A Microfluidic Channel Method for Rapid Drug-Susceptibility Testing of Pseudomonas aeruginosa

Rapid screening of positive blood cultures for extended-spectrum β-lactamases and metallo-β-lactamases using a drug susceptibility testing microfluidic method

OBJECTIVES

An increasing number of drug-resistant bacteria have been identified recently. In particular, drug-resistant bacteria have been linked to unfavorable prognoses in patients with bacteremia, highlighting the need for rapid testing. Our previous studies have focused on the utility of a drug susceptibility testing microfluidic (DSTM) method using microfluidic channels. A system with this DSTM method for screening for β-lactamases can rapidly detect extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs). In this study, we have evaluated the clinical utility of pre-treatment for screening positive blood cultures using the DSTM method.

METHODS

A total of 178 positive blood cultures and five simulated samples of MBL-producing bacteria were prepared at Kochi University Hospital, Japan. The pretreatment consisted of a two-step centrifugation. The obtained sediments were screened with the DSTM method for the production of β-lactamase based on morphological changes in the bacteria after 3 h of incubation.

RESULTS

The pretreatment functioned properly for all samples. Of the 25 ESBL samples, 21 were positive for ESBLs. Four false-negative samples, all obtained from the same patient, contained CTX-M-2 enzyme-producing Proteus mirabilis and showed insusceptibility to an ESBL inhibitor. The simulated samples prepared for MBL screening were positive for MBLs.

CONCLUSIONS

When combined with a method for rapidly identifying bacterial species, DSTM may enable patients with bloodstream infections to start receiving appropriate treatment within 4 h after positive blood cultures are screened.

Significant reduction of the culturing time required for bacterial identification and antibiotic susceptibility determination by infrared spectroscopy

Rapid testing of bacteria for antibiotic susceptibility is essential for effective treatment and curbing the emergence of multidrug-resistant bacteria. The misuse of antibiotics, coupled with the time-consuming classical testing methods, intensifies the threat of antibiotic resistance, a major global health concern. In this study, employing infrared spectroscopy-based machine learning techniques, we significantly shortened the time required for susceptibility testing to 10 hours, a significant improvement from the 24 hours in our previous studies as well as the conventional methods that typically take at least 48 hours. This remarkable reduction in turnaround time (from 48 hours to 10 hours), achieved by minimizing the culturing period, offers a game-changing advantage for clinical applications. Our study involves a dataset comprising 400 bacterial samples (200 E. coli, 100 Klebsiella pneumoniae, and 100 Pseudomonas aeruginosa) with an impressive 96% accuracy in the taxonomic classification at the species level and up to 82% accuracy in bacterial susceptibility to various antibiotics.

cmpX overexpression in Pseudomonas aeruginosa affects biofilm formation and cell morphology in response to shear stress

Pseudomonas aeruginosa is an opportunistic pathogen causing chronic infections that are related to its ability to form biofilms. Mechanosensitive ion channels (Mcs) are cytoplasmic membrane proteins whose opening depends on a mechanical stress impacting the lipid bilayer. CmpX is a homologue of the small conductance MscS of Escherichia coli. The cmpX gene is part of a transcriptional cfrX-cmpX unit that is under the control of the cell envelope stress response ECF sigma factor SigX. CmpX was shown to regulate the activity of the hybrid sensor kinase PA1611 involved in the regulation of transition from a planktonic to a biofilm lifestyle. The deletion of cmpX leads to increased biofilm formation under static conditions. Herein, the effect of cmpX overexpression was investigated by confocal laser scanning microscopy in terms of biofilm formation and architecture, and matrix components production, in dynamic conditions. We show that overexpression of cmpX in P. aeruginosa leads to enhanced and altered biofilm architecture that seems to be associated to increased matrix components and the emergence of filamentous cells. These phenotypic alterations might occur potentially through a shear stress induced by the medium flow rate.

Importance

CmpX is involved in biofilm formation and cell filamentation with regards to the medium flow.

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.

Computer vision meets microfluidics: a label-free method for high-throughput cell analysis

In this paper, we review the integration of microfluidic chips and computer vision, which has great potential to advance research in the life sciences and biology, particularly in the analysis of cell imaging data. Microfluidic chips enable the generation of large amounts of visual data at the single-cell level, while computer vision techniques can rapidly process and analyze these data to extract valuable information about cellular health and function. One of the key advantages of this integrative approach is that it allows for noninvasive and low-damage cellular characterization, which is important for studying delicate or fragile microbial cells. The use of microfluidic chips provides a highly controlled environment for cell growth and manipulation, minimizes experimental variability and improves the accuracy of data analysis. Computer vision can be used to recognize and analyze target species within heterogeneous microbial populations, which is important for understanding the physiological status of cells in complex biological systems. As hardware and artificial intelligence algorithms continue to improve, computer vision is expected to become an increasingly powerful tool for in situ cell analysis. The use of microelectromechanical devices in combination with microfluidic chips and computer vision could enable the development of label-free, automatic, low-cost, and fast cellular information recognition and the high-throughput analysis of cellular responses to different compounds, for broad applications in fields such as drug discovery, diagnostics, and personalized medicine.

Early appropriate diagnostics and treatment of MDR Gram-negative infections

The term difficult-to-treat resistance has been recently coined to identify Gram-negative bacteria exhibiting resistance to all fluoroquinolones and all β-lactam categories, including carbapenems. Such bacteria are posing serious challenges to clinicians trying to identify the best therapeutic option for any given patient. Delayed appropriate therapy has been associated with worse outcomes including increase in length of stay, increase in total in-hospital costs and ∼20% increase in the risk of in-hospital mortality. In addition, time to appropriate antibiotic therapy has been shown to be an independent predictor of 30 day mortality in patients with resistant organisms. Improving and anticipating aetiological diagnosis through optimizing not only the identification of phenotypic resistance to antibiotic classes/agents, but also the identification of specific resistance mechanisms, would have a major impact on reducing the frequency and duration of inappropriate early antibiotic therapy. In light of these considerations, the present paper reviews the increasing need for rapid diagnosis of bacterial infections and efficient laboratory workflows to confirm diagnoses and facilitate prompt de-escalation to targeted therapy, in line with antimicrobial stewardship principles. Rapid diagnostic tests currently available and future perspectives for their use are discussed. Early appropriate diagnostics and treatment of MDR Gram-negative infections require a multidisciplinary approach that includes multiple different diagnostic methods and further consensus of algorithms, protocols and guidelines to select the optimal antibiotic therapy.

Bioremediation on a chip: A portable microfluidic device for efficient screening of bacterial biofilm with polycyclic aromatic hydrocarbon removal capacity

Polycyclic aromatic hydrocarbons (PAHs) are pollutants of critical environmental and public health concern and their elimination from contaminated sites is significant for the environment. Biodegradation studies have demonstrated the ability of bacteria in biofilm conformation to enhance the biodegradation of pollutants. In this study, we used our newly developed microfluidic platform to explore biofilm development, properties, and applications of fluid flow, as a new technique for screening PAHs-degrading biofilms. The optimization and evaluation of the flow condition in the microchannels were performed through computational fluid dynamics (CFD). The formation of biofilms by PAHs-degrading bacteria Pseudomonas sp. P26 and Gordonia sp. H19, as pure cultures and co-culture, was obtained in the developed microchips. The removal efficiencies of acenaphthene, fluoranthene and pyrene were determined by HPLC. All the biofilms formed in the microchips removed all tested PAHs, with the higher removal percentages observed with the Pseudomonas sp. P26 biofilm (57.4% of acenaphthene, 40.9% of fluoranthene, and 28.9% of pyrene). Pseudomonas sp. P26 biofilm removed these compounds more efficiently than planktonic cultures. This work proved that the conformation of biofilms enhances the removal rate. It also provided a new tool to rapid and low-cost screen for effective pollutant-degrading biofilms.

Metabolic preference assay for rapid diagnosis of bloodstream infections

Bloodstream infections (BSIs) cause >500,000 infections and >80,000 deaths per year in North America. The length of time between the onset of symptoms and administration of appropriate antimicrobials is directly linked to mortality rates. It currently takes 2–5 days to identify BSI pathogens and measure their susceptibility to antimicrobials – a timeline that directly contributes to preventable deaths. To address this, we demonstrate a rapid metabolic preference assay (MPA) that uses the pattern of metabolic fluxes observed in ex-vivo microbial cultures to identify common pathogens and determine their antimicrobial susceptibility profiles. In a head-to-head race with a leading platform (VITEK 2, BioMérieux) used in diagnostic laboratories, MPA decreases testing timelines from 40 hours to under 20. If put into practice, this assay could reduce septic shock mortality and reduce the use of broad spectrum antibiotics.

It is currently slow to identify bloodstream infection pathogens. Here the authors report a rapid metabolic preference assay that uses the pattern of metabolic fluxes observed in ex-vivo microbial cultures to identify common pathogens and determine their antimicrobial susceptibility profiles.

Microfluidic devices for studying bacterial taxis, drug testing and biofilm formation

Some bacteria have coevolved to establish symbiotic or pathogenic relationships with plants, animals or humans. With human association, the bacteria can cause a variety of diseases. Thus, understanding bacterial phenotypes at the single-cell level is essential to develop beneficial applications. Traditional microbiological techniques have provided great knowledge about these organisms; however, they have also shown limitations, such as difficulties in culturing some bacteria, the heterogeneity of bacterial populations or difficulties in recreating some physical or biological conditions. Microfluidics is an emerging technique that complements current biological assays. Since microfluidics works with micrometric volumes, it allows fine-tuning control of the test conditions. Moreover, it allows the recruitment of three-dimensional (3D) conditions, in which several processes can be integrated and gradients can be generated, thus imitating physiological 3D environments. Here, we review some key microfluidic-based studies describing the effects of different microenvironmental conditions on bacterial response, biofilm formation and antimicrobial resistance. For this aim, we present different studies classified into six groups according to the design of the microfluidic device: (i) linear channels, (ii) mixing channels, (iii) multiple floors, (iv) porous devices, (v) topographic devices and (vi) droplet microfluidics. Hence, we highlight the potential and possibilities of using microfluidic-based technology to study bacterial phenotypes in comparison with traditional methodologies.

Novel approach for rapid detection of extended spectrum β-lactamase and metalloid-β-lactamase using drug susceptibility testing microfluidic device (DSTM)

BACKGROUND/PURPOSE

Rapid detection of β-lactamases is important in a recent situation where resistant bacteria are increasing. By using the drug susceptibility testing microfluidic device (DSTM), rapid screening of extended spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) has become possible.

METHODS

β-lactams and β-lactamase inhibitors were pre-fixed in the DSTM for use. A bacterial suspension in Mueller-Hinton broth (McF 0.25) was introduced into the device, and the effects of β-lactamase inhibitor on morphological changes caused by β-lactam were evaluated after 3 h incubation.

RESULTS

Clinical isolates genetically confirmed to produce β-lactamase were used. Of the 84 ESBL-producing strains, 80 strains (95%) turned to be ESBL positive, and five strains (6%) of them MBL were positive as well as ESBL. Four strains (5%) were negative for both ESBL and MBL. Of the 24 MBL-producing strains, 23 strains (96%) were positive for MBL. All the 43 AmpC-producing strains were negative for both ESBL and MBL. Of the 156 ESBL- and MBL-nonproducing strains, 155 strains (99%) were negative for both ESBL and MBL, and one strain was positive for ESBL. With this method, the detection sensitivity was 95% and the specificity was 100% for ESBL, whereas the detection sensitivity was 96% and the specificity was 98% for MBL. These results were not significantly different from the results of the disc diffusion method.

CONCLUSION

The DSTM method allows rapid detection of β-lactamases in 3 h and may be a useful replacement for the disc diffusion method.

Miniaturised broth microdilution for simplified antibiotic susceptibility testing of Gram negative clinical isolates using microcapillary devices

Miniaturised antibiotic susceptibility testing: 100 times smaller microcapillary broth microdilution gives equivalent result to standard microplate broth microdilution.

Antibiotic susceptibility test under a linear concentration gradient using travelling surface acoustic waves

An efficient and accurate antibiotic susceptibility test (AST) is indispensable for measuring the antimicrobial resistance of pathogenic bacteria. A minimal inhibitory concentration (MIC) can be obtained without performing repeated dilutions of the antibiotic by forming a linear antibiotic concentration gradient in a microfluidic channel. We demonstrated a device designed to use travelling surface acoustic waves (TSAWs) to enable a rapid formation of an antibiotic gradient in a few seconds. The TSAWs produced by a focused interdigital transducer deposited on the surface of a piezoelectric (LiNbO₃) substrate generated an acoustic streaming flow inside a microfluidic channel, which mixed confluent streams of antibiotics in a controlled fashion. The growth of bacteria exposed to the antibiotic gradient was determined by measuring the MIC, which was used as an indicator of the effectiveness of the AST. The concentration gradient produced using our device was linear, a feature that enhanced the reliability of measurements throughout the microchannel. Two ASTs, namely Pseudomonas aeruginosa against gentamicin and levofloxacin were chosen for the case of slowly proliferating bacteria, and one AST, namely Escherichia coli against gentamicin, were chosen for the rapidly proliferating case. Appropriate antibiotic doses for Pseudomonas aeruginosa and Escherichia coli were each obtained in an efficient manner.

On the Wireless Microwave Sensing of Bacterial Membrane Potential in Microfluidic-Actuated Platforms

The investigation of the electromagnetic properties of biological particles in microfluidic platforms may enable microwave wireless monitoring and interaction with the functional activity of microorganisms. Of high relevance are the action and membrane potentials as they are some of the most important parameters of living cells. In particular, the complex mechanisms of a cell’s action potential are comparable to the dynamics of bacterial membranes, and consequently focusing on the latter provides a simplified framework for advancing the current techniques and knowledge of general bacterial dynamics. In this work, we provide a theoretical analysis and experimental results on the microwave detection of microorganisms within a microfluidic-based platform for sensing the membrane potential of bacteria. The results further advance the state of microwave bacteria sensing and microfluidic control and their implications for measuring and interacting with cells and their membrane potentials, which is of great importance for developing new biotechnologically engineered systems and solutions.

Rapid Methods for Antimicrobial Resistance Diagnostics

Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.

3D microfluidic gradient generator for combination antimicrobial susceptibility testing

Microfluidic concentration gradient generators (µ-CGGs) have been utilized to identify optimal drug compositions through antimicrobial susceptibility testing (AST) for the treatment of antimicrobial-resistant (AMR) infections. Conventional µ-CGGs fabricated via photolithography-based micromachining processes, however, are fundamentally limited to two-dimensional fluidic routing, such that only two distinct antimicrobial drugs can be tested at once. This work addresses this limitation by employing Multijet-3D-printed microchannel networks capable of fluidic routing in three dimensions to generate symmetric multidrug concentration gradients. The three-fluid gradient generation characteristics of the fabricated 3D µ-CGG prototype were quantified through both theoretical simulations and experimental validations. Furthermore, the antimicrobial effects of three highly clinically relevant antibiotic drugs, tetracycline, ciprofloxacin, and amikacin, were evaluated via experimental single-antibiotic minimum inhibitory concentration (MIC) and pairwise and three-way antibiotic combination drug screening (CDS) studies against model antibiotic-resistant Escherichia coli bacteria. As such, this 3D µ-CGG platform has great potential to enable expedited combination AST screening for various biomedical and diagnostic applications.

Bacterial Isolation Microwell-Plug (μWELLplug) for Rapid Antibiotic Susceptibility Testing Using Morphology Analysis

The rapid and accurate diagnosis of infectious diseases with high morbidity rates is crucial because it can minimize the misuse and overuse of antibiotics and increase survival rates in dreadful conditions. The conventional antibiotic susceptibility test (AST) systems used to choose appropriate antibiotics require long wait times to obtain results and cannot prevent the misuse or overuse of antibiotics by clinicians who need to quickly treat patients and cannot wait to identify the underlying cause of their symptoms. Therefore, several rapid AST (rAST) methods have been developed to provide quick test results, but they are complicated to operate, require additional equipment or materials, and give less accurate results than the conventional AST methods. In this study, we propose an rAST method that can obtain precise outcomes from a simple process with a short running time using a bacterial isolation microwell-plug (μWELLplug) in a conventional 96-well plate. The specifically designed hydrogel component of the μWELLplug provides a simple process for cell isolation and the observation of bacterial growth and morphological changes induced by a variety of antibiotic concentrations. The μWELLplug is placed over each well of the 96-well plate, and then bacterial or eukaryotic cells are isolated in the microwells and treated with different antibiotic concentrations to observe their effects. Saccharomyces cerevisiae (yeast, eukaryote), Streptomyces atratus (actinomycetes, prokaryote), Escherichia coli, Staphylococcus aureus, and methicillin-resistant S. aureus were cultivated and tested using the μWELLplug. The minimum inhibitory concentration values from this system were obtained in 3-4 h and correlated well with those from the conventional AST methods whose running time is 18-24 h.

Current state of the art in rapid diagnostics for antimicrobial resistance

Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.

Capillary-Driven Flow Microfluidics Combined with Smartphone Detection: An Emerging Tool for Point-of-Care Diagnostics

Point-of-care (POC) or near-patient testing allows clinicians to accurately achieve real-time diagnostic results performed at or near to the patient site. The outlook of POC devices is to provide quicker analyses that can lead to well-informed clinical decisions and hence improve the health of patients at the point-of-need. Microfluidics plays an important role in the development of POC devices. However, requirements of handling expertise, pumping systems and complex fluidic controls make the technology unaffordable to the current healthcare systems in the world. In recent years, capillary-driven flow microfluidics has emerged as an attractive microfluidic-based technology to overcome these limitations by offering robust, cost-effective and simple-to-operate devices. The internal wall of the microchannels can be pre-coated with reagents, and by merely dipping the device into the patient sample, the sample can be loaded into the microchannel driven by capillary forces and can be detected via handheld or smartphone-based detectors. The capabilities of capillary-driven flow devices have not been fully exploited in developing POC diagnostics, especially for antimicrobial resistance studies in clinical settings. The purpose of this review is to open up this field of microfluidics to the ever-expanding microfluidic-based scientific community.

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance

Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.

Bacteria encapsulation and rapid antibiotic susceptibility test using a microfluidic microwell device integrating surface-enhanced Raman scattering

The antibiotic susceptibility test (AST) is a general laboratory procedure for bacterial identification and characterization and can be utilized to determine effective antimicrobials for individual patients. Due to the low bacterial concentration, conventional AST usually requires a prolonged bacterial culture time and a labor-intensive sample pretreatment process. Therefore, it cannot perform timely diagnosis or treatment, which results in a high mortality rate for seriously infected patients. To address this problem, we developed a microfluidic microwell device integrating surface-enhanced Raman scattering (SERS) technology, or the so called the Microwell-SERS system, to enable a rapid and high-throughput AST. Our results show that the Microwell-SERS system can successfully encapsulate bacteria in a miniaturized microwell with a greatly increased effective bacteria concentration, resulting in a shorter bacterial culture time. By attaching a microchannel onto the microwell, a smooth liquid and air exchange can purify the surrounding buffer and isolate bacteria in an individual microwell for independent SERS measurement. For proof-of-concept, we demonstrated a 2 h AST on susceptible and resistant E. coli and S. aureus with a concentration of 103 CFU mL-1 in the Microwell-SERS system, whereas the previous SERS-AST method required 108 CFU mL-1 bacterial suspension droplets dispensing on a SERS substrate. Based on the above features, we envision that the Microwell-SERS system could achieve highly sensitive, label-free, bacteria detection and rapid AST to enable timely and accurate bacterial infection disease diagnosis.

Identification and Antimicrobial Susceptibility Testing of Campylobacter Using a Microfluidic Lab-on-a-Chip Device

Campylobacter spp. have been recognized as major foodborne pathogens worldwide. An increasing frequency of antibiotic-resistant pathogens, including Campylobacter spp., have been identified to transmit from food products to humans and cause severe threats to public health. To better mitigate the antibiotic resistance crisis, rapid detection methods are required to provide timely antimicrobial resistance surveillance data for agri-food systems. Herein, we developed a polymer-based microfluidic device for the identification and antimicrobial susceptibility testing (AST) of Campylobacter spp. An array of bacterial incubation chambers were created in the microfluidic device, where chromogenic medium and antibiotics were loaded. The growth of Campylobacter spp. was visualized by color change due to chromogenic reactions. This platform achieved 100% specificity for Campylobacter identification. Sensitive detection of multiple Campylobacter species (C. jejuni, C. coli, and C. lari) was obtained in artificially contaminated milk and poultry meat, with detection limits down to 1 × 102 CFU/ml and 1 × 104 CFU/25 g, respectively. On-chip AST determined Campylobacter antibiotic susceptibilities by the lowest concentration of antibiotics that can inhibit bacterial growth (i.e., no color change observed). High coincidences (91% to 100%) of on-chip AST and the conventional agar dilution method were achieved against several clinically important antibiotics. For a presumptive colony, on-chip identification and AST were completed in parallel within 24 h, whereas standard methods, including biochemical assays and traditional culture-based AST, take several days for multiple sequential steps. In conclusion, this lab-on-a-chip device can achieve rapid and reliable detection of antibiotic-resistant Campylobacter spp.IMPORTANCE Increasing concerns of antibiotic-resistant Campylobacter spp. with regard to public health emphasize the importance of efficient and fast detection. This study described the timely identification and antimicrobial susceptibility testing of Campylobacter spp. by using a microfluidic device. Our developed method not only reduced the total analysis time, but it also simplified food sample preparation and chip operation for end users. Due to the miniaturized size of the lab-on-a-chip platform, the detection was achieved by using up to 1,000 times less of the reagents than with standard reference methods, making it a competitive approach for rapid screening and surveillance study in food industries. In addition, multiple clinically important Campylobacter species (C. jejuni, C. coli, and C. lari) could be tested by our device. This device has potential for wide application in food safety management and clinical diagnostics, especially in resource-limited regions.

Development of a rapid phenotypic test on a microfluidic device for carbapenemase detection using the chromogenic compound nitrocefin

Routine identification of carbapenemase-producing bacterial isolates is a lengthy process often taking up to 72 h to generate results with standard culture-based tests. Here we describe a rapid test based on the hydrolysis of nitrocefin to identify isolates producing β-lactamase enzymes. A cocktail of inhibitors has been optimized in the reaction mix to provide specificity for carbapenemase enzymes. The developed assay has also been translated to a microfluidic platform with an optical readout (optofluidic chip). The chip has a long absorbance path (25 mm) to provide high sensitivity. A sample-to-answer has been achieved in under 30 min on these chips using colonies from culture plates. The test on this platform has the potential to provide a rapid indicative (presumptive positive) test for carbapenemase producers direct from bacteria isolated from patient samples, to rapidly trigger infection control measures and identify samples that should be prioritized for more specialized carbapenemase diagnostic assays.

Direct antibiotic susceptibility testing of blood cultures of gram-negative bacilli using the Drug Susceptibility Testing Microfluidic (DSTM) device

Proper treatment of bloodstream infections requires rapid, early determination of appropriate antibiotic agents, emphasizing the need for more rapid drug susceptibility testing. The Drug Susceptibility Testing Microfluidic (DSTM) device represents a novel method in which a small amount of bacterial suspension is injected into the microchip-like device and cultured for 3 h. However, it remains unknown whether the DSTM method can directly determine antibiotic susceptibilities from positive blood cultures. Here, we developed a new approach to directly assess drug susceptibility, using the DSTM method for positive blood cultures. We compare the utility and accuracy of DSTM with those of conventional susceptibility testing methods. Fifty positive blood cultures identified as gram-negative bacilli were used herein. The outcomes of drug susceptibility and resistance assays for positive blood cultures were compared to those of conventional susceptibility testing methods to evaluate their utility and accuracy. Method agreement rates between DSTM and standard methods often exceed 90%, suggesting a high positive correlation with conventional methods. Furthermore, our results show that a combination of multiple drugs in the DSTM device helps identify extended-spectrum β-lactamase (ESBL)- and AmpC-β-lactamase (AmpC-)-producing microorganisms. In conclusion, DSTM method enables effective drug susceptibility and resistance screening within 3 h from positive blood cultures and is suitable for the rapid and personalized determination of the antimicrobial regimen.

Chitosan Films for Microfluidic Studies of Single Bacteria and Perspectives for Antibiotic Susceptibility Testing

Current microfluidic techniques are powerful to study bacteria and determine their response to antibiotic treatment, but they are currently limited by their complex manipulation. Chitosan films are fully biocompatible and could thus be a viable replacement for existing commercial devices that currently use polylysine. Thus, the low cost of chitosan slides and their simple implementation make them highly versatile for research as well as clinical use.

Single-cell microfluidics is a powerful method to study bacteria and determine their susceptibility to antibiotic treatment. Glass treatment by adhesive molecules is a potential solution to immobilize bacterial cells and perform microscopy, but traditional cationic polymers such as polylysine deeply affect bacterial physiology. In this work, we chemically characterized a class of chitosan polymers for their biocompatibility when adsorbed to glass. Chitosan chains of known length and composition allowed growth of Escherichia coli cells without any deleterious effects on cell physiology. Combined with a machine learning approach, this method could measure the antibiotic susceptibility of a diversity of clinical strains in less than 1 h and with higher accuracy than current methods. Finally, chitosan polymers also supported growth of Klebsiella pneumoniae, another bacterial pathogen of clinical significance.

Antibiotic Susceptibility Test with Surface-Enhanced Raman Scattering in a Microfluidic System

Antibiotic susceptibility test (AST) is essential in clinical diagnosis of serious bacterial infection, such as sepsis, while it typically takes 2-5 days for sample culture, antibiotic treatment, and reading result. Detecting metabolites secreted from bacteria with surface-enhanced Raman scattering (SERS) enables rapid determination of antibiotic susceptibility, reducing the AST time to 1-2 days. However, it still requires 1 day of culture time to obtain sufficient quantity of bacteria for sample washing, bacterial extraction, and antibiotic treatment. Additionally, the whole procedure, manually performed in open environment, often suffers from contamination and human error. To address the above problems, a microfluidic system integrating membrane filtration and the SERS-active substrate (MF-SERS) was developed to perform on-chip bacterial enrichment, metabolite collection, and in situ SERS measurements for antibiotic susceptibility test. Using Escherichia coli as the prototype bacterium, the lowest SERS detection limit of bacterial concentration of the MF-SERS system is 10³ CFU/mL, which is 4 orders of magnitude lower than that using centrifugation-purification procedure, significantly shortening the bacterial culture time. The bacteria and secreted metabolites are enclosed during bacterial trapping, metabolite filtration, and SERS detection, thus minimizing possible contamination and human errors. Finally, the successful demonstration of AST on E. coli with a concentration of 10³ CFU/mL is presented. Overall, the MF-SERS system with a miniature size and well-confined microenvironment allows the integration of multiple bacteria processes for bacterial enrichment, culture, and determination of AST.

Toward point-of-care assessment of patient response: a portable tool for rapidly assessing cancer drug efficacy using multifrequency impedance cytometry and supervised machine learning

We present a novel method to rapidly assess drug efficacy in targeted cancer therapy, where antineoplastic agents are conjugated to antibodies targeting surface markers on tumor cells. We have fabricated and characterized a device capable of rapidly assessing tumor cell sensitivity to drugs using multifrequency impedance spectroscopy in combination with supervised machine learning for enhanced classification accuracy. Currently commercially available devices for the automated analysis of cell viability are based on staining, which fundamentally limits the subsequent characterization of these cells as well as downstream molecular analysis. Our approach requires as little as 20 μL of volume and avoids staining allowing for further downstream molecular analysis. To the best of our knowledge, this manuscript presents the first comprehensive attempt to using high-dimensional data and supervised machine learning, particularly phase change spectra obtained from multi-frequency impedance cytometry as features for the support vector machine classifier, to assess viability of cells without staining or labelling.

Advancing Infectious Diseases Diagnostic Testing and Applications to Antimicrobial Therapy in the ICU

Treatment of suspected infections in critically ill patients requires the timely initiation of appropriate antimicrobials and rapid de-escalation of unnecessary broad-spectrum coverage. New advances in rapid diagnostic tests can now offer earlier detection of pathogen and potential resistance mechanisms within hours of initial culture growth. These technologies, combined with pharmacist antimicrobial stewardship efforts, may result in shorten time to adequate coverage or earlier de-escalation of unnecessary broad spectrum antimicrobials, which could improve patient outcomes and lower overall treatment cost. Furthermore, de-escalation of antimicrobials may lead to decreased emergence of resistant organisms and adverse events associated with antimicrobials. Clinical pharmacists should be aware of new rapid diagnostic tests, including their application, clinical evidence, and limitations, in order to implement the most appropriate clinical treatment strategy when patients have positive cultures. This review will focus on commercially available rapid diagnostic tests for infections that are routinely encountered by critically ill patients, including gram-positive and gram-negative bacterial blood stream infections, Candida, and Clostridioides difficile.

Progress in antibiotic susceptibility tests: a comparative review with special emphasis on microfluidic methods

Antibiotic susceptibility test (AST) is an umbrella term for techniques to determine the susceptibility of bacteria to antibiotics. The antibiotic-resistant bacteria are a major threat to public health and a directed therapy based on accurate AST results is paramount in resistance control. Here we have briefly covered the progress of conventional, molecular, and automated AST tools and their limitations. Various aspects of microfluidic AST such as optical, electrochemical, colorimetric, and mechanical methods have been critically reviewed. We also address the future requirements of the microfluidic devices for AST. Cumulatively, we have outlined the overview of AST that can help to expand and improve the existing techniques and emphasize that microfluidics could be the future of AST and introduction of microtechnologies in AST will be extremely advantageous, especially for point-of-care testing.

Sensitive, Real-time and Non-Intrusive Detection of Concentration and Growth of Pathogenic Bacteria using Microfluidic-Microwave Ring Resonator Biosensor

Infection diagnosis and antibiotic susceptibility testing (AST) are time-consuming and often laborious clinical practices. This paper presents a microwave-microfluidic biosensor for rapid, contactless and non-invasive device for testing the concentration and growth of Escherichia Coli (E. Coli) in medium solutions of different pH to increase the efficacy of clinical microbiology practices. The thin layer interface between the microfluidic channel and the microwave resonator significantly enhanced the detection sensitivity. The microfluidic chip, fabricated using standard soft lithography, was injected with bacterial samples and incorporated with a microwave microstrip ring resonator sensor with an operation frequency of 2.5 GHz and initial quality factor of 83 for detecting the concentration and growth of bacteria. The resonator had a coupling gap area on of 1.5 × 1.5 mm² as of its sensitive region. The presence of different concentrations of bacteria in different pH solutions were detected via screening the changes in resonant amplitude and frequency responses of the microwave system. The sensor device demonstrated near immediate response to changes in the concentration of bacteria and maximum sensitivity of 3.4 MHz compared to a logarithm value of bacteria concentration. The minimum prepared optical transparency of bacteria was tested at an OD₆₀₀ value of 0.003. The sensor’s resonant frequency and amplitude parameters were utilized to monitor bacteria growth during a 500-minute time frame, which demonstrated a stable response with respect to detecting the bacterial proliferation. A highly linear response was demonstrated for detecting bacteria concentration at various pH values. The growth of bacteria analyzed over the resonator showed an exponential growth curve with respect to time and concurred with the lag-log-stationary-death model of cell growth. This biosensor is one step forward to automate the complex AST workflow of clinical microbiology laboratories for rapid and automated detection of bacteria as well as screening the bacteria proliferation in response to antibiotics.

Rapid Phenotypic Antibiotic Susceptibility Testing of Uropathogens Using Optical Signal Analysis on the Nanowell Slide

Achieving fast antimicrobial susceptibility results is a primary goal in the fight against antimicrobial resistance. Standard antibiotic susceptibility testing (AST) takes, however, at least a day from patient sample to susceptibility profile. Here, we developed and clinically validated a rapid phenotypic AST based on a miniaturized nanotiter plate, the nanowell slide, that holds 672 wells in a 500 nl format for bacterial cultivation. The multitude of nanowells allows multiplexing with a panel of six antibiotics relevant for urinary tract infections. Inclusion of seven concentrations per antibiotic plus technical replicates enabled us to determine a precise minimum inhibitory concentration for 70 clinical uropathogenic Escherichia coli isolates. By combining optical recordings of bacterial growth with an algorithm for optical signal analysis, we calculated T_lag, the point of transition from lag to exponential phase, in each nanoculture. Algorithm-assisted analysis determined antibiotic susceptibility as early as 3 h 40 min. In comparison to standard disk diffusion assays, the nanowell AST showed a total categorical agreement of 97.9% with 2.6% major errors and 0% very major errors for all isolate-antibiotic combination tested. Taking advantage of the optical compatibility of the nanowell slide, we performed microscopy to illustrate its potential in defining susceptibility profiles based on bacterial morphotyping. The excellent clinical performance of the nanowell AST, combined with a short detection time, morphotyping, and the very low consumption of reagents clearly show the advantage of this phenotypic AST as a diagnostic tool in a clinical setting.

Microfluidic detection of movements of Escherichia coli for rapid antibiotic susceptibility testing

Various nanomechanical movements of bacteria provide a signature of bacterial viability. Most notably, bacterial movements have been observed to subside rapidly and dramatically when the bacteria are exposed to effective antibiotics. Thus, monitoring bacterial movements, if performed with high fidelity, could offer a path to various clinical microbiological applications, including antibiotic susceptibility tests. Here, we introduce a robust and ultrasensitive electrical transduction technique for detecting the nanomechanical movements of bacteria. The technique is based on measuring the electrical fluctuations in a microfluidic channel, which the bacteria populate. The swimming of planktonic bacteria and the random oscillations of surface-immobilized bacteria both cause small but detectable electrical fluctuations. We show that this technique provides enough sensitivity to detect even the slightest movements of a single cell; we also demonstrate an antibiotic susceptibility test in a biological matrix. Given that it lends itself to smooth integration with other microfluidic methods and devices, the technique can be developed into a functional antibiotic susceptibility test, in particular, for urinary tract infections.

Drug screening of cancer cell lines and human primary tumors using droplet microfluidics

Precision Medicine in Oncology requires tailoring of therapeutic strategies to individual cancer patients. Due to the limited quantity of tumor samples, this proves to be difficult, especially for early stage cancer patients whose tumors are small. In this study, we exploited a 2.4 × 2.4 centimeters polydimethylsiloxane (PDMS) based microfluidic chip which employed droplet microfluidics to conduct drug screens against suspended and adherent cancer cell lines, as well as cells dissociated from primary tumor of human patients. Single cells were dispersed in aqueous droplets and imaged within 24 hours of drug treatment to assess cell viability by ethidium homodimer 1 staining. Our results showed that 5 conditions could be screened for every 80,000 cells in one channel on our chip under current circumstances. Additionally, screening conditions have been adapted to both suspended and adherent cancer cells, giving versatility to potentially all types of cancers. Hence, this study provides a powerful tool for rapid, low-input drug screening of primary cancers within 24 hours after tumor resection from cancer patients. This paves the way for further technological advancement to cutting down sample size and increasing drug screening throughput in advent to personalized cancer therapy.

Rapid antibiotic sensitivity testing in microwell arrays

The widespread bacterial resistance to a broad range of antibiotics necessitates rapid antibiotic susceptibility testing before effective treatment could start in the clinic. Among resistant bacteria, Staphylococcus aureus is one of the most important, and Methicillin-resistant (MRSA) strains are a common cause of life threatening infections. However, standard susceptibility testing for S. aureus is time consuming and thus the start of effective antibiotic treatment is often delayed. To circumvent the limitations of current susceptibility testing systems, we designed an assay that enables measurements of bacterial growth with higher spatial and temporal resolution than standard techniques. The assay consists of arrays of microwells that confine small number of bacteria in small spaces, where their growth is monitored with high precision. These devices enabled us to investigate the effect of different antibiotics on S. aureus growth. We measured the Minimal Inhibitory Concentration (MIC) in less than 3 hours. In addition to being significantly faster than the 48 hours needed for traditional microbiological methods, the assay is also capable of differentiating the specific effects of different antibiotic classes on S. aureus growth. Overall, this assay has the potential to become a rapid, sensitive, and robust tool for use in hospitals and laboratories to assess antibiotic sensitivity.

Advances in Rapid Identification and Susceptibility Testing of Bacteria in the Clinical Microbiology Laboratory: Implications for Patient Care and Antimicrobial Stewardship Programs

Early availability of information on bacterial pathogens and their antimicrobial susceptibility is of key importance for the management of infectious diseases patients. Currently, using traditional approaches, it usually takes at least 48 hours for identification and susceptibility testing of bacterial pathogens. Therefore, the slowness of diagnostic procedures drives prolongation of empiric, potentially inappropriate, antibacterial therapies. Over the last couple of years, the improvement of available techniques (e.g. for susceptibility testing, DNA amplification assays), and introduction of novel technologies (e.g. MALDI-TOF) has fundamentally changed approaches towards pathogen identification and characterization. Importantly, these techniques offer increased diagnostic resolution while at the same time shorten the time-to-result, and are thus of obvious importance for antimicrobial stewardship. In this review, we will discuss recent advances in medical microbiology with special emphasis on the impact of novel techniques on antimicrobial stewardship programs.

[Advances in diagnostic microbiology : Opportunities and limitations]

In the light of ever increasing problems related to the emergence of multidrug-resistant bacteria, rapid microbiological diagnostics are of growing importance. Timely pathogen detection and availability of susceptibility data are essential for optimal treatment, but are even more crucial for de-escalation of broad spectrum empiric therapies. Medical microbiology is, thus, an integral part of antimicrobial stewardship programs. Traditional microbiological techniques for species identification and susceptibility testing rely on bacterial growth and are, thus, characterized by inherent slowness. Time-to-report is usually 48 h or longer, and typically delays optimization of therapeutic regimens. Constant improvement of available techniques (e. g., molecular methods) and introduction of novel methods (e. g., matrix-assisted laser desorption ionization time-of-flight [MALDI-ToF] mass spectrometry) have fundamentally changed diagnostic procedures. As a consequence, sensitivity and specificity as well as time-to-report have been dramatically improved. In this manuscript, key methodological advances in medical microbiology are discussed, emphasizing consequences for daily management of infectious disease patients.

Microfluidics: innovative approaches for rapid diagnosis of antibiotic-resistant bacteria

The emergence of antibiotic-resistant bacteria has become a major global health concern. Rapid and accurate diagnostic strategies to determine the antibiotic susceptibility profile prior to antibiotic prescription and treatment are critical to control drug resistance. The standard diagnostic procedures for the detection of antibiotic-resistant bacteria, which rely mostly on phenotypic characterization, are time consuming, insensitive and often require skilled personnel, making them unsuitable for point-of-care (POC) diagnosis. Various molecular techniques have therefore been implemented to help speed up the process and increase sensitivity. Over the past decade, microfluidic technology has gained great momentum in medical diagnosis as a series of fluid handling steps in a laboratory can be simplified and miniaturized on to a small platform, allowing marked reduction of sample amount, high portability and tremendous possibility for integration with other detection technologies. These advantages render the microfluidic system a great candidate to be developed into an easy-to-use sample-to-answer POC diagnosis suitable for application in remote clinical settings. This review provides an overview of the current development of microfluidic technologies for the nucleic acid based and phenotypic-based detections of antibiotic resistance.

Microfluidic advances in phenotypic antibiotic susceptibility testing

A strong natural selection for microbial antibiotic resistance has resulted from the extensive use and misuse of antibiotics. Though multiple factors are responsible for this crisis, the most significant factor - widespread prescription of broad-spectrum antibiotics - is largely driven by the fact that the standard process for determining antibiotic susceptibility includes a 1-2-day culture period, resulting in 48-72 h from patient sample to final determination. Clearly, disruptive approaches, rather than small incremental gains, are needed to address this issue. The field of microfluidics promises several advantages over existing macro-scale methods, including: faster assays, increased multiplexing, smaller volumes, increased portability for potential point-of-care use, higher sensitivity, and rapid detection methods. This Perspective will cover the advances made in the field of microfluidic, phenotypic antibiotic susceptibility testing (AST) over the past two years. Sections are organized based on the functionality of the chip - from simple microscopy platforms, to gradient generators, to antibody-based capture devices. Microfluidic AST methods that monitor growth as well as those that are not based on growth are presented. Finally, we will give our perspective on the major hurdles still facing the field, including the need for rapid sample preparation and affordable detection technologies.

Microfluidics for Antibiotic Susceptibility and Toxicity Testing

The recent emergence of antimicrobial resistance has become a major concern for worldwide policy makers as very few new antibiotics have been developed in the last twenty-five years. To prevent the death of millions of people worldwide, there is an urgent need for a cheap, fast and accurate set of tools and techniques that can help to discover and develop new antimicrobial drugs. In the past decade, microfluidic platforms have emerged as potential systems for conducting pharmacological studies. Recent studies have demonstrated that microfluidic platforms can perform rapid antibiotic susceptibility tests to evaluate antimicrobial drugs’ efficacy. In addition, the development of cell-on-a-chip and organ-on-a-chip platforms have enabled the early drug testing, providing more accurate insights into conventional cell cultures on the drug pharmacokinetics and toxicity, at the early and cheaper stage of drug development, i.e., prior to animal and human testing. In this review, we focus on the recent developments of microfluidic platforms for rapid antibiotics susceptibility testing, investigating bacterial persistence and non-growing but metabolically active (NGMA) bacteria, evaluating antibiotic effectiveness on biofilms and combinatorial effect of antibiotics, as well as microfluidic platforms that can be used for in vitro antibiotic toxicity testing.