MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification.

Motivation: State-of-the-art tools for classifying metagenomic sequencing reads provide both rapid and accurate options, although the combination of both in a single tool is a constantly improving area of research. The machine learning-based Naïve Bayes Classifier (NBC) approach provides a theoretical basis for accurate classification of all reads in a sample.

Results: We developed the multithreaded Minimizer-based Naïve Bayes Classifier (MNBC) tool to improve the NBC approach by applying minimizers, as well as plurality voting for closely related classification scores.

A multi-provincial outbreak of Newport infections associated with red onions: A report of the largest outbreak in Canada in over 20 years.

An investigation into an outbreak of Newport infections in Canada was initiated in July 2020. Cases were identified across several provinces through whole-genome sequencing (WGS). Exposure data were gathered through case interviews.

Transition to Whole Genome Sequencing Surveillance: The Impact on National Outbreak Detection and Response for , , Shiga Toxin-Producing , and Clusters in Canada, 2015-2021.

Between 2017 and 2019, pulsed-field gel electrophoresis was replaced by whole genome sequencing (WGS) for identifying enteric disease clusters in Canada. The number and characteristics of all clusters of , , Shiga toxin-producing (STEC), and spp. between 2015 and 2021 were analyzed.

Evaluating disinfectant efficacy on mixed biofilms comprising Shiga toxigenic , lactic acid bacteria, and spoilage microorganisms.

This study aimed to investigate the impact of temperature and the presence of other microorganisms on the susceptibility of STEC to biocides. Mature biofilms were formed at both 10°C and 25°C. An inoculum of planktonic bacteria comprising 10 CFU/mL of spoilage bacteria and 10 CFU/mL of a single strain (O157, O111, O103, and O12) was used to form mixed biofilms.

The state of integrated disease surveillance in seven countries: a synthesis report.

Objectives: Integrated disease surveillance (IDS) offers the potential for better use of surveillance data to guide responses to public health threats. However, the extent of IDS implementation worldwide is unknown. This study sought to understand how IDS is operationalized, identify implementation challenges and barriers, and identify opportunities for development.

Competitive interference among rhizobia reduces benefits to hosts.

The capacity of beneficial microbes to compete for host infection-and the ability of hosts to discriminate among them-introduces evolutionary conflict that is predicted to destabilize mutualism. We investigated fitness outcomes in associations between legumes and their symbiotic rhizobia to characterize fitness impacts of microbial competition. Diverse Bradyrhizobium strains varying in their capacity to fix nitrogen symbiotically with a common host plant, Acmispon strigosus, were tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations.

Sex-specific effects of voluntary wheel running on behavior and the gut microbiota-immune-brain axis in mice.

Physical exercise has been positioned as a promising strategy to prevent and/or alleviate anxiety and depression, but the biological processes associated with its effects on mental health have yet to be entirely determined. Although the prevalence of depression and anxiety in women is about twice that of men, very few studies have examined whether physical exercise could affect mental health differently according to sex. This study examined, in singly-housed mice, the sex-specific effects of voluntary exercise on depressive- and anxiety-like behaviors as well as on different markers along the gut microbiota-immune-brain axis.

Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.

Background: The reliability of culture-independent pathogen detection in foods using metagenomics is contingent on the quality and composition of the reference database. The inclusion of microbial sequences from a diverse representation of taxonomies in universal reference databases is recommended to maximize classification precision for pathogen detection. However, these sizable databases have high memory requirements that may be out of reach for some users.

A multi-provincial Typhimurium outbreak in Canada associated with exposure to pet hedgehogs, 2017-2020.

Background: In October 2020, an investigation began in Canada on an outbreak of Typhimurium infections of the same strain as a concomitant outbreak in the United States (US) that was linked to pet hedgehogs. The objective of this article is to identify the source of the outbreak, determine if there was a link between the Canadian and US outbreaks and identify risk factors for infection to inform public health interventions.

Methods: Cases were identified through whole genome sequencing of Typhimurium isolates.

Impact of the COVID-19 Pandemic on the Reported Incidence of Select Bacterial Enteric Diseases in Canada, 2020.

The aim of this study was to describe the impact of the COVID-19 pandemic on reported cases and clusters of select enteric diseases in Canada, for the period of March 2020 to December 2020. Weekly counts of laboratory confirmed cases of , , Shiga toxin-producing (STEC), and were obtained from laboratory surveillance data. These data were supplemented with epidemiological information on the suspected source of illness, collected for cases identified within whole genome sequencing clusters.

Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada's public health laboratories.

Background: Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada's public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic.

Formation and Transfer of Multi-Species Biofilms Containing O103:H2 on Food Contact Surfaces to Beef.

Interactions of Shiga toxin-producing (STEC; O103:H2) with lactic acid bacteria (LAB) or spoilage bacteria (SP) multispecies biofilms on polyurethane (TPU) and stainless-steel (SS) were assessed at 10 and 25°C under wet and dry conditions after 6, 30, and 60 days of storage. One LAB T1: + , and two SP T2: + T3: + were assessed for their ability to form multispecies biofilms with O103:H2. O103:H2 single-species biofilms served as a control positive (T4).

PulseNet International Survey on the Implementation of Whole Genome Sequencing in Low and Middle-Income Countries for Foodborne Disease Surveillance.

PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for real-time identification and subtyping of foodborne pathogens to strengthen preparedness and response and lower the burden of disease. Several countries in North America and Europe have experienced significant benefits in disease mitigation after implementing WGS.

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in in Canada Using Staramr.

Whole genome sequencing (WGS) of supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in ( = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard.

Population structure, case clusters, and genetic lesions associated with Canadian Salmonella 4,[5],12:i:- isolates.

Monophasic Salmonella 4,[5]:12:i:- are a major public health problem because they are one of the top five Salmonella serotypes isolated from clinical cases globally and because they can carry resistance to multiple antibiotics. A total of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium whole genome sequences (WGS) were generated.

Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019.

BackgroundWhole genome sequencing (WGS) is increasingly used for pathogen identification and surveillance.AimWe evaluated costs and benefits of routine WGS through case studies at eight reference laboratories in Europe and the Americas which conduct pathogen surveillance for avian influenza (two laboratories), human influenza (one laboratory) and food-borne pathogens (five laboratories).MethodsThe evaluation focused on the institutional perspective, i.

Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype.

Salmonella 4,[5],12:i:- are monophasic S. Typhimurium variants incapable of producing the second-phase flagellar antigen. They have emerged since the mid-1990s to become one of the most prevalent Salmonella serotypes causing human disease world-wide.

Source Tracking Based on Core Genome SNV and CRISPR Typing of Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012.

Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method.

Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America.

Two separate human outbreaks of serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated serotype. A total of 988 isolates of U.

Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing along Segments of the One Health Continuum.

Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase (ESBL-EC) from cattle feces ( = 40), feedlot catch basins ( = 42), surrounding streams ( = 21), a beef processing plant ( = 4), municipal sewage ( = 30), and clinical patients ( = 25) are described.

CPHLN recommendations for the laboratory detection of Shiga toxin-producing (O157 and non-O157).

Shiga toxin-producing (STEC) are important enteric pathogens responsible for sporadic cases and outbreaks of gastroenteritis. O157:H7/NM (STEC O157) are the most commonly known STEC serotypes but it is now increasingly apparent that non-O157 STEC serotypes have been underreported in the past because they were not part of routine screening in many front-line laboratories. The Canadian Public Health Laboratory Network (CPHLN) has identified the need for improved detection and surveillance of non-O157 STEC and has developed the following recommendations to assist in the decision-making process for clinical and reference microbiology laboratories.