Analysis of Microbial Composition of Edible Insect Products Available for Human Consumption within the United States Using Traditional Microbiological Methods and Whole Genome Sequencing.

Edible insects offer a promising protein source for humans, but their food safety risks have not been previously investigated within the United States. Therefore, the aim of this study was to investigate the microbial content of processed edible insect products. A total of eight different types of edible insect products, including diving beetles, silkworms, grasshoppers, Jamaican crickets, mealworms, mole crickets, whole roasted crickets, and 100% pure cricket powder, were purchased from a large online retailer for the analysis.

Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices.

Meat from broilers raised without the use of antibiotics is becoming increasingly popular among consumers. Consequently, interest in the microbial profiling of chickens produced under nonconventional practices is growing, however, research on this topic is lacking. The current study was designed to characterize the dynamics of gut microbial populations of broilers raised under conventional and no antibiotics ever (NAE) practices.

Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species "L. swaminathanii".

Recently, a new Listeria species, "Listeria swaminathanii", was proposed. Here, we phenotypically and genotypically characterize two additional strains that were previously obtained from soil samples and compare the results to the type strain. Complete genomes for both strains were assembled from hybrid Illumina and Nanopore sequencing reads and annotated.

SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data.

Laboratories that run Whole Genome Sequencing (WGS) produce a tremendous amount of data, up to 10 gigabytes for some common instruments. There is a need to standardize the quality assurance and quality control process (QA/QC). Therefore we have created SneakerNet to automate the QA/QC for WGS.

Draft Genome Sequences of Two Lactobacillus johnsonii and Three Ligilactobacillus salivarius Strains Isolated from Intestinal Microbiomes of Chickens.

This report describes the genome sequences of two Lactobacillus johnsonii strains (AER105 and AER25) and three Ligilactobacillus salivarius strains (AER35, AER36, and AER04) recovered from broiler chicken gastrointestinal tracts in the southeastern United States. These genome sequences will enhance our understanding of the ecology of lactobacilli in the chicken gut microbiome.

Heat Inactivation of Listeria monocytogenes on Pecans, Macadamia Nuts, and Sunflower Seeds.

This project was undertaken to determine the kinetic parameters of thermal inactivation of Listeria monocytogenes on pecans, macadamia nuts, and sunflower seeds subjected to heat treatments simulating industry processes. Five strains were grown in nonselective medium, mixed, and resuspended before inoculating macadamia nuts, pecans, and sunflower seeds (6 to 9 Log CFU/g). Redried inoculated pecans and macadamia nuts were heated in an oven at a temperature range of 90 to 140°C.

High-Resolution Genomic Comparisons within Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period.

Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as one of the primary sources of -related outbreaks. Pathogenicity and antibiotic resistance of are highly serotype and subpopulation specific, which makes it essential to understand high-resolution population dynamics in cattle. Time of year, source of cattle, pen, and sample type (i.

Phylogeny of the Bacillus altitudinis Complex and Characterization of a Newly Isolated Strain with Antilisterial Activity.

Abstract: Bacillus strain UTK D1-0055 was isolated from a laboratory environment and appeared to have antilisterial activity. The genome was sequenced, the strain was identified as Bacillus altitudinis, and a high-quality complete annotated genome was produced. The taxonomy was evaluated for this and related Bacillus species (B.

Complete Genome Sequences of Three Listeria monocytogenes Bacteriophage Propagation Strains.

Bacteriophages can be used as a biocontrol for the foodborne pathogen Propagation of phages is a necessary step for their use in experimental studies and biocontrol applications. Here, we present the complete genomes of three strains commonly used as propagation hosts for phages.

Complete Genome Sequence of a Serotype 7 Listeria monocytogenes Strain, FSL R9-0915.

serotype 7 lacks glycosidic constituents in wall teichoic acids. Here, we present the complete genome sequence of serotype 7 strain FSL R9-0915 and an analysis of genes known to affect antigenicity. This strain is used as a control strain in phage host range analyses.

Sepia, a taxonomy oriented read classifier in Rust.

Here we present Sepia, a fast and accurate read classifier. It is implemented in Rust, has the ability to switch between different taxonomies, can detect inconsistencies in taxonomies, and can estimate similarities between organisms in a query dataset and reference sequences in the index.

Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing.

Food safety is a new area for novel applications of metagenomics analysis, which not only can detect and subtype foodborne pathogens in a single workflow but may also produce additional information with in-depth analysis capabilities. In this study, we applied a quasimetagenomic approach by combining short-term enrichment, immunomagnetic separation (IMS), multiple-displacement amplification (MDA), and nanopore sequencing real-time analysis for simultaneous detection of and in wheat flour. Tryptic soy broth was selected for the 12-h enrichment of samples at 42°C.

Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracycline.

Antibiotic use in beef cattle is a risk factor for the expansion of antimicrobial-resistant Salmonella populations. However, actual changes in the quantity of Salmonella in cattle feces following antibiotic use have not been investigated. Previously, we observed an overall reduction in Salmonella prevalence in cattle feces associated with both ceftiofur crystalline-free acid (CCFA) and chlortetracycline (CTC) use; however, during the same time frame the prevalence of multidrug-resistant Salmonella increased.

Survival of Salmonella enterica and Escherichia coli O157:H7 Sprayed onto the Foliage of Field-Grown Cabbage Plants.

To reduce the number of cabbage pathogen outbreaks, it is essential to understand the fate of enteric pathogens that contaminate plants in the field. To assist in that effort, two independent trials were conducted with a red cultivar (cv. Red Dynasty) and a green cultivar (cv.

Ultrafast search of all deposited bacterial and viral genomic data.

Exponentially increasing amounts of unprocessed bacterial and viral genomic sequence data are stored in the global archives. The ability to query these data for sequence search terms would facilitate both basic research and applications such as real-time genomic epidemiology and surveillance. However, this is not possible with current methods.

Complete Genome Sequences of Four Salmonella enterica Strains (Including Those of Serotypes Montevideo, Mbandaka, and Lubbock) Isolated from Peripheral Lymph Nodes of Healthy Cattle.

Salmonella enterica serotype Lubbock emerged most likely from a Salmonella enterica serotype Mbandaka ancestor that acquired by recombination the operon from Salmonella enterica serotype Montevideo. Here, we report the complete genome sequence of two Lubbock, one Montevideo, and one Mbandaka strain isolated from bovine lymph nodes.

Pre-harvest internalization and surface survival of Salmonella and Escherichia coli O157:H7 sprayed onto different lettuce cultivars under field and growth chamber conditions.

Plant genotype has been advocated to have an important role in the fate of enteric pathogens residing in lettuce foliage. This study was therefore undertaken under the premise that different pathogen responses could occur in lettuce cultivars with cultivar selection being one of several hurdles in an overall strategy for controlling foodborne pathogens on field-grown produce. Up to eight lettuce cultivars ('Gabriella', 'Green Star', 'Muir', 'New Red Fire', 'Coastal Star', 'Starfighter', 'Tropicana', and 'Two Star') were examined in these experiments in which the plants were subjected to spray contamination of their foliage with pathogens.

Genomic Diversity of Isolated from Clinical and Non-Clinical Samples in Chile.

is the causative agent of listeriosis, which is an uncommon but severe infection associated with high mortality rates in humans especially in high-risk groups. This bacterium survives a variety of stress conditions (e.g.

Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.

Unlabelled: Listeria monocytogenes is a bacterial pathogen that is found in a wide variety of anthropogenic and natural environments. Genome sequencing technologies are rapidly becoming a powerful tool in facilitating our understanding of how genotype, classification phenotypes, and virulence phenotypes interact to predict the health risks of individual bacterial isolates. Currently, 57 closed L.

Carbapenem-Resistant Bacteria Recovered from Faeces of Dairy Cattle in the High Plains Region of the USA.

Objective: A study was conducted to recover carbapenem-resistant bacteria from the faeces of dairy cattle and identify the underlying genetic mechanisms associated with reduced phenotypic susceptibility to carbapenems.

Methods: One hundred and fifty-nine faecal samples from dairy cattle were screened for carbapenem-resistant bacteria. Phenotypic screening was conducted on two media containing ertapenem.

Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.

As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-called next-generation sequencing (NGS) technologies that have made whole-genome sequencing (WGS) of foodborne bacterial pathogens a realistic and superior alternative to traditional subtyping methods. Routine, real-time, and widespread application of WGS in food safety and public health is on the horizon. Technological, operational, and policy challenges are still present and being addressed by an international and multidisciplinary community of researchers, public health practitioners, and other stakeholders.

Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing.

We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or "epidemic clones" that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones.