Development and utility of the FDA 'GutProbe' DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics.

Aim: Lactic acid bacteria are beneficial microbes added to many food products and dietary supplements for their purported health benefits. Proper identification of bacteria is important to assess safety as well as proper product labelling. A custom microarray (FDA GutProbe) was developed to verify accurate labelling in commercial dietary supplements.

Whole-Genome Sequences of 12 Clinical Strains of Listeria monocytogenes.

Listeria monocytogenes is a foodborne pathogen of global concern due to the high mortality rate among immunocompromised patients. Whole-genome sequences of 12 strains of L. monocytogenes from humans were reported.

Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport.

Multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Newport has been a long-standing public health concern in the United States. We present the complete sequences of six IncA/C plasmids from animal-derived MDR S.

An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella.

Comparative genomics based on whole genome sequencing (WGS) is increasingly being applied to investigate questions within evolutionary and molecular biology, as well as questions concerning public health (e.g., pathogen outbreaks).

The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.

Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs.

The forensic analysis of foodborne bacterial pathogens in the age of whole-genome sequencing.

The forensic evaluation of bacterial pathogens presents new challenges to the forensic science community. This review examines bacterial pathogens as objects of forensic comparison, focusing on their nucleic acid sequences as an important aspect of the comparison process. Because of the clonal propagation of most bacterial pathogens, a phylogenetic approach to understanding the diversity and using this understanding to address common forensic questions is explored.

Rapid determination of hexapeptides by hydrophilic interaction LC-MS/MS for in vitro skin-penetration studies.

Background: A sensitive analytical method is needed for assessing penetration of topically applied peptides for in vitro skin-penetration studies.

Results: A rapid hydrophilic interaction LC (HILIC)-MS/MS method for analyzing the polar peptides Ac-EEMQRR-amide and H2N-EEMQRR-amide in various skin layers and matrices has been developed and evaluated. The matrices included emulsion, receptor fluids, cotton-tipped applicators, stratum corneum tape strips, epidermis and dermis of the skin.

Fully assembled genome sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.

We report a closed genome of Salmonella enterica subsp. enterica serovar Javiana (S. Javiana).

Analysis of pulsed field gel electrophoresis profiles using multiple enzymes for predicting potential source reservoirs for strains of Salmonella Enteritidis and Salmonella Typhimurium isolated from humans.

We reported previously on a highly discriminatory pulsed field gel electrophoresis-based (PFGE) subtyping scheme for Salmonella enterica serovar Enteritidis (SE) and Salmonella Typhimurium (ST) that relies on combined cluster analysis of up to six restriction enzymes. This approach allowed for the high-resolution separation of numerous poultry-derived SE and ST isolates into several distinct clusters that sorted along several geographical and host-linked boundaries. In this study, 101 SE and 151 ST strains isolated from poultry, swine, beef, mouse, and produce origins were combined with 62 human SE and ST isolates of unknown sources.

Colonization and internalization of Salmonella enterica in tomato plants.

The consumption of fresh tomatoes has been linked to numerous food-borne outbreaks involving various serovars of Salmonella enterica. Recent advances in our understanding of plant-microbe interactions have shown that human enteric pathogenic bacteria, including S. enterica, are adapted to survive in the plant environment.

Draft genome sequences of 21 Salmonella enterica serovar enteritidis strains.

Salmonella enterica subsp. enterica serovar Enteritidis is a common food-borne pathogen, often associated with shell eggs and poultry. Here, we report draft genomes of 21 S.

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach.

Background: Next-Generation Sequencing (NGS) is increasingly being used as a molecular epidemiologic tool for discerning ancestry and traceback of the most complicated, difficult to resolve bacterial pathogens. Making a linkage between possible food sources and clinical isolates requires distinguishing the suspected pathogen from an environmental background and placing the variation observed into the wider context of variation occurring within a serovar and among other closely related foodborne pathogens. Equally important is the need to validate these high resolution molecular tools for use in molecular epidemiologic traceback.

The influence of body weight on social network ties among adolescents.

Evidence of negative stereotypes, prejudice and discrimination towards obese individuals has been widely documented. However, the effect of a larger body size on social network ties or friendship formations is less well understood. In this paper, we explore the extent to which higher body weight results in social marginalization of adolescents.

Simultaneous analysis of multiple enzymes increases accuracy of pulsed-field gel electrophoresis in assigning genetic relationships among homogeneous Salmonella strains.

Due to a highly homogeneous genetic composition, the subtyping of Salmonella enterica serovar Enteritidis strains to an epidemiologically relevant level remains intangible for pulsed-field gel electrophoresis (PFGE). We reported previously on a highly discriminatory PFGE-based subtyping scheme for S. enterica serovar Enteritidis that relies on a single combined cluster analysis of multiple restriction enzymes.

Detection of type A, B, E, and F Clostridium botulinum neurotoxins in foods by using an amplified enzyme-linked immunosorbent assay with digoxigenin-labeled antibodies.

An amplified enzyme-linked immunosorbent assay (ELISA) for the detection of Clostridium botulinum complex neurotoxins was evaluated for its ability to detect these toxins in food. The assay was found to be suitable for detecting type A, B, E, and F botulinum neurotoxins in a variety of food matrices representing liquids, solid, and semisolid food. Specific foods included broccoli, orange juice, bottled water, cola soft drinks, vanilla extract, oregano, potato salad, apple juice, meat products, and dairy foods.

Exploring genotypic and phenotypic diversity of microbes using microarray approaches.

Application of genome-scale analysis like DNA microarray technology has revolutionized multiple scientific disciplines. Herein, a next generation of DNA microarrays, a DNA tiling approach that allows high throughput sampling of genomes with single-nucleotide precision, is described. As methods revealing a genomic scale examination of cellular phenotypes offer keen insights for genomic analyses, a high throughput system for whole cell phenotyping is similarly detailed.

Molecular applications for identifying microbial pathogens in the post-9/11 era.

Rapid advances in molecular and optical technologies over the past 10 years have dramatically impacted the way biologic research is conducted today. Examples include microarrays, capillary sequencing, optical mapping and real-time sequencing (Pyrosequencing). These technologies are capable of rapidly delivering massive amounts of genetic information and are becoming routine mainstays of many laboratories.

Effects of dietary taurocholate, fat and protein on the storage and metabolism of dietary beta-carotene and alpha-tocopherol in ferrets.

Dietary factors affecting tissue storage of beta-carotene (BC), alpha-tocopherol (alpha-T), and retinol (ROL) in mammals include taurocholate, protein, and fat. Few studies have examined the effects of these factors on the storage of BC, retinyl esters, and alpha-T in a mammalian system that is similar to humans. The main objective of the study was to investigate the effects of taurocholate (TC), fat, and protein on the absorption and metabolism of BC and alpha-T in ferret tissues.

Genomic variability among enteric pathogens: the case of the mutS-rpoS intergenic region.

The mutS-rpoS intergenic region of enteric bacteria ranges in size from 88 bp in Yersinia to > 12000 bp in Salmonella. We interpret this expansion as the result of the horizontal transfer of segments of DNA from diverse origins. Both comparative genomic analysis and selective sequencing of a variety of Escherichia coli pathogens have provided additional evidence for reassortment of segments within this region.

From farm to table to brain: foodborne pathogen infection and the potential role of the neuro-immune-endocrine system in neurotoxic sequelae.

The American diet is among the safest in the world; however, diseases transmitted by foodborne pathogens (FBPs) still pose a public health hazard. FBPs are the second most frequent cause of all infectious illnesses in the United States. Numerous anecdotal and clinical reports have demonstrated that central nervous system inflammation, infection, and adverse neurological effects occur as complications of foodborne gastroenteritis.

Three R's of bacterial evolution: how replication, repair, and recombination frame the origin of species.

The genetic diversity of bacteria results not only from errors in DNA replication and repair but from horizontal exchange and recombination of DNA sequences from similar and disparate species as well. New individuals carrying adaptive changes are thus being spawned constantly among the population at large. When new selection pressures appear, these are the individuals that survive, at the expense of the general population, to forge new populations.

Phylogenetic evidence for horizontal transfer of mutS alleles among naturally occurring Escherichia coli strains.

mutS mutators accelerate the bacterial mutation rate 100- to 1,000-fold and relax the barriers that normally restrict homeologous recombination. These mutators thus afford the opportunity for horizontal exchange of DNA between disparate strains. While much is known regarding the mutS phenotype, the evolutionary structure of the mutS(+) gene in Escherichia coli remains unclear.

Testing the potential of flaxseed to affect spermatogenesis: morphometry.

Quantitative information was collected on male reproductive effects of maternal and postnatal dietary exposure to flaxseed (20 or 40%), flaxmeal (13 or 26%) or standard NIH AIN-93 feed (0% flaxseed control). Measurements were made on the testes of F1 generation males rats (1) whose mothers were exposed to the diets designated above, and (2) who, after weaning, were placed on the same diet as their mothers for an additional 70 days. The seminiferous tubules comprised 86%, 84%, 84%, 84% and 85% of the total testis volume while the interstitial space comprised 12%, 14%, 14%, 14%, 13% of the total testis volume for the 0% flaxseed/flaxmeal, 20% flaxseed, 13% flaxmeal, 40% flaxseed and 26% flaxmeal groups, respectively.