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.

Comparison of rectal swabs and fecal samples for the detection of infections with a new in-house PCR assay.

Unlabelled: The detection of infections (CDI) relies on testing the stool of patients by toxin antigen detection or PCR methods. Although PCR and antigenic methods have significantly reduced the time to results, delays in stool collection can significantly add to the turnaround time. The use of rectal swabs to detect could considerably reduce the time to diagnosis of CDI.

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.

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.

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.

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.

Comparison of MI, Chromocult coliform, and Compass CC chromogenic culture-based methods to detect Escherichia coli and total coliforms in water using 16S rRNA sequencing for colony identification.

The MI, Chromocult coliform, and Compass CC chromogenic culture-based methods used to assess water quality by the detection of Escherichia coli and total coliforms were compared in terms of their specificity and sensitivity, using 16S rRNA sequencing for colony identification. A sewage water sample was divided in 2-μL subsamples for testing by all three culture-based methods. All growing colonies were harvested and subjected to 16S rRNA sequencing.

Rapid molecular identification of fecal origin-colonies growing on Enterococcus spp.-specific culture methods.

The mEI, Chromocult enterococci, and m-Enterococcus culture-based methods used to assess water quality by the detection of Enterococcus spp. were first compared in terms of sensitivity using (1) 41 different type strains of Enterococcus spp. and (2) environmental colonies identified by 16S rRNA sequencing.

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.

The initial state of the human gut microbiome determines its reshaping by antibiotics.

Microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. However, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. To specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers.

Abilities of the mCP Agar method and CRENAME alpha toxin-specific real-time PCR assay to detect Clostridium perfringens spores in drinking water.

We first determined the analytical specificity and ubiquity (i.e., the ability to detect all or most strains) of a Clostridium perfringens-specific real-time PCR (rtPCR) assay based on the cpa gene (cpa rtPCR) by using a bacterial strain panel composed of C.

Polythiophene biosensor for rapid detection of microbial particles in water.

Most microbial particles have a negatively charged surface and in this work, we describe a water quality monitoring application of a cationic polythiophene derivative (AH-35) for the rapid assessment of microbial contamination of water. Using E. coli as a prototype microbial particle, we demonstrate that the AH-35 polymer can provide a qualitative assessment of water if exposed to more than 500 CFU/mL, thereby paving the way to a new family of biosensors potentially useful for monitoring drinking water distribution systems.

Comparative analysis of classical and molecular microbiology methods for the detection of Escherichia coli and Enterococcus spp. in well water.

The microbiological quality of 165 1 litre well water samples collected in the Québec City region was assessed by culture-based methods (mFC agar, Chromocult coliform agar, Colilert(®), MI agar, Chromocult enterococci, Enterolert™, and mEI agar) and by a molecular microbiology strategy, dubbed CRENAME-rtPCR, developed for the detection of Escherichia coli, Enterococcus spp., Enterococcus faecalis/faecium, and Bacillus atrophaeus subsp. globigii.

Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples.

In this work, we used a rapid, simple, and efficient concentration-and-recovery procedure combined with a DNA enrichment method (dubbed CRENAME [concentration and recovery of microbial particles, extraction of nucleic acids, and molecular enrichment]), that we coupled to an Escherichia coli/Shigella-specific real-time PCR (rtPCR) assay targeting the tuf gene, to sensitively detect E. coli/Shigella in water. This integrated method was compared to U.

Ability of three DNA-based assays to identify presumptive Escherichia coli colonies isolated from water by the culture-based mFC agar method.

We tested the ability of three PCR assays, targeting uidA and tuf genes to correctly identify Escherichia coli colonies isolated from water and we compared them to two β-glucuronidase-based culture methods (Colilert(®) and Readycult(®)), in terms of specificity and sensitivity. E. coli isolates recovered on mFC agar were first tested for the presence of the uidA positive colonies were presumed to be E.

Method for rapid and sensitive detection of Enterococcus sp. and Enterococcus faecalis/faecium cells in potable water samples.

We have developed a rapid and robust technological solution including a membrane filtration and dissolution method followed by a molecular enrichment and a real-time PCR assay, for detecting the presence of Enterococcus sp. or Enterococcus faecalis/faecium per 100 mL of water in less than 5 h and we compared it to Method 1600 on mEI agar in terms of specificity, sensitivity, and limit of detection. The mEI and the Enterococcus sp.