Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain.

Pistachios have been implicated in two salmonellosis outbreaks and multiple recalls in the U.S. This study performed an in-depth retrospective data analysis of Salmonella associated with pistachios as well as a storage study to evaluate the survivability of Salmonella on inoculated inshell pistachios to further understand the genetics and microbiological dynamics of this commodity-pathogen pair. The retrospective data analysis on isolates associated with pistachios was performed utilizing short-read and long-read sequencing technologies. The sequence data were analyzed using two methods: the FDA's Center for Food Safety and Applied Nutrition Single Nucleotide Polymorphism (SNP) analysis and Whole Genome Multilocus Sequence Typing (wgMLST). The year-long storage study evaluated the survival of five strains of Salmonella on pistachios stored at 25 °C at 35% and 54% relative humidity (RH). Our results demonstrate: i) evidence of persistent Salmonella Senftenberg and Salmonella Montevideo strains in pistachio environments, some of which may be due to clonal resident strains and some of which may be due to preharvest contamination; ii) presence of the Copper Homeostasis and Silver Resistance Island (CHASRI) in Salmonella Senftenberg and Montevideo strains in the pistachio supply chain; and iii) the use of metagenomic analysis is a novel tool for determining the composition of serovar survival in a cocktail inoculated storage study.

Complete Genome Sequences of Four Salmonella enterica Strains Associated with Pistachios Assembled Using a Combination of Short- and Long-Read Sequencing.

Here, we report the genomes of two Salmonella enterica subsp. enterica serovar Montevideo strains (CFSAN005645 and FCC0123) and two Salmonella enterica subsp. enterica serovar Senftenberg strains (FSW0104 and CFSAN087304) isolated from pistachios. The genomes were closed using a hybrid assembly method using short- and long-read sequencing technology.

Erratum for Haendiges et al., "Complete Genome Sequences of Five Salmonella enterica Strains Used in Inoculation Cocktails in Low-Moisture Food Storage Studies".

[This corrects the article DOI: 10.1128/MRA.01588-18.].

Complete Genome Sequences of Five Salmonella enterica Strains Used in Inoculation Cocktails in Low-Moisture Food Storage Studies.

Survival kinetics of Salmonella enterica have been previously studied using an inoculum cocktail composed of different strains that have been associated with low-moisture foods. Here, we report the closed genome sequences of five strains of Salmonella enterica that are commonly used in these storage studies.

First Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Worthington Strain CFSAN051295, Isolated from Pistachio.

We report here, using third-generation, single-molecule, real-time DNA sequencing, the first complete genome sequence of Salmonella enterica serovar Worthington CFSAN051295, isolated from pistachios in the United States. The genome consists of a single 4.9-Mb chromosome.

Complete Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Senftenberg and Montevideo Isolates Associated with a 2016 Multistate Outbreak in the United States.

A multistate outbreak of 11 Salmonella infections linked to pistachio nuts occurred in 2016. In this announcement, we report the complete genome sequences of four Salmonella enterica subsp. enterica serovar Senftenberg and S. enterica subsp. enterica serovar Montevideo isolates from pistachios collected during the 2016 outbreak investigation.

Closed Genome Sequences of Two Clostridium botulinum Strains Obtained by Nanopore Sequencing.

Here we report the genome sequences of two toxin-producing Clostridium botulinum strains, one environmental sample (83F) and one clinical sample (CDC51232). The genomes were closed by a combination of long-read and short-read sequencing. The strains belong to C. botulinum sequence type 4 (ST4) and ST7, respectively.

Asymmetric transfer efficiencies between fomites and fingers: Impact on model parameterization.

BACKGROUND: Healthcare-associated infections (HAIs) affect millions of patients every year. Pathogen transmission via fomites and healthcare workers (HCWs) contribute to the persistence of HAIs in hospitals. A critical parameter needed to assess risk of environmental transmission is the pathogen transfer efficiency between fomites and fingers. Recent studies have shown that pathogen transfer is not symmetric. In this study,we evaluated how the commonly used assumption of symmetry in transfer efficiency changes the dynamics of pathogen movement between patients and rooms and the exposures to uncolonized patients. METHODS: We developed and analyzed a deterministic compartmental model of Acinetobacter baumannii describing the contact-mediated process among HCWs, patients, and the environment. We compared a system using measured asymmetrical transfer efficiency to 2 symmetrical transfer efficiency systems. RESULTS: Symmetric models consistently overestimated contamination levels on fomites and underestimated contamination on patients and HCWs compared to the asymmetrical model. The magnitudes of these miscalculations can exceed 100%. Regardless of the model, relative percent reductions in contamination declined after hand hygiene compliance reached approximately 60% in the large fomite scenario and 70% in the small fomite scenario. CONCLUSIONS: This study demonstrates how healthcare facility-specific data can be used for decision-making processes. We show that the incorrect use of transfer efficiency data leads to biased effectiveness estimates for intervention strategies. More accurate exposure models are needed for more informed infection prevention strategies.

Nutrition in the management of gastrointestinal diseases and disorders: the evidence for the low FODMAP diet.

A growing interest from both physicians and patients is fueling research in the interaction of symptoms related to irritable bowel syndrome (IBS) and diet, particularly the low FODMAP diet. Recent studies further define the role of these short-chain fermentable carbohydrates on IBS symptoms and their effects in different parts of the gastrointestinal tract. Mounting evidence supports the use of a low FODMAP diet in the clinical setting, but this dietary approach is not without potential drawbacks. This review illustrates the mechanisms by which the low FODMAP diet leads to improvement in IBS symptoms, summarizes the available clinical evidence, and offers practical advice regarding implementation of this dietary strategy.

Zebrafish as a model host for streptococcal pathogenesis.

Streptococcal pathogens continue to evade concerted efforts to determine clear-cut virulence mechanisms, although numerous genes have been implicated in pathogenesis. A single species can infect a diversity of tissues, suggesting the expression of specific virulence factors based on the local tissue environment or stage of infection. In an effort to identify the interactions that occur between the host and pathogen that lead to activation of virulence mechanisms and contribute to specific streptococcal disease states, we have developed a unique animal model, the zebrafish (Danio rerio), to characterize specific virulence mechanisms utilized within various tissues in vivo. We are using this model host to study infection by two streptococcal species that represent two forms of streptococcal disease: a natural pathogen of fish and humans, Streptococcus iniae and a human-specific pathogen, Streptococcus pyogenes. S. iniae primarily causes a fatal systemic disease in the zebrafish following intra-muscular injection, with similar pathologies to that seen in human infections caused by Streptococcus agalactiae and S. pneumoniae. While the fatal infection by S. pyogenes causes a locally spreading necrotic disease confined to the muscle with pathology similar to what is observed in a human infection of necrotizing fasciitis. By studying pathogens that are virulent for both fish and humans and that mediate disease states in the zebrafish that are identical to those found in human streptococcal infections, we will be able to identify common virulence strategies shared by a number of Gram-positive pathogens.

Analysis of the polysaccharide capsule of the systemic pathogen Streptococcus iniae and its implications in virulence.

Systemic pathogens have developed numerous strategies for evading the defenses of the host, permitting dissemination and multiplication in various tissues. One means of survival in the host, particularly in the bloodstream, has been attributed to the ability to avoid phagocytosis via capsular polysaccharide. To further define the virulence capacity of Streptococcus iniae, a zoonotic pathogen with the ability to cause severe systemic disease in both fish and humans, we performed an analysis of the capsule locus. The initial analysis included cloning and sequencing of the capsule synthesis operon, which revealed an approximately 21-kb region that is highly homologous to capsule operons of other streptococci. A genetic comparison of S. iniae virulent strain 9117 and commensal strain 9066 revealed that the commensal strain does not have the central region of the capsule operon composed of several important capsule synthesis genes. Four 9117 insertion or deletion mutants with mutations in the beginning, middle, or end of the capsule locus were analyzed to determine their capsule production and virulence. Virulence profiles were analyzed for each mutant using three separate criteria, which demonstrated the attenuation of each mutant in several tissue environments. These analyses also provided insight into the different responses of the host to each mutant strain compared to a wild-type infection. Our results demonstrate that capsule is not required for all host environments, while excess capsule is also not optimal, suggesting that for an "ideal" systemic infection, capsule production is most likely regulated while the bacterium is in different environments of the host.

Large-scale screen highlights the importance of capsule for virulence in the zoonotic pathogen Streptococcus iniae.

Zoonotic pathogens have the unique ability to cross the species barrier, causing disease in both humans and specific animal hosts. Streptococcus iniae is a zoonotic pathogen of both fish and humans, and the clinical presentations of S. iniae infections in fish and humans are very similar to those caused by various human-specific streptococcal pathogens. Virulence mechanisms required for infection by this pathogen of either host have yet to be determined. Using the previously reported zebrafish infectious disease model, we performed a large-scale screening to determine genes required for systemic infection. Screening 1,128 signature-tagged transposon mutants through the zebrafish model allowed identification of 41 potential mutants that were unable to survive within the host environment. Greater than 50% of the mutants that could be identified through homology searches were highly homologous to genes found in other human-specific streptococcal pathogens, while 32% were found to have no homology to any sequences found in the databases, suggesting as yet unknown gram-positive bacterial virulence factors. A large percentage of the insertions were found to be located in several putative capsule synthesis genes, an important virulence component for other systemic pathogens. Density gradient assays demonstrated that several of these putative capsule mutants have dissimilar buoyant densities, suggesting different levels of capsule synthesis. Putative capsule mutants were also less resistant to phagocytosis in whole-blood assays than wild-type S. iniae. Our initial large-scale characterization of S. iniae virulence highlights the importance of the capsule for successful infection.