Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in .

We have developed a targeted, amplicon-based next-generation sequencing method to detect and analyze 227 virulence genes (VG) of (AmpliSeq) for assessing the pathogenicity potential of . The procedure was developed using 80 reference genomes representing 75 epidemiologically-relevant serovars associated with human salmonellosis. We applied the AmpliSeq assay to (a) 35 previously characterized field strains of consisting of serovars commonly incriminated in foodborne illnesses and (b) 34 strains with undisclosed serological or virulence attributes, and were able to divide VGs into two groups: core VGs and variable VGs.

Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology.

Background: Structural variants (SVs), including deletions, insertions, duplications, and inversions, are relatively long genomic variations implicated in a diverse range of processes from human disease to ecology and evolution. Given their complex signatures, tendency to occur in repeated regions, and large size, discovering SVs based on short reads is challenging compared to single-nucleotide variants. The increasing availability of long-read technologies has greatly facilitated SV discovery; however, these technologies remain too costly to apply routinely to population-level studies.

A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection.

The lactococcal virulent phage p2 is a model for studying the genus, the most prevalent group of phages causing milk fermentation failures in cheese factories worldwide. This siphophage infects MG1363, a model strain used to study Gram-positive lactic acid bacteria. The structural proteins of phage p2 have been thoroughly described, while most of its non-structural proteins remain uncharacterized.

The Plasmidome as a Reservoir of Antibiotic Resistance.

The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades. The increase in antimicrobial resistance has been expanding via plasmids as mobile genetic elements encoding antimicrobial resistance (AMR) genes that are transferred vertically and horizontally. This study focuses on , one of the leading foodborne pathogens in industrialized countries.

Culture-Dependent Bioprospecting of Bacterial Isolates From the Canadian High Arctic Displaying Antibacterial Activity.

The goal of this study was to isolate, screen, and characterize Arctic microbial isolates from Expedition Fjord, Axel Heiberg Island, Nunavut, Canada capable of inhibiting the growth of foodborne and clinically relevant pathogens. Arctic bacteria were isolated from twelve different high Arctic habitats pertaining to active layer permafrost soil, saline spring sediments, lake sediments, and endoliths. This was achieved using (1) the cryo-iPlate, an innovative cultivation device within active layer permafrost soil and (2) bulk plating of Arctic samples by undergraduate students that applied standard culturing methods.

Species interactions and distinct microbial communities in high Arctic permafrost affected cryosols are associated with the CH and CO gas fluxes.

Microbial metabolism of the thawing organic carbon stores in permafrost results in a positive feedback loop of greenhouse gas emissions. CO and CH fluxes and the associated microbial communities in Arctic cryosols are important in predicting future warming potential of the Arctic. We demonstrate that topography had an impact on CH and CO flux at a high Arctic ice-wedge polygon terrain site, with higher CO emissions and lower CH uptake at troughs compared to polygon interior soils.

Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.

Non-typhoidal is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated strains.