High-Throughput Flow-Through Direct Immunoassays for Targeted Bacteria Detection

Unraveling the Possibilities: Recent Progress in DNA Biosensing

Due to the advantages of its numerous modification sites, predictable structure, high thermal stability, and excellent biocompatibility, DNA is the ideal choice as a key component of biosensors. DNA biosensors offer significant advantages over existing bioanalytical techniques, addressing limitations in sensitivity, selectivity, and limit of detection. Consequently, they have attracted significant attention from researchers worldwide. Here, we exemplify four foundational categories of functional nucleic acids: aptamers, DNAzymes, i-motifs, and G-quadruplexes, from the perspective of the structure-driven functionality in constructing DNA biosensors. Furthermore, we provide a concise overview of the design and detection mechanisms employed in these DNA biosensors. Noteworthy advantages of DNA as a sensor component, including its programmable structure, reaction predictility, exceptional specificity, excellent sensitivity, and thermal stability, are highlighted. These characteristics contribute to the efficacy and reliability of DNA biosensors. Despite their great potential, challenges remain for the successful application of DNA biosensors, spanning storage and detection conditions, as well as associated costs. To overcome these limitations, we propose potential strategies that can be implemented to solve these issues. By offering these insights, we aim to inspire subsequent researchers in related fields.

Phage-Displayed Nanobody as a Sensitive Nanoprobe to Enhance Chemiluminescent Immunoassay for Cronobacter sakazakii Detection in Dairy Products

The exploitation of stable, high-affinity, and low-cost nanoprobes is essential to develop immunoassays for real-time monitoring of foodborne pathogens, so as to safeguard human health. The possible interaction of the Fc fragment of antibodies with spA protein on Staphylococcus aureus will result in unexpected interference. To address this consideration, we described herein for the first time the development of nanobodies that by definition are devoid of the Fc fraction. These nanobodies directed against Cronobacter sakazakii (C. sakazakii) were retrieved from a dedicated immune phage-displayed nanobody library. The binders showed superiority of low cost, strong stability, high binding affinity, and adequate load capacity. Thereafter, a phage-mediated sandwich enzyme-linked immunosorbent assay (ELISA) was constructed by using Cs-Nb2 as an antigen-capturing antibody and phage-displayed Cs-Nb1 as a detection probe. To further enhance the sensitivity, a chemiluminescent enzyme immunoassay (CISA) was established by replacing the substrate from 3,3',5,5'-tetramethylbenzidine (TMB) to luminol, providing a limit of detection of 1.04 × 104 CFU/mL, with a recovery of 98.15-114.63% for the detection of C. sakazakii in dairy products. The proposed nanobody-based phage-mediated sandwich CLISA shows various advantages, including high sensitivity, cost effectiveness, enhanced loading capacity of the enzyme, and high resistance to the matrix effect, providing a strategy for the design of immunoassays toward foodborne pathogens.

Urchin-Shaped Au-Ag@Pt Sensor Integrated Lateral Flow Immunoassay for Multimodal Detection and Specific Discrimination of Clinical Multiple Bacterial Infections

A new lateral flow immunoassay strip (LFIA) combining sensitive detection and identification of multiple bacteria remains a huge challenge. In this study, we first developed multifunctional urchin-shaped Au-Ag@Pt nanoparticles (UAA@P NPs) with a unique combination of colorimetric-SERS-photothermal-catalytic (CM/SERS/PT/CL) properties and integrated them with LFIA for multiplexed detection and specific discrimination of pathogenic bacteria in blood samples. Unlike the conventional LFIA that relied on antibody (Ab), this novel LFIA introduced 4-mercaptophenylboronic acid (4-MPBA) as an ideal Ab replacer that was functionalized on UAA@P NPs (UAA@P/M NPs) with outstanding binding and enrichment capacities toward bacteria. Taking Staphylococcus aureus (S. aureus) as model bacteria, the limit of detection (LOD) was 3 CFU/mL for SERS-LFIA, 27 CFU/mL for PT-LFIA, and 18 CFU/mL for CL-LFIA, three of which were over 330-fold, 37-fold, and 55-fold more sensitive than ordinary visual CM-LFIA, respectively. Besides, this SERS-LFIA is capable of identifying three types of bacterial spiked blood samples (E. coli, S. aureus, and P. aeruginosa) effectively according to specific bacterial Raman "fingerprints" by partial least-squares-discriminant analysis (PLS-DA). More importantly, this LFIA was successfully applied to blood samples with satisfactory recoveries from 90.3% to 108.8% and capable of identifying the infected patients (N = 4) from healthy subjects (N = 2) with great accuracy. Overall, the multimodal LFIA incorporates bacteria discrimination and quantitative detection, offering an avenue for early warning and diagnosis of bacterial infection.

Mycobacteriophage Derived Lipoarabinomannan Binding Protein for Recognizing Non-Tuberculosis Mycobacteria

Non-tuberculosis mycobacteria (NTM) is one family of pathogens usually leading to nosocomial infections. Exploration of high-performance biological recognition agent plays a pivotal role for the development of point-of-care testing device and kit for detecting NTM. Mycobacterium smegmatis (M. smegmatis) is a NTM which has been frequently applied as an alternative model for highly pathogenic mycobacteria. Herein, a recombinant tail protein derived from mycobacteriophage SWU1 infecting M. smegmatis was expressed with Escherichia coli system and noted as GP89. It shows a fist-like structure according to the results of homology modeling and ab initio modeling. It is confirmed as a lipoarabinomannan (LAM) binding protein, which can recognize studied NTM genus since abundant LAM constructed with d-mannan and d-arabinan is distributed over the mycobacterial surface. Meanwhile an enhanced green fluorescent protein (eGFP)-fused GP89 protein was acquired with a fusion expression technique. Then GP89 and eGFP-fused GP89 were applied to establish a sensitive and rapid method for fluorescent detection of M. smegmatis with a broad linear range of 1.0 × 10² to 1.0 × 10⁶ CFU mL^-1 and a low detection limit of 69 CFU mL^-1. Rapid and reliable testing of antimicrobial susceptibility was achieved by the GP89-based fluorescent method. The present work provides a promising recognition agent for studied NTM and opens an avenue for clinical diagnosis of NTM-induced infections.

Colorimetric nano-beacon and magnetic separation-based rapid and visual assay for gram-negative bacteria

Food-borne diseases caused by pathogenic bacteria are one of the serious factors affecting human health. However, the most commonly used detection methods for pathogenic bacteria not only require expensive instruments, but also take a long time due to the complicated and cumbersome detection process. Therefore, the development of a fast, simple, and low-cost detection method for pathogenic bacteria is crucial for food safety and human health. In this work, based on the high binding ability of antimicrobial peptide (AMP) and polymyxin B (PMB) to bacteria, combined with magnetic separation technology, a new enzyme-free colorimetric strategy was constructed to achieve visual detection of Gram-negative bacteria in complex samples. The sensor system was divided into the following two parts: a colorimetric signal amplification nanoprobe, which was modified with AMP to enable effective binding of the colorimetric probe to the surface of bacteria, and a PMB-modified magnetic nanobead (MNB), which was used as the capture and enrichment unit of Gram-negative bacteria, as a result of which PMB could effectively distinguish Gram-negative bacteria from Gram-positive bacteria. Under optimized conditions, the detection limit of the method for Gram-negative bacteria (e.g. E. coli (G^-)) was as low as 10 CFU/mL, and it was successfully applied to complex real samples. In addition, the developed colorimetric sensor offered advantages, such as fast response, less time consumption, high sensitivity, and low cost. It can be expected to become a new diagnostic tool for on-site detection of pathogenic bacteria in remote areas.

Isothermal RNA Amplification for the Detection of Viable Pathogenic Bacteria to Estimate the Salmonella Virulence for Causing Enteritis

Viable foodborne pathogens can cause intestinal infection and food poisoning. Herein, we reported an RNA assay allowing for sensitive (close to 1 CFU and 1% viable bacteria detectable) and rapid (within 2.5 h) detection of viable pathogenic bacteria by coupling isothermal RNA amplification (nucleic acid sequence-based amplification, NASBA) with a CRISPR/Cas13a system. NASBA allowed direct amplification of 16S rRNA extracted from viable S. enterica (RNAs degrade rapidly in dead bacteria), and the specificity of amplification was ensured using Cas13a/crRNA to recognize the amplicons. We used the CRISPR/Cas13-based NASBA assay (termed cNASBA assay) to investigate the in vivo colonization and intestinal infection of S. enterica in mice. We found that S. enterica was mainly colonized at the cecum, colon, and rectum, and the severity of enteritis caused by S. enterica was determined by the number of viable S. enterica rather than the total count of S. enterica. The cNASBA assay can quantify viable S. enterica and thus can improve the accuracy of virulence estimation compared to qPCR. It shows promise as a reliable tool for monitoring pathogen contamination and biosafety control.