infection sources. However, an effective implementation of WGS methods for large-scale microbial pathogen detection and surveillance has been hampered by the lack of standardized methods, uniform quality criteria and strategies for data sharing, all of which are essential for a successful interpretation of sequencing data from different sources. To overcome these challenges, the national GenoSalmSurv project aims to establish a working model for an integrated genome-based surveillance system of Salmonella spp. in Germany, based on a decentralized data analysis. Backbone of the model is the harmonization of laboratory procedures and sequencing protocols, the implementation of open-source bioinformatics tools for data analysis at each institution and the establishment of routine practices for cross-sectoral data sharing for a uniform result interpretation. With this model, we present a working solution for cross-sector interpretation of sequencing data from different sources (such as human, veterinarian, food, feed and environmental) and outline how a decentralized data analysis can contribute to a uniform cluster detection and facilitate outbreak investigations.
format Online
Article
Text
id pubmed-7902525
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-79025252021-02-25 Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany Uelze, Laura Becker, Natalie Borowiak, Maria Busch, Ulrich Dangel, Alexandra Deneke, Carlus Fischer, Jennie Flieger, Antje Hepner, Sabrina Huber, Ingrid Methner, Ulrich Linde, Jörg Pietsch, Michael Simon, Sandra Sing, Andreas Tausch, Simon H. Szabo, Istvan Malorny, Burkhard Front Microbiol Microbiology Despite extensive monitoring programs and preventative measures, Salmonella spp. continue to cause tens of thousands human infections per year, as well as many regional and international food-borne outbreaks, that are of great importance for public health and cause significant socio-economic costs. In Germany, salmonellosis is the second most common cause of bacterial diarrhea in humans and is associated with high hospitalization rates. Whole-genome sequencing (WGS) combined with data analysis is a high throughput technology with an unprecedented discriminatory power, which is particularly well suited for targeted pathogen monitoring, rapid cluster detection and assignment of possible infection sources. However, an effective implementation of WGS methods for large-scale microbial pathogen detection and surveillance has been hampered by the lack of standardized methods, uniform quality criteria and strategies for data sharing, all of which are essential for a successful interpretation of sequencing data from different sources. To overcome these challenges, the national GenoSalmSurv project aims to establish a working model for an integrated genome-based surveillance system of Salmonella spp. in Germany, based on a decentralized data analysis. Backbone of the model is the harmonization of laboratory procedures and sequencing protocols, the implementation of open-source bioinformatics tools for data analysis at each institution and the establishment of routine practices for cross-sectoral data sharing for a uniform result interpretation. With this model, we present a working solution for cross-sector interpretation of sequencing data from different sources (such as human, veterinarian, food, feed and environmental) and outline how a decentralized data analysis can contribute to a uniform cluster detection and facilitate outbreak investigations. Frontiers Media S.A. 2021-02-10 /pmc/articles/PMC7902525/ /pubmed/33643254 http://dx.doi.org/10.3389/fmicb.2021.626941 Text en Copyright © 2021 Uelze, Becker, Borowiak, Busch, Dangel, Deneke, Fischer, Flieger, Hepner, Huber, Methner, Linde, Pietsch, Simon, Sing, Tausch, Szabo and Malorny. 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
Uelze, Laura
Becker, Natalie
Borowiak, Maria
Busch, Ulrich
Dangel, Alexandra
Deneke, Carlus
Fischer, Jennie
Flieger, Antje
Hepner, Sabrina
Huber, Ingrid
Methner, Ulrich
Linde, Jörg
Pietsch, Michael
Simon, Sandra
Sing, Andreas
Tausch, Simon H.
Szabo, Istvan
Malorny, Burkhard
Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
title Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
title_full Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
title_fullStr Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
title_full_unstemmed Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
title_short Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany
title_sort toward an integrated genome-based surveillance of salmonella enterica in germany
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902525/
https://www.ncbi.nlm.nih.gov/pubmed/33643254
http://dx.doi.org/10.3389/fmicb.2021.626941
work_keys_str_mv AT uelzelaura towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT beckernatalie towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT borowiakmaria towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT buschulrich towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT dangelalexandra towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT denekecarlus towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT fischerjennie towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT fliegerantje towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT hepnersabrina towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT huberingrid towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT methnerulrich towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT lindejorg towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT pietschmichael towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT simonsandra towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT singandreas towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT tauschsimonh towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT szaboistvan towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany
AT malornyburkhard towardanintegratedgenomebasedsurveillanceofsalmonellaentericaingermany