Bacterial Trapping for infection diagnosis

Over the last decade, optical resonators integrated into "lab-on-chip" devices have emerged as suitable structures for biological analysis, due to their small footprint and especially their ability to trap objects at low power below the damage threshold of biological entities. The resonant nature of optical cavities allows the simultaneous acquisition of information about the trapped object, such as size, refractive index and morphology, through a feedback effect induced by the sample trapped by the electromagnetic field trapping itself. At the same time, the massive and inappropriate use of antibiotics since the 1950s has led to antimicrobial resistance. This misuse of antibiotic therapy is partly due to time-consuming and expensive diagnostic tools often based on a large number of bacteria, obtained after a culture step. To overcome this problem, the development of non-destructive techniques at the (statistical) single-cell scale is of crucial interest. This work carried out on Silicon On Insulator (SOI) substrate at 1.55 µm in collaboration with CEA/INAC/SiNaPs and CEA/LETI/DTBS falls within this framework.

(I) Linear microcavity for the identification of single bacteria (a) SEM photograph of the microcavity and study bacteria (Diplococcus S. epidermidis (orange curve) - E. coli (blue) - B. subtilis (red)) (b) Spatial study of trapping (Brownian/trapped) by microscopy column (c) Temporal study by spectroscopy. (II) Photonic crystal device for differentiation of bacterial gram type (a) Microcavity and optical measurement principle (b) Resonance shift and transmission change during trapping of bacteria (c) Differentiation of 7 types of bacteria according to their gram type (>5 different measurements per bacteria).

A first study [LATE Appl. Phys. Let. 2016] allowed us to demonstrate the trapping of a single bacteria by the evanescent field of a correctly modeled microcavity. Two analysis methodologies have been developed to precisely study the behavior of the bacteria in the trap: the spatial method which analyzes the movement of the trapped bacteria and the temporal method (optical transmission measurement) (Fig. 4 (Ia)) . The spatial signature demonstrates that the morphological properties of the 3 types of bacteria studied (size, shape and presence of flagella) can be identified using the parameter known as the confinement factor (Fig. 4 (Ib)). The temporal signature concerns the analysis of fluctuations in the optical signal transmitted over time during the trapping of bacteria, fluctuations which depend on the movement of the bacteria in the trap. This method allowed us to identify the phenotypes of the bacteria (Fig. 4 (Ic)). Compared to spatial characterization, the label-free temporal method only requires optical transmission measurements and is therefore likely to be miniaturized.

To go further in bacterial identification, we compared this methodology with the Gram test (in collaboration with EPFL). This classic bacterial test carried out in a hospital environment makes it possible to obtain a very first characterization of the pathogen to be identified. It consists of differential staining which makes it possible to classify bacteria into two groups, Gram positive and Gram negative, based on the chemical and physical properties of the cell wall and to guide initial treatment. From a hollow cavity coupled to a two-dimensional photonic crystal guide (Fig. 4 (IIa)), the trapped bacteria induces a shift in the resonance and therefore a modification of the transmitted power (Fig. 4 (IIb)). Different bacteria are selected to represent the 4 main categories of pathogens (Gram+/- cocci, Gram+/- bacillus). Statistical measurements (characteristics of the interaction between the electromagnetic field of the cavity and the cell membrane) clearly show separation by Gram type [THERISOD Appl. Phys. Let. 2018].

More recently, a two-laser trapping device was also implemented to allow detailed analysis of the state of an E. coli bacteria subjected to thermal stress without resorting to the standard culture step in a Petri dish. The small amount of suspension required, as well as the speed of a simple transmission measurement, make this technique a promising tool for the rapid, label-free and non-destructive identification of bacterial species at the cellular scale.