Sources and Transmission Routes of Carbapenem-Resistant : Study Design and Methodology of the SAMPAN Study.

: The global spread of carbapenem-resistant (CRPA) warrants collaborative action. Guidance should come from integrated One Health surveillance; however, a surveillance strategy is currently unavailable due to insufficient knowledge on the sources and transmission routes of CRPA. The aim of the SAMPAN study ("A Smart Surveillance Strategy for Carbapenem-resistant ") is to develop a globally applicable surveillance strategy.

Honeybee gut bacterial strain improved survival and gut microbiota homeostasis in exposed to clothianidin.

Unlabelled: Pesticides are causing honeybee mortality worldwide. Research carried out on honeybees indicates that application of pesticides has a significant impact on the core gut community, which ultimately leads to an increase in the growth of harmful pathogens. Disturbances caused by pesticides also affect the way bacterial members interact, which results in gut microbial dysbiosis.

Evolution and host-specific adaptation of .

The major human bacterial pathogen causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups.

Characterization of gill bacterial microbiota in wild Arctic char () across lakes, rivers, and bays in the Canadian Arctic ecosystems.

Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors.

Complete genome sequence of multidrug-resistant 0-E.

Here, we present the complete 4.77 Mb genome of 0-E assembled with Oxford Nanopore long reads. This genome harbors 19 antimicrobial resistance genes, including and decreasing permeability to carbapenems.

Mitochondrial genome sequence of the protist Kent, 1881 (Ancyromonadida) from the Sugluk Inlet, Hudson Strait, Nunavik, Québec.

Introduction: There is little information on evolutionarily ancient eukaryotes, which are often referred to as basal eukaryotes, in Arctic waters. Despite earlier studies being conducted in the Russian White Sea, only few have been reported.

Methods: Following a shotgun sequence survey of diatom cultures from Sugluk Inlet off the Hudson Strait in Northern Québec, we obtained the complete mitochondrial genome and the operon of nuclear ribosomal RNA genes from a strain that matches that of (Kent, 1881).

Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing.

With the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach for real-time, early detection of cHAB outbreaks. We present how the proposed workflow offers consistent taxonomic identification of water samples in comparison to traditional microscopic analyses in a few hours and discuss how the generated data can be used to deepen our understanding on cyanobacteria ecology and forecast HABs events.

Complete genome sequence of strain OST1911 isolated from oil sand tailing pond water in Alberta, Canada.

Here, we report the complete genome sequence of strain OST1911, recovered from oil sand process-affected water accumulated in tailing ponds. This water contains numerous organic and inorganic compounds of environmental significance. The genome size is 6,435,955 bp with a G+C content of 61.

Draft genome sequences of six spp. and one sp. isolated from oil sands process-affected water from Alberta, Canada.

We report the draft genomes of seven bacterial strains (six spp. and one sp.) isolated from environmental water samples from oil sands tailings ponds that have accumulated a wide variety of organic compounds, salts and metals.

Draft genome sequences of six bacterial strains isolated from Cannabis rhizosphere soil.

Although bacterial isolates from Cannabis flowers were reported and sequenced, few from its rhizosphere have been characterized. Here we report the draft genomes of six bacterial strains isolated from Cannabis rhizosphere soil samples. These sequences may shed light on plant-microbe interactions in the Cannabis rhizosphere at the molecular level.

Draft genome sequence of sp. ER28, a cyclohexane pentanoic acid degrader isolated from oil sands process-affected water from Alberta, Canada.

We report the draft genome sequence of sp. ER28, capable of utilizing the model naphthenic acid, cyclohexane pentanoic acid, as its sole carbon source. It was recovered from oil sands process-affected water containing cyclic and acyclic naphthenic acids.

Post-COVID symptoms are associated with endotypes reflecting poor inflammatory and hemostatic modulation.

Introduction: Persistent symptoms after COVID-19 infection ("long COVID") negatively affects almost half of COVID-19 survivors. Despite its prevalence, its pathophysiology is poorly understood, with multiple host systems likely affected. Here, we followed patients from hospital to discharge and used a systems-biology approach to identify mechanisms of long COVID.

Complete genome sequences of agricultural azole-resistant encoding CYP51A and ERG11 paralogues.

Azoles are major antifungals in agriculture and medicine. However, the surge of intrinsic azole resistance is critical for public health. Here, we present the complete long-read sequencing of three azole-resistant from food crops.

Predicting severity in COVID-19 disease using sepsis blood gene expression signatures.

Severely-afflicted COVID-19 patients can exhibit disease manifestations representative of sepsis, including acute respiratory distress syndrome and multiple organ failure. We hypothesized that diagnostic tools used in managing all-cause sepsis, such as clinical criteria, biomarkers, and gene expression signatures, should extend to COVID-19 patients. Here we analyzed the whole blood transcriptome of 124 early (1-5 days post-hospital admission) and late (6-20 days post-admission) sampled patients with confirmed COVID-19 infections from hospitals in Quebec, Canada.

Dietary Contamination with a Neonicotinoid (Clothianidin) Gradient Triggers Specific Dysbiosis Signatures of Microbiota Activity along the Honeybee () Digestive Tract.

Pesticides are increasing honeybee () death rates globally. Clothianidin neonicotinoid appears to impair the microbe-immunity axis. We conducted cage experiments on newly emerged bees that were 4-6 days old and used a 16S rRNA metataxonomic approach to measure the impact of three sublethal clothianidin concentrations (0.

Genome evolution drives transcriptomic and phenotypic adaptation in during 20 years of infection.

The opportunistic pathogen chronically infects the lungs of patients with cystic fibrosis (CF). During infection the bacteria evolve and adapt to the lung environment. Here we use genomic, transcriptomic and phenotypic approaches to compare multiple isolates of collected more than 20 years apart during a chronic infection in a CF patient.

Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods.

Background: The past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes the large-scale, systematic validation vital to the continued development and use of optical microscopy impossible.

New-method: We provide a new framework for evaluating two-photon microscopy methods via in silico Neural Anatomy and Optical Microscopy (NAOMi) simulation.

Evenness-Richness Scatter Plots: a Visual and Insightful Representation of Shannon Entropy Measurements for Ecological Community Analysis.

Shannon's entropy is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent on both those parameters, there is theoretically an infinite number of richness/evenness value combinations translating into the same index score. By decoupling both components measured by Shannon's entropy, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot.

Complete Genome Sequence of a Species Isolated from Tailings Pond Water in Alberta, Canada.

We report the complete genome sequence of strain OST1909, belonging to a species. The genome size is 6,306,352 bp, with a G+C content of 59.6%.

Stimulated Growth and Innate Immunity in Brook Charr () Treated with a General Probiotic (Bactocell) and Two Endogenous Probiotics That Inhibit In Vitro.

subsp. is a Gram-negative bacterium causing furunculosis, an opportunistic infection of farmed salmonid fish. Current treatment methods against furunculosis rely heavily on antibiotherapy.

A brief history of bioinformatics.

It is easy for today's students and researchers to believe that modern bioinformatics emerged recently to assist next-generation sequencing data analysis. However, the very beginnings of bioinformatics occurred more than 50 years ago, when desktop computers were still a hypothesis and DNA could not yet be sequenced. The foundations of bioinformatics were laid in the early 1960s with the application of computational methods to protein sequence analysis (notably, de novo sequence assembly, biological sequence databases and substitution models).

Strong Genomic and Phenotypic Heterogeneity in the Species Complex.

is a mesophilic motile aeromonad currently depicted as an opportunistic pathogen, despite increasing evidence of mutualistic interactions in salmonid fish. However, the determinants of its host-microbe associations, either mutualistic or pathogenic, remain less understood than for other aeromonad species. On one side, there is an over-representation of pathogenic interactions in the literature, of which only three articles to date report mutualistic interactions; on the other side, genomic characterization of this species is still fairly incomplete as only two draft genomes were published prior to the present work.

Walleye Autochthonous Bacteria as Promising Probiotic Candidates against .

Walleye () is the second most fished freshwater species in Canada. While much sought by anglers, walleye also supports substantial commercial fisheries. To cope with the recent decline of wild walleye populations, fish farmers produce juveniles for lake stocking.