Critical issues in detecting viable Listeria monocytogenes cells by real-time reverse transcriptase PCR

Advancements in Detection Methods for Salmonella in Food: A Comprehensive Review

Non-typhoidal Salmonella species are one of the leading causes of gastrointestinal disease in North America, leading to a significant burden on the healthcare system resulting in a huge economic impact. Consequently, early detection of Salmonella species in the food supply, in accordance with food safety regulations, is crucial for protecting public health, preventing outbreaks, and avoiding serious economic losses. A variety of techniques have been employed to detect the presence of this pathogen in the food supply, including culture-based, immunological, and molecular methods. The present review summarizes these methods and highlights recent updates on promising emerging technologies, including aptasensors, Surface Plasmon Resonance (SPR), and Surface Enhanced Raman Spectroscopy (SERS).

Advances in detection methods for viable Salmonella spp.: current applications and challenges

Salmonella is a common intestinal pathogen that can cause food poisoning and intestinal disease. The high prevalence of Salmonella necessitates efficient and sensitive methods for its identification, detection, and monitoring, especially of viable Salmonella. Conventional culture methods need to be more laborious and time-consuming. And they are relatively limited in their ability to detect Salmonella in the viable but non-culturable status if present in the sample to be tested. As a result, there is an increasing need for rapid and accurate techniques to detect viable Salmonella spp. This paper reviewed the status and progress of various methods reported in recent years that can be used to detect viable Salmonella, such as culture-based methods, molecular methods targeting RNAs and DNAs, phage-based methods, biosensors, and some techniques that have the potential for future application. This review can provide researchers with a reference for additional method options and help facilitate the development of rapid and accurate assays. In the future, viable Salmonella detection approaches will become more stable, sensitive, and fast and are expected to play a more significant role in food safety and public health.

A Review of Modern Methods for the Detection of Foodborne Pathogens

Despite the recent advances in food preservation techniques and food safety, significant disease outbreaks linked to foodborne pathogens such as bacteria, fungi, and viruses still occur worldwide indicating that these pathogens still constitute significant risks to public health. Although extensive reviews of methods for foodborne pathogens detection exist, most are skewed towards bacteria despite the increasing relevance of other pathogens such as viruses. Therefore, this review of foodborne pathogen detection methods is holistic, focusing on pathogenic bacteria, fungi, and viruses. This review has shown that culture-based methods allied with new approaches are beneficial for the detection of foodborne pathogens. The current application of immunoassay methods, especially for bacterial and fungal toxins detection in foods, are reviewed. The use and benefits of nucleic acid-based PCR methods and next-generation sequencing-based methods for bacterial, fungal, and viral pathogens' detection and their toxins in foods are also reviewed. This review has, therefore, shown that different modern methods exist for the detection of current and emerging foodborne bacterial, fungal, and viral pathogens. It provides further evidence that the full utilization of these tools can lead to early detection and control of foodborne diseases, enhancing public health and reducing the frequency of disease outbreaks.

Novel neurolisteriosis therapy using SPION as a drivable nanocarrier in gallic acid delivery to CNS

Neurolisteriosis is an infectious disease of the central nervous system (CNS) with a high mortality rate caused by Listeria monocytogenes. The CNS disorders suffer from inadequacy of drugs accessibility. An experimental in vivo model of neurolisteriosis was developed by oral administration of the bacteria in Wistar rats. It's speculated the capability of magnetite nanoparticles (MNPs) in ferrying gallic acid (GA), as a natural antimicrobial agent, through the blood-brain barrier (BBB) with the assistance of an external magnetic field (EMF). The capability of the formulated nanodrug in traversing through the BBB was approved by detecting blue spots in the Perls' Prussian staining of the brain tissue sections and by an increased iron content of the brain determined by the inductively coupled plasma spectroscopy. The GA release pattern and the nanodrug toxicity assay were promising. Anti-listeriosis effect of the formulated nanodrug was evaluated by molecular quantification of the relative abundance of survived bacteria in brain tissue samples. Besides, the relative expression of the listeriolysin O-encoding hly gene, the prominent virulence factor of L. monocytogenes, was determined using the rplD gene as a reference gene. The nanodrug-received rats showed a significantly less viable bacteria (13.2 ± 7.6%) and a 4.4-fold reduction in the relative expression of the hly gene in comparison to the sham group. Magnetite nanoparticles (MNPs) were synthesized by co-precipitation method, functionalized with GA, and finally coated with Tween 80. The physicochemical properties of the bare and surface modified materials were investigated using different techniques including X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopies, transmission electron microscopy (TEM), field-emission scanning electron microscopy (FESEM), dynamic light scattering (DLS) and Zeta Potential analyses, and vibrating sample magnetometry. In conclusion, MNPs displayed a considerable potential for drug delivery intentions to various target sites such as the CNS. Gallic acid exhibited a binary anti-listerial effect, the destruction of L. monocytogenes bacteria in addition to reducing the expression of the hly gene, which in turn causes reduced survivability of the bacteria in the CNS.

Methods for detection of viable foodborne pathogens: current state-of-art and future prospects

The ability to rapidly detect viable pathogens in food is important for public health and food safety reasons. Culture-based detection methods, the traditional means of demonstrating microbial viability, tend to be laborious, time consuming and slow to provide results. Several culture-independent methods to detect viable pathogens have been reported in recent years, including both nucleic acid-based (PCR combined with use of cell viability dyes or reverse-transcriptase PCR to detect messenger RNA) and phage-based (plaque assay or phage amplification and lysis plus PCR/qPCR, immunoassay or enzymatic assay to detect host DNA, progeny phages or intracellular components) methods. Some of these newer methods, particularly phage-based methods, show promise in terms of speed, sensitivity of detection and cost compared with culture for food testing. This review provides an overview of these new approaches and their food testing applications, and discusses their current limitations and future prospects in relation to detection of viable pathogens in food. KEY POINTS: • Cultural methods may be 'gold standard' for assessing viability of pathogens, but they are too slow. • Nucleic acid-based methods offer speed of detection but not consistently proof of cell viability. • Phage-based methods appear to offer best alternative to culture for detecting viable pathogens.

Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION - Promising Strategies for Multiplex Identification of Viable Pathogens in Food

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in food remains a major challenge. A novel strategy is developed through direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION to achieve real-time multiplex identification of viable pathogens in food. Specifically, this study reports an optimized universal Nanopore sample extraction and library preparation protocol applicable to both Gram-positive and Gram-negative pathogenic bacteria, demonstrated using a cocktail culture of E. coli O157:H7, Salmonella enteritidis, and Listeria monocytogenes, which were selected based on their impact on economic loss or prevalence in recent outbreaks. Further evaluation and validation confirmed the accuracy of direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing using Sanger sequencing and selective media. The study also included a comparison of different bioinformatic pipelines for metatranscriptomic and amplicon genomic analysis. MEGAN without rRNA mapping showed the highest accuracy of multiplex identification using the metatranscriptomic data. EPI2ME also demonstrated high accuracy using multiplex RT-PCR amplicon sequencing. In addition, a systemic comparison was drawn between Nanopore sequencing of the direct metatranscriptome RNA-seq and RT-PCR amplicons. Both methods are comparable in accuracy and time. Nanopore sequencing of RT-PCR amplicons has higher sensitivity, but Nanopore metatranscriptome sequencing excels in read length and dealing with complex microbiome and non-bacterial transcriptome backgrounds.

In Vitro Gene Transcription of Listeria monocytogenes after Exposure to Human Gastric and Duodenal Aspirates

The aim of the present study was to assess, for the first time to our knowledge, Listeria monocytogenes CFU changes, as well as to determine the transcription of key virulence genes, namely, sigB, prfA, hly, plcA, plcB, inlA, inlB, inlC, inlJ, inlP, and lmo2672 after in vitro exposure to human gastric and duodenal aspirates. Furthermore, investigations of the potential correlation between CFU changes and gene regulation with factors influencing gastric (proton pump inhibitor intake and presence of gastric atrophy) and duodenal pH were the secondary study aims. Gastric and duodenal fluids that were collected from 25 individuals undergoing upper gastrointestinal endoscopy were inoculated with L. monocytogenes serotype 4b strain LQC 15257 at 9 log CFU·mL-1 and incubated at 37°C for 100 min and 2 h, respectively, with the time corresponding to the actual exposure time to gastric and duodenal fluids in the human gastrointestinal tract. Sampling was performed upon gastric fluid inoculation, after incubation of the inoculated gastric fluids, upon pathogen resuspension in duodenal fluids and after incubation of the inoculated duodenal fluids. L. monocytogenes CFU changes were assessed by colony counting, as well as reverse transcription quantitative PCR by using inlB as a target. Gene transcription was assessed by reverse transcription quantitative PCR. In 56% of the cases, reduction of the pathogen CFU occurred immediately after exposure to gastric aspirate. Upregulation of hly and inlC was observed in 52 and 58% of the cases, respectively. On the contrary, no upregulation or downregulation was noticed regarding sigB, prfA, plcA, plcB, inlA, inlB, inlJ, inlP, and lmo2672. In addition, sigB and plcA transcription was positively and negatively associated, respectively, with an increase of the pH value, and inlA transcription was negatively associated with the presence of gastric atrophy. Finally, a positive correlation between the transcriptomic responses of plcB, inlA, inlB, inlC, inlJ, inlP, and lmo2672 was detected. This study revealed that the CFU of the pathogen was negatively affected after exposure to human gastroduodenal aspirates, as well as significant correlations between the characteristics of the aspirates with the virulence potential of the pathogen.

RNA-Based Detection Does not Accurately Enumerate Living Escherichia coli O157:H7 Cells on Plants

The capacity to distinguish between living and dead cells is an important, but often unrealized, attribute of rapid detection methods for foodborne pathogens. In this study, the numbers of enterohemorrhagic Escherichia coli O157:H7 after inoculation onto Romaine lettuce plants and on plastic (abiotic) surfaces were measured over time by culturing, and quantitative PCR (qPCR), propidium monoazide (PMA)-qPCR, and reverse transcriptase (RT)-qPCR targeting E. coli O157:H7 gapA, rfbE, eae, and lpfA genes and gene transcripts. On Romaine lettuce plants incubated at low relative humidity, E. coli O157:H7 cell numbers declined 10⁷-fold within 96 h according to culture-based assessments. In contrast, there were no reductions in E. coli levels according to qPCR and only 100- and 1000-fold lower numbers per leaf by RT-qPCR and PMA-qPCR, respectively. Similar results were obtained upon exposure of E. coli O157:H7 to desiccation conditions on a sterile plastic surface. Subsequent investigation of mixtures of living and dead E. coli O157:H7 cells strongly indicated that PMA-qPCR detection was subject to false-positive enumerations of viable targets when in the presence of 100-fold higher numbers of dead cells. RT-qPCR measurements of killed E. coli O157:H7 as well as for RNaseA-treated E. coli RNA confirmed that transcripts from dead cells and highly degraded RNA were also amplified by RT-qPCR. These findings show that neither PMA-qPCR nor RT-qPCR provide accurate estimates of bacterial viability in environments where growth and survival is limited.

Molecular Methods in Food Safety Microbiology: Interpretation and Implications of Nucleic Acid Detection

Because of increasing demand for rapid results, molecular techniques are now applied for the detection of microorganisms in foodstuffs. However, interpretation problems can arise for the results generated by molecular methods in relation to the associated public health risk. Discrepancies between results obtained by molecular and conventional culture methods stem from the difference in target, namely nucleic acids instead of actively growing microorganisms. Nucleic acids constitute 5% to 15% of the dry weight of all living cells and are relatively stable, even after cell death, so they may be present in a food matrix after the foodborne microorganisms have been inactivated. Therefore, interpretation of the public health significance of positive results generated by nucleic acid detection methods warrants some additional consideration. This review discusses the stability of nucleic acids in general and highlights the persistence of microbial nucleic acids after diverse food‐processing techniques based on data from the scientific literature. Considerable amounts of DNA and RNA (intact or fragmented) persist after inactivation of bacteria and viruses by most of the commonly applied treatments in the food industry. An overview of the existing adaptations for molecular assays to cope with these problems is provided, including large fragment amplification, flotation, (enzymatic) pretreatment, and various binding assays. Finally, the negligible risks of ingesting free microbial nucleic acids are discussed and this review ends with the future perspectives of molecular methods such as next‐generation sequencing in diagnostic and source attribution food microbiology.