Taxonomy, ecology, and relevance to food safety of the genus Listeria with a particular consideration of new Listeria species described between 2010 and 2022

Since 2010, the genus Listeria has had the addition of 22 new species that more than tripled the number of species identified until 2010. Sixteen of these 22 new species are distantly related to the type species, Listeria monocytogenes, and several of these present phenotypes that distinguish them from classical Listeria species (L. monocytogenes, Listeria innocua, Listeria ivanovii, Listeria seeligeri, Listeria welshimeri, and Listeria grayi). These 22 newly described species also show that Listeria is more genetically diverse than previously estimated. While future studies and surveys are needed to clarify the distribution of these species, at least some of these species may not be widely spread, while other species may be frequently found spread to human-related settings (e.g., farms and processing facilities), and others may be adapted to specific environmental habitats. Here, we review the taxonomic, phylogenetic, and ecological characteristics of these new Listeria species identified since 2010 and re-iterate the suggestion of re-classification of some species into three new genera: Murraya, Mesolisteria, and Paenilisteria. We also provide a review of current detection issues and the relevance to food safety related to the identification of these new species. For example, several new non-pathogenic species could be misidentified as the pathogen L. monocytogenes, based on methods that do not target L. monocytogenes-specific virulence genes/factors, leading to unnecessary product recalls. Moreover, eight species in the proposed new genus Mesolisteria are not good indicators of environmental conditions that could allow L. monocytogenes to grow since Mesolisteria species are unable to grow at low temperatures.

Development of a method based on ATR-FTIR spectroscopy to detect maple syrup adulterated with added syrups

BACKGROUND

Food adulteration is a global concern, whether it takes place intentionally or incidentally. In Canada, maple syrup is susceptible to being adulterated with cheaper syrups such as corn, beet, cane syrups, and many more due to its high price and economic importance.

RESULTS

In this study, the use of attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was investigated to detect maple syrups adulterated with 15 different sugar syrups at different concentration levels. The spectra were collected in the range of 4000-650 cm-1 in the absorbance unit. These spectra were used to build six libraries and three models. A method that is capable of performing a qualitative library search using a similarity search, which is based on the first derivative correlation search algorithm, was developed. This method was further evaluated and proved to be able to capture adulterated and reject non-adulterated maple syrups, belonging to the color grades golden and amber maple syrups, with an accuracy of 93.9% and 92.3%, respectively. However, for the maple syrup belonging to the dark color grade, this method demonstrated low specificity of 33.3%, and for this reason it was only able to adequately detect adulterated samples from the non-adulterated ones with an accuracy of 81.4%.

CONCLUSION

This simple and rapid method has strong potential for implementation in different stages of the maple syrup supply chain for early adulteration detection, particularly for golden and amber samples. Further evaluation and improvements are required for the dark color grade. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Rapid methods for identifying barriers and solutions to improve access to community health services: a scoping review

BACKGROUND

The advancement of universal health coverage (UHC) is largely based on identifying and addressing barriers to accessing community health services. Traditional qualitative research approaches provide excellent insights but have unfeasibly high resource requirements for most care providers.

AIM

To identify, categorise, and evaluate methods that have been used to identify barriers to and/or solutions for improving access to community-based health services, grounded in engagement with affected communities, excluding approaches that take >14 days.

DESIGN & SETTING

This was a scoping review.

METHOD

Following Joanna Briggs Institute (JBI) guidelines, a search was undertaken using the Cochrane Library, Ovid MEDLINE, Ovid Embase, Ovid Global Health, and Google Scholar. An information specialist designed the search, and dual independent review and data charting were used.

RESULTS

In total, 44 studies were included from 30 countries, reporting on 18 different clinical services. Thirty studies used self-described 'rapid' approaches; however, the majority of these did not justify what they meant by this term. Nearly half of the studies used mixed- or multi-methods and triangulation to verify early findings. All of the qualitative studies used interviews and/or focus groups, which were often supplemented with observations, document review, and mapping activities. The use of in situ snowball and convenience sampling; community members as data collectors and cultural guides; collaborative summarisation (review of findings with community members and end-users); and deductive framework analysis expedited the research processes. There were no data on costs.

CONCLUSION

There are a wide range of methods that can be used to deliver timely information about barriers to access. The methods employed in the articles reviewed tended to use traditional data collection approaches in innovative ways.

Oxygen Sensor-Based Respirometry and the Landscape of Microbial Testing Methods as Applicable to Food and Beverage Matrices

The current status of microbiological testing methods for the determination of viable bacteria in complex sample matrices, such as food samples, is the focus of this review. Established methods for the enumeration of microorganisms, particularly, the 'gold standard' agar plating method for the determination of total aerobic viable counts (TVC), bioluminescent detection of total ATP, selective molecular methods (immunoassays, DNA/RNA amplification, sequencing) and instrumental methods (flow cytometry, Raman spectroscopy, mass spectrometry, calorimetry), are analyzed and compared with emerging oxygen sensor-based respirometry techniques. The basic principles of optical O₂ sensing and respirometry and the primary materials, detection modes and assay formats employed are described. The existing platforms for bacterial cell respirometry are then described, and examples of particular assays are provided, including the use of rapid TVC tests of food samples and swabs, the toxicological screening and profiling of cells and antimicrobial sterility testing. Overall, O₂ sensor-based respirometry and TVC assays have high application potential in the food industry and related areas. They detect viable bacteria via their growth and respiration; the assay is fast (time to result is 2-8 h and dependent on TVC load), operates with complex samples (crude homogenates of food samples) in a simple mix-and-measure format, has low set-up and instrumentation costs and is inexpensive and portable.

Development of a Rapid and Non-Destructive Method for the Detection of Water Addition in Octopus Species (Octopus vulgaris and Eledone cirrhosa) Using Time Domain Reflectometry (TDR)

Consumer expectations regarding the quality of octopus are often frustrated and dissatisfaction is frequent, namely due to the excessive reduction in weight after cooking. Therefore, a rapid and non-destructive method based in time domain reflectometry (TDR) was developed for the control of water added to octopus (Octopus vulgaris and Eledone cirrhosa). O. vulgaris had significant higher values of moisture content, moisture/protein ratio, and cooking loss than E. cirrhosa. Immersion in freshwater increased the weight of O. vulgaris in ca. 32% after 32 h, and of E. cirrhosa in ca. 21% after 36 h, and cooking losses increased about 13.9% and 26.1%, respectively. The results reveal how consumers can be misled by abusive water addition. Changes in electrical conductivity and TDR curves were linked with the increasing incorporation of water and dilution effect of salts from octopus muscle. TDR technology and linear discriminant analysis were combined to detect added water in octopus. The classification model developed was cross-validated and 98.6% of samples were correctly classified. The method can be used to proof the authenticity of octopus (O. vulgaris and E. cirrhosa) or to detect fraudulent practices regarding added water.

Rapid evaluation of COVID-19 related service and practice changes in health and human services using tailored methods

The COVID-19 pandemic required substantive delivery and practice changes for government services under tight timeframes and high public scrutiny. These urgently implemented service changes provided the opportunity for evaluators to support decision-makers to understand the impact of adaptations for those delivering and receiving health and human services. Tailored rapid evaluation methods (REM) provide a pragmatic approach to generating timely information for evidence-based policy and decision-making under these conditions. Drawing from features of a range of existing rapid evaluation models, as well as developmental and utilization-focussed evaluation theory, this article outlines the design and implementation of a novel REM approach and considers the benefits of both tailoring and standardizing rapid evaluation approaches to meet end-user needs. The tailored REM approach and mixed methods are contextualized and compared to other documented rapid evaluation models to demonstrate the purpose and value of customization. This article builds on previous descriptions of the implementation of a novel REM approach to provide a comparative account of tailored rapid evaluation methods. The article outlines the drivers that led to the selected tailoring of the REM approach, and shares lessons learned in the context of the COVID-19 pandemic by a large internal government evaluation unit (Department of Health and Human Services) in Victoria, Australia. The customized features of REM ensure that it can consider the experiences of those delivering and receiving services, and inform near-term decision-making on programme and policy design in emergency and fast-paced contexts. The article shares a case study of a rapid evaluation of telehealth in pediatric care to demonstrate insights from tailoring the REM approach in practice. The REM method was utilized with the aim of delivering findings in a time-sensitive manner to rapidly inform decision making for policy-makers. Key enablers for the tailored REM protocol include the use of multi-disciplinary teams, flexible evaluation design, and a participatory approach that facilitates stakeholder involvement throughout delivery. Insights from the case study and methods presented seek to inform practice for evaluators who intend to or may want to tailor their own rapid evaluation model in resource and time-limited settings.

SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods

Since the beginning of COVID-19 pandemic the Real Time sharing of genome sequences of circulating virus supported the diagnostics and surveillance of SARS-CoV-2 and its transmission dynamics. SARS-CoV-2 straightaway showed its tendency to mutate and adapt to the host, culminating in the emergence of variants; so it immediately became of crucial importance to be able to detect them quickly but also to be able to monitor in depth the changes on the whole genome to early identify the new possibly emerging variants. In this scenario, this manuscript aims to provide an overview of the existing methods for the identification of SARS-CoV-2 variants (from rapid method based on identification of one or more specific mutations to Whole Genome sequencing approach-WGS), taking into account limitations, advantages and applications of them in the field of diagnosis and surveillance of SARS-CoV-2.

Recent Advances and Applications of Rapid Microbial Assessment from a Food Safety Perspective

Unsafe food is estimated to cause 600 million cases of foodborne disease, annually. Thus, the development of methods that could assist in the prevention of foodborne diseases is of high interest. This review summarizes the recent progress toward rapid microbial assessment through (i) spectroscopic techniques, (ii) spectral imaging techniques, (iii) biosensors and (iv) sensors designed to mimic human senses. These methods often produce complex and high-dimensional data that cannot be analyzed with conventional statistical methods. Multivariate statistics and machine learning approaches seemed to be valuable for these methods so as to "translate" measurements to microbial estimations. However, a great proportion of the models reported in the literature misuse these approaches, which may lead to models with low predictive power under generic conditions. Overall, all the methods showed great potential for rapid microbial assessment. Biosensors are closer to wide-scale implementation followed by spectroscopic techniques and then by spectral imaging techniques and sensors designed to mimic human senses.

Digital Assessment and Classification of Wine Faults Using a Low-Cost Electronic Nose, Near-Infrared Spectroscopy and Machine Learning Modelling

The winemaking industry can benefit greatly by implementing digital technologies to avoid guesswork and the development of off-flavors and aromas in the final wines. This research presents results on the implementation of near-infrared spectroscopy (NIR) and a low-cost electronic nose (e-nose) coupled with machine learning to detect and assess wine faults. For this purpose, red and white base wines were used, and treatments consisted of spiked samples with 12 faults that are traditionally formed in wines. Results showed high accuracy in the classification models using NIR and e-nose for red wines (94–96%; 92–97%, respectively) and white wines (96–97%; 90–97%, respectively). Implementing new and emerging digital technologies could be a turning point for the winemaking industry to become more predictive in terms of decision-making and maintaining and increasing wine quality traits in a changing and challenging climate.

Quantitation of Water Addition in Octopus Using Time Domain Reflectometry (TDR): Development of a Rapid and Non-Destructive Food Analysis Method

A rapid and non-destructive method based in time domain reflectometry analysis (TDR), which detects and quantifies the water content in the muscle, was developed for the control of abusive water addition to octopus. Common octopus samples were immersed in freshwater for different periods (0.5−32 h) to give a wide range of moisture contents, representing different commercial conditions. Control and water-added octopus were analyzed with a TDR sensor, and data correlated with moisture content were used for calibration and method validation. A maximum limit of moisture content of 85.2 g/100 g in octopus is proposed for conformity assessment, unless the label indicates that water (>5%) was added. Calibration results showed that TDR analysis can discriminate control and water-added octopus, especially for octopus immersed for longer periods (32 h). In addition, moisture content can be quantified in octopus using only TDR analysis (between 80 and 90 g/100 g; RMSE = 1.1%). TDR data and correlation with moisture content show that this non-destructive methodology can be used by the industry and quality control inspections for assessment of octopus quality and to verify compliance with legislation, promoting fair trade practices, and further contributing to a sustainable use of resources.

Applying a scoping review approach for identifying effective implementation strategies in oral health settings

Dental service providers have limited capacity to identify strategies to implement evidence-based practices (EBPs). We developed a rigorous yet parsimonious scoping review approach to identify, select, and rate implementation strategies based on an oral health system context. From 153 strategies identified, we selected the top 11 strategies, which had a moderate level of support of evidence and where managers were the main actors. The main actions were to educate, remind, structure, and influence. Targets included dentists, dental hygienists, and assistants and managers from a large prepaid dental care delivery system. This approach responds to calls for rapid and innovative methods to implement EBPs in oral health.

Development of species-specific primers for rapid identification by PCR of the ecologically important pathogen Fusarium keratoplasticum from isolated and environmental samples

The genus Fusarium contains many fungal species known to be pathogenic to animals and plants alike. One species complex within this genus, the Fusarium solani species complex (FSSC), is of particular concern due to its high numbers of pathogenic members. FSSC members are known to contribute significantly to plant, human and other animal fungal disease. One member of the FSSC, Fusarium keratoplasticum, is of particular ecological concern and has been implicated in low hatching success of endangered sea turtle eggs, as well as contribute to human and other animal Fusarium pathogenesis. Species-specific primers for molecular identification of F. keratoplasticum currently do not exist to our knowledge, making rapid identification, tracking and quantitation of this pathogenic fungus difficult. The objective of this study was to develop primers specific to F. keratoplasticum that could be applied to DNA from isolated cultures as well as total (mixed) DNA from environmental samples. RPB2 sequence from 109 Fusarium isolates was aligned and analysed to determine nucleotide polymorphisms specific to F. keratoplasticum useful for primer design. A set of primers were generated and found to be effective for identification of F. keratoplasticum from total DNA extracted from sand surrounding sea turtle nesting sites.

Influence of Sample Matrix on Determination of Histamine in Fish by Surface Enhanced Raman Spectroscopy Coupled with Chemometric Modelling

Histamine fish poisoning is a foodborne illness caused by the consumption of fish products with high histamine content. Although intoxication mechanisms and control strategies are well known, it remains by far the most common cause of seafood-related health problems. Since conventional methods for histamine testing are difficult to implement in high-throughput quality control laboratories, simple and rapid methods for histamine testing are needed to ensure the safety of seafood products in global trade. In this work, the previously developed SERS method for the determination of histamine was tested to determine the influence of matrix effect on the performance of the method and to investigate the ability of different chemometric tools to overcome matrix effect issues. Experiments were performed on bluefin tuna (Thunnus thynnus) and bonito (Sarda sarda) samples exposed to varying levels of microbial activity. Spectral analysis confirmed the significant effect of sample matrix, related to different fish species, as well as the extent of microbial activity on the predictive ability of PLSR models with R² of best model ranging from 0.722–0.945. Models obtained by ANN processing of factors derived by PCA from the raw spectra of the samples showed excellent prediction of histamine, regardless of fish species and extent of microbial activity (R² of validation > 0.99).

Qualitative determination of histamine in canned yellowfin tuna (Thunnus albacares) marketed in Sardinia (Italy) by rapid screening methods

Histamine is produced by the bacterial decarboxylation of histidine, an ammino acid present in large amount especially in scombroid fish such as tuna. Fish containing high levels of histamine have been associated with many instances of “scombroid poisoning”. Since histamine is heat resistant, its presence has been used as an indicator of the good manufacturing practice and of the preservation state of canned tuna. In this study we have applied a rapid screening method to determine the presence of histamine in canned tuna marketed in Sardinia (Italy). A total of 165 samples of canned tuna were screened for the qualitative determination of histamine by HistaSure™ Fish Rapid Test. The results were consistently in agreement with the food safety criteria (<100 mg/kg of histamine) laid down in EC Regulation 2073/2005 (as amended). The HistaSure™ kit was confirmed as a rapid screening method for the presence of histamine in canned tuna.

Accurate method for rapid biomass quantification based on specific absorbance of microalgae species with biofuel importance

The development of microalgae culture technology has been an integral part to produce biomass feedstock to biofuel production. Due to this, numerous attempts have been made to improve some operational parameters of microalgae production. Despite this, specialized research in cell growth monitoring, considered as a fundamental parameter to achieve profitable applications of microalgae for biofuels production, presents some opportunity areas mainly related to the development of specific and accurate methodologies for growth monitoring. In this work, predictive models were developed through statistical tools that correlate a specific micro-algal absorbance with cell density measured by cell count (cells∙per ml), for three species of interest for biofuels production. The results allow the precise prediction of cell density through a logistic model based on spectrophotometry, valid for all the kinetics analysed. The adjusted determination coefficients ( r adj 2 ) for the developed models were 0·993, 0·995 and 0·994 for Dunaliella tertiolecta, Nannochloropsis oculata and Chaetoceros muelleri respectively. The results showed that the equations obtained here can be used with an extremely low error (≤2%) for all the cell growth ranges analysed, with low operational cost and high potential of automation. Finally, a user-friendly software was designed to give practical use to the developed predictive models.

Histamine Control in Raw and Processed Tuna: A Rapid Tool Based on NIR Spectroscopy

The present study was designed to investigate whether near infrared (NIR) spectroscopy with minimal sample processing could be a suitable technique to rapidly measure histamine levels in raw and processed tuna fish. Calibration models based on orthogonal partial least square regression (OPLSR) were built to predict histamine in the range 10–1000 mg kg⁻¹ using the 1000–2500 nm NIR spectra of artificially-contaminated fish. The two models were then validated using a new set of naturally contaminated samples in which histamine content was determined by conventional high-performance liquid chromatography (HPLC) analysis. As for calibration results, coefficient of determination (r²) > 0.98, root mean square of estimation (RMSEE) ≤ 5 mg kg⁻¹ and root mean square of cross-validation (RMSECV) ≤ 6 mg kg⁻¹ were achieved. Both models were optimal also in the validation stage, showing r² values > 0.97, root mean square errors of prediction (RMSEP) ≤ 10 mg kg⁻¹ and relative range error (RER) ≥ 25, with better results showed by the model for processed fish. The promising results achieved suggest NIR spectroscopy as an implemental analytical solution in fish industries and markets to effectively determine histamine amounts.

A diagnostic test that uses isothermal amplification and lateral flow detection sdaA can detect tuberculosis in 60 min

AIMS

Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is now the leading cause of death from infectious disease, thus rapid diagnostic and screening techniques for TB are urgently needed.

METHODS AND RESULTS

Here, a detection of MTB using multiple cross displacement amplification coupling with nanoparticles-based lateral flow device (MCDA-LFD) was developed and validated, targeting the specific sdaA gene. The whole detection procedure, including rapid genomic DNA extraction (15 min), amplification (30 min) and result reporting (2 min), was completed within 50 min. No cross-reaction with non-mycobacteria and non-tuberculous mycobacteria (NTM) strains was observed. The sensitivity of sdaA-MCDA-LFD, Xpert MTB/RIF assay and culture results was 81·6, 48·3 and 37·9%, respectively, in TB patients. Among positive culture samples, the sensitivity of sdaA-MCDA-LFD and Xpert MTB/RIF assay was 93·9% (31/33) and 81·8% (27/33), respectively. Among culture-negative samples, the sensitivity of sdaA-MCDA-LFD and Xpert MTB/RIF assay was 74·1% (40/54) and 27·8% (15/54), respectively. The specificity of sdaA-MCDA-LFD and Xpert MTB/RIF was 95·4% (62/65) and 100% (65/65) in clinical samples from non-TB patients.

CONCLUSION

The sdaA-MCDA-LFD assay was a rapid, simple, specific and sensitive TB diagnostic test.

SIGNIFICANCE AND IMPACT OF THE STUDY

The sdaA-MCDA-LFD assay holds promise for application as a useful point-of-care test to detect MTB, and will play an important role in controlling and preventing TB.

Advances in Foodborne Pathogen Analysis

As the world population has grown, new demands on the production of foods have been met by increased efficiencies in production, from planting and harvesting to processing, packaging and distribution to retail locations. These efficiencies enable rapid intranational and global dissemination of foods, providing longer “face time” for products on retail shelves and allowing consumers to make healthy dietary choices year-round. However, our food production capabilities have outpaced the capacity of traditional detection methods to ensure our foods are safe. Traditional methods for culture-based detection and characterization of microorganisms are time-, labor- and, in some instances, space- and infrastructure-intensive, and are therefore not compatible with current (or future) production and processing realities. New and versatile detection methods requiring fewer overall resources (time, labor, space, equipment, cost, etc.) are needed to transform the throughput and safety dimensions of the food industry. Access to new, user-friendly, and point-of-care testing technologies may help expand the use and ease of testing, allowing stakeholders to leverage the data obtained to reduce their operating risk and health risks to the public. The papers in this Special Issue on “Advances in Foodborne Pathogen Analysis” address critical issues in rapid pathogen analysis, including preanalytical sample preparation, portable and field-capable test methods, the prevalence of antibiotic resistance in zoonotic pathogens and non-bacterial pathogens, such as viruses and protozoa.

Reevaluating limits of detection of 12 lateral flow immunoassays for the detection of Yersinia pestis, Francisella tularensis, and Bacillus anthracis spores using viable risk group-3 strains

AIM

Rapid detection of biological agents in biodefense is critical for operational, tactical and strategic levels as well as for medical countermeasures. Yersinia pestis, Francisella tularensis, and Bacillus anthracis are high priority agents of biological warfare or bioterrorism and many response forces use lateral flow assays (LFAs) for their detection. Several companies produce these assays, which offer results in short time and are easy to use. Despite their importance, only few publications on the limits of detection (LOD) for LFAs are available. Most of these studies used inactivated bacteria or risk group-2 strains. As the inactivation process in previous studies might have affected the tests' performances, it was our aim in this study to determine and compare the LOD of several commercially available LFAs using viable risk group-3 strains.

METHODS AND RESULTS

Lateral flow assays from four different companies for the detection of following bacteria were evaluated: Y. pestis, F. tularensis and B. anthracis spores. Two independent quantification methods for each target organism were applied, in order to ensure high quantification accuracy. LODs varied greatly between tests and organisms and ranged between 10⁴ for Y. pestis-tests and as high as >10⁹ for one B. anthracis-test.

CONCLUSION

This work precisely determined the LODs of LFAs from four commercial suppliers. The herein determined LODs differed from results of previous studies. This illustrates the need for using accurately quantified viable risk group 3-strains for determining such LODs.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our work bridges an important knowledge gap with regard to LFA LOD. The LODs determined in this study will facilitate better assessment of LFA-results. They illustrate that a negative LFA result is not suited to exclude the presence of the respective agent in the analyzed sample.

Development of a combined immunochromatographic lateral flow assay for accurate and rapid Escherichia coli O157:H7 detection

Escherichia coli O157:H7 is an important pathogenic Bacterium that threatens human health. A convenient, sensitive and specific method for the E. coli O157:H7 detection is necessary. We developed two pairs of monoclonal antibodies through traditional hybridoma technology, one specifically against E. coli O157 antigen and the other specifically against E. coli H7 antigen. Using these two pairs of antibodies, we developed two rapid test kits to specifically detect E. coli O157 antigen and E. coli H7 antigen, respectively. The detection sensitivity for O157 positive E. coli is 1 × 10³ CFU per ml and for H7 positive E. coli is 1 × 10⁴ CFU per ml. Combining these two pairs of antibodies together, we developed a combo test strip that can specifically detect O157: H7, with a detection sensitivity of 1 × 10⁴ CFU per ml, when two detection lines are visible to the naked eye. This is currently the only rapid detection reagent that specifically detects O157: H7 by simultaneously detecting O157 antigen and H7 antigens of E. coli. Our product has advantages of simplicity and precision, and can be a very useful on-site inspection tool for accurate and rapid detection of E. coli O157:H7 infection.

From hazard analysis to risk control using rapid methods in microbiology: A practical approach for the food industry

The prevention of foodborne diseases is one of the main objectives of health authorities. To this effect, analytical techniques to detect and/or quantify the microbiological contamination of foods prior to their release onto the market are required. Management and control of foodborne pathogens have generally been based on conventional detection methodologies, which are not only time-consuming and labor-intensive but also involve high consumable materials costs. However, this management perspective has changed over time given that the food industry requires efficient analytical methods that obtain rapid results. This review covers the historical context of traditional methods and their passage in time through to the latest developments in rapid methods and their implementation in the food sector. Improvements and limitations in the detection of the most relevant pathogens are discussed from a perspective applicable to the current situation in the food industry. Considering efforts that are being done and recent developments, rapid and accurate methods already used in the food industry will be also affordable and portable and offer connectivity in near future, which improves decision-making and safety throughout the food chain.

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.

Review of Research into the Determination of Acrylamide in Foods

Acrylamide (AA) is produced by high-temperature processing of high carbohydrate foods, such as frying and baking, and has been proved to be carcinogenic. Because of its potential carcinogenicity, it is very important to detect the content of AA in foods. In this paper, the conventional instrumental analysis methods of AA in food and the new rapid immunoassay and sensor detection are reviewed, and the advantages and disadvantages of various analysis technologies are compared, in order to provide new ideas for the development of more efficient and practical analysis methods and detection equipment.

Poultry processing and the application of microbiome mapping

Chicken is globally one of the most popular food animals. However, it is also one of the major reservoirs for foodborne pathogens, annually resulting in continued morbidity and mortality incidences worldwide. In an effort to reduce the threat of foodborne disease, the poultry industry has implemented a multifaceted antimicrobial program that incorporates not only chemical compounds, but also extensive amounts of water application and pathogen monitoring. Unfortunately, the pathogen detection methods currently used by the poultry industry lack speed, relying on microbiological plate methods and molecular detection systems that take time and lack precision. In many cases, the time to data acquisition can take 12 to 24 h. This is problematic if shorter-term answers are required which is becoming more likely as the public demand for chicken meat is only increasing, leading to new pressures to increase line speed. Therefore, new innovations in detection methods must occur to mitigate the risk of foodborne pathogens that could result from faster slaughter and processing speeds. Future technology will have 2 tracks: rapid methods that are meant to detect pathogens and indicator organisms within a few hours, and long-term methods that use microbiome mapping to evaluate sanitation and antimicrobial efficacy. Together, these methods will provide rapid, comprehensive data capable of being applied in both risk-assessment algorithms and used by management to safeguard the public.

Evaluation of MASTDISCS combi Carba plus for the identification of metallo-β-lactamases, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae clinical isolates

The increasing frequency of class A KPC enzymes, class B metallo-β-lactamases (MBLs) and class D OXA-48 enzymes in Enterobacteriaceae makes their early identification urgent. A simple commercial MASTDISCS combi Carba plus disc system (MAST-Carba plus) was designed for the identification of MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae. To validate the MAST-Carba plus, a total of 77 isolates of carbapenemase-producing Enterobacteriaceae (CPE) and 84 isolates of noncarbapenemase-producing Enterobacteriaceae (non-CPE) were selected for differentiation of the genes of Enterobacteriaceae by MAST-Carba plus. Meanwhile, the carbapenemase genes such as bla_KPC , bla_IMP , bla_VIM , bla_NDM-1 and bla_OXA-48 were detected by PCR (polymerase chain reaction). Thus, when considered on the basis of PCR results, the sensitivity of MAST-Carba plus detection of KPC strains is 82·3%, the specificity is 100·0%, the positive predictive value is 100·0% and the negative predictive value is 92·4%. For MBLs strains, the sensitivity is 100·0%, the specificity is 97·1%, the positive predictive value is 84·6% and the negative predictive value is 100·0%. For OXA-48 strains, the sensitivity is 100·0%, the specificity is 99·4%, the positive predictive value is 80·0% and the negative predictive value is 100·0%. Our findings suggest that MAST-Carba plus is a rapid and promising method for identifying the MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae, which could be exploited in basic microbiology laboratory to prevent the transmission of CPE. SIGNIFICANCE AND IMPACT OF THE STUDY: Not only detection of carbapenemases but also identification of their genes accurately and rapidly in Enterobacteriaceae is still a major challenge for clinical laboratories in order to prevent the transmission of carbapenemase-producing Enterobacteriaceae (CPE). Therefore, this study aimed to evaluate the performance of a new rapid method (MASTDISCS combi Carba plus) for the identification of metallo-β-lactamases (MBLs), KPC and OXA-48 carbapenemase genes in Enterobacteriaceae clinical isolates.

Development of an IgY-based lateral flow immunoassay for detection of fumonisin B in maize

Fumonisin is one of the most prevalent mycotoxins in maize, causing substantial economic losses and potential health risks in human and animals. In the present study, in-house polyclonal IgY antibody against fumonisin group B (FB) was applied for the development of a competitive lateral flow immunoassay detecting these mycotoxins in maize grains with the limit of detection of 4000 µg/kg, which corresponds to the maximum residue limit adopted by The International Codex Alimentarius Commission. To this end, factors affecting the test performance including nitrocellulose membrane type, dilution factor of maize homogenates in running buffer, amount of detection conjugate, and incubation time between detection conjugate and samples were optimized. Under the optimal condition (UniSart ^®CN140 nitrocellulose membrane, FB ₁-BSA immobilized at 1 µg/cm, 1:10 dilution factor, 436 ng of gold nanoparticle conjugate, 30 minutes of incubation), the developed test could detect both FB ₁ and FB ₂ in maize with limit of detection of 4000 µg/kg, and showed no cross-reactivity to deoxynivalenol, ochratoxin A, aflatoxin B1 and zearalenone. When applied to detect FB ₁ and FB ₂ in naturally contaminated maize samples, results obtained from the developed assay were in good agreement with those from the high-performance liquid chromatography method. This lateral flow immunoassay is particularly suitable for screening of fumonisins in maize because of its simplicity and cost-effectiveness.

Development of an IgY-based lateral flow immunoassay for detection of fumonisin B in maize

Fumonisin is one of the most prevalent mycotoxins in maize, causing substantial economic losses and potential health risks in human and animals. In the present study, in-house polyclonal IgY antibody against fumonisin group B (FB) was applied for the development of a competitive lateral flow immunoassay detecting these mycotoxins in maize grains with the limit of detection of 4000 µg/kg, which corresponds to the maximum residue limit adopted by The International Codex Alimentarius Commission. To this end, factors affecting the test performance including nitrocellulose membrane type, dilution factor of maize homogenates in running buffer, amount of detection conjugate, and incubation time between detection conjugate and samples were optimized. Under the optimal condition (UniSart ®CN140 nitrocellulose membrane, FB 1-BSA immobilized at 1 µg/cm, 1:10 dilution factor, 436 ng of gold nanoparticle conjugate, 30 minutes of incubation), the developed test could detect both FB 1 and FB 2 in maize with limit of detection of 4000 µg/kg, and showed no cross-reactivity to deoxynivalenol, ochratoxin A, aflatoxin B1 and zearalenone. When applied to detect FB 1 and FB 2 in naturally contaminated maize samples, results obtained from the developed assay were in good agreement with those from the high-performance liquid chromatography method. This lateral flow immunoassay is particularly suitable for screening of fumonisins in maize because of its simplicity and cost-effectiveness.

A loop-mediated isothermal amplification assay for the diagnosis of pulmonary tuberculosis

Quantitated Mycobacterium tuberculosis (M.tb) H37Rv DNA was used to analyse the sensitivity and the specificity was assessed using DNA isolated from the reference strain H37Rv, 12 nontuberculous mycobacterium (NTM) species and five nonmycobacterium species. Furthermore, performance of the assay was evaluated on the sputum samples and compared with smear microscopy, culture and PCR. mpt64 (also called mpb64 or Rv1980c) loop-mediated isothermal amplification (LAMP) successfully detected 1 pg DNA within 40 min and successfully rejected NTMs and other bacterial species tested. It specifically detected all the 119 confirmed TB cases and 100 of the 104 control cases. The resulting sensitivity and specificity of LAMP assay was found to be 100% (95% CI: 96·79-100%) and 96·15% (95% CI; 90·44-98·94%) respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Loop-mediated isothermal amplification (LAMP) is a technique for isothermal DNA amplification suitable for cost-limited settings as it prevents the use of sophisticated instruments. Using mpt64 antigenic protein gene, we developed a LAMP assay especially for organisms of the M. tuberculosis complex. mpt64 LAMP assay showed 100% sensitivity and detected all the bacteriologically and clinically positive TB cases not detected by smear, culture or PCR methods.

Contemporary microbiology and identification of Corynebacteria spp. causing infections in human

The Corynebacterium is a genus of bacteria of growing clinical importance. Progress in medicine results in growing population of immunocompromised patients and growing number of infections caused by opportunistic pathogens. A new infections caused by new Corynebacterium species and species previously regarded as commensal micro-organisms have been described. Parallel with changes in Corynebacteria infections, the microbiological laboratory diagnostic possibilities are changing. But identification of this group of bacteria to the species level remains difficult. In the paper, we present various manual, semi-automated and automated assays used in clinical laboratories for Corynebacterium identification, such as API Coryne, RapID CB Plus, BBL Crystal Gram Positive ID System, MICRONAUT-RPO, VITEK 2, BD Phoenix System, Sherlock Microbial ID System, MicroSeq Microbial Identification System, Biolog Microbial Identification Systems, MALDI-TOF MS systems, polymerase chain reaction (PCR)-based and sequencing-based assays. The presented assays are based on various properties, like biochemical tests, specific DNA sequences, composition of cellular fatty acids, protein profiles and have specific limitations.

SIGNIFICANCE AND IMPACT OF THE STUDY

The number of opportunistic infections caused by Corynebacteria is increasing due to increase in number of immunocompromised patients. New Corynebacterium species and new human infections, caused by this group of bacteria, has been described recently. However, identification of Corynebacteria is still a challenge despite application of sophisticated laboratory methods. In the study we present possibilities and limitations of various commercial systems for identification of Corynebacteria.

Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms

Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (2000Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro‐organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro‐organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real‐time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro‐organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.

Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens

AIMS

To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens.

METHODS AND RESULTS

The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection.

CONCLUSIONS

The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.

Rapid Prediction of Moisture Content in Intact Green Coffee Beans Using Near Infrared Spectroscopy

Moisture content (MC) is one of the most important quality parameters of green coffee beans. Therefore, its fast and reliable measurement is necessary. This study evaluated the feasibility of near infrared (NIR) spectroscopy and chemometrics for rapid and non-destructive prediction of MC in intact green coffee beans of both Coffea arabica (Arabica) and Coffea canephora (Robusta) species. Diffuse reflectance (log 1/R) spectra of intact beans were acquired using a bench top Fourier transform NIR instrument. MC was determined gravimetrically according to The International Organization for Standardization (ISO) 6673. Samples were split into subsets for calibration (n = 64) and independent validation (n = 44). A three-component partial least squares regression (PLSR) model using raw NIR spectra yielded a root mean square error of prediction (RMSEP) of 0.80% MC; a four component PLSR model using scatter corrected spectra yielded a RMSEP of 0.57% MC. A simplified PLS model using seven selected wavelengths (1155, 1212, 1340, 1409, 1724, 1908, and 2249 nm) yielded a similar accuracy (RMSEP: 0.77% MC) which opens the possibility of creating cheaper NIR instruments. In conclusion, NIR diffuse reflectance spectroscopy appears to be suitable for rapid and reliable MC prediction in intact green coffee; no separate model for Arabica and Robusta species is needed.

A novel broth medium for enhanced growth of Francisella tularensis

Francisella tularensis is a fastidious organism that requires a lengthy incubation time in liquid growth media for detection. The objective of this study was to develop a medium formulation using readily available supplements that enhanced early growth of F. tularensis. Francisella tularensis live vaccine strain was used to evaluate the growth responses for each of the media formulations tested. Growth in brain heart infusion broth supplemented with 2% Vitox, 10% Fildes and 1% histidine (BVFH) resulted in a significant increase in growth after 8 h incubation compared to other media formulations tested (P < 0·001). Virulent strains of F. tularensis grown in BVFH medium demonstrated similar enhanced early growth. Cell densities of 3·9-5·2 log₁₀ CFU per ml were obtained after 24 h of growth in BVFH from a 1-2 cell ml^-1 starting inoculum of the virulent Type A Schu4 strain, indicating the suitability of this medium in rapidly amplifying low starting titres of F. tularensis. Collectively, these results indicate that the novel formulation of the BVFH medium was capable of producing enhanced growth response for F. tularensis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The need for rapid cultivation of Francisella tularensis is essential for detection and monitoring during natural outbreak events or intentional bioterrorism attacks. The addition of selected supplements into the base medium BHI (BVFH) developed in this study enhanced growth of F. tularensis Type A1, A2 and B strains compared to BHI alone. Growth of these organisms in BVFH will allow for improved response time should a natural or intentional contamination event occur.

Development of a qualitative real-time PCR for microbiological quality control testing in mammalian cell culture production

AIMS

The aim of this study was to develop and evaluate a real-time PCR technology for microbiological control methods to examine individualized cell therapeutics, an emerging class of pharmaceutical formulations.

METHODS AND RESULTS

Oligonucleotide primers and hybridization probe for bacterial detection targeting the 16SrRNA gene were adapted based on Nadkarni et al. [Microbiology148 (2002) 257]. For detection of yeast and moulds, primers and probe were designed from conserved sequences of the 18SrRNA gene in this study. The real-time PCR assays were tested on genomic DNA of Escherichia coli and Candida albicans to assess efficiency and linear dynamic range. After successful establishment of robust real-time PCRs, applicability of the assays was evaluated by extracting microbial target DNA from cell-based preparations. Different commercial DNA extraction methods were compared identifying the MagNA Pure DNA Isolation Kit III as the method of choice. Sensitivity was examined for different strains and a detection limit of 10² -10³ CFU per ml in a sample containing ~10⁶ mammalian cells per ml was achieved.

CONCLUSIONS

This study reports the successful establishment of two qualitative real-time PCR assays, enabling in general the broad-range detection of microbial contaminants in a cell-based sample matrix.

SIGNIFICANCE AND IMPACT OF THE STUDY

Individualized cell therapeutics tend to have a short shelf life. Due to lengthy incubation periods, compendial testing according to current pharmacopoeial guidelines may not be applicable. We report a suitable alternative method upon which future microbiological quality control methods for such products could be based on. However, to implement valid rapid microbiological testing methods using real-time PCR technology, further challenges need to be addressed.

Exploring MALDI-TOF MS approach for a rapid identification of Mycobacterium avium ssp. paratuberculosis field isolates

AIMS

The aim of the study was to explore the suitability of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for a rapid and correct identification of Mycobacterium avium ssp. paratuberculosis (MAP) field isolates.

METHODS AND RESULTS

MALDI-TOF MS approach is becoming one of the most popular tests for the identification of intact bacterial cells which has been shown to be fast and reliable. For this purpose, 36 MAP field isolates were analysed through MALDI-TOF MS and the spectra compared with two different databases: one provided by the vendor of the system employed (Biotyper ver. 3·0; Bruker Daltonics) and a homemade database containing spectra from both tuberculous and nontuberculous Mycobacteria. Moreover, principal component analysis procedure was employed to confirm the ability of MALDI-TOF MS to discriminate between very closely related subspecies. Our results suggest MAP can be differentiated from other Mycobacterium species, both when the species are very close (M. intracellulare) and when belonging to different subspecies (M. avium ssp. avium and M. avium ssp. silvaticum).

CONCLUSIONS

The procedure applied is fast, easy to perform, and achieves an earlier accurate species identification of MAP and nontuberculous Mycobacteria in comparison to other procedures.

SIGNIFICANCE AND IMPACT OF THE STUDY

The gold standard test for the diagnosis of paratuberculosis is still isolation of MAP by cultural methods, but additional assays, such as qPCR and subculturing for determination of mycobactin dependency are required to confirm its identification. We have provided here evidence pertaining to the usefulness of MALDI-TOF MS approach for a rapid identification of this mycobacterium among other members of M. avium complex.

A loop-mediated isothermal amplification method for rapid direct detection and differentiation of nonpathogenic and verocytotoxigenic Escherichia coli in beef and bovine faeces

AIM

To develop a multiplex loop-mediated isothermal amplification (LAMP) assay capable of quantifying Escherichia coli and differentiating verocytotoxigenic E. coli (VTEC).

METHODS AND RESULTS

Primer sets were selected to amplify the phoA gene (all E. coli strains) and stx1 and/or stx2 genes (VTEC strains only). LAMP calibration curves demonstrated good quantification capability compared with conventional culture. The limits of detection 50% (LOD₅₀ ) of the multiplex LAMP assay were 2·8 (95% CI 2·4-3·3), 3·2 (95% CI 2·5-3·9) and 2·8-3·2 (95% CI 2·1-3·5) log CFU per g for the phoA, stx1 and stx2 genes, respectively. When validated by testing retail beef and bovine faeces samples, good correlation between E. coli counts indicated by the LAMP assay and culture was observed; however, false-negative LAMP assay results were obtained for 12·5-14·7% of samples.

CONCLUSIONS

A rapid, multiplex LAMP assay for direct quantification of E. coli and specific detection of VTEC in beef and faeces was successfully developed. Further optimisation of the assay would be needed to improve detection sensitivity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The multiplex LAMP assay represents a rapid alternative to culture for monitoring E. coli levels on beef for hygiene monitoring purposes, and, potentially, a method for detection of VTEC in beef and faeces.

Group detection of DON and its modified forms by an ELISA kit

Deoxynivalenol (DON) and its modified forms (3-, and 15-acetyl-DON, DON-3-glucoside) are commonly analysed by chromatographic methods. Indeed, coupled with proper extraction and clean-up, LC-MS represents the best approach for multi-mycotoxin measurements. On the other hand, immunochemistry-based methods are possibly able to detect a family of structurally related compounds, although the determination of single contributions is not possible so far. However, ELISA methods often lead to an apparent overestimation of the mycotoxins content because modified forms and matrix components can potentially cross-react with the antibodies (designed for the parent toxin). Several data about the possible cross-reactivity of commercial DON-detecting ELISA kit are reported in the literature so far. Data are commonly obtained in buffer solutions or in matrix-matched solutions, but comparison of a set of naturally incurred samples has never been reported. In the present work the accuracy of a commercial DON-detecting ELISA kit was evaluated on naturally incurred soft wheat (n = 15) and maize (n = 15), taking into account the matrix effect. Recovery was calculated considering the DON concentration found by LC-MS/MS and the total DON concentration, expressed as the sum of DON and its modified forms found by LC-MS/MS. The obtained data clearly show that, when 3-modified forms of DON occur in the sample, the ELISA kit does actually detect them, thus returning an apparent overestimation if only DON content is considered. When the ELISA recovery is calculated on the total DON content, the accuracy of the analysis increases and the variability decreases. According to our data, the ELISA kit seems to be a promising group detection tool for the accurate evaluation of DON and its modified forms, expressed as sum of DON, DON-3Glc and 3Ac-DON, for soft wheat and maize samples.

Membrane filtration immobilization technique-a simple and novel method for primary isolation and enrichment of bacteriophages

AIM

To develop a method for the isolation and enrichment of bacteriophages selectively against specific bacteria coupled with a membrane filtration technique.

METHODS AND RESULTS

Rapid isolation and concentration of host-specific bacteriophages was achieved by exposure of the sample suspected to contain bacteriophages to a specific host immobilized on a 0·45 μm membrane in a membrane filtration unit. The principle behind this method is the exploitation of host-specific interaction of bacteriophages with their host and maximizing this interaction using a classic membrane filtration method. This provides a chance for each bacteriophage in the sample to interact with the specific host on the membrane filter fitted with a vacuum pump. Specific bacteriophages of the host are retained on the membrane along with its host cells due to the effect of adsorption and these adsorbed bacteriophages (along with their hosts) on the filter disc are then amplified and enriched in regular nutritive broth tryptose soya broth by incubation. With the help of the plaque assay method, host-specific phages of various bacterial species were isolated, segregated and enriched.

CONCLUSIONS

The phage concentration method coupled with membrane filtration immobilization of host bacteria was able to isolate and enrich the host-specific bacteriophages by several fold using a lower quantity of an environmental water sample, or other phage suspensions. Enrichment of phages from single plaques was also achieved.

SIGNIFICANCE AND IMPACT OF THE STUDY

The isolation and detection of host-specific bacteriophages from a low density bacteriophage water sample in a single step by the use of a simple and basic microbiological technique can be achieved. Enrichment of phages from low phage titre suspensions is also achieved very effectively.

Fast detection of both O157 and non-O157 shiga-toxin producing Escherichia coli by real-time optical immunoassay

Among bacterial pathogens involved in food-illnesses, seven serogroups (O26, O45, O103, O111, O121, O145 and O157) of Shiga-toxin producing Escherichia coli (STEC), are frequently identified. During such outbreak, and due to the perishable property of most foodstuff, the time laps for the identification of contaminated products and pathogens is thus critical to better circumvent their spread. Traditional detection methods using PCR or culture plating are time consuming and may present some limitations. In this study, we present a multiplexed immunoassay for the optical detection of most commonly enterohemorrhagic E. coli serogroups: O26, O45, O103, O111, O121, O145 and O157:H7 in a single device. The use of Surface Plasmon Resonance imaging not only enabled the label-free analysis of the samples but gave results in a real-time manner. A dedicated protocol was set up for the detection of both low contaminating bacterial concentrations of food samples (5 CFU per 25 g) and postenrichment aliquots. By combining one single device for the detection of O157 and non-O157 STEC in a label-free manner, this rapid approach may have an important economic and societal impact.

SIGNIFICANCE AND IMPACT OF THE STUDY

This article presents a simple-to-operate immunoassay for the specific detection of Shiga-toxin producing Escherichia coli (STEC). This approach consists in the on-chip assay detection of viable cells on a specifically designed antibody microarray. By skipping any enrichment step and avoiding the use of labelling agent, this approach based on the Surface Plasmon Resonance imaging of the microarrays turns out to be much faster and more cost effective by comparison with standardized methods.

Direct identification of mycobacteria from clinical specimens by multiplex real-time PCR

AIMS

To directly identify clinically relevant mycobacteria from clinical specimens, we have developed a multiplex real-time PCR assay with hydrolysis probes that can identify 20 mycobacterial species.

METHODS AND RESULTS

The assay was initially evaluated using 248 strains, including both reference strains and clinical isolates. Then, the assay was implemented according to a scheme in our laboratory. The scheme based on the clinical differences between the Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) consisted of three stepwise PCRs. MTC and NTM were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and step 3 PCRs. During a 2·5-year period, 1877 isolates of MTC (1142 directly recovered from clinical specimens) and 596 isolates of NTM (143 directly recovered from clinical specimens) were detected, and the species of 590 (99·0%) of the 596 NTM isolates were identified.

CONCLUSIONS

Our experience shows that this is a new paradigm for rapidly and accurately identifying clinically relevant mycobacteria, in which a multiplex real-time PCR assay is directly applied to clinical specimens in a stepwise fashion.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first report of a multiplex real-time PCR assay for identifying clinically important mycobacterial species directly from clinical specimens and its application in a clinical microbiology laboratory.

Advancements in IR spectroscopic approaches for the determination of fungal derived contaminations in food crops

Infrared spectroscopy is a rapid, nondestructive analytical technique that can be applied to the authentication and characterization of food samples in high throughput. In particular, near infrared spectroscopy is commonly utilized in the food quality control industry to monitor the physical attributes of numerous cereal grains for protein, carbohydrate, and lipid content. IR-based methods require little sample preparation, labor, or technical competence if multivariate data mining techniques are implemented; however, they do require extensive calibration. Economically important crops are infected by fungi that can severely reduce crop yields and quality and, in addition, produce mycotoxins. Owing to the health risks associated with mycotoxins in the food chain, regulatory limits have been set by both national and international institutions for specific mycotoxins and mycotoxin classes. This article discusses the progress and potential of IR-based methods as an alternative to existing chemical methods for the determination of fungal contamination in crops, as well as emerging spectroscopic methods.

Evaluation of a membrane filtration method for the rapid enumeration of confirmed Clostridium perfringens from water

A modification of the UK reference and ISO 14189 TSCA medium for the enumeration of Clostridium perfringens from water coupled with a membrane filter transfer technique for testing for production of acid phosphatase was evaluated. The new tryptose cycloserine agar (TCA) medium, which lacks sodium metabisulphite but contains sodium pyruvate to improve recovery, allows the isolation and confirmation of Cl. perfringens within 18-24 h of sample processing. Data from a multilaboratory study analysed according to ISO 17994 showed that TCA was equivalent to TSCA for the enumeration of Cl. perfringens. The identification of acid phosphatase-negative isolates revealed a false-negative rate for the TCA method of 0.8%. The TCA membrane filter transfer procedure provides confirmed Cl. perfringens counts in half the time of the TSCA method and is simple to undertake.

SIGNIFICANCE AND IMPACT OF THE STUDY

The testing of drinking water for Clostridium perfringens is a regulatory parameter in Europe and the UK. Current UK and ISO methods employ membrane filtration (MF) and TSCA medium followed by subculture and confirmation of isolates by testing for acid phosphatase. This takes 48 h. We present here the results of a multilaboratory evaluation of a MF method that features a simplified isolation medium (TCA) and a membrane transfer procedure for the acid phosphatase test resulting in confirmed results being available in 18-24 h. This development significantly reduces the time to confirmed results for Cl. perfringens from water samples.

Comparison of viable plate count, turbidity measurement and real-time PCR for quantification of Porphyromonas gingivalis

The viable plate count (VPC) is considered as the reference method for bacterial enumeration in periodontal microbiology but shows some important limitations for anaerobic bacteria. As anaerobes such as Porphyromonas gingivalis are difficult to culture, VPC becomes time-consuming and less sensitive. Hence, efficient normalization of experimental data to bacterial cell count requires alternative rapid and reliable quantification methods. This study compared the performance of VPC with that of turbidity measurement and real-time PCR (qPCR) in an experimental context using highly concentrated bacterial suspensions. Our TaqMan-based qPCR assay for P. gingivalis 16S rRNA proved to be sensitive and specific. Turbidity measurements offer a fast method to assess P. gingivalis growth, but suffer from high variability and a limited dynamic range. VPC was very time-consuming and less repeatable than qPCR. Our study concludes that qPCR provides the most rapid and precise approach for P. gingivalis quantification. Although our data were gathered in a specific research context, we believe that our conclusions on the inferior performance of VPC and turbidity measurements in comparison to qPCR can be extended to other research and clinical settings and even to other difficult-to-culture micro-organisms.

SIGNIFICANCE AND IMPACT OF THE STUDY

Various clinical and research settings require fast and reliable quantification of bacterial suspensions. The viable plate count method (VPC) is generally seen as 'the gold standard' for bacterial enumeration. However, VPC-based quantification of anaerobes such as Porphyromonas gingivalis is time-consuming due to their stringent growth requirements and shows poor repeatability. Comparison of VPC, turbidity measurement and TaqMan-based qPCR demonstrated that qPCR possesses important advantages regarding speed, accuracy and repeatability.

A decade with nucleic acid-based microbiological methods in safety control of foods

In the last decade, nucleic acid-based methods gradually started to replace or complement the culture-based methods and immunochemical assays in routine laboratories involved in food control. In particular, real-time polymerase chain reaction (PCR) was technically developed to the stage of good speed, sensitivity and reproducibility, at minimized risk of carry-over contamination. Basic advantages provided by nucleic acid-based methods are higher speed and added information, such as subspecies identification, information on the presence of genes important for virulence or antibiotic resistance. Nucleic acid-based methods are attractive also to detect important foodborne pathogens for which no classical counterparts are available, namely foodborne pathogenic viruses. This review briefly summarizes currently available or developing molecular technologies that may be candidates for involvement in microbiological molecular methods in the next decade. Potential of nonamplification as well as amplification methods is discussed, including fluorescent in situ hybridization, alternative PCR chemistries, alternative amplification technologies, digital PCR and nanotechnologies.

Surface plasmon resonance-based real-time bioaerosol detection

AIMS

Rapid and precise bioaerosol detection in different environments has become an important research and technological issue over last decades. Previously, we employed a real-time PCR protocol in conjunction with personal bioaerosol sampler for rapid detection of airborne viruses. The approach has been proved to be specific and sensitive. However, a period of time required for entire procedure was in manner of hours. Some new developments are required to decrease the detection time down to real-time protocols.

METHODS AND RESULTS

Presently, a surface plasmon resonance (SPR)-based immunosensor that coupled with a specific antigen-antibody reaction could offer sensitive, specific, rapid and label-free detection. This study describes the possibility of combining the personal sampler with SPR technology for qualitative and extremely rapid detection of airborne micro-organisms. Common viral surrogate MS2 bacteriophage, frequently used in bioaerosol studies, was employed as a model organism. The results of the sensor functionalizing procedure with monoclonal anti-MS2 antibody and optimization of the chip performance are presented. The SPR-based detection of the airborne virus was found to be very fast; the viral presence was detected in less than 2 min, and the entire procedure (sampling and analysis) was undertaken in 6 min, which could be considered as real-time detection for this type of measurements.

CONCLUSIONS

The combination of SPR with the personal sampler targeted towards bioaerosol detection was proven to be feasible. The SPR sensor was found to be highly stable and suitable for multiple utilizations without significant decrease in response. The suggested approach opens new possibilities for the development of portable and rapid (almost real time) bioaerosol monitors.

SIGNIFICANCE AND IMPACT OF THE STUDY

This technology is the first in the world real-time bioaerosol monitor. This outcome would be of strong interest to individuals representing public health, biosecurity, defence forces, environmental sciences and many others.

Detection of Salmonella sp in chicken cuts using immunomagnetic separation

The immunomagnetic separation (IMS) is a technique that has been used to increase sensitivity and specificity and to decrease the time required for detection of Salmonella in foods through different methodologies. In this work we report on the development of a method for detection of Salmonella in chicken cuts using in house antibody-sensitized microspheres associated to conventional plating in selective agar (IMS-plating). First, protein A-coated microspheres were sensitized with polyclonal antibodies against lipopolysacharide and flagella from salmonellae and used to standardize a procedure for capturing Salmonella Enteritidis from pure cultures and detection in selective agar. Subsequently, samples of chicken meat experimentally contaminated with S. Enteritidis were analyzed immediately after contamination and after 24h of refrigeration using three enrichment protocols. The detection limit of the IMS-plating procedure after standardization with pure culture was about 2x10 CFU/mL. The protocol using non-selective enrichment for 6-8h, selective enrichment for 16-18h and a post-enrichment for 4h gave the best results of S. Enteritidis detection by IMS-plating in experimentally contaminated meat. IMS-plating using this protocol was compared to the standard culture method for salmonellae detection in naturally contaminated chicken cuts and yielded 100% sensitivity and 94% specificity. The method developed using in house prepared magnetic microespheres for IMS and plating in selective agar was able to diminish by at least one day the time required for detection of Salmonella in chicken products by the conventional culture method.

24-Hour Presumptive Enumeration of Escherichia coli O157:H7 in Foods by Using the ISO-GRID® Method with SD-39 Agar

Two 24-hour presumptive enumeration methods for Escherichia coli O157:H7 organisms based on the hydrophobic grid membrane filter (ISO-GRID) and using SD-39 agar, a new selective and differential culture medium, were developed and compared to a 3-tube MPN (most probable number) method using modified tryptone soy broth enrichment. The comparative study comprised 22 combinations of storage conditions and food products, including a variety of raw and cooked meats and several dairy products. The ISO-GRID direct filtration method produced counts which were equivalent to or significantly higher than the 3-tube MPN method for all food-storage combinations except for frozen pasteurized whole egg. The ISO-GRID resuscitation method produced counts equivalent to the 3-tube MPN method for the frozen egg.

Detection of Molds in Foods and Feeds: Potential Rapid and Selective Methods †

Most laboratories still rely on traditional microbiological methods to detect molds in foods and feed. These methods are modified bacteriological methods. Plate count techniques are time consuming and do not detect dead fungi, which are a sign of past contamination. Development of rapid methods to detect molds in foods is still in its embryonic stage. Recently mycologists have begun to develop media that are differential and selective for particular mold species. The use of these media is of great value for the detection of specific groups of fungi such as toxigenic fungi. Other potential rapid methods include chemical and biochemical assays for, e.g., chitin and ergosterol, and immunological and electrical impedance methods.

Sensitivity and specificity of different methods for the isolation of Salmonella from pigs

Three different selective enrichment media, Rappaport-Vassiliadis broth (RV), selenite broth (SB) and Müller-Kauffmann tetrathionate broth (MKTB), in combination with plating on modified brilliant green agar (BGA), were compared for the isolation of Salmonella from samples of pig feces. These conventional methods were also compared with a new ELISA kit in conjunction with RV and SB enrichment. Of the conventional methods, enrichment in RV had a higher sensitivity and selectivity than SB and MKTB. Recovery of S. typhimurium from MKTB was significantly poorer than recovery of other serotypes. The combination of RV enrichment and ELISA was as good as the conventional method involving RV enrichment, with a similar high sensitivity and specificity.