Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples

Rapid Universal Detection of High-Risk and Low-Abundance Microbial Contaminations in CAR-T Cell Therapy

Live microbial contamination poses high risks to cell and gene therapies, threatening manufacturing processes and patient safety. Rapid, sensitive detection of live microbes in complex environments, such as CAR-T cell cultures, remains an urgent need. Here, an innovative sample-to-result workflow is introduced using digital loop-mediated isothermal amplification (dLAMP), enhanced by Electrostatic Microfiltration (EM)-based enrichment, for rapid sterility testing. By rationally designing primers targeting 16S and 18S rRNA, dLAMP assay enables both universal detection (covering >80% of known species) and strain-specific identification of bacterial and fungal contaminants in CAR-T cell spent medium and final products, directly from microorganism lysates. Enhanced by EM-based enrichment of low-abundance live microbes, the workflow achieves unparalleled sensitivity and speed, detecting contamination levels as low as 1 CFU/mL in complex CAR-T cell cultures within 6 h. Compared to qPCR and 14-day compendial methods, the approach demonstrates superior accuracy and significantly faster turnaround times. This workflow holds transformative potential for real-time monitoring in cell therapy manufacturing and rapid safety assessments of CAR-T cell products prior to patient infusion. Beyond cell therapy, the method is broadly applicable to infectious disease diagnostics, biomanufacturing monitoring, food safety, and environmental surveillance.

A Self-Calibrating Chemiluminescence Sensor for Rapid and Precise Antibiotic Prescribing Guidelines on Urinary Tract Infections

Traditional antimicrobial-susceptibility testing methodologies, including the isolation and culture of bacteria from urine samples and antibiotic-susceptibility test (AST), are expensive and time-consuming. Therefore, a rapid, user-friendly phenotypic AST is urgently needed to guide treatment strategies. Several novel phenotypic AST platforms based on the physiological characteristics of bacteria obtained directly from clinical urine samples have been proposed as promising methods as rapid AST and appropriate antibiotic treatments. However, inaccurate bacterial quantification can lead to false results when high-accuracy quantitative assays are required using these procedures. Coupling the expression of catalase by pathogens with a chemiluminescence-based analytical method enables a convenient and low-cost operation. Herein, we demonstrate a rapid self-calibrating chemiluminescence sensor that can measure bacterial viability through the variation in catalase activity and its response to hydrogen peroxide after treatment with antibiotics. This rapid nanosensor platform can be utilized to determine the antibiotic susceptibility of uropathogenic Escherichia coli and Klebsiella pneumoniae, which account for 80% of all urinary tract infections, directly from clinical urine samples within 40 min without bacterial quantification. The proposed ultrafast and highly accurate AST can enable the precise guidance of antibiotic prescriptions and shorten the time required for clinical decision-making.

An integrated microfluidic chip for rapid and multiple antimicrobial susceptibility testing

The overuse and misuse of antibiotics have caused the development of antimicrobial resistance (AMR), which poses a significant threat to human health. Antimicrobial susceptibility testing (AST) serves as an effective tool for assessing the susceptibility of pathogens infecting patients and guiding the precise use of antibiotics. The conventional AST method, however, is limited by prolonged incubation times and high reagent consumption. In this study, we introduce an integrated microfluidic platform, enabling multiple AST and minimum inhibitory concentration (MIC) determination after 2 hours of incubation. Sample loading is achieved using a self-priming and vacuum-driven approach, enhancing operational feasibility and preventing cross-contamination during reagent pre-coating. Moreover, the use of chips with pre-coated antibiotics minimizes the need for reagent handling off-chip, thereby enhancing the flexibility of the microfluidic device and making the platform easy to use. The AST on-chip results for Klebsiella pneumoniae (K. pneumoniae) S1 correlate well with broth dilution methods. This integrated microfluidic platform offers a novel approach for rapid AST, demonstrating improved customization and efficiency for AST assays. It holds potential for addressing multi-drug resistant bacterial strains and accommodating diverse screening scenarios in modern clinical diagnostics.

Droplet microfluidics: unveiling the hidden complexity of the human microbiome

The human body harbors diverse microbial communities essential for maintaining health and influencing disease processes. Droplet microfluidics, a precise and high-throughput platform for manipulating microscale droplets, has become vital in advancing microbiome research. This review introduces the foundational principles of droplet microfluidics, its operational capabilities, and wide-ranging applications. We emphasize its role in enhancing single-cell sequencing technologies, particularly genome and RNA sequencing, transforming our understanding of microbial diversity, gene expression, and community dynamics. We explore its critical function in isolating and cultivating traditionally unculturable microbes and investigating microbial activity and interactions, facilitating deeper insight into community behavior and metabolic functions. Lastly, we highlight its broader applications in microbial analysis and its potential to revolutionize human health research by driving innovations in diagnostics, therapeutic development, and personalized medicine. This review provides a comprehensive overview of droplet microfluidics' impact on microbiome research, underscoring its potential to transform our understanding of microbial dynamics and their relevance to health and disease.

Rapid and Visual Detection of Urinary Pathogens by Employing Bifunctional Deoxyribonucleic Acid Sensors and Aggregation of Gold Nanoparticles

A simple, rapid, and visual approach is developed to perform diagnosis of urinary tract infection (UTI) and antimicrobial susceptibility testing (AST) by employing smart bifunctional DNA (bfDNA) sensors, exonuclease III, concatermers of CuO nanoparticles (CuONPs), and gold NPs (AuNPs) aggregation [AuNPs agglutination (AA)], namely, the bfDEC-AA method. The bfDNA sensors serve as probes for identifying 16S rRNA genes of bacterium or 18S rRNA of fungus and as mediators connecting the concatermers of CuONPs. The AA as a signal source is triggered by Cu(I)-catalyzed azide-alkyne cycloaddition click chemistry. In this study, the urine samples are analyzed directly, eliminating the need for overnight incubation or bacterial isolation. A crucial color change from red to purple occurs at the UTI diagnostic threshold of 104 CFU mL-1; thus the results of UTI diagnosis can be qualitatively interpreted by the unaided eyes. Similarly, AST was performed visually under our optimal conditions. The color shift can also be quantified using a point-of-care (POC) device. UTI identification, bacteria strain identification, and AST were achieved within 55, 55, and 145 min for 96 samples, respectively. Here, 128 urine samples from suspected UTI patients were tested. Notably, the sensitivity and specificity of our method were 99% and 100% for Gram-negative bacteria (G-) infection, 100% and 100% for Gram-positive bacteria (G+) infection, and 98% and 100% for AST, respectively. Furthermore, the low cost of our POC device (US$156) is friendly to underdeveloped regions.

Platinum nanoparticles-based electrochemical H2O2 sensor for rapid antibiotic susceptibility testing

With the increase of antimicrobial resistance, rapid antibiotic susceptibility testing (AST) to guide precise antibiotic administration has become increasingly important. However, current gold standard AST approaches tend to take up to 24-48 h. In this work, based on the nature of catalase-positive bacteria decomposing H2O2, we developed a rapid, portable, straightforward, and cost-effective phenotypic AST approach by detecting residual H2O2 using a Pt nanoparticles-based electrochemical sensor. The pulse current of the sensor exhibited a linear increase with rising H2O2 concentration, demonstrating a high sensitivity of ∼382.2 μA cm-2 mM-1. This approach showed superb diagnostic performance, with an area under the curve of 1 for 24 clinical samples of Escherichia coli and Staphylococcus aureus, with a total detection time of 60 and 45 min, respectively. Furthermore, the performance of the sensor showed no degradation even after 100 detections, promising a substantial reduction in AST costs. Overall, the proposed approach exhibited immense potential for diagnosing bacterial antibiotic resistance.

Nanoplasmonic Rapid Antimicrobial-Resistance Point-of-Care Identification Device: RAPIDx

The emergence of antibiotic resistance has become a global health crisis, and everyone must arm themselves with wisdom to effectively combat the "silent tsunami" of infections that are no longer treatable with antibiotics. However, the overuse or inappropriate use of unnecessary antibiotics is still routine for administering them due to the unavailability of rapid, precise, and point-of-care assays. Here, a rapid antimicrobial-resistance point-of-care identification device (RAPIDx) is reported for the accurate and simultaneous identification of bacterial species (genotype) and target enzyme activity (phenotype). First, a contamination-free active target enzyme is extracted via the photothermal lysis of preconcentrated bacteria cells on a nanoplasmonic functional layer on-chip. Second, the rapid, precise identification of pathogens is achieved by the photonic rolling circle amplification of DNA on a chip. Third, the simultaneous identification of bacterial species (genotype) and target enzyme activity (phenotype) is demonstrated within a sample-to-answer 45 min operation via the RAPIDx. It is believed that the RAPIDx will be a valuable method for solving the bottleneck of employing on-chip nanotechnology for antibiotic-resistant bioassay and other infectious diseases.

Point-of-Care Diagnosis of Tuberculosis Using a Portable Nucleic Acid Test with Distance-Based Readout

Rapid and accurate diagnosis of tuberculosis (TB) infection in resource-limited settings is critically needed to stop the spread of the disease but remains difficult to achieve. Herein, we report a fast, inexpensive nucleic acid test with distance-based readout (FINDR) for TB. Based on the unique chromatographic behavior of DNA intercalating dye on unmodified cellulose paper, our FINDR platform converted the amplicons of loop-mediated isothermal amplification (LAMP) into the migration distance on a paper-based analytical device. A suite of innovations were further introduced to enhance the accessibility of FINDR, including (1) screening optimal LAMP primers for distance-based readout; (2) developing a chip-on-cover design capable of streamlining LAMP amplification and distance-based detection in a fully sealed FINDR chip with a simple hand-based swirling for liquid transfer; and (3) integrating FINDR with an upstream portable pipetting-free DNA extractor and a downstream smartphone app to simplify sample processing and data interpretation. With these innovations, FINDR demonstrated a high clinical sensitivity (96.6%) and specificity (100%) upon validation against clinical sputum samples. Successful clinical validation was also achieved when FINDR was deployed as a point-of-care test for detecting TB under resource-limited conditions.

AI-empowered visualization of nucleic acid testing

AIMS

The visualization of nucleic acid testing (NAT) results plays a critical role in diagnosing and monitoring infectious and genetic diseases. The review aims to review the current status of AI-based NAT result visualization. It systematically introduces commonly used AI-based methods and techniques for NAT, emphasizing the importance of result visualization for accessible, clear, and rapid interpretation. This highlights the importance of developing a NAT visualization platform that is user-friendly and efficient, setting a clear direction for future advancements in making nucleic acid testing more accessible and effective for everyday applications.

METHOD

This review explores both the commonly used NAT methods and AI-based techniques for NAT result visualization. The focus then shifts to AI-based methodologies, such as color detection and result interpretation through AI algorithms. The article presents the advantages and disadvantages of these techniques, while also comparing the performance of various NAT platforms in different experimental contexts. Furthermore, it explores the role of AI in enhancing the accuracy, speed, and user accessibility of NAT results, highlighting visualization technologies adapted from other fields of experimentation.

SIGNIFICANCE

This review offers valuable insights for researchers and everyday users, aiming to develop effective visualization platforms for NAT, ultimately enhancing disease diagnosis and monitoring.

Atmospheric Pressure Enhanced Self-Sealing Rotation-SlipChip with Programmable Concentration Gradient Generation for Microbiological Applications

In microbiological research, traditional methods for bacterial screening and antibiotic susceptibility testing are resource-intensive. Microfluidics offers an efficient alternative with rapid results and minimal sample consumption, but the demand for cost-effective, user-friendly platforms persists in communities and hospitals. Inspired by the Magdeburg hemispheres, the strategy adapts to local conditions, leveraging omnipresent atmospheric pressure for self-sealing of Rotation-SlipChip (RSC) equipped with a 3D circular Christmas tree-like microfluidic concentration gradient generator. This innovative approach provides an accessible and adaptable platform for microbiological research and testing in diverse settings. The RSC can avoid leakage concerns during multiple concentration gradient generation, chip-rotating, and final long-term incubation reaction (≥24 h). Furtherly, RSC subtypes adapted to different reactions can be fabricated in less than 15 min with cost less than $1, the result can be read through designated observational windows by naked-eye. Moreover, the RSC demonstrates its capability for evaluating bacterial biomarker activity, enabling the rapid assessment of β-galactosidase concentration and enzyme activity within 30 min, and the limit of detection can be reduced by 10-fold. It also rapidly determines the minimum antibiotic inhibitory concentration and antibiotic combined medications results within 4 h. Overall, these low-cost and user-friendly RSC make them invaluable tools in determinations at previously impractical environment.

Exploiting β-Lactams-Induced Lysis and DNA Fragmentation for Rapid Molecular Antimicrobial Susceptibility Testing of Neisseria Gonorrhoeae via Dual-Digital PCR

The evolution of antimicrobial resistance (AMR) presents substantial challenges to global medical health systems. Neisseria gonorrhoeae (N. gonorrhoeae), in particular, has developed resistance to all currently available antimicrobials. Addressing this issue necessitates not only discovering new antimicrobials but also deepening the understanding of bacterial responses to these agents, which can lead to new markers for rapid antimicrobial susceptibility testing (AST). Such advancements can enhance treatment outcomes and promote antimicrobial stewardship. In this study, single-cell techniques, including live-cell imaging, flow cytometry, and digital polymerase chain reaction (PCR) are utilized, to investigate the lysis dynamics and molecular features of N. gonorrhoeae upon exposure to β-lactam antimicrobials. Distinct patterns of bacterial lysis and DNA fragmentation are uncovered in susceptible strains. Leveraging these discoveries, a microfluidic dual-digital PCR approach that combines single-cell and single-molecule analyses, facilitate rapid and efficient phenotypic molecular AST for N. gonorrhoeae against β-lactams is developed. This proof-of-concept validation demonstrates the effectiveness of the method in accessing antimicrobial susceptibility across a range of bacterial strains, contributing valuable insights for advancing the battle against AMR.

Next-generation rapid phenotypic antimicrobial susceptibility testing

Slow progress towards implementation of conventional clinical bacteriology in low resource settings and strong interest in greater speed for antimicrobial susceptibility testing (AST) more generally has focused attention on next-generation rapid AST technologies. In this Review, we systematically synthesize publications and submissions to regulatory agencies describing technologies that provide phenotypic AST faster than conventional methods. We characterize over ninety technologies in terms of underlying technical innovations, technology readiness level, extent of clinical validation, and time-to-results. This work provides a guide for technology developers and clinical microbiologists to understand the rapid phenotypic AST technology landscape, current development pipeline, and AST-specific validation milestones.

A new therapeutic strategy for infectious diseases against intracellular multidrug-resistant bacteria

Bacterial infections result in 7,700,000 deaths per year globally, with intracellular bacteria causing repeated and resistant infection. No drug is currently licenced for the treatment of intracellular bacteria. A new screening platform mimicking the host milieu has been established to explore phytochemical antibiotic adjuvants. Previously neglected isoprenylated flavonoids were found to be effective against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Specifically, the synergistic effect between glabrol and streptomycin against intracellular bacteria was observed for the first time. The glabrol-streptomycin combination targets bacterial inner membrane phospholipids, disrupts arginine biosynthesis, inhibits cell wall proteins and biofilm formation genes (agrA/B/C/D), and promotes ROS production, causing subsequent membrane and wall damage. To enhance the selective uptake of combination drug into infected cells, hyaluronic acid-streptomycin-lipoic acid-glabrol nanoparticles (HSLGS-S) were designed and synthesized to trigger the intracellular delivery of the glabrol-streptomycin combination. Thus, the treatment can be transported into the infected intracellular region and selectively release the glabrol-streptomycin combination to the bacterial at site. The bioactivity of HSLGS-S in clearing intracellular bacteria was 20-fold higher than that of the glabrol-streptomycin combination alone in vitro and 2- to 10-fold higher in vivo.

Diagnosis of extraintestinal pathogenic Escherichia coli pathogenesis in urinary tract infection

Extra-intestinal pathogenic Escherichia coli (ExPEC) is a virulent pathogen found in humans that causes the majority of urinary tract infections, and other infections such as meningitis and sepsis. ExPEC can enter the urinary tract through two modes: ascending from the bladder or descending from the kidneys. Human anatomical structures generally prevent the transmission of pathogens between the extra-intestinal area, kidneys, bladder, and urinary tract. However, adhesins, a virulence protein of ExPEC, promote the initial bacterial attachment and invasion of host cells. In addition to adhesion proteins, ExPEC contains iron acquisition systems and toxins to evade the host immune system, acquire essential nutrients, and gain antibiotic resistance. The presence of antibiotic-resistant genes makes treating ExPEC in urinary tract infections (UTIs) more complicated. Therefore, screening for the presence of ExPEC among other uropathogens in UTI patients is essential, as it can potentially aid in the effective treatment and mitigation of ExPEC pathogens. Several diagnostic techniques are available for detecting ExPEC, including urine culture, polymerase chain reaction, serological testing, loop-mediated isothermal amplification, and biochemical tests. This review addresses strain-specific diagnostic techniques for screening ExPEC in UTI patients.

Phenotypic and genotypic perspectives on detection methods for bacterial antimicrobial resistance in a One Health context: research progress and prospects

The widespread spread of bacterial antimicrobial resistance (AMR) and multidrug-resistant bacteria poses a significant threat to global public health. Traditional methods for detecting bacterial AMR are simple, reproducible, and intuitive, requiring long time incubation and high labor intensity. To quickly identify and detect bacterial AMR is urgent for clinical treatment to reduce mortality rate, and many new methods and technologies were required to be developed. This review summarizes the current phenotypic and genotypic detection methods for bacterial AMR. Phenotypic detection methods mainly include antimicrobial susceptibility tests, while genotypic detection methods have higher sensitivity and specificity and can detect known or even unknown drug resistance genes. However, most of the current tests are either genotypic or phenotypic and rarely combined. Combining the advantages of phenotypic and genotypic methods, combined with the joint application of multiple rapid detection methods may be the trend for future AMR testing. Driven by rapid diagnostic technology, big data analysis, and artificial intelligence, detection methods of bacterial AMR are expected to constantly develop and innovate. Adopting rational detection methods and scientific data analysis can better address the challenges of bacterial AMR and ensure human health and social well-being.

Blood culture-free ultra-rapid antimicrobial susceptibility testing

Treatment assessment and patient outcome for sepsis depend predominantly on the timely administration of appropriate antibiotics1-3. However, the clinical protocols used to stratify and select patient-specific optimal therapy are extremely slow4. In particular, the major hurdle in performing rapid antimicrobial susceptibility testing (AST) remains in the lengthy blood culture procedure, which has long been considered unavoidable due to the limited number of pathogens present in the patient's blood. Here we describe an ultra-rapid AST method that bypasses the need for traditional blood culture, thereby demonstrating potential to reduce the turnaround time of reporting drug susceptibility profiles by more than 40-60 h compared with hospital AST workflows. Introducing a synthetic beta-2-glycoprotein I peptide, a broad range of microbial pathogens are selectively recovered from whole blood, subjected to species identification or instantly proliferated and phenotypically evaluated for various drug conditions using a low-inoculum AST chip. The platform was clinically evaluated by the enrolment of 190 hospitalized patients suspected of having infection, achieving 100% match in species identification. Among the eight positive cases, six clinical isolates were retrospectively tested for AST showing an overall categorical agreement of 94.90% with an average theoretical turnaround time of 13 ± 2.53 h starting from initial blood processing.

Integrated Droplet-Based Digital Loop-Mediated Isothermal Amplification Microfluidic Chip with Droplet Generation, Incubation, and Continuous Fluorescence Detection

This study integrated sample partition, incubation, and continuous fluorescence detection on a single microfluidic chip for droplet-based digital Loop-Mediated Isothermal Amplification (LAMP) of nucleic acids. This integration eliminated the need to transfer reactions between different platforms, avoiding sample contamination and loss. Prior to the reaction, filling the channels with an oil phase and adding a glass cover slip on top of the chip overcame the problem of bubble generation in the channels during the LAMP reaction due to heating. Additionally, using two fluorescence intensity thresholds enabled simultaneous detection and counting of positive and negative droplets within a single fluorescence detection channel. The chip can partition approximately 6000 droplets from a 5 µL sample within 10 min, with a droplet diameter of around 110 µm and a coefficient of variation (CV) value of 0.82%. Staphylococcus aureus was quantified via the proposed platform. The results demonstrated a highly accurate correlation coefficient (R = 0.9998), and the detection limit reached a concentration of 1.7 × 102 copies/µL. The entire process of the droplet digital LAMP reaction, from droplet generation to incubation to quantitative results, took a maximum of 70 min.

Nucleic Acid Target Sensing Using a Vibrating Sharp-Tip Capillary and Digital Droplet Loop-Mediated Isothermal Amplification (ddLAMP)

Nucleic acid tests are key tools for the detection and diagnosis of many diseases. In many cases, the amplification of the nucleic acids is required to reach a detectable level. To make nucleic acid amplification tests more accessible to a point-of-care (POC) setting, isothermal amplification can be performed with a simple heating source. Although these tests are being performed in bulk reactions, the quantification is not as accurate as it would be with digital amplification. Here, we introduce the use of the vibrating sharp-tip capillary for a simple and portable system for tunable on-demand droplet generation. Because of the large range of droplet sizes possible and the tunability of the vibrating sharp-tip capillary, a high dynamic range (~2 to 6000 copies/µL) digital droplet loop-mediated isothermal amplification (ddLAMP) system has been developed. It was also noted that by changing the type of capillary on the vibrating sharp-tip capillary, the same mechanism can be used for simple and portable DNA fragmentation. With the incorporation of these elements, the present work paves the way for achieving digital nucleic acid tests in a POC setting with limited resources.

Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium

Antimicrobial resistance (AMR) is a growing public health crisis that requires innovative solutions. Current susceptibility testing approaches limit our ability to rapidly distinguish between antimicrobial-susceptible and -resistant organisms. Salmonella Typhimurium (S. Typhimurium) is an enteric pathogen responsible for severe gastrointestinal illness and invasive disease. Despite widespread resistance, ciprofloxacin remains a common treatment for Salmonella infections, particularly in lower-resource settings, where the drug is given empirically. Here, we exploit high-content imaging to generate deep phenotyping of S. Typhimurium isolates longitudinally exposed to increasing concentrations of ciprofloxacin. We apply machine learning algorithms to the imaging data and demonstrate that individual isolates display distinct growth and morphological characteristics that cluster by time point and susceptibility to ciprofloxacin, which occur independently of ciprofloxacin exposure. Using a further set of S. Typhimurium clinical isolates, we find that machine learning classifiers can accurately predict ciprofloxacin susceptibility without exposure to it or any prior knowledge of resistance phenotype. These results demonstrate the principle of using high-content imaging with machine learning algorithms to predict drug susceptibility of clinical bacterial isolates. This technique may be an important tool in understanding the morphological impact of antimicrobials on the bacterial cell to identify drugs with new modes of action.

Microfluidic technologies for advanced antimicrobial susceptibility testing

Antimicrobial resistance is getting serious and becoming a threat to public health worldwide. The improper and excessive use of antibiotics is responsible for this situation. The standard methods used in clinical laboratories, to diagnose bacterial infections, identify pathogens, and determine susceptibility profiles, are time-consuming and labor-intensive, leaving the empirical antimicrobial therapy as the only option for the first treatment. To prevent the situation from getting worse, evidence-based therapy should be given. The choosing of effective drugs requires powerful diagnostic tools to provide comprehensive information on infections. Recent progress in microfluidics is pushing infection diagnosis and antimicrobial susceptibility testing (AST) to be faster and easier. This review summarizes the recent development in microfluidic assays for rapid identification and AST in bacterial infections. Finally, we discuss the perspective of microfluidic-AST to develop the next-generation infection diagnosis technologies.

Sensitive and Extraction-Free Detection of Methicillin-Resistant Staphylococcus aureus through Ag+ Aptamer-Based Color Reaction

Refractory infections, such as hospital-acquired pneumonia, can be better diagnosed with the assistance of precise methicillin-resistant Staphylococcus aureus (MRSA) testing. However, traditional methods necessitate high-tech tools, rigorous temperature cycling, and the extraction of genetic material from MRSA cells. Herein, we propose a sensitive, specific, and extraction-free strategy for MRSA detection by integrating allosteric probe-based target recognition and exonuclease-III (Exo-III)-enhanced color reaction. The penicillin-binding protein 2a (PBP2a) aptamer in the allosteric probe binds with MRSA to convert protein signals to nucleic acid signals. This is followed by the DNA polymerase-assisted target recycle and the production of numerous single-strand DNA (ssDNA) chains which bind with silver ion (Ag+) aptamer to form a blunt terminus that can be identified by Exo-III. As a result, the Ag+ aptamer pre-coupled to magnetic nanoparticles is digested. After magnetic separation, the Ag+ in liquid supernatant catalyzes 3,3',5,5'-tetramethylbenzidine (TMB) for a color reaction. In addition, a concentration of 54 cfu/mL is predicted to be the lowest detectable value. Based on this, our assay has a wide linear detection range, covering 5 orders of magnitude and demonstrating a high specificity, which allows it to accurately distinguish the target MRSA from other microorganisms.

Metabolism-Triggered Plasmonic Nanosensor for Bacterial Detection and Antimicrobial Susceptibility Testing of Clinical Isolates

Antimicrobial resistance (AMR) is predicted to become the leading cause of death worldwide in the coming decades. Rapid and on-site antibiotic susceptibility testing (AST) is crucial for guiding appropriate antibiotic choices to combat AMR. With this in mind, we have designed a simple and efficient plasmonic nanosensor consisting of Cu2+ and cysteine-modified AuNP (Au/Cys) that utilizes the metabolic activity of bacteria toward Cu2+ for bacterial detection and AST. When Cu2+ is present, it induces the aggregation of Au/Cys. However, in the presence of bacteria, Cu2+ is metabolized to varying extents, resulting in distinct levels of aggregation. Moreover, the metabolic activity of bacteria can be influenced by their antibiotic susceptibility, allowing us to differentiate between susceptible and resistant strains through direct color changes from the Cu2+-Au/Cys platform over approximately 3 h. These color changes can be easily detected using naked-eye observation, smartphone analysis, or absorption readout. We have validated the platform using four clinical isolates and six types of antibiotics, demonstrating a clinical sensitivity and specificity of 95.8%. Given its simplicity, low cost, high speed, and high accuracy, the plasmonic nanosensor holds great potential for point-of-care detection of antibiotic susceptibility across various settings.

Rapid, Ultrasensitive, and Visual Detection of Pathogens Based on Cation Dye-Triggered Gold Nanoparticle Electrokinetic Agglutination Analysis

Rapid prescribing of the right antibiotic is the key to treat infectious diseases and decelerate the challenge of bacterial antibiotic resistance. Herein, by targeting the 16S rRNA of bacteria, we developed a cation dye-triggered electrokinetic gold nanoparticle (AuNP) agglutination (CD-TEAA) method, which is rapid, visual, ultrasensitive, culture-independent, and low in cost. The limit of detection (LOD) is as low as 1 CFU mL-1 Escherichia coli. The infection identifications of aseptic fluid samples (n = 11) and urine samples with a clinically suspected urinary tract infection (UTI, n = 78) were accomplished within 50 and 30 min for each sample, respectively. The antimicrobial susceptibility testing (AST) of UTI urine samples was achieved within 2.5 h. In ROC analysis of urine, the sensitivity and specificity were 100 and 96% for infection identification, and 100 and 98% for AST, respectively. Moreover, the overall cost of materials for each test is about US$0.69. Therefore, the CD-TEAA method is a superior approach to existing, time-consuming, and expensive methods, especially in less developed areas.

Performance of an innovative culture-based digital dipstick for detection of bacteriuria

IMPORTANCE

In this study, we explore the transformative potential of UTI-lizer, an emerging technology not yet commercially available. Our manuscript shows that UTI-lizer is a promising alternative for detecting the five main pathogens that cause urinary tract infections (UTIs). The results also indicate that digital dipsticks have the potential to uniquely provide UTI diagnostic quality on par with that of gold-standard testing, with the added benefits of ease of testing, rapid test handling time, and simple test equipment. This technology can be helpful in quickly ruling out bacterial infections and reducing the unnecessary use of antibiotics, especially in primary care settings or at the point of care. Moreover, the UTI-lizer test can reduce the number of negative urine samples sent to central laboratories, thus easing the burden of UTI diagnostics on the healthcare system. We believe our study, as well as current and upcoming research based on this technology, is highly relevant for clinical microbiologists, microbiology scientists, general practitioners, and urologists.

Rapid Drug Susceptibility Testing to Preserve Antibiotics

Antibiotic resistance is a global challenge likely to cost trillions of dollars in excess costs in the health system and more importantly, millions of lives every year. A major driver of resistance is the absence of susceptibility testing at the time a healthcare worker needs to prescribe an antimicrobial. The effect is that many prescriptions are unintentionally wasted and expose mutable organisms to antibiotics increasing the risk of resistance emerging. Often simplistic solutions are applied to this growing issue, such as a naïve drive to increase the speed of drug susceptibility testing. This puts a spotlight on a technological solution and there is a multiplicity of such candidate DST tests in development. Yet, if we do not define the necessary information and the speed at which it needs to be available in the clinical decision-making progress as well as the necessary integration into clinical pathways, then little progress will be made. In this chapter, we place the technological challenge in a clinical and systems context. Further, we will review the landscape of some promising technologies that are emerging and attempt to place them in the clinic where they will have to succeed.

Digital Recombinase Polymerase Amplification, Digital Loop-Mediated Isothermal Amplification, and Digital CRISPR-Cas Assisted Assay: Current Status, Challenges, and Perspectives

Digital nucleic acid detection based on microfluidics technology can quantify the initial amount of nucleic acid in the sample with low equipment requirements and simple operations, which can be widely used in clinical and in vitro diagnosis. Recently, isothermal amplification technologies such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats-CRISPR associated proteins (CRISPR-Cas) assisted technologies have become a hot spot of attention and state-of-the-art digital nucleic acid chips have provided a powerful tool for these technologies. Herein, isothermal amplification technologies including RPA, LAMP, and CRISPR-Cas assisted methods, based on digital nucleic acid microfluidics chips recently, have been reviewed. Moreover, the challenges of digital isothermal amplification and possible strategies to address them are discussed. Finally, future directions of digital isothermal amplification technology, such as microfluidic chip and device manufacturing, multiplex detection, and one-pot detection, are outlined.

Inoculum size-insensitive susceptibility determination of urine sample based on in-situ measurement of inducible enzyme activity after 20 min of antibiotic exposure

BACKGROUND

The empirical antibiotic therapies for bacterial infections cause the emergence and propagation of multi-drug resistant bacteria, which not only impair the effectiveness of existing antibiotics but also raise healthcare costs. To reduce the empirical treatments, rapid antimicrobial susceptibility testing (AST) of causative microorganisms in clinical samples should be conducted for prescribing evidence-based antibiotics. However, most of culture-based ASTs suffer from inoculum effect and lack differentiation of target pathogen and commensals, hampering their adoption for evidence-based antibiotic prescription. Therefore, rapid ASTs which can specifically determine pathogens' susceptibilities, regardless of the bacterial load in clinical samples, are in urgent need.

RESULTS

We present a pathogen-specific and inoculum size-insensitive AST to achieve the reliable susceptibility determination on Escherichia coli (E. coli) in urine samples. The developed AST is featured with an 1 h sample-to-result workflow in a filter, termed on-filter AST. The AST results can be obtained by using an inducible enzymatic assay to in-situ measure the cell response of E. coli collected from urine after 20 min of antibiotic exposure. The calculated detection limit of our AST (1.95 × 104 CFU/mL) is much lower than the diagnosis threshold of urinary tract infections. The specific expression of the inducible enzyme enables on-filter AST to correctly profile the susceptibilities of target pathogen to multi-type antibiotics without the interference from commensals. We performed the on-filter AST on 1 mL urine samples with bacterial loads varying from 105 CFU/mL to 107 CFU/mL and compared the results to that of standard method, demonstrating its insensitivity to inoculum size.

SIGNIFICANCE

The developed AST is demonstrated to be of high sensitivity, specificity, and insensitive to inoculum size. With further developments for additional bacteria and clinical validation, on-filter AST is promising as a rapid and reliable surrogate of culture-based AST to promote the evidence-based prescription at the first visit and minimize the emergency of new multi-drug resistant microorganisms.

Enzymatic Antimicrobial Susceptibility Testing with Bacteria Identification in 30 min

Rapid antimicrobial susceptibility testing (AST) with the ability of bacterial identification is urgently needed for evidence-based antibiotic prescription. Herein, we propose an enzymatic AST (enzyAST) that employs β-d-glucuronidase as a biomarker to identify pathogens and profile phenotypic susceptibilities simultaneously. EnzyAST enables to offer binary AST results within 30 min, much faster than standard methods (>16 h). The general applicability of enzyAST was verified by testing the susceptibility of two Escherichia coli strains to three antibiotics with different action mechanisms. The pilot study also shows that the minimal inhibitory concentrations can be determined by enzyAST with the statistical analysis of enzymatic activity of the bacteria population exposed to varying antibiotic concentrations. With further development of multiple bacteria and sample treatment, enzyAST could be able to evaluate the susceptibility of pathogens in clinical samples directly to facilitate the evidence-based therapy.

Accurate Prediction of Antimicrobial Susceptibility for Point-of-Care Testing of Urine in Less than 90 Minutes via iPRISM Cassettes

The extensive and improper use of antibiotics has led to a dramatic increase in the frequency of antibiotic resistance among human pathogens, complicating infectious disease treatments. In this work, a method for rapid antimicrobial susceptibility testing (AST) is presented using microstructured silicon diffraction gratings integrated into prototype devices, which enhance bacteria-surface interactions and promote bacterial colonization. The silicon microstructures act also as optical sensors for monitoring bacterial growth upon exposure to antibiotics in a real-time and label-free manner via intensity-based phase-shift reflectometric interference spectroscopic measurements (iPRISM). Rapid AST using clinical isolates of Escherichia coli (E. coli) from urine is established and the assay is applied directly on unprocessed urine samples from urinary tract infection patients. When coupled with a machine learning algorithm trained on clinical samples, the iPRISM AST is able to predict the resistance or susceptibility of a new clinical sample with an Area Under the Receiver Operating Characteristic curve (AUC) of ∼ 0.85 in 1 h, and AUC > 0.9 in 90 min, when compared to state-of-the-art automated AST methods used in the clinic while being an order of magnitude faster.

Rapid and sensitive detection of miRNA via light scatter-aided emulsion-based isothermal amplification using a custom low-cost device

MicroRNAs are likely to be a next-generation clinical biomarker for many diseases. While gold-standard technologies, e.g., reverse transcription-quantitative polymerase chain reaction (RT-qPCR), exist for microRNA detection, there is a need for rapid and low-cost testing. Here, an emulsion loop-mediated isothermal amplification (eLAMP) assay was developed for miRNA that compartmentalizes a LAMP reaction and shortens the time-to-detection. The miRNA was a primer to facilitate the overall amplification rate of template DNA. Light scatter intensity decreased when the emulsion droplet got smaller during the ongoing amplification, which was utilized to moitor the amplification non-invasively. A custom low-cost device was designed and fabricated using a computer cooling fan, a Peltier heater, an LED, a photoresistor, and a temperature controller. It allowed more stable vortexing and accurate light scatter detection. Three miRNAs, miR-21, miR-16, and miR-192, were successfully detected using the custom device. Specifically, new template and primer sequences were developed for miR-16 and miR-192. Zeta potential measurements and microscopic observations confirmed emulsion size reduction and amplicon adsorption. The detection limit was 0.01 fM, corresponding to 2.4 copies per reaction, and the detection could be made in 5 min. Since the assays were rapid and both template and miRNA + template could eventually be amplified, we introduced the success rate (compared to the 95% confidence interval of the template result) as a new measure, which worked well with lower concentrations and inefficient amplifications. This assay brings us one step closer to allowing circulating miRNA biomarker detection to become commonplace in the clinical world.

Droplet-Based Microfluidics: Applications in Pharmaceuticals

Droplet-based microfluidics offer great opportunities for applications in various fields, such as diagnostics, food sciences, and drug discovery. A droplet provides an isolated environment for performing a single reaction within a microscale-volume sample, allowing for a fast reaction with a high sensitivity, high throughput, and low risk of cross-contamination. Owing to several remarkable features, droplet-based microfluidic techniques have been intensively studied. In this review, we discuss the impact of droplet microfluidics, particularly focusing on drug screening and development. In addition, we surveyed various methods of device fabrication and droplet generation/manipulation. We further highlight some promising studies covering drug synthesis and delivery that were updated within the last 5 years. This review provides researchers with a quick guide that includes the most up-to-date and relevant information on the latest scientific findings on the development of droplet-based microfluidics in the pharmaceutical field.

Prospects of Microfluidic Technology in Nucleic Acid Detection Approaches

Conventional diagnostic techniques are based on the utilization of analyte sampling, sensing and signaling on separate platforms for detection purposes, which must be integrated to a single step procedure in point of care (POC) testing devices. Due to the expeditious nature of microfluidic platforms, the trend has been shifted toward the implementation of these systems for the detection of analytes in biochemical, clinical and food technology. Microfluidic systems molded with substances such as polymers or glass offer the specific and sensitive detection of infectious and noninfectious diseases by providing innumerable benefits, including less cost, good biological affinity, strong capillary action and simple process of fabrication. In the case of nanosensors for nucleic acid detection, some challenges need to be addressed, such as cellular lysis, isolation and amplification of nucleic acid before its detection. To avoid the utilization of laborious steps for executing these processes, advances have been deployed in this perspective for on-chip sample preparation, amplification and detection by the introduction of an emerging field of modular microfluidics that has multiple advantages over integrated microfluidics. This review emphasizes the significance of microfluidic technology for the nucleic acid detection of infectious and non-infectious diseases. The implementation of isothermal amplification in conjunction with the lateral flow assay greatly increases the binding efficiency of nanoparticles and biomolecules and improves the limit of detection and sensitivity. Most importantly, the deployment of paper-based material made of cellulose reduces the overall cost. Microfluidic technology in nucleic acid testing has been discussed by explicating its applications in different fields. Next-generation diagnostic methods can be improved by using CRISPR/Cas technology in microfluidic systems. This review concludes with the comparison and future prospects of various microfluidic systems, detection methods and plasma separation techniques used in microfluidic devices.

Moving microcapillary antibiotic susceptibility testing (mcAST) towards the clinic: unravelling kinetics of detection of uropathogenic E. coli, mass-manufacturing and usability for detection of urinary tract infections in human urine

Innovation in infection based point-of-care (PoC) diagnostics is vital to avoid unnecessary use of antibiotics and the development of antimicrobial resistance. Several groups including our research team have in recent years successfully miniaturised phenotypic antibiotic susceptibility tests (AST) of isolated bacterial strains, providing validation that miniaturised AST can match conventional microbiological methods. Some studies have also shown the feasibility of direct testing (without isolation or purification), specifically for urinary tract infections, paving the way for direct microfluidic AST systems at PoC. As rate of bacteria growth is intrinsically linked to the temperature of incubation, transferring miniaturised AST nearer the patient requires building new capabilities in terms of temperature control at PoC, furthermore widespread clinical use will require mass-manufacturing of microfluidic test strips and direct testing of urine samples. This study shows for the first-time application of microcapillary antibiotic susceptibility testing (mcAST) directly from clinical samples, using minimal equipment and simple liquid handling, and with kinetics of growth recorded using a smartphone camera. A complete PoC-mcAST system was presented and tested using 12 clinical samples sent to a clinical laboratory for microbiological analysis. The test showed 100% accuracy for determining bacteria in urine above the clinical threshold (5 out of 12 positive) and achieved 95% categorical agreement for 5 positive urines tested with 4 antibiotics (nitrofurantoin, ciprofloxacin, trimethoprim and cephalexin) within 6 h compared to the reference standard overnight AST method. A kinetic model is presented for metabolization of resazurin, demonstrating kinetics of degradation of resazurin in microcapillaries follow those observed for a microtiter plate, with time for AST dependent on the initial CFU ml^-1 of uropathogenic bacteria in the urine sample. In addition, we show for the first time that use of air-drying for mass-manufacturing and deposition of AST reagents within the inner surface of mcAST strips matches results obtained with standard AST methods. These results take mcAST a step closer to clinical application, for example as PoC support for antibiotic prescription decisions within a day.

Direct single-cell antimicrobial susceptibility testing of Escherichia coli in urine using a ready-to-use 3D microwell array chip

Empirical antibiotic therapies are prescribed for treating uncomplicated urinary tract infections (UTIs) due to the long turnaround time of conventional antimicrobial susceptibility testing (AST), leading to the prevalence of multi-drug resistant pathogens. We present a ready-to-use 3D microwell array chip to directly conduct comprehensive AST of pathogenic agents in urine at the single-cell level. The developed device features a highly integrated 3D microwell array, offering a dynamic range from 10² to 10⁷ CFU mL^-1, and a capillary valve-based flow distributor for flow equidistribution in dispensing channels and uniform sample distribution. The chip with pre-loaded reagents and negative pressure inside only requires the user to initiate AST by loading samples (∼3 s) and can work independently. We demonstrate an accessible sample-to-result workflow, including syringe filter-based bacteria separation and rapid single-cell AST on chip, which enables us to bypass the time-consuming bacteria isolation and pre-culture, speeding up the AST in ∼3 h from 2 days of conventional methods. Moreover, the bacterial concentration and AST with minimum inhibitory concentrations can be assessed simultaneously to provide comprehensive information on infections. With further development for multiple antibiotic conditions, the Dsc-AST assay could contribute to timely prescription of targeted drugs for better patient outcomes and mitigation of the threat of drug-resistant bacteria.

Rapid Phenotypic Antimicrobial Susceptibility Testing Using a Coulter Counter and Proliferation Rate Discrepancy

The rapid determination of antimicrobial susceptibility and evidence-based antimicrobial prescription is necessary to combat widespread antimicrobial resistance and promote effectively treatment for bacterial infections. This study developed a rapid phenotypic antimicrobial susceptibility determination method competent for seamless clinical implementation. A laboratory-friendly Coulter counter-based antimicrobial susceptibility testing (CAST) was developed and integrated with bacterial incubation, population growth monitoring, and result analysis to quantitatively detect differences in bacterial growth between resistant and susceptible strains following a 2 h exposure to antimicrobial agents. The distinct proliferation rates of the different strains enabled the rapid determination of their antimicrobial susceptibility phenotypes. We evaluated the performance efficacy of CAST for 74 clinically isolated Enterobacteriaceae subjected to 15 antimicrobials. The results were consistent with those obtained via the 24 h broth microdilution method, showing 90.18% absolute categorical agreement.

A 3D Scalable Chamber-Array Chip for Digital LAMP

As an absolute quantification method at the single-molecule level, digital PCR (dPCR) offers the highest accuracy. In this work, we developed a 3D scalable chamber-array chip that multiplied the number of partitions by stacking chamber-array layers and realized digital loop-mediated isothermal amplification to quantify DNA molecules. It greatly increases the number of partitions to improve the performance of dPCR without increasing the chip size, the operation workflow complicity, and operation time. For the three-chamber-array-layer chip which contains 200,000 reactors of a 0.125 nL volume, it has been proved that the reagent filling and partition were finished within 3 min, and the whole detection could be finished within 1 h. The method demonstrated that it could be scalable to a six-chamber-array layer, which contains 400,000 reactors without increasing the size of the chip and the complication of filling/partition workflow but only takes an additional hour for scanning. Due to its potential for high throughput, low cost, and simple operation, our device may significantly expand the clinical application range of dPCR.

Single-cell pathogen diagnostics for combating antibiotic resistance

Bacterial infections and antimicrobial resistance are a major cause for morbidity and mortality worldwide. Antimicrobial resistance often arises from antimicrobial misuse, where physicians empirically treat suspected bacterial infections with broad-spectrum antibiotics until standard culture-based diagnostic tests can be completed. There has been a tremendous effort to develop rapid diagnostics in support of the transition from empirical treatment of bacterial infections towards a more precise and personalized approach. Single-cell pathogen diagnostics hold particular promise, enabling unprecedented quantitative precision and rapid turnaround times. This Primer provides a guide for assessing, designing, implementing and applying single-cell pathogen diagnostics. First, single-cell pathogen diagnostic platforms are introduced based on three essential capabilities: cell isolation, detection assay and output measurement. Representative results, common analysis methods and key applications are highlighted, with an emphasis on initial screening of bacterial infection, bacterial species identification and antimicrobial susceptibility testing. Finally, the limitations of existing platforms are discussed, with perspectives offered and an outlook towards clinical deployment. This Primer hopes to inspire and propel new platforms that can realize the vision of precise and personalized bacterial infection treatments in the near future.

High-Throughput Antimicrobial Susceptibility Testing of Escherichia coli by Wide-Field Mid-Infrared Photothermal Imaging of Protein Synthesis

Antimicrobial resistance poses great threats to global health and economics. Current gold-standard antimicrobial susceptibility testing (AST) requires extensive culture time (36-72 h) to determine susceptibility. There is an urgent need for rapid AST methods to slow down antimicrobial resistance. Here, we present a rapid AST method based on wide-field mid-infrared photothermal imaging of protein synthesis from ¹³C-glucose in Escherichia coli. Our wide-field approach achieved metabolic imaging for hundreds of bacteria at the single-cell resolution within seconds. The perturbed microbial protein synthesis can be probed within 1 h after antibiotic treatment in E. coli cells. The susceptibility of antibiotics with various mechanisms of action has been probed through monitoring protein synthesis, which promises great potential of the proposed platform toward clinical translation.

Cell-Free Production Systems in Droplet Microfluidics

The use of cell-free production systems in droplet microfluidic devices has gained significant interest during the last decade. Encapsulating DNA replication, RNA transcription, and protein expression systems in water-in-oil drops allows for the interrogation of unique molecules and high-throughput screening of libraries of industrial and biomedical interest. Furthermore, the use of such systems in closed compartments enables the evaluation of various properties of novel synthetic or minimal cells. In this chapter, we review the latest advances in the usage of the cell-free macromolecule production toolbox in droplets, with a special emphasis on new on-chip technologies for the amplification, transcription, expression, screening, and directed evolution of biomolecules.

All-In-One Escherichia coli Viability Assay for Multi-dimensional Detection of Uncomplicated Urinary Tract Infections

The urinary tract infections by antibiotic-resistant bacteria have been a serious public health problem and increase the healthcare costs. The conventional technologies of diagnosis and antimicrobial susceptibility testing (AST) relying on multiple culture-based assays are time-consuming and labor-intensive and thus compel the empirical antimicrobial therapies to be prescribed, fueling the prevalence of antimicrobial resistance. Herein, we propose an all-in-one Escherichia coli viability assay in an enclosed 3D microwell array chip, termed digital β-d-glucuronidase (GUS)-AST assay. It employs GUS, a specific metabolism-related enzyme, to convert the presence of E. coli into bright fluorescence. The random distribution of single bacteria in microwell array enables to quantify the E. coli concentrations by counting the positive microwells. We incorporate the most probable number with digital quantification to lower the limit of detection and expand the dynamic range to 7 orders. The digital GUS-AST assay is able to indicate the potency of antibiotics and determine the minimum inhibitory concentrations. A streamlined procedure of urine removal, bacterial separation, and digital GUS-AST is established to perform the direct analysis of bacteria population in urine. The sample-to-result workflow can be finished in 4.5 h with a limit of detection of 39 CFU/mL. With further development for additional pathogens and multiple antibiotic conditions, the digital GUS-AST assay could help physicians to prescribe timely targeted therapies for better patient outcomes and the minimum emergence of resistant bacteria.

Loop-Mediated Isothermal Amplification: From Theory to Practice

Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.

Rapid Antimicrobial Susceptibility Testing Based on a Bio-Inspired Chemiluminescence Sensor

Indiscriminate usage of antibiotics has caused accelerating growth and global expansion of antimicrobial resistance. Therefore, rapid antimicrobial susceptibility testing (AST) for guiding antibiotic prescription and preventing the spread of antimicrobial resistance is in urgent need. Phenotypic AST is the clinical gold standard method; however, no phenotypic AST has realized a colony-to-answer at about 1 h by utilizing the chemiluminescence sensor to detect the enzyme expressed by bacteria. Inspired by the bubble formation in the mixture of Escherichia coli and H₂O₂, we demonstrate a strategy based on the chemiluminescence sensor for rapid AST. Compared with the gold standard methods, the values of AUC are 0.960 for E. coli and 0.950 for Staphylococcus aureus, close to 1, indicating superb diagnostic performance as an AST method. The whole process from colonies to answer is 55 min for E. coli and 70 min for S. aureus. The chemiluminescence readout is based on the common equipment in the laboratory of the hospital, which is conducive to follow-up clinical promotion. Our sensor promises great potential in rapid AST, facilitating antimicrobial stewardship.

Bioinspired Plasmonic Nanosensor for on-Site Antimicrobial Susceptibility Testing in Urine Samples

Delayed use of appropriate antibiotics for superbugs, particularly for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pn), has caused extensive morbidity and mortality worldwide. Therefore, rapid and on-site antimicrobial susceptibility testing (AST) is urgently required. Unfortunately, currently, no phenotypic AST can realize a sample-to-answer result within 2 h directly from a clinical sample and without using laboratory equipment or customized devices. Inspired by observing that E. coli and K. pn can rapidly catalyze H₂O₂, we developed a plasmonic nanosensor that responds to the proliferation of bacteria for realizing rapid AST. The results can be determined with the naked eye, digitized using a smartphone, and validated using ultraviolet-visible spectrometry. Our assay achieved superb area under the curves of 0.9752 and 1 in a receiver operating characteristic analysis directly obtained from uncultured clinical urine samples infected by E. coli and K. pn, respectively. The entire process from sample collection to analysis takes 100 min for E. coli and 85 min for K. pn detection. Our platform provides a practical approach for performing on-site AST in clinics to improve the survival of patients. It releases the burden of superbugs and avoids the abuse of antibiotics.

Picoliter Droplet Generation and Dense Bead-in-Droplet Encapsulation via Microfluidic Devices Fabricated via 3D Printed Molds

Picoliter-scale droplets have many applications in chemistry and biology, such as biomolecule synthesis, drug discovery, nucleic acid quantification, and single cell analysis. However, due to the complicated processes used to fabricate microfluidic channels, most picoliter (pL) droplet generation methods are limited to research in laboratories with cleanroom facilities and complex instrumentation. The purpose of this work is to investigate a method that uses 3D printing to fabricate microfluidic devices that can generate droplets with sizes <100 pL and encapsulate single dense beads mechanistically. Our device generated monodisperse droplets as small as ~48 pL and we demonstrated the usefulness of this droplet generation technique in biomolecule analysis by detecting Lactobacillus acidophillus 16s rRNA via digital loop-mediated isothermal amplification (dLAMP). We also designed a mixer that can be integrated into a syringe to overcome dense bead sedimentation and found that the bead-in-droplet (BiD) emulsions created from our device had <2% of the droplets populated with more than 1 bead. This study will enable researchers to create devices that generate pL-scale droplets and encapsulate dense beads with inexpensive and simple instrumentation (3D printer and syringe pump). The rapid prototyping and integration ability of this module with other components or processes can accelerate the development of point-of-care microfluidic devices that use droplet-bead emulsions to analyze biological or chemical samples with high throughput and precision.

Rapid antibiotic susceptibility testing and species identification for mixed samples

Antimicrobial resistance is an increasing problem on a global scale. Rapid antibiotic susceptibility testing (AST) is urgently needed in the clinic to enable personalized prescriptions in high-resistance environments and to limit the use of broad-spectrum drugs. Current rapid phenotypic AST methods do not include species identification (ID), leaving time-consuming plating or culturing as the only available option when ID is needed to make the sensitivity call. Here we describe a method to perform phenotypic AST at the single-cell level in a microfluidic chip that allows subsequent genotyping by in situ FISH. By stratifying the phenotypic AST response on the species of individual cells, it is possible to determine the susceptibility profile for each species in a mixed sample in 2 h. In this proof-of-principle study, we demonstrate the operation with four antibiotics and mixed samples with combinations of seven species.

Combinatorial screening SlipChip for rapid phenotypic antimicrobial susceptibility testing

Antimicrobial resistance (AMR) by bacteria is a serious global threat, and a rapid, high-throughput, and easy-to-use phenotypic antimicrobial susceptibility testing (AST) method is essential for making timely treatment decisions and controlling the spread of antibiotic resistant micro-organisms. Traditional culture-based methods are time-consuming, and their capability to screen against a large number of different conditions is limited; meanwhile genotypic based methods, including sequencing and PCR based methods, are constrained by rarely identified resistance genes and complicated resistance mechanisms. Here, a combinatorial-screening SlipChip (cs-SlipChip) containing 192 nanoliter-sized compartments is developed which can perform high-throughput phenotypic AST within three hours by monitoring the bacterial growth within nanoliter-sized droplets with bright-field imaging and analyzing the changes in bacterial number and morphology. The minimum inhibitory concentration (MIC) of Escherichia coli ATCC 25922 against four antibiotics (ampicillin, ciprofloxacin, ceftazidime, and nitrofurantoin) can be measured in one chip within 3 hours. Furthermore, five antibiotic-resistant E. coli strains were isolated from patients diagnosed with urinary tract infections (UTIs), and an individual isolate was tested using four antibiotics and eleven antibiotic combinations simultaneously with three different concentrations of each. The results from the cs-SlipChip agree with those of a VITEK 2 automated system. This cs-SlipChip provides a practical high-throughput and rapid phenotypic method for AST and can also be used to screen different chemicals and antibiotic combinations for the treatment of multiple antibiotic-resistant bacteria.

Microfluidics for antibiotic susceptibility testing

The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.