Complete genome sequence of multidrug-resistant strain RT01-5M1 isolated from farmed salmon in Canada.

The genome sequence of multidrug-resistant RT01-5M1 strain isolated from Canadian farmed salmon was determined using Oxford nanopore and Illumina MiSeq sequencers. The assembled chromosome was estimated at 5,699,993 bp in size, with two plasmids, 164,879 bp and 82,046 bp. The chromosome and smaller plasmid contained antimicrobial resistance genes.

An integrated strategy involving high-throughput sequencing to characterize an unknown GM wheat event in Canada.

Glyphosate-resistant wheat plants were discovered in southern Alberta in 2017, representing an unauthorized GM release in Canada. The Canadian Food Inspection Agency undertook a series of experiments to characterize and identify this unknown GM wheat, as well as to develop and validate construct-specific and event-specific qPCR assays. Results of PCR-based assays and Sanger sequencing indicated the presence of CaMV 35S promoter (p35S), Rice Actin 1 intron (RactInt1), CP4-EPSPS gene and nopaline synthase terminator (tNOS) elements in the unknown GM wheat.

Complete Genome Sequence of an Endemic Mycobacterium bovis Strain from Wood Bison in Wood Buffalo National Park, Canada.

Mycobacterium bovis is the primary causative agent of bovine tuberculosis, a zoonotic infectious disease of concern for human health, livestock, and wildlife conservation. We report a complete genome sequence of an endemic Mycobacterium bovis strain affiliated with a wildlife reservoir of bovine tuberculosis found in wood bison in Wood Buffalo National Park, Canada.

Application of prophage sequence analysis to investigate a disease outbreak involving Adjame, a rare serovar and implications for the population structure.

Introduction: Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of , creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Adjame was caused by multiple strains of the organism as revealed by single-nucleotide polymorphism (SNP) variation. The use of highly discriminatory prophage analysis to characterize strains of should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis.

Complete Genome Sequences of Mycobacterium bovis Strains Affiliated with Bovine Tuberculosis Outbreaks in Canada in 2016 and 2018.

Mycobacterium bovis is the primary causative agent of bovine tuberculosis, a zoonotic infectious disease that presents a risk to public health, livestock, and wildlife. Here, we report complete genome sequences of two Mycobacterium bovis strains affiliated with bovine tuberculosis outbreaks in Canadian cattle farms in 2016 and 2018.

Complete Genome Sequence of a Listeria monocytogenes Strain from a Sample of Kale Salad.

Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium that is an important foodborne bacterial pathogen for humans worldwide, with high mortality rates. Here, we report the complete genome sequence of a Listeria monocytogenes strain that was isolated from kale salad in Canada.

Complete Genome Sequences of Three Listeria monocytogenes Strains from Microgreens Obtained with MinION and MiSeq Sequencing.

Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an important foodborne bacterial pathogen for human worldwide with 20-30% mortality. Here, we report circular complete genome sequences of three Listeria monocytogenes strains isolated from the samples of microgreens in Canada.

Complete Genome Sequence of a Listeria monocytogenes Strain Isolated from Sprouts and Carrying an Antimicrobial Resistance Gene.

Listeria monocytogenes, a Gram-positive, rod-shaped, non-spore-forming bacterium, is an important foodborne bacterial pathogen for humans worldwide, with a high mortality rate. Here, we report the complete genome sequence of a Listeria monocytogenes strain with an antimicrobial resistance (AMR) gene, isolated from sprouts in Canada.

Complete Genome Sequence of a Listeria monocytogenes Strain with Antimicrobial Resistance Genes Isolated from Lettuce in Canada.

Listeria monocytogenes, a Gram-positive, rod-shaped, non-spore-forming bacterium, is an important foodborne bacterial pathogen for humans worldwide. Here, we report the complete genome sequence of a Canadian Listeria monocytogenes strain with an antimicrobial resistance (AMR) gene that was isolated from lettuce.

High female mortality caused by an atypical species closely related to the complex in a colony of bearded dragons .

A commercial breeding colony of bearded dragons experienced an increase in mortality that affected females only. Before death, the animals had lost appetite and weight, were dehydrated, and some had labored breathing. Necropsy revealed granulomas in many organs (ovaries, lungs, liver, kidneys, heart, bone marrow) in which numerous acid-fast bacteria were identified.

Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada.

Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous.

Cross-reactivity and inclusivity analysis of CRISPR-based diagnostic assays of coronavirus SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is the cause of the novel coronavirus disease 2019 (COVID-19) pandemic. Its diagnosis relies on the molecular detection of the viral RNA by polymerase chain reaction (PCR) while newer rapid CRISPR-based diagnostic tools are being developed. As molecular diagnostic assays rely on the detection of unique sequences of viral nucleic acid, the target regions must be common to all coronavirus SARS-CoV-2 circulating strains, yet unique to SARS-CoV-2 with no cross-reactivity with the genome of the host and other normal or pathogenic organisms potentially present in the patient samples.

A comparison of fourteen fully characterized mammalian-associated isolates suggests that loss of defense mechanisms contribute to high genomic plasticity and subspecies evolution.

is currently classified into three main subspecies, but only two of these, subspecies and subsp. v originate principally from ruminants where they inhabit different niches and cause distinct pathogenicity. Their importance as pathogens in international trade and reporting is also different yet the criteria defining these properties have never been fully substantiated nor understood.

Complete Genome Sequence of a Canadian Klebsiella michiganensis Strain, Obtained Using Oxford Nanopore Technologies Sequencing.

is a Gram-negative opportunistic pathogen that is associated with many hospital-acquired infections in humans. Here, we report the complete genome sequence of a strain isolated from a Canadian wastewater treatment facility.

Complete Genome Assemblies of the Rare Salmonella enterica Serovar Adjame Using Nanopore and Illumina Sequence Reads.

The complete genome sequences of 12 isolates of the rare serovar Adjame were determined by combining Nanopore and Illumina sequence reads. Chromosome sizes ranged from 4,597,011 bp to 4,678,052 bp, and the GC content was 52.3%.

An Unusual Enteritidis Strain Carrying a Modified Virulence Plasmid Lacking the Gene Represents a Geographically Widely Distributed Lineage.

This study identifies a strain of subspecies serovar Enteritidis that harbors a highly unusual virulence plasmid. During the characterisation of a group of Enteritidis isolates, 10 isolates recovered from Canadian duck production facilities, of which seven were phage type 9b and three were closely related atypical phage types, failed detection by a PCR targeting the gene, a marker located on the virulence plasmid often employed for identification of this serovar. Comparison to + isolates by several standard genetic typing tools, further revealed their distinctive genomic makeup.

Closed Genome Sequences and Antimicrobial Resistance Profiles of Eight Wild Bird Isolates Obtained with MinION and Illumina MiSeq Sequencing.

Complete genome sequences of eight isolates of subsp. from Canadian wild birds were determined by MinION and Illumina MiSeq sequencing. Assembled chromosomes had an average size of 4,833,662 bp.

A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of in Lettuce.

The rapid detection of foodborne microbial pathogens contaminating fresh fruits and vegetables during the intervening period between harvest and consumption could revolutionize microbial quality assurance of food usually consumed raw and those with a limited shelf life. We have developed a sensitive, shotgun whole genome sequencing protocol capable of detecting as few as 1 colony forming unit (cfu) of serovar Typhimurium spiked on 25 g of lettuce. The Ion Torrent sequencing platform was used to generate reads of globally amplified DNA from microbes recovered from the surface of lettuce followed by bioinformatic analyses of the nucleotide sequences to detect the presence of .

Draft Genome Sequences of Eight Canadian Citrobacter braakii and Citrobacter freundii Strains.

and are Gram-negative opportunistic pathogens associated with many infectious diseases, including septicemia, in humans and animals. Here, we report the draft genome sequences of seven strains and one strain isolated from Canadian wastewater treatment facilities.

Screening for Exotic Forest Pathogens to Increase Survey Capacity Using Metagenomics.

Anthropogenic activities have a major impact on the global environment. Canada's natural resources are threatened by the spread of fungal pathogens, which is facilitated by agricultural practices and international trade. Fungi are introduced to new environments and sometimes become established, in which case they can cause disease outbreaks resulting in extensive forest decline.

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.