Real-Time PCR Method for the Rapid Detection and Quantification of Pathogenic Staphylococcus Species Based on Novel Molecular Target Genes

Prevalence and types of methicillin-resistant Staphylococcus aureus (MRSA) in meat and meat products from retail outlets and in samples of animal origin collected in farms, slaughterhouses and meat processing facilities. A review

Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of nosocomial and community infections, in some cases severe and difficult to treat. In addition, there are strains of MRSA that are specifically associated with food-producing animals. For this reason, in recent years special attention has been paid to the role played by foodstuffs of animal origin in infections by this microorganism. With the aim of gaining knowledge on the prevalence and types of MRSA in meat and meat products, a review was undertaken of work published on this topic since 2001, a total of 259 publications, 185 relating to meat samples from retail outlets and 74 to samples of animal origin collected in farms, slaughterhouses and meat processing facilities. Strains of MRSA were detected in 84.3% reports (156 out of 185) from retail outlets and 86.5% reports (64 out of 74) from farms, slaughterhouses and meat processing facilities, although in most of the research this microorganism was detected in under 20% of samples from retail outlets, and under 10% in those from farms, slaughterhouses and meat processing facilities. The meat and meat products most often contaminated with MRSA were pork and chicken. In addition to the mecA gene, it is crucial to take into consideration the mecB and mecC genes, so as to avoid misidentification of strains as MSSA (methicillin-susceptible Staphylococcus aureus). The great variety of methods used for the determination of MRSA highlights the need to develop a standardized protocol for the study of this microorganism in foods.

Association of coagulase-negative staphylococci with orthopedic infections detected by in-house multiplex real-time PCR

Introduction

Clinical significance of coagulase-negative staphylococci (CoNS) has been gradually acknowledged in both healthcare and clinical research, but approaches for their precise discrimination at the species level remain scarce. The current study aimed to evaluate the association of CoNS with orthopedic infections, where accurate and prompt identification of etiology is crucial for appropriate diagnosis and treatment decision-making.

Methods

A 16S rRNA-based quantitative PCR (qPCR) assay was developed for the detection of Staphylococcus genus and two panels of 3-plex qPCR assays for further differentiation of six CoNS species with remarkable clinical significance, including S. epidermidis, S. haemolyticus, S. simulans, S. hominis, S. capitis, and S. caprae. All the assays exhibited excellent analytical performance. ΔCq (quantification cycle) between 16S rRNA and CoNS species-specific targets was established to determine the primary CoNS. These methods were applied to detect CoNS in wound samples from orthopedic patients with and without infection.

Results and discussion

Overall, CoNS were detected in 17.8% (21/118) of patients with clinically suspected infection and in 9.8% (12/123) of patients without any infection symptom (p < 0.05). Moreover, the association with infection was found to be bacterial quantity dependent. S. epidermidis was identified as the predominant species, followed by S. simulans, S. haemolyticus, and S. hominis. Male sex, open injury, trauma, and lower extremity were determined as risk factors for CoNS infections. CoNS-positive patients had significantly longer hospitalization duration (20 days (15, 33) versus 13 days (7, 22) for Staphylococcus-negative patients, p = 0.003), which could be a considerable burden for healthcare and individual patients. Considering the complex characteristics and devastating consequences of orthopedic infections, further expanding the detection scope for CoNS may be pursued to better understand the etiology of orthopedic infections and to improve therapeutic strategies.

A simple and rapid colorimetric detection of Staphylococcus aureus relied on the distance-dependent optical properties of silver nanoparticles

The quick and accurate diagnosis of pathogens has appeared as a pressing issue in clinical diagnostics, environmental monitoring, and food safety. The available assays are suffering from limited capacities in simple, fast, low-cost, and on-site detection to increase prevention and proper treatment. Herein, we address these challenges by developing a simple, speedy, affordable, and ultrasensitive nanoplasmonic biosensor for colorimetric detection of cDNA from staphylococcal RNA relying on the distance-dependent optical features of silver nanostructures for the measurement of color variations and spectral shifts owing to the plasmon coupling generated by the cross-linking accumulation of AgNPs. The method described utilizes silver nanoparticles (AgNPs) immobilized with two different single-stranded oligonucleotides (ssDNA1 and ssDNA2) that specifically recognize the target DNA. Sandwich hybridization of target DNA with ssDNA1 and ssDNA2 induced color variations and spectral shifts of AgNPs, whereas test samples without the target DNA remained yellow as the initial color of colloidal silver. The designed nanoplasmonic biosensor demonstrated high specificity with the detection limit (LOD) of ∼1.8 amol target DNA (∼106 molecules per test) in the broad linear dynamic range from 0.01 to 100 nM, and LOD down to a few cells was attained for amplified bacterial nucleic acids and a linear range from 102 CFU mL-1 to 107 CFU mL-1. The sensing approach showed great potential for the timely diagnosis of pathogens in low-density samples, and it has considerable merits over traditional culture approaches and qPCR techniques.

Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

This article presents a review of recent advancements in the utilization of NAA-based techniques for detecting foodborne pathogens in food products, focusing on studies conducted within the past five years. This review revealed that recent research efforts have primarily aimed at enhancing sensitivity and specificity by improving sample pre-treatment/preparation, DNA isolation, and readout methods. Isothermal-based amplification methods, such as LAMP, RPA, RAA, and RCA, have emerged as promising approaches, providing rapid results within one h and often demonstrating comparable or superior sensitivity to conventional or qPCR methods. However, the attention paid to specific pathogens varies, with Salmonella spp., Listeria spp., E. coli, and V. parahaemolyticus receiving more focus than norovirus and other similar pathogens. NAA-based methods have the potential to significantly contribute to food safety and public health protection. However, further advancements are necessary to fully realize their benefits.

Rapid identification of Staphylococcus aureus based on a fluorescence imaging/detection platform that combines loop mediated isothermal amplification assay and the smartphone-based system

Food associated diseases pose significant public health threat in the United States. Health risks associated with food-borne pathogens drive the need for constant monitoring of food products. An efficient method that can diagnose food-borne pathogens rapidly will be invaluable and in high demand. In this study, we showed the feasibility of a novel rapid detection platform based on fluorescence imaging/detection that combines a user-friendly, portable loop mediated isothermal amplification (LAMP) reaction device and a smartphone-based detection system. The proposed platform was used to detect Staphylococcus aureus which is one of the most important food-borne pathogen especially dairy products. The complete protocol is quicker; the reaction is performed under isothermal conditions and completed in 1 h or less. Experimental results show that LAMP assays were ten-fold more sensitive than PCR-based detection. The proposed smartphone detection system was able to detect and quantify LAMP assay samples containing three different concentrations of S. aureus from 10⁹ CFU/mL down to 10³ CFU/mL. The present proof-of-concept study demonstrated that this platform offers a portable, easy to use method for measuring target pathogens with LAMP amplification.

Development and Evaluation of Duplex MIRA-qPCR Assay for Simultaneous Detection of Staphylococcus aureus and non-aureus Staphylococci

Staphylococcus spp., especially Staphylococcus aureus (S. aureus), is an important pathogen in hospital-acquired infection and food poisoning. Here, we developed a multienzyme isothermal rapid amplification combined with duplex quantitative PCR (duplex MIRA-qPCR) method, which can simultaneously detect the S. aureus species-specific conserved gene FMN-bgsfp and the Staphylococcus genus-specific conserved gene tuf. This assay enabled the amplification of DNA within 20 min at a constant temperature of 39 °C. Specificity analysis indicated that all nine common Staphylococcus species were positive and non-Staphylococcus spp. were negative for tuf gene, whereas S. aureus was positive, non-aureus Staphylococci species and non-Staphylococcus spp. were negative for FMN-bgsfp gene, suggesting that duplex MIRA-qPCR exhibited high specificity. Meanwhile, the sensitivity was tested and the limit of detection (LoD) was 3 × 102 CFU/mL. The coefficient variation values ranged from 0.13% to 2.09%, indicating that the assay had good repeatability. Furthermore, all the nine common Staphylococcus species (including S. aureus) could be detected from four kinds of simulated samples and the LoD of S. aureus was 8.56 × 103 CFU/mL. In conclusion, the duplex MIRA-qPCR has advantages of stronger specificity, lower detection threshold, shorter detection time, and simpler operation, which is an effective tool to detect S. aureus and non-aureus Staphylococci spp. infections rapidly.

Antibiofilm Effect of Silver Nanoparticles in Changing the Biofilm-Related Gene Expression of Staphylococcus epidermidis

Nowadays, antibiotic resistance is a major public health problem. Among staphylococci, infections caused by Staphylococcus epidermidis (S. epidermidis) are frequent and difficult to eradicate. This is due to its ability to form biofilm. Among the antibiotic substances, nanosilver is of particular interest. Based on this information, we decided to investigate the effect of nanosilver on the viability, biofilm formation and gene expression of the icaADBC operon and the icaR gene for biofilm and non-biofilm S. epidermidis strains. As we observed, the viability of all the tested strains decreased with the use of nanosilver at a concentration of 5 µg/mL. The ability to form biofilm also decreased with the use of nanosilver at a concentration of 3 µg/mL. Genetic expression of the icaADBC operon and the icaR gene varied depending on the ability of the strain to form biofilm. Low concentrations of nanosilver may cause increased biofilm production, however no such effect was observed with high concentrations. This confirms that the use of nanoparticles at an appropriately high dose in any future therapy is of utmost importance. Data from our publication confirm the antibacterial and antibiotic properties of nanosilver. This effect was observed phenotypically and also by levels of gene expression.