Genetic changes are introduced by repeated exposure of Salmonella spiked in low water activity and high fat matrix to heat.

WGS is used to define if isolates are "in" or "out" of an outbreak and/or microbial root cause investigation. No threshold of genetic differences is fixed and the conclusions on similarity between isolates are mainly based on the knowledge generated from previous outbreak investigations and reported mutation rates. Mutation rates in Salmonella when exposed to food processing conditions are lacking.

Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation.

Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required to accurately process and understand the data has limited its adoption at a wider scale. Additionally, the time needed to obtain actionable information is often seen as an impairment for the application and use of the information generated via WGS.

Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an Platform Using Whole Genome Sequencing Data.

is one of the most common causes of food-borne diseases worldwide. While molecular subtyping by Whole Genome Sequencing (WGS) is increasingly used for outbreak and source tracking investigations, serotyping remains as a first-line characterization of isolates. The traditional phenotypic method for serotyping is logistically challenging, as it requires the use of more than 150 specific antisera and well trained personnel to interpret the results.

Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination.

In 2013, during a routine laboratory analysis performed on food samples, one finished product from a European factory was tested positive for Salmonella Hadar. At the same period, one environmental isolate in the same laboratory was serotyped Salmonella Hadar. Prior to this event, the laboratory performed a proficiency testing involving a sample spiked with NCTC 9877 Salmonella Hadar.

A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of and .

Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations.

Genome Sequence of Lactobacillus fermentum Strain NCC2970 (CNCM I-5068).

Lactobacillus fermentum NCC2970 (CNCM I-5068) is a lactic acid bacterium originating from the Nestle Culture Collection. Here, we disclose its full 1.9-Gb genome sequence comprising one chromosome with no plasmid.

Fully Closed Genome Sequences of Five Type Strains of the Genus Cronobacter and One Cronobacter sakazakii Strain.

Cronobacteris associated with infant infections and the consumption of reconstituted infant formula. Here we sequenced and closed six genomes ofC. condimenti(T),C.

Safety analysis of a Russian phage cocktail: from metagenomic analysis to oral application in healthy human subjects.

Phage therapy has a long tradition in Eastern Europe, where preparations are comprised of complex phage cocktails whose compositions have not been described. We investigated the composition of a phage cocktail from the Russian pharmaceutical company Microgen targeting Escherichia coli/Proteus infections. Electron microscopy identified six phage types, with numerically T7-like phages dominating over T4-like phages.

Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh.

The genomic diversity of 99 T4-like coliphages was investigated by sequencing an equimolar mixture with Illumina technology and screening them against different databases for horizontal gene transfer and undesired genes. A 9-phage cocktail was given to 15 healthy adults from Bangladesh at a dose of 3×10(9) and 3×10(7) plaque-forming units and placebo respectively. Phages were detected in 64% of the stool samples when subjects were treated with higher titer phage, compared to 30% and 28% with lower-titer phage and placebo, respectively.

Genome sequence of the lantibiotic bacteriocin producer Streptococcus salivarius strain K12.

Streptococcus salivarius is a prevalent commensal species of the oropharyngeal tract. S. salivarius strain K12 is an isolate from the saliva of a healthy child, used as an oral probiotic.

Gut microbiota: methodological aspects to describe taxonomy and functionality.

The human gut is populated by a rich and diverse microbiota that has been described as a human metabolic organ. Its composition has an impact on the health status of the host and could be the target or effector of dietary health effects. The advent of high-throughput sequencing technologies and their integration with advanced analysis methods enables the development of new approaches to characterize the gut microbiota composition and initiates the understanding of its functionality.

Campylobacter jejuni group III phage CP81 contains many T4-like genes without belonging to the T4-type phage group: implications for the evolution of T4 phages.

CP81 is a virulent Campylobacter group III phage whose linear genome comprises 132,454 bp. At the nucleotide level, CP81 differs from other phages. However, a number of its structural and replication/recombination proteins revealed a relationship to the group II Campylobacter phages CP220/CPt10 and to T4-type phages.

T4 phages against Escherichia coli diarrhea: potential and problems.

A combination of in vitro and in vivo experiments with comparative phage genomics was used for the rational design of a phage cocktail against E. coli diarrhea. Orally applied T4 coliphages representing three different subgroups (T4-, RB49- and JS98-like phages) had no negative impact on the murine gut microbiota.

The role of prophage for genome diversification within a clonal lineage of Lactobacillus johnsonii: characterization of the defective prophage LJ771.

Two independent isolates of the gut commensal Lactobacillus johnsonii were sequenced. These isolates belonged to the same clonal lineage and differed mainly by a 40.8-kb prophage, LJ771, belonging to the Sfi11 phage lineage.

Genome analysis of phage JS98 defines a fourth major subgroup of T4-like phages in Escherichia coli.

Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (g23) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E.

Global transcriptome analysis of the heat shock response of Bifidobacterium longum.

Bifidobacteria are natural inhabitants of the human gastrointestinal tract and have been widely used as functional foods in different products. During industrial processing, bacterial cells undergo several stresses that can limit large-scale production and stability of the final product. To better understand the stress-response mechanisms of bifidobacteria, microarrays were used to obtain a global transcriptome profile of Bifidobacterium longum NCC2705 exposed to a heat shock treatment at 50 degrees C for 3, 7 and 12 min.

Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics.

A set of lactobacilli were investigated by polyphasic analysis. Multilocus sequence analysis, DNA typing, microarray analysis, and in silico whole-genome alignments provided a remarkably consistent pattern of similarity within the Lactobacillus acidophilus complex. On microarray analysis, 17 and 5% of the genes from Lactobacillus johnsonii strain NCC533 represented variable and strain-specific genes, respectively, when tested against four independent isolates of L.

The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.

Lactobacillus johnsonii NCC 533 is a member of the acidophilus group of intestinal lactobacilli that has been extensively studied for their "probiotic" activities that include, pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into its physiology and identify genes potentially involved in interactions with the host, we sequenced and analyzed the 1.99-Mb genome of L.