Nanophotonics for bacterial detection and antimicrobial susceptibility testing

Photonic biosensors are a major topic of research that continues to make exciting advances. Technology has now improved sufficiently for photonics to enter the realm of microbiology and to allow for the detection of individual bacteria. Here, we discuss the different nanophotonic modalities used in this context and highlight the opportunities they offer for studying bacteria. We critically review examples from the recent literature, starting with an overview of photonic devices for the detection of bacteria, followed by a specific analysis of photonic antimicrobial susceptibility tests. We show that the intrinsic advantage of matching the optical probed volume to that of a single, or a few, bacterial cell, affords improved sensitivity while providing additional insight into single-cell properties. We illustrate our argument by comparing traditional culture-based methods, which we term macroscopic, to microscopic free-space optics and nanoscopic guided-wave optics techniques. Particular attention is devoted to this last class by discussing structures such as photonic crystal cavities, plasmonic nanostructures and interferometric configurations. These structures and associated measurement modalities are assessed in terms of limit of detection, response time and ease of implementation. Existing challenges and issues yet to be addressed will be examined and critically discussed

Photonic crystal resonances for sensing and imaging

This review provides an insight into the recent developments of photonic crystal (PhC)-based devices for sensing and imaging, with a particular emphasis on biosensors. We focus on two main classes of devices, namely sensors based on PhC cavities and those on guided mode resonances (GMRs). This distinction is able to capture the richness of possibilities that PhCs are able to offer in this space. We present recent examples highlighting applications where PhCs can offer new capabilities, open up new applications or enable improved performance, with a clear emphasis on the different types of structures and photonic functions. We provide a critical comparison between cavity-based devices and GMR devices by highlighting strengths and weaknesses. We also compare PhC technologies and their sensing mechanism to surface plasmon resonance, microring resonators and integrated interferometric sensors

Multiparameter antibiotic resistance detection based on hydrodynamic trapping of individual E. coli

There is an urgent need to develop novel methods for assessing the response of bacteria to antibiotics in a timely manner. Antibiotics are traditionally assessed via their effect on bacteria in a culture medium, which takes 24-48 h and exploits only a single parameter, i.e. growth. Here, we present a multiparameter approach at the single-cell level that takes approximately an hour from spiking the culture to correctly classify susceptible and resistant strains. By hydrodynamically trapping hundreds of bacteria, we simultaneously monitor the evolution of motility and morphology of individual bacteria upon drug administration. We show how this combined detection method provides insights into the activity of antimicrobials at the onset of their action which single parameter and traditional tests cannot offer. Our observations complement the current growth-based methods and highlight the need for future antimicrobial susceptibility tests to take multiple parameters into account

Exploring the Limit of Multiplexed Near-Field Optical Trapping

Optical trapping has revolutionized our understanding of biology by manipulating cells and single molecules using optical forces. Moving to the near-field creates intense field gradients to trap very smaller particles, such as DNA fragments, viruses, and vesicles. The next frontier for such optical nanotweezers in biomedical applications is to trap multiple particles and to study their heterogeneity. To this end, we have studied dielectric metasurfaces that allow the parallel trapping of multiple particles. We have explored the requirements for such metasurfaces and introduce a structure that allows the trapping of a large number of nanoscale particles (>1000) with a very low total power P < 26 mW. We experimentally demonstrate the near-field enhancement provided by the metasurface and simulate its trapping performance. We have optimized the metasurface for the trapping of 100 nm diameter particles, which will open up opportunities for new biological studies on viruses and extracellular vesicles, such as studying heterogeneity, or to massively parallelize analyses for drug discovery

Developing photonic, microfluidic and electrical systems to study the antibiotic susceptibility of individual Escherichia coli

Antimicrobial Resistance (AMR) is an important societal and medical burden being faced by every healthcare system in the world. The large overuse of antibiotics favours bacterial resistance, thereby causing drugs to become ineffective. While traditional susceptibility tests are well established, they are slow at informing prescriptions, which means that many antibiotics are prescribed without proper diagnostics. This inefficacy stems from the detection of bacterial growth at the bulk colony level. In addition, averaging over bulk colonies masks any cell-to-cell difference even though it is well known that bacterial populations and their response to antibiotics are heterogenous. These differences need to be considered to correctly assess the efficacy of any microbial agent in a timely manner. This thesis presents a multiparameter approach for profiling the susceptibility of individual bacteria to antibiotics. Hydrodynamic trapping provides the mechanism for retaining and examining hundreds of single E. coli in a microfluidic channel. The multiparameter aspect consists of the simultaneous assessment of bacterial motility and morphology upon exposure to antibiotics. This combined approach allows us to detect susceptibility and resistance of E. coli MG1655 in as little as 1 hour from spiking the culture. Standard microdilution assays and bacteria counts confirmed the validity of the classification. Additionally, the richness of single-cell data enables us to study the dynamics of population killing and the mode of action of the antibiotics. The methodological approach presented here has the potential to complement traditional susceptibility tests by providing a deeper understanding of the drugs’ action and a more rapid way of assessing the bacterial response to antimicrobial agents. More generally, the assay provides a platform for monitoring the behaviour of hundreds of single bacteria over time, while preserving the individuality of each microorganism

Integrating cell on chip : novel waveguide platform employing ultra-long optical paths

Optical waveguides are the most fundamental building blocks of integrated optical circuits. They are extremely well understood, yet there is still room for surprises. Here, we introduce a novel 2D waveguide platform which affords a strong interaction of the evanescent tail of a guided optical wave with an external medium while only employing a very small geometrical footprint. The key feature of the platform is its ability to integrate the ultra-long path lengths by combining low propagation losses in a silicon slab with multiple reflections of the guided wave from photonic crystal (PhC) mirrors. With a reflectivity of 99.1% of our tailored PhC-mirrors, we achieve interaction paths of 25 cm within an area of less than 10 mm2. This corresponds to 0.17 dB/cm effective propagation which is much lower than the state-of-the-art loss of approximately 1 dB/cm of single mode silicon channel waveguides. In contrast to conventional waveguides, our 2D-approach leads to a decay of the guided wave power only inversely proportional to the optical path length. This entirely different characteristic is the major advantage of the 2D integrating cell waveguide platform over the conventional channel waveguide concepts that obey the Beer-Lambert law

Backscattering design for a focusing grating coupler with fully etched slots for transverse magnetic modes

Grating couplers are a fundamental building block of integrated optics as they allow light to be coupled from free-space to on-chip components and vice versa. A challenging task in designing any grating coupler is represented by the need for reducing back reflections at the waveguide-grating interface, which introduce additional losses and undesirable interference fringes. Here, we present a design approach for focusing TM grating couplers that minimizes these unwanted reflections by introducing a modified slot that fulfills an anti-reflection condition. We show that this antireflection condition can be met only for the Bloch mode of the grating that concentrates in the dielectric. As a consequence the light is scattered from the grating coupler with a negative angle, referred to as “backscattering design”. Our analytic model shows that the anti-reflection condition is transferrable to grating couplers on different waveguide platforms and that it applies for both TE and TM polarizations. Our experimentally realized focusing grating coupler for TM-modes on the silicon photonics platform has a coupling loss of (3.95 ± 0.15) dB at a wavelength of 1.55 µm. It has feature sizes above 200 nm and fully etched slots. The reflectivity between the grating coupler and the connected waveguide is suppressed to below 0.16%