Rapid detection of live methicillin-resistant Staphylococcus aureus by using an integrated microfluidic system capable of ethidium monoazide pre-treatment and molecular diagnosis

Nucleic acid amplification-based microfluidic approaches for antimicrobial susceptibility testing

Because of the global spread of antimicrobials, there is an urgent need to develop rapid and effective tools for antimicrobial susceptibility testing to help clinicians prescribe accurate and appropriate antibiotic doses sooner. The conventional methods for antimicrobial susceptibility testing are usually based on bacterial culture methods, which are time-consuming, complicated, and labor-intensive. Therefore, other approaches are needed to address these issues. Recently, microfluidic technology has gained significant attention in infection management due to its advantages including rapid detection, high sensitivity and specificity, highly automated assay, simplicity, low cost, and potential for point-of-care testing in low-resource areas. Microfluidic advances for antimicrobial susceptibility testing can be classified into phenotypic (usually culture-based) and genotypic tests. Genotypic antimicrobial susceptibility testing is the detection of resistant genes in a microorganism using methods such as nucleic acid amplification. This review (with 107 references) surveys the different forms of nucleic acid amplification-based microdevices used for genotypic antimicrobial susceptibility testing. The first section reviews the serious threat of antimicrobial-resistant microorganisms and the urgent need for fast check-ups. Next, several conventional antimicrobial susceptibility testing methods are discussed, and microfluidic technology as a promising candidate for rapid detection of antimicrobial-resistant microorganisms is briefly introduced. The next section highlights several advancements of microdevices, with an emphasis on their working principles and performance. The review concludes with the importance of fully integrated microdevices and a discussion on future perspectives.

A sample-to-answer, portable platform for rapid detection of pathogens with a smartphone interface

Emerging and re-emerging infectious diseases pose global threats to human health. Although several conventional diagnostic methods have been widely adopted in the clinic, the long turn-around times of "gold standard" culture-based techniques, as well as the limited sensitivity of lateral-flow strip assays, thwart medical progress. In this study, a smartphone-controlled, automated, and portable system was developed for rapid molecular diagnosis of pathogens (including viruses and bacteria) via the use of a colorimetric loop-mediated isothermal amplification (LAMP) approach on a passive, self-driven microfluidic device. The system was capable of 1) purifying viral or bacterial samples with specific affinity reagents that had been pre-conjugated to magnetic beads, 2) lysing pathogens at low temperatures, 3) executing isothermal nucleic acid amplification, and 4) quantifying the results of colorimetric assays for detection of pathogens with an integrated color sensor. The entire, 40 min analytical process was automatically performed with a novel punching-press mechanism that could be controlled and monitored by a smartphone. As a proof of concept, the influenza A (H1N1) virus and methicillin-resistant Staphylococcus aureus bacteria were used to characterize and optimize the device, and the limits of detection were experimentally found to be 3.2 × 10^-3 hemagglutinating units (HAU) per reaction and 30 colony-forming units (CFU) per reaction, respectively; both such values represent high enough sensitivity for clinical adoption. Moreover, the colorimetric assay could be both qualitative and quantitative for detection of pathogens. This is the first instance of an easy-to-use, automated, and portable system for accurate and sensitive molecular diagnosis of either viruses or bacteria, and it is envisioned that this smartphone-controlled apparatus may serve as a platform for clinical, point-of-care pathogen detection, particularly in resource-limited settings.

Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology

Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.

Quantitative Polymerase Chain Reaction Coupled With Sodium Dodecyl Sulfate and Propidium Monoazide for Detection of Viable Streptococcus agalactiae in Milk

Streptococcus agalactiae is an important pathogen causing bovine mastitis. The aim of this study was to develop a simple and specific method for direct detection of S. agalactiae from milk products. Propidium monoazide (PMA) and sodium dodecyl sulfate (SDS) were utilized to eliminate the interference of dead and injured cells in qPCR. Lysozyme (LYZ) was adopted to increase the extraction efficiency of target bacteria DNA in milk matrix. The specific primers were designed based on cfb gene of S. agalactiae for qPCR. The inclusivity and exclusivity of the assay were evaluated using 30 strains. The method was further determined by the detection of S. agalactiae in spiked milk. Results showed significant differences between the SDS–PMA–qPCR, PMA–qPCR and qPCR when a final concentration of 10 mg/ml (R² = 0.9996, E = 95%) of LYZ was added in DNA extraction. Viable S. agalactiae was effectively detected when SDS and PMA concentrations were 20 μg/ml and 10 μM, respectively, and it was specific and more sensitive than qPCR and PMA–qPCR. Moreover, the SDS–PMA–qPCR assay coupled with LYZ was used to detect viable S. agalactiae in spiked milk, with a limit of detection of 3 × 10³ cfu/ml. Therefore, the SDS–PMA–qPCR assay had excellent sensitivity and specificity for detection of viable S. agalactiae in milk.

Vancomycin-resistant gene identification from live bacteria on an integrated microfluidic system by using low temperature lysis and loop-mediated isothermal amplification

Vancomycin-resistant Enterococcus (VRE) is a kind of enterococci, which shows resistance toward antibiotics. It may last for a long period of time and meanwhile transmit the vancomycin-resistant gene (vanA) to other bacteria. In the United States alone, the resistant rate of Enterococcus to vancomycin increased from a mere 0.3% to a whopping 40% in the past two decades. Therefore, timely diagnosis and control of VRE is of great need so that clinicians can prevent patients from becoming infected. Nowadays, VRE is diagnosed by antibiotic susceptibility test or molecular diagnosis assays such as matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and polymerase chain reaction. However, the existing diagnostic methods have some drawbacks, for example, time-consumption, no genetic information, or high false-positive rate. This study reports an integrated microfluidic system, which can automatically identify the vancomycin resistant gene (vanA) from live bacteria in clinical samples. A new approach using ethidium monoazide, nucleic acid specific probes, low temperature chemical lysis, and loop-mediated isothermal amplification (LAMP) has been presented. The experimental results showed that the developed system can detect the vanA gene from live Enterococcus in joint fluid samples with detection limit as low as 10 colony formation units/reaction within 1 h. This is the first time that an integrated microfluidic system has been demonstrated to detect vanA gene from live bacteria by using the LAMP approach. With its high sensitivity and accuracy, the proposed system may be useful to monitor antibiotic resistance genes from live bacteria in clinical samples in the near future.

Advances and Challenges in Viability Detection of Foodborne Pathogens

Foodborne outbreaks are a serious public health and food safety concern worldwide. There is a great demand for rapid, sensitive, specific, and accurate methods to detect microbial pathogens in foods. Conventional methods based on cultivation of pathogens have been the gold standard protocols; however, they take up to a week to complete. Molecular assays such as polymerase chain reaction (PCR), sequencing, microarray technologies have been widely used in detection of foodborne pathogens. Among molecular assays, PCR technology [conventional and real-time PCR (qPCR)] is most commonly used in the foodborne pathogen detection because of its high sensitivity and specificity. However, a major drawback of PCR is its inability to differentiate the DNA from dead and viable cells, and this is a critical factor for the food industry, regulatory agencies and the consumer. To remedy this shortcoming, researchers have used biological dyes such as ethidium monoazide and propidium monoazide (PMA) to pretreat samples before DNA extraction to intercalate the DNA of dead cells in food samples, and then proceed with regular DNA preparation and qPCR. By combining PMA treatment with qPCR (PMA-qPCR), scientists have applied this technology to detect viable cells of various bacterial pathogens in foods. The incorporation of PMA into PCR-based assays for viability detection of pathogens in foods has increased significantly in the last decade. On the other hand, some downsides with this approach have been noted, particularly to achieve complete suppression of signal of DNA from the dead cells present in some particular food matrix. Nowadays, there is a tendency of more and more researchers adapting this approach for viability detection; and a few commercial kits based on PMA are available in the market. As time goes on, more scientists apply this approach to a broader range of pathogen detections, this viability approach (PMA or other chemicals such as platinum compound) may eventually become a common methodology for the rapid, sensitive, and accurate detection of foodborne pathogens. In this review, we summarize the development in the field including progress and challenges and give our perspective in this area.

Toward a Molecular Understanding of the Antibacterial Mechanism of Copper-Bearing Titanium Alloys against Staphylococcus aureus

The antibacterial mechanism of the Cu-containing materials has not been fully understood although such understanding is crucial for the sustained clinical use of Cu-containing antibacterial materials such as bone implants. The aim of this study is to investigate the molecular mechanisms by which the Gram-positive Staphylococcus aureus is inactivated through Cu-bearing titanium alloys (Ti6Al4V5Cu). Cu ions released from the alloys are found to contribute to lethal damage of bacteria. They destroy the permeability of the bacterial membranes, resulting in the leakage of reducing sugars and proteins from the cells. They also promote the generation of bacteria-killing reactive oxygen species (ROS). The ROS production is confirmed by several assays including fluorescent staining of intracellular oxidative stress, detection of respiratory chain activity, and measurement of the levels of lipid peroxidation, catalase, and glutathione. Furthermore, the released Cu ions show obvious genetic toxicity by interfering the replication of nuc (species-specific) and 16SrRNA genes, but with no effect on the genome integrity. All of these effects lead to the antibacterial effect of Ti6Al4V5Cu. Collectively, our work reconciles the conflicting antibacterial mechanisms of Cu-bearing metallic materials or nanoparticles reported in the literature and highlights the potential use of Ti6Al4V5Cu alloys in inhibiting bacterial infections.

An automated microfluidic system for single-stranded DNA preparation and magnetic bead-based microarray analysis

We present an integrated microfluidic device capable of performing single-stranded DNA (ssDNA) preparation and magnetic bead-based microarray analysis with a white-light detection for detecting mutations that account for hereditary hearing loss. The entire operation process, which includes loading of streptavidin-coated magnetic beads (MBs) and biotin-labeled polymerase chain reaction products, active dispersion of the MBs with DNA for binding, alkaline denaturation of DNA, dynamic hybridization of the bead-labeled ssDNA to a tag array, and white-light detection, can all be automatically accomplished in a single chamber of the microchip, which was operated on a self-contained instrument with all the necessary components for thermal control, fluidic control, and detection. Two novel mixing valves with embedded polydimethylsiloxane membranes, which can alternately generate a 3-μl pulse flow at a peak rate of around 160 mm/s, were integrated into the chip for thoroughly dispersing magnetic beads in 2 min. The binding efficiency of biotinylated oligonucleotides to beads was measured to be 80.6% of that obtained in a tube with the conventional method. To critically test the performance of this automated microsystem, we employed a commercial microarray-based detection kit for detecting nine mutation loci that account for hereditary hearing loss. The limit of detection of the microsystem was determined as 2.5 ng of input K562 standard genomic DNA using this kit. In addition, four blood samples obtained from persons with mutations were all correctly typed by our system in less than 45 min per run. The fully automated, "amplicon-in-answer-out" operation, together with the white-light detection, makes our system an excellent platform for low-cost, rapid genotyping in clinical diagnosis.

Propidium monoazide combined with real-time PCR for selective detection of viable Staphylococcus aureus in milk powder and meat products

Staphylococcus aureus is a spherical, gram-positive, pathogenic bacterium commonly associated with bovine mastitis and clinical infections. It is also recognized as a pathogen that causes outbreaks of food poisoning. The objective of this study was to develop and evaluate a rapid and reliable technique that combines propidium monoazide (PMA) staining with real-time quantitative (q)PCR to detect and quantify viable cells of Staph. aureus in milk powder and meat products. The inclusivity and exclusivity of the assay were evaluated using 58 strains belonging to 14 species. Serial dilutions of Staph. aureus cells were used to establish a standard curve and to confirm the effect of PMA treatment. Milk powder and meat products were used as the spiked foods, and the ability of PMA-qPCR to eliminate nonviable cells was determined in milk powder. Furthermore, meat products were inoculated with different concentrations of Staph. aureus and 10(5) cfu/g of Bacillus cereus and Salmonella enterica to test the interference by nontarget microorganisms. When PMA treatment was applied before DNA extraction, we were able to eliminate false-positive results with little effect on viable cells. The PMA-qPCR assay was specific and more sensitive than conventional PCR, and the level of detection was 3.0×10(2) cfu/g in spiked milk powder. Additionally, we observed no significant interference for the detection of viable Staph. aureus from other nontarget bacteria. The PMA-qPCR protocol is an effective and rapid method to quantify viable cells of Staph. aureus in food samples. The PMA-qPCR assay is specific and reliable, offering a valuable diagnostic tool for routine analysis in food and clinical diagnostic research at a reasonable cost.

Hydrogel-based microfluidic incubator for microorganism cultivation and analyses

This work presents an array of microfluidic chambers for on-chip culturing of microorganisms in static and continuous shear-free operation modes. The unique design comprises an in-situ polymerized hydrogel that forms gas and reagent permeable culture wells in a glass chip. Utilizing a hydrophilic substrate increases usability by autonomous capillary priming. The thin gel barrier enables efficient oxygen supply and facilitates on-chip analysis by chemical access through the gel without introducing a disturbing flow to the culture. Trapping the suspended microorganisms inside a gel well allows for a much simpler fabrication than in conventional trapping devices as the minimal feature size does not depend on cell size. Nutrients and drugs are provided on-chip in the gel for a self-contained and user-friendly handling. Rapid antibiotic testing in static cultures with strains of Enterococcus faecalis and Escherichia coli is presented. Cell seeding and diffusive medium supply is provided by phaseguide technology, enabling simple operation of continuous culturing with a great flexibility. Cells of Saccharomyces cerevisiae are utilized as a model to demonstrate continuous on-chip culturing.

Rapid isolation and diagnosis of live bacteria from human joint fluids by using an integrated microfluidic system

Arthroplasty is a general approach for improving the life quality for patients with degenerative or injured joints. However, post-surgery complications including periprosthetic joint infection (PJI) poses a serious drawback to the procedure. Several methods are available for diagnosing PJI, but they are time-consuming or have poor sensitivity and specificity. Alternatively, reverse-transcription PCR can detect live bacteria and reduce false-positive results but cannot avoid the cumbersome RNA handling and human contamination issues. In response, an integrated microfluidic system capable of detecting live bacteria from clinical PJI samples within 55 minutes is developed in this study. This system employs an ethidium monoazide (EMA)-based assay and a PCR with universal bacterial primers and probes to isolate and detect only the live bacteria that commonly cause PJI. The experimental results indicated that the developed system can detect bacteria in human joint fluids with a detection limit of 10(4) colony formation unit mL(-1). Furthermore, nine clinical samples were analyzed using the microfluidic system. The results obtained from the microfluidic system were negative for all culture-negative cases, indicating that the proposed system can indeed reduce false-positive results. In addition, experimental results showed that the EMA sample pre-treatment process was crucial for successful detection of live bacteria. The culture-positive cases were diagnosed as positive by the proposed system only when the clinical samples were treated with EMA immediately after being sampled from patients. Based on these promising results, the developed microfluidic system can be a useful tool to detect PJI and potentially be applied in other clinical situations.

A pneumatic valve controlled microdevice for bioanalysis

This paper describes a pneumatic valve controlled microdevice for performing mixing and reaction. This microdevice combined the degassed polydimethylsiloxane (PDMS) pumping method with a syringe-actuated valve system to control the dispensing and mixing of nanoliter solutions. The syringe was used to manually generate vacuum and to open the valves. Upon the opening of the valve, the microchamber was filled with the solution, which was driven by the external atmosphere through the degassed PDMS microchannel. With this microdevice, the enzymatic kinetics of alkaline phosphatase converting the fluorescein diphosphate was studied, and the Michaelis-Menten kinetics was analyzed. The microdevice has the advantages of simplicity and low cost in fabrication and operation.

Experimental validation of numerical study on thermoelectric-based heating in an integrated centrifugal microfluidic platform for polymerase chain reaction amplification

A comprehensive study involving numerical analysis and experimental validation of temperature transients within a microchamber was performed for thermocycling operation in an integrated centrifugal microfluidic platform for polymerase chain reaction (PCR) amplification. Controlled heating and cooling of biological samples are essential processes in many sample preparation and detection steps for micro-total analysis systems. Specifically, the PCR process relies on highly controllable and uniform heating of nucleic acid samples for successful and efficient amplification. In these miniaturized systems, the heating process is often performed more rapidly, making the temperature control more difficult, and adding complexity to the integrated hardware system. To gain further insight into the complex temperature profiles within the PCR microchamber, numerical simulations using computational fluid dynamics and computational heat transfer were performed. The designed integrated centrifugal microfluidics platform utilizes thermoelectrics for ice-valving and thermocycling for PCR amplification. Embedded micro-thermocouples were used to record the static and dynamic thermal responses in the experiments. The data collected was subsequently used for computational validation of the numerical predictions for the system response during thermocycling, and these simulations were found to be in agreement with the experimental data to within ∼97%. When thermal contact resistance values were incorporated in the simulations, the numerical predictions were found to be in agreement with the experimental data to within ∼99.9%. This in-depth numerical modeling and experimental validation of a complex single-sided heating platform provide insights into hardware and system design for multi-layered polymer microfluidic systems. In addition, the biological capability along with the practical feasibility of the integrated system is demonstrated by successfully performing PCR amplification of a Group B Streptococcus gene.