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Salmonella contamination in food production and processing is a serious threat to consumer health. More and more rapid detection methods have been proposed to compensate for the inefficiency of traditional bacterial cultures to suppress the high prevalence of Salmonella more efficiently. The contamination of Salmonella in foods can be identified by recognition elements and screened using rapid detection methods with different measurable signals (optical, electrical, etc.). Therefore, the different signal transduction mechanisms and Salmonella recognition elements are the key of the sensitivity, accuracy and specificity for the rapid detection methods. In this review, the bioreceptors for Salmonella were firstly summarized and described, then the current promising Salmonella rapid detection methods in foodstuffs with different signal transduction were objectively summarized and evaluated. Moreover, the challenges faced by these methods in practical monitoring and the development prospect were also emphasized to shed light on a new perspective for the Salmonella rapid detection methods applications.

Rapid assessment methods (RAMs) have become an integral part of state and federal wetland programs by providing a consistent method for monitoring and prioritizing wetland conservation efforts. RAMs evaluate condition along an anthropogenic disturbance gradient based on qualitative and quantitative measures of wetland indicators. However, RAM applicability outside of the intended region may be difficult or inappropriate due to differences in wetland types, natural variability, and types of stressors. Given the influence of regional and wetland variability on the effectiveness of RAMs, our approach focused on the development and validation of a method applicable to specific wetland types found in Oklahoma and other regions in the Central Great Plains. We applied the Oklahoma Rapid Assessment Method (OKRAM) in 28 depressional wetlands across the state and evaluated the method’s ability to detect condition along a disturbance gradient. We found consistent relationships between OKRAM scores and plant data (e.g., Floristic Quality Index, species richness, and diversity) and with a landscape assessment of anthropogenic disturbance. Based on our results, OKRAM has utility as a tool for differentiating between high and low quality depressional wetlands in Oklahoma, with potential for applicability across other regions of the Central Great Plains.

Salmonella is a major cause of foodborne illness throughout the world and has resulted in a serious of public health issues over the past decades. The conventional culture methods for Salmonella detection are laborious and time-consuming; thus a variety of new methods have been developed to enable rapid detection. Among them, immuno- and nucleic acid-based methods are fast developing because the advancing of molecular science provides more target antibodies and genes for Salmonella detection. These new targets might enable a lower detection limit and higher sensitivity/specificity and, therefore shorten the detection period while ensuring the detection accuracy. This review emphasizes the effect of current immuno- and nucleic acid-based techniques for Salmonella detection. The target antibodies and target genes identified and applied during the latest research are also listed out as a reference. Besides, the main features of various immune- and nucleic acid-based techniques used for Salmonella detection in food are also summarized and compared. This review would provide the in-time and comprehensive guidance to achieve rapid and accurate detection of foodborne Salmonella.

Harmful algal blooms (HABs) are major ecological and environmental problems in China’s coastal waters and seriously threaten the stability of the marine ecosystem and human health. Gymnodinium catenatum is a toxic red tide dinoflagellate. It can produce paralytic shellfish toxins (PSP), which cause serious hazards to marine organisms, public health, and safety. In this paper, a test strip based on colloidal gold immunochromatography (GICG) was developed for the rapid detection of Gymnodinium catenatum . The experimental results showed that the test strip has good specificity and sensitivity. It not only detects the different components of Gymnodinium catenatum but also may detect algal toxins. The lowest density of Gymnodinium catenatum that can be detected by this test strip is approximately 120 cells/mL. Cross-reaction indicated that the test strip had a high specificity for Gymnodinium catenatum. This test strip provides a rapid method for in situ detection of Gymnodinium catenatum and a reference method for the monitoring of other harmful algae to serve as an early warning of upcoming red tides. It also provides a new way to prepare more detection methods for toxic algal toxins.

Background Perkinsosis, a disease caused by the protist Perkinsus , is responsible for mass mortalities of many molluscan species worldwide. The rapid, early and accurate detection of Perkinsus infection is necessary to react to outbreaks, and manage disease transmission. Current methods for diagnosis of Perkinsus spp. are time-consuming or require professional equipment and experienced personnel, rendering them unsuitable for field application. Recombinase polymerase amplification (RPA) assay is a highly sensitive and selective isothermal amplification technique that operates at temperatures of 37–42 °C, requires minimal sample preparation, and is capable of amplifying as low as 1–10 target DNA copies in less than 20 minutes. Methods We report a novel RPA assay that amplifies the internal transcriber spacer (ITS) region of P. beihaiensis , which, followed by rapid detection of amplicons using a lateral flow (LF) strip, enables easy visualization of results by the naked eye. Results The LF-RPA assay successfully amplified P. beihaiensis DNA using a set of primers of 20–25 bp in length. After incubation at 37 °C for 25 min, results were read within 5 min by the naked eye on a lateral flow strip. Our LF-RPA assay was comparably sensitive to qPCR assay, and capable of detecting as few as 26 copies of P. beihaiensis DNA. Cross-amplification occurred with other two Perkinsus species, P. olseni and P. chesapeaki , but not with other potential pathogen taxa in culture environments. We compared the performance of LF-RPA, conventional PCR and qPCR assays on 60 oyster samples. While LF-RPA assay results were 86.2% as sensitive, 77.4% as specific, and generally in agreement with those of conventional PCR results, they were more (93.3%) sensitive, (86.7%) specific, and agreed better with qPCR assay results. Future research should focus on developing simple DNA extraction methods that do not require professional laboratories and complicated extraction procedures, to facilitate application of this LF-RPA assay in the field. Conclusions Our LF-RPA assay provides a rapid and efficient method for detecting species of Perkinsus . This novel assay has potential to be used in field applications.

In eutrophic waters, harmful algal blooms (HAB) are particularly prone to occur, which will affect the ecological environment and public health and safety. How to quickly detect and monitor marine microalgae is the key to preventing and managing HAB. Our innovative application of colloidal gold immunochromatography (GICG) technology to detect the dominant species in red tide, Skeletonema pseudocostatum , to monitor the outbreak of red tide. The experimental results show that the method and the prepared test strips are extremely sensitive and can specifically detect the presence of Skeletonema pseudocostatum . The approximate concentration of algae cells is judged by establishing a fitting relationship between the degree of color development and the concentration of algae cells. This test strip provides a quick and easy method for routine environmental monitoring, fishery water quality monitoring, and field testing of red tide monitoring. It effectively warns of the outbreak of red tides and also provides a new application direction for GICG technology.

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1–10 min. Testing FCS-GX on artificially fragmented genomes demonstrates high sensitivity and specificity for diverse contaminant species. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination, comprising 0.16% of total bases, with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/ or https://doi.org/10.5281/zenodo.10651084 .

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

Foodborne diseases caused by pathogenic bacteria pose a serious threat to human health. Early and rapid detection of foodborne pathogens is an urgent task for preventing disease outbreaks. Microfluidic devices are simple, automatic, and portable miniaturized systems. Compared with traditional techniques, microfluidic devices have attracted much attention because of their high efficiency and convenience in the concentration and detection of foodborne pathogens. This article firstly reviews the bio-recognition elements integrated on microfluidic chips in recent years and the progress of microfluidic chip development for pathogen pretreatment. Furthermore, the research progress of microfluidic technology based on optical and electrochemical sensors for the detection of foodborne pathogenic bacteria is summarized and discussed. Finally, the future prospects for the application and challenges of microfluidic chips based on biosensors are presented.

Raspberries have lately caused several human norovirus (HuNoV) outbreaks in Europe. In this study, we developed and evaluated for HuNoV reverse transcription (RT)-PCR detection in frozen raspberries extraction methods that have equal sensitivity but are less time-consuming than widely used methods based on polyethylene glycol (PEG) precipitation and chloroform–butanol purification. One method was applied to stored frozen raspberries linked to previous HuNoV outbreaks and berries on sale. In the virus elution-based Method 1, sparkling water eluted viruses most efficiently from the berries. Method 2, based on direct nucleic acid extraction with minor PEG supplement, yielded the highest number of positive findings (4 out of 9) at low virus concentration level of 100 genome copies HuNoV genogroup II per 25 g raspberries. Both methods showed approximately equal sensitivity to a method including PEG precipitation and chloroform–butanol purification. Two naturally contaminated berry samples linked to HuNoV outbreaks in 2006 and 2009 were still positive for HuNoV genogroup I, but all berry products purchased from a local store remained negative for HuNoV. In conclusion, this study presents two efficient and rapid methods which can be used in urgent HuNoV outbreak investigations, since the results of the virus analysis are available in a few hours.