The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.

Streptococcus thermophilus is a lactic acid bacterium widely used by the dairy industry for the manufacture of yogurt and specialty cheeses. It is also a Gram-positive bacterial model to study phage-host interactions. CRISPR-Cas systems are one of the most prevalent phage resistance mechanisms in S. thermophilus. Little information is available about other host factors involved in phage replication in this food-grade streptococcal species. We used the model strain S. thermophilus SMQ-301 and its virulent phage DT1, harboring the anti-CRISPR protein AcrIIA6, to show that a host gene coding for a methionine aminopeptidase (metAP) is necessary for phage DT1 to complete its lytic cycle. A single mutation in metAP provides S. thermophilus SMQ-301 with strong resistance against phage DT1. The mutation impedes a late step of the lytic cycle since phage adsorption, DNA replication, and protein expression were not affected. When the mutated strain was complemented with the wild-type version of the gene, the phage sensitivity phenotype was restored. When this mutation was introduced into other S. thermophilus strains it provided resistance against cos-type (Sfi21dt1virus genus) phages but replication of pac-type (Sfi11virus genus) phages was not affected. The mutation in the gene coding for the MetAP induces amino acid change in a catalytic domain conserved across many bacterial species. Introducing the same mutation in Streptococcus mutans also provided a phage resistance phenotype, suggesting the wide-ranging importance of the host methionine aminopeptidase in phage replication.

The lytic Escherichia coli phage Ebrios was isolated from a water sample collected in Ebrie Lagoon on the Adiopodoumé River in Abidjan (Republic of Côte d’Ivoire, West Africa). The linear genome of this Podoviridae family member contains 39,752 bp, has a G+C content of 52.9%, is composed of 53 open reading frames, and is related to the Stenotrophomonas maltophilia phage IME15.

Multi-drug resistant (MDR) Salmonella enterica Enteritidis is one of the major causes of foodborne illnesses worldwide. This non-typhoidal Salmonella (NTS) serovar is mainly transmitted to humans through poultry products. Bacteriophages (phages) offer an alternative to antibiotics for reducing the incidence of MDR NTS in poultry farms. Phages that survive the harsh environment of the chicken gastrointestinal tract (cGIT), which have low pH, high temperatures, and several enzymes, may have a higher therapeutic or prophylactic potential. In this study, we analysed the stability of 10 different S. Enteritidis phages isolated from Kenyan poultry farms in different pH-adjusted media, incubation temperatures, as well as simulated gastric and intestinal fluids (SGF and SIF, respectively). Furthermore, their ability to persist in water sources available in Kenya, including river, borehole, rain and tap water, was assessed. All phages were relatively stable for 12 h at pHs ranging from 5 to 9 and at temperatures ranging from 25 °C to 42 °C. At pH 3, a loss in viral titre of up to three logs was observed after 3 h of incubation. In SGF, phages were stable for 20 min, after which they started losing infectivity. Phages were relatively stable in SIF for up to 2 h. The efficacy of phages to control Salmonella growth was highly reduced in pH 2- and pH 3-adjusted media and in SGF at pH 2.5, but less affected in SIF at pH 8. River water had the most significant detrimental effect on phages, while the other tested waters had a limited impact on the phages. Our data suggest that these phages may be administered to chickens through drinking water and may survive cGIT to prevent salmonellosis in poultry.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.