Standardization of diagnostic PCR for the detection of foodborne pathogens

Surface Blocking-Based Potentiometric Biosensor for Detection of E. coli ATCC 15597 Using Phage MS2 as a Receptor

Nowadays, using a potentiometric ion sensor to achieve detection of biological analytes is still a big challenge, since these analytes usually do not yield a measurable ion signal. To address this challenge, a simple and robust potentiometric sensing protocol based on a delayed Nernstian response is proposed for the label-free detection of biological analytes. The proposed sensor platform is composed of two layers: the surface recognition layer and the indicator-ion-selective electrode (ISE) membrane layer. It is based on a surface blocking mechanism in which the surface recognition interactions between the surface recognition element and the target can impede the diffusion of the indicator ion from the aqueous phase to the sensing membrane phase to reach the final Nernstian-response equilibrium, thus resulting in a delayed potential change. Such a potential change could be used to measure the concentration of a biological target in the sample. Thus, a sensing system was designed by using phage MS2, its host bacterium Escherichia coli ATCC 15597(abbreviated as E. coli H), and a solid-contact butyrylcholine ISE as a surface recognition element, a target, and an indicator electrode, respectively. This new concept offers a simple, sensitive, and extremely selective potentiometric method for detection of E. coli H with a detection limit of 100 CFU mL-1. It can be expected that the present approach may pave the way to using ISEs to detect various important nonionic biological targets in clinical and environmental applications.

Comparison of real-time PCR and nested PCR based on the HlyA gene for the detection of Listeria monocytogenes. Application on cheese samples

The aim of the present study was to compare the performance of a nested polymerase chain reaction (nPCR) and a real-time PCR based on the amplification of the HlyA gene from Listeria monocytogenes using a plasmid DNA standard. Nested PCR was developed with an internal amplification control (IAC). Both techniques were validated in soft cheese samples by comparing their results with the results of the microbiological reference method ISO 11290-1:2017. Cheese samples artificially contaminated with 3.5 to 3,500 UFC/25 g were processed by ISO 11290-1:2017 and, at several times of culture, DNA samples were extracted. All cheeses contaminated with L. monocytogenes were positive for the microbiological method 96 h post contamination and for nPCR and real-time PCR 48 h post contamination. At this time, the HlyA gene was amplified in all contaminated samples. Both molecular techniques showed the same sensitivity, 30 copies/reaction or 3.5 UFC/25 g, when plasmid DNA standard or artificially contaminated cheese samples were used. Finally, eighty soft cheese samples obtained from local retail stores and tested by three methods were negative, indicating a 100% concordance in results. The development of an nPCR with IAC reinforces the reliability of the negative results without increasing the costs of the reaction. Besides, nPCR showed less sensitivity to the presence of inhibitory substances in the reaction. The use of one of these molecular techniques could be easily coupled to the microbiological method, serving as a screening method in the food industry for hygiene monitoring and early identification of contaminated foods.

Recent Advances in Aptamer-Based Biosensors for Bacterial Detection

The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.

Occurrence of Salmonella spp. in animal patients and the hospital environment at a veterinary academic hospital in South Africa

Background and Aims

Nosocomial infections caused by Salmonella spp. are common in veterinary facilities. The early identification of high-risk patients and sources of infection is important for mitigating the spread of infections to animal patients and humans. This study investigated the occurrence of Salmonella spp. among patients at a veterinary academic hospital in South Africa. In addition, this study describes the environmental factors that contribute to the spread of Salmonella spp. in the veterinary facility.

Materials and Methods

This study used a dataset of Salmonella-positive animals and environmental samples submitted to the bacteriology laboratory between 2012 and 2019. The occurrence of Salmonella isolates at the veterinary hospital was described based on source, month, season, year, and location. Proportions and 95% confidence intervals were calculated for each variable.

Results

A total of 715 Salmonella isolates were recorded, of which 67.6% (483/715) came from animals and the remainder (32.4%, 232/715) came from environmental samples. The highest proportion (29.2%) of Salmonella isolates was recorded in 2016 and most isolates were reported in November (17.4%). The winter season had the lowest (14.6%) proportion of isolates reported compared to spring (31.3%), summer (27.8%), and autumn (26.4%). Salmonella Typhimurium (20.0%) was the most frequently reported serotype among the samples tested, followed by Salmonella Anatum (11.2%). Among the positive animal cases, most (86.3%) came from equine clinics. Most reported isolates differed based on animal species with S. Typhimurium being common in equines and S. Anatum in bovines.

Conclusion

In this study, S. Typhimurium emerged as the predominant strain in animal and environmental samples. Equines were the most affected animals; however, Salmonella serotypes were also detected in the production animals. Environmental contamination was also a major source of Salmonella species in this study. To reduce the risk of transmission, strict infection prevention and control measures (biosecurity) must be implemented.

Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection

Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.

Hyperspectral Imaging and Selected Biological Control Agents for the Management of Fusarium Head Blight in Spring Wheat

Fusarium spp. are important pathogens on cereals, capable of causing considerable yield losses and significantly reducing the quality of harvested grains due to contamination with mycotoxins. The European Union intends to reduce the use of chemical-synthetic plant protection products (csPPP) by up to 50% by the year 2030. To realize this endeavor without significant economic losses for farmers, it is crucial to have both precise early detection of pathogens and effective alternatives for csPPP. To investigate both the early detection of Fusarium head blight (FHB) and the efficacy of selected biological control agents (BCAs), a pot experiment with spring wheat (cv. 'Servus') was conducted under semi-field conditions. Spikes were sprayed with different BCAs prior to inoculation with a mixture of F. graminearum and F. culmorum conidia. While early detection of FHB was investigated by hyperspectral imaging (HSI), the efficiency of the fungal (Trichoderma sp. T10, T. harzianum T16, T. asperellum T23 and Clonostachys rosea CRP1104) and bacterial (Bacillus subtilis HG77 and Pseudomonas fluorescens G308) BCAs was assessed by visual monitoring. Evaluation of the hyperspectral images using linear discriminant analysis (LDA) resulted in a pathogen detection nine days post inoculation (dpi) with the pathogen, and thus four days before the first symptoms could be visually detected. Furthermore, support vector machines (SVM) and a combination of LDA and distance classifier (DC) were also able to detect FHB symptoms earlier than manual rating. Scoring the spikes at 13 and 17 dpi with the pathogen showed no significant differences in the FHB incidence among the treatments. Nevertheless, there is a trend suggesting that all BCAs exhibit a diminishing effect against FHB, with fungal isolates demonstrating greater efficacy compared to bacterial ones.

Hybrid Autofluorescence and Optoacoustic Microscopy for the Label-Free, Early and Rapid Detection of Pathogenic Infections in Vegetative Tissues

Agriculture plays a pivotal role in food security and food security is challenged by pests and pathogens. Due to these challenges, the yields and quality of agricultural production are reduced and, in response, restrictions in the trade of plant products are applied. Governments have collaborated to establish robust phytosanitary measures, promote disease surveillance, and invest in research and development to mitigate the impact on food security. Classic as well as modernized tools for disease diagnosis and pathogen surveillance do exist, but most of these are time-consuming, laborious, or are less sensitive. To that end, we propose the innovative application of a hybrid imaging approach through the combination of confocal fluorescence and optoacoustic imaging microscopy. This has allowed us to non-destructively detect the physiological changes that occur in plant tissues as a result of a pathogen-induced interaction well before visual symptoms occur. When broccoli leaves were artificially infected with Xanthomonas campestris pv. campestris (Xcc), eventually causing an economically important bacterial disease, the induced optical absorption alterations could be detected at very early stages of infection. Therefore, this innovative microscopy approach was positively utilized to detect the disease caused by a plant pathogen, showing that it can also be employed to detect quarantine pathogens such as Xylella fastidiosa.

Electrochemical Biosensors for Pathogen Detection: An Updated Review

Electrochemical biosensors are a family of biosensors that use an electrochemical transducer to perform their functions. In recent decades, many electrochemical biosensors have been created for pathogen detection. These biosensors for detecting infections have been comprehensively studied in terms of transduction elements, biorecognition components, and electrochemical methods. This review discusses the biorecognition components that may be used to identify pathogens. These include antibodies and aptamers. The integration of transducers and electrode changes in biosensor design is a major discussion topic. Pathogen detection methods can be categorized by sample preparation and secondary binding processes. Diagnostics in medicine, environmental monitoring, and biothreat detection can benefit from electrochemical biosensors to ensure food and water safety. Disposable and reusable biosensors for process monitoring, as well as multiplexed and conformal pathogen detection, are all included in this review. It is now possible to identify a wide range of diseases using biosensors that may be applied to food, bodily fluids, and even objects' surfaces. The sensitivity of optical techniques may be superior to electrochemical approaches, but optical methods are prohibitively expensive and challenging for most end users to utilize. On the other hand, electrochemical approaches are simpler to use, but their efficacy in identifying infections is still far from satisfactory.

A MoS2 platform and thionine-carbon nanodots for sensitive and selective detection of pathogens

This work focuses on the combination of molybdenum disulfide (MoS₂) and à la carte functionalized carbon nanodots (CNDs) for the development of DNA biosensors for selective and sensitive detection of pathogens. MoS₂ flakes prepared through liquid-phase exfoliation, serves as platform for thiolated DNA probe immobilization, while thionine functionalized carbon nanodots (Thi-CNDs) are used as electrochemical indicator of the hybridization event. Spectroscopic and electrochemical studies confirmed the interaction of Thi-CNDs with DNA. As an illustration of the pathogen biosensor functioning, DNA sequences from InIA gen of Listeria monocytogenes bacteria and open reading frame sequence (ORF1ab) of SARS-CoV-2 virus were detected and quantified with a detection limit of 67.0 fM and 1.01 pM, respectively. Given the paradigmatic selectivity of the DNA hybridization, this approach allows pathogen detection in the presence of other pathogens, demonstrated by the detection of Listeria monocytogenes in presence of Escherichia coli. We note that this design is in principle amenable to any pathogen for which the DNA has been sequenced, including other viruses and bacteria. As example of the application of the method in real samples it has been used to directly detect Listeria monocytogenes in cultures without any DNA Polymerase Chain Reaction (PCR) amplification process.

Prevalence, typing and antimicrobial resistance of Salmonella isolates from commercial shellfish in the North coast of Morocco

Salmonellosis is one of the most common foodborne illnesses in the world. The irrational use of antibiotics in medicine and in animal nutrition has greatly favored the emergence and spread of resistant strains of non-typhoid Salmonella. This study aims the determination of the prevalence of Salmonella in bivalve mollusks in Northern Morocco, as well as the molecular typing and antibiotic susceptibility testing of the strains isolated from positive samples. In total, 150 samples from shellfish composed of mussels (Mytilus galloprovincialis), clams (Callista chione and Ruditapes descussatus) and oysters (Magallana gigas). Isolated Salmonella were characterized by Molecular techniques PCR, MLST and MLVA, phylogenetically grouped by MLSA, and susceptibilities were determined for 30 antimicrobial drugs using microdilution method by the BD Phoenix Automated Microbiology System. Prevalence of Salmonella enterica subsp. enterica was 12.67%, grouped in four serovars identified as Chester, Hadar, Typhimurium and Kentucky. Five different MLST STs (sequence types) were detected, ST1954 being the most common, which was mostly found in Chester isolates. Forty-two percent of the isolates showed resistance to more than one antibiotic, especially trimethoprim, sulfa drugs, quinolones and β-lactam. There was a marked change in the serovars and antimicrobial resistance profiles of the Salmonella isolates in this study compared to those in previous studies.

Molecular diagnostic of toxigenic Corynebacterium diphtheriae strain by DNA sensor potentially suitable for electrochemical point-of-care diagnostic

The presented study is focused on the development of electrochemical genosensor for detection of tox gene fragment of toxigenic Corynebacterium diphtheriae strain. Together with our previous studies it fulfils the whole procedure for fast and accurate diagnostic of diphtheria at its early stage of infection with the use of electrochemical methods. The developed DNA sensor potentially can be used in more sophisticated portable device. After the electrochemical stem-loop probe structure optimization the conditions for real asymmetric PCR (aPCR) product detection were selected. As was shown it was crucial to optimize the magnesium and organic solvent concentrations in detection buffer. Under optimal conditions it was possible to selectively detect as low as 20.8 nM of complementary stand in 5 min or 0.5 nM in 30 min with sensitivity of 12.81 and 0.24 1⋅μM^-1 respectively. The unspecific biosensor response was elucidated with the use of new electrode blocking agent, diethyldithiocarbamate. Its application in electrochemical genosensors lead to significant higher current values and the biosensor response even in conditions with magnesium ion depletion. The developed biosensor selectivity was examined using samples containing genetic material originated from a number of non-target bacterial species which potentially can be present in the human upper respiratory tract.

Baleen-Mimicking Virtual Filters for Rapid Detection of Pathogenic Bacteria in Water Using Magnetic Nanoparticle Chains and a Halbach Ring

We have developed a virtual filter that quickly and efficiently captures and detects pathogenic bacteria in large amounts of water. The virtual filter comprised magnetic nanoparticle chains (MNCs) obtained by cross-linking alginate-coated magnetic nanoparticles (MNPs). When the MNC solution in a disposable plastic tube was exposed to an external magnetic field, the MNCs were aligned along the magnetic field lines, forming a filter similar to a whale's baleen filtering system. A Halbach ring that increased the magnetic field inside the ring was used as the source of an external magnetic field. The Halbach ring produced a more uniform and denser alignment of MNCs than any other ring array. To demonstrate the performance of the virtual filter comprising MNCs, Escherichia coli (E. coli) O157-spiked water was injected into the virtual filter comprising polyethyleneimine-coated MNCs, and the concentration of E. coli O157 captured by electrostatic interaction was determined using qPCR analysis. The bacterial capture efficiency using MNCs was 90% at a flow rate of 5 mL/min, and the detection limit after 10 min of preconcentration of bacteria was 10 cfu/mL, which is 100 times lower than that obtained using qPCR alone.

Recent advances on functional nucleic acid-based biosensors for detection of food contaminants

It has seen increasing development of reliable, robust, and flexible biosensors for rapid food-safety analysis in the past few decades. Recently, functional nucleic acid-based biosensors have attracted attention because of their programmability, bottom-up characteristics, and structural switches. However, few systematic reviews devoted to categorizing the potential of DNA nanostructures and devices were found for detecting food contaminants. Hence, the applications of functional nucleic acid-based biosensors were reviewed for analyzing food contaminants, including foodborne pathogen bacteria, biotoxins, heavy metals, and et al. In addition to categorizing the various biosensors, multiple signal readout strategies, such as optical, electrochemical, and mass-based signals were also examined. Finally, the future changes and potential opportunities, as well as practical applications of functional nucleic acid-based biosensors were discussed.

Electrochemical biosensors for pathogen detection

Recent advances in electrochemical biosensors for pathogen detection are reviewed. Electrochemical biosensors for pathogen detection are broadly reviewed in terms of transduction elements, biorecognition elements, electrochemical techniques, and biosensor performance. Transduction elements are discussed in terms of electrode material and form factor. Biorecognition elements for pathogen detection, including antibodies, aptamers, and imprinted polymers, are discussed in terms of availability, production, and immobilization approach. Emerging areas of electrochemical biosensor design are reviewed, including electrode modification and transducer integration. Measurement formats for pathogen detection are classified in terms of sample preparation and secondary binding steps. Applications of electrochemical biosensors for the detection of pathogens in food and water safety, medical diagnostics, environmental monitoring, and bio-threat applications are highlighted. Future directions and challenges of electrochemical biosensors for pathogen detection are discussed, including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, reusable biosensors for process monitoring applications, and low-cost, disposable biosensors.

Development and Evaluation of a Novel Armored RNA Technology Using Bacteriophage Qβ

Foodborne viruses are a global threat to food safety. Real-time reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used method to detect viral RNA in food. Armored RNA (AR) prepared using the MS2 phage system is a successful positive control for detecting foodborne viruses and is an important quality control process when using real-time RT-PCR. In this study, we report a novel technology for preparing AR using bacteriophage Qβ and compare its stability with AR prepared using the MS2 phage system for packaging norovirus detection target RNA. AR could be successfully and efficiently produced using the developed bacteriophage Qβ system. Two types of AR-AR-QNoV prepared using the Qβ system and AR-MNoV prepared using the MS2 system-were stored at different temperatures for different durations. After incubating at - 20 °C for 360 days, the copy numbers of AR-QNoV and AR-MNoV decreased by 8.9% and 35.9%, respectively. After incubating at 4 °C for 60 days, the copy numbers of AR-QNoV and AR-MNoV decreased by 12.0% and 38.9%, respectively. After incubating at 45 °C, the copy numbers of AR-QNoV decreased by 71.8% after 5 days, whereas those of AR-MNoV decreased by 92.9% after only 4 days. After 5 days, AR-MNoV could not be detected using real-time RT-PCR. There was a significant difference in copy numbers decrease rate between AR-QNoV and AR-MNoV at three different temperatures (P < 0.05 ). Therefore, AR prepared using the new bacteriophage Qβ system is more stable than the traditional AR, making the developed strategy a good candidate for AR preparation and quality control.

Molecular viability testing of viable but non-culturable bacteria induced by antibiotic exposure

Nucleic acid amplification-based methods are limited by their inability to discriminate between viable and dead cells. To overcome this drawback, propidium monoazide (PMA) combined with qPCR has been used to differentiate viable from nonviable cells in environmental samples. However, assessing bacterial physiology using PMA-qPCR remains a challenge due to its incapability of detecting metabolic activities, leading to overestimation of the viable bacteria population under an inactivation condition (e.g. antibiotic treatments). A recent advanced technique to amplify ribosomal RNA precursors (pre-rRNA) has been shown to detect viable cells because pre-rRNAs are intermediates in rRNA synthesis. This study investigated the effect of different types of antibiotics on the bacterial viability or viable but non-culturable (VBNC) state using both PMA-qPCR and pre-rRNA analyses with Pseudomonas aeruginosa. This study demonstrated that P. aeruginosa was more sensitive to colistin than it was to carbenicillin, gentamicin and levofloxacin. We could discriminate VBNCP. aeruginosa cells using PMA-qPCR when antibiotic pressure induced the VBNC state. Also, pre-rRNA was able to distinguish viable cells from colistin-inactivated bacteria cells, and it could detect the presence of VBNC and persister cells. Our results showed that these two molecular methods could successfully eliminate false-positive signals derived from antibiotics-inactivated cells.

Survey of Salmonella spp. in beef meat for export at slaughterhouses in Brazil

ABSTRACT: The aim of the present study was to investigate the presence of Salmonella spp. in samples collected from beef meat at three points of the slaughter line (after skinning, washing and cooling) at three slaughterhouses in Brazil that export meat. Detection was based on ISO 6579:2002 and confirmed by PCR and qPCR. The isolates were typified using slide agglutination tests and PFGE. The antibiotic sensitivity profile was determined using the disk diffusion method. Contamination was detected in only one slaughterhouse. The overall frequency of contamination by Salmonella spp. was 6.7% of carcasses (6/90) and 2.6% of carcass surface samples (7/270). All isolates were confirmed by PCR and qPCR. The serological analysis and the PFGE showed a single profile: Typhimurium. The strains demonstrated 100% susceptibility to ampicillin, cefotaxime, ciprofloxacin, chloramphenicol, gentamicin and tetracycline. Positive carcasses after cooling pose a direct risk to consumers, since the meat is considered ready to be marketed after this process.

Presence and Persistence of Salmonella in Water: The Impact on Microbial Quality of Water and Food Safety

Salmonella ranks high among the pathogens causing foodborne disease outbreaks. According to the Centers for Disease Control and Prevention, Salmonella contributed to about 53.4% of all foodborne disease outbreaks from 2006 to 2017, and approximately 32.7% of these foodborne Salmonella outbreaks were associated with consumption of produce. Trace-back investigations have suggested that irrigation water may be a source of Salmonella contamination of produce and a vehicle for transmission. Presence and persistence of Salmonella have been reported in surface waters such as rivers, lakes, and ponds, while ground water in general offers better microbial quality for irrigation. To date, culture methods are still the gold standard for detection, isolation and identification of Salmonella in foods and water. In addition to culture, other methods for the detection of Salmonella in water include most probable number, immunoassay, and PCR. The U.S. Food and Drug Administration (FDA) issued the Produce Safety Rule (PSR) in January 2013 based on the Food Safety Modernization Act (FSMA), which calls for more efforts toward enhancing and improving approaches for the prevention of foodborne outbreaks. In the PSR, agricultural water is defined as water used for in a way that is intended to, or likely to, contact covered produce, such as spray, wash, or irrigation. In summary, Salmonella is frequently present in surface water, an important source of water for irrigation. An increasing evidence indicates irrigation water as a source (or a vehicle) for transmission of Salmonella. This pathogen can survive in aquatic environments by a number of mechanisms, including entry into the viable but nonculturable (VBNC) state and/or residing within free-living protozoa. As such, assurance of microbial quality of irrigation water is critical to curtail the produce-related foodborne outbreaks and thus enhance the food safety. In this review, we will discuss the presence and persistence of Salmonella in water and the mechanisms Salmonella uses to persist in the aquatic environment, particularly irrigation water, to better understand the impact on the microbial quality of water and food safety due to the presence of Salmonella in the water environment.

Solid-Phase Microextraction of DNA from Mycobacteria in Artificial Sputum Samples To Enable Visual Detection Using Isothermal Amplification

Point-of-care (POC) technologies for the detection of pathogens in clinical samples are highly valued due to their speed, ease of use, and cost-effectiveness. Furthermore, they are ideally suited for resource-limited settings where expensive and sophisticated laboratory equipment may not be readily available. In this study, a rapid method based on solid-phase microextraction (SPME) of mycobacterial DNA with subsequent isothermal amplification and visual detection was developed. Direct coupling of the SPME desorption solution (1 M NaCl) to the isothermal reaction system was achieved to circumvent dilution steps and improve detection limits. Using this method, DNA was preconcentrated from lysed mycobacteria in just 2 min, subjected to isothermal multiple-self-matching-initiated amplification (IMSA), and the amplicons were detected visually. With a total analysis times of less than 2 h, the optimized method was capable of extracting and visually detecting mycobacterial DNA from artificial sputum samples containing clinically relevant concentrations of mycobacteria (10⁷ colony forming units/mL), demonstrating its potential for future POC applications.

Molecular discrimination of Bacillus cereus group species in foods (lettuce, spinach, and kimbap) using quantitative real-time PCR targeting groEL and gyrB

The aim of the study was to identify and evaluate specific biomarkers to differentiate within Bacillus cereus group species from contaminated food samples with the use of real-time PCR. A total of 120 strains, comprising of 28 reference, 2 type, 78 wild strains of B. cereus and B. thuringiensis along with 12 strains representing 2 bacterial groups - B. mycoides, B. pseudomycoides, B. weihenstephanensis (B. cereus group); B. amyloliquefaciens, B. subtilis, Enterococcus faecalis, Escherichia coli, Listeria monocytogenes, Micrococcus luteus, Salmonella enterica, Staphylococcus aureus, Streptococcus pyogenes (non-Bacillus sp.) were identified by applying valid biomarkers (groEL and gyrB). In addition, the presence of B. cereus group was determined in three different artificially contaminated vegetable samples (lettuce, spinach, and kimbap), using prominent biomarkers targeting on chaperonin protein (GroEL) and topoisomerase enzyme protein (gyrB). Direct analysis of samples revealed the specificity towards identification and characterization of the B. cereus group among wild, reference and type strains and the type strain inoculated in vegetables. Our results demonstrated two existing biomarkers groEL and gyrB with a high specificity of 98% and 96% respectively to analyze the total B. cereus group. Further, we also reported the detection limit of groEL and gyrB in food samples was 3.5 and 3.7 log CFU/g respectively. Thus, the developed real-time PCR approach can be a reliable and effective tool for the identification of B. cereus group strains present in environment and food samples. This does not require band isolation, re-amplification, sequencing or sequence identification, thus reducing the time and cost of analysis.

Unique biomarkers as a potential predictive tool for differentiation of Bacillus cereus group based on real-time PCR

The aim of the study was to develop unique biomarkers for qPCR detection of Bacillus cereus group. Clinical and soil isolates were identified by specifically designed biomarkers - Lipoprotein (OPL-114-lipo), Methyltransferase (MT-17) and S-layer homology domain protein (151-1BC). In order to design biomarkers, we used 120 bacterial strains grouped into B. cereus and non-Bacillus group. The B. cereus group was confirmed by 108 strains of B. cereus and B. thuringiensis (30 reference and 78 wild), along with 3 strains of B. mycoides, B. pseudomycoides, and B. weihenstephanensis; while the non-Bacillus group was composed of 9 Gram-positive and Gram-negative strains. Direct analysis of samples revealed specificity towards identification and characterization of B. cereus group. The newly developed markers OPL-114-lipo and MT-17 showed specificity of 95% and 81%, respectively in identification of B. cereus. They are efficient tools to identify contaminated sources and the degree of bacterial contamination. Environmental and food samples do not require band isolation, re-amplification, sequencing or sequence identification. Thus, reducing the time and cost of analysis. Hence, it will be an alternative approach to traditional culture methods. Commercial food processing industries will be able to employ these biomarkers specific for B. cereus group as a detection tool to reduce economic loss due to B. cereus contamination.

Nucleic Acid Biosensor Synthesis of an All-in-One Universal Blocking Linker Recombinase Polymerase Amplification with a Peptide Nucleic Acid-Based Lateral Flow Device for Ultrasensitive Detection of Food Pathogens

In this study, a whole-course nucleic-acid-constructed biosensor that combines the all-in-one concepts of the universal blocking linker recombinase polymerase amplification (UBLRPA) and a peptide nucleic acid (PNA)-based lateral flow device (PLFD) has been developed for the ultrasensitive detection of food pathogens. Using the preamplification UBLRPA principle, a universal linker and C3 space blocker were utilized to produce the universal linker single-duplex DNA products. The developed amplification system was employed to convert duplex products to a single strand. In the signal recognition strategy, a special PNA probe was successfully employed in the portable PLFD. The UBLRPA products were identified visually using the PLFD through dual hybridization (a PNA probe on the gold nanoparticle (Au-NP) was combined with a universal linker on the end of the products; a PNA capture probe was used on the test line and a universal linker on the other end of the products). The accumulation of Au-NPs produced a characteristic red band, enabling the visual detection of a food pathogen without further testing. To demonstrate the value of the all-in-one biosensor, Salmonella enterica subsp. enterica serovar typhimurium was used as a model organism. The biosensor showed high selectivity and extraordinary repeatability using S. typhimurium, and the limit of detection was 4 CFU mL^-1. Furthermore, when milk samples artificially contaminated with S. typhimurium were analyzed, the analysis was completed within 30 min without complicated instrumentation. The results exhibited good precision and recovery. This portable all-in-one biosensor demonstrates great promise for the screening of pathogens in food and environmental samples.

Novel motB as a potential predictive tool for identification of B. cereus, B. thuringiensis and differentiation from other Bacillus species by triplex real-time PCR

Quantitative triplex real-time PCR (qPCR) offers an alternative method for detection of bacterial contamination. It provides quantitation of the number of gene copies. In our study, we established a qPCR assay to detect and quantify the specificity towards Bacillus cereus and B. thuringiensis. The assay was designed to detect a 280 bp fragment of motB gene encoding the flagellar motor protein, specific for detection of B. cereus and B. thuringiensis, excluding other group species B. pseudomycoides, B. mycoides and B. weihenstephanensis. Specificity of the assay was confirmed with 111 strains belonging to Bacillus cereus group and performed against 58 B. cereus, 50 B. thuringiensis, 3 other Bacillus bacteria and 9 non-Bacillus bacteria. Detection limit was determined for each assay. Direct analysis of samples revealed the specificity towards identification and characterization of B. cereus group cultured in nutrient media. Based on results, it was observed that motB showed 97% specificity towards B. cereus strains, 98% for B. thuringiensis but other B. cereus group showed less sensitivity (0%), thus, provides an efficient tool to identify B. cereus and B. thuringiensis. Further, environmental and food samples do not require band isolation, re-amplification or sequence identification. Thus, reducing the time and cost of analysis.

Neonatal listeriosis: Uncommon or misdiagnosed?

The incidence of perinatal and neonatal Listeriosis is underestimated due undiagnosed stillbirths, misdiagnosis of NL and underreporting of single case reports. Recent outbreaks reinforce the need for better surveillance and targeted health education in certain population groups especially during pregnancy.

Influence of Pichia pastoris cellular material on polymerase chain reaction performance as a synthetic biology standard for genome monitoring

Advances in synthetic genomics are now well underway in yeasts due to the low cost of synthetic DNA. These new capabilities also bring greater need for quantitating the presence, loss and rearrangement of loci within synthetic yeast genomes. Methods for achieving this will ideally; i) be robust to industrial settings, ii) adhere to a global standard and iii) be sufficiently rapid to enable at-line monitoring during cell growth. The methylotrophic yeast Pichia pastoris (P. pastoris) is increasingly used for industrial production of biotherapeutic proteins so we sought to answer the following questions for this particular yeast species. Is time-consuming DNA purification necessary to obtain accurate end-point polymerase chain reaction (e-pPCR) and quantitative PCR (qPCR) data? Can the novel linear regression of efficiency qPCR method (LRE qPCR), which has properties desirable in a synthetic biology standard, match the accuracy of conventional qPCR? Does cell cultivation scale influence PCR performance? To answer these questions we performed e-pPCR and qPCR in the presence and absence of cellular material disrupted by a mild 30s sonication procedure. The e-pPCR limit of detection (LOD) for a genomic target locus was 50pg (4.91×10(3) copies) of purified genomic DNA (gDNA) but the presence of cellular material reduced this sensitivity sixfold to 300pg gDNA (2.95×10(4) copies). LRE qPCR matched the accuracy of a conventional standard curve qPCR method. The presence of material from bioreactor cultivation of up to OD600=80 did not significantly compromise the accuracy of LRE qPCR. We conclude that a simple and rapid cell disruption step is sufficient to render P. pastoris samples of up to OD600=80 amenable to analysis using LRE qPCR which we propose as a synthetic biology standard.

Prevalence of Salmonella and E. coli in neonatal diarrheic calves

Neonatal calf diarrhea remains one of the most important problems faced by livestock, causing great economic losses. This study investigated the prevalence of Salmonella and Escherichia coli, especially enterotoxigenic E.  coli (ETEC), in diarrheic calves. Fecal samples were collected from 127 diarrheic calves up to 3 months of age at 12 farms from different governorates in Egypt. 119 bacterial isolates (93.7%) were recovered and the prevalences of Salmonella and E.  coli in diarrheic calves were 18.1% and 75.6%, respectively. Serotyping of Salmonella isolates revealed that S. Enteritidis and S. Typhimurium were the most prevalent serotypes, representing 60.9% and 30.4%, respectively, while S. Dublin was 8.7%. Serogrouping of E.  coli isolates showed that 10 O-serogroups were obtained where O₂₆ and O₁₀₃ were the most prevalent (17.7% of each). Salmonella serotypes showed positive results with PCR test using oligonucleotide primer amplifying 521 bp fragment of invA gene of Salmonella while 70% of E.  coli serogroups possessed ETEC virulent gene (K99). The in-vitro antibiotic sensitivity test indicated that Salmonella serotypes showed high sensitivity against enrofloxacin, spectinomycin and neomycin while E.  coli isolates showed high sensitivities against marbofloxacin, spectinomycin and neomycin only.

A two-stage microresistive pulse immunosensor for pathogen detection

We present a two-stage immunosensor for pathogen detection in a mixed population. In this approach, antibody-conjugated microparticles were used to functionalize the surface of the capture chamber via a convenient magnetic method and a two-stage resistive pulse sensor was used to detect and quantify pathogen cells. We firstly tested the capture efficiency of the functionalized capture chamber. The specific capture efficiency of S. cerevisiae is greater than 94.8%, while the non-specific capture efficiency is 3.4%. We showed that the device can accurately measure pure S. cerevisiae at concentrations ranging from 1.0 to 8.0 × 10(3) cells per μL. We performed S. cerevisiae measurements in a mixture with Chlorella. Both cells have similar sizes. For S. cerevisiae to Chlorella ratios ranging from 1.0 to 2.0, the measurement error was less than 7%, while the error became 20% to 32% for lower ratios ranging from 0.1 to 0.5 caused by nonspecific attachment. We demonstrated that this device is able to isolate target cells and quantitatively measure the cell population in a short time. This device can be potentially used for pathogen detection in the food industry, biological research and clinical applications.

The Development and Use of Internal Amplification Controls (IACs) with DNA Profiling Kits for Forensic DNA Analysis

Biological samples recovered for forensic investigations are often degraded and/or have low amounts of DNA; in addition, in some instances the samples may be contaminated with chemicals that can act as PCR inhibitors. As a consequence this can make interpretation of the results challenging with the possibility of having partial profiles and false negative results. Because of the impact of DNA analysis on forensic investigations, it is important to monitor the process of DNA profiling, in particular the amplification reaction. In this chapter we describe a method for the in-house generation and use of internal amplification controls (IACs) with DNA profiling kits to monitor the success of the PCR proces. In the example we show the use of the SGM Plus® kit. These controls can also be used to aid the interpretation of the DNA profile.

Growth of Stressed Strains of Four Non-O157 Shiga Toxin-Producing Escherichia coli Serogroups in Five Enrichment Broths

The purpose of this study was to evaluate (i) the behavior of several strains of non-O157 Shiga toxin-producing Escherichia coli (STEC) serogroups (O26, O103, O111, and O145) exposed to different stress conditions and (ii) the growth dynamics of stressed and nonstressed non-O157 STEC cells in five enrichment media. STEC strains were exposed to acid, cold, and freeze stresses. Lethal and sublethal injuries were determined by plating in parallel on selective and nonselective agar media. Freeze stress (8 days, 20°C) caused the most lethal (95.3% ± 2.5%) injury, as well as the most sublethal (89.1% ± 8.8%) injury in the surviving population. Growth of stressed and nonstressed pure cultures of non-O157 STEC on modified tryptic soy broth, buffered peptone water (BPW), BPW with sodium pyruvate, Brila, and STEC enrichment broth (SEB) was determined using total viable counts. To compare growth capacities, growth after 7 and 24 h of enrichment was measured; lag phases and maximum growth rates were also calculated. In general, growth on BPW resulted in a short lag phase followed by a high maximum growth rate during the enrichment of all tested strains when using all three stress types. Furthermore, BPW ensured the highest STEC count after 7 h of growth. Supplementing the medium with sodium pyruvate did not improve the growth dynamics. The two selective media, Brila and SEB, were less efficient than BPW, but Brila's enrichment performance was remarkably better than that of SEB. This study shows that irrespective of the effect of background flora, BPW is still recommended for resuscitation of non-O157 STEC.

Genome Wide Search for Biomarkers to Diagnose Yersinia Infections

Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4-6 base cutters). Yersinia species have 6-7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences-carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.