Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species.

Roseburia species are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genus Roseburia have examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genus Roseburia with respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content among Roseburia species and strains was most significant for cofactor biosynthesis. Unlike all other species of Roseburia that we analysed, Roseburia inulinivorans strains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities in R. intestinalis strains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of the Roseburia spp. genomes may influence in vivo gut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology of Roseburia spp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species.

Salmonella enterica subsp. enterica Serovar Heidelberg Food Isolates Associated with a Salmonellosis Outbreak Have Enhanced Stress Tolerance Capabilities.

Salmonella enterica serovar Heidelberg is currently the 12th most common serovar of Salmonella enterica causing salmonellosis in the United States and results in twice the average incidence of blood infections caused by nontyphoidal salmonellae. Multiple outbreaks of salmonellosis caused by Salmonella Heidelberg resulted from the same poultry processor, which infected 634 people during 2013 and 2014. The hospitalization and invasive illness rates were 38% and 15%, respectively. We hypothesized that the outbreak strains of Salmonella Heidelberg had enhanced stress tolerance and virulence capabilities. We sourced nine food isolates collected during the outbreak investigation and three reference isolates to assess their tolerance to heat and sanitizers, ability to attach to abiotic surfaces, and invasiveness in vitro We performed RNA sequencing on three isolates (two outbreak-associated isolates and a reference Salmonella Heidelberg strain) with various levels of heat tolerance to gain insight into the mechanism behind the isolates' enhanced heat tolerance. We also performed genomic analyses to determine the genetic relationships among the outbreak isolates. Ultimately, we determined that (i) six Salmonella Heidelberg isolates associated with the foodborne outbreak had enhanced heat tolerance, (ii) one outbreak isolate with enhanced heat tolerance also had an enhanced biofilm-forming ability under stressful conditions, (iii) exposure to heat stress increased the expression of Salmonella Heidelberg multidrug efflux and virulence genes, and (iv) outbreak-associated isolates were likely transcriptionally primed to better survive processing stresses and, potentially, to cause illness.IMPORTANCE This study provides a deep analysis of the intrinsic stress tolerance and virulence capabilities of Salmonella Heidelberg that may have contributed to the length and severity of a recent salmonellosis outbreak. Additionally, this study provides a comprehensive analysis of the transcriptomic response of S. enterica strains to heat stress conditions and compares baseline stationary-phase gene expression among outbreak- and non-outbreak-associated Salmonella Heidelberg isolates. These data can be used in assay development to screen isolates for stress tolerance and subsequent survival. This study adds to our understanding of the strains associated with the outbreak and informs ongoing regulatory discussions on Salmonella in poultry.

Hydrogen peroxide and sodium hypochlorite disinfectants are more effective against Staphylococcus aureus and Pseudomonas aeruginosa biofilms than quaternary ammonium compounds.

Background: Antimicrobial disinfectants are used as primary treatment options against pathogens on surfaces in healthcare facilities to help prevent healthcare associated infections (HAIs). On many surfaces, pathogenic microorganisms exist as biofilms and form an extracellular matrix that protects them from the antimicrobial effects of disinfectants. Disinfectants are used as all-purpose antimicrobials though very few specifically make biofilm efficacy claims. The objective of this study was to evaluate the efficacy of eight registered disinfectants (six registered by the Environmental Protection Agency and two products registered in by the European Chemical Agency) with general bactericidal claims, but currently no biofilm efficacy claims, against Staphylococcus aureus ATTC-6538 and Pseudomonas aeruginosa ATCC-15442 biofilms. We hypothesized that hydrogen peroxide and sodium hypochlorite disinfectant products would be more effective than quaternary ammonium chlorides. Methods: This study tested the bactericidal efficacy of eight registered disinfectant products against S. aureus ATCC-6538 and P. aeruginosa ATCC-15442 grown on glass coupons using a Center for Disease Control (CDC) biofilm reactor and EPA MLB SOP MB-19. Bactericidal efficacy was determined after treating coupons with disinfectants following standard EPA MLB SOP MB-20. Results: Overall, sodium hypochlorite and hydrogen peroxide disinfectants had significantly higher bactericidal efficacies than quaternary ammonium chloride disinfectants. We also found that all tested disinfectants except for quaternary ammonium chloride disinfectants met and exceeded the EPA standard for bactericidal efficacy against biofilms. Conclusion: In general, bactericidal efficacy against biofilms differed by active ingredient. The efficacies of sodium hypochlorite and hydrogen peroxide disinfectants did not vary between strains, but there were significant differences between strains treated with quaternary ammonium chloride disinfectants.