The effect of pH on the growth rate of Bacillus cereus sensu lato: Quantifying strain variability and modelling the combined effects of temperature and pH.

In this study, the effect of pH, alone or in combination with temperature, on the maximum growth rate (μ) of B. cereus sensu lato was investigated. In phase 1, the effect of pH at 30 °C was studied for 16 mesophilic strains and 2 psychrotrophic strains of Bacillus cereus sensu lato.

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.

Identification of Closely Related Listeria monocytogenes Isolates with No Apparent Evidence for a Common Source or Location: A Retrospective Whole Genome Sequencing Analysis.

Abstract: Public health and regulatory agencies worldwide sequence all Listeria monocytogenes isolates obtained as part of routine surveillance and outbreak investigations. Many of these entities submit the sequences to the National Center for Biotechnology Information Pathogen Detection (NCBI PD) database, which groups the L. monocytogenes isolates into single nucleotide polymorphism (SNP) clusters based on a pairwise SNP difference threshold of 50 SNPs.

Evolution of Listeria monocytogenes in a Food Processing Plant Involves Limited Single-Nucleotide Substitutions but Considerable Diversification by Gain and Loss of Prophages.

Whole-genome sequencing (WGS) is becoming the standard method for subtyping Interpretation of WGS data for isolates from foods and associated environments is, however, challenging due to a lack of detailed data on evolution in processing facilities. Here, we used previously collected WGS data for 40 isolates obtained from a cold-smoked salmon processing facility between 1998 and 2015 to probe the molecular evolution in this facility, combined with phenotypic assessment of selected isolates. Isolates represented three clusters (1, 2, and 3); cluster 3 isolates ( = 32) were obtained over 18 years.

Implications of Mobile Genetic Elements for Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations.

Single-nucleotide polymorphisms (SNPs) are widely used for whole-genome sequencing (WGS)-based subtyping of foodborne pathogens in outbreak and source tracking investigations. Mobile genetic elements (MGEs) are commonly present in bacterial genomes and may affect SNP subtyping results if their evolutionary history and dynamics differ from that of the bacterial chromosomes. Using as a model organism, we surveyed major categories of MGEs, including plasmids, phages, insertion sequences, integrons, and integrative and conjugative elements (ICEs), in 990 genomes representing 21 major serotypes of We evaluated whether plasmids and chromosomal MGEs affect SNP subtyping with 9 outbreak clusters of different serotypes found in the United States in 2018.

Comparative Analysis of Tools and Approaches for Source Tracking in a Food Facility Using Whole-Genome Sequence Data.

As WGS is increasingly used by food industry to characterize pathogen isolates, users are challenged by the variety of analysis approaches available, ranging from methods that require extensive bioinformatics expertise to commercial software packages. This study aimed to assess the impact of analysis pipelines (i.e.

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.

Optimization of subculture and DNA extraction steps within the whole genome sequencing workflow for source tracking of Salmonella enterica and Listeria monocytogenes.

This work shows that an incubation time reduced to 4-5 h to prepare a culture for DNA extraction followed by an automated DNA extraction can shorten the hands-on time, the turnaround time by 30% and increase the throughput while maintaining the WGS quality assessed by high quality Single Nucleotide Polymorphism analysis.

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.

Evaluation of Whole Genome Mapping as a Fast and Automated Molecular Epidemiological Tool for the Study of Cronobacter spp. in Powdered Infant Formula Processing Facilities.

Cronobacter has been identified as the causative agent of outbreaks or sporadic cases of meningitis, necrotizing enterocolitis, and septicemia associated with powdered infant formula. Food processing environments may provide a possible contamination route. The purpose of this study was to evaluate whole genome mapping (WGM) as a fast and automated molecular epidemiological method for characterizing Cronobacter spp.

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.

A quantitative exposure model simulating human norovirus transmission during preparation of deli sandwiches.

Human noroviruses (HuNoVs) are a major cause of food borne gastroenteritis worldwide. They are often transmitted via infected and shedding food handlers manipulating foods such as deli sandwiches. The presented study aimed to simulate HuNoV transmission during the preparation of deli sandwiches in a sandwich bar.

Norovirus transfer between foods and food contact materials.

Human infective noroviruses (NoVs) are a worldwide leading cause of foodborne illness and are frequently spread via infected food handlers preparing and manipulating food products such as deli sandwiches. The objective of the current study was to determine the efficiencies whereby NoV could be transferred between surfaces associated with the preparation of manually prepared foods such as deli sandwiches. Nonfood surfaces included gloves and stainless steel discs, and boiled ham, lettuce, and a sandwich bun were the ingredients of the deli sandwich.

Inactivation of food-borne viruses using natural biochemical substances.

Food-borne viruses such as human Noroviruses (NoVs), hepatitis A virus (HAV), Rotaviruses (RoVs) are a public health concern worldwide. Biochemical substances, which occur naturally in plants, animals or microorganisms, might possess considerable antimicrobial properties. In this study, the reported effects of biochemical substances on food-borne viruses are reviewed.

Molecular detection and genotyping of noroviruses.

Noroviruses (NoVs) are a major cause of gastroenteritis worldwide in humans and animals and are known as very infectious viral agents. They are spread through feces and vomit via several transmission routes involving person-to-person contact, food, and water. Investigation of these transmission routes requires sensitive methods for detection of NoVs.

A review of known and hypothetical transmission routes for noroviruses.

Human noroviruses (NoVs) are considered a worldwide leading cause of acute non-bacterial gastroenteritis. Due to a combination of prolonged shedding of high virus levels in feces, virus particle shedding during asymptomatic infections, and a high environmental persistence, NoVs are easily transmitted pathogens. Norovirus (NoV) outbreaks have often been reported and tend to affect a lot of people.

Evaluation of viral concentration methods from irrigation and processing water.

Four viral concentration methods were evaluated for their efficiency in recovering murine norovirus-1 (MNV-1) (surrogate for human noroviruses (NoV)) and MS2 bacteriophages from processing water (1L) and four different types of irrigation water (bore hole water, rain water, open well and river water) (2-5L). Three methods were based on the viral adsorption and elution principle, two methods using an electronegative HA-membrane (Katayama et al., 2002), one method using an electropositive Zetapor membrane according to CEN/TC275/WG6/TAG4 and the fourth method was based on size exclusion using a tangential flow filtration system.

Effects of a variety of food extracts and juices on the specific binding ability of norovirus GII.4 P particles.

The effects of 13 food extracts and juices, including shellfish, fruits, and vegetables, on the binding ability of human norovirus (NoV) were examined, using P particles of human NoV GII.4 as a research surrogate. The enhancements (positive values) or reductions (negative values) of NoV P particle detection (changes in optical density at 450 nm) in the presence of different food extracts and juices as compared with P particles diluted in phosphate-buffered saline were tested by saliva-binding, enzyme-linked immunosorbent assay in triplicate.

Effect of grape seed extract on human norovirus GII.4 and murine norovirus 1 in viral suspensions, on stainless steel discs, and in lettuce wash water.

The anti-norovirus (anti-NoV) effect of grape seed extract (GSE) was examined by plaque assay for murine norovirus 1 (MNV-1), cell-binding reverse transcription-PCR for human NoV GII.4, and saliva-binding enzyme-linked immunosorbent assay for human NoV GII.4 P particles, with or without the presence of interfering substances (dried milk and lettuce extract).

Evaluation of methods measuring the capsid integrity and/or functions of noroviruses by heat inactivation.

Attempts were made to evaluate methods measuring the capsid integrity and/or functions of noroviruses (NoVs) following heat treatment. Intact viruses (Murine Norovirus-1 [MNV-1] and human NoV GII.4), virus like particles (VLPs) and P particles (expressed in vitro from the protruding domain of the viral capsid) of NoVs were used in this study.

Extraction of food-borne viruses from food samples: a review.

Detection of food-borne viruses such as noroviruses, rotaviruses and hepatitis A virus in food products differs from detection of most food-borne bacteria, as most of these viruses cannot be cultivated in cell culture to date. Therefore, detection of food-borne viruses in food products requires multiple steps: first, virus extraction; second, purification of the viral genomic material (RNA for the majority of food-borne viruses); and last, molecular detection. This review is focused on the first step, the virus extraction.

Critical studies on binding-based RT-PCR detection of infectious Noroviruses.

Attempts were made to discriminate between infectious and non-infectious Noroviruses (NoVs) based on their viral binding properties followed by reverse transcription polymerase chain reaction (RT-PCR). Murine norovirus-1 (MNV-1) was employed as a surrogate to test the principle. Detection of both infectious and inactivated MNV-1 was investigated by the plaque assay, RT-PCR and binding-based RT-PCRs.