Complete genome sequence of a strain of serovar Agona associated with an outbreak in France.

We report here the complete genome of one Agona strain isolated in 2017 from a dried milk powder in France.

Tell me if you prefer bovine or poultry sectors and I'll tell you who you are: Characterization of subsp. serovar Mbandaka in France.

Introduction: In north-western France, susp. serovar Mbandaka (. Mbandaka) is most frequently isolated from bovine and dairy samples.

Countrywide multi-serotype outbreak of Bovismorbificans ST142 and monophasic Typhimurium ST34 associated with dried pork sausages in France, September 2020* to January 2021.

The French National Reference Centre for and (FNRC-ESS) detected two human clusters of 33 cases (median age: 10 years; 17 females) infected by serotype Bovismorbificans, ST142, HC5_243255 (EnteroBase HierCC‑cgMLST scheme) in September-November 2020 and of 11 cases (median age: 11 years; seven males) infected by serotype 4,12:i:-, ST34, HC5_198125 in October-December 2020. Epidemiological investigations conducted by Santé publique France linked these outbreaks to the consumption of dried pork sausages from the same manufacturer.  Bovismorbificans and  4,12:i:- were isolated by the National Reference Laboratory from different food samples, but both strains were identified in a single food sample only by qPCR.

Polyphyly in widespread serovars and using genomic proximity to choose the best reference genome for bioinformatics analyses.

is the most common cause of gastroenteritis in the world. Over the past 5 years, whole-genome analysis has led to the high-resolution characterization of clinical and foodborne responsible for typhoid fever, foodborne illness or contamination of the agro-food chain. Whole-genome analyses are simplified by the availability of high-quality, complete genomes for mapping analysis and for calculating the pairwise distance between genomes, but unfortunately some difficulties may still remain.

Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks.

Background: Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirmed human cases.

Retrieving Good-Quality Genomes From the GenBank Database Using a Python Tool, SalmoDEST.

With the advent of next-generation whole-genome sequencing (WGS), the need for good-quality and well-characterised genomes has increased over the past years. Good-quality complete genomes are often required for assembly reference mapping or phylogenetic single nucleotide polymorphism (SNP) analysis. Complete genomes or contigs from specific sources or serovars are also searched for clustering analysis or source attribution studies.

Closed Genome Sequence of a Salmonella enterica Serovar Bovismorbificans Strain Isolated from Dried Pork Sausage Associated with an Outbreak in France.

We report here the closed genome sequence of one Salmonella enterica subsp. serovar Bovismorbificans strain isolated from dried pork sausage consumed by a patient suffering from salmonellosis.

The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Circulating in Europe.

The European epidemic monophasic variant of enterica serovar (. 1,4,[5],12:i:-) characterized by the multi sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this in Europe.

Source Attribution Study of Sporadic Derby Cases in France.

subsp. serovar Derby is one of the most frequent causes of gastroenteritis in humans. In Europe, this pathogen is one of the top five most commonly reported serovars in human cases.

AB_SA: Accessory genes-Based Source Attribution - tracing the source of Typhimurium environmental strains.

The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g.

A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale - Application to Retrospective Foodborne Outbreak Investigations.

The investigation of foodborne outbreaks (FBOs) from genomic data typically relies on inspecting the relatedness of samples through a phylogenomic tree computed on either SNPs, genes, kmers, or alleles (i.e., cgMLST and wgMLST).

Genetic Diversity of Derby from the Poultry Sector in Europe.

Derby (. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK).

Whole-Genome Sequences of Two Salmonella enterica Serovar Dublin Strains That Harbor the , , and Loci of the Vi Antigen.

Here, we report the genome sequences of two serovar Dublin strains, 03EB8736SAL and 03EB8994SAL, isolated from raw-milk cheese and milk filtrate, respectively. Analysis of the draft genomes of the two isolates reveals the presence of the , and loci of the Vi capsular polysaccharide antigen (Vi antigen).

Disentangling a complex nationwide Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016.

On 18 January 2016, the French National Reference Centre for reported to Santé publique France an excess of serotype Dublin ( Dublin) infections. We investigated to identify the source of infection and implement control measures. Whole genome sequencing (WGS) and multilocus variable-number tandem repeat analysis (MLVA) were performed to identify microbiological clusters and links among cases, animal and food sources.

Correction for Sévellec et al., "Complete Genome Sequence of Salmonella enterica subsp. Serotype Derby, Associated with the Pork Sector in France".

[This corrects the article DOI: 10.1128/MRA.01027-18.

Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Dublin Strains from St. Nectaire and Morbier Cheeses Characterized by Multilocus Variable-Number Tandem-Repeat Analysis Profiles Associated with Two Fatal Outbreaks in France.

We report here the draft genome sequences of 2 Salmonella enterica subsp. enterica serovar Dublin strains from St. Nectaire and Morbier cheeses having multilocus variable-number tandem-repeat analysis (MLVA) profiles identified during the fatal outbreaks that occurred in France in 2012 and 2015 to 2016, respectively.

Complete Genome Sequence of Salmonella enterica subsp. enterica Serotype Derby, Associated with the Pork Sector in France.

In the European Union, Salmonella enterica subsp. enterica serovar Derby is the most abundant serotype isolated from pork. Recent studies have shown that this serotype is polyphyletic.

Polyphyletic Nature of Serotype Derby and Lineage-Specific Host-Association Revealed by Genome-Wide Analysis.

In France, Derby is one of the most prevalent serotypes in pork and poultry meat. Since 2006, it has ranked among the 10 most frequent serotypes isolated in humans. In previous publications, Derby isolates have been characterized by pulsed field gel electrophoresis (PFGE) and antimicrobial resistance (AMR) profiles revealing the existence of different pulsotypes and AMR phenotypic groups.

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers.

Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity.

MLVA for subsp. Serovar Dublin: Development of a Method Suitable for Inter-Laboratory Surveillance and Application in the Context of a Raw Milk Cheese Outbreak in France in 2012.

subspecies Dublin (. Dublin) figures among the most frequently isolated strains in humans in France. This serovar may affect production and animal health mainly in cattle herds with corresponding high economic losses.

Outbreak of Salmonella Enteritidis linked to the consumption of frozen beefburgers received from a food bank and originating from Poland: northern France, December 2014 to April 2015.

A prolonged outbreak of Salmonella enterica serotype Enteritidis occurred in northern France between December 2014 and April 2015. Epidemiological investigations following the initial notification on 30 December 2014 of five cases of salmonellosis (two confirmed S. Enteritidis) in young children residing in the Somme department revealed that all cases frequented the same food bank A.