Multifunctional Paper-Based Analytical Device for In Situ Cultivation and Screening of Escherichia coli Infections

Microfluidic systems for infectious disease diagnostics

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.

The use of biological fluids in microfluidic paper-based analytical devices (μPADs): Recent advances, challenges and future perspectives

The use of microfluidic paper-based analytical devices (μPADs) for aiding medical diagnosis is a growing trend in the literature mainly due to their low cost, easy use, simple manufacturing, and great potential for application in low-resource settings. Many important biomarkers (proteins, ions, lipids, hormones, DNA, RNA, drugs, whole cells, and more) and biofluids are available for precise detection and diagnosis. We have reviewed the advances μPADs in medical diagnostics have achieved in the last few years, focusing on the most common human biofluids (whole blood/plasma, sweat, urine, tears, and saliva). The challenges of detecting specific biomarkers in each sample are discussed, along with innovative techniques that overcome such limitations. Finally, the difficulties of commercializing μPADs are considered, and future trends are presented, including wearable devices and integrating multiple steps in a single platform.

Gold Nanomaterial-Based Microfluidic Paper Analytical Device for Simultaneous Quantification of Gram-Negative Bacteria and Nitrite Ions in Water Samples

This study presents a rapid microfluidic paper-based analytical device (μPAD) capable of simultaneously monitoring Gram-negative bacteria and nitrite ions (NO2-) for water quality monitoring. We utilize gold nanoparticles (AuNPs) functionalized with polymyxin molecules (AuNPs@polymyxin) to cause color change due to aggregation for the detection of Gram-negative bacteria, and antiaggregation in the presence of o-phenylenediamine (OPD) for NO2- detection. In this study, Escherichia coli (E. coli) serves as the model of a Gram-negative bacterium. Using the developed μPADs, the color changes resulting from aggregation and antiaggregation reactions are measured using a smartphone application. The linear detection ranges from 5.0 × 102 to 5.0 × 105 CFU/mL (R2 = 0.9961) for E. coli and 0.20 to 2.0 μmol/L (R2 = 0.995) for NO2-. The detection limits were determined as 2.0 × 102 CFU/mL for E. coli and 0.18 μmol/L for NO2-. Notably, the newly developed assay exhibited high selectivity with no interference from Gram-positive bacteria. Additionally, we obtained acceptable recovery for monitoring E. coli and NO2- in drinking water samples with no significant difference between our method and a commercial assay by t test validation. The sensor was also employed for assessing the quality of the pond and environmental water source. Notably, this approach can also be applied to human urine samples with satisfactory accuracy. Furthermore, the assay's stability is extended due to its reliance on AuNPs rather than reagents like antibodies and enzymes, reducing costs and ensuring long-term viability. Our cost-effective μPADs therefore provide a real-time analysis of both contaminants, making them suitable for assessing water quality in resource-limited settings.

Review of paper-based microfluidic analytical devices for in-field testing of pathogens

Pathogens cause various infectious diseases and high morbidity and mortality which is a global public health threat. The highly sensitive and specific detection is of significant importance for the effective treatment and intervention to minimise the impact. However, conventional detection methods including culture and molecular method gravely depend on expensive equipment and well-trained skilled personnel, limiting in the laboratory. It remains challenging to adapt in resource-limiting areas, e.g., low and middle-income countries (LMICs). To this end, low-cost, rapid, and sensitive detection tools with the capability of field testing e.g., a portable device for identification and quantification of pathogens, has attracted increasing attentions. Recently, paper-based microfluidic analytical devices (μPADs) have shown a promising tool for rapid and on-site diagnosis, providing a cost-effective and sensitive analytical approach for pathogens detection. The fast turn-round data collection may also contribute to better understanding of the risks and insights on mitigation method. In this paper, critical developments of μPADs for in-field detection of pathogens both for clinical diagnostics and environmental surveillance are reviewed. The future development, and challenges of μPADs for rapid and onsite detection of pathogens are discussed, including using the cross-disciplinary development with, emerging techniques such as deep learning and Internet of Things (IoT).

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.

Detection of Oxacillin/Cefoxitin Resistance in Staphylococcus aureus Present in Recurrent Tonsillitis

Background: Recurrent tonsillitis is one of the most common diseases in childhood, caused many times by ß-lactam-resistant S. aureus. The objective of this study was to investigate an alternative method to identify resistance to oxacillin/cefoxitin in S. aureus from hospitalized children with recurrent tonsillitis. Methods: The samples of S. aureus came from patients with recurrent tonsillitis and were used in 16S rRNA sequencing and an antibiogram test for identification and verifying resistance, after which HSI methodology were applied for separation of S. aureus resistances. Results: The S. aureus isolated showed sensitivity to oxacillin/cefoxitin and the diagnostic images show a visual description of the resistance different groups formed, that may be related to sensitivity and resistance to oxacillin/cefoxitin, characterizing the MRSA S. aureus. Conclusions: Samples that showed phenotypic resistance to oxacillin/cefoxitin were clearly separated from samples that did not show this resistance. A PLS-DA model predicted the presence of resistance to oxacillin/cefoxitin in S. aureus samples and it was possible to observe the pixels classified as MRSA. The HSI was able to successfully discriminate samples in replicas that were sensitive and resistant, based on the calibration model it received.

Paper-based sensors for bacteria detection

The detection of pathogenic bacteria is essential to prevent and treat infections and to provide food security. Current gold-standard detection techniques, such as culture-based assays and polymerase chain reaction, are time-consuming and require centralized laboratories. Therefore, efforts have focused on developing point-of-care devices that are fast, cheap, portable and do not require specialized training. Paper-based analytical devices meet these criteria and are particularly suitable to deployment in low-resource settings. In this Review, we highlight paper-based analytical devices with substantial point-of-care applicability for bacteria detection and discuss challenges and opportunities for future development.

Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter

The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.

Emerging Bioanalytical Devices and Platforms for Rapid Detection of Pathogens in Environmental Samples

The development of robust bioanalytical devices and biosensors for infectious pathogens is progressing well with the advent of new materials, concepts, and technology. The progress is also stepping towards developing high throughput screening technologies that can quickly identify, differentiate, and determine the concentration of harmful pathogens, facilitating the decision-making process for their elimination and therapeutic interventions in large-scale operations. Recently, much effort has been focused on upgrading these analytical devices to an intelligent technological platform by integrating them with modern communication systems, such as the internet of things (IoT) and machine learning (ML), to expand their application horizon. This review outlines the recent development and applications of bioanalytical devices and biosensors to detect pathogenic microbes in environmental samples. First, the nature of the recent outbreaks of pathogenic microbes such as foodborne, waterborne, and airborne pathogens and microbial toxins are discussed to understand the severity of the problems. Next, the discussion focuses on the detection systems chronologically, starting with the conventional methods, advanced techniques, and emerging technologies, such as biosensors and other portable devices and detection platforms for pathogens. Finally, the progress on multiplex assays, wearable devices, and integration of smartphone technologies to facilitate pathogen detection systems for wider applications are highlighted.

A review on urinary tract infections diagnostic methods: Laboratory-based and point-of-care approaches

Urinary tract infections (UTIs) are among the most common infectious diseases worldwide. This type of infections can be healthcare-associated or community-acquired and affects millions of people every year. Different diagnostic procedures are available to detect pathogens in urine and they can be divided into two main categories: laboratory-based and point-of-care (POC) detection techniques. Traditional methodologies are often time-consuming, thus, achieving a rapid and accurate identification of pathogens is a challenging feature that has been pursued by many research groups and companies operating in this area. The purpose of this review is to compare and highlight advantages and disadvantages of the traditional and currently most used detection methods, as well as the emerging POC approaches and the relevant advances in on-site detection of pathogens´ mechanisms, suitable to be adapted to UTI diagnosis. Lately, the commercially available UTI self-testing kits and devices are helping in the diagnosis of urinary infections as patients or care givers are able to perform the test, easily and comfortably at home and, upon the result, decide when to attend an appointment/Urgent Health Care Unit.

Paper and thread as media for the frugal detection of urinary tract infections (UTIs)

Urinary tract infections (UTIs) make up a significant proportion of the global burden of disease in vulnerable groups and tend to substantially impair the quality of life of those affected, making timely detection of UTIs a priority for public health. However, economic and societal barriers drastically reduce accessibility of traditional lab-based testing methods for critical patient groups in low-resource areas, negatively affecting their overall healthcare outcomes. As a result, cellulose-based materials such as paper and thread have garnered significant interest among researchers as substrates for so-called frugal analytical devices which leverage the material's portability and adaptability for facile and reproducible diagnoses of UTIs. Although the field may be only in its infancy, strategies aimed at commercial penetration can appreciably increase access to more healthcare options for at-risk people. In this review, we catalogue recent advances in devices that use cellulose-based materials as the primary housing or medium for UTI detection and chart out trends in the field. We also explore different modalities employed for detection, with particular emphasis on their ability to be ported onto discreet casings such as sanitary products.

An origami paper-based peptide nucleic acid device coupled with label-free DNAzyme probe hybridization chain reaction for prostate cancer molecular screening test

Prostate cancer associated 3 (PCA3) assay has been used to improve prostate cancer diagnosis and reduce unnecessary biopsies. In this work, we successfully developed a new PCA3 assay on an origami paper-based peptide nucleic acid device (oPAD). The PCA3 oPAD comprises an acrylic cassette and shutter slides to facilitate the molecular reaction and liquid control occurring on the paper surface. To quantify PCA3, a pyrrolidinyl peptide nucleic acid (acpcPNA) was immobilized onto the aldehyde-modified oPAD surface as a selective capture probe. A G-quadruplex (GQD) DNAzyme reporter probe was designed so that the PCA3 gene target binding triggered the hybridization chain reaction of the reporter probe, resulting in the accumulation of the GQD on the oPAD. The peroxidase activity of the GQD-hemin generated a deep green color of the oxidized ABTS substrate. Image analyses were performed in Adobe Photoshop CS6. The proposed oPAD was successfully applied in PCA3 detection ranges of 1-5 μM (r² = 0.982) with a limit of detection of 0.5 μM. Our proposed oPAD was demonstrated to measure PCA3 samples in both urine matrix and human cancer cell lines. The results reveal the great potential of our origami paper-based platform to be an alternative approach for facile, rapid, and low-cost detection of PCA3 in real samples.

Pumpless three-dimensional photo paper-based microfluidic analytical device for automatic detection of thioredoxin-1 using enzyme-linked immunosorbent assay

Microfluidic-based biosensors have been developed for their precise automatic reaction control. However, these biosensors require external devices that are difficult to transport and use. To overcome this disadvantage, our group made an easy-to-use, cheap, and light pumpless three-dimensional photo paper-based microfluidic analytical device (3D-μPAD; weight: 1.5 g). Unlike conventional paper-based microfluidic analytical devices, the 3D-μPAD can be used to control fluid flow in a 3D manner, thus allowing sophisticated multi-step reaction control. This device can control fluid flow speed and direction accurately using only the capillary-driven flow without an external device like a pump. The flow speed is controlled by the width of the microfluidic channel and its surface property. In addition, fluid speed control and 3D-bridge structure enable the control of fluid flow direction. Using these methods, multi-step enzyme-linked immunosorbent assay (ELISA) can be done automatically in sequence by injecting solutions (sample, washing, and enzyme's substrate) at the same time in the 3D-μPAD. All the steps can be performed in 14 min, and data can be analyzed immediately. To test this device, thioredoxin-1 (Trx-1), a biomarker of breast cancer, is used as the target. In the 3D-μPAD, it can detect 0-200 ng/mL of Trx-1, and the prepared 3D-μPAD Trx-1 sensor displays excellent selectivity. Moreover, by analyzing the concentration of Trx-1 in real patients and healthy individuals' blood serum samples using the 3D-μPAD, and comparing results to ELISA, it can be confirmed that the 3D-μPAD is a good tool for cancer diagnosis.

Lab-on-Paper Devices for Diagnosis of Human Diseases Using Urine Samples-A Review

In recent years, microfluidic lab-on-paper devices have emerged as a rapid and low-cost alternative to traditional laboratory tests. Additionally, they were widely considered as a promising solution for point-of-care testing (POCT) at home or regions that lack medical infrastructure and resources. This review describes important advances in microfluidic lab-on-paper diagnostics for human health monitoring and disease diagnosis over the past five years. The review commenced by explaining the choice of paper, fabrication methods, and detection techniques to realize microfluidic lab-on-paper devices. Then, the sample pretreatment procedure used to improve the detection performance of lab-on-paper devices was introduced. Furthermore, an in-depth review of lab-on-paper devices for disease measurement based on an analysis of urine samples was presented. The review concludes with the potential challenges that the future development of commercial microfluidic lab-on-paper platforms for human disease detection would face.

Usability as a guiding principle for the design of paper-based, point-of-care devices - A review

Due to their portability, versatility for supporting multiple assay formats, and potential for resulting in low-cost assays, paper-based analytical devices (PADs) are an increasingly popular format as a platform for the development of point-of-care tests. However, very few PADs have been translated successfully to their intended environments outside of academic settings. Often overlooked as a factor that inhibits translation, usability is a vital characteristic of any successful point-of-care test. Recent advancements in PAD design have demonstrated improved usability by simplifying various aspects of user operation, including sample collection, sample processing, device operation, detection, and readout/interpretation. Field testing at various stages of device design can offer critical feedback about device usability, especially when it involves the proposed end-user or other stakeholders. By highlighting advances in usability, we aim to encourage thoughtful and rigorous design at the academic prototyping stage to address one outstanding hurdle that limits the number of PADs that make it from the benchtop to the point-of-care.

Biomarker discovery and beyond for diagnosis of bladder diseases

Molecular biosignatures of altered cellular landscapes and functions have been casually linked with pathological conditions, which imply the promise of biomarkers specific to bladder diseases, such as bladder cancer and other dysfunctions. Urinary biomarkers are particularly attractive due to costs, time, and the minimal and noninvasive efforts acquiring urine. The evolution of omics platforms and bioinformatics for analyzing the genome, epigenome, transcriptome, proteome, lipidome, metabolome, etc., have enabled us to develop more sensitive and disease-specific biomarkers. These discoveries broaden our understanding of the complex biology and pathophysiology of bladder diseases, which can ultimately be translated into the clinical setting. In this short review, we will discuss current efforts on identification of promising urinary biomarkers of bladder diseases and their roles in diagnosis and monitoring. With these considerations, we also aim to provide a prospective view of how we can further utilize these bladder biomarkers in developing ideal and smart medical devices that would be applied in the clinic.

Paper-Based Analytical Device for Real-Time Monitoring of Egg Hatching in the Model Nematode Caenorhabditis elegans

Caenorhabditis elegans is an in vivo model known for its easy handling and maintenance and lack of associated ethical issues. The release of chitinase can be used to monitor the egg-laying stage in C. elegans. The aim of this study was to develop a simple and cost-effective device to monitor the activity of chitinase in embryos of C. elegans. Colloid chitin azure (CCA), a substrate for chitinase, was preimmobilized on the detection area of paper, forming a purple region, to generate a CCA paper-based analytical device (CCA-PAD). The degradation of CCA by chitinase could be observed as the purple color became faint and the filter paper eventually became colorless. Under the optimum conditions, the proposed device quantified the chitinase enzyme in the range of 15.625-125 mU/mL within 48 h (R² = 0.993). In this work, 10 young adult-staged wild-type C. elegans (Bristol N2) worms were analyzed on the CCA-PAD, which was supplemented with the laboratory food source E. coli OP50 on a gauze layer. The same strain treated with 5-fluoro-2'-deoxyuridine was used to prevent egg production in C. elegans. A significant difference in the color intensity was observed between these two groups at the end of the experiment (P = <0.001, independent t-test, n = 3). We successfully developed a simple and effective method for monitoring chitinase activity. The device may have potential applications in drug-screening studies as it efficiently distinguishes drugs that can impact egg laying.

Preoperative urine nitrite versus urine culture for predicting postoperative fever following flexible ureteroscopic lithotripsy: a propensity score matching analysis

PURPOSE

Multiple studies have reported that preoperative positive urine culture is an independent risk factor for postoperative fever (POF) after ureteroscopy (URS). Urine nitrite is associated urinary tract infections (UTIs). However, none of studies has explored the role of urine nitrite in the prediction of POF after flexible URS (fURS).

METHODS

Patients who underwent fURS by the same surgeon between 2009 and 2019 were screened. Sensitivity and specificity of urine culture and urine nitrite were calculated. Propensity score (PS) matching was performed to get a baseline-balanced retrospective cohort to avoid potential bias. Receiver operating characteristic-area under the curve (ROC-AUC) calculated was used to determine the predictive power of models. Decision curve analysis (DCA) was plotted to obtain the clinical benefit of the models.

RESULTS

Poseoperative fever (POF) is defined as the temperature of the patient higher than 38 ℃ within 72 h after operation, with no sign of infection in other systems. 31(2.8%) of 1095 cases had POF after fURL. Urine nitrite had a better specificity than urine culture for POF diagnosis (P < 0.001). After the PS matching, a well-balanced cohort of 24 POF group and 96 no-POF group was produced. The mean AUC from the bootstrap resampling method for urine nitrite model (AUC: 0.8736; 95% CI: 0.8731-0.8743) was significantly increased than that of the urine culture model (AUC: 0.8385; 95% CI: 0.8378-0.8392). The application of two kinds of POF predicting models could bring clinical net benefit when the probability is < 35%. However, urine nitrite model showed a better clinical net benefit acquirement compared to the urine culture model.

CONCLUSION

Preoperative positive urine nitrite may play a pivotal role in the prediction of POF after fURS and needs to be validated by future evidence.

Laser-patterned paper-based sensors for rapid point-of-care detection and antibiotic-resistance testing of bacterial infections

Antimicrobial resistance (AMR) has been identified by the World Health Organisation as a global threat that currently claims at least 25,000 deaths each year in Europe and 700,000 globally; the number is projected to reach 10 million per year between 2015 and 2050. Therefore, there is an urgent need for low-cost but reliable point-of-care diagnostics for early screening of infections especially in developing countries lacking in basic infrastructure and trained personnel. This work is aimed at developing such a device, a paper-based microfluidic device for infection testing by an unskilled user in a low resource setting. Here, we present our work relating to the use of our laser-patterned paper-based devices for detection and susceptibility testing of Escherichia coli, via a simple visually observable colour change. The results indicate the suitability of our integrated paper devices for timely identification of bacterial infections at the point-of-care and their usefulness in providing a hugely beneficial pathway for accurate antibiotic prescribing and thus a novel route to tackling the global challenge of AMR.

One-Step Biotinylation of Cellulose Paper by Polymer Coating to Prepare a Paper-Based Analytical Device

Cellulose paper has strong potential as an analytical platform owing to its unique characteristics. In the present study, we investigated a procedure for functionalizing the surface of cellulose paper by dip-coating a mixture of a functional polymer and a perfluoroalkylated surfactant (surfactant 1). The functional polymer comprised a mixture of methyl methacrylate and poly(ethylene glycol) methacrylate monomers. The monomer ratio in the functional polymer affected the hydrophilicity and water absorbance of the cellulose paper after dip-coating. Furthermore, the presence of surfactant 1 during dip-coating promoted the surface segregation of poly(ethylene glycol) (PEG) moieties in the polymer, which enhanced the hydrophilicity, prevented nonspecific protein adsorption, and maintained the water absorbance of the dip-coated cellulose paper. Dip-coating with another functional polymer containing biotin groups produced a cellulose paper with a biotin-decorated surface in a one-step procedure. The displayed biotin groups immobilized avidin on the surface, and the PEG moieties in the polymer prevented nonspecific protein adsorption. We then immobilized a thrombin-binding DNA aptamer on the avidin-immobilized cellulose paper to prepare a paper-based analytical device. It is possible to visualize thrombin in model solutions and serum using the paper-based analytical device.

Paper-Based Diagnostic System Facilitating Escherichia coli Assessments by Duplex Coloration

Laboratory support for low-resource regions is a rising global issue. As microbiological contamination is closely associated with other issues like food safety, water supply sustainability, and public health, bacterial assessments in this setting need to be improved. Herein, we demonstrate a paper-based diagnostic device for point-of-need testing, in which fecal-indicating Escherichia coli and highly pathogenic E. coli are detected by duplex coloration. This device was functionalized by mixing different chromogenic substrates that reflect each bacterial enzymatic phenotype. In the final part of the paper, we describe this microbiological diagnostic system tested with bacteria-contaminated food samples. The device sensitivity was shown to have greatly reduced the total analysis time (below to 4 h) when combined with an enrichment amplification procedure. Notably, this paper device successfully detected 10 cfu/mL of target bacteria in a contaminated milk sample. Our diagnostic system shows acceptable accuracy, short analysis time, and a user-friendly interface, thereby eliminating demands for high-end equipment and a highly trained staff. We expect that this diagnostic system will be a sustainable solution in supporting microbiological or clinical laboratories in low-income countries.