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.

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.

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.

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.

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.

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.

ampG gene of Pseudomonas aeruginosa and its role in β-lactamase expression.

In enterobacteria, the ampG gene encodes a transmembrane protein (permease) that transports 1,6-GlcNAc-anhydro-MurNAc and the 1,6-GlcNAc-anhydro-MurNAc peptide from the periplasm to the cytoplasm, which serve as signal molecules for the induction of ampC β-lactamase. The role of AmpG as a transporter is also essential for cell wall recycling. Pseudomonas aeruginosa carries two AmpG homologues, AmpG (PA4393) and AmpGh1 (PA4218), with 45 and 41% amino acid sequence identity, respectively, to Escherichia coli AmpG, while the two homologues share only 19% amino acid identity.

Analytical limits of three beta-glucosidase-based commercial culture methods used in environmental microbiology, to detect enterococci.

The enzyme-based test methods Enterolert, Chromocult Enterococci agar, and mEI agar, used to assess water quality through the detection Enterococcus spp., have been compared in terms of their analytical specificity and their ability to detect various enterococcal strains. To achieve this goal, we have tested 110 different non-enterococcal bacterial strains and 101 strains of Enterococcus spp.

Vancomycin-modified nanoparticles for efficient targeting and preconcentration of Gram-positive and Gram-negative bacteria.

A series of vancomycin-modified nanoparticles were developed and employed in magnetic confinement assays to isolate a variety of Gram-positive and Gram-negative bacteria from aqueous solution. We determined that the orientation/architecture of vancomycin on the surface of the nanoparticles and the overall surface coverage is critical in mediating fast and effective interactions between the nanoparticle and the pathogen cell wall surface and only one orientation/architecture in a series of modified nanoparticles leads to the efficient and reproducible capture of several important pathogenic bacteria. Interestingly, as the nanoparticles increase in diameter (from approximately 50 to 2800 nm), it is necessary to incorporate a long linker between the nanoparticle surface and the vancomycin moiety in order for the surface bound probe to efficiently confine Gram-positive bacteria.

Plastic polymers for efficient DNA microarray hybridization: application to microbiological diagnostics.

Fabrication of microarray devices using traditional glass slides is not easily adaptable to integration into microfluidic systems. There is thus a need for the development of polymeric materials showing a high hybridization signal-to-background ratio, enabling sensitive detection of microbial pathogens. We have developed such plastic supports suitable for highly sensitive DNA microarray hybridizations.

A low-cost, disposable card for rapid polymerase chain reaction.

A low-cost, disposable card for rapid polymerase chain reaction (PCR) was developed in this work. Commercially available, adhesive-coated aluminum foils and polypropylene films were laminated with structured polycarbonate films to form microreactors in a card format. Ice valves [1] were employed to seal the reaction chambers during thermal cycling and a Peltier-based thermal cycler was configured for rapid thermal cycling and ice valve actuation.

Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid.

The hybridization behavior of small oligonucleotides arrayed on glass slides is currently unpredictable. In order to examine the hybridization efficiency of capture probes along target nucleic acid, 20-mer oligonucleotide probes were designed to hybridize at different distances from the 5' end of two overlapping 402- and 432-bp ermB products amplified from the target DNA. These probes were immobilized via their 5' end onto glass slides and hybridized with the two labeled products.

Identification of methicillin-resistant Staphylococcus aureus carriage in less than 1 hour during a hospital surveillance program.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) has spread worldwide and is responsible for significant morbidity, mortality, and health care costs. Control strategies to limit the emergence and spread of this organism rely on rapid and sensitive tests for detection of MRSA carriage. However, the standard surveillance culture method for detecting MRSA is labor intensive and time-consuming (2-3 days per procedure).

Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species.

A 761-bp portion of the tuf gene (encoding the elongation factor Tu) from 28 clinically relevant streptococcal species was obtained by sequencing amplicons generated using broad-range PCR primers. These tuf sequences were used to select Streptococcus-specific PCR primers and to perform phylogenetic analysis. The specificity of the PCR assay was verified using 102 different bacterial species, including the 28 streptococcal species.

Real-time PCR assay for detection of fluoroquinolone resistance associated with grlA mutations in Staphylococcus aureus.

Resistance to fluoroquinolones among clinical isolates of Staphylococcus aureus has become a clinical problem. Therefore, a rapid method to identify S. aureus and its susceptibility to fluoroquinolones could provide clinicians with a useful tool for the appropriate use of these antimicrobial agents in the health care settings.