Rapid identification and specific quantification of Staphylococcus epidermidis by 5' nuclease real-time polymerase chain reaction with a minor groove binder probe

Rapid Identification and Quantification of Lactobacillus rhamnosus by Real-Time PCR Using a TaqMan Probe

Lactobacillus rhamnosus is a gram-positive, rod-shaped bacterium and is commonly used as a probiotic to maintain intestinal health. Recently, surveillance of Lactobacillus bacteremia was conducted using a biochemical test and conventional PCR assay; however, these assays are unable to quantify the target and might yield a false positive result. In this study, we developed an L. rhamnosus-specific quantitative PCR assay, which yields accurate and reproducible results on the basis of the specificity of a TaqMan probe targeting the unique 16S rDNA sequence of L. rhamnosus. The assay specifically detected the target bacterium, L. rhamnosus, and no nonspecific signals were generated under the assay conditions. With genomic DNA from the cells of L. rhamnosus (10¹ to 10⁶ cells), the threshold cycle values showed a linear dependence (R² = 0.9993). This L. rhamnosus-specific quantitative PCR assay can advance the research into the effects of this microorganism on microflora, microbial infections, and on the host.

Thiolated AuNP probes and multiplex PCR for molecular detection of Staphylococcus epidermidis

The emergence of nanotechnology in biology helps to apply the gold nanoparticle probes for fast and accurate identification of pathogens compared to the time-consuming and non-precise phenotypic methods. In this study, two molecular methods have been established for the accurate identification of staphylococcus epidermidis from other coagulase-negative staphylococci. Multiplex PCR was performed using designed primers for Gmk2 and pta housekeeping genes, and SESB specific gene of S. epidermidis. Colorimetric detection by gold nanoparticle probes was carried out using two 20-base thiolated probes designed based on the sequence of pta housekeeping gene of S. epidermidis. The specificity of multiplex PCR and colorimetric assays were determined using genomic DNA of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii as negative controls and no alteration was detected. To investigate the sensitivity of the primers and gold nanoparticle probes, different concentrations of the extracted DNA from S. epidermidis were used. Based on the results, the minimum required quantity of target DNA for multiplex PCR amplification was 1 ng/μL and for color and absorption alteration of solution in colorimetric assay was 20 ng/μL. Our results revealed that both methods were sufficiently specific and sensitive to detect S. epidermidis.

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis

The microbiome can promote or disrupt human health by influencing both adaptive and innate immune functions. We tested whether bacteria that normally reside on human skin participate in host defense by killing Staphylococcus aureus, a pathogen commonly found in patients with atopic dermatitis (AD) and an important factor that exacerbates this disease. High-throughput screening for antimicrobial activity against S. aureus was performed on isolates of coagulase-negative Staphylococcus (CoNS) collected from the skin of healthy and AD subjects. CoNS strains with antimicrobial activity were common on the normal population but rare on AD subjects. A low frequency of strains with antimicrobial activity correlated with colonization by S. aureus The antimicrobial activity was identified as previously unknown antimicrobial peptides (AMPs) produced by CoNS species including Staphylococcus epidermidis and Staphylococcus hominis These AMPs were strain-specific, highly potent, selectively killed S. aureus, and synergized with the human AMP LL-37. Application of these CoNS strains to mice confirmed their defense function in vivo relative to application of nonactive strains. Strikingly, reintroduction of antimicrobial CoNS strains to human subjects with AD decreased colonization by S. aureus These findings show how commensal skin bacteria protect against pathogens and demonstrate how dysbiosis of the skin microbiome can lead to disease.

Developments for improved diagnosis of bacterial bloodstream infections

Bloodstream infections (BSIs) are associated with high mortality and increased healthcare costs. Optimal management of BSI depends on several factors including recognition of the disease, laboratory tests and treatment. Rapid and accurate identification of the etiologic agent is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates. Furthermore, appropriate treatment might slow down the emergence of antibiotic resistant strains. Culture-based methods are still considered to be the "gold standard" for the detection and identification of pathogens causing BSI. Positive blood cultures are used for Gram-staining. Subsequently, positive blood culture material is subcultured on solid media, and (semi-automated) biochemical testing is performed for species identification. Finally, a complete antibiotic susceptibility profile can be provided based on cultured colonies, which allows the start of pathogen-tailored antibiotic therapy. This conventional workflow is extremely time-consuming and can take up to several days. Furthermore, fastidious and slow-growing microorganisms, as well as antibiotic pre-treated samples can lead to false-negative results. The main aim of this review is to present different strategies to improve the conventional laboratory diagnostic steps for BSI. These approaches include protein-based (MALDI-TOF mass spectrometry) and nucleic acid-based (polymerase chain reaction [PCR]) identification from subculture, blood cultures, and whole blood to decrease time to results. Pathogen enrichment and DNA isolation methods, to enable optimal pathogen DNA recovery from whole blood, are described. In addition, the use of biomarkers as patient pre-selection tools for molecular assays are discussed.

The microbiome extends to subepidermal compartments of normal skin

Commensal microbes on the skin surface influence the behavior of cells below the epidermis. We hypothesized that bacteria or their products exist below the surface epithelium and thus permit physical interaction between microbes and dermal cells. Here, to test this hypothesis, we employed multiple independent detection techniques for bacteria including qPCR, Gram-staining, immunofluorescence, and in situ hybridization. Bacteria were consistently detectable within the dermis and dermal adipose of normal human skin. Sequencing of DNA from dermis and dermal adipose tissue identified bacterial 16S rRNA reflective of a diverse and partially distinct microbial community in each skin compartment. These results show the microbiota extends within the dermis, therefore enabling physical contact between bacteria and various cells below the basement membrane. These observations show that normal commensal bacterial communities directly communicate with the host in a tissue previously thought to be sterile.

Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization

Commensal bacteria are known to inhibit pathogen colonization; however, complex host-microbe and microbe-microbe interactions have made it difficult to gain a detailed understanding of the mechanisms involved in the inhibition of colonization. Here we show that the serine protease Esp secreted by a subset of Staphylococcus epidermidis, a commensal bacterium, inhibits biofilm formation and nasal colonization by Staphylococcus aureus, a human pathogen. Epidemiological studies have demonstrated that the presence of Esp-secreting S. epidermidis in the nasal cavities of human volunteers correlates with the absence of S. aureus. Purified Esp inhibits biofilm formation and destroys pre-existing S. aureus biofilms. Furthermore, Esp enhances the susceptibility of S. aureus in biofilms to immune system components. In vivo studies have shown that Esp-secreting S. epidermidis eliminates S. aureus nasal colonization. These findings indicate that Esp hinders S. aureus colonization in vivo through a novel mechanism of bacterial interference, which could lead to the development of novel therapeutics to prevent S. aureus colonization and infection.