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View article: SARS-CoV-2 detection is independent of microbiome composition on surfaces in a major Ontario hospital
SARS-CoV-2 detection is independent of microbiome composition on surfaces in a major Ontario hospital Open
The SARS-CoV-2 pandemic has resulted in considerable mortality in hospital settings. Built environment surveillance can provide a non-invasive indicator of SARS-CoV-2 status in hospitals, but we have a limited understanding of SARS-CoV-2’s…
View article: Nearly a century of discoveries in bacterial genetics and their continuing impact on the field
Nearly a century of discoveries in bacterial genetics and their continuing impact on the field Open
View article: A multicentre study to predict COVID-19 outbreaks in long-term care homes using wastewater surveillance and environmental surface sampling for SARS-CoV-2
A multicentre study to predict COVID-19 outbreaks in long-term care homes using wastewater surveillance and environmental surface sampling for SARS-CoV-2 Open
Background Floor swabs can be an effective environmental sampling method for proactive SARS-CoV-2 surveillance in congregate settings like long-term care homes (LTCHs). Concurrent assessment of additional variables such as wastewater surve…
View article: Pleotropic Effects of Antibiotic Resistance Mutation
Pleotropic Effects of Antibiotic Resistance Mutation Open
Antibiotic resistance mutations (AMRs) alter the phenotypic (physical) characteristics of an organism, which may result in enhanced fitness under antibiotic stress. However, these mutations often infer trade-offs in the organism’s fitness …
View article: City-wide built environment SARS-CoV-2 detection for COVID-19 surveillance
City-wide built environment SARS-CoV-2 detection for COVID-19 surveillance Open
Built environment surveillance has shown promise for monitoring COVID-19 burden at granular geographic scales, but its utility for surveillance across larger areas and populations is unknown. Our study aims to evaluate the role of built en…
View article: The ionophore resistance genes <i>narA</i> and <i>narB</i> are geographically widespread and linked to resistance to medically important antibiotics
The ionophore resistance genes <i>narA</i> and <i>narB</i> are geographically widespread and linked to resistance to medically important antibiotics Open
Ionophores are a class of antibiotics used widely in animal production as anti-coccidials and for growth promotion. Since ionophores are not used in human medicine, it has largely been assumed that they do not contribute to medically impor…
View article: SARS-CoV-2 detection is independent of microbiome composition on surfaces in a major Ontario hospital
SARS-CoV-2 detection is independent of microbiome composition on surfaces in a major Ontario hospital Open
The SARS-CoV-2 pandemic has resulted in considerable mortality in hospital settings. Built environment surveillance can provide a non-invasive indicator of SARS-CoV-2 status in hospitals, but we have a limited understanding of SARS-CoV-2's…
View article: Predicting COVID-19 cases across a large university campus using built environment surveillance
Predicting COVID-19 cases across a large university campus using built environment surveillance Open
Background: Environmental surveillance of SARS-CoV-2 via wastewater has become an invaluable tool for population-level surveillance. Built environment sampling may provide complementary spatially refined detection for viral surveillance in…
View article: Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets
Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets Open
We used simulated and published shotgun sequencing datasets containing Salmonella-derived reads to explore the appearance and mitigation of false positive results using the popular taxonomic annotation softwares Kraken2 and Metaphlan4. Usi…
View article: Limit of detection of <i>Salmonella</i> ser. Enteritidis using culture-based versus culture-independent diagnostic approaches
Limit of detection of <i>Salmonella</i> ser. Enteritidis using culture-based versus culture-independent diagnostic approaches Open
To prevent the spread of foodborne illnesses, the presence of pathogens in the food chain is monitored by government agencies and food producers. The culture-based methods currently employed are sensitive but time- and labor-intensive, lea…
View article: SARS-CoV-2 burden on the floor was associated with COVID-19 cases and outbreaks in two acute care hospitals: a prospective cohort study
SARS-CoV-2 burden on the floor was associated with COVID-19 cases and outbreaks in two acute care hospitals: a prospective cohort study Open
Background: Recent work demonstrated that detection of SARS-CoV-2 on the floor of long-term care facilities is associated with impending COVID-19 outbreaks. It is unknown if similar results will be observed in hospitals. Methods: Floor swa…
View article: Systematic <i>in vitro</i> optimization of antimicrobial peptides against <i>Escherichia coli</i>
Systematic <i>in vitro</i> optimization of antimicrobial peptides against <i>Escherichia coli</i> Open
Objectives Antimicrobial resistance is a growing concern and claims over 1 million lives per year. The discovery of new antimicrobial drugs is expensive and often generates low profitability, with very low success rates. One way to combat …
View article: Detection of SARS-CoV-2 in schools using built environment testing in Ottawa, Canada: A multi-facility prospective surveillance study
Detection of SARS-CoV-2 in schools using built environment testing in Ottawa, Canada: A multi-facility prospective surveillance study Open
Classroom and staffroom floor swabs across six elementary schools in Ottawa, Canada were tested for SARS-CoV-2. Environmental test positivity did not correlate with student grade groups, school-level absenteeism, pediatric COVID-19-related…
View article: Overcoming Microbial Inhibition of S. Sonnei Through the Exploitation of Genomically Predicted Antibiotic Resistance Profiles for the Development of Food Enrichment Media
Overcoming Microbial Inhibition of S. Sonnei Through the Exploitation of Genomically Predicted Antibiotic Resistance Profiles for the Development of Food Enrichment Media Open
Linking outbreaks of Shigella spp. to specific foods is challenging due to poor selectivity of current enrichment media. We have previously shown that enrichment media, tailored to the genomically-predicted antimicrobial resistance (AMR) o…
View article: Strain-specific Recovery of S. sonnei from Artificially Contaminated Baby Carrots: Enhancing Food-safety Investigations with a Customized Shigella Detection Method Based on Genomically predicted Antibiotic Resistance Traits
Strain-specific Recovery of S. sonnei from Artificially Contaminated Baby Carrots: Enhancing Food-safety Investigations with a Customized Shigella Detection Method Based on Genomically predicted Antibiotic Resistance Traits Open
Shigella spp. are Gram-negative gastrointestinal bacterial pathogens that cause bacillary dysentery or shigellosis in humans. Isolation of Shigella from outbreak-associated foods is often problematic due to the lack of selectivity of cultu…
View article: Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in <i>Escherichia coli</i>
Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in <i>Escherichia coli</i> Open
The evolution of antimicrobial resistance (AMR) in bacteria is a major public health concern, and antibiotic restriction is often implemented to reduce the spread of resistance. These measures rely on the existence of deleterious fitness e…
View article: Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database
Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database Open
Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection databa…
View article: Environmental surveillance of SARS-CoV-2 for COVID-19 outbreak detection in hospital: a single-centre prospective study
Environmental surveillance of SARS-CoV-2 for COVID-19 outbreak detection in hospital: a single-centre prospective study Open
View article: Draft genomes of meropenem-resistant <i>Pseudomonads</i> from the cloacae of turtles in Lake Opinicon, Canada
Draft genomes of meropenem-resistant <i>Pseudomonads</i> from the cloacae of turtles in Lake Opinicon, Canada Open
We report the draft genome sequences of seven meropenem-resistant bacterial isolates from the cloacae of painted and musk turtles at Lake Opinicon, Canada. This study improves our understanding of the spread of meropenem-resistant bacteria…
View article: Limit of detection of<i>Salmonella</i>ser. Enteritidis using culture-based versus culture-independent diagnostic approaches
Limit of detection of<i>Salmonella</i>ser. Enteritidis using culture-based versus culture-independent diagnostic approaches Open
In order to prevent the spread of foodborne illnesses, the presence of pathogens in the food chain is monitored by government agencies and food producers. The culture-based methods currently employed are sensitive but time-and labour-inten…
View article: Predicting COVID-19 cases across a large university campus using complementary built environment and wastewater surveillance approaches
Predicting COVID-19 cases across a large university campus using complementary built environment and wastewater surveillance approaches Open
Background Environmental surveillance of SARS-CoV-2 via wastewater has become an invaluable tool for population-level surveillance. Built environment sampling may provide complementary spatially-refined detection for viral surveillance in …
View article: Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools
Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools Open
Background Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologie…
View article: 2303. Detection of COVID-19 Outbreaks in Hospitals Using Built Environment Testing for SARS-CoV-2
2303. Detection of COVID-19 Outbreaks in Hospitals Using Built Environment Testing for SARS-CoV-2 Open
Background Environmental testing for SARS-CoV-2 including assessment of wastewater and the built environment is a useful tool for population-level surveillance for COVID-19. Detection of SARS-CoV-2 on the floor of healthcare facilities has…
View article: 1711. Prospective Environmental Surveillance of Floors in a Pediatric Emergency Department During a Respiratory Syncytial Virus Surge in Ottawa, Canada
1711. Prospective Environmental Surveillance of Floors in a Pediatric Emergency Department During a Respiratory Syncytial Virus Surge in Ottawa, Canada Open
Background Annual respiratory syncytial virus (RSV) epidemics disproportionately impact infants and young children. Clinical surveillance is often restricted to laboratory-confirmed hospitalizations. Built environmental surveillance throug…
View article: Unpredictability of the fitness effects of antimicrobial resistance mutations across environments in<i>Escherichia coli</i>
Unpredictability of the fitness effects of antimicrobial resistance mutations across environments in<i>Escherichia coli</i> Open
The evolution of antimicrobial resistance (AMR) in bacteria is a major public health concern. When resistant bacteria are highly prevalent in microbial populations, antibiotic restriction protocols are often implemented to reduce their spr…
View article: Modeling the Limits of Detection for Antimicrobial Resistance Genes in Agri-Food Metagenomic Samples
Modeling the Limits of Detection for Antimicrobial Resistance Genes in Agri-Food Metagenomic Samples Open
Background Despite the potential for dissemination of antimicrobial resistance (AMR) through food and food production, there are few studies of the prevalence of AMR organisms (AROs) in various agri-food products. Sequencing technologies a…
View article: Environmental surveillance for SARS-CoV-2 for outbreak detection in hospital: A single centre prospective study
Environmental surveillance for SARS-CoV-2 for outbreak detection in hospital: A single centre prospective study Open
Identifying COVID-19 outbreaks in hospitals at an early stage requires active surveillance. Our objective was to assess whether floor swabs correlated with COVID-19 outbreak status in hospital. We swabbed the floors of an inpatient ward at…
View article: An Optimized Pipeline for Detection of Salmonella Sequences in Shotgun Metagenomics Datasets
An Optimized Pipeline for Detection of Salmonella Sequences in Shotgun Metagenomics Datasets Open
Background Culture-independent diagnostic tests (CIDTs) are gaining popularity as tools for detecting pathogens in food. Shotgun sequencing holds substantial promise for food testing as it provides abundant information on microbial communi…
View article: Locust gut epithelia do not become more permeable to fluorescent dextran and bacteria in the cold
Locust gut epithelia do not become more permeable to fluorescent dextran and bacteria in the cold Open
The insect gut, which plays a role in ion and water balance, has been shown to leak solutes in the cold. Cold stress can also activate insect immune systems, but it is unknown whether the leak of the gut microbiome is a possible immune tri…
View article: Collateral sensitivity profiling in drug-resistant Escherichia coli identifies natural products suppressing cephalosporin resistance
Collateral sensitivity profiling in drug-resistant Escherichia coli identifies natural products suppressing cephalosporin resistance Open