Application of quasimetagenomics methods to define microbial diversity and subtype in dairy and seafood production facilities.

In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as , and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of culture enrichments of environmental swabs collected from dairy and seafood production facilities.

Draft Genome Sequences of 18 Streptococcus Strains Isolated from Live Dietary Supplements and Cultured Food Products.

We present the genome sequences of 18 Streptococcus isolates from 8 different dietary supplements and 9 cultured food products. Strains from this species naturally colonize the human mouth and upper respiratory tract. Studies have shown that S.

Draft Genome Sequences of Nine Strains and Two Strains Isolated from Live Dietary Supplements and a Cultured Food Product.

We present the genome sequences of nine isolates and two isolates from 10 different dietary supplements and one cultured food product. Strains of these species have been associated with health benefits when ingested by humans, due to their ability to survive the stomach's acidic environment and colonize the intestinal tract.

Variability in the Occupancy of O157 Integration Sites by Shiga Toxin-Encoding Prophages.

O157:H7 strains often produce Shiga toxins encoded by genes on lambdoid bacteriophages that insert into multiple loci as prophages. O157 strains were classified into distinct clades that vary in virulence. Herein, we used PCR assays to examine Shiga toxin (Stx) prophage occupancy in , , , and among 346 O157 strains representing nine clades.

Comparative Transcriptomics of Shiga Toxin-Producing and Commensal and Cytokine Responses in Colonic Epithelial Cell Culture Infections.

Ingestion of Shiga toxin-producing (STEC) can result in a range of illness severity from asymptomatic to hemorrhagic colitis and death; thus risk assessment of STEC strains for human pathogenicity is important in the area of food safety. Illness severity depends in part on the combination of virulence genes carried in the genome, which can vary between strains even of identical serotype. To better understand how core genes are regulated differently among strains and to identify possible novel STEC virulence gene candidates that could be added to the risk assessment repertoire, we used comparative transcriptomics to investigate global gene expression differences between two STEC strains associated with severe illness and a commensal strain during intestinal epithelial cell (IEC) infections.

Development and Validation of a Quantitative PCR Method for Species Verification and Serogroup Determination of Listeria monocytogenes Isolates.

Abstract: Listeria monocytogenes (Lm) is one of the leading causes of death because of foodborne illness, affecting the elderly, pregnant women, neonates, and people who are immunocompromised. Serologically, Lm can be classified into 13 serotypes, although only 4 are typically linked with food contamination and illness. Since 2000, a shift in serotypes involved in listeriosis outbreaks has been observed, suggesting that tracking of serotypes could help identify emerging trends.

Draft Genome Sequences of Isolates of Diverse Host Origin from the E. coli Reference Center at Penn State University.

strains present a vast genomic diversity. We report the draft genome sequences of 1,000 isolates from the Reference Center at Penn State University. These strains were originally isolated from multiple animal and environmental sources over the past 50 years.

gndDb, a Database of Partial Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing.

The use of culture methods to detect diversity does not provide sufficient resolution to identify strains present at low levels. Here, we target the hypervariable gene and describe a database containing 534 distinct partial sequences and associated O groups for use with culture-independent community analysis.

Microbiota of the Hickey Run Tributary of the Anacostia River.

Water from the Hickey Run Tributary of the Anacostia River is being collected quarterly (beginning August 2018) and analyzed to create high-resolution baseline taxonomic profiles of microbiota associated with this important aquatic ecosystem, which has a long history of exposure to residential and commercial effluents from Washington, DC. These United States National Arboretum Microbial Observatory data are available under NCBI BioProject number PRJNA498951.

Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella enterica from Dairy Cattle Farms in the Wakiso District, Uganda: A Cross-Sectional Study.

Enterobacteriaceae producing β-lactamases have spread rapidly worldwide and pose a serious threat to human-animal-environment interface. In this study, we present the presence of Salmonella enterica (1.3%) and commensal Escherichia coli (96.

Draft Genome Sequences of 72 Isolates from All Four Species of .

Shigella is a genus of Gram-negative enteric pathogenic bacteria which has four species, Shigella dysenteriae, S. flexneri, S. boydii, and S.

Draft Genome Sequences of the Escherichia coli Reference (ECOR) Collection.

Here, we report the genomes of all 72 isolates belonging to the Escherichia coli reference (ECOR) collection. Strains in this collection were isolated from diverse hosts and geographic locations and have been used for more than 30 years to represent the phylogenetic diversity of E. coli.

Interlaboratory Evaluation of the U.S. Food and Drug Administration Escherichia coli Identification Microarray for Profiling Shiga Toxin-Producing Escherichia coli.

The U.S. Food and Drug Administration Escherichia coli Identification (FDA-ECID) microarray provides rapid molecular characterization of E.

Fifty-Six Draft Genome Sequences of 10 Lactobacillus Species from 22 Commercial Dietary Supplements.

Here, we present the genome sequences of 56 isolates of 10 species of the genus that are considered beneficial components of the gut microbiota. The isolates examined were found in commercially available dietary supplements in the U.S.

Draft Genome Sequences of Bifidobacterium Strains Isolated from Dietary Supplements and Cultured Food Products.

Here, we present the genome sequences of 23 isolates from several commercially available dietary supplements and cultured food products. Strains of this genus are natural inhabitants of the mammalian mouth, gastrointestinal tract, and vagina. Some species are considered beneficial to human health.

Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.

We report here the genome sequences of 55 strains belonging to the genus from multiple animal and environmental sources. These strains include representatives of , , and six additional genetically distinct lineages of spp., one of which is newly discovered and is being reported for the first time here.

Species-Wide Collection of Isolates for Examination of Genomic Diversity.

Pathogenic and nonpathogenic strains present a vast genomic diversity. We report the genome sequences of 2,244 isolates from multiple animal and environmental sources. Their phylogenetic relationships and potential risk to human health were examined.

Shiga Toxin-Producing Serogroup O91 Escherichia coli Strains Isolated from Food and Environmental Samples.

Shiga toxin-producing (STEC) strains of the O91:H21 serotype have caused severe infections, including hemolytic-uremic syndrome. Strains of the O91 serogroup have been isolated from food, animals, and the environment worldwide but are not well characterized. We used a microarray and other molecular assays to examine 49 serogroup O91 strains (environmental, food, and clinical strains) for their virulence potential and phylogenetic relationships.

Plasma -fatty acid concentrations in fasting adults declined from NHANES 1999-2000 to 2009-2010.

The consumption of fatty acids (TFAs) is associated with an increased risk of cardiovascular disease, and reducing their consumption is a major public health objective. Food intake studies have provided estimates for TFA concentrations in the US population; however, there is a need for data on TFA blood concentrations in the population. The objective of this study was to determine plasma TFA concentrations in a nationally representative group of fasted adults in the US population in NHANES samples from 1999-2000 and 2009-2010.

Challenges and Lessons Learned in Generating and Interpreting NHANES Nutritional Biomarker Data.

For the past 45 y, the National Center for Health Statistics at the CDC has carried out nutrition surveillance of the US population by collecting anthropometric, dietary intake, and nutritional biomarker data, the latter being the focus of this publication. The earliest biomarker testing assessed iron and vitamin A status. With time, a broad spectrum of water- and fat-soluble vitamins was added and biomarkers for other types of nutrients (e.

Use of the Escherichia coli Identification Microarray for Characterizing the Health Risks of Shiga Toxin-Producing Escherichia coli Isolated from Foods.

More than 470 serotypes of Shiga toxin-producing Escherichia coli (STEC) have been identified, but not all cause severe illness in humans. Most STEC that cause severe diseases can adhere to epithelial cells, produce specific stx subtypes, and belong to certain serotypes; therefore, these traits appear to be critical STEC risk factors. However, testing for these traits is labor intensive, and serotyping is inadequate because of extensive variations among E.

Characterization and Virulence Potential of Serogroup O113 Shiga Toxin-Producing Escherichia coli Strains Isolated from Beef and Cattle in the United States.

Shiga toxin-producing Escherichia coli (STEC) of serotype O113:H21 have caused severe diseases but are unusual in that they do not produce the intimin protein required for adherence to intestinal epithelial cells. Strains of serogroup O113 are one of the most common STEC found in ground beef and beef products in the United States, but their virulence potential is unknown. We used a microarray to characterize 65 O113 strains isolated in the United States from ground beef, beef trim, cattle feces, and fresh spinach.

Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in Spinach Using Metagenomic Sequencing.

Consumption of fresh bagged spinach contaminated with Shiga toxin-producing Escherichia coli (STEC) has led to severe illness and death; however current culture-based methods to detect foodborne STEC are time consuming. Since not all STEC strains are considered pathogenic to humans, it is crucial to incorporate virulence characterization of STEC in the detection method. In this study, we assess the comprehensiveness of utilizing a shotgun metagenomics approach for detection and strain-level identification by spiking spinach with a variety of genomically disparate STEC strains at a low contamination level of 0.

Applying inappropriate cutoffs leads to misinterpretation of folate status in the US population.

Background: Folate cutoffs for risk of deficiency compared with possible deficiency were originally derived differently (experimental compared with epidemiologic data), and their interpretations are different. The matching of cutoffs derived from one assay with population-based data derived from another assay requires caution.

Objective: We assessed the extent of folate-status misinterpretation with the use of inappropriate cutoffs.