Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I–VI toxin–antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods

Fate of Salmonella enterica in a Mixed Ingredient Salad Containing Lettuce, Cheddar Cheese, and Cooked Chicken Meat

Food service and retail sectors offer consumers a variety of mixed ingredient salads that contain fresh-cut vegetables and other ingredients such as fruits, nuts, cereals, dairy products, cooked seafood, cooked meat, cured meats, or dairy products obtained from external suppliers. Little is known about the behavior of enteric bacterial pathogens in mixed ingredient salads. A model system was developed to examine the fate of Salmonella enterica (inoculum consisting of S. enterica serovars Agona, Typhimurium, Enteritidis, Brandenberg, and Kentucky) on the surface of romaine lettuce tissues incubated alone and in direct contact with Cheddar cheese or cooked chicken. S. enterica survived but did not grow on lettuce tissues incubated alone or in contact with Cheddar cheese for 6 days at either 6 or 14\ub0C. In contrast, populations increased from 2.01 \ub1 0.22 to 9.26 \ub1 0.22 CFU/cm2 when lettuce washed in water was incubated in contact with cooked chicken at 14\ub0C. Populations on lettuce leaves were reduced to 1.28 \ub1 0.14 CFU/cm2 by washing with a chlorine solution (70 ppm of free chlorine) but increased to 8.45 \ub1 0.22 CFU/cm2 after 6 days at 14\ub0C. Experimentation with a commercial product in which one third of the fresh-cut romaine lettuce was replaced with inoculated lettuce revealed that S. enterica populations increased by 4 log CFU/g during storage for 3 days at 14uC. These findings indicate that rapid growth of bacterial enteric pathogens may occur in mixed ingredient salads; therefore, strict temperature control during the manufacture, distribution, handling, and storage of these products is critical

Natural soil reservoirs for human pathogenic and fecal indicator bacteria

Prod ? EA UB INRA BIOMEInternational audiencerésumé du livre : Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field. Thoroughly updated and revised, the Manuall is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradation and biotransformation. This wealth of information is divided into 18 sections each containing chapters written by acknowledged topical experts from the international community. Specifically, this new edition of the Manual Contains completely new sections covering microbial risk assessment, quality control, and microbial source tracking Incorporates a summary of the latest methodologies used to study microorganisms in various environments Synthesizes the latest information on the assessment of microbial presence and microbial activity in natural and artificial environments Contains a completely revamped section covering The Manual of Environmental Microbiology is an essential reference for environmental microbiologists, microbial ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater treatment, and biotechnology

Natural soil reservoirs for human pathogenic and fecal indicator bacteria

EAMERSUBSoils receive inputs of human pathogenic and indicator bacteria through land application of animal manures or sewage sludge, and inputs by wildlife. Soil is an extremely heterogeneous substrate and contains meso- and macrofauna that may be reservoirs for bacteria of human health concern. The ability to detect and quantify bacteria of human health concern is important in risk assessments and in evaluating the efficacy of agricultural soil management practices that are protective of crop quality and protective of adjacent water resources. The present chapter describes the distribution of selected Gram-positive and Gram-negative bacteria in soils. Methods for detecting and quantifying soilborne bacteria including extraction, enrichment using immunomagnetic capture, culturing, molecular detection and deep sequencing of metagenomic DNA to detect pathogens are overviewed. Methods for strain phenotypic and genotypic characterization are presented, as well as how comparison with clinical isolates can inform the potential for human health ris

Comparative examination of Escherichia coli O157:H7 survival on romaine lettuce and in soil at two independent experimental sites

Little is known about the influence of abiotic factors such as climate and soil chemistry on the survival of Escherichia coli O157:H7 in field lettuce. We applied a nalidixic acid-resistant derivative of strain ATCC 700728 to field-grown romaine lettuce in two regions in Canada characterized by large variances in soil type and climate. Surviving populations in soil and on lettuce leaves were estimated on sorbitol MacConkey agar supplemented with nalidixic acid. Data were fitted with the Weibull decline function to permit comparison of decay rates in the two experimental sites. E. coli O157:H7 populations fell from 10 5 to <10 2 CFU/g on leaves, and <10 3 CFU/g in soil within 7 days after inoculation. Analysis revealed there was no significant difference between decay rates at the two experimental sites in either environment. The results of this study suggest that the inherent ecological fitness of E. coli O157:H7 ATCC 700728 determines the extent of survival in the production environment

Bacteriophage-Insensitive Mutants of Antimicrobial-Resistant Salmonella Enterica are Altered in their Tetracycline Resistance and Virulence in Caco-2 Intestinal Cells

Bacteriophages have shown promise as therapeutic alternatives to antibiotics for the control of infectious bacteria, including the human pathogen Salmonella. However, the development of effective phage-based applications requires the elucidation of key interactions between phages and target hosts, particularly since host resistance to phage is inevitable. Little is known about the alteration of host phenotypes following the development of resistance to phage. The aim of this study is to evaluate the antibiotic susceptibility and virulence of a Salmonella isolate following the development of resistance to bacteriophage SI1. We observed enhanced susceptibility to tetracycline and decreased invasion capacity in a differentiated Caco-2 intestinal cell line. Whole genome sequence analysis revealed an array of mutations, most notably, truncations in vgrG1_2, a core gene involved in Type VI secretion and mutations in the lipopolysaccharide, thereby indicating the plausible attachment site of phage SI1. These findings shed light on understanding the underlying mechanism for phage immunity within the host. Importantly, we reveal an associated genetic cost to the bacterial host with developing resistance to phages. Taken together, these results will aid in advancing strategies to delay or eliminate the development of host resistance when designing informed phage-based antimicrobials.Land and Food Systems, Faculty ofOther UBCNon UBCReviewedFacult