Differential detection of pathogenic Yersinia spp. by fluorescence in situ hybridization

Fluorescent In Situ Hybridization for the Detection of Intracellular Bacteria in Companion Animals

FISH techniques have been applied for the visualization and identification of intracellular bacteria in companion animal species. Most frequently, these techniques have focused on the identification of adhesive-invasive Escherichia coli in gastrointestinal disease, although various other organisms have been identified in inflammatory or neoplastic gastrointestinal disease. Previous studies have investigated a potential role of Helicobacter spp. in inflammatory gastrointestinal and hepatic conditions. Other studies evaluating the role of infectious organisms in hepatopathies have received some attention with mixed results. FISH techniques using both eubacterial and species-specific probes have been applied in inflammatory cardiovascular, urinary, and cutaneous diseases to screen for intracellular bacteria. This review summarizes the results of these studies.

Establishment of a Real-Time Recombinase Polymerase Amplification for Rapid Detection of Pathogenic Yersinia enterocolitica

Yersinia enterocolitica is a zoonotic proto-microbe that is widespread throughout the world, causes self-limiting diseases in humans or animals and even leads to sepsis and death in patients with severe cases. In this study, a real-time recombinase polymerase amplification (RPA) assay for pathogenic Y. enterocolitica was established based on the ail gene. The results showed that the RPA detection for Y. enterocolitica could be completed within 20 min at an isothermal temperature of 38 °C by optimizing the conditions in the primers and Exo probe. Moreover, the sensitivity of the current RT-RPA was 10^-4 ng/μL, and the study found that the assay was negative in the application of the genomic DNA of other pathogens. These suggest the establishment of a rapid and sensitive real-time RPA method for the detection of pathogenic Y. enterocolitica, which can provide new understandings for the early diagnosis of the pathogens.

The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection

Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.

Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review

As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.

Combination of Direct Viable Count and Fluorescent In Situ Hybridization (DVC-FISH) as a Potential Method for Identifying Viable Vibrio parahaemolyticus in Oysters and Mussels

Vibrio parahaemolyticus is a human food-borne pathogen with the ability to enter the food chain. It is able to acquire a viable, non-cultivable state (VBNC), which is not detected by traditional methods. The combination of the direct viable count method and a fluorescent in situ hybridization technique (DVC-FISH) makes it possible to detect microorganisms that can present VBNC forms in complex samples The optimization of the in vitro DVC-FISH technique for V. parahaemolyticus was carried out. The selected antibiotic was ciprofloxacin at a concentration of 0.75 μg/mL with an incubation time in DVC broth of 5 h. The DVC-FISH technique and the traditional plate culture were applied to detect and quantify the viable cells of the affected pathogen in artificially contaminated food matrices at different temperatures. The results obtained showed that low temperatures produced an important logarithmic decrease of V. parahaemolyticus, while at 22 °C, it proliferated rapidly. The DVC-FISH technique proved to be a useful tool for the detection and quantification of V. parahaemolyticus in the two seafood matrices of oysters and mussels. This is the first study in which this technique has been developed to detect viable cells for this microorganism.

Development of a fixation-free fluorescence in situ hybridization for the detection of Salmonella species

Salmonella is one of the most important infectious bacteria causing severe gastroenteritis and deaths in humans and animals, and the prompt diagnosis is crucial for effective control and treatment. The detection of Salmonella still depends principally on culture-based methods, which is time-consuming and laborious. Recently, polyhexamethylene biguanide (PHMB) was discovered to have cellular delivery properties and its combination with the fluorescence in situ hybridization (FISH) method was exploited for oligomer delivery and the rapid detection of Salmonella spps in this study. Cell-associated fluorescence was quantified using Volocity® 3-D image analysis software (Volocity 6.3, PerkinElmer, Inc.). PHMB complexed with fluorophore-labelled species-specific oligomers permeabilized freshly grown viable strains of Salmonella cells and mediated strong cell-associated fluorescence signals. This strategy further enabled a fixation-free protocol and hybridization in a single reaction. Using the modified FISH method, monoculture Salmonella strains were validated as well as detected in artificially contaminated water and milk within a turnaround period of 5 h. The method was observed to be comparable with the standard FISH technique (sFISH; P > 0.05). The findings suggest that fixation-free delivery and hybridization of oligomers using PHMB can provide a simplified and prompt strategy for Salmonella detection at the species level, and promote early management responses to the disease and appropriate antimicrobial therapy.

Recent methods and biosensors for foodborne pathogen detection in fish: progress and future prospects to sustainable aquaculture systems

The aquaculture industry has advanced toward sustainable recirculating systems, in where parameters of food quality are strictly monitored. Despite that, as in the case of conventional aquaculture practices, the recirculating systems also suffer threats from Aeromonas spp., Vibrio spp., Streptococcus spp., among other foodborne pathogens infecting farmed fish. The aquaculture pathogens are routinely detected by conventional PCR methods or antibody-based tests, with the detection protocols confined to laboratory use. Emerging assay technologies and biosensors recently reported in the literature open new opportunities to the development of sensitive, specific, and portable analytical devices to use in the field. Techniques of DNA/RNA analysis, immunoassays and other nanomolecular technologies have been facing important advances in response time, sensitivity, and enhanced power of discrimination among and within species. Moreover, the recent developments of electrochemical and optical signal transduction have facilitated the incorporation of the innovative assays to practical miniaturized devices. In this work, it is provided a critical review over foodborne pathogen detection by existing and promising methods and biosensors applied to fish samples and extended to other food matrices. While isothermal DNA/RNA amplification methods can be highlighted among the assay methods for their promising analytical performance and suitability for point-of-care testing, the electrochemical transduction provides a way to achieve cost-effective biosensors amenable to use in the aquaculture field. The adoption of new methods and biosensors would constitute a step forward in securing sustainable aquaculture systems.

Miniaturized Paper-Supported 3D Cell-Based Electrochemical Sensor for Bacterial Lipopolysaccharide Detection

Sensitive detection of lipopolysaccharides (LPSs), which are present on the outer wall of Gram-negative bacteria, is important to reflect the degree of bacterial contamination in food. For indirect assessment of the LPS content, a miniaturized electrochemical cell sensor consisting of a screen-printed paper electrode, a three-dimensional cells-in-gels-in-paper culture system, and a conductive jacket device was developed for in situ detection of nitric oxide released from LPS-treated mouse macrophage cells (Raw264.7). Nafion/polypyrrole/graphene oxide with excellent selectivity, high conductivity, and good biocompatibility functionalized on the working electrode via electrochemical polymerization could enhance sensing. Raw264.7 cells encapsulated in the alginate hydrogel were immobilized on a Nafion/polypyrrole/graphene oxide/screen-printed carbon electrode in paper fibers as a biorecognition element. Differential impulse voltammetry was employed to record the current signal as-influenced by LPS. Results indicated that LPS from Salmonella enterica serotype Enteritidis caused a significant increase in peak current, varying from 1 × 10^-2 to 1 × 10⁴ ng/mL, dose-dependently. This assay had a detection limit of 3.5 × 10^-3 ng/mL with a linear detection range of 1 × 10^-2 to 3 ng/mL. These results were confirmed by analysis of nitric oxide released from Raw264.7 via the Griess method. The miniaturized sensor was ultimately applied to detect LPSs in fruit juice samples. The results indicated that the method exhibited high recovery and relative standard deviation lower than 2.65% and LPSs in samples contaminated with 10²-10⁵ CFU/mL bacteria could be detected, which proved the practical value of the sensor. Thus, a novel, low-cost, and highly sensitive approach for LPS detection was developed, providing a method to assess Gram-negative bacteria contamination in food.

NOTIFy (non-toxic lyophilized field)-FISH for the identification of biological agents by Fluorescence in situ Hybridization

The rapid and reliable diagnostics of highly pathogenic bacteria under restricted field conditions poses one of the major challenges to medical biodefense, especially since false positive or false negative reports might have far-reaching consequences. Fluorescence in situ hybridization (FISH) has the potential to represent a powerful microscopy-based addition to the existing molecular-based diagnostic toolbox. In this study, we developed a set of FISH-probes for the fast, matrix independent and simultaneous detection of thirteen highly pathogenic bacteria in different environmental and clinical sample matrices. Furthermore, we substituted formamide, a routinely used chemical that is toxic and volatile, by non-toxic urea. This will facilitate the application of FISH under resource limited field laboratory conditions. We demonstrate that hybridizations performed with urea show the same specificity and comparable signal intensities for the FISH-probes used in this study. To further simplify the use of FISH in the field, we lyophilized the reagents needed for FISH. The signal intensities obtained with these lyophilized reagents are comparable to freshly prepared reagents even after storage for a month at room temperature. Finally, we show that by the use of non-toxic lyophilized field (NOTIFy)-FISH, specific detection of microorganisms with simple and easily transportable equipment is possible in the field.

A comprehensive review on the prevalence, pathogenesis and detection ofYersinia enterocolitica

Food safety is imperative for a healthy life, but pathogens are still posing a significant life threat. “Yersiniosis” is caused by a pathogen named Yersinia enterocolitica and is characterized by diarrheal, ileitis, and mesenteric lymphadenitis types of sicknesses. This neglected pathogen starts its pathogenic activity by colonizing inside the intestinal tract of the host upon the ingestion of contaminated food. Y. enterocolitica remains a challenge for researchers and food handlers due to its growth habits, low concentrations in samples, morphological similarities with other bacteria and lack of rapid, cost-effective, and accurate detection methods. In this review, we presented recent information about its prevalence, biology, pathogenesis, and existing cultural, immunological, and molecular detection approaches. Our ultimate goal is to provide updated knowledge regarding this pathogen for the development of quick, effective, automated, and sensitive detection methods for the systematic detection of Y. enterocolitica.

Food safety is imperative for a healthy life, but pathogens are still posing a significant life threat.

Designing a new biosensor "DNA ELISA" to detect Escherichia coli using genomic DNA and comparison of this method to PCR-ELISA

In this experiment, DNA-ELISA biosensor was introduced, bearing the ability to detect specific bacteria in about 4 h. This is a more rapid system in comparison to conventional methods, like colony counting method. Moreover, this method does not require any amplification and directly detects genomic DNA of bacteria, giving a lower limit to the sensitivity of 40,000 bacteria. In this study, two specific probes capture (biotin labelled) and detector (dig labelled), were used against special regions of 16s rRNA gene of Escherichia coli ATCC 25922. The capture probe has the ability to trap the target bacterial DNA from a pool of other kinds of bacteria under specific conditions. The detector probe then was used to hybridize to the genome of trapped bacteria. The detection proceeds by adding HRP-anti dig enzyme and its substrate, ABTS to emit light. Light absorbance is measured for verifying the detection.