Recent trends in the detection of pathogenic Escherichia coli O157 : H7

In silico screening of ssDNA aptamer against Escherichia coli O157:H7: A machine learning and the Pseudo K-tuple nucleotide composition based approach

This study was planned to in silico screening of ssDNA aptamer against Escherichia coli O157:H7 by combination of machine learning and the PseKNC approach. For this, firstly a total numbers of 47 validated ssDNA aptamers as well as 498 random DNA sequences were considered as positive and negative training data respectively. The sequences then converted to numerical vectors using PseKNC method through Pse-in-one 2.0 web server. After that, the numerical vectors were subjected to classification by the SVM, ANN and RF algorithms available in Orange 3.2.0 software. The performances of the tested models were evaluated using cross-validation, random sampling and ROC curve analyzes. The primary results demonstrated that the ANN and RF algorithms have appropriate performances for the data classification. To improve the performances of mentioned classifiers the positive training data was triplicated and re-training process was also performed. The results confirmed that data size improvement had significant effect on the accuracy of data classification especially about RF model. Subsequently, the RF algorithm with accuracy of 98% was selected for aptamer screening. The thermodynamics details of folding process as well as secondary structures of the screened aptamers were also considered as final evaluations. The results confirmed that the selected aptamers by the proposed method had appropriate structure properties and there is no thermodynamics limit for the aptamers folding.

Immunosensing Based on Optical Fiber Technology: Recent Advances

The evolution of optical fiber technology has revolutionized a variety of fields, from optical transmission to environmental monitoring and biomedicine, given their unique properties and versatility. For biosensing purposes, the light guided in the fiber core is exposed to the surrounding media where the analytes of interest are detected by different techniques, according to the optical fiber configuration and biofunctionalization strategy employed. These configurations differ in manufacturing complexity, cost and overall performance. The biofunctionalization strategies can be carried out directly on bare fibers or on coated fibers. The former relies on interactions between the evanescent wave (EW) of the fiber and the analyte of interest, whereas the latter can comprise plasmonic methods such as surface plasmon resonance (SPR) and localized SPR (LSPR), both originating from the interaction between light and metal surface electrons. This review presents the basics of optical fiber immunosensors for a broad audience as well as the more recent research trends on the topic. Several optical fiber configurations used for biosensing applications are highlighted, namely uncladded, U-shape, D-shape, tapered, end-face reflected, fiber gratings and special optical fibers, alongside practical application examples. Furthermore, EW, SPR, LSPR and biofunctionalization strategies, as well as the most recent advances and applications of immunosensors, are also covered. Finally, the main challenges and an outlook over the future direction of the field is presented.

Review: Trends in point-of-care diagnosis for Escherichia coli O157:H7 in food and water

Escherichia coli O157:H7, a Shiga-producing E. coli is a major pathogenic E. coli strain which since the early 1980s has become a crucial food and water-borne pathogen. Several management strategies can be applied to control the spread of infection; however early diagnosis represents the optimum preventive strategy to minimize the infection. Therefore, it is crucial to detect this pathogen in a fast and efficient manner in order to reduce the morbidity and mortality. Currently used gold standard tests rely on culture and pre-enrichment of E. coli O157:H7 from the contaminated source; they are time consuming and laborious. Molecular methods such as polymerase chain reaction are sensitive; however, they require expensive instrumentation. Therefore, there is a requirement for Accurate, Sensitive, Specific, User friendly, Rapid, Equipment free and Deliverable (ASSURED) detection methods for use in the laboratory and in the field. Emerging technologies such as isothermal amplification methods, biosensors, surface enhanced Raman Spectroscopy, paper-based diagnostics and smartphone-based digital methods are recognized as new approaches in the field of E. coli O157:H7 diagnostics and are discussed in this review. Mobile PCR and CRISPR-Cas diagnostic platforms have been identified as new tools in E. coli O157:H7 POC diagnostics with the potential for implementation by industry. This review describes advances and progress in the field of E. coli O157:H7 diagnosis in the context of food and water industry. The focus is on emerging high throughput point-of-care (POC) E. coli O157:H7 diagnostics and the requirement for the transformation to service routine diagnostics in the food and water industry.

Highly Sensitive Optical Detection of Escherichia coli Using Terbium-Based Metal-Organic Framework

Metal-organic frameworks (MOFs) are envisaged as highly useful for the development of biosensors. Herein, for the first time, we report the optical detection of Escherichia coli using a water-dispersible terbium MOF (Tb-BTC; BTC, 1,3,5-benzenetricarboxylic acid). The successful synthesis of Tb-BTC is verified using spectroscopic and morphological techniques like UV-vis, fluorescence and FTIR spectroscopy, X-ray diffraction analysis, and electron microscopy. Tb-BTC has been bio-interfaced with anti-E. coli antibodies and then investigated as a biosensor for E. coli. The biosensor displays detection ability in an analyte concentration range of 1.3 × 10² to 1.3 × 10⁸ cfu/mL with a detection limit of 3 cfu/mL, having a response time of 5 min and a total analysis time of about 20-25 min. The results are also found to be reproducible and specific in the presence of some other interfering bacterial species. As demonstrated, the present sensor provides highly sensitive and specific detection of E. coli in fruit juice sample. To the best of our knowledge, this is the first report to showcase the potential of the MOF-based fluorescent biosensor for the detection of E. coli.

DNA aptamer-based non-faradaic impedance biosensor for detecting E. coli

Developing a real-time, portable, and inexpensive sensor for pathogenic bacteria is crucial since the conventional detection approaches such as enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) assays are high cost, time-consuming, and require an expert operator. Here we present a portable, inexpensive, and convenient impedance-based biosensor using Interdigitated Electrode (IDE) arrays to detect Escherichia coli (E. coli) as a model to demonstrate the feasibility of an impedance-based biosensor. We manipulated the affinity of the IDE array towards E. coli (E. coli BL21 series) by functionalizing the IDEs' surface with an E. coli outer membrane protein (OMP) Ag1 Aptamer. To determine the dominant factors affecting the sensitivity and the performance of the biosensor in detecting E. coli, we investigated the roles of the substrate material used in the fabrication of the IDE, the concentration of the aptamer, and the composition of the carboxy aliphatic thiol mixture used in the pre-treatment of the IDE surface. In the sensing experiments we used an E. coli concentration range of 25-1000 cfu mL-1 and confirmed the binding of the OMP Ag1 Aptamer to the outer membrane protein of the E. coli by Field Emission Scanning Electron Microscopy (FESEM), Optical Microscopy, and Atomic Force Microscopy (AFM). By tuning the surface chemistry, the IDEs' substrate material, and the concentration of the OMP Ag1 Aptamer, our sensor could detect E. coli with the analytical sensitivity of approximately 1.8 Ohm/cfu and limit of detection of 9 cfu mL-1. We found that the molecular composition of the self-assembled monolayer (SAM) formed on the top of the IDEs before the attachment of the OMP Ag1 Aptamer significantly impacted the sensitivity of the sensor. Notably, with straightforward changes to the molecular recognition elements, this platform device can be used to detect a wide range of other microorganisms and chemicals relevant for environmental monitoring and public health.

Dark Field Microscopy-Based Biosensors for the Detection of E. coli in Environmental Water Samples

Development of sensitive methods for the determination of E. coli bacteria contamination in water distribution systems is of paramount importance to ensure the microbial safety of drinking water. This work presents a new sensing platform enabling the fast detection of bacteria in field samples by using specific antibodies as the biorecognition element and dark field microscopy as the detection technique. The development of the sensing platform was performed using non-pathogenic bacteria, with the E. coli DH5α strain as the target, and Bacillus sp. 9727 as the negative control. The identification of the captured bacteria was made by analyzing the dark field microscopy images and screening the detected objects by using object circularity and size parameters. Specificity tests revealed the low unspecific attachment of either E. coli over human serum albumin antibodies (negative control for antibody specificity) and of Bacillus sp. over E. coli antibodies. The system performance was tested using field samples, collected from a wastewater treatment plant, and compared with two quantification techniques (i.e., Colilert-18 test and quantitative polymerase chain reaction (qPCR)). The results showed comparable quantification capability. Nevertheless, the present method has the advantage of being faster, is easily adaptable to in-field analysis, and can potentially be extended to the detection of other bacterial strains.

Terminal deoxynucleotidyl transferase (TdT)-catalyzed homo-nucleotides-constituted ssDNA: Inducing tunable-size nanogap for core-shell plasmonic metal nanostructure and acting as Raman reporters for detection of Escherichia coli O157:H7

Core-shell plasmonic metal nanoparticles with interior nanogaps are superior nanostructures owing to their large signal enhancement for Surface enhanced Raman spectroscopy (SERS). Herein, we incorporated Terminal deoxynucleotidyl transferase (TdT)-catalyzed DNA in the preparation of core-shell nanostructures for the detection of Escherichia coli O157:H7 (E. coli O157:H7) cells. The elongated products-homo-nucleotides-composed of long single DNA strands (hn-D) are used not only to induce tunable-size nanogaps but also as Raman reporters with consistent and uniform signal enhancement. Using this synthetic process of hn-D-embedded core-shell nanoparticles (hn-DENPs), we found that the length of hn-D strands affects the size of the nanogap. In addition, performances of the specific Raman imaging of E. coli O157:H7, high detection sensitivity of 2 CFU/mL, and the recovery of 98.1%-105.2% measured in the real food samples, make hn-DENP a biosensor that will be widely used in biological detection.

National outbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to mixed salad leaves, United Kingdom, 2016

We investigated a large outbreak of Escherichia coli O157 in the United Kingdom (UK) with 165 cases between 31 May and 29 July 2016. No linked cases were reported in other countries. Cases were predominately female (n = 128) and adult (n = 150), 66 attended hospital and nine had features of haemorrhagic uraemic syndrome. A series of epidemiological studies (case-control, case-case, ingredients-based and venue-based studies) and supply chain investigations implicated mixed salad leaves from Supplier A as the likely outbreak vehicle. Whole genome sequencing (WGS) indicated a link with strains from the Mediterranean and informed the outbreak control team to request that Supplier A cease distributing salad leaves imported from Italy. Microbiological tests of samples of salad leaves from Supplier A were negative. We were unable to confirm the source of contamination or the contaminated constituent leaf although our evidence pointed to red batavia received from Italy as the most likely vehicle. Variations in Shiga toxin-producing E.coli surveillance and diagnosis may have prevented detection of cases outside the UK and highlights a need for greater standardisation. WGS was useful in targeting investigations, but greater coverage across Europe is needed to maximise its potential.

Enterohaemorrhagic and other Shiga toxin-producing Escherichia coli (STEC): Where are we now regarding diagnostics and control strategies?

Escherichia coli comprises a highly diverse group of Gram-negative bacteria and is a common member of the intestinal microflora of humans and animals. Generally, such colonization is asymptomatic; however, some E. coli strains have evolved to become pathogenic and thus cause clinical disease in susceptible hosts. One pathotype, the Shiga toxigenic E. coli (STEC) comprising strains expressing a Shiga-like toxin is an important foodborne pathogen. A subset of STEC are the enterohaemorrhagic E. coli (EHEC), which can cause serious human disease, including haemolytic uraemic syndrome (HUS). The diagnosis of EHEC infections and the surveillance of STEC in the food chain and the environment require accurate, cost-effective and timely tests. In this review, we describe and evaluate tests now in routine use, as well as upcoming test technologies for pathogen detection, including loop-mediated isothermal amplification (LAMP) and whole-genome sequencing (WGS). We have considered the need for improved diagnostic tools in current strategies for the control and prevention of these pathogens in humans, the food chain and the environment. We conclude that although significant progress has been made, STEC still remains an important zoonotic issue worldwide. Substantial reductions in the public health burden due to this infection will require a multipronged approach, including ongoing surveillance with high-resolution diagnostic techniques currently being developed and integrated into the routine investigations of public health laboratories. However, additional research requirements may be needed before such high-resolution diagnostic tools can be used to enable the development of appropriate interventions, such as vaccines and decontamination strategies.

Functional Graphene Nanomaterials Based Architectures: Biointeractions, Fabrications, and Emerging Biological Applications

Functional graphene nanomaterials (FGNs) are fast emerging materials with extremely unique physical and chemical properties and physiological ability to interfere and/or interact with bioorganisms; as a result, FGNs present manifold possibilities for diverse biological applications. Beyond their use in drug/gene delivery, phototherapy, and bioimaging, recent studies have revealed that FGNs can significantly promote interfacial biointeractions, in particular, with proteins, mammalian cells/stem cells, and microbials. FGNs can adsorb and concentrate nutrition factors including proteins from physiological media. This accelerates the formation of extracellular matrix, which eventually promotes cell colonization by providing a more beneficial microenvironment for cell adhesion and growth. Furthermore, FGNs can also interact with cocultured cells by physical or chemical stimulation, which significantly mediate their cellular signaling and biological performance. In this review, we elucidate FGNs-bioorganism interactions and summarize recent advancements on designing FGN-based two-dimensional and three-dimensional architectures as multifunctional biological platforms. We have also discussed the representative biological applications regarding these FGN-based bioactive architectures. Furthermore, the future perspectives and emerging challenges will also be highlighted. Due to the lack of comprehensive reviews in this emerging field, this review may catch great interest and inspire many new opportunities across a broad range of disciplines.

Specific detection of live Escherichia coli O157:H7 using tetracysteine-tagged PP01 bacteriophage

Sensitive and rapid detection of Escherichia coli O157:H7, one of the most notorious bacterial pathogens, is urgently needed for public health protection. Yet, the existing methods are either lack of speed or limited in discriminating viable and dead cells. Using a recombinant bacteriophage, here we report the development of a rapid and sensitive method for live E. coli O157:H7 detection. First, the wild-type PP01 phage was engineered with a tetracysteine (TC)-tag fused with the small outer capsid (SOC) protein. Then, this PP01-TC phage was used to inoculate bacterial sample for 30min. Specific infection and rapid replication of PP01-TC phage in viable E. coli O157:H7 host cell yields a large number of progeny phages with capsids displaying TC tags that can be fluorescently labeled by a membrane permeable biarsenical dye (FlAsH). The bright green fluorescence of single E. coli O157:H7 cells can be readily detected by flow cytometry (FCM) and fluorescence microscopy. High specificity of the assay was verified with seven other bacterial strains. Practical application in E. coli O157:H7 detection in drinks was successfully demonstrated with artificially contaminated 100% apple juice. In less than three hours (including sample preconcentration) and with 40mL of sample volume, as low as 1cfu/mL E. coli O157:H7 can be detected in the presence of large excess of other nontarget bacteria via fluorescence microscopic measurement. The as-developed TC-PP01-FlAsH approach shows a great potential in the safeguard of liquid food products by providing rapid, sensitive, and specific detection of live E. coli O157:H7.