Comparison of real-time PCR, reverse transcriptase real-time PCR, loop-mediated isothermal amplification, and the FDA conventional microbiological method for the detection of Salmonella spp. in produce

Development of a Novel Nested-RT-LAMP Assay for the Rapid and Accurate Coronavirus Disease-2019 Diagnosis

Background and Aims: Coronavirus disease 2019 (COVID-19), an emerging life-threatening viral disease, has rapidly spread worldwide, exerting a detrimental impact on public health. We aimed to devise an innovative platform based on the loop-mediated isothermal amplification (LAMP) method, having priorities over real-time PCR (RT-PCR) in terms of sensitivity, specificity, and low running costs. Methods: To develop a novel assay, a new primer set plus four primer sets were designed targeting the N gene of the COVID-19 agent, resulting in the sensitivity reinforcement. The limit of detection (LOD) of the developed approach was determined and compared to those of the standard RT-LAMP and RT-PCR. Two hundred confirmed positive and negative samples initially tested by RT-PCR were recruited to assess the nested-RT-LAMP assay. Furthermore, for the one-step nested-RT-LAMP assay, positive samples were tested directly without the need for RNA extraction. Results: The LOD of nested-RT-LAMP, LAMP, and RT-PCR were 5, 15, and 15 copies/μL, respectively. The findings of the investigation illustrated 100% sensitivity and 98% specificity for both LAMP assays. Moreover, respectively, 94% and 97% sensitivity and specificity were determined regarding the one-step nested-RT-LAMP assay. Conclusion: We offered a novel approach with more sensitivity compared to RT-PCR and common RT-LAMP, not only being a simple, accurate, cost-effective alternative diagnostic tool for RT-PCR but also being able to detect asymptomatic or mildly symptomatic patients more accurately in 2 h by naked eyes.

Viral Involvement in Oral Potentially Malignant Disorders: A Scoping Review

Purpose

The purpose of this scoping review was to investigate which viruses other than HPV and EBV-associated with OPMDs and investigate whether viruses are linked solely to the etiology of OPMDs, their malignant transformation (MT), or both.

Methods

A scoping review following PRISMA-ScR methodological framework was used during the process. We conducted thorough searches in the EBSCOhost and PubMed databases. The inclusion criteria were publications that described viruses in OPMDs and identified pertinent research published between 2014 and 2023. The articles included underwent a thorough analysis and synthesis process to map out viruses in OPMDs. Pertinent characteristics such as research domains, publication dates, authors, type of research studies, sample sizes, gender ratios, types of OPMDs lesions, detected viruses, and methodological detection approaches were incorporated into the analysis.

Results

A total of twenty-eight articles were eligible for inclusion. The prevalence of viruses detected in OPMDs was found to be 78.57%. Viruses detected in this study, including HPV (0% to 86.6%), EBV (8% to 95.7%), hepatitis B virus (HBV) (6.71%) and herpes simplex virus (HSV) (1%). The biggest risk factor for OPMDs found in this study was tobacco use.

Conclusion

Given that 90% of oral cancers worldwide are attributable to OSCC, it is crucial to understand the role of viruses such as HPV, EBV, HBV, and HSV, along with unhealthy risk factors like tobacco and alcohol, which may contribute to the etiology and progression of lesions into OPMDs. Global data indicate that these viruses play varying roles in the etiology of OPMDs, with significant geographic variability, co-infections, and interactions with lifestyle factors influencing their oncogenic potential. Although this study found that virus positivity rates were higher in the malignant stage (OSCC) than in OPMDs and that there is a high prevalence of viruses in OPMDs, further research is needed to clarify the direct causality of virus-induced malignant transformation in OPMDs.

Tunable control of Cas12 activity promotes universal and fast one-pot nucleic acid detection

The CRISPR-based detection methods have been widely applied, yet they remain limited by the non-universal nature of one-pot diagnostic approaches. Here, we report a universal one-pot fluorescent method for the detection of epidemic pathogens, delivering results within 15-20 min. This method uses heparin sodium to precisely tunes the cis-cleavage capability of Cas12 via interference with the Cas12a-crRNA binding process, thereby generating significant fluorescence due to the accumulation of isothermal amplification products. Additionally, this universal assay accommodates both classic and suboptimal PAMs, as well as various Cas12a subtypes such as LbCas12a, AsCas12a, and AapCas12b. Such a robust method demonstrates sensitivity and specificity exceeding 95% in the detection of monkeypox pseudovirus, influenza A virus, and SARS-CoV-2 from saliva or wastewater samples, when compared with qPCR or RT-qPCR. Moreover, the cost of heparin sodium per thousand uses is $0.01 to $0.04 only. Collectively, this universal and fast one-pot approach based on heparin sodium offers potential possibilities for point-of-care testing.

A drop dispenser for simplifying on-farm detection of foodborne pathogens

Nucleic-acid biosensors have emerged as useful tools for on-farm detection of foodborne pathogens on fresh produce. Such tools are specifically designed to be user-friendly so that a producer can operate them with minimal training and in a few simple steps. However, one challenge in the deployment of these biosensors is delivering precise sample volumes to the biosensor's reaction sites. To address this challenge, we developed an innovative drop dispenser using advanced 3D printing technology, combined with a hydrophilic surface chemistry treatment. This dispenser enables the generation of precise sample drops, containing DNA or bacterial samples, in volumes as small as a few micro-liters (∼20 to ∼33 μL). The drop generator was tested over an extended period to assess its durability and usability over time. The results indicated that the drop dispensers have a shelf life of approximately one month. In addition, the device was rigorously validated for nucleic acid testing, specifically by using loop-mediated isothermal amplification (LAMP) for the detection of Escherichia coli O157, a prevalent foodborne pathogen. To simulate real-world conditions, we tested the drop dispensers by integrating them into an on-farm sample collection system, ensuring they deliver samples accurately and consistently for nucleic acid testing in the field. Our results demonstrated similar performance to commercial pipettors in LAMP assays, with a limit of detection of 7.8×106 cells/mL for whole-cell detection. This combination of precision, ease of use, and durability make our drop dispenser a promising tool for enhancing the effectiveness of nucleic acid biosensors in the field.

Surface monitoring of L. monocytogenes by real-time fluorescence and colorimetric LAMP

Listeria monocytogenes is a major foodborne pathogen affecting developing, and developed countries. The analysis of food contact surfaces in food industries is key for better controlling this pathogen. The current study focused on the development, optimization, and evaluation of a rapid and simple method for the detection of L. monocytogenes on stainless steel surfaces, suitable for decentralized setups, taking advantage of Loop-mediated isothermal amplification (LAMP). This was accomplished using a general pre-enrichment broth (TSB), with a simple DNA extraction based on a chelating resin, and final isothermal amplification. Two different detection strategies were tested, real-time fluorescence and naked-eye colorimetric, which were evaluated after 5, 7, and 24 h of pre-enrichment. Regardless the detection chemistry selected, after 5-7 h of pre-enrichment, 103-104 CFU/cm2 were needed to obtain a positive result, while after 24 h, it was possible to detect concentrations below 10 CFU/cm2. Within each given time, all the performance parameters calculated, relative sensitivity, specificity, and accuracy, reached values higher than 80-90%; likewise, a Cohen's k of concordance with a culture-based approach higher than 0.8. Overall, the most sensitive assay can be performed in roughly 25 h. This time-to-result outperforms commercial kits with the added value of specifically detecting L. monocytogenes instead of Listeria spp. KEY POINTS: • Real-time fluorescence and naked-eye colorimetric, were compared for the novel assay. • An LOD50 of 3.4 CFU/cm2 and 4.2 CFU/cm2 was calculated for the two assays. • Three pre-enrichment times were compared providing 24 h better results.

Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications

Salmonella, the prevailing zoonotic pathogen within the Enterobacteriaceae family, holds the foremost position in global bacterial poisoning incidents, thereby signifying its paramount importance in public health. Consequently, the imperative for expeditious and uncomplicated detection techniques for Salmonella in food is underscored. After more than two decades of development, loop-mediated isothermal amplification (LAMP) has emerged as a potent adjunct to the polymerase chain reaction, demonstrating significant advantages in the realm of isothermal amplification. Its growing prominence is evident in the increasing number of reports on its application in the rapid detection of Salmonella. This paper provides a systematic exposition of the technical principles and characteristics of LAMP, along with an overview of the research progress made in the rapid detection of Salmonella using LAMP and its derivatives. Additionally, the target genes reported in various levels, including Salmonella genus, species, serogroup, and serotype, are summarized, aiming to offer a valuable reference for the advancement of LAMP application in Salmonella detection. Finally, we look forward to the development direction of LAMP and expect more competitive methods to provide strong support for food safety applications.

Development of a closed-tube, calcein-based loop-mediated isothermal amplification assay to detect Salmonella spp. in raw meat samples

Foodborne pathogens compromise food safety and public health, and Salmonella spp. are among the major pathogenic bacteria that cause outbreaks worldwide. Proper surveillance through timely and cost-effective detection methods across the food animal production chain is crucial to prevent Salmonella outbreaks and agricultural losses. Traditional culture methods are labor- and resource-intensive, with lengthy turnaround times. Meanwhile, conventional molecular tools, such as PCR and qPCR, are expensive and require technical skills and equipment. Loop-mediated isothermal amplification (LAMP) is a simple, rapid, inexpensive, highly sensitive, and specific molecular assay that does not require expensive equipment. Hence, this study developed and optimized a closed-tube, calcein-based LAMP assay to detect Salmonella using the invA gene and performed evaluation and validation against conventional PCR. The LAMP assay showed high specificity and sensitivity. It showed 10-fold higher sensitivity than conventional PCR, at <1 ng/μL DNA concentrations. Meanwhile, for CFU/mL, LAMP assay showed 1000-fold higher sensitivity than conventional PCR at 4.8 × 103 cells/mL than 4.8 × 107 cells/mL, respectively. For parallel testing of 341 raw meat samples, after conventional culture enrichment (until Rappaport-Vassiliadis broth), the optimized LAMP assay showed 100% detection on all samples while conventional PCR showed 100%, 99.04%, and 96.64% for raw chicken, beef, and pork samples, respectively. Meanwhile, a shortened enrichment protocol involving 3-h incubation in buffered peptone water only, showed lower accuracy in tandem with the optimized LAMP assay ranging from 55 to 75% positivity rates among samples. These suggest that the optimized LAMP assay possesses higher sensitivity over conventional PCR for invA gene detection when coupled with conventional enrichment culture methods. Hence, this assay has potential as a powerful complementary or alternative Salmonella detection method to increase surveillance capacity and protect consumer food safety and public health worldwide.

Salmonella detection with LAMP and qPCR and identification of serovars of interest by multiplex qPCR in poultry carcasses

Salmonella is present in the poultry production chain and is a major challenge in terms of food safety and animal health. The early Salmonella detection is one of the main tools to control and prevent the transmission of this pathogen. Microbiological isolation and serotyping to identify and differentiate Salmonella serovars are laborious processes, time-consuming, and expensive. Therefore, molecular diagnostic methods can be rapid and efficient alternatives to the detection of this pathogen. Thus, the aim herein was to standardize and evaluate the use of loop-mediated isothermal amplification (LAMP) in comparison with real-time PCR (qPCR) for detection of Salmonella associated with a multiplex qPCR for simultaneous identification and differentiation of S. Enteritidis, S. Typhimurium, S. Pullorum, and S. Gallinarum. The LAMP, qPCR, and multiplex qPCR assays were comparable in specificity. The three techniques were evaluated for specificity for 16 different serovars of Salmonella and for 37 strains of the serovars of interest. The limit of detection and the efficiency of the LAMP, qPCR, and multiplex qPCR reactions were determined. The techniques were applied to 33 samples of chicken carcasses and compared to the results of conventional microbiology for validation. As results, LAMP was specific in the detection of different Salmonella serovars but presented lower limit of detection ranging from 101 to 104 CFU/reaction. In comparison, qPCR could detect less cells (100 to 102 CFU/reaction), reaching equal specificity and better repeatability in the assays. The qPCR multiplexing for identification of the different serovars also showed good specificity, with the detection threshold between entre 101 and 102 CFU/reaction. The results obtained in the analyses on poultry carcasses suggested a correspondence between the results obtained in molecular methods and in conventional microbiology. Thus, the proposed assays are promising for the diagnosis of Salmonella in poultry carcasses, already proved to be faster and more efficient than conventional diagnostics techniques, being of great interest for poultry production, animal, and public health.

Microbial Inoculants as Plant Biostimulants: A Review on Risk Status

Modern agriculture systems are copiously dependent on agrochemicals such as chemical fertilizers and pesticides intended to increase crop production and yield. The indiscriminate use of these chemicals not only affects the growth of plants due to the accumulation of toxic compounds, but also degrades the quality and life-supporting properties of soil. There is a dire need to develop some green approach that can resolve these issues and restore soil fertility and sustainability. The use of plant biostimulants has emerged as an environmentally friendly and acceptable method to increase crop productivity. Biostimulants contain biological substances which may be capable of increasing or stimulating plant growth in an eco-friendly manner. They are mostly biofertilizers that provide nutrients and protect plants from environmental stresses such as drought and salinity. In contrast to the protection of crop products, biostimulants not only act on the plant's vigor but also do not respond to direct actions against pests or diseases. Plant biostimulants improve nutrient mobilization and uptake, tolerance to stress, and thus crop quality when applied to plants directly or in the rhizospheric region. They foster plant growth and development by positively affecting the crop life-cycle starting from seed germination to plant maturity. Legalized application of biostimulants causes no hazardous effects on the environment and primarily provides nutrition to plants. It nurtures the growth of soil microorganisms, which leads to enhanced soil fertility and also improves plant metabolism. Additionally, it may positively influence the exogenous microbes and alter the equilibrium of the microfloral composition of the soil milieu. This review frequently cites the characterization of microbial plant biostimulants that belong to either a high-risk group or are closely related to human pathogens such as Pueudomonas, Klebsiella, Enterobacter, Acinetobacter, etc. These related pathogens cause ailments including septicemia, gastroenteritis, wound infections, inflammation in the respiratory system, meningitis, etc., of varied severity under different conditions of health status such as immunocompromized and comorbidity. Thus it may attract the related concern to review the risk status of biostimulants for their legalized applications in agriculture. This study mainly emphasizes microbial plant biostimulants and their safe application concerns.

Point-of-care diagnosis of invasive non-typhoidal Salmonella enterica in bloodstream infections using immunomagnetic capture and loop-mediated isothermal amplification

Invasive non-typhoidal salmonellosis is gaining worldwide attention as an emerging disease cluster among bloodstream infections. The disease has the highest burden among immunocompromised and malnourished children in resource-limited areas due to poor access to reliable and rapid diagnostics. Point-of-care (POC) diagnostics are promising for use in such low infrastructure laboratory settings. However, there still remains a major challenge for POC testing to deal with the complexity of blood matrices in rapid detection of an extremely low concentration of blood-borne pathogens. In this work, the challenges were addressed by combining magnetic bead based pathogen concentration and Loop Mediated Isothermal Amplification (LAMP) technology. Sensitivity and performance of the combined approach were determined and compared with a direct PCR method. A direct visual detection strategy, adapted using SYTO-24 DNA intercalating dye, resulted in a limit of detection (LoD) as low as 14 CFU/mL in blood samples with a total analysis time of less than 2 h, including sample preparation. This approach has the potential for wide application as a high-throughput POC testing method to analyze pathogens in clinical, food, feed and environmental samples.

Genetic identification of bat species for pathogen surveillance across France

With more than 1400 chiropteran species identified to date, bats comprise one-fifth of all mammalian species worldwide. Many studies have associated viral zoonoses with 45 different species of bats in the EU, which cluster within 5 families of bats. For example, the Serotine bats are infected by European Bat 1 Lyssavirus throughout Europe while Myotis bats are shown infected by coronavirus, herpesvirus and paramyxovirus. Correct host species identification is important to increase our knowledge of the ecology and evolutionary pattern of bat viruses in the EU. Bat species identification is commonly determined using morphological keys. Morphological determination of bat species from bat carcasses can be limited in some cases, due to the state of decomposition or nearly indistinguishable morphological features in juvenile bats and can lead to misidentifications. The overall objective of our study was to identify insectivorous bat species using molecular biology tools with the amplification of the partial cytochrome b gene of mitochondrial DNA. Two types of samples were tested in this study, bat wing punches and bat faeces. A total of 163 bat wing punches representing 22 species, and 31 faecal pellets representing 7 species were included in the study. From the 163 bat wing punches tested, a total of 159 were genetically identified from amplification of the partial cyt b gene. All 31 faecal pellets were genetically identified based on the cyt b gene. A comparison between morphological and genetic determination showed 21 misidentifications from the 163 wing punches, representing ~12.5% of misidentifications of morphological determination compared with the genetic method, across 11 species. In addition, genetic determination allowed the identification of 24 out of 25 morphologically non-determined bat samples. Our findings demonstrate the importance of a genetic approach as an efficient and reliable method to identify bat species precisely.

Rapid, Sensitive, Specific, and Visual Detection of Salmonella in Retail Meat with Loop-Mediated Isothermal Amplification, Targeting the invA Gene

ABSTRACT

Salmonella is one of the major pathogenic bacteria causing foodborne diseases. The rapid detection of Salmonella in food is of great significance to food safety. In this study, the loop-mediated isothermal amplification (LAMP) method was developed, and primers were designed targeting the invA gene of Salmonella. Standard samples of recombinant invA-plasmid and 100 retail meat samples were tested by LAMP and compared with the results tested by conventional PCR and the routine Chinese National Food Safety Standard-Microbiological Examination of Food-Examination of Salmonella, respectively. The results showed that Salmonella strains of eight different serotypes were amplified successfully by the developed LAMP assay, and it was 1,000-fold more sensitive than conventional PCR, with the analytical sensitivity of 8 × 102 copies per μL of the standard sample of invA-plasmid. The results were visualized directly by adding calcein and MnCl2 in the LAMP reaction tube, and the positively amplified products turned green after an incubation of 2 min. In parallel detection, the positive rate of Salmonella by the LAMP assay was highly correlated with the routine Chinese national standard method. The results of the study demonstrated that the developed LAMP assay is a simple, rapid, strongly specific, highly sensitive, and visual detection method for Salmonella.

HIGHLIGHTS

Occurrence of Salmonella enterica in grey-headed flying foxes from New South Wales

Salmonella enterica and Campylobacter jejuni are significant foodborne zoonotic pathogens causing gastroenteritis in humans. Domestic animals are commonly implicated as reservoirs of S. enterica and C. jejuni, but both are also detected in wild animals. Salmonella enterica serovar Typhimurium is the most common cause of human salmonellosis in Australia; however, Salmonella enterica serovar Wangata is associated with sporadic human outbreaks in New South Wales and wild animals may be a potential reservoir. To determine if wild grey-headed flying foxes (GHFF; Pteropus poliocephalus) are reservoirs of Salmonella and Campylobacter, faecal samples were collected from three GHFF colonies in New South Wales and cultured for the presence of Salmonella and Campylobacter. One Salmonella isolate was cultured from 254 GHFF faecal samples (0.39%). Whole genome sequencing was used to genetically characterise the Salmonella isolate and perform phylogenetic analysis. The GHFF isolate was determined to be Salmonella Typhimurium ST19. The GHFF isolate carried a virulence plasmid and other virulence factors, but did not exhibit antimicrobial resistance. Phylogenetic analysis determined that the GHFF isolate was most closely related to a cluster of six isolates: four from human salmonellosis cases in Queensland and two from Australian livestock. Neither Campylobacter nor Salmonella Wangata were cultured from the 254 GHFF faecal samples. This study concluded that wild GHFF in New South Wales are not major reservoirs for Salmonella, and the zoonotic risks associated with S. enterica carriage by urban GHFF are low for the general public.

RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19

The global pandemic of coronavirus disease 2019 (COVID-19) highlights the shortcomings of the current testing paradigm for viral disease diagnostics. Here, we report a stepwise protocol for an RNA-extraction-free nano-amplified colorimetric test for rapid and naked-eye molecular diagnosis of COVID-19. The test employs a unique dual-prong approach that integrates nucleic acid (NA) amplification and plasmonic sensing for point-of-care detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a sample-to-assay response time of <1 h. The RNA-extraction-free nano-amplified colorimetric test utilizes plasmonic gold nanoparticles capped with antisense oligonucleotides (ASOs) as a colorimetric reporter to detect the amplified nucleic acid from the COVID-19 causative virus, SARS-CoV-2. The ASOs are specific for the SARS-CoV-2 N-gene, and binding of the ASOs to their target sequence results in the aggregation of the plasmonic gold nanoparticles. This highly specific agglomeration step leads to a change in the plasmonic response of the nanoparticles. Furthermore, when tested using clinical samples, the accuracy, sensitivity and specificity of the test were found to be >98.4%, >96.6% and 100%, respectively, with a detection limit of 10 copies/μL. The test can easily be adapted to diagnose other viral infections with a simple modification of the ASOs and primer sequences. It also provides a low-cost, rapid approach requiring minimal instrumentation that can be used as a screening tool for the diagnosis of COVID-19 at point-of-care settings in resource-poor situations. The colorimetric readout of the test can even be monitored using a handheld optical reader to obtain a quantitative response. Therefore, we anticipate that this protocol will be widely useful for the development of biosensors for the molecular diagnostics of COVID-19 and other infectious diseases.

Evaluation of a commercial loop-mediated isothermal amplification assay, 3MTM Molecular Detection Assay 2 - Campylobacter, for the detection of Campylobacter from poultry matrices

1. The objective of this study was to evaluate performance of a commercial loop-mediated isothermal amplification (LAMP) method as an alternative method for the detection of Campylobacter spp. in primary production samples, poultry rinses and raw poultry products, as compared to the US Department of Agriculture Food Inspection Service Microbiology Laboratory Guide Book PCR reference method, MLG 41A.2. The Campylobacter spp. LAMP was used in conjunction with a ready-to-use enrichment broth that does not require microaerophilic incubation. After enrichment, boot swabs from poultry farms, carcase rinses and raw poultry products were tested by the LAMP method and the MLG 41A PCR method.3. The ready-to-use enrichment broth enabled the growth of Campylobacter spp. within 22 to 28 hours under aerobic incubation conditions. The LAMP method enabled Campylobacter detection in the enriched samples of various poultry matrices and had equivalent sensitivity and specificity to the MLG 41A PCR method.4. No significant difference (95% confidence interval) was found between the alternative and the MLG 41A PCR method, as determined by probability of detection analysis, except for neutralising buffered peptone water post-chill rinsates. For the post-chill neutralising buffered peptone water rinsates, the LAMP method had significantly higher confirmed portions.

Conserved CRISPR arrays in Salmonella enterica serovar Infantis can serve as qPCR targets to detect Infantis in mixed serovar populations

Salmonellosis is a leading bacterial cause of foodborne illness, and numerous Salmonella enterica serovars have been responsible for foodborne outbreaks. In the United States outbreaks are often linked to poultry and poultry-related products. The prevalence of Salmonella serovar Infantis has been increasing in poultry processing facilities over the past few years and in 2018 was identified as the causative agent for a large multistate outbreak linked to raw chicken. CRISPR-typing is a subtyping approach based on PCR and the sequencing of two Salmonella loci, CRISPR1 and CRISPR2. CRISPR-typing was used to interrogate 138 recent (2018-2019) isolates and genomes of ser. Infantis. Results show that the CRISPR elements are remarkably conserved in this serovar. The most conserved spacers, and those also unique to ser. Infantis, were used as targets to develop a ser. Infantis-specific qPCR assay. This assay was able to detect ser. Infantis in mixed serovar cultures of Salmonella, down to 0·1% of the population, highlighting the utility of this molecular approach in improving surveillance sensitivity for this important food safety pathogen. SIGNIFICANCE AND IMPACT OF THE STUDY: The incidence of human salmonellosis cases caused by Salmonella enterica serovar Infantis (ser. Infantis) has been increasing, as has its prevalence in broiler chickens, which are a frequent reservoir of Salmonella. A cluster of ser. Infantis genetically linked to an outbreak strain have been identified in numerous processing facilities. A qPCR assay targeting CRISPR elements that are unique to ser. Infantis has been developed and can detect this serovar directly from mixed cultures. This assay is sensitive enough to reveal ser. Infantis within a mixed Salmonella population where it constitutes only 0·1% of the population. The rapid nature of qPCR lends this assay to high-throughput screening of poultry samples to detect this important pathogen.

COVID-19: Current Trends in Invitro Diagnostics

The novel coronavirus SARS-CoV-2 is the seventh known species of coronavirus, infectious to human beings. The pandemic COVID-19 spread all over the world with an unprecedented spreading rate after its first appearance in Wuhan, China. As a novel viral disease there in no antiviral treatment or vaccine for the COVID-19. At present, the early detection and the quarantine of infected patients are the ways to stop the spreading of the disease. This review will discuss about the current invitro diagnostic methods used worldwide for the early and accurate diagnosis of COVID-19. Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment.

Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters

Foodborne contamination and associated illness in the United States is responsible for an estimated 48 million cases per year. Increased food demand, global commerce of perishable foods, and the growing threat of antibiotic resistance are driving factors elevating concern for food safety. Foodborne illness is often associated with fresh-cut, ready-to-eat produce commodities due to the perishable nature of the product and relatively minimal processing from farm to the consumer. The research presented here optimizes and evaluates the utility of microfluidic droplets, also termed ultra-miniaturized bioreactors, for rapid detection of viable Salmonella enterica ser. Typhimurium in a shredded lettuce wash water acquired from a major Mid-Atlantic produce processing facility (denoted as Producer) in the U.S. Using a fluorescently-labeled anti-S. Typhimurium antibody and relative fluorescence intensities, paired with in-droplet incubation, S. Typhimurium was detected and identified with 100% specificity in less than 5 h. In initial optimization experiments using S. Typhimurium-spiked sterile water, the relative fluorescence intensity of S. Typhimurium was approximately two times that of the observed relative intensities of five non-S. Typhimurium negative controls at 4-h incubation in droplets containing Rappaport-Vasiliadis (RV) broth at 37°C: relative fluorescence intensity for S. Typhimurium = 2.36 (95% CI: 2.15-2.58), Enterobacter aerogens 1.12 (95% CI: 1.09-1.16), Escherichia coli 700609 = 1.13 (95% CI: 1.09-1.17), E. coli 13706 1.13 (95% CI: 1.07-1.19), E. coli 700891 1.05 (95% CI: 1.03-1.07) and Citrobacter freundii 1.04 (95% CI: 1.03-1.05). S. Typhimurium- and E. aerogens-spiked shredded lettuce wash waters acquired from the Producer were then incubated 4 h in-droplet at 37°C with RV broth. The observed relative fluorescence of S. Typhimurium was significantly higher than that of E. aerogens, 1.56 (95% CI: 1.42-1.71) and 1.10 (95% CI: 1.08-1.12), respectively. While further optimization focusing on compatible concentration methodologies for highly-dilute produce water samples is needed, this application of droplet microfluidics shows great promise in dramatically shortening the time necessary-from days to hours-to confirm viable bacterial contamination in ready-to-eat produce wash waters used throughout the domestic and international food industry.

Optical Temperature Control Unit and Convolutional Neural Network for Colorimetric Detection of Loop-Mediated Isothermal Amplification on a Lab-On-A-Disc Platform

Lab-on-a-disc (LOD) has emerged as a promising candidate for a point-of-care testing (POCT) device because it can effectively integrate complex fluid manipulation steps using multiple layers of polymeric substrates. However, it is still highly challenging to design and fabricate temperature measurement and heating system in non-contact with the surface of LOD, which is a prerequisite to successful realization of DNA amplification especially with a rotatable disc. This study presents a Lab-on-a-disc (LOD)-based automatic loop-mediated isothermal amplification (LAMP) system, where a thermochromic coating (<~420 µm) was used to distantly measure the chamber’s temperature and a micro graphite film was integrated into the chamber to remotely absorb laser beam with super high efficiency. We used a deep learning network to more consistently analyze the product of LAMP than we could with the naked eye. Consequently, both temperature heating and measurement were carried out without a physical contact with the surface of LOD. The experimental results show that the proposed approach, which no previous work has attempted, was highly effective in realizing LAMP in LOD.

Loop-Mediated Isothermal Amplification for Salmonella Detection in Food and Feed: Current Applications and Future Directions

Loop-mediated isothermal amplification (LAMP) has become a powerful alternative to polymerase chain reaction (PCR) for pathogen detection in clinical specimens and food matrices. Nontyphoidal Salmonella is a zoonotic pathogen of significant food and feed safety concern worldwide. The first study employing LAMP for the rapid detection of Salmonella was reported in 2005, 5 years after the invention of the LAMP technology in Japan. This review provides an overview of international efforts in the past decade on the development and application of Salmonella LAMP assays in a wide array of food and feed matrices. Recent progress in assay design, platform development, commercial application, and method validation is reviewed. Future perspectives toward more practical and wider applications of Salmonella LAMP assays in food and feed testing are discussed.

Methods for the detection and identification of pathogenic bacteria: past, present, and future

In order to retard the rate of development of antibacterial resistance, the causative agent must be identified as rapidly as possible, so that directed patient treatment and/or contact precautions can be initiated. This review highlights the challenges associated with the detection and identification of pathogenic bacteria, by providing an introduction to the techniques currently used, as well as newer techniques that are in development. Focusing on the chemical basis for these techniques, the review also provides a comparison of their advantages and disadvantages.

Diagnosis of schistosomiasis mansoni: an evaluation of existing methods and research towards single worm pair detection

The inadequacy of current diagnostics for the detection of low worm burdens in humans means that schistosomiasis mansoni is more widespread than previously acknowledged. With the inception of mass drug treatment programmes aimed at disease elimination and the advent of human vaccine trials, the need for more sensitive diagnostics is evident. In this review, we evaluate the merits and limitations of the principal diagnostic methods, namely detection of eggs in faeces; anti-schistosome antibodies in serum; parasite-derived proteins and glycans in serum or urine; parasite DNA in blood, faeces or urine. Only in the baboon model, where actual worm burden is determined by portal perfusion, have faecal smear and circulating antigen methods been calibrated, and shown to have thresholds of detection of 10-19 worm pairs. There is scope for improvement in all the four methods of detection, e.g. the identification of single targets for host antibodies to improve the specificity of enzyme linked immunosorbent assay. Despite recent advances in the definition of the schistosome secretome, there have been no comprehensive biomarker investigations of parasite products in the urine of infected patients. Certainly, the admirable goal of eliminating schistosomiasis will not be achieved unless individuals with low worm burdens can be diagnosed.

Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples

The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation). Despite having a detection limit less than the threshold recommended for effective remediation, the application of the assay was limited because of the semi-quantitative nature of the data. Moreover, the assay was prone to false positives due to the aerosolization of amplicons. In this study, deoxyuridine triphosphate (dUTP) and uracil DNA glycosylase (UNG) were incorporated into the assay to reduce the probability of false positives. Optimization experiments revealed a UNG concentration of 0.2units per reaction was adequate for degrading trace levels of AUGC based contamination (~1.4×10⁴ gene copies/reaction) without significant changes to the detection limit (~100 gene copies/reaction). Additionally, the optimized assay was used with the most probable number (MPN) method to quantify RDase genes (vcrA and tceA) in multiple groundwater samples from a chlorinated solvent contaminated site. Using this approach, gene concentrations were significantly correlated to concentrations obtained using traditional methods (qPCR and DNA templates). Although the assay underestimated RDase genes concentrations, a strong correlation (R²=0.78 and 0.94) was observed between the two data sets. The regression equations obtained will be valuable to determine gene copies in groundwater using the newly developed, low cost and time saving method.

Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater

TaqMan probe-based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes is a widely accepted molecular biological tool (MBT) for determining the abundance of Dehalococcoides sp. in groundwater samples from chlorinated solvent-contaminated sites. However, there are significant costs associated with this MBT. In this study, we describe an approach that requires only low-cost laboratory equipment (a bench top centrifuge and a water bath) and requires less time and resources compared to qPCR. The method involves the concentration of biomass from groundwater, without DNA extraction, and loop-mediated isothermal amplification (LAMP) of the cell templates. The amplification products are detected by a simple visual color change (orange/green). The detection limits of the assay were determined using groundwater from a contaminated site. In addition, the assay was tested with groundwater from three additional contaminated sites. The final approach to detect RDase genes, without DNA extraction or a thermal cycler, was successful to 1.8 × 10⁵ gene copies per L for vcrA and 1.3 × 10⁵ gene copies per L for tceA. Both values are below the threshold recommended for effective in situ dechlorination.

Exploiting a host-commensal interaction to promote intestinal barrier function and enteric pathogen tolerance

Commensal intestinal bacteria can prevent pathogenic infection; however, limited knowledge of the mechanisms by which individual bacterial species contribute to pathogen resistance has restricted their potential for therapeutic application. Here, we examined how colonization of mice with a human commensal Enterococcus faecium protects against enteric infections. We show that E. faecium improves host intestinal epithelial defense programs to limit Salmonella enterica serotype Typhimurium pathogenesis in vivo in multiple models of susceptibility. E. faecium protection is mediated by a unique peptidoglycan hydrolase, SagA, and requires epithelial expression of pattern recognition receptor components and antimicrobial peptides. Ectopic expression of SagA in non-protective and probiotic bacteria is sufficient to enhance intestinal barrier function and confer resistance against S. Typhimurium and Clostridium difficile pathogenesis. These studies demonstrate that specific factors from commensal bacteria can be used to improve host barrier function and limit the pathogenesis of distinct enteric infections.

Recombinant plasmid-based quantitative Real-Time PCR analysis of Salmonella enterica serotypes and its application to milk samples

The aim of the current study was to develop, a new, rapid, sensitive and quantitative Salmonella detection method using a Real-Time PCR technique based on an inexpensive, easy to produce, convenient and standardized recombinant plasmid positive control. To achieve this, two recombinant plasmids were constructed as reference molecules by cloning the two most commonly used Salmonella-specific target gene regions, invA and ttrRSBC. The more rapid detection enabled by the developed method (21 h) compared to the traditional culture method (90 h) allows the quantitative evaluation of Salmonella (quantification limits of 10(1)CFU/ml and 10(0)CFU/ml for the invA target and the ttrRSBC target, respectively), as illustrated using milk samples. Three advantages illustrated by the current study demonstrate the potential of the newly developed method to be used in routine analyses in the medical, veterinary, food and water/environmental sectors: I--The method provides fast analyses including the simultaneous detection and determination of correct pathogen counts; II--The method is applicable to challenging samples, such as milk; III--The method's positive controls (recombinant plasmids) are reproducible in large quantities without the need to construct new calibration curves.

Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9

Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures.

Effects of climate change on Salmonella infections

BACKGROUND

Climate change and global warming have been reported to increase spread of foodborne pathogens. To understand these effects on Salmonella infections, modeling approaches such as regression analysis and neural network (NN) were used.

METHODS

Monthly data for Salmonella outbreaks in Mississippi (MS), Tennessee (TN), and Alabama (AL) were analyzed from 2002 to 2011 using analysis of variance and time series analysis. Meteorological data were collected and the correlation with salmonellosis was examined using regression analysis and NN.

RESULTS

A seasonal trend in Salmonella infections was observed (p<0.001). Strong positive correlation was found between high temperature and Salmonella infections in MS and for the combined states (MS, TN, AL) models (R(2)=0.554; R(2)=0.415, respectively). NN models showed a strong effect of rise in temperature on the Salmonella outbreaks. In this study, an increase of 1°F was shown to result in four cases increase of Salmonella in MS. However, no correlation between monthly average precipitation rate and Salmonella infections was observed.

CONCLUSION

There is consistent evidence that gastrointestinal infection with bacterial pathogens is positively correlated with ambient temperature, as warmer temperatures enable more rapid replication. Warming trends in the United States and specifically in the southern states may increase rates of Salmonella infections.

Evaluation of Two Loop-mediated Isothermal Amplification Methods for the Detection of Salmonella Enteritidis and Listeria Monocytogenes in Artificially Contaminated Ready-to-Eat Fresh Produce

In the present study, the effectiveness of two loop-mediated isothermal amplification (LAMP) assays was evaluated. Samples of romaine lettuce, strawberries, cherry tomatoes, green onions and sour berries were inoculated with known dilutions (100-108 CFU/g of produce) of S. Enteritidis and L. monocytogenes. With LAMP, assay pathogens can be detected in less than 60 min. The limits of detection of S. Enteritidis and L. monocytogenes depended on the food sample tested and on the presence of enrichment step. After enrichment steps, all food samples were found positive even at low initial pathogen levels. The developed LAMP, assays, are expected to become a valuable, robust, innovative, powerful, cheap and fast monitoring tool, which can be extensively used for routine analysis, and screening of contaminated foods by the food industry and the Public Food Health Authorities.

Efficient Detection of Pathogenic Leptospires Using 16S Ribosomal RNA

Pathogenic Leptospira species cause a prevalent yet neglected zoonotic disease with mild to life-threatening complications in a variety of susceptible animals and humans. Diagnosis of leptospirosis, which primarily relies on antiquated serotyping methods, is particularly challenging due to presentation of non-specific symptoms shared by other febrile illnesses, often leading to misdiagnosis. Initiation of antimicrobial therapy during early infection to prevent more serious complications of disseminated infection is often not performed because of a lack of efficient diagnostic tests. Here we report that specific regions of leptospiral 16S ribosomal RNA molecules constitute a novel and efficient diagnostic target for PCR-based detection of pathogenic Leptospira serovars. Our diagnostic test using spiked human blood was at least 100-fold more sensitive than corresponding leptospiral DNA-based quantitative PCR assays, targeting the same 16S nucleotide sequence in the RNA and DNA molecules. The sensitivity and specificity of our RNA assay against laboratory-confirmed human leptospirosis clinical samples were 64% and 100%, respectively, which was superior then an established parallel DNA detection assay. Remarkably, we discovered that 16S transcripts remain appreciably stable ex vivo, including untreated and stored human blood samples, further highlighting their use for clinical detection of L. interrogans. Together, these studies underscore a novel utility of RNA targets, specifically 16S rRNA, for development of PCR-based modalities for diagnosis of human leptospirosis, and also may serve as paradigm for detection of additional bacterial pathogens for which early diagnosis is warranted.

Ecological prevalence, genetic diversity, and epidemiological aspects of Salmonella isolated from tomato agricultural regions of the Virginia Eastern Shore

Virginia is the third largest producer of fresh-market tomatoes in the United States. Tomatoes grown along the eastern shore of Virginia are implicated almost yearly in Salmonella illnesses. Traceback implicates contamination occurring in the pre-harvest environment. To get a better understanding of the ecological niches of Salmonella in the tomato agricultural environment, a 2-year study was undertaken at a regional agricultural research farm in Virginia. Environmental samples, including tomato (fruit, blossoms, and leaves), irrigation water, surface water and sediment, were collected over the growing season. These samples were analyzed for the presence of Salmonella using modified FDA-BAM methods. Molecular assays were used to screen the samples. Over 1500 samples were tested. Seventy-five samples tested positive for Salmonella yielding over 230 isolates. The most commonly isolated serovars were S. Newport and S. Javiana with pulsed-field gel electrophoresis yielding 39 different patterns. Genetic diversity was further underscored among many other serotypes, which showed multiple PFGE subtypes. Whole genome sequencing (WGS) of several S. Newport isolates collected in 2010 compared to clinical isolates associated with tomato consumption showed very few single nucleotide differences between environmental isolates and clinical isolates suggesting a source link to Salmonella contaminated tomatoes. Nearly all isolates collected during two growing seasons of surveillance were obtained from surface water and sediment sources pointing to these sites as long-term reservoirs for persistent and endemic contamination of this environment.

A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods

Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR). There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These ‘isothermal’ methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT), akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP) assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

Detection of Salmonella spp. by a loop-mediated isothermal amplification (LAMP) method targeting bcfD gene

In this study, we developed and validated a loop-mediated isothermal amplification (LAMP) assay for Salmonella detection targeting bcfD gene, a conserved fimbrial operon gene existing in Salmonella. The Salmonella LAMP assay we developed successfully amplified 44 Salmonella strains (14 standard strains and 30 clinical isolates), but none of 9 non-Salmonella standard strains (Proteus mirabilis, Listeria monocytogenes, Escherichia coli, Pseudomonas aeruginosa, Shigella flexneri, Shigella sonnei, Klebsiella pneumoniae, Campylobacter jejuni and Vibrio parahemolyticus). The detection limit was 5 CFU of Salmonella pure culture or 200 CFU of artificially spiked faeces per reaction system (equivalent to 5000 CFU g(-1) of faeces), and this method could directly detect Salmonella in chicken faeces free of pre-enrichment in a reaction time of 25 min. Our experiments show that the LAMP method we developed is a rapid, sensitive, specific and practical method for Salmonella detection. The Salmonella LAMP assay can potentially serve as new on-site diagnostics in the food and agricultural industries.

SIGNIFICANCE AND IMPACT OF THE STUDY

A loop-mediated isothermal amplification (LAMP) assay was established to detect Salmonella targeting bcfD gene, a conserved fimbrial operon gene. The detection limit was 5 CFU of Salmonella pure culture or 200 CFU of artificially spiked faeces per reaction system (equivalent to 5000 CFU g(-1) of faeces), and this method could directly detect Salmonella in chicken faeces free of pre-enrichment in a reaction time of 25 min. The Salmonella LAMP assay is a rapid, sensitive, specific and practical method for Salmonella detection and can potentially serve as new on-site diagnostics in the food and agricultural industries.

Differentiation of Salmonella strains from the SARA, SARB and SARC reference collections by using three genes PCR-RFLP and the 2100 Agilent Bioanalyzer

Rapid molecular typing methods are important tools in surveillance and outbreak investigations of human Salmonella infections. Here we described the development of a three-genes PCR-RFLP typing method for the differentiation of Salmonella species, subspecies and serovars using the Agilent 2100 Bioanalyzer. The fliC, gnd, and mutS genes were PCR-amplified in 160 Salmonella strains representing the two Salmonella species, six subspecies, and 41 different serovars of S. enterica subspecies enterica. PCR products were individually cut with two different restriction enzymes and the resulting 930 restriction patterns were collected using the Agilent 2100 Bioanalyzer followed by cluster analysis. Both species of Salmonella were differentiated by conventional PCR. All of S. bongori tested were gnd PCR negative due to a mismatch at the 3'-end in one the PCR primers. Salmonella subspecies were differentiated into third-teen homogeneous groups representing each of the six subspecies by cluster analysis of restriction patterns generated from the mutS gene cut with AciI. S. enterica subspecies enterica serovars were further differentiated by the combination of the three target genes and five out the six sets of restriction patterns with a discriminatory power of 0.9725 by cluster analysis. The combined RFLP results of five sets of restriction patterns allowed us to assign each of the 160 strains to one of 128 restriction types. During inoculation studies we were able to identify S. Saintpaul and Typhimurium from 24 h pre-enrichment samples using the described method. The use of fliC, gnd, and mutS PCR-RFLP with the Agilent 2100 Bioanalyzer can provide an accessible and automated alternative method for differentiation of Salmonella pathogens.