Application of Microfluidics for Bacterial Identification

Abstract

Bacterial infections continue to pose serious public health challenges. Though anti-bacterial therapeutics are effective remedies for treating these infections, the emergence of antibiotic resistance has imposed new challenges to treatment. Often, there is a delay in prescribing antibiotics at initial symptom presentation as it can be challenging to clinically differentiate bacterial infections from other organisms (e.g., viruses) causing infection. Moreover, bacterial infections can arise from food, water, or other sources. These challenges have demonstrated the need for rapid identification of bacteria in liquids, food, clinical spaces, and other environments. Conventional methods of bacterial identification rely on culture-based approaches which require long processing times and higher pathogen concentration thresholds. In the past few years, microfluidic devices paired with various bacterial identification methods have garnered attention for addressing the limitations of conventional methods and demonstrating feasibility for rapid bacterial identification with lower biomass thresholds. However, such culture-free methods often require integration of multiple steps from sample preparation to measurement. Research interest in using microfluidic methods for bacterial identification is growing; therefore, this review article is a summary of current advancements in this field with a focus on comparing the efficacy of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and emerging spectroscopic methods.

Keywords: bacterial identification; loop-mediated isothermal amplification (LAMP); matrix-assisted laser deposition/ionization mass spectroscopy (MALDI-ToF MS); microfluidics; polymerase chain reaction (PCR); raman spectroscopy.

Figure 1

The figure indicates a growing interest in microfluidics-enabled devices for bacterial identification over the past decade by using the metric of number of research articles published over the last decade with keywords “microfluidics” and “bacterial identification”. Data obtained from Scopus using a keyword search.

Figure 2

Cross-sectional schematic of a curvilinear microchannel showing the generation of Dean vortices and the forces that act on particles to cause lateral migration in low $Re$ flows, along with inertial lift force and drag forces which affect positional equilibrium of particles within the microchannel. Adapted from M.-L. Lee and D.-J. Yao, Inventions 2018, 3, 40; licensed under a Creative Commons Attribution (CC BY) license.

Figure 3

Example depiction of CF-PCR-based chip. (A) General sampling and extraction methods used for obtaining experimental periodontal pathogens tested for identification using the device. (B) Diagram of the microfluidic chip containing serpentine channels mixing the PCR reagents with the extracted sample above a thermocycler heating system. (C) Explicit definition of the three divisions and stages of the device. (D) Overall image of the device. Reproduced with permission Lab on a Chip, 2022, 22, 733–737. Copyright 2022 Royal Society of Chemistry.

Figure 4

LAMP-based dual-sample microfluidic chip that allow for simultaneous amplification and real-time detection of genetic material from 10 waterborne pathogens. (A) Image of the dual-sample microfluidic chip that consist of two identical half units containing 11 reaction wells each. (B) Methodology of sample amplification and path of reaction mixture flow through channel. At 63 °C, their slim capillary channels narrow and fuse together, preventing contamination of reaction mixture. (C) CapitalBio RTisochip-A apparatus used for isothermal heating fluorescent acquisition. (D) Fluorescent plot with time to positive amplification on the x-axis and intensity of fluorescence on the y-axis. Reproduced with permission from Analytical Methods 2021, 13, 2710–2721. Copyright 2021 Royal Society of Chemistry.

Figure 5

Graphic representation of the experimental workflow of the inertial separation spiral microfluidic device created by Condina et al., where it can be seen that larger Saccharomyces pastorianus position near the inner channel wall and smaller Lactobacillus brevis concentrate at the outer wall. Reproduced with permission from Lab on a Chip. 2019, 19, 1961–1970. Copyright 2019 Royal Society of Chemistry.

Figure 6

Microfluidic chip utilizing a herringbone design and vancomycin modified magnetic beads (VMB) to enrich bacteria for MALDI-ToF identification. The herringbone design aids in generating chaotic flow for more efficient mixing and interaction of VMBs and bacteria. (A) Microfluidic model assembly displaying the staggered herringbone design. (B) Image of assembled microfluidic setup and its serpentine channels. (C) Work process for pathogen identification. Reproduced with permission from Analyst. 2021, 146, 4146–4153. Copyright 2021 Royal Society of Chemistry.