Inhibition and facilitation of nucleic acid amplification

Detection of Mycobacterium ulcerans with IS2404 loop-mediated isothermal amplification and a fluorescent reporter probe

An exquisitely sensitive quantitative PCR (qPCR) assay targeting the high-copy number insertion sequence, IS2404, is the gold standard diagnostic test for Mycobacterium ulcerans, the agent of the neglected tropical skin disease Buruli ulcer. Here, we designed and tested an alternative M. ulcerans diagnostic test, a fluorescent probe-based, loop-mediated isothermal amplification (P-LAMP) assay that also targets IS2404. Benchmarked against IS2404 qPCR, P-LAMP was equally specific and nearly as sensitive (analytical sensitivity of four vs two M. ulcerans genome copies). Clinical and environmental specimen validation against IS2404 qPCR showed P-LAMP had 100% sensitivity and specificity. P-LAMP was twice as fast as qPCR with an average time-to-positive at the limit-of-detection of 19 minutes. P-LAMP targeting IS2404 is a versatile assay that addresses the performance issues of previously described IS2404 LAMP formats. This study tackles a key research priority for Buruli ulcer and represents another avenue for the development of rapid and accessible molecular diagnostics for this neglected tropical disease.IMPORTANCEBuruli ulcer is a neglected tropical disease caused by infection with Mycobacterium ulcerans. Correct diagnosis is essential before appropriate treatment for Buruli ulcer can be started. Development of a portable, easy-to-use diagnostic test for M. ulcerans has been identified by the World Health Organization as a research priority. Buruli ulcer most commonly occurs in remote, rural areas; therefore, an ideal test is one that can be used at (or near) the point of care (community health centres) without the need for specialized laboratories. Here, we describe a molecular test using loop-mediated isothermal amplification (LAMP) to detect DNA specific to M. ulcerans and show that this new test has equivalent performance to the gold standard M. ulcerans PCR test currently used worldwide. Our new test is rapid (30 minutes to run), simple to perform, and could be further developed into a robust, portable format to provide accessible and affordable M. ulcerans diagnostics anywhere.

Enteroviruses in Water: Epidemiology, Detection and Inactivation

Enteroviruses are small non-enveloped RNA viruses commonly found in environmental water samples. Worldwide analysis of water provides evidence of the broad distribution of enteroviruses. In addition to their medical importance, they are used as markers of faecal contamination of water. This review focuses on water-borne human enteroviruses and their transmission. Methods for detecting enteroviruses in water are also presented as well as current strategies to control these enteric viruses in water.

Recovery of human DNA from fly larvae (Order: Diptera) using Powersoil® Pro

Forensic entomology, the use of insects in criminal and civil investigations, is commonly associated with the estimation of the postmortem interval (PMI). Dipteran larvae found on decomposing bodies can be used for PMI estimations, and as a potential source of human DNA to identify individuals and establish scene-to-victim connections. The ability to use fly larvae for multiple purposes would increase their evidentiary value and help investigations. This study investigates the use of DNeasy® Powersoil® Pro (QIAGEN) paired with various forensic genotyping methods to assess the recovery of useful human and fly DNA. Fly larvae were collected at the Southeast Texas Applied Forensic Science (STAFS) Facility from cadavers to process crops and whole fly larvae. Human DNA was quantified using Quantifiler™ Trio (Applied Biosystems™) and short tandem repeat (STR) profiles were recovered with Investigator® 24plex QS (QIAGEN). Human and fly larval mitochondrial DNA were sequenced for HVI and II and CO1, respectively. Genotyping with ForenSeq® MainstAY SE was also attempted to assess the possibility of using next generation sequencing on human DNA recovered from fly larvae. Full and partial STR profiles from crop and whole fly larvae were recovered. Human mtDNA analysis was successful, recovering full sequences and haplogroups for samples that failed STR typing. CO1 sequencing and MainstAY SE yielded additional information for investigative purposes. PMI estimates were provided using species specific development and Total Body Score (TBS). Fly larvae as a source of human DNA can allow laboratories to attempt various genotyping methods on an extract to aid investigations.

Comparison of Fecal DNA Extraction Kits for the Giant Panda (Ailuropoda melanoleuca) by Short Tandem Repeat Genotype Analysis

Genetic analysis of short tandem repeat (STR) loci using noninvasive fecal samples is currently the most widely used method in genetic surveys of giant pandas (Ailuropoda melanoleuca). However, low-quality fecal DNA obtained from fecal samples may affect the accuracy of short tandem repeat (STR) genotyping results and pose a challenge to accurately identify individuals. The aim of this study was thus to compare the efficiency of DNA extraction kits in obtaining high-quality fecal host DNA from giant panda fecal samples. In this study, six commercial kits widely used in fecal DNA extraction, the QIAamp Fast DNA Stool Mini Kit (Q kit), Beaver Beads Stool DNA Kit (H kit), Mag-MK Soil & Stool Genome DNA Extraction kit (S kit), Magnetic Soil And Stool DNA Kit (T kit), E.Z.N.A Mag-Bind Stool DNA Kit (O kit) and Mag Beads Fast DNA Kit for Feces (M kit) were compared. Fecal DNA concentration and purity were measured, and STR genotyping was performed using blood and fecal DNA from captive giant pandas to compare the genotype matches at 11 STR loci. Our results show that the most efficient extraction kits were the Q and T kits, and the Q kit had a greater ability to remove PCR inhibitors than other kits. Careful selection of DNA extraction kits is required to achieve optimal genotyping accuracy across different STR genotyping systems. For STR genotyping systems with smaller PCR product sizes (< 200 bp, such as GPL-29, GP-08, GP-01, Panda-40 and Panda-05), all six kits demonstrated high genotype matching rates (GMR > 80%). In contrast, for STR genotyping systems with longer PCR product sizes (> 200 bp), the choice of DNA extraction kit significantly influenced GMR, with the H kit and O kit performing well for gpy-5 but the Q kit and O kit being less suitable for GPL-08.

Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification with Xylenol Orange Targeting Nucleocapsid Gene for Detection of Feline Coronavirus Infection

Feline infectious peritonitis (FIP), a devastating disease with near-complete mortality, is caused by the feline coronavirus (FCoV) and affects domestic cats worldwide. Herein, we report the development of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay incorporating xylenol orange (XO) as a visual indicator for FCoV detection. The assay employed six oligonucleotide primers targeting regions of the nucleocapsid (N) gene. Under optimized conditions (65 °C, 60 min), amplification products were detected through pH-dependent colour changes in the XO dye. The RT-LAMP-XO assay exhibited high specificity for FCoV, with no cross-reactivity against other common feline viral pathogens. While the detection limit (1.7 × 101 copies/µL) was an order of magnitude higher than that of qPCR, the method offered advantages in simplicity and speed compared to existing diagnostic approaches. Although less sensitive than qPCR, the RT-LAMP-XO assay may serve as a rapid screening tool when used in combination with additional primer sets. These findings demonstrate the potential utility of XO-based RT-LAMP as a simple, visual detection method for FCoV infection.

Development and Characterization of a Polyvalent Polyclonal Antibody as a Common Capture Antibody for the Detection of Enterotoxigenic Escherichia coli in a Sandwich ELISA

Due to its low cost and simplicity, the sandwich enzyme-linked immunosorbent assay (sELISA) is a traditional technique for identifying foodborne pathogens. However, most sELISAs are designed for single foodborne pathogen detection using two specific antibodies, which capture and detect the target bacteria. This study aimed to produce and characterize a common capture polyclonal antibody for Enterotoxigenic Escherichia coli (ETEC), Salmonella Typhimurium, and Shigella flexneri (S. flexneri) by a sELISA. Rabbit polyclonal antibodies (pAbs) were generated against recombinant proteins of CsgA, FhuA, and OmpA, which we called anti-mix. The recombinant proteins generated are conserved in Escherichia coli (E. coli), Salmonella enterica serovar Typhimurium, and S. flexneri species, but not in Listeria monocytogenes (L. monocytogenes) and Enterococcus faecalis (E. faecalis). The anti-mix serum gave a title higher than 1:32,000 by an indirect ELISA using purified recombinant proteins and whole bacteria cultures of the bacteria expressing the antigens but failed to recognize L. monocytogenes and E. faecalis. In addition, a recombinant protein A was purified and used to orient the capture antibodies (anti-mix) in the sELISA. However, no statistically significant difference was found in the assay sensitivity for ETEC detection in spiked milk samples with or without protein A. The assay linearity of sELISA for ETEC detection in Phosphate-buffered saline (PBS) was from 1 × 108 to 1 × 104 cells/mL, and for spiked milk samples was 1 × 108 to 1 × 105 cells/mL. In spiked milk samples, the detection limit of ETEC was lower than PBS, which suggests a negative effect from the matrix analyzed (milk) compared to PBS.

Development of a Rapid Surveillance System for Ross River Virus in Mosquitoes Through Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP)

The global rise in arboviral diseases can be attributed to the ongoing effects of climate change. Ross River virus (RRV) is an illustrative example of such diseases, with case reports in Australia experiencing a significant surge since 2020. RRV is transmitted to susceptible species, such as horses and humans, through multiple mosquito vectors, namely Culex annulirostris, Aedes camptorhynchus, and more recently Ae. notoscriptus. This disease is not only endemic to Australia but has caused outbreaks in surrounding countries such as Fiji and Papua New Guinea. Currently, there are no therapeutic regimes or vaccinations available for RRV, leaving public health warning systems and advice relying upon disease prediction and surveillance. Commonly utilised methods, such as predictive modelling, are experiencing challenges resulting from an increased mosquito presence and extreme weather patterns, often yielding inaccurate advice. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) provided a promising solution to mitigate these challenges and is now considered the gold standard in many Australian states. However, this method must be performed in a laboratory setting and requires expensive machinery, thus rendering it inadequate for resource-poor or rural communities. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) serves as a simple and field-deployable substitute with comparable sensitivities and specificity to RT-qPCR, whilst possessing the ability to provide rapid results within 20 min. This paper describes a novel RRV RT-LAMP assay that can detect RRV in as little as one mosquito, with a limit of detection of 1 × 10-7 ng/µl (~620 copies/µl) and a clinical sensitivity of 84%. Through the addition of tetramethylammonium chloride (TMAC), our assay achieved a 100% specificity and was able to detect RRV RNA as early as 2 min in crude field samples. The simplistic sampling method coupled with our RRV RT-LAMP assay can provide an in-field and low-cost alternative to current routine surveillance techniques.

A Contracted Channel Droplet Reinjection Chip-Based Simple Integrated ddpcr System for SARS-CoV-2 and H1N1 Detection

Droplet microfluidics is a powerful method for digital droplet polymerase chain reaction (ddPCR) applications. However, precise droplet control, bulky peripherals, and multistep operation usually required in droplet detection process hinder the broad application of ddPCR. Here, a contracted channel droplet reinjection chip is presented, where droplets can be self-separated and detected one by one at intervals. Based on that, a Simple Integrated ddPCR (SI-ddPCR) system is established, including surface-wetting-based droplet generation, tube heating, and droplet signal detection. To assess the system's performance, we quantified SARS-CoV-2 and H1N1 simultaneously using duplex-ddPCR. The results exhibited a good linearity (R2 = 0.999) at concentrations ranging from 101 to 104 copies/μL. By employing the SI-ddPCR system, we detected SARS-CoV-2 and H1N1 in clinical samples isolated from 20 swab specimens with an accuracy of 97.5%. Thus, the developed SI-ddPCR system offers simple droplet detection, eliminates complicated peripherals and multistep operations, and promises to be a portable, low-cost, and easy-to-deploy toolbox for high-accuracy ddPCR.

Comparative evaluation of various DNA extraction methods and analysis of DNA degradation levels in commercially marketed Chestnut rose juices and beverages

BACKGROUND

Food safety is a significant global study subject that is strongly intertwined with human life and well-being. The utilization of DNA-based methods for species identification is a valuable instrument in the field of food inspection and regulation. It is particularly significant for traceability purposes, as it enables the monitoring of a specific item at every level of the food chain regulation. However, obtaining amplifiable genomic DNA in this process is a significant obstacle in gene studies. To date, there is a lack of literature on DNA extraction from processed juice or beverages, and no data exist on simultaneous comparisons of various extraction processes. This study aimed to optimize and compare four DNA extraction methods for Chestnut rose juices and beverages. Furthermore, we also conducted a comparison and analysis of the extent of DNA degradation in Chestnut rose juice or beverage by utilizing the amplicon size.

METHODS

The quantity and quality of the extracted DNA were assessed using NanoDrop One spectrophotometer, gel electrophoresis, and real-time polymerase chain reaction (real-time PCR or qPCR) assays. An assessment was conducted on the processing time, labor intensity, and cost associated with each approach. The degree of DNA degradation in Chestnut rose juice or beverage was also assessed using TaqMan real-time PCR methods.

RESULTS

The non-commercial modified CTAB-based approach yielded a high DNA concentration. However, spectrophotometric results and real-time PCR analysis showed poor DNA quality. The combination approach showed the greatest performance among the extraction methods, while being comparatively time-consuming and costly in contrast to the other methods. Additionally, the analytical findings of DNA degradation suggested that the integrity of sample DNA could be influenced by the intricacy of processing methods used by various manufacturers.

CONCLUSIONS

To achieve precise DNA quantification, selecting suitable extraction strategies for the given matrix is necessary. The combination approach was identified as the most effective DNA extraction technique and is suggested for extracting DNA from Chestnut rose juices and beverages. This comparative assessment can be particularly valuable for extracting and identifying processed Juices and Beverages in a diverse range of food compositions.

Magnetic Carbon Bead-Based Concentration Method for SARS-CoV-2 Detection in Wastewater

Wastewater surveillance for pathogens is important to monitor disease trends within communities and maintain public health; thus, a quick and reliable protocol is needed to quantify pathogens present in wastewater. In this study, a method using a commercially available magnetic carbon bead-based kit, i.e., the Carbon Prep (C.prep) method (Life Magnetics), was employed to detect and quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as bacteriophage Phi6 and pepper mild mottle virus (PMMoV) in wastewater samples. The performance of this method was evaluated by modifying several steps and comparing it with the polyethylene glycol (PEG) precipitation method to demonstrate its applicability to virus detection in wastewater. The protocol of the C.prep method, based on the manufacturer's instructions, could not detect SARS-CoV-2 RNA, while the optimized protocol could detect it in the tested samples at concentrations that were not significantly different from those obtained using the PEG precipitation method. However, the optimized C.prep method performed more poorly in recovering Phi6 and detecting PMMoV than the PEG precipitation method. The results of this study indicated that the full workflow of the C.prep method was not sufficient to detect the target viruses in wastewater and that an additional RNA extraction step was needed to increase its detection sensitivity.

Maximizing viral nucleic acid yield from passive samplers: Evaluating elution and extraction protocols

The COVID-19 pandemic has underscored the need for effective viral tracking in aqueous environments, particularly for non-enteric viruses. Despite advances in wastewater monitoring, surveillance of viruses in freshwater remains limited due to traditional sampling challenges. This study refines GAC-based passive sampling protocols by determining optimal extraction and elution methods for enhancing the recovery of viral nucleic acids in freshwater. Three commercially available total nucleic acid (TNA) extraction kits and four elution buffers were assessed for their ability to recover SARS-CoV-2 and bacteriophage MS2 from GAC-based samplers. The Promega Wizard® Enviro Total Nucleic Acid Kit, paired with a Tween®20-based buffer, provided the highest virus recovery efficiency for GAC-based passive sampling. Field-scale applications demonstrated the effectiveness of GAC-based passive samplers in capturing SARS-CoV-2, INFA, RSV, and MeV using the optimized protocols. The combination of the Tween®20 based buffer and the Promega kit led to increased detection frequencies in grab samples, which remained lower in recovery than passive sampling. This study underscores the importance of selecting appropriate TNA extraction kits and elution buffers to maximize virus recovery from passive samples. By optimizing these protocols, we enhance the sensitivity and reliability of viral surveillance in freshwater ecosystems.

Enhanced Blastocystis subtyping from stool samples using semi-nested barcode PCR: validation with an NGS-based approach

In 2006, a PCR method was introduced to subtype Blastocystis by Sanger sequencing of an ≈610 bp amplicon of the 18S rRNA gene. This method, known as barcoding-PCR, has become widespread, although the primer pair used can amplify non-Blastocystis sequences, which can result in false positives. Barcoding-PCR is most effective with DNA extracted from Blastocystis cultures, limiting its sensitivity when used directly with stool samples. As a result, barcoding-PCR can sometimes yield negative results for stool samples confirmed as Blastocystis-positive by microscopy. To improve subtyping from stool-derived DNA, we developed a Semi-Nested barcode PCR that amplifies the barcoding region in a second reaction. Our study shows that this Semi-Nested approach outperforms classical barcoding-PCR, detecting Blastocystis more reliably from stool samples with stronger gel signals and no false positives. This was confirmed by near-complete concordance (68/70 samples) with the Santin-PCR coupled to Next-Generation Sequencing (NGS) as reference standard for Blastocystis subtyping. Of particular interest, one amplicon matched the only previous report of ST35, marking this as the second global detection of ST35 and the first in Colombia. Overall, Semi-Nested barcoded PCR offers a more robust and sensitive alternative compared to classical barcoding-PCR for subtyping Blastocystis directly from stool samples.

Development, Optimization, and Validation of a Quantitative PCR Assay for Borrelia burgdorferi Detection in Tick, Wildlife, and Human Samples

Tick-borne pathogens are growing in importance for human and veterinary research worldwide. We developed, optimized, and validated a reliable quantitative PCR (qPCR; real-time PCR) assay to assess Borrelia burgdorferi infection by targeting two B. burgdorferi genes, ospA and flaB. When assessing previously tested tick samples, its performance surpassed the nested PCR in efficiency, sensitivity, and specificity. Since the detection of Borrelia is more difficult in mammalian samples, the qPCR assay was also assessed using wildlife tissues. For wildlife samples, the sensitivity and specificity of ospA primers, with the incorporation of a pre-amplification step, was equivalent or superior to the nested PCR. For human samples, no primer set was successful with human tissue without culture, but we detected Borrelia with ospA and flaB primers in 50% of the Lyme culture samples, corresponding to 60% of the participants with a Lyme disease diagnosis or suspicion. The specificity of amplification was confirmed by Sanger sequencing. The healthy participant culture samples were negative. This PCR-based direct detection assay performs well for the detection of Borrelia in different biological samples. Advancements in detection methods lead to a better surveillance of Borrelia in vectors and hosts, and, ultimately, enhance human and animal health.

Innovative omics strategies in fermented fruits and vegetables: Unveiling nutritional profiles, microbial diversity, and future prospects

Fermented fruits and vegetables (FFVs) are not only rich in essential nutrients but also contain distinctive flavors, prebiotics, and metabolites. Although omics techniques have gained widespread recognition as an analytical strategy for FFVs, its application still encounters several challenges due to the intricacies of biological systems. This review systematically summarizes the advances, obstacles and prospects of genomics, transcriptomics, proteomics, metabolomics, and multi-omics strategies in FFVs. It is evident that beyond traditional applications, such as the exploration of microbial diversity, protein expression, and metabolic pathways, omics techniques exhibit innovative potential in deciphering stress response mechanisms and uncovering spoilage microorganisms. The adoption of multi-omics strategies is paramount to acquire a multidimensional network fusion, thereby mitigating the limitations of single omics strategies. Although substantial progress has been made, this review underscores the necessity for a comprehensive repository of omics data and the establishment of universal databases to ensure precision in predictions. Furthermore, multidisciplinary integration with other physical or biochemical approaches is imperative, as it enriches our comprehension of this intricate process.

A low-cost and versatile paramagnetic bead DNA extraction method for Mycobacterium ulcerans environmental surveillance

In Australia, native possums are a major wildlife reservoir for Mycobacterium ulcerans, the causative agent of the neglected tropical skin disease Buruli ulcer (BU). Large-scale possum excreta surveys that use PCR to detect M. ulcerans in 100-1,000 s of excreta specimens are an important tool that can inform geospatial modeling and predict locations of future human BU risk. However, the significant expense of commercial kits used to extract DNA from specimens is a major barrier to routine implementation. Here, we developed a low-cost method for DNA extraction from possum excreta, possum tissue, and pure mycobacterial cultures, using a guanidinium isothiocyanate lysis solution and paramagnetic beads. In a 96-well plate format for high-throughput processing, the paramagnetic bead DNA extraction method was threefold less sensitive but only 1/6 the cost of a commonly used commercial kit. Applied to tissue swabs, the method was fourfold more sensitive and 1/5 the cost of a commercial kit. When used for preparing DNA from pure mycobacterial cultures, the method yielded purified genomic DNA with quality metrics comparable to more lengthy techniques. Our paramagnetic bead method is an economical means to undertake large-scale M. ulcerans environmental surveillance that will directly inform efforts to halt the spread of BU in Victoria, Australia, with potential for applicability in other endemic countries.

IMPORTANCE

Buruli ulcer (BU) is a neglected tropical skin disease, with an incidence that has dramatically increased in temperate southeastern Australia over the last decade. In southeastern Australia, BU is a zoonosis with native possums the major wildlife reservoir of the causative pathogen, Mycobacterium ulcerans. Infected possums shed M. ulcerans in their excreta, and excreta surveys using PCR to screen for the presence of pathogen DNA are a powerful means to predict future areas of Buruli ulcer risk for humans. However, excreta surveys across large geographic areas require testing of many thousands of samples. The cost of commercial DNA extraction reagents used for preparing samples for PCR testing can thus become prohibitive to effective surveillance. Here, we describe a simple, low-cost method for extracting DNA from possum excreta using paramagnetic beads. The method is versatile and adaptable to a variety of other sample types including swabs collected from possum tissues and pure cultures of mycobacteria.

Interference-resistant gold nanoparticle assay for detecting Enterococcus in fresh and marine waters

Enterococci are common indicators of fecal contamination and are used to assess the quality of fresh and marine water, sand, soil, and sediment. However, samples collected from these environments contain various cells and other factors that can interfere with the assays used to detect enterococci. We developed a novel assay for the sensitive and specific detection of enterococci that is resistant to interference from other cells and environmental factors. Our interference-resistant assay used 30-nm gold nanoparticles (AuNPs), streptavidin, and a biotinylated Enterococcus antibody. Enterococci inhibited the interaction between streptavidin and biotin and led to the disaggregation of AuNPs. The absence of enterococci led to the aggregation of AuNPs, and this difference was easily detected by spectrophotometry. This interference-resistant AuNP assay was able to detect whole cells of Enterococcus in the range of 10 to 107 CFU/mL within 3 h, had high specificity for enterococci, and was unaffected by the presence of other intestinal bacteria, such as Escherichia coli. Our examination of fresh and marine water samples demonstrated no interference from other cells or environmental factors. The interference-resistant AuNP assay described here has the potential to be used as a rapid, simple, and effective method for monitoring enterococci in diverse environmental samples.

From capture to detection: A critical review of passive sampling techniques for pathogen surveillance in water and wastewater

Water quality, critical for human survival and well-being, necessitates rigorous control to mitigate contamination risks, particularly from pathogens amid expanding urbanization. Consequently, the necessity to maintain the microbiological safety of water supplies demands effective surveillance strategies, reliant on the collection of representative samples and precise measurement of contaminants. This review critically examines the advancements of passive sampling techniques for monitoring pathogens in various water systems, including wastewater, freshwater, and seawater. We explore the evolution from conventional materials to innovative adsorbents for pathogen capture and the shift from culture-based to molecular detection methods, underscoring the adaptation of this field to global health challenges. The comparison highlights passive sampling's efficacy over conventional techniques like grab sampling and its potential to overcome existing sampling challenges through the use of innovative materials such as granular activated carbon, thermoplastics, and polymer membranes. By critically evaluating the literature, this work identifies standardization gaps and proposes future research directions to augment passive sampling's efficiency, specificity, and utility in environmental and public health surveillance.

Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.

Identification of Diptera Puparia in Forensic and Archeo-Funerary Contexts

Diptera identification is fundamental in forensic entomology as well as in funerary archeoentomology, where the challenge is exacerbated by the presence of immature stages such as larvae and puparia. In these two developmental stages, specimens possess a very limited number of diagnostic features, and for puparia, there is also a lack of identification tools such as descriptions and identification keys. Morphological analysis, DNA-based techniques, and cuticular chemical analyses all show good potential for species identification; however, they also have some limitations. DNA-based identification is primarily hindered by the incompleteness of genetic databases and the presence of PCR inhibitors often co-extracted from the puparial cuticle. Chemical analysis of the cuticle is showing promising results, but this approach is also limited by the insufficient profile database and requires specific, expensive equipment, as well as trained personnel. Additionally, to ensure the repeatability of the analysis-a critical aspect in forensic investigations-and to preserve precious and unique specimens from museum collections, non-invasive protocols and techniques must be prioritized for species identification.

A syndromic diagnostic assay on a macrochannel-to-digital microfluidic platform for automatic identification of multiple respiratory pathogens

The worldwide COVID-19 pandemic has changed people's lives and the diagnostic landscape. The nucleic acid amplification test (NAT) as the gold standard for SARS-CoV-2 detection has been applied in containing its transmission. However, there remains a lack of an affordable on-site detection system at resource-limited areas. In this study, a low cost "sample-in-answer-out" system incorporating nucleic acid extraction, purification, and amplification was developed on a single macrochannel-to-digital microfluidic chip. The macrochannel fluidic subsystem worked as a world-to-chip interface receiving 500-1000 μL raw samples, which then underwent bead-based extraction and purification processes before being delivered to DMF. Electrodes actuate an eluent dispensed to eight independent droplets for reverse transcription quantitative polymerase chain reaction (RT-qPCR). By reading with 4 florescence channels, the system can accommodate a maximum of 32 detection targets. To evaluate the proposed platform, a comprehensive assessment was conducted on the microfluidic chip as well as its functional components (i.e., extraction and amplification). The platform demonstrated a superior performance. In particular, using clinical specimens, the chip targeting SARS-CoV-2 and Flu A/B exhibited 100% agreement with off-chip diagnoses. Furthermore, the fabrication of chips is ready for scaled-up manufacturing and they are cost-effective for disposable use since they are assembled using a printed circuit board (PCB) and prefabricated blocks. Overall, the macrochannel-to-digital microfluidic platform coincides with the requirements of point-of-care testing (POCT) because of its advantages: low-cost, ease of use, comparable sensitivity and specificity, and availability for mass production.

Inhibitors of LAMP used to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease in Akoya pearl oysters, and additives to reduce the effect of the inhibitors

Black-spot shell disease is an unresolved disease that decreases pearl quality and threatens pearl oyster survival. In previous studies, the bacterium Tenacibaculum sp. strain Pbs-1 was isolated from diseased Akoya pearl oysters Pinctada fucata, and a rapid, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay for detecting this pathogen was established. This technology has considerable potential for routine diagnosis of strain Pbs-1 in oyster hatcheries and/or pearl farms; therefore, it is vital to identify substances in environmental samples that might inhibit LAMP and to find additives that can reduce the inhibition. In this study, we investigated the effects of six chemicals or proteins, otherwise known as conventional PCR inhibitors, on LAMP, using the DNA of strain Pbs-1 as template: humic acid, urea, iron (III) chloride hexahydrate, melanin, myoglobin, and Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA; pH 6.5). Next, to reduce the effects of identified inhibitors, we tested the addition of bovine serum albumin (BSA) or T4 gene 32 protein (gp32) to the LAMP assay. When 50 ng of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, and 10 mM of EDTA (pH 6.5) inhibited the LAMP reaction, whereas myoglobin, urea, and FeCl3 had no effect. When 50 pg of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, 4 μg/μL of myoglobin, 10 μg/μL of urea, and 10 mM of EDTA inhibited the LAMP reaction. Thus, it was shown that the gene-amplification inhibitory effect of melanin, humic acid, and urea could be reduced by adding BSA or gp32 to the LAMP reaction mixture. This technique could be applied as part of a protocol to prevent mass mortalities of pearl oysters; moreover, the results enhance our knowledge about substances that inhibit LAMP and methods to reduce the inhibition, which have rarely been reported.

Sample preparation and detection methods in point-of-care devices towards future at-home testing

Timely and accurate diagnosis is critical for effective healthcare, yet nearly half the global population lacks access to basic diagnostics. Point-of-care (POC) testing offers partial solutions by enabling low-cost, rapid diagnosis at the patient's location. At-home POC devices have the potential to advance preventive care and early disease detection. Nevertheless, effective sample preparation and detection methods are essential for accurate results. This review surveys recent advances in sample preparation and detection methods at POC. The goal is to provide an in-depth understanding of how these technologies can enhance at-home POC devices. Lateral flow assays, nucleic acid tests, and virus detection methods are at the forefront of POC diagnostic technology, offering rapid and sensitive tools for identifying and measuring pathogens, biomarkers, and viral infections. By illuminating cutting-edge research on assay development for POC diagnostics, this review aims to accelerate progress towards widely available, user-friendly, at-home health monitoring tools that empower individuals in personalized healthcare in the future.

Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility

BACKGROUND

There is a growing demand for fast and reliable plant biomolecular analyses. DNA extraction is the major bottleneck in plant nucleic acid-based applications especially due to the complexity of tissues in different plant species. Conventional methods for plant cell lysis and DNA extraction typically require extensive sample preparation processes and large quantities of sample and chemicals, elevated temperatures, and multiple sample transfer steps which pose challenges for high throughput applications.

RESULTS

In a prior investigation, an ionic liquid (IL)-based modified vortex-assisted matrix solid phase dispersion approach was developed using the model plant, Arabidopsis thaliana (L.) Heynh. Building upon this foundational study, the present study established a simple, rapid and efficient protocol for DNA extraction from milligram fragments of plant tissue representing a diverse range of taxa from the plant Tree of Life including 13 dicots and 4 monocots. Notably, the approach was successful in extracting DNA from a century old herbarium sample. The isolated DNA was of sufficient quality and quantity for sensitive molecular analyses such as qPCR. Two plant DNA barcoding markers, the plastid rbcL and nuclear ribosomal internal transcribed spacer (nrITS) regions were selected for DNA amplification and Sanger sequencing was conducted on PCR products of a representative dicot and monocot species. Successful qPCR amplification of the extracted DNA up to 3 weeks demonstrated that the DNA extracted using this approach remains stable at room temperature for an extended time period prior to downstream analysis.

CONCLUSIONS

The method presented here is a rapid and simple approach enabling cell lysis and DNA extraction from 1.5 mg of plant tissue across a broad range of plant taxa. Additional purification prior to DNA amplification is not required due to the compatibility of the extraction solvents with qPCR. The method has tremendous potential for applications in plant biology that require DNA, including barcoding methods for agriculture, conservation, ecology, evolution, and forensics.

Molecular Methods: Clinical Utilization and Designing a Test Menu

Pre-analytical factors in molecular oncology diagnostics are reviewed. Issues around sample collection, storage, and transport that might affect the stability of nucleic acids and the ability to perform molecular testing are addressed. In addition, molecular methods used commonly in clinical diagnostic laboratories, including newer technologies such as next-generation sequencing and digital droplet polymerase chain reaction, as well as their applications, are reviewed. Finally, we discuss considerations in designing a molecular test menu to deliver accurate and timely results in an efficient and cost-effective manner.

A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements

Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.

Comparative analysis of three next-generation sequencing techniques to measure nosZ gene abundance in Missouri claypan soils

Quantitative next-generation sequencing techniques have been critical in gaining a better understanding of microbial ecosystems. In soils, denitrifying microorganisms are responsible for dinitrogen (N2) production. The nosZ gene codes for nitrous oxide reductase, the enzyme facilitating the reduction of nitrous oxide (N2O) to N2. The objectives of this research were to: 1) understand how soil depth influences RNA concentration and nosZ gene abundance; 2) assess the spatial dependence of nosZ gene abundance in two claypan soil fields; and 3) compare and evaluate multiple RNA-based sequencing methods for quantifying nosZ gene abundance in soils in relation to dinitrogen (N2) production. Research sites consisted of two intensively studied claypan soil fields in Central Missouri, USA. Soil cores were collected from two landscape transects across both fields and analyzed for extractable soil RNA at two depths (0-15 cm and 15-30 cm). Measurements of nosZ gene abundance were obtained using real-time quantitative polymerase chain reaction (RT-qPCR), droplet digital polymerase chain reaction (ddPCR), and nanostring sequencing (NS). In both fields, soil RNA concentrations were significantly greater at 0-15 cm depth compared to 15-30 cm. These data indicated low overall soil microbial activity below 15 cm. Due to low quantities of extractable soil RNA in the subsoil, nosZ gene abundance was only determined in the 0-15 cm depth. Sequencing method comparisons of average nosZ gene abundance showed that NS results were constrained to a narrow range and were 10-20-fold lower than ddPCR and RT-qPCR at each landscape position within each field. Droplet digital PCR appears to be the most promising method, as it reflected changes in N2 production across landscape position.

John Cunningham Virus and Progressive Multifocal Leukoencephalopathy: A Falsely Played Diagnosis

Progressive Multifocal Leukoencephalopathy (PML) is a possibly fatal demyelinating disease and John Cunningham Polyomavirus (JCPyV) is believed to cause this condition. The so-called JCPyV was initially reported in lymphoma and Human Immunodeficiency Virus (HIV) cases, whereas nowadays, its incidence is increasing in Multiple Sclerosis (MS) cases treated with natalizumab (Tysabri). However, there are conflicting literature data on its pathology and diagnosis, whereas some misdiagnosed reports exist, giving rise to further questions towards the topic. In reality, the so-called PML and the supposed JCPyV are not what they seem to be. In addition, novel and more frequent PML-like conditions may be reported, especially after the Coronavirus Disease 2019 (COVID-19) pandemic.

Implementing L-DNA analogs as mirrors of PCR reactant hybridization state: theoretical and practical guidelines for PCR cycle control

In previous reports, we described a PCR cycle control approach in which the hybridization state of optically labeled L-DNA enantiomers of the D-DNA primers and targets determined when the thermal cycle was switched from cooling to heating and heating to cooling. A consequence of this approach is that it also "adapts" the cycling conditions to compensate for factors that affect the hybridization kinetics of primers and targets. It assumes, however, that the hybridization state of the labeled L-DNA analogs accurately reflects the hybridization state of the D-DNA primers and targets. In this report, the Van't Hoff equation is applied to determine the L-DNA concentration and ratio of L-DNA strands required by this assumption. Simultaneous fluorescence and temperature measurements were taken during L-DNA controlled cycling, and the optical and thermal switch points compared as a function of both total L-DNA concentration and ratio of strands. Based on the Van't Hoff relationship and these experimental results, L-DNA best mirrors the hybridization of PCR primers and targets when total L-DNA concentration is set equal to the initial concentration of the D-DNA primer of interest. In terms of strand ratios, L-DNA hybridization behavior most closely matches the behavior of their D-DNA counterparts throughout the reaction when one of the L-DNA strands is far in excess of the other. The L-DNA control algorithm was then applied to the practical case of the SARS-CoV-2 N2 reaction, which has been shown to fail or have a delayed Cq when PCR was performed without nucleic acid extraction. PCR Cq values for simulated "unextracted" PCR samples in a nasopharyngeal background and in an NaCl concentration similar to that of viral transport media were determined using either the L-DNA control algorithm (N = 6) or preset cycling conditions (N = 3) and compared to water background controls run in parallel. For preset cycling conditions, the presence of nasopharyngeal background or a high salt background concentration significantly increased Cq, but the L-DNA control algorithm had no significant delay. This suggests that a carefully designed L-DNA-based control algorithm "adapts" the cycling conditions to compensate for hybridization errors of the PCR D-DNA reactants that produce false negatives.

Metal-DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis

Forensic DNA analysis continues to be hampered by the complex interactions between metals and DNA. Metal ions may cause direct DNA damage, inhibit DNA extraction and polymerase chain reaction (PCR) amplification or both. This study evaluated the impact of metal ions on DNA extraction, quantitation, and short tandem repeat profiling using cell-free and cellular (saliva) DNA. Of the 11 metals assessed, brass exhibited the strongest PCR inhibitory effects, for both custom and Quantifiler Trio quantitation assays. Metal ion inhibition varied across the two quantitative PCR assays and the amount of DNA template used. The Quantifiler Trio internal PCR control (IPC) only revealed evidence of PCR inhibition at higher metal ion concentrations, limiting the applicability of IPC as an indicator of the presence of metal inhibitor in a sample. Notably, ferrous ions were found to significantly decrease the extraction efficiency of the DNA-IQ DNA extraction system. The amount of DNA degradation and inhibition in saliva samples caused by metal ions increased with a dilution of the sample, suggesting that the saliva matrix provides protection from metal ion effects.

Detection of equine herpesvirus-1 (EHV-1) in urine samples during outbreaks of equine herpesvirus myeloencephalopathy

BACKGROUND

Real-time PCR is the diagnostic technique of choice for the diagnosis and control of equine herpesvirus-1 (EHV-1) in an outbreak setting. The presence of EHV-1 in nasal swabs (NS), whole blood, brain and spinal cord samples has been extensively described; however, there are no reports on the excretion of EHV-1 in urine, its DNA detection patterns, and the role of urine in viral spread during an outbreak.

OBJECTIVES

To determine the presence of EHV-1 DNA in urine during natural infection and to compare the DNA detection patterns of EHV-1 in urine, buffy coat (BC) and NS.

STUDY DESIGN

Descriptive study of natural infection.

METHODS

Urine and whole blood/NS samples were collected at different time points during the hospitalisation of 21 horses involved in two EHV-1 myeloencephalopathy outbreaks in 2021 and 2023 in Spain. Quantitative real-time PCR was performed to compare the viral DNA load between BC-urine samples in 2021 and NS-urine samples in 2023. Sex, age, breed, presence of neurological signs, EHV-1 vaccination status and treatment data were recorded for all horses.

RESULTS

A total of 18 hospitalised horses during the 2021 and 2023 outbreaks were positive for EHV-1, and viral DNA was detected in urine samples from a total of 11 horses in both outbreaks. Compared with BC samples, DNA presence was detected in urine samples for longer duration and with slightly higher concentration; however, compared with NS, detection of EHV-1 in urine was similar in duration with lower DNA concentrations.

MAIN LIMITATIONS

Limited sample size, different sampling times and protocols (BC vs. NS) in two natural infection outbreak settings.

CONCLUSIONS

EHV-1 was detected in the urine from naturally infected horses. Urine should be considered as complimentary to blood and NS in diagnosis of EHV-1 infection.

Mitochondrial DNA marker: A PCR approach for tracking rat (Rattus rattus and Rattus norvegicus) fecal pollution in surface water systems

Rats act as reservoirs for a wide range of zoonotic pathogens and can negatively impact human health. In this study, we developed a novel dye base mitochondrial DNA (mtDNA) PCR-assay (RatMt) specifically targeting a 180 bp fragment of the NADH dehydrogenase subunit 2 gene for detecting fecal pollution from two species of rats (Rattus rattus and Rattus norvegicus) in environmental samples. Estimation of Escherichia coli concentrations in Rattus norvegicus fecal pellets suggested that there were approximately 2.24 × 10 4 ± 4.86 × 103 MPN/g of fecal pellet. The RatMt PCR assay was robust, had a detection limit of rat feces in water of 0.274 ± 0.14 mg/100 mL and was 100 % specific for detecting Rattus rattus and Rattus norvegicus fecal mtDNA. Fecal Indicator Bacteria (FIB) along an urbanized gradient in Pensacola-Bay was assessed by the IDEXX Colilert™ - 18 and indicated that the majority of the fifteen sampling sites in the Pensacola-Bay area had E. coli concentrations >410 MPN/100 mL. Rattus rattus and Rattus norvegicus mtDNA were detected in all the urban marine sites, three of the urban freshwater sampling areas, and three of the forested sampling sites. The RatMt PCR assay is a useful tool for rapidly detecting Rattus rattus and Rattus norvegicus fecal pollution in environmental samples.

Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research

The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.

CRISPR-based platforms for the specific and dual detection of defoliating/nondefoliating strains of Verticillium dahliae

BACKGROUND

Verticillium dahliae is a soil-borne pathogenic fungus that causes Verticillium wilt disease on more than 400 plant species worldwide. Because of its broad host range and its ability to survive long term in the soil, there are few effective control measures for V. dahliae once it has become established. Accurate, sensitive, and rapid detection of V. dahliae is crucial for limiting pathogen entry into new regional environments and early management of Verticillium wilt.

RESULTS

In this study, we developed a method to detect V. dahliae based on recombinase polymerase amplification (RPA) and CRISPR/Cas technology and used fluorescence and lateral flow test strips to monitor the outcomes. Through the establishment and optimization of RPA-CRISPR/Cas13a detection, the sensitivity of the fluorescence method was 1 am for genomic DNA (gDNA) within 20 min, whereas the sensitivity of the lateral flow strip method was 100 am for gDNA in 30 min. The field applicability of RPA-CRISPR/Cas13a was also validated by the detection of V. dahliae on smoke trees (Cotinus coggygria) in Xiangshan Park, Beijing, China. Finally, diplex detection for defoliating and nondefoliating pathotypes of V. dahliae was established by combining CRISPR-Cas12a/Cas13a with specific target genes.

CONCLUSION

Taken together, this study achieved rapid, sensitive, and accurate detection of V. dahliae and the differentiation of defoliating and nondefoliating pathotypes and provides potential for field-deployable diagnostic tools for rapid and ultrasensitive detection. © 2023 Society of Chemical Industry.

Ultrasensitive colorimetric detection of Staphylococcus aureus using wheat germ agglutinin and IgY as a dual-recognition strategy

A novel colorimetric platform was designed for the determination of S. aureus by utilizing a dual-recognition strategy, where wheat germ agglutinin (WGA)-functionalized magnetic beads were served as separation elements to capture and enrich S. aureus efficiently from the matrix. Horseradish peroxidase (HRP) labeled chicken anti-protein A IgY (HRP-IgY) was used to label the captured S. aureus. A chicken IgY was introduced as a signal tracer to bind with staphylococcal protein A (SPA) on the surface of S. aureus, which can circumvent the interference from protein G-producing Streptococcus. Subsequently, the colorimetric signal was achieved by an HRP-catalyzed reaction, which was amplified by HRP-IgY bound by approximately 80,000 SPA molecules on one S. aureus. The entire detection process could be accomplished within 90 min. Under optimal conditions, the linear response of different S. aureus concentrations ranged from 7.8 × 102 to 2.0 × 105 CFU/mL and the limit of detection reached down to 3.9 × 102 CFU/mL. Some common non-target bacteria yielded negative results, indicating the excellent specificity of the method. The developed strategy was successfully applied to the determination of S. aureus in various types of samples with satisfactory recoveries. Therefore, the novel dual-recognition strategy possessed the advantages of high sensitivity, specificity, and low cost and exhibited considerable potential as a promising tool to defend public health.

A Deep Ensemble Dynamic Learning Network for Corona Virus Disease 2019 Diagnosis

Corona virus disease 2019 is an extremely fatal pandemic around the world. Intelligently recognizing X-ray chest radiography images for automatically identifying corona virus disease 2019 from other types of pneumonia and normal cases provides clinicians with tremendous conveniences in diagnosis process. In this article, a deep ensemble dynamic learning network is proposed. After a chain of image preprocessing steps and the division of image dataset, convolution blocks and the final average pooling layer are pretrained as a feature extractor. For classifying the extracted feature samples, two-stage bagging dynamic learning network is trained based on neural dynamic learning and bagging algorithms, which diagnoses the presence and types of pneumonia successively. Experimental results manifest that using the proposed deep ensemble dynamic learning network obtains 98.7179% diagnosis accuracy, which indicates more excellent diagnosis effect than existing state-of-the-art models on the open image dataset. Such accurate diagnosis effects provide convincing evidences for further detections and treatments.

Magnetic capture device for large volume sample analysis

Immunomagnetic separation (IMS) techniques employing superparamagnetic particles can successfully isolate various components from mixtures. However, their utility can be limited for large-volume samples, viscous samples, or those containing a high density of particulate matter because of the need to generate high field gradients for particle recovery. Therefore, a new class of immunomagnetic particles was devised utilizing a single, macroscopic Pyrex spinbar conjugated with biorecognition elements to address these limitations. Advantages include an inherent capacity for effective mixing, an almost instantaneous recovery of the spinbar that can be performed without expensive equipment and with no loss of magnetic particles during processing, and reduced transfer of sample matrix. As a result, spinbars can provide an effective means for IMS with large-volume assays composed of complex matrices.

Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water

The quantity and quality of DNA isolated from environmental samples are crucial for getting robust high-throughput sequencing data commonly used for microbial community analysis. The differences in the nature and physicochemical properties of environmental samples impact DNA yields, and therefore, an optimisation of the protocols is always recommended. For instance, samples collected from corroded areas contain high concentrations of metals, salts, and hydrocarbons that can interfere with several steps of the DNA extraction protocols, thereby reducing yield and quality. In this study, we compared the efficiency of commercially available DNA extraction kits and laboratory-adopted methods for microbial community analysis of iron incrustations and oilfield-produced water samples. Modifications to the kits manufacturers' protocols were included to maximise the yield and quality. For iron incrustations, the modified protocol for FastDNA Spin Kit for Soil yielded higher DNA and resulted in higher diversity, including the recovery of low-abundant and rare taxa in the samples, compared to DNeasy PowerSoil Pro Kit. The DNA extracted with modified phenol-chloroform methods yielded higher DNA but failed to pass quality control PCR for 16S sequencing with and without purification. The protocols mentioned here can be used to maximise DNA recovery from iron incrustations and oilfield-produced water samples.

An improved protocol for metagenomic DNA isolation from low microbial biomass alkaline hot-spring sediments and soil samples

High-quality, humic-acid-free pure DNA is a prerequisite for functional and sequence-based approaches of metagenomics. In the present investigation, an improved extraction buffer was developed by making a combination of powdered activated charcoal (2%; w/v), polyvinyl poly pyrrolidone (2%; w/v), and CaCl2 (2%; w/v). This trio significantly improved the purity and yield of the metagenomic DNA from the hot spring's hot and alkaline soil. The quality of extracted metagenomic DNA was successfully validated by PCR amplification and restriction enzymes. Besides, the thermophilic amylase encoding genes were also retrieved from these soil DNA samples. Extreme habitats I harbour low microbial biomass and, therefore, demand in-situ lysis of the microbial cells to access their genomes. The protocol can potentially extract DNA from geothermal spring habitats where the count of microbial cells is low.

Comparison of kits for SARS-CoV-2 extraction in liquid and passive samples

Effective extraction and detection of viral nucleic acids from sewage are fundamental components of a successful SARS-CoV-2 sewage surveillance programme. As there is no standard method employed in sewage surveillance, understanding the performance of different extraction kits in the recovery of SARS-CoV-2 and the impact that PCR inhibitors have on quantification is essential to minimize data discrepancies caused by sample extraction. Three commercial nucleic acid extraction kits: the RNeasy PowerSoil Total RNA Kit (PS), the RNeasy PowerMicrobiome Kit (PMB), and the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (MM), with minor modifications, were evaluated. Their efficacy in recovering viral ribonucleic acid and removal of PCR inhibitors was assessed using two South Australian wastewater matrices-one from a major metropolitan site and one from a regional centre. Both had SARS-CoV-2 present due to active COVID-19 cases in these communities. Overall, the MM kit had a higher recovery of SARS-CoV-2 from the samples tested, followed by PMB and PS. The PMB kit performance was strongly influenced by the sample matrix when compared to the MM kit. It is recommended to assess the performance of extraction kits using different local wastewater matrices to ensure the accuracy and reliability of monitoring results to avoid false reporting.

Cultivation-free sample preparation and DNA purification for direct real-time qPCR of intracellular or spore-like Coxiella burnetii in beef, goat, and lamb meat

Coxiella burnetii is a zoonotic pathogen that has been associated with foodborne outbreaks in products with ruminant origins. However, a method to detect C. burnetii in meat has been merely studied, and commercial kits cannot efficiently fulfill this purpose. In this study, an in-house preparation method for direct real-time qPCR of C. burnetii in beef, goat, and lamb meat was designed. In the sample preparation step (step 1), trypsin digestion and cell disruption techniques were introduced to target C. burnetii in an obligate intracellular or spore-like form. Afterward, 16 DNA purification protocols involving the following steps (steps 2-3) were assessed: the precipitation of meat proteins (step 2; using 2.5, 5.0 M NaCl or 1:1, 2:1 ethanol as the precipitant) and binding of DNA to silicon dioxide particles with chaotropic salts (step 3; using 2.5, 5.0 M NaCl or 2.5, 5.0 M guanidine thiocyanate as the salt). The protocols with superior performance in high-spiked loins (estimated 4-5 log cells/g) were verified in low-spiked (1-2 log cells/g) or Bacillus thuringiensis spore-inoculated (1-2 log CFU/g) loins, ribs, and hind legs. During the protein precipitation, 5.0 M NaCl induced significantly lower protein level as demonstrated by A280, when compared to 2.5 M NaCl or ethanol (P < 0.05). For the DNA binding step, Ct values were lowered in high-spiked goat or lamb loins (3.5-6.0▾; P < 0.05) when the concentration of NaCl was doubled or guanidine thiocyanate was introduced instead of NaCl as a chaotropic salt. Based on these results, two protocols using 5.0 M NaCl as the protein precipitant and 5.0 M NaCl (N2 + N2) or guanidine thiocyanate (N2 + G2) as the chaotropic salt were selected, which demonstrated successful detection in low-spiked (Ct values of N2 + N2, 32.9-35.6; N2 + G2, 32.3-36.4) or spore-inoculated meat (N2 + N2, 30.9-37.5; N2 + G2, 29.7-32.7). Verification in low-spiked meat showed that meat type/part significantly impacted the Ct values of N2 + G2 but not those of N2 + N2. To our knowledge, this is the first study that developed a highly accessible method for detecting C. burnetii in meat which could reveal the possibility of meat-borne Q fever in humans.

Development and validation of a duplex RT-qPCR assay for norovirus quantification in wastewater samples

Norovirus (NoV) is a highly contagious enteric virus that causes widespread outbreaks and a substantial number of deaths across communities. As clinical surveillance is often insufficient, wastewater-based epidemiology (WBE) may provide novel pathways of tracking outbreaks. To utilise WBE, it is important to use accurate and sensitive methods for viral quantification. In this study, we developed a one-step duplex RT-qPCR assay to simultaneously test the two main human pathogenic NoV genogroups, GI and GII, in wastewater samples. The assay had low limits of detection (LOD), namely 0.52 genome copies (gc)/µl for NoVGI and 1.37 gc/µl for NoVGII. No significant concentration-dependent interactions were noted for both NoVGI and for NoVGII when the two targets were mixed at different concentrations in the samples. When tested on wastewater-derived RNA eluents, no significant difference between duplex and singleplex concentrations were found for either target. Low levels of inhibition (up to 32 %) were noted due to organic matter present in the wastewater extracts. From these results we argue that the duplex RT-qPCR assay developed enables the sensitive detection of both NoVGI and NoVGII in wastewater-derived RNA eluents, in a time and cost-effective way and may be used for surveillance to monitor public and environmental health.

An enhanced activity and thermostability of chimeric Bst DNA polymerase for isothermal amplification applications

Loop-mediated isothermal amplification (LAMP) is a widely used method for clinical diagnosis, customs quarantine, and disease prevention. However, the low catalytic activity of Bst DNA polymerase has made it challenging to develop rapid and reliable point-of-care testing. Herein, we developed a series of Bst DNA polymerase mutants with enhanced activity by predicting and analyzing the activity sites. Among these mutants, single mutants K431D and K431E showed a 1.93- and 2.03-fold increase in catalytic efficiency, respectively. We also created a chimeric protein by fusing the DNA-binding domain of DNA ligase from Pyrococcus abyssi (DBD), namely DBD-K431E, which enabled real-time LAMP at high temperatures up to 73 ℃ and remained active after heating at 70 ℃ for 8 h. The chimeric DBD-K431E remained active in the presence of 50 U/mL heparin, 10% ethanol, and up to 100 mM NaCl, and showed higher activity in 110 mM (NH4)2SO4, 110 mM KCl, and 12 mM MgSO4. Notably, it generated a fluorescence signal during the detection of Salmonella typhimurium at 2 × 102 ag/μL of genomic DNA and 1.24 CFU/mL of bacterial colony, outperforming the wild type and the commercial counterpart Bst 2.0. Our results suggest that the DBD-K431E variant could be a promising tool for general molecular biology research and clinical diagnostics. KEY POINTS: • Residue K431 is probably a key site of Bst DNA polymerase activity • The chimeric DBD-K431E is more inhibitor tolerant and thermostable than Bst-LF • The DBD-K431E variant can detect Salmonella typhimurium at 102 ag/μL or 100 CFU/mL.

Development of a PNA-LNA-LAMP Assay to Detect an SNP Associated with QoI Resistance in Erysiphe necator

The repetitive use of quinone outside inhibitor fungicides (QoIs, strobilurins; Fungicide Resistance Action Committee [FRAC] 11) to manage grape powdery mildew has led to development of resistance in Erysiphe necator. While several point mutations in the mitochondrial cytochrome b gene are associated with resistance to QoI fungicides, the substitution of glycine to alanine at codon 143 (G143A) has been the only mutation observed in QoI-resistant field populations. Allele-specific detection methods such as digital droplet PCR and TaqMan probe-based assays can be used to detect the G143A mutation. In this study, a peptide nucleic acid-locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA-LAMP) assay consisting of an A-143 reaction and a G-143 reaction, was designed for rapidly detecting QoI resistance in E. necator. The A-143 reaction amplifies the mutant A-143 allele faster than the wild-type G-143 allele, while the G-143 reaction amplifies the G-143 allele faster than the A-143 allele. Identification of resistant or sensitive E. necator samples was determined by which reaction had the shorter time to amplification. Sixteen single-spore QoI-resistant and -sensitive E. necator isolates were tested using both assays. Assay specificity in distinguishing the single nucleotide polymorphism (SNP) approached 100% when tested using purified DNA of QoI-sensitive and -resistant E. necator isolates. This diagnostic tool was sensitive to one-conidium equivalent of extracted DNA with an R2 value of 0.82 and 0.87 for the G-143 and A-143 reactions, respectively. This diagnostic approach was also evaluated against a TaqMan probe-based assay using 92 E. necator samples collected from vineyards. The PNA-LNA-LAMP assay detected QoI resistance in ≤30 min and showed 100% agreement with the TaqMan probe-based assay (≤1.5 h) for the QoI-sensitive and -resistant isolates. There was 73.3% agreement with the TaqMan probe-based assay when samples had mixed populations with both G-143 and A-143 alleles present. Validation of the PNA-LNA-LAMP assay was conducted in three different laboratories with different equipment. The results showed 94.4% accuracy in one laboratory and 100% accuracy in two other laboratories. The PNA-LNA-LAMP diagnostic tool was faster and required less expensive equipment relative to the previously developed TaqMan probe-based assay, making it accessible to a broader range of diagnostic laboratories for detection of QoI resistance in E. necator. This research demonstrates the utility of the PNA-LANA-LAMP for discriminating SNPs from field samples and its utility for point-of-care monitoring of plant pathogen genotypes.

Rapid Diagnostic of Streptococcus suis in Necropsy Samples of Pigs by thrA-Based Loop-Mediated Isothermal Amplification Assay

Streptococcus (S.) suis presents a serious threat to the pig industry as well as food safety and public health. Although several LAMP assays have been developed for the identification of S. suis, no universal assay is so far available for the field-suitable examination of clinical pig specimens. Based on the thrA housekeeping gene, a new loop-mediated isothermal amplification (LAMP) assay was developed and validated for the detection of S. suis in the brain and joints of pigs. For this LAMP assay, two different methods for the extraction of DNA from brain and joint swabs were compared. Using the LPTV boiling method, the detection limit of LAMP was 1.08 CFU/reaction, while the detection limit was 53.8 CFU/reaction using a commercial DNA extraction kit. The detection limits of thrA-LAMP in combination with the LPTV boiling method were 104-105 CFU/swab in the presence of brain tissue and 103-104 CFU/swab in the presence of joint tissue. The diagnostic quality criteria of LAMP were determined by the examination of 49 brain swabs and 34 joint swabs obtained during routine diagnostic necropsies. Applying the LPTV boiling method to brain swabs, the sensitivity, specificity, and positive and negative predictive values of thrA-LAMP were 88.0, 95.8, 95.7, and 88.5% using cultural investigation as a reference method, and 76.7, 100, 100, and 73.1% using real-time PCR as a reference method. Based on these results, the thrA-LAMP assay combined with the LPTV boiling method is suitable for rapid detection of S. suis from brain swabs.

Multi-laboratory validation study of a real-time PCR method for detection of Salmonella in baby spinach

The FDA Bacteriological Analytical Manual (BAM) Salmonella culture method takes at least 3 days for a presumptive positive result. The FDA developed a quantitative PCR (qPCR) method to detect Salmonella from 24-h preenriched cultures, using ABI 7500 PCR system. The qPCR method has been evaluated as a rapid screening method for a broad range of foods by single laboratory validation (SLV) studies. The present multi-laboratory validation (MLV) study was aimed to measure the reproducibility of this qPCR method and compare its performance with the culture method. Sixteen laboratories participated in two rounds of MLV study to analyze twenty-four blind-coded baby spinach test portions each. The first round yielded ∼84% and ∼82% positive rates across laboratories for the qPCR and culture methods, respectively, which were both outside the fractional range (25%-75%) required for fractionally inoculated test portions by the FDA's Microbiological Method Validation Guidelines. The second round yielded ∼68% and ∼67% positive rates. The relative level of detection (RLOD) for the second-round study was 0.969, suggesting that qPCR and culture methods had similar sensitivity (p > 0.05). The study demonstrated that the qPCR yields reproducible results and is sufficiently sensitive and specific for the detection of Salmonella in food.

Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications

BACKGROUND

Accurate, high-confidence data is critical for assessing potential biothreat incidents. In a biothreat event, false-negative and -positive results have serious consequences. Worst case scenarios can result in unnecessary shutdowns or fatalities at an exorbitant monetary and psychological cost, respectively. Quantitative PCR assays for agents of interest have been successfully used for routine biosurveillance. Recently, there has been increased impetus for adoption of amplicon sequencing (AS) for biosurveillance because it enables discrimination of true positives from near-neighbor false positives, as well as broad, simultaneous detection of many targets in many pathogens in a high-throughput scheme. However, the high sensitivity of AS can lead to false positives. Appropriate controls and workflow reporting can help address these challenges.

OBJECTIVES

Data reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection.

METHODS

We present a set of standards, Amplicon Sequencing Minimal Information (ASqMI), developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program on Agent Detection Assays for making actionable calls in biosurveillance applications. In addition to the first minimum information guidelines for AS, we provide a controls checklist and scoring scheme to assure AS run quality and assess potential sample contamination.

RESULTS

Adoption of the ASqMI guidelines will improve data quality, help track workflow performance, and ultimately provide decision makers confidence to trust the results of this new and powerful technology.

CONCLUSION

AS workflows can provide robust, confident calls for biodetection; however, due diligence in reporting and controls are needed. The ASqMI guideline is the first AS minimum reporting guidance document that also provides the means for end users to evaluate their workflows to improve confidence.

HIGHLIGHTS

Standardized reporting guidance for actionable calls is critical to ensuring trustworthy data.

Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor

To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.

A simple method for testing and controlling inhibition in soil and sediment samples for qPCR

The presence of polymerase-chain-reaction (PCR) inhibitors in many environmental samples can make reliable and repeatable quantitative-polymerase-chain-reaction (qPCR) analysis difficult without sample dilution. To estimate an optimal sample dilution for qPCR and reduce effects of inhibition, a simple test based on multiple dilution series of samples is presented that avoids the use of internal controls and standards reducing complexity and cost.

Droplet magnetic-controlled microfluidic chip integrated nucleic acid extraction and amplification for the detection of pathogens and tumor mutation sites

Traditional nucleic acid extraction and detection is based on open operation, which may cause cross-contamination and aerosol formation. This study developed a droplet magnetic-controlled microfluidic chip integrated nucleic acid extraction, purification and amplification. The reagent is sealed in oil to form a droplet, and the nucleic acid is extracted and purified by controlling the movement of the magnetic beads (MBs) through a permanent magnet, ensuring a closed environment. This chip can automatically extract nucleic acid from multiple samples within 20 min, and can be directly placed in the in situ amplification instrument for amplification without further transfer of nucleic acid, characterized by simple, fast, time-saving and labor-saving. The results showed that the chip was able to detect <10 copies/test SARS-CoV-2 RNA, and EGFR exon 21 L858R mutations were detected in H1975 cells as low as 4 cells. In addition, on the basis of the droplet magnetic-controlled microfluidic chip, we further developed a multi-target detection chip, which used MBs to divide the nucleic acid of the sample into three parts. And the macrolides resistance mutations A2063G and A2064G, and the P1 gene of mycoplasma pneumoniae (MP) were successfully detected in clinical samples by the multi-target detection chip, providing the possibility for future application in the detection of multiple pathogens.

Detecting the Minimum Limit on Wheat Stripe Rust in the Latent Period Using Proximal Remote Sensing Coupled with Duplex Real-Time PCR and Machine Learning

Wheat stripe rust (WSR) is an airborne disease that causes severe damage to wheat. The rapid and early detection of WSR is essential for the prevention and control of this disease. The minimum detection limit (MDL) is one of the most important characteristics of quantitative methods that can be used to determine the scope and applicability of a measurement technique. Three wheat cultivars were inoculated with Puccinia striiformis f.sp. tritici (Pst), and a spectrometer was used to collect the canopy hyperspectral data, and the Pst content was obtained via a duplex real-time polymerase chain reaction (PCR) during the latent period, respectively. The disease index (DI) and molecular disease index (MDI) were calculated. The regression tree algorithm was used to determine the MDL of the Pst based on hyperspectral feature parameters. The logistic, IBK, and random committee algorithms were used to construct the classification model based on the MDL. The results showed that when the MDL was 0.7, IBK had the best recognition accuracy. The optimal model, which used the spectral feature R_2nd.dv ((the second derivative of the original hyperspectral value)) and the modeling ratio 2:1, had an accuracy of 91.67% on the testing set and 90.67% on the 10-fold cross-validation. Thus, during the latent period, the MDL of Pst was determined using hyperspectral technology as 0.7.