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Uelze L, Becker N, Borowiak M, Busch U, Dangel A, Deneke C, Fischer J, Flieger A, Hepner S, Huber I, Methner U, Linde J, Pietsch M, Simon S, Sing A, Tausch SH, Szabo I, Malorny B. Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany. Front Microbiol 2021; 12:626941. [PMID: 33643254 PMCID: PMC7902525 DOI: 10.3389/fmicb.2021.626941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/21/2021] [Indexed: 02/03/2023] Open
Abstract
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.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Natalie Becker
- Department of Food, Feed and Commodities, Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Antje Flieger
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Hepner
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Michael Pietsch
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sandra Simon
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Meinen A, Simon S, Banerji S, Szabo I, Malorny B, Borowiak M, Hadziabdic S, Becker N, Luber P, Lohr D, Harms C, Plenge-Bönig A, Mellou K, Mandilara G, Mossong J, Ragimbeau C, Weicherding P, Hau P, Dědičová D, Šafaříková L, Nair S, Dallman TJ, Larkin L, McCormick J, De Pinna E, Severi E, Kotila S, Niskanen T, Rizzi V, Deserio D, Flieger A, Stark K. Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017. Euro Surveill 2019; 24:1800543. [PMID: 31507266 PMCID: PMC6737830 DOI: 10.2807/1560-7917.es.2019.24.36.1800543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/29/2019] [Indexed: 11/20/2022] Open
Abstract
In spring 2016, Greece reported an outbreak caused by a previously undescribed Salmonella enterica subsp. enterica serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presumptive vehicle. Subsequently, Germany, Czech Republic, Luxembourg and the United Kingdom (UK) reported infections with this novel serotype via EPIS-FWD. Concerned countries in collaboration with the European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA) adopted a common outbreak case definition. An outbreak case was defined as a laboratory-confirmed notification of the novel Salmonella serotype. Between March 2016 and April 2017, 47 outbreak cases were notified (Greece: n = 22; Germany: n = 13; Czech Republic: n = 5; Luxembourg: n = 4; UK: n = 3). Whole genome sequencing revealed the very close genetic relatedness of isolates from all affected countries. Interviews focusing on sesame product consumption, suspicious food item testing and trace-back analysis following Salmonella spp. detection in food products identified a company in Greece where sesame seeds from different countries were processed. Through European collaboration, it was possible to identify and recall sesame spread as one contaminated food item serving as vehicle of infection and trace it back to its origin.
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Affiliation(s)
- Anika Meinen
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
- These authors contributed equally
| | - Sandra Simon
- These authors contributed equally
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Sangeeta Banerji
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Istvan Szabo
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Sead Hadziabdic
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Natalie Becker
- Federal Office of Consumer Protection and Food Safety, Crisis Unit Office, Foodborne Outbreaks, Prevention, Berlin, Germany
| | - Petra Luber
- Federal Office of Consumer Protection and Food Safety, Crisis Unit Office, Foodborne Outbreaks, Prevention, Berlin, Germany
| | - Dorothee Lohr
- Baden-Wuerttemberg State Health Office, Stuttgart, Germany
| | - Carolin Harms
- Institute for Hygiene and Environment Hamburg, Department of Microbiology, Hamburg, Germany
| | - Anita Plenge-Bönig
- Institute for Hygiene and Environment Hamburg, Infectious Disease Surveillance Unit, Hamburg, Germany
| | - Kassiani Mellou
- Hellenic National Public Health Organization, Athens, Greece
| | - Georgia Mandilara
- National School of Public Health, National Reference Centre for Salmonella, Athens, Greece
| | - Joël Mossong
- Laboratoire National de Santé, Département de Microbiologie, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Département de Microbiologie, Dudelange, Luxembourg
| | | | - Patrick Hau
- Direction de la Santé, Luxembourg, Luxembourg
| | - Daniela Dědičová
- Státní zdravotní ústav (National Institute of Public Health), Prague, Czech Republic
| | - Lucie Šafaříková
- Státní zdravotní ústav (National Institute of Public Health), Prague, Czech Republic
| | | | | | | | | | | | - Ettore Severi
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | - Saara Kotila
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | - Taina Niskanen
- European Centre for Disease Prevention and Control (ECDC), Surveillance and Response Support, Stockholm, Sweden
| | | | | | - Antje Flieger
- Robert Koch Institute, Department of Infectious Diseases, National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Klaus Stark
- Robert Koch Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
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