Biosensors for Bacteria Detection

The task of rapid detection and identification of bacteria remains a major challenge in both medicine and industry. As current bacteria detection methods rely on lengthy laboratory-based techniques, there is an urgent need for developing biosensing platforms that will allow for rapid detection at point-of-care settings. Our lab designs different optical biosensors that can detect and quantify bacteria in real-time.

Porous Si photonic crystals for rapid bacteria detection:

The sensor is based on a two-dimensional periodic structure of porous Si photonic crystals, developed in collaboration with Prof. Sa’ar from the Hebrew University, in which the pore size is adjusted to fit the target bacteria cells. Bacteria capture within the pores using different surface functionalities measurable induces changes in the zero-order reflectivity spectrum collected from the periodic structure, as shown below.


Bacterial cells presence within thepores
Bacterial cells presence within the pores (A) affects the refractive index of the porous layer as function of the relative volume they occupy. The bacteria fraction in the pores is monitored in real time by collecting the effective optical thickness (EOT); (B) as this property is determined by the bacteria contribution to the refractive index, n.

Confocal laser microscopy and electron microscopy confirm that the target bacteria cells are individually imprisoned within the porous array. A simple model is suggested to correlate the optical readout and the bacteria concentration and its predictions are found to be in good agreement with experimental results.

In addition, we demonstrate that sensing scheme can be easily modified to potentially allow monitoring of concentration, growth and physiological state of bacteria cells. This generic platform can be tailored to target different microorganisms by tuning the array periodicity and its surface chemistry for rapid and label-free detection outside the laboratory environment.

High-resolution scanning electron micrographs of the biosensor, demonstrating bacteria cells confined within the pores.
High-resolution scanning electron micrographs of the biosensor, demonstrating bacteria cells confined within the pores. Some of the bacteria cells are false-colored to ease observation.

Selected Publications:

  1. Massad-Ivanir N., Mirsky Y., Nahor A., Eitan Edrei, Bonanno-Young L.M, Ben Dov N., Sa’ar A., Segal E., Trap and Track: Designing Self-Reporting Porous Si Photonic Crystals for Rapid Bacteria Detection, Analyst, 139, 3885-3894 (2014).
  2. Mirsky Y., Nahor A., Edrei E., Massad-Ivanir N., Bonanno L.M., Segal E., Sa’ar A., Optical Biosensing of Bacteria and Cells using Porous Silicon-based Photonic Lamellar Gratings, Appl. Phys. Lett., 103 (3), 033702-033704 (2013).

Silicon diffraction gratings for monitoring bacterial responses and rapid antibiotic susceptibility testing

We have developed label-free biosensors based on two-dimensional photonic crystals of periodic micron-sized pores and pillars. The spacing between the structures allows for bacteria capture, inducing measurable changes in the zero-order reflectivity spectrum collected from the periodic structures.

The optical signal allows for real-time readouts of bacterial responses and activity, such as growth and death. Thus, in collaboration with Bnai Zion Medical Center, we have recently demonstrated that these sensors can be used as a platform for rapid antibiotic susceptibility testing in order to determine the most effective antibiotic for an infection. While in the clinic this test takes more than 8 hours, in our platform, the assay takes 2 hours to perform, encouraging the correct prescription of antibiotics to ill patients in a timely manner.

An electron micrograph of bacterial cells colonized on silicon micropillar arrays (left) and a confocal scanning laser microscopy image (right) of antibiotic-induced filamentous E. coli cells (red) growing on top of the micropillars (blue).


  1. Leonard H., Colodner R., Halachmi S., Segal E., Recent Advances in the Race to Design a Rapid Diagnostic Test for Antimicrobial Resistance, ACS Sensors, 3(11), 2202-2217 (2018).
  2. Leonard H., Halachmi S., Ben-Dov N., Nativ O., Segal E., Antimicrobial Susceptibility of Bacterial Networks on Micropillar Architectures Using Intrinsic Phase-Shift SpectroscopyACS Nano, 11, 6167-6177 (2017).

Nanostructured porous Si for bacteria detection:

Nanostructured porous silicon (PSi) Fabry–Pérot thin films are used as the optical transducer element to monitor changes in the reflectivity spectrum upon target bacteria binding. We have established the feasibility of antibody-conjugated oxidized PSi for optical detection of bacteria via the ‘direct-cell-capture’ approach (Massad-Ivanir et al., 2010, 2011).

Exposure of these biosensors to the target bacteria results in their capture onto the porous surface, inducing predictable changes in the thin-film optical interference spectrum of the nanostructure, i.e., a decrease in the intensity of the reflected light, allowing for rapid detection of low bacterial concentrations.

Recently, we used a novel peptidemimetic compound, as the recognition element (Tenenbaum, 2015). The sequence K-[C12K]7 (referred to as K-7α12, shown below), which is a synthetic antimicrobial peptide is tethered to the porous nanostructure. The K-7α12 compound is a member of a family of oligomers of acylated lysines (OAKs), mimicking the hydrophobicity and charge of natural antimicrobial peptides.

Changes in the reflectivity spectrum of the biosensor are monitored upon exposure to different bacteria and their lysate suspensions. We show that capture of bacterial cell fragments induce changes in the reflectivity spectrum, proportional to the E. coli concentration, thereby enabling rapid, sensitive and reproducible detection of E. coli at concentrations as low as 103 cells per mL.

High-resolution scanning electron micrographs of the OAK-modified biosensor after incubation with E. coli bacterial lysate suspension: an intact cell is captured onto the nanostructure.
High-resolution scanning electron micrographs of the OAK-modified biosensor after incubation with E. coli bacterial lysate suspension, showing an intact cell captured onto the nanostructure.

Selected Publications:

  1. Massad-Ivanir N., Shtenberg G., Raz N., Gazenbeek C., Budding D., Bos M.P, Segal E., Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry, Scientific Reports, 6, Article number: 38099 (2016).
  2. K Urmann, S Arshavsky-Graham, JG Walter, T Scheper, E Segal., Whole-cell detection of live lactobacillus acidophilus on aptamer-decorated porous silicon biosensorsAnalyst 141 (18), 5432-5440 (2016).
  3. Tenenbaum E. and Segal E., Optical Biosensors for Bacteria Detection by a Peptidomimetic Antimicrobial Compound, Analyst, 140, 7726-7733 (2015).
  4. Massad-Ivanir N., Shtenberg G., Segal E., Biosensors for Bacteria Detection, Journal of Visualized Experiments. (81), e50805, doi:10.3791/50805 (2013).
  5. Massad N., Shtenberg G., Tzur A., Krepker M., Segal E., Engineering Nanostructured Porous SiO2 Surfaces for Bacteria Detection via “Direct-Cell-Capture”, Anal. Chem., 83, 3282–3289 (2011).
  6. Massad N., Shtenberg G., Zeidman T., Segal E., Construction and Characterization of Porous SiO2/Hydrogel Hybrids as Optical Biosensors for Rapid Detection of Bacteria, Adv. Funct. Mater., 20, 2269-2277 (2010).

Researchers: Talya Borkom and Dr. Naama Massad-Ivanir 





Novel Antimicrobial Polymeric Systems

The emergence of antibiotic resistance of pathogenic bacteria has led to renewed interest in exploring the potential of plant-derived antimicrobials e.g., essential oils (EOs), as an alternative strategy to reduce microbial contamination. However, the volatile nature of EOs presents a major challenge in their incorporation into polymers by conventional high-temperature processing techniques.

We employ nanomaterials such as, Halloysite nanotubes (HNTs), as efficient nano-carriers for essential oils. Using various pre-compounding processes, we encapsulate essential oils within HNTs. This step imparts enhanced thermal stability to the essential oil, allowing for its subsequent melt compounding with different polymers e.g., low-density polyethylene (LDPE).

High-resolution scanning electron micrograhs of neat HNTs and a schematic illustration of halloysite nanotubes loaded with carvacrol molecules
High-resolution scanning electron micrograhs of neat HNTs (prior to hybrid formation) and A schematic illustration of halloysite nanotubes (HNTs) loaded with carvacrol molecules (a model antimicrobial EO) as achievedby a pre-compounding step in which HNTs/carvacrol hybrids are produced.

The resulting polymer nanocomposites exhibit outstanding antimicrobial properties with a broad spectrum of inhibitory activity against Escherichia coli, Listeria innocua in biofilms, and Alternaria alternata. Their antimicrobial effectiveness is also successfully demonstrated in complex model food systems (such as soft cheese and bread). This superior activity, compared to other studied essential oil-containing films, is induced by the significantly higher oil content in the film as well as its slower out-diffusion from the hybrid system.

Thus, these new active polymer nanocomposites presents an immense potential in controlling microbial contamination and biofilm related adverse effects, rendering them as excellent candidate materials for a wide range of applications.

Storage experiment demonstrating complete eradication of the fungus when the bread is stored in a package based on our antimicrobial hybrid films.
Storage experiment of fungi-inoculated sliced bread (preservative-free) demonstrating complete eradication of the fungus when the bread is stored (11 days) in a package based on our new antimicrobial hybrid films.


  1. Krepker M., Zhang C., Nitzan N., Prinz-Setter O., Massad-Ivanir N., Olah A., Baer E., Segal E., Antimicrobial LDPE/EVOH Layered Films Containing Carvacrol Fabricated by Multiplication Extrusion, Polymers, 10 (8), 864 (2018).
    Open access
  2. Krepker M., Prinz-Setter O., Shemesh R., Vaxman A., Alperstein D., Segal E., Antimicrobial Carvacrol-Containing Polypropylene Films: Composition, Structure and Function, Polymers, 10 (1), 79 (2018).
    Open Access
  3. Krepker M., Shemesh R., Danin-Poleg Y., Kashi Y., Vaxman A., Segal E., Active Food Packaging Films with Synergistic Antimicrobial Activity, Food Control, 76, 117–126 (2017).
  4. Shemesh R., Krepker M., Nitzan N., Vaxman A., Segal E., Active packaging containing encapsulated carvacrol for control of postharvest decayPostharvest Biology and Technology, 118, 175-182
  5. Shemesh R., Krepker M., Nathan M., Banin E., Danin-Poleg Y., Kashi Y., Nitzan N., Vaxman A., Segal E., Novel LDPE/Halloysite Nanotubes Films with Sustained Carvacrol Release for Broad-Spectrum Antimicrobial Activity, RSC Advances, 5, 87108–87117 (2015).
  6. Shemesh R., Goldman D., Krepker M., Danin-Poleg Y., Kashi Y., Vaxman A., Segal E., LDPE/Clay/Carvacrol Nanocomposites with Prolonged Antimicrobial Activity, J. Appl. Polym. Sci., 132(2), 41261-41269 (2015).
  7. Shemesh R., Krepker M., Goldman D., Danin-Poleg Y., Kashi Y., Nitzan N., Vaxman A., Segal E., Antibacterial and Antifungal LDPE Films for Active Packaging, Polym. Adv. Tech., 26(1), 110-116 (2015).

Researchers: Dr. Andy Sand and Dr. Naama Massad-Ivanir.

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Lab-on-a-chip Systems

The incorporation of porous silicon (PSi) biosensors into lab-on-a-chip devices present great promise for sensitive and real-time detection of biological targets, offering significant advantages in terms of high throughput, small sample volumes, and rapid operation time.

We design novel microfluidic devices and assays that integrate PSi optical biosensor with electrokinetic techniques (in collaboration with Prof. Moran Bercovici, Technion) for highly sensitive label-free detection.

Recently, we demonstrated a highly-sensitive lab-on-a-chip device for DNA and protein detection. The DNA/protein target molecules are focused using an electric field within a finite and confined zone, and this highly concentrated analyte is delivered to an on-chip PSi Fabry–Pérot optical transducer, pre-functionalized with capture probes. Using reflective interferometric Fourier transform spectroscopy real-time monitoring, a 1000-fold improvement in the limit of detection (LoD) is demonstrated compared to a standard assay, using the same biosensor.

A measured limit of detection of 1 × 10 −9 M and 7.5 nM is achieved without compromising specificity for DNA and protein target respectively. To the best of our knowledge, this is the lowest LoD measured to date by any PSi biosensor for DNA.

This is the first time that electrokinetic isotachophoresis (ITP) technique has been applied for DNA and protein focusing on PSi biosensors, as well as the utilization of immobilized aptamers as capture probes in an ITP assay.

In addition, the assay is successfully performed in complex media, such as bacteria lysate samples, while the selectivity of the biosensor is retained.

Schematic illustration of lab-on-a-chip device
Schematic illustration of lab-on-a-chip device
 for optical DNA detection using electrokinetic focusing.

Left: Relative optical signal changes vs time of the aptamer-based biosensor during a typical ITP experiment with E. coli lysate suspension spiked or nonspiked with the target protein.
Right: Averaged relative optical signal changes for ITP biosensing experiments of neat target protein, E. coli lysate spiked with the target protein, and neat E. coli lysate (no target protein), demonstrating great performance and selectivity of the assay in a highly complex media.

The concepts presented herein can be readily applied to other ionic targets, paving way for the development of other highly sensitive chemical and biochemical assays.



  1. Arshavsky-Graham S., Massad-Ivanir N., Paratore F., Scheper T., Bercovici M., Segal E., On Chip Protein Pre-Concentration for Enhancing the Sensitivity of Porous Silicon Biosensors, ACS Sensors, 2 (12), 1767–1773 (2017).
  2. Vilenski R., Bercovici M., Segal E., Oxidized Porous Silicon Nanostructures enabling Electrokinetic Transport for Enhanced DNA DetectionAdv. Funct. Mater., 25, 6725–6732 (2015). Featured on the cover page of Advanced Functional Materials  – Vol. 25, No. 43

Researchers: Dr. Naama Massad-Ivanir and Sofi Arshavski