LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections.

Urinary tract infections (UTIs) are a worldwide health problem. Fast and accurate detection of bacterial infection is essential to provide appropriate antibiotherapy to patients and to avoid the emergence of drug-resistant pathogens. While the gold standard requires 24 h to 48 h of bacteria culture prior to MALDI-TOF species identification, we propose a culture-free workflow, enabling bacterial identification and quantification in less than 4 h using 1 ml of urine.

Tackling Infectious Diseases with Rapid Molecular Diagnosis and Innovative Prevention.

Infectious diseases (IDs) are a leading cause of death. The diversity and adaptability of microbes represent a continuing risk to health. Combining vision with passion, our transdisciplinary medical research team has been focussing its work on the better management of infectious diseases for saving human lives over the past five decades through medical discoveries and innovations that helped change the practice of medicine.

A systematic review of tools for predicting complications in patients with influenza-like illness.

Objective: To identify tools that predict the risk of complications for patients presenting to an outpatient clinic or an emergency department (ED) with influenza-like illness.

Methods: We searched Medline, Embase, Cochrane Library and CINAHL from inception to July 2023. We included articles reporting on the derivation or validation of a score or algorithm used to stratify the risk of hospitalization or mortality among patients with influenza-like illness in the ED or outpatient clinic.

Characterization of vancomycin-resistance gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.

Objectives: To characterize vancomycin-resistance gene clusters and potential -carrying bacteria in the intestinal microbiota of healthy volunteers exposed or not to β-lactam antibiotics.

Methods: Stool samples were collected before and after 7 days of cefprozil β-lactam antibiotic exposure of 18 participants and six control participants who were not exposed to the antibiotic at the same time points. Metagenomic sequencing and culture-enriched metagenomic sequencing (with and without β-lactam selection) were used to characterize gene clusters and determine potential -carrying bacteria.

Infectious diseases genomic surveillance capacity in the Caribbean: A retrospective analysis of SARS-CoV-2.

Background: The ongoing coronavirus diseases 2019 (COVID-19) pandemic with its numerous variants of concern has shown the need to have a robust and complete global infectious diseases genomic surveillance network worldwide. Various clinical and research institutions have stepped up to perform SARS-CoV-2 sequencing thus enhancing the understanding of this virus' global evolution. However, given that genomic sequencing capacities and capabilities are not available in every region or country, significant gaps exist, which lead to geographic blind spots.

Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts.

Comparative metagenomics studies have highlighted differences in microbiome community structure among human populations over diverse lifestyles and environments. With their unique environmental and historical backgrounds, Nunavik Inuit have a distinctive gut microbiome with undocumented health-related implications. Using shotgun metagenomics, we explored the taxonomic and functional structure of the gut microbiome from 275 Nunavik Inuit ranging from 16 to 30-year-old.

A systematic review of tools for predicting complications in patients with acute infectious diarrhea.

Objective: To identify tools that predict the risk of complications in patients presenting to outpatient clinics or emergency departments (ED) with acute infectious diarrhea.

Methods: Medline, Embase, Cochrane Library, Web of Science and CINAHL were searched from inception to July 2021. Articles reporting on the derivation or validation of a score to stratify the risk of intravenous rehydration or hospitalization among patients with acute infectious diarrhea in the ED or outpatient clinic were retained for analysis.

Antimicrobial Resistance in the Environment: Towards Elucidating the Roles of Bioaerosols in Transmission and Detection of Antibacterial Resistance Genes.

Antimicrobial resistance (AMR) is continuing to grow across the world. Though often thought of as a mostly public health issue, AMR is also a major agricultural and environmental problem. As such, many researchers refer to it as the preeminent One Health issue.

Complete Genome Sequences of and , KPC-2-Producers Serially Isolated from a Single Patient.

Carbapenemase-producing including KPC-2 producers, have become a major clinical problem. During an outbreak in Quebec City, Canada, KPC-2-producing and were isolated from a patient six weeks apart. We determined their complete genome sequences.

Real-time monitoring of bead-based DNA hybridization in a microfluidic system: study of amplicon hybridization behavior on solid supports.

DNA hybridization phenomena occurring on solid supports are not understood as clearly as aqueous phase hybridizations and mathematical models cannot predict some empirically obtained results. Ongoing research has identified important parameters but remains incomplete to accurately account for all interactions. It has previously been shown that the length of the overhanging (dangling) end of the target DNA strand following hybridization to the capture probe is correlated to interactions with the complementary strand in solution which can result in unbinding of the target and its release from the surface.

gen. nov., sp. nov., a new member of the family , isolated from human clinical samples.

A rod-shaped, motile anaerobic bacterium, designated CCRI-22567, was isolated from a vaginal sample of a woman diagnosed with bacterial vaginosis and subjected to a polyphasic taxonomic study. The novel strain was capable of growth at 30-42 °C (optimum, 42 °C), at pH 5.5-8.

A Sensitive and Accurate Recombinase Polymerase Amplification Assay for Detection of the Primary Bacterial Pathogens Causing Bovine Respiratory Disease.

Rapid and accurate diagnosis of bovine respiratory disease (BRD) presents a substantial challenge to the North American cattle industry. Here we utilize recombinase polymerase amplification (RPA), a fast and sensitive isothermal DNA-based technology for the detection of four BRD pathogens (), genes coding antimicrobial resistance (AMR) and integrative conjugative elements (ICE) which can harbor AMR genes. Eleven RPA assays were designed and validated including: a) one conventional species-specific multiplex assay targeting the 4 BRD pathogens, b) two species-specific real-time multiplex RPA assays targeting / and /, respectively with a novel competitive internal amplification control, c) seven conventional assays targeting AMR genes (), and d) one real-time assay targeting ICE.

"Researcher for a Day": Creating and Shaping a New Generation of Scientific and Medical Researchers.

Science is the engine of prosperity, helping society respond to the important issues it faces. We are presently witnessing a worldwide decline in high school students' interest in science, regardless of gender. To overcome this problem, developing science promotion programs and activities that inspire young people to become the scientists of tomorrow is critical.

Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning.

Fast identification of microbial species in clinical samples is essential to provide an appropriate antibiotherapy to the patient and reduce the prescription of broad-spectrum antimicrobials leading to antibioresistances. MALDI-TOF-MS technology has become a tool of choice for microbial identification but has several drawbacks: it requires a long step of bacterial culture before analysis (≥24 h), has a low specificity and is not quantitative. We developed a new strategy for identifying bacterial species in urine using specific LC-MS/MS peptidic signatures.

Culture-enriched human gut microbiomes reveal core and accessory resistance genes.

Background: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens.

Method for isolation of both lactose-fermenting and - non-fermenting Escherichia albertii strains from stool samples.

Initially, Escherichia albertii has been described as a non-lactose fermenting bacterium and methods used to isolate it were first based on this phenotypic property. However, a recent study showed a variable lactose fermentation phenotype for E. albertii suggesting that this microorganism could have been underestimated by previous studies using isolation methods based on lactose fermentation.

Draft Genome Sequence of a Sporulating and Motile Strain of Isolated from Water in Québec City, Canada.

CCRI-19302 belongs to the genus The strain was isolated from a water sample harvested in Québec City, Canada. The genome assembly comprised 4,694,231 bp, with 34.6% GC content.

Draft Genome Sequence of sp. nov. Strain CCRI-22766, Isolated from Coastal Estuarine Mud.

The sp. nov. CCRI-22766 strain was isolated from coastal estuarine mud in New Zealand.

Draft Genome Sequence of sp. nov. Strain CCRI-19649 Isolated from Surface Water.

sp. nov. CCRI-19649 belongs to the genus The strain was isolated from a water sample harvested in Québec City, Québec, Canada.

Use of phylogenetical analysis to predict susceptibility of pathogenic Candida spp. to antifungal drugs.

Successful treatment of a Candida infection relies on 1) an accurate identification of the pathogenic fungus and 2) on its susceptibility to antifungal drugs. In the present study we investigated the level of correlation between phylogenetical evolution and susceptibility of pathogenic Candida spp. to antifungal drugs.

Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial Vaginosis.

Criibacterium bergeronii gen. nov., sp.

Partial recovery of microbiomes after antibiotic treatment.

Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment.

Recombinase Polymerase Amplification for Diagnostic Applications.

Background: First introduced in 2006, recombinase polymerase amplification (RPA) has stirred great interest, as evidenced by 75 publications as of October 2015, with 56 of them just in the last 2 years. The widespread adoption of this isothermal molecular tool in many diagnostic fields represents an affordable (approximately 4.3 USD per test), simple (few and easy hands-on steps), fast (results within 5-20 min), and sensitive (single target copy number detected) method for the identification of pathogens and the detection of single nucleotide polymorphisms in human cancers and genetically modified organisms.