Deciphering the Molecular Mechanism of Peracetic Acid Response in Listeria monocytogenes.

Peracetic acid (PAA), a strong oxidizing agent, has been widely used as a disinfectant in food processing settings as it does not produce harmful chlorinated by-products. In the present study, the transcriptional response of Listeria monocytogenes to a sub-lethal concentration of PAA (2.5 ppm) was assessed using RNA-sequencing (RNA-seq).

associated with agricultural animals exhibit diverse evolutionary rates and show evidence of recent clonal expansion.

Unlabelled: Most foodborne salmonellosis outbreaks are linked to agricultural animal products with a few serovars accounting for most isolated from specific animal products, suggesting an adaptation to the corresponding animal hosts and their respective environments. Here, we utilized whole-genome sequence (WGS) data to analyze the evolution and population genetics of seven serovars frequently isolated from ground beef (Montevideo, Cerro, and Dublin), chicken (Kentucky, Infantis, and Enteritidis), and turkey (Reading) in the United States. In addition, publicly available metadata were used to characterize major clades within each serovar with regard to public health significance.

Utilizing whole-genome sequencing to characterize Listeria spp. persistence and transmission patterns in a farmstead dairy processing facility and its associated farm environment.

Farmstead dairy processing facilities may be particularly susceptible to Listeria spp. contamination due to the close physical proximity of their processing environments (PE) to associated dairy farm environments (FE). In this case study, we supported the implementation of interventions focused on improving (1) cleaning and sanitation efficacy, (2) hygienic zoning, and (3) sanitary equipment and facility design and maintenance in a farmstead dairy processing facility, and evaluated their effect on Listeria spp.

Application of Environmental Monitoring Programs and Root Cause Analysis to Identify and Implement Interventions to Reduce or Eliminate Listeria Populations in Apple Packinghouses.

Controlling Listeria in produce packinghouses can be challenging due to the large number of potential contamination routes. For example, repeated isolation of the same Listeria subtype in a packinghouse could indicate persistence in the packinghouse or reintroduction of the same Listeria from an upstream source. To improve understanding of Listeria transmission patterns in packinghouses, we performed a longitudinal study in four apple packinghouses, including testing of 1,339 environmental sponges and whole genome sequencing (WGS)-based characterization of 280 isolates.

Strain-specific Growth Parameters are Important to Accurately Model Bacterial Growth on Baby Spinach in Simulation Models.

Digital tools to predict produce shelf life have the potential to reduce food waste and improve consumer satisfaction. To address this need, we (i) performed an observational study on the microbial quality of baby spinach, (ii) completed growth experiments of bacteria that are representative of the baby spinach microbiota, and (iii) developed an initial simulation model of bacterial growth on baby spinach. Our observational data showed that the predominant genera found on baby spinach were Pseudomonas, Pantoea and Exiguobacterium.

Intensive Environmental Sampling and Whole Genome Sequence-based Characterization of Listeria in Small- and Medium-sized Dairy Facilities Reveal Opportunities for Simplified and Size-appropriate Environmental Monitoring Strategies.

Small- and medium-sized dairy processing facilities (SMDFs) may face unique challenges with respect to controlling Listeria in their processing environments, e.g., due to limited resources.

Taxonomy, ecology, and relevance to food safety of the genus with a particular consideration of new species described between 2010 and 2022.

Since 2010, the genus has had the addition of 22 new species that more than tripled the number of species identified until 2010. Sixteen of these 22 new species are distantly related to the type species, , and several of these present phenotypes that distinguish them from classical species (, , , , and ). These 22 newly described species also show that is more genetically diverse than previously estimated.

Role of Whole Genome Sequencing in Assessing Resident and Transient Listeria monocytogenes in a Produce Packinghouse.

Whole genome sequencing (WGS) is a powerful tool that may be used to assist in identifying Listeria contamination sources and movement within environments, and to assess persistence. This study investigated sites in a produce packinghouse where Listeria had been historically isolated; and aimed to characterize dispersal patterns and identify cases of transient and resident Listeria. Environmental swab samples (n = 402) were collected from 67 sites at two time-points on three separate visits.

Phenotypic and genomic characterizations of Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata strains reveal no clear association between genetic content and ropy phenotype.

Ropy defect of pasteurized fluid milk is a type of spoilage which manifests itself by an increased viscosity, slimy body, and string-like flow during pouring. This defect has, among other causes, been attributed to the growth, proliferation and exopolysaccharide production by coliform bacteria, which are most commonly introduced in milk as post-pasteurization contaminants. As we identified both Klebsiella pneumoniae ssp.

serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle.

subsp () serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.

Whole-Genome Sequencing-Based Characterization of Isolates from Produce Packinghouses and Fresh-Cut Facilities Suggests Both Persistence and Reintroduction of Fully Virulent L. monocytogenes.

The contamination of ready-to-eat produce with Listeria monocytogenes (LM) can often be traced back to environmental sources in processing facilities and packinghouses. To provide an improved understanding of sources and transmission in produce operations, we performed whole-genome sequencing (WGS) of LM ( = 169) and other spp. ( = 107) obtained from 13 produce packinghouses and three fresh-cut produce facilities.

Development of a Modeling Tool To Assess and Reduce Regulatory and Recall Risks for Cold-Smoked Salmon Due to Listeria monocytogenes Contamination.

Abstract: Although public health risk assessments for Listeria monocytogenes (Lm) have been published for various foods, firm-level decision making on interventions targeting Lm involves considerations of both public health and enterprise risks. Smoked seafood is a ready-to-eat product with a high incidence of Lm contamination and has been associated with several recalls. We used cold-smoked salmon as a model product to develop a decision support tool (the regulatory and recall risk [3R] model) to estimate (i) baseline regulatory and recall (RR) risks (i.

Soil Collected in the Great Smoky Mountains National Park Yielded a Novel Species, .

Soil samples collected in the Great Smoky Mountains National Park yielded a isolate that could not be classified to the species level. Whole-genome sequence-based average nucleotide identity BLAST and DNA-DNA Hybridization analyses confirmed this isolate to be a novel species with the highest similarity to (ANI = 93.9%, isDDH = 55.

The Number and Type of Chaperone-Usher Fimbriae Reflect Phylogenetic Clade Rather than Host Range in Salmonella.

Salmonella is one of the most successful foodborne pathogens worldwide, owing in part to its ability to colonize or infect a wide range of hosts. Salmonella serovars are known to encode a variety of different fimbriae (hairlike organelles that facilitate binding to surfaces); however, the distribution, number, and sequence diversity of fimbriae encoded across different lineages of Salmonella were unknown. We queried whole-genome sequence (WGS) data for 242 Salmonella enterica subsp.

Characterization of Listeria monocytogenes isolated from wildlife in central New York.

Background: Listeria monocytogenes (Lm) present in farming soil and food-processing facilities threatens food safety, but little is known about the carriage of Lm by wildlife.

Objectives: We estimated the prevalence of faecal Lm shedding among wildlife admitted to a veterinary medical teaching hospital in central New York and characterized a subset of the Lm isolates.

Methods: Wildlife samples were collected between May 2018 and December 2019.

Development of a Genomics-Based Approach To Identify Putative Hypervirulent Nontyphoidal Salmonella Isolates: Salmonella enterica Serovar Saintpaul as a Model.

While differences in human virulence have been reported across nontyphoidal (NTS) serovars and associated subtypes, a rational and scalable approach to identify subtypes with differential ability to cause human diseases is not available. Here, we used NTS serovar Saintpaul ( Saintpaul) as a model to determine if metadata and associated whole-genome sequence (WGS) data in the NCBI Pathogen Detection (PD) database can be used to identify (i) subtypes with differential likelihoods of causing human diseases and (ii) genes and single nucleotide polymorphisms (SNPs) potentially responsible for such differences. Saintpaul SNP clusters ( = 211) were assigned different epidemiology types (epi-types) based on statistically significant over- or underrepresentation of human clinical isolates, including human associated (HA;  = 29), non-human associated (NHA;  = 23), and other ( = 159).

Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Serovars.

The zoonotic pathogen includes >2,600 serovars, which differ in the range of hosts they infect and the severity of disease they cause. To further elucidate the mechanisms behind these differences, we performed transcriptomic comparisons of nontyphoidal (NTS) serovars with the model for NTS pathogenesis, . Typhimurium.

Sequence Analyses and Phenotypic Characterization Revealed Multidrug Resistant Gene Insertions in the Genomic Region Encompassing Phase 2 Flagellin Encoding Genes in Monophasic Variant Serovar 4,5,12:i:- Isolates From Various Sources in Thailand.

serovar 4,5,12:i:- (. 4,5,12:i:-), a monophasic variant of Typhimurium (STm) lacking the phase 2 flagellin encoding genes , has become increasingly prevalent worldwide. The increasing trends in multidrug resistant (MDR) .

Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil.

Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of Heidelberg isolated from Brazilian poultry farms.

Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in under Stationary Phase Stress Condition.

can regulate and fine-tune gene expression, to adapt to diverse stress conditions encountered during foodborne transmission. To further understand the contributions of alternative sigma (σ) factors to the regulation of gene expression, RNA-Seq was performed on strain 10403S and five isogenic mutants (four strains bearing in-frame null mutations in three out of four alternative σ factor genes, ΔCHL, ΔBHL, ΔBCL, and ΔBCH, and one strain bearing null mutations in all four genes, ΔBCHL), grown to stationary phase. Our data showed that 184, 35, 34, and 20 genes were positively regulated by σ, σ, σ, and σ (posterior probability > 0.

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.

Pre-growth conditions and strain diversity affect nisin treatment efficacy against Listeria monocytogenes on cold-smoked salmon.

Listeria monocytogenes is a human pathogen that is commonly found in environments associated with cold-smoked salmon. Nisin is a natural antimicrobial that can be used as a food preservative. While nisin is active against a number of Gram-positive bacteria, including L.

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica.

Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host- and geographic-associated population structure.

Paenibacillus odorifer, the Predominant Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways.

is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of spp., we first used allelic typing data for a preexisting collection of 1,228 species isolates collected from raw and processed milk, milk products, and dairy environmental sources.

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.