Lab on a stick: multi-analyte cellular assays in a microfluidic dipstick

A new microfluidic concept for multi-analyte testing in a dipstick format is presented, termed “Lab-on-a-Stick”, that combines the simplicity of dipstick tests with the high performance of microfluidic devices. Lab-on-a-Stick tests are ideally suited to analysis of particulate samples such as mammalian or bacterial cells, and capable of performing multiple different parallel microfluidic assays when dipped into a single sample with results recorded optically. The utility of this new diagnostics format was demonstrated by performing three types of multiplex cellular assays that are challenging to perform in conventional dipsticks: 1) instantaneous ABO blood typing; 2) microbial identification; and 3) antibiotic minimum inhibitory (MIC) concentration measurement. A pressure balance model closely predicted the superficial flow velocities in individual capillaries, that were overestimated by up to one order of magnitude by the Lucas-Washburn equation conventionally used for wicking in cylindrical pores. Lab-on-a-stick provides a cost-effective, simple, portable and flexible multiplex platform for a range of assays, and will deliver a new generation of advanced yet affordable point-of-care tests for global diagnostics

Covalent immobilisation of antibodies in Teflon-FEP microfluidic devices for sensitive quantification of clinically relevant protein biomarkers

This study reports for the first time sensitive colorimetric and fluorescence detection of clinically relevant protein biomarkers by sandwich immunoassays using covalent immobilisation of antibodies onto the fluoropolymer surface inside Teflon®-FEP microfluidic devices. Teflon®-FEP has outstanding optical transparency ideal for high-sensitivity colorimetric and fluorescence bioassays, however this thermoplastic is regarded as chemically inert and very hydrophobic. Covalent immobilisation can offer benefits over passive adsorption to plastic surfaces by allowing better control over antibody density, orientation and analyte binding capacity, and so we tested a range of different and novel covalent immobilisation strategies. We first functionalised the inner surface of a 10-bore, 200 µm internal diameter FEP microcapillary film with high-molecular weight polyvinyl alcohol (PVOH) without changing the outstanding optical transparency of the device delivered by the matched refractive index of FEP and water. Glutaraldehyde immobilisation was compared with use of photoactivated linkers and NHS-ester crosslinkers for covalently immobilising capture antibodies onto PVOH. Three clinically relevant sandwich ELISAs were tested, against the cytokine IL-1ß, the myocardial infarct marker cardiac troponin I (cTnI), and the chronic heart failure marker brain natriuretic peptide (BNP). Overall, glutaraldehyde immobilisation was effective for BNP assays, but yielded unacceptable background for IL-1ß and cTnI assays caused by direct binding of biotinylated detection antibody to the modified PVOH surface. We found NHS-ester groups reacted with APTES-treated PVOH coated fluoropolymer. This facilitated a novel method for capture antibody immobilisation onto fluoropolymer devices using a bifunctional NHS-maleimide crosslinker. The density of covalently immobilised capture antibodies achieved using PVOH/APTES/NHS/Maleimide approached levels seen with passive adsorption, and sensitive and quantitative assay performance was achieved using this method. Overall, PVOH coating provided an excellent surface for controlled covalent antibody immobilisation onto Teflon®-FEP for performing high-sensitivity immunoassays

Exploiting open source 3D printer architecture for laboratory robotics to automate high-throughput time-lapse imaging for analytical microbiology

Growth in open-source hardware designs combined with the low-cost of high performance optoelectronic and robotics components has supported a resurgence of in-house custom lab equipment development. We describe a low cost (below USD700), open-source, fully customizable high-throughput imaging system for analytical microbiology applications. The system comprises a Raspberry Pi camera mounted on an aluminium extrusion frame with 3D-printed joints controlled by an Arduino microcontroller running open-source Repetier Host Firmware. The camera position is controlled by simple G-code scripts supplied from a Raspberry Pi singleboard computer and allow customized time-lapse imaging of microdevices over a large imaging area. Open-source OctoPrint software allows remote access and control. This simple yet effective design allows high-throughput microbiology testing in multiple formats including formats for bacterial motility, colony growth, microtitre plates and microfluidic devices termed ‘lab-on-a-comb’ to screen the effects of different culture media components and antibiotics on bacterial growth. The open-source robot design allows customization of the size of the imaging area; the current design has an imaging area of ~420 × 300mm, which allows 29 ‘lab-on-a-comb’ devices to be imaged which is equivalent 3480 individual 1μl samples. The system can also be modified for fluorescence detection using LED and emission filters embedded on the PiCam for more sensitive detection of bacterial growth using fluorescent dyes

Label-free smartphone quantitation of bacteria by darkfield imaging of light scattering in fluoropolymer micro capillary film allows portable detection of bacteriophage lysis

Conventional methods for the detection and quantitation of bacteria are slow, laborious and require a laboratory. Microfluidic systems offer faster and portable testing, and smartphone cameras can record colorimetric or fluorometric bioassays, but this requires dye addition. Here, we demonstrate for the first time label-free smartphone detection of bacterial light scattering by darkfield microfluidic imaging to measure bacteria and bacteriophage lysis. A single LED and portable 3D printed imaging box allowed bacterial concentration and growth to be measured by direct imaging of bacterial light scattering. Bacteriophage lysis was detected within a 10-channel microfluidic device made from melt-extruded fluoropolymer micro capillary film, allowing rapid detection of host specificity. Elimination of unwanted reflections and optimising illumination angle are critical for successful darkfield bacterial imaging, with 15° giving maximal intensity. Bacterial sedimentation was directly observed within microfluidic devices, and detection sensitivity significantly increased by allowing bacteria to sediment for 30 min. With this simple, low-cost, 3D printed system bacterial concentrations down to an optical density of 0.1 could be measured corresponding to 8 × 104 colony forming units (CFU) per microdevice, approaching the sensitivity of conventional spectrophotometers. Bacteriophage lysis could be detected at a range of starting cell concentrations. With a low starting cell concentration, the increase in light scatter signal with incubation was prevented in the presence of bacteriophage. Conversely, with high starting cell concentration, the light scatter signal detected at the start was clearly eliminated when phage were added, indicating this simple system allows direct visualisation of bacteriophage eliminating light scattering by lysis

Development and first applications of a bacterial cell sorting method by labeling DNA with magnetic nanoparticles to study bacterial diversity and in situ horizontal gene transfer

En dépit de leur importance, la caractérisation des communautés bactériennes dans l’environnement reste encore très incomplète. Les principales raisons sont, d’une part, la difficulté d’appréhender la totalité de la communauté bactérienne quand plus de 99% des bactéries demeurent récalcitrantes à la culture in vitro et ne peuvent donc être étudiées par les approches classiques de microbiologie. D’autre part, la métagénomique, censée contourner cette méthode de culture en s’intéressant à l’ensemble des génomes extraits des milieux d’études, demeure elle aussi imparfaite du fait de limitations techniques (biais d’extraction de l'ADN, de clonage, de PCR, de séquençage et d’assemblage des génomes etc.) et conceptuelles, inhérentes à la complexité et l’hétérogénéité des environnements. Pour compenser les limites de chacune de ces techniques, des méthodes de tri cellulaire appliquées en conjonction avec les deux premières pourraient aider à un meilleur décryptage de la diversité microbienne. Basée sur la sélection spécifique (taxonomique et/ou fonctionnelle) et l’isolement direct des cellules bactériennes ciblées à partir d’un échantillon environnemental complexe, l’étude est restreinte à une population spécifique, voire à une cellule isolée. Pourront alors être appliquées les approches classiques de mise en culture ou d’extraction de l’ADN pour une étude restreinte à l’ADN ou l’ARN, leur répétition sur les différentes populations devant à terme (lointain) approcher l’exhaustivité. C’est dans ce contexte que s’est positionné ce travail de thèse visant dans un premier temps à mettre au point un nouvel outil de tri cellulaire basé sur l’intégration de micro-aimants permanents dans un canal microfluidique. A partir de ce système de tri magnétique miniaturisé, offrant de nombreux avantages (dispositif portable, peu coûteux, nécessitant de faibles volumes réactionnels et potentiellement intégrable en « laboratoire sur puce »), une technique d’isolement sélectif de cellules bactériennes marquées magnétiquement a alors été développée. Ciblées sur des critères taxonomiques après hybridation in situ avec des sondes d’acides nucléiques biotinylés complémentaires d’une région spécifique du gène 23S rRNA, des cellules bactériennes ont été marquées magnétiquement après réaction de la sonde avec des nanoparticules magnétiques fonctionnalisées par des molécules de streptavidine. Les premiers résultats montrent l’établissement d’une méthode de tri suffisamment spécifique et sensible pour piéger les cellules marquées diluées (0,04%) au sein d’une suspension, à des niveaux compatibles avec l’isolement futur de populations d’intérêt à partir de communautés d’environnements complexes. Sur un principe comparable, l’approche a été adaptée à l’étude des transferts horizontaux de gènes in situ. Les applications d’un tri cellulaire grâce au marquage par des nanoparticules magnétiques et l’emploi de micro-aimants intégrés dans des microsystèmes fluidiques semblent donc très prometteuses pour le développement de la microbiologie environnementale.Despite their importance, bacterial communities in the environment remain poorly characterized. On the one hand, it is difficult to gain knowledge of the community as a whole because over 99% of bacteria are recalcitrant to in vitro culture, rendering classic microbiological approaches imposible to carry out. On the other hand, metagenomics, which can be used to circumvent culture-based approaches by extracting all the genomes from a given environment, is also problematic given the associated technical limitations (biases related to DNA extraction, cloning, PCR, genome sequencing and assembling etc.), and conceptual difficulties related to the complexity and the homogeneity of the environments. In order to overcome some of the limitations of these approaches, bacterial cell selection methods have been developed and can be used to improve our understanding of microbial diversity. Based on taxonomic and/or functional selection and the direct isolation of bacterial cells from an environmental sample, bacterial cell selection can be used to reduce microbial community complexity by targeting specific populations, or even an isolated cell. A variety of classic approaches such as cultivation or DNA/RNA extraction can then be carried out. This cycle can theoretically be repeated until all members of the community are characterized. The aim of this doctoral thesis was to design a novel cell selection tool based on the permanent integration of micro-magnets into a microfluidic canal. In conjunction with a new miniaturized magnetic selection system that provides several advantages over larger systems (portable, low cost, requiring smaller reaction volumes and can be potentially integrated on “laboratory on a chip” systems), a method for selective bacterial cell isolation using magnetic labeling was developed. The bacterial cells were targeted based on taxonomic criteria; biotin-labeled probes were developed for a specific region of the 23S rRNA gene. Following in situ hybridization with the probes, baceterial cells were labeled with streptavidin-functionalized magnetic nanoparticles. First results showed that the tool was specific and sensitive enough to trap labeled and diluted (0,04%) cells from a suspension at levels that are comparible to populations of interest found in complex environmental communities. This tool has also been adapted to study in situ horizontal gene transfer as well. The application of a cellular selection tool that labels targets with magnetic nanoparticles coupled to fluidic microsystems with integrated nano-magnets looks very promising for future studiesin environmental microbiology

LIGHTNING-ASSISTED ENVIRONMENTAL GENETIC THERAPY

Remediation of polluted environmental media presents an ongoing challenge, with each contaminated site requiring a thorough description to choose an appropriate remediation technology. One popular remediation technique is monitored natural attenuation (MNA), which relies on the ability of indigenous microbes to degrade or sequester contaminants. However, if the indigenous population lacks the biochemical makeup or genes to tackle the pollutants, which is common with xenobiotic compounds, then other - often more costly - remediation efforts are necessary. In mammals, the idea of gene therapy involves the introduction of a gene into cells to correct a disease state resulting from improper gene function. Our research proposes using the same idea to augment the function of a soil community via gene delivery to facilitate degradation of a contaminant. Previous research has successfully used microbes containing degradation genes to inoculate indigenous microbes via horizontal gene transfer. However, direct addition of the genes using naked DNA in lieu of a microbial vector might make the process more efficient and circumvent the issue of adding genetically modified organisms (GMOs) to the existing community. In this research, we added a lindane-degrading gene (linA) in a broad-host range plasmid, resulting in the plasmid pBLN, to a microbial soil community that lacked the ability to degrade lindane. We attempted to increase the rate of transformation by electroporation in liquid media or application of simulated lightning in a soil medium. In the first round of experiments, we extracted bacteria from soil, mixed the bacteria with pBLN, and electroporated the liquid mixture. We then incubated the electroporated cells in a liquid medium with lindane, and monitored lindane degradation via an increase in chloride concentration. Soil microbes, either electroporated with pBLN or simply incubated for a 2 hour period with pBLN, displayed an increased ability to degrade lindane as compared to a negative control. The presence of linA in the samples with increased degradation was verified using PCR. In the second phase of this work, the bacterial transformation in a soil matrix, using a lightning generator to provide the electric shock to the soil bacteria in situ, simulates a potential mechanism for site treatment. This research demonstrates the feasibility of environmental gene therapy to remediate xenobiotic-contaminated sites

High Dynamic Range Bacterial Cell Detection in a Novel “Lab-In-A-Comb” for High-Throughput Antibiotic Susceptibility Testing of Clinical Urine Samples

ABSTRACTAntibiotic resistance in urinary tract infection is a major global challenge, and improved cost-effective and rapid antibiotic susceptibility tests (AST) are urgently needed to inform correct antibiotic selection. Although microfluidic technology can miniaturise AST, the high dynamic range of pathogen density found in clinical urine samples makes direct testing of clinical samples – rather than testing colonies from overnight agar plates – extremely challenging. We evaluated for the first time how pathogen concentration in urine affects microfluidic AST using a novel microplate-compatible high-throughput microfluidic AST system termed “Lab-on-a-Comb”. When tested with clinical E. coli isolates at standardised density, these devices gave identical antibiotic susceptibility profiles to standard disc diffusion and microtitre plate tests. Bacterial detection directly in synthetic urine spiked with clinical E. coli UTI isolates was possible over a very large dynamic range of starting cell densities, from 103 – 108 CFU/mL which covers the range of pathogen cell densities found in patient urine. The lowest cell density where cell growth was reproducibly detected optically was 9.6x102 CFU/mL, corresponding to one single CFU detected in a 1 μL microcapillary-an unprecedented level of sensitivity. Cell growth kinetics followed a simple Monod model with fast growth limited by the substrate availability and an estimated doubling time of 24.5 min, indicating optimal E. coli growth conditions within these microfluidic devices. There was a trade-off between sensitivity and speed of detection, with 105 CFU/mL detection possible within 2h, but 6h incubation required at 103 CFU/mL.</jats:p

Bioremediation via In Situ Electrotransformation

International audienceBioremediation of polluted sites relies on bacteria to degrade or transform contaminants into less noxious chemicals. To do so, bacteria require genes that encode the degradation enzymes and the capacity to properly express them, which may be lacking in indigenous bacteria. To increase the ability of indigenous bacteria to bioremediate a contaminated site, this research proposes the use of electrotransformation to facilitate bacterial uptake of exogenous degradation genes. As a proof of concept, a lindane degradation gene (linA) located on a broad host-spectrum expression plasmid (pBLN) was introduced into soil bacteria by electroporation both in vitro, in liquid media, and in situ, in soil. In both cases, the electrotransformed bacteria displayed an increase in lindane degradation and an increase in the linA gene copy number. The use of in situ electrotransformation could improve pollutant degradation rates and could provide another tool for bioremediation

Magnetic microfluidic device as a complementary tool for investigating microbial diversity

National audienc