Disentangling outbreaks using whole-genome sequencing: concurrent multistate outbreaks of <i>Salmonella</i> Kottbus in Germany, 2017

Enkelmann, Julia; Laer, Anja von; Simon, Sandra; Fruth, Angelika; Lachmann, Raskit; Michaelis, Kai; Blettner, Maria; Lassen, Sofie Gillesberg; Frank, Christina

doi:10.1017/s0950268820000394

Cited by 5 publications

(2 citation statements)

References 12 publications

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“…In 2017, a multi-state outbreak of the rare serotype S. Kottbus in Germany involved 69 cases ( Enkelmann et al, 2020 ). WGS enabled the differentiation of isolates belonging to the potential outbreak into three independent co-circulating clusters.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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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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Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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“…enterica serovar Kottbus is a rare serovar, accounting for ca 1% of all NTS-cases registered over the past 20 years (https://statistik.ssi.dk). S. Kottbus has been isolated from poultry, cattle, pigs and reptiles [1] and has been identified in several outbreaks [2][3][4][5]. Carbapenems are not first-choice drugs for the treatment of Salmonella.…”

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A case of blaNDM-1-positive Salmonella Kottbus, Denmark, November 2020

et al. 2021

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We present a case of carbapenemase-producing blaNDM-1-positive Salmonella Kottbus in an 82-year-old Danish man. The blaNDM-1 was also identified in Escherichia coli and Citrobacter freundii in the same patient on the same 43 kb IncN2 plasmid, suggesting in vivo inter-species plasmid transfer. A NCBI BLAST analysis of the plasmid (pAMA003584_NDM-1) identified 12 highly similar plasmids, all originating from east and south-east Asia. This case could be the first confirmed case of blaNDM-1-positive Salmonella not related to travel outside Europe.

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Whole-genome sequencing for food safety

French

2023

Present Knowledge in Food Safety

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Disentangling outbreaks using whole-genome sequencing: concurrent multistate outbreaks of Salmonella Kottbus in Germany, 2017

Cited by 5 publications

References 12 publications

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

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

A case of blaNDM-1-positive Salmonella Kottbus, Denmark, November 2020

Whole-genome sequencing for food safety

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