PCR inhibitors - occurrence, properties and removal

A simple detection method for potato viruses combining template preparation by heat treatment of homogenate with primers and one-step multiplex RT-PCR

Potatoes are susceptible to viral diseases, and widespread viral infections lead to reduced production yields. Potato leaf roll virus, potato virus S, potato virus X, and potato virus Y are important viruses predominant in potato fields and cause significant economic damage in Japan. In this study, to reduce the labor and cost of virus testing in seed certification program, a simple molecular diagnostic assay for these potato viruses was developed. This method consists of template preparation by heat-treating a mixture of leaf homogenate and a newly designed primer set, followed by one-step conventional multiplex RT-PCR (mRT-PCR). In particular, to simplify RNA extraction, a procedure was adopted in which leaf homogenates in PBST were diluted 100-fold in RNase-free water, heat-treated with primers for 5 min at 70°C and subjected to one-step mRT-PCR. Interestingly, heat treatment of a mixture of the homogenate and primers improved the detection sensitivity for the virus. This new method's detection sensitivity of each virus was 10-100 times higher than that of ELISA using commercial kits and 1-10 times higher than that of one-step mRT-PCR with filter paper-based RNA extraction. The heat-treated homogenate with primers was also applicable for detecting eight other potato viruses by one-step conventional mRT-PCR and four potato viruses by real-time mRT-PCR which our research group previously developed. New direct RT-PCR method for potato viruses can be applied to seed certification programs, where a large number of samples need to be tested.

Catalytic hairpin assembly-and-cyclization aptasensing for AND-logic detection of protein- and RNA-targets in ribonucleoprotein

Both immunological and molecular diagnostics are essential in disease control. However, due to the different technical routes, existing diagnostic tools mainly focus on either immunological or molecular targets at a time, resulting in restricted information for assessment. Herein, we report a DNA operational amplifier circuit for AND-logic analysis of nucleoprotein and RNA of SARS-CoV-2 ribonucleoprotein. The operator is realized using an aptamer-hairpin probe and a padlock-hairpin probe for nucleoprotein- and ligase-catalyzed hairpin assembly-and-cyclization (CHAC). Given approximately 1000 nucleoproteins per virion in coronavirus, a rolling circle amplification (RCA)-based preamplifier is applied to adjust the input bias by converting the target sequence into an aptamer-hairpin input for CHAC. After CHAC, cyclized padlock-hairpin probes trigger another round of RCA as a post-operator amplifier, producing amplicon coils that aggregate detection probe-modified magnetic nanoparticles. These stepwise homogeneous reaction processes are conducted in a single tube for optomagnetic sensing, offering detection limits of 0.07 ng/mL and 1.5 fM for the protein and the molecular targets of SARS-CoV-2, respectively. The stability, specificity, and accuracy of the circuit are validated by testing serum samples, salmon sperm samples, biased inputs, and 33 clinical nasopharyngeal swab specimens, demonstrating the practicability of simultaneously analyzing immunological and molecular targets for accurate diagnostics.

Evaluation of loop mediated isothermal amplification, quantitative real-time PCR, conventional PCR methods for identifying Ascaris lumbricoides in human stool samples

Ascariasis, caused by Ascaris lumbricoides, is a widespread parasitic infection. Traditional diagnostic methods, such as microscopy, can miss infections with low worm burdens, leading to false negatives. This study compares four diagnostic methods-microscopy, conventional PCR, real-time PCR, and loop-mediated isothermal amplification (LAMP)-for detecting A. lumbricoides in 400 stool samples from children aged 2-16. Microscopy methods (direct wet mount, Kato-Katz, and concentration) detected 17, 23, and 21 positive samples, respectively. Molecular techniques identified 23 positive samples by conventional PCR, 29 by real-time PCR, and 25 by LAMP. Notably, real-time PCR detected two samples missed by microscopy, while conventional PCR failed to detect three samples positive by real-time PCR and LAMP. In limit-of-detection assays, conventional PCR detected A. lumbricoides DNA down to 150 pg, while qPCR and LAMP could detect as low as 15 fg. For egg number analysis, conventional PCR detected DNA from 100 eggs, while qPCR and LAMP identified DNA from just 10 eggs. The methods specifically targeted A. lumbricoides, without cross-reacting with other co-occurring parasites. Sensitivity and specificity analysis revealed that microscopy had sensitivities of 81.3 %, while conventional PCR, qPCR, and LAMP had sensitivities of 81.1 %, 99.2 %, and 88.1 %, respectively. Microscopy and conventional PCR had 100 % specificity, while qPCR and LAMP had 99.2 % and 99.9 % specificity. While Kato-Katz is advantageous for detecting active infections, molecular techniques, particularly LAMP's field applicability in resource-limited settings makes it a promising tool for surveillance and control of low-intensity infections.

Bringing the heat: Thermostable analogs of Bst polymerase allow high-temperature LAMP

BACKGROUND

Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that gained prominence during the early months of the COVID-19 pandemic due to its simplicity, sensitivity and robustness. However, this technique is susceptible to non-specific amplifications, raising concerns about false-positive results and reduced diagnostic accuracy. A primary contributor to false-positive testing is primer dimerization, which can theoretically be mitigated by performing reactions at higher temperatures. Unfortunately, the strand-displacing DNA polymerases typically used in LAMP, such as Bst, exhibit reduced efficiency at elevated temperatures. To address this limitation, we hypothesised that naturally occurring thermophilic analogs of Bst may be capable of supporting LAMP at higher temperatures, thereby improving reaction specificity.

METHODS

Bioinformatics and recombinant enzyme production allowed the identification and synthesis of several Bst analogs. These were tested in real-time LAMP assays to detect diverse targets, in a wide range of reaction temperatures (63°C-75°C) and in the presence of typical qPCR inhibitors.

RESULTS

Three polymerases-Bst_7, Bst_8 and Bst_15-demonstrated exceptional activity and robust stability at higher temperature conditions (up to 72.5°C), while displaying considerable resistance to common qPCR inhibitors.

CONCLUSIONS

The identified thermophilic Bst analogs represent a potential solution for the mitigation of non-specific amplification in LAMP, further boosting the application of this technique in molecular diagnostic settings.

Assessing the Effectiveness of Immunoelectric Method in Detecting Mycobacterium avium Subspecies paratuberculosis in Cow Faeces With Paratuberculosis

Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease in ruminants, is typically transmitted through the faecal-oral route. This study aimed to optimize and evaluate an immunoelectric (IE) method for detecting MAP in faecal samples from infected cows. The necessary polyclonal antibodies were extracted from hyperimmune donkeys and rabbits using affinity chromatography. Furthermore, cross-reactive antibodies were eliminated through absorption with Mycobacterium phlei. The binding of donkey antibodies to a polystyrene filter and rabbit antibodies to Fe nanoparticles was facilitated by a diethylenetriaminepentaacetic acid (DTPA) linker. The trapping of bacteria on the filter and the fixation of Fe nanoparticles attached to specific antibodies led to a modification in the electrical resistance of the filter. This alteration in electrical resistance can be quantified using a high-precision electrical meter. In this research, MAP was identified through both polymerase chain reaction (PCR) and the IE methods in faecal samples from dairy cows, producing varied outcomes in the enzyme-linked immunosorbent assay (ELISA) test. The sensitivity and specificity of the ELISA approach for detection of the serum antibodies in comparison to the PCR technique were determined to be 75% and 72%, respectively. In contrast, the sensitivity and specificity of the IE method relative to the PCR approach were found to be 96% and 95%, respectively. With a detection time of less than 60 min, cost-effectiveness per sample, user-friendly operation utilizing an IE device, no requirement for specialized machinery and applicability in farm or dairy settings, this technique emerges as a promising alternative to traditional bacterial detection methods.

Kareniaceae in focus: A molecular survey of harmful algal dinoflagellates in the South China Sea

In recent years, species of the family Kareniaceae have been forming algal blooms worldwide, leading to significant fish mortality. The biodiversity of this group of dinoflagellates has been underestimated, primarily due to their highly similar morphologies. In this study, using high-throughput sequencing (HTS) targeted the large subunit ribosomal DNA (LSU rDNA) of dinoflagellates, 21 Kareniaceae species were identified from the South China Sea (SCS), including nine species newly recorded in Chinese coastal waters. Additionally, species-specific real-time fluorescent quantitative PCR (qPCR) assays targeting the internal transcribed spacer (ITS) for three Karenia species (Karenia longicanalis, K. papilionacea, and K. selliformis) isolated from the SCS were established. Karenia longicanalis and K. papilionacea were identified as the most prevalent Karenia species in summer in the Zhujiang Estuary via qPCR. Further qPCR analysis during a Karenia spp. bloom in the Beibu Gulf on August 3, 2023, revealed K. selliformis as the most abundant species, followed by K. longicanalis, K. mikimotoi, and K. papilionacea. Both HTS and qPCR methods successfully detected the targeted Karenia species in field samples; however, qPCR assays identified them at more stations than HTS. The integration of qPCR assays with HTS provides a comprehensive and precise assessment of the diversity of Kareniaceae species and harmful dinoflagellates. This multi-method approach enhances our understanding and management of harmful algal blooms, thereby contributing to the improved protection of marine ecosystems.

Colorimetric dual DNAzyme reaction triggered by loop-mediated isothermal amplification for the visual detection of Shiga toxin-producing Escherichia coli in food matrices

Shiga toxin-producing Escherichia coli (STEC) is causing outbreaks worldwide and a rapid detection method is urgently needed. Loop-mediated isothermal amplification (LAMP) has attracted attention in the development of pathogen detection methods; however, current methods for the detection of LAMP amplicon suffer some drawbacks. In this study, we designed a new LAMP method by incorporating peroxidase-mimicking G-quadruplex DNAzyme for a simple colorimetric detection of the LAMP amplicon. As the new method produces LAMP amplicon containing two DNAzyme molecules per amplification unit, the method was termed colorimetric Dual DNAzyme LAMP (cDDLAMP). cDDLAMP was developed targeting 3 common STEC's virulence genes (stx1, stx2, and eae) that are associated with serious human illnesses such hemorrhagic colitis and hemolytic-uremic syndrome. Immunomagnetic enrichment was used for specific, ultrasensitive, and fast detection of STEC in food samples (leafy vegetables and milk). The sensitivity of cDDLAMP ranged from 1-100 CFU/mL in pure culture to 100-103 CFU/mL in spiked milk, and 104-109 CFU/25g of lettuce. No cross-reaction with other generic E. coli strains and non-E. coli bacteria was observed. The color signal could be observed by the naked eye or analyzed by either UV-Vis spectra or smartphone platforms. Therefore, the cDDLAMP assay is a cost-effective method for detecting STEC strains without expensive machines or extraction methods.

Impact of Pre-Extraction Methods on Apple Blossom Microbiome Analysis

This study examines the effect of pre-extraction methods, namely, sonication, grinding, and lyophilization, and the use of peptide nucleic acid (PNA) blockers on the DNA recovery, diversity, and taxonomic resolution of bacterial and fungal communities in apple blossoms. Sonication was the most successful in recovering bacterial 16S and fungal ITS reads across all the collection points and plots. Lyophilization and grinding led to a significant reduction in fungal read counts, while PNA enhanced the recovery of bacterial 16S reads. Sonication improved the efficiency of DNA extraction and yielded greater diversity in the recovered microbial community. Sonicated samples showed greater sensitivity to temporal shifts in microbial community composition. Communities in sonicated samples contained a larger number of bacterial genera, such as Bacillus, Staphylococcus, and Erwinia, and fungal genera, including Didymellaceae and Cladosporium. In contrast, lyophilization and grinding led to a reduction in detected taxa. The indicator species analysis determined that 35 bacterial and 21 fungal genera were closely related to sonication, whereas no other pre-extraction method had any associated genera. Our findings suggest that sonication is the most appropriate pre-extraction method for analyzing blossom-associated microbiomes, and that the use of PNA blockers can improve the recovery of bacteria and minimize contamination by host DNA.

Survey of pathogens and human fecal markers in stormwater across a highly populated urban region

Microbial contamination of urban stormwater, rivers, and creeks during rainstorms is a persistent and widespread problem. Remediation of these waters has proven to be challenging since there are many potential sources for the fecal indicator bacteria on which water quality is regulated. Microbial source tracking markers have allowed for improved identification and quantification of the sources of contamination, but the majority of the source-attributed microbial targets are not responsible for causing the illnesses associated with waterborne human fecal contamination. Thus there is a need to better understand the relationships of human pathogens and human fecal markers in stormwater. In this study, we used a spatially-intensive sampling approach (31 sites) across southern California for the analysis of stormwater. During three storms from 2021-2023, we used droplet digital PCR to quantify the human fecal markers HF183 and Lachno3 along with human adenovirus, human norovirus, Campylobacter spp., and Salmonella spp. This spatially intensive sampling design captures information from a 5900 km2 area with ∼22 million people. We detected human markers HF183 and Lachno3 genes at 90% and 97% of the sites; concentrations ranged from below detection to 104 and 105 gene copies per 100 mL, respectively. We found variable concentrations of human bacterial and viral pathogen genes. HF183 was significantly correlated to human adenovirus and Lachno3. Lachno3 was also significantly correlated with Salmonella. We reported PCR inhibition in 83-90% of the samples but found that separating sediment and adding proteinase K during lysis improved DNA/RNA extraction efficiency and reduced inhibition.

A rapid and high-yield method for nucleic acid extraction

We report a magnetic silica bead-based nucleic acid extraction method which is rapid (6 - 7 min) and efficient (extracts nearly all the nucleic acid in the sample). We call this method SHIFT-SP (Silica bead based HIgh yield Fast Tip based Sample Prep). Factors such as pH during binding of nucleic acid to bead, the mode of bead movement during binding, the duration of binding, pH, temperature and duration of elution affect the final yield of the method. We have compared the method developed here to commercially available bead and column-based methods. The commercially available bead-based method took about 40 minutes from lysed sample to extracted nucleic acid and had a similar DNA yield as SHIFT-SP. The commercially available column-based method took 25 minutes with half the DNA yield as SHIFT-SP. In addition to a favorable time and yield, all steps in this developed method are automation compatible. We demonstrated a similar efficiency and speed of extraction for both DNA and RNA and showed that the performance of SHIFT-SP was unaffected by DNA size. SHIFT-SP was also able to extract DNA from low concentrations of microbes from enriched whole blood, for downstream whole genome amplification and sequencing.

Airborne Influenza Virus Surveillance Platform Using Paper-Based Immunosensors and a Growth-Based Virus Aerosol Concentrator

The measurement of respiratory viruses in indoor air is critical for effectively preventing the spread of diseases. This is typically accomplished by counting the nucleic acids or plaques of air-sampled viruses. Herein, we present a growth-based airborne virus surveillance (G-AVS) platform based on paper-based electrochemical immunosensors for targeting hemagglutinin (HA) and nucleoprotein (NP), and water-condensation air sampling for the quantitative measurement of airborne influenza viruses. The measurements, compared with RT-qPCR, demonstrated consistency between the two. In the measurements of airborne influenza viruses conducted in an elementary school using G-AVS, 23% (4/17) of indoor air samples were positive, with concentrations ranging from 1.7 × 104 to 1.6 × 106 gene copies/m3, while losses in the HA relative to NP were 48-75% at a relative humidity of 27.0-36.8% and 60 min air sampling, similar to infectivities reported in the literature. This platform has the potential for rapid and cost-effective airborne virus measurement.

Evaluating postmortem tongue fluids as a tool for monitoring PRRSV and IAV in the post-wean phases of swine production

BACKGROUND

Porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV) are swine pathogens that can significantly impact the performance of post-weaning pigs. While oral fluid (OF) samples are widely used for monitoring these viruses, postmortem tongue fluid (TF) samples present a cost-effective alternative with potential advantages in viral detection. This study aimed to compare the performance of TF and OF samples collected from nursery and finishing pig herds in detecting PRRSV and IAV using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A Bayesian latent class model was used to estimate diagnostic sensitivity and specificity for TF and OF under the assumption of conditional independence. The study also examined the relationship between mortality rates and RT-qPCR outcomes, the success rate of Sanger sequencing for the PRRSV ORF-5 region, and the effect of pooling daily aggregated TF samples on the probability of PRRSV detection.

RESULTS

IAV was detected in 34.9% of OF samples and 30.2% of TF samples, while PRRSV was identified in 67.4% of OF and 53.5% of TF samples. TF samples had a significantly lower mean Ct for PRRSV (29.1) compared to OF samples (32.8) but had a similar Ct (30.9) to OF (29.7) for IAV. The hierarchical latent class Bayesian model estimated the sensitivity and specificity values for OF as 37.3% and 61.7% for IAV, and 64.3% and 35.1% for PRRSV. The estimated sensitivity and specificity values for TF were 33.5% and 66.0% for IAV, and 53.0% and 47.0% for PRRSV. Among 22 matched TF and OF pairs submitted for PRRSV sequencing, 45.5% of OF samples and 63.6% of TF samples were successfully sequenced, with the higher success rate for TF attributed to having lower Ct values. Additionally, mortality rates were notably higher when PRRSV was detected, especially in cases with concurrent IAV detection. Regarding sample pooling, our results indicated that pooling TF samples significantly increased detection probabilities, with a 1/7 dilution achieving a 79% RT-qPCR detection rate, compared to a detection rate of 14.3% when testing a single day's TF sample from a week with only one positive day.

CONCLUSION

The findings support the use of TF samples as a viable complement or alternative to OF samples for PRRSV and IAV surveillance in post-weaning pigs when mortalities are available. The cost-efficiency of TF sampling can enhance monitoring compliance, improve early pathogen detection, and facilitate timely responses to emerging threats in swine production. This study advocates for the adoption of TF as a risk-based sampling strategy in nursery and grow-finish settings, complementing live animal samples such as OF, ultimately contributing to better herd health management.

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.

An SDS-NaOH-based method to isolate genome of recombinant adeno-associated virus vectors for physical titer measurement

Recombinant adeno-associated viruses (rAAVs) vectors are promising for their safety and sustained expression of genetic payloads across various tissues. These vectors consist of a protein capsid enclosing a 4.7 kb single-stranded DNA genome. Rapid and accurate determination of the physical titers of rAAV vector is crucial for quality control in rAAV manufacturing and precise drug dosage in clinical trials. To prepare vector DNA for genome titer assessment, it is essential to completely degrade unencapsulated DNA and dissociate the capsid. Conventional methods typically involve co-incubation with DNase I to degrade unencapsidated DNA, followed by co-incubation with Proteinase K to cleave protein shells. Here, we present a "Benzonase & SDS-NaOH" pretreatment as an effective alkaline lysis for releasing the vector DNA. In the presence of producer cell crude extract, Benzonase demonstrated superior efficacy in degrading unencapsidated DNA compared to DNase I. Additionally, the use of SDS-NaOH, effective at 65 °C for 30 min, significantly reduces the time required compared to that of Proteinase K at 56 °C for 2 hours. We also showed that the "Benzonase & SDS-NaOH" pretreatment is applicable for vector genome titration in rAAV production, harvest, and purified stock. Moreover, our method is effective for both scAAV and ssAAV forms and across all serotypes, including the thermally stable rAAV5. Overall, this method offers a rapid and straightforward solution to determine rAAV vector genome titers in both purified preparations and during the manufacturing process.

Simplifying SARS-CoV-2 wastewater-based surveillance using an automated FDA EUA assay

Wastewater-based surveillance (WBS) can track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in communities. Laboratory methods for this testing involve labor-intensive, multi-step processes. This study assessed the feasibility of performing WBS with an off-label use of an automated commercial SARS-CoV-2 assay that had received Emergency Use Authorization for human diagnostic testing from the United States Food and Drug Administration (FDA EUA). Twenty-four-hour composite samples of primary influent wastewater from seven municipalities in New Hampshire and Vermont were collected between September 2020 and February 2021, and were centrifuged upon receipt. An aliquot of fresh supernatant was immediately tested with the Abbott m2000 RealTime SARS-CoV-2 assay (Abbott Molecular, Des Plaines, IL, USA). Corresponding aliquots were then stored at -80°C until they were thawed, polyethylene glycol (PEG) concentrated, and tested by two PCR-based laboratory-developed tests (LDTs). Wastewater samples (103) were tested with successful detection of SARS-CoV-2 viral RNA by all three methods. Bland-Altman analysis showed overall concordant results with a bias of -0.13 and -0.42 log copies/mL detected by the FDA EUA assay compared to the LDTs. Specimen stability assessment demonstrated a decrease of 33.9% measurable viral RNA after three freeze-thaw cycles. SARS-CoV-2 detection in wastewater using an FDA EUA assay on an automated commercial testing platform performed comparably but with more efficient workflow when compared to two LDTs. This sample-to-answer automated method could save time and labor for surveillance testing, but further validation of its ability to quantitate SARS-CoV-2 viral RNA is necessary.IMPORTANCEThis proof-of-principle study evaluates an off-label use of an automated United States Food and Drug Administration (FDA) Emergency Use Authorization (EUA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human diagnostic assay for wastewater surveillance. Compared to standard, labor-intensive, multi-step methods currently in use for wastewater surveillance testing, an off-label use of an FDA EUA assay on an automated platform offers a sample-to-answer testing requiring less labor and a faster turnaround time.

Accuracy of real-time PCR for the detection of paratuberculosis in actual samples: A systematic review and meta-analysis

Paratuberculosis, an infectious and chronic ailment that affects ruminants, causes significant annual economic losses to the livestock industry. Early diagnosis and prompt culling are the primary measures for controlling this disease, highlighting the need for accurate and rapid diagnostic methods. This systematic review and meta-analysis aimed to evaluate the efficacy of quantitative PCR (qPCR) in the diagnosis of paratuberculosis. We searched for and selected articles from databases including PubMed, Web of Science, Elsevier ScienceDirect, Wiley-Blackwell, Springerlink, AGRICOLA, and CAB Abstracts, with VETQUADAS (VQ) employed to assess the quality of the literature. Meta-analysis and heterogeneity investigation were conducted using the "Meta4diag" package in "R" software, Meta-Disc 2.0, and Meta-Disc, while the Deeks' test was utilized to detect publication bias. The studies included in the systematic review displayed a moderate level of heterogeneity (I² = 48.6 %) with no significant publication bias (p = 0.998). The pooled sensitivity was determined to be 0.92 [95 % confidence interval [CI], 0.85-0.96], and the specificity was 0.85 [95 % CI, 0.77-0.91], with a summary receiver operating characteristic area under the curve (SROCAUC) of 0.95 [95 % CI, 0.91-0.98]. These findings indicate that the qPCR method has high diagnostic value for identifying paratuberculosis in animals. Subgroup analysis revealed satisfactory stability in these studies; however, the current single-target qPCR detection strategy still has limitations, as it fails to simultaneously ensure both sensitivity and specificity. Future developments should focus on multi-target detection strategies to provide more reliable qPCR testing methods for controlling paratuberculosis.

Rapid and sensitive isolation of Campylobacter jejuni using immunomagnetic separation from patient specimens exposed to oxygen

This study describes a method for detecting Campylobacter jejuni in patient stools with subsequent isolation using antibody-magnetic beads in conjunction with selective culture and PCR. Monoclonal antibodies specific for the flagellin A and major outer membrane protein of C. jejuni were generated; two clones (1C7 and 4B2) were used to coat magnetic beads for immunomagnetic separation (IMS). C. jejuni strain NCTC11168 was recovered from human stool samples spiked with varying concentrations (101-105 CFU/mL) by Campylobacter (Campy)-IMS or a conventional culture-based method and plated on modified charcoal-cefoperazone-deoxycholate agar; the number of colonies was enumerated. The detection limits of Campy-IMS and conventional culture-based method with spiked stool samples were 102 and 104 CFU/mL, respectively. The sensitivity of IMS-PCR was 10-10,000-fold higher than that of direct PCR. The recovery rate of C. jejuni from spiked stools stored for 12 to 72 h decreased from 72.3 to 5.9% with Campy-IMS and from 48.5 to 0.1% with the conventional culture-based method. Importantly, of 20 PCR (+)/bacterial culture (-) samples that were diagnosed as probable cases according to general criteria, 95% (19/20) were confirmed positive by Campy-IMS. Thus, this study suggests a solution to overcome the problems caused by the inconsistency between probable and confirmed cases of Campylobacter infection.

IMPORTANCE

The isolation, cultivation, and maintenance of Campylobacter spp. are difficult because of the microaerophilic conditions and specific medium needed. Although selective media are useful for the initial isolation of Campylobacter, subsequent exposure of the sample to oxygen has a detrimental effect on the positive culture rate of Campylobacter, significantly lowering the isolation rate from patient samples. In this study, the detection limit was improved by combining immunomagnetic separation and PCR methods to quickly detect Campylobacter jejuni in clinical patient stool samples using antibody-magnetic beads. Therefore, this study is expected to improve confirmation of C. jejuni infection where diagnosis would previously fail with patient samples because of oxygen exposure, inappropriate diagnostic methods, and interference from other bacteria in the sample.

Development of multiplex PCR for detection of foodborne pathogens in fresh produce

Foodborne pathogens present a significant public health concern where fresh produce is a key agricultural product. Rapid and sensitive detection methods are essential to ensure the safety of such produce. This study aimed to develop and optimize a modified multiplex polymerase chain reaction (mPCR) assay, which incorporates enhancements to conventional PCR, for the simultaneous detection of Escherichia coli, Salmonella, and Listeria monocytogenes in fresh produce. The specificity of each primer pair was validated using 15 strains, confirming 100% accurate detection of pathogenic strains without cross-reactivity. Since no false positives were observed, the assay demonstrated 100% precision, highlighting its reliability in distinguishing target pathogens. The sensitivity of the mPCR assay was demonstrated through serial dilutions, detecting Salmonella down to 10 fg µl-1, L. monocytogenes to 100 fg µl-1, and E. coli to 1 pg µl-1. The mPCR assay was then successfully applied to romaine lettuce and kale, demonstrating its effectiveness in detecting pathogens in mixed samples inoculated at varying concentrations (109-101 CFU ml-1). Kale exhibited greater sensitivity, detecting pathogens at lower levels, while romaine lettuce also provided consistent detection. This study highlights the potential of mPCR for enhancing food safety by providing rapid and sensitive pathogen detection in fresh produce.

A streamlined procedure for advancing the detection and isolation of Listeria monocytogenes from artificially contaminated ground beef in a single working day

Listeria monocytogenes, a rod-shaped Gram-positive bacterium widely distributed in nature, can contaminate foods and represents a foodborne pathogen of public health significance causing a high mortality rate of 20%-30%. Rapid and reliable identification of foods and food-processing environments contaminated with L. monocytogenes is a crucial step in implementing effective intervention strategies to ensure food safety and limit the transmission of bacteria to humans. This study designed and refined a practical workflow to streamline and accelerate the detection of a low level of L. monocytogenes present in ground beef. The workflow coupled an abbreviated 5 h culture enrichment in PALCAM liquid medium with physical separation (filtration and centrifugation) to preprocess enrichment samples. Specific capture was achieved using magnetic separation with a bacteriophage endolysin-derived cell wall-binding domain in a Hyglos Listeria capture kit. Molecular detection was performed using a MicroSEQ L. monocytogenes RTi-PCR detection kit combined with a nested PCR strategy. Preprocessing of enrichment culture samples using a multi-stage filtration system constructed for the study or commercially available BagFilter Pull-up filter bags, in conjunction with centrifugation, enabled the recovery of ~30 colony-forming units (CFUs) from the enrichment culture of a 25 g ground beef sample artificially contaminated with 1 CFU of L. monocytogenes. Integration of magnetic separation into the workflow for capturing L. monocytogenes cells specifically from preprocessed samples and further cleaning up the samples yielded bacterial counts similar to those obtained by direct plating of preprocessed samples. The RTi-PCR-based molecular detection method integrated into the workflow was capable of detecting pure cultures of L. monocytogenes as low as 12.5 CFUs. Evaluation of the workflow using artificially ground beef demonstrated the consistent detection of L. monocytogenes within an 8 h workday in a 25 g sample unit containing the cell count as low as 2 CFU following a 5 h culture enrichment.

IMPORTANCE

Consuming foods contaminated with the bacterial pathogen Listeria monocytogenes can lead to the development of human listeriosis, a severe and life-threatening foodborne illness. Timely detection of L. monocytogenes present at a low level in foods and food processing environments is a necessary measure to prevent the spread of the Listeria-associated illness. This study designed and evaluated a multi-step workflow for testing L. monocytogenes in artificially contaminated food samples. The workflow was composed of a short 5 h culture enrichment, filtration-based sample preprocessing, magnetic separation, a single-tube nested RTi-PCR, and culture plating. It allowed L. monocytogenes to be detected within 8 h from a 25 g ground beef sample containing the target cells as low as 2 colony-forming units, significantly improving and streamlining the detection methods for this important foodborne pathogen.

Detection of hepatitis delta virus RNA in cervical swab and seminal plasma of chronic hepatitis delta patients

OBJECTIVES

Hepatitis delta virus (HDV) is the smallest human virus that causes the most severe form of viral hepatitis. However, the virus's biological features, transmission routes and causes of endemicity in particular populations are not yet fully understood. HDV shares the hepatitis B virus (HBV) parenteral mode of transmission with HBV; therefore, sexual transmissions are also possible. However, data on sexual transmission of HDV are limited.

METHODS

This study included 60 patients with chronic HBV/HDV coinfection. The median age (IQR) of patients was 35 (23-47) years, and all were Mongolian. HDV-RNA, HBV-DNA and hepatitis B surface antigens were tested in serum, seminal plasma and cervical swab samples collected at the Liver Centre, Mongolia. Binary logistic regression analysis was used to create a model that predicts the possibility of HDV detection in seminal plasma and cervical swab samples based on HDV-RNA levels in serum samples.

RESULTS

HDV-RNA was detected in cervical swab samples from 24 of 30 patients (80%) and in seminal plasma from 15 of 30 patients (50%) (Fisher's exact test, p=0.03). Patients with detectable HDV-RNA in either seminal or cervical fluid samples showed higher levels of HDV-RNA in serum ((females: 6.44 vs 4.21 log IU/mL (p<0.0001); males: 6.69 vs 5.65 log IU/mL (p<0.0001)). A correlation between HDV-RNA levels in the serum was identified in females (r=0.56, p=0.004; 95% CI 0.206 to 0.788) but not in males (r=0.38, p=0.15, 95% CI -0.15 to 0.75). The regression model identified threshold points of serum HDV-RNA levels that can be used to predict HDV-RNA detection in seminal plasma and cervical swabs.

CONCLUSIONS

HDV-RNA can be detected in cervical swabs and seminal plasma of patients with HBV/HDV coinfection, and the detection was more common in females than in males. The probability of HDV-RNA detection in male seminal plasma and female cervical swab samples can be predicted based on the HDV viral load in serum.

Multiplexed Detection of Salmonella, Escherichia coli, Campylobacter, and Listeria in Raw Poultry

The detection of foodborne pathogens is a critical aspect of ensuring food safety. Traditional methods rely on time-intensive enrichment steps and pathogen-specific assays, extending testing timelines and limiting throughput. This study evaluates an enrichment-free, multiplexed pathogen detection workflow combining the Pathotrak system for bacterial separation and the Neogen Molecular Detection System (MDS) for detection. The workflow enables simultaneous detection of Salmonella, Escherichia coli O157, Listeria monocytogenes, Listeria spp., and Campylobacter in poultry samples, significantly reducing the time taken to screen samples requiring further evaluation. The system's performance was assessed using inoculated chicken samples over a range of bacterial concentrations (102-108 CFU/mL). The MDS system demonstrated robust detection for most pathogens, with strong correlations between theoretical inoculation levels and MDS-calculated concentrations (R2 > 0.85 for all pathogens). However, detection variability was observed at lower concentrations for Salmonella and Listeria monocytogenes. The system maintained high sensitivity and specificity, achieving a Cohen's Kappa coefficient for E. coli and Campylobacter. This study highlights the potential of enrichment-free, multiplex detection to streamline food safety testing by reducing the time to results, enhancing efficiency, and providing reliable pathogen quantification across multiple targets.

Optimization of a 6-plex Crystal Digital PCR® assay and its application to simultaneous surveillance of enteric and respiratory viruses in wastewater

Multiplex digital PCR (dPCR) approaches are commonly employed in wastewater-based epidemiology (WBE) studies. However, optimizing the dPCR workflow is a critical step to ensure its reliability and accuracy before application. In this study, a 6-plex Crystal Digital PCR® (cdPCR) workflow was optimized for the simultaneous detection of six epidemiologically important pathogens, including three enteric viruses, noroviruses of genogroups I and II (NoV-GI and GII) and enteroviruses (EnV), and three respiratory viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), influenza A virus (InfA), and respiratory syncytial virus B (RSVB), in wastewater. Four cDNA input ratios (20 %-70 %) and two extraction kits were evaluated for optimization, with 30 % cDNA input and the AllPrep PowerViral DNA/RNA Kit (Qiagen) exhibiting optimal performance. The optimized 6-plex cdPCR assay was applied to a year-long wastewater surveillance study in Japan (n = 52), revealing distinct trends and prevalence ratios for enteric and respiratory viruses. NoV-GII was detected in 96 % of the samples with the highest mean concentration (6.1 ± 0.6 log10 copies/L), while SARS-CoV-2 and InfA were detected in 60 % and 50 % of the samples, respectively, which reflected the circulation of these pathogens within the community. Notably, RSVB was detected less frequently (25 %), in line with the fewer cases of RSVB reported during the study period. The wastewater concentrations of EnV and InfA showed significant positive correlations with hand foot and mouth disease and herpangina and influenza cases, respectively. However, no positive correlations were observed for RSV and COVID-19, possibly due to the testing of RSVB while RSVA was more prevalent and also due to cluster outbreaks. These findings demonstrated the utility of the 6-plex cdPCR assay in detecting pathogens and provided insights into community disease trends, representing an advancement in WBE.

In-house isolation protocol from human serum samples demonstrates the circulating of a broad diversity of Leptospira serogroups in Costa Rica

The isolation of pathogenic Leptospira is fundamental for a comprehensive characterization of circulating strains in endemic regions. Unfortunately, culture methods of Leptospira spp. are laborious and challenging. Here, we present a method for the isolation of these pathogenic bacteria from non-fresh serum samples, previously stored at 4-8 °C for several days. Briefly, 730 serum samples collected from leptospirosis-suspected patients (presenting acute signs) were screened for Leptospira DNA by real-time PCR. Thirty-one PCR-positive sera were then assessed for Leptospira isolation on specialized media for up to 6 months. Using this methodology, 11 Leptospira isolates were obtained, resulting in an isolation rate of 35.4% (11/31). Through whole-genome analysis, ten strains were identified as Leptospira santarosai and one strain as Leptospira borgpertersenii. The isolates were classified into six different serogroups, namely Hebdomadis, Shermani, Tarassovi, Pyrogenes, Ballum, and Grippotyphosa, demonstrating a wide diversity of Leptospira strains circulating in Costa Rica. This study reveals that serum is a suitable sample for Leptospira isolation in patients with positive PCR results, even after maintenance at cold conditions, promoting the use of serum for Leptospira isolation in reference laboratories around the world.

Artificial intelligence-driven quantification of antibiotic-resistant Bacteria in food by color-encoded multiplex hydrogel digital LAMP

Antibiotic-resistant bacteria pose considerable risks to global health, particularly through transmission in the food chain. Herein, we developed the artificial intelligence-driven quantification of antibiotic-resistant bacteria in food using a color-encoded multiplex hydrogel digital loop-mediated isothermal amplification (LAMP) system. The quenching of unincorporated amplification signal reporters (QUASR) was first introduced in multiplex digital LAMP. During amplification, primers labeled with different fluorophores were integrated into amplicons, generating color-specific fluorescent spots. While excess primers were quenched by complementary quenching probes. After amplification, fluorescent spots in red, green, and blue emerged in hydrogels, which were automatically identified and quantified using a deep learning model. Methicillin-resistant Staphylococcus aureus and carbapenem-resistant Escherichia coli in real fruit and vegetable samples were also successfully detected. This artificial intelligence-driven color-encoded multiplex hydrogel LAMP offers promising potential for the digital quantification of antibiotic-resistant bacteria in the food industry.

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.

A Streamlined Point-of-Care CRISPR Test for Tuberculosis Detection Directly from Sputum

Mycobacterium tuberculosis (Mtb) is a major threat to global health and is responsible for over one million deaths each year. To stem the tide of cases and maximize opportunities for early interventions, there is an urgent need for affordable and simple means of tuberculosis diagnosis in under-resourced areas. We sought to develop a CRISPR-based isothermal assay coupled with a compatible, straightforward sample processing technique for point-of-care use. Here, we combine Recombinase Polymerase Amplification (RPA) with Cas13a and Cas12a, to create two parallelised one-pot assays that detect two conserved elements of Mtb (IS6110 and IS1081) and an internal control targeting human DNA. These assays were shown to be compatible with lateral flow and can be readily lyophilized. Our finalized assay exhibited sensitivity over a wide range of bacterial loads (105 to 102 CFU/mL) in sputum. The limit of detection (LoD) of the assay was determined to be 69.0 (51.0 - 86.9) CFU/mL for Mtb strain H37Rv spiked in sputum and 80.5 (59.4 - 101.6) CFU/mL for M. bovis BCG. Our assay showed no cross reactivity against a wide range of bacterial/fungal isolates. Clinical tests on 13 blinded sputum samples revealed 100% (6/6) sensitivity and 100% (7/7) specificity compared to culture. Our assay exhibited comparable sensitivity in clinical samples to the microbiological gold standard, TB culture, and to the nucleic acid state-of-the-art, GeneXpert MTB/RIF Ultra. This technology streamlines TB diagnosis from sample extraction to assay readout in a rapid and robust format, making it the first test to combine amplification and detection while being compatible with both lateral flow and lyophilization.

Diagnostic value of SAT-TB in stool and urine samples for intestinal and urinary tuberculosis

BACKGROUND

The simultaneous amplification/testing for tuberculosis (SAT-TB) targets specific 16s rRNA for detecting Mycobacterium tuberculosis in real-time.

OBJECTIVE

To evaluate SAT-TB's performance in detecting intestinal and urinary TB using stool and urine samples.

METHODS

Stool (94) and urine samples (69) (From 2021 to 2022), were collected from pulmonary combined with suspected intestinal or urinary tuberculosis. Simultaneous detection of Mycobacterium tuberculosis was performed using the SAT-TB method, Xpert MTB/RIF assay, and MGIT960 culture.

RESULTS

For stool samples, the sensitivity, specificity, and area under the curve (AUC) were 53.33 %, 93.88 %, and 0.736 for SAT-TB; 60 %, 81.63 %, and 0.708 for Xpert; and 40 %, 95.92 %, and 0.680 for MGIT960. For urine samples, the sensitivity, specificity, and AUC for SAT-TB, Xpert, and MGIT960 were 27.27 %, 98.28 %, 0.628; 54.55 %, 96.35 %, 0.755; and 45.45 %, 100 %, 0.727, respectively.

CONCLUSION

ROC analysis indicated that SAT-TB had the highest diagnostic efficacy for stool samples when tested individually.

Ultrafast PCR assay for identification of three king crabs-Chionoecetes japonicus, Chionoecetes opilio, and Paralithodes camtschaticus

Identifying the species of king crab in processed products is crucial to prevent food fraud and harm to consumers. A rapid real-time PCR method was developed to identify three crab species (Chionoecetes japonicus, Chionoecetes opilio, and Paralithodes camtschaticus) in crab products within 30 min. The method involved direct DNA extraction and utilized species-specific primer sets targeting mitochondrial cytochrome C oxidase subunit I (COI) and internal transcribed spacer (ITS1) for the three crab species. Specificity and sensitivity tests demonstrated consistent melting temperatures and cycle threshold values and a detection limit of 0.001 ng DNA. The ultrafast PCR successfully distinguished the three crab species in 24 commercial products, indicating its rapid, specific, and sensitive potential for on-site identification of crab species in commercial food products.

Optimization of a DNA extraction protocol from fingerprints for the analysis of nuclear STR and mitochondrial DNA genetic profiles

Most of the cells found in fingerprints belong to the cornified barrier of the epidermis (stratum corneum), lack nuclei and cytoplasmic organelles, and are filled with keratin. Nuclear and mitochondrial DNA is degraded and embedded in the keratin mesh, a very resistant protein that is difficult to remove during DNA extraction. In this work, we studied the possible negative effect of keratin on Polymerase Chain Reaction (PCR) reactions and the influence of keratinase and proteinase K on the extraction of DNA from fingerprints. The role of glycogen in the DNA yield during the precipitation step and the importance of washing the obtained DNA with 70% ethanol were also studied. DNA was extracted from 96 fingerprints corresponding to recent prints and stored for 0, 1, 5, and 18 months from six individuals. No differences were observed in the concentration of extracted DNA or in the number of nuclear Short Tandem Repeat (STR) alleles in the genetic profiles of fingerprints stored during different times. However, sex differences were observed in both the concentration of DNA obtained and the number of nuclear STR alleles detected, being lower in females than in males. In 80% of the fingerprints genetic profiles were obtained with at least half of the STR nuclear markers and, in 50% of the fingerprints genetic profiles were obtained with more than 90% of the markers, which would allow an unambiguous identification of the donor. In all fingerprints where mitochondrial DNA was analyzed, complete sequencing of the HV1 and HV2 regions was possible, which increases the accuracy of the results obtained. The optimized protocol allowed obtaining a complete STR nuclear genetic profile of a 20-year-old palmprint.

Key points

The presence of keratin negatively influences PCR reactions.The addition of keratinase in latent fingerprint DNA extraction protocol improves the yield and quality of the DNA obtained.The use of glycogen for DNA precipitation and 70% ethanol for washing the precipitate influence the yield and quality of the DNA isolated from fingerprint.The DNA obtained is useful for STR marker profiling and HV1 and HV2 hypervariable regions of mitochondrial DNA analysis.The amount of DNA obtained and the number of STR markers detected from fingerprints depend on the sex of the individual, but not on the time elapsed. The optimized protocol is efficient in analysis of a 20-year-old sample.

Comparative evaluation of PCR and loop-mediated isothermal amplification (LAMP) assays for detecting Pasteurella multocida in poultry

AIMS

To develop a colourimetric loop-mediated isothermal amplification (LAMP) assay for the detection of Pasteurella multocida in clinical poultry samples and compare the performance of this assay with PCR. A secondary aim was to evaluate a simple DNA extraction method that could enable LAMP-based testing in the field without the need for specialised laboratory equipment.

METHODS

Primer sets for both LAMP and PCR were designed to amplify the KMT1 gene of P. multocida. DNA was extracted from 12 P. multocida isolates using a commercial extraction kit, and subjected to analysis using both LAMP and PCR. The analytical specificity of the LAMP assay was evaluated by testing it against a panel of 12 unrelated bacterial species, and the analytical sensitivity (limit of detection) was determined through testing of serial dilutions of the target DNA and compared to that of PCR. Subsequently, cloacal swabs (n = 40) from a commercial turkey flock were subjected to analysis using both LAMP and PCR assays, using a rapid DNA extraction method and a commercial extraction kit. Clinical sensitivity and specificity of the LAMP assay were calculated in comparison to PCR.

RESULTS

A single DNA fragment of the expected size (∼ 200 base pairs), was amplified by PCR from 12 P. multocida isolates, which were also all positive by the LAMP assay. The identity of all PCR amplicons was confirmed by sequencing. Both PCR and LAMP showed similar analytical sensitivity, with a LOD of 20 pg of target DNA. As neither PCR nor LAMP assays produced positive results with 12 non-related bacterial species, the analytical specificity was assessed as 100%. However, LAMP demonstrated lower clinical specificity (94.74%) compared to PCR (100%) when 40 clinical samples were tested. None of the DNA samples extracted using the simplified DNA extraction method were amplified by either LAMP or PCR.

CONCLUSION

The LAMP assay developed in this study exhibits comparable performance to PCR in detecting P. multocida.

CLINICAL RELEVANCE

The use of a rapid and portable DNA extraction method, in conjunction with LAMP assays, could create opportunities for point-of-care testing for fowl cholera in field settings.

Occurrence and molecular identification of haemotropic Mycoplasma species in grey wolves (Canis lupus) from southern Europe

Although wild and domestic carnivores share some haemotropic Mycoplasma species, information about the circulation of this pathogen in grey wolves (Canis lupus) populations is still very limited. Thus, a geographically broad-based investigation was performed for determining the occurrence and diversity of Mycoplasma spp. in three different wolf populations from southern Europe. Between 2001 and 2023, spleen samples from 285 grey wolves from Spain (n = 129), Italy (n = 113), and Portugal (n = 43) were collected. The presence of haemotropic Mycoplasma was assessed targeting the 16S rRNA gene using two PCR assays in parallel; in addition, the 16S-23S rRNA intergenic spacer was analysed for further identification of the positive samples. The influence of the sampling country, sex, and age of the animals on the prevalence of Mycoplasma spp. was also assessed by a generalized linear model analysis. The percentage of positive wolves was 13.3 % (38/285), and the occurrence was significantly higher in Spain (20.9 %) than in Italy (8.0 %) and Portugal (4.7 %). Mycoplasma haemocanis (10.5 %) and Candidatus M. haematoparvum (2.1 %), were identified; in addition, an uncultured Mycoplasma sp. was also detected (0.7 %). Our results confirm the circulation of potentially zoonotic Mycoplasma in wolf populations from southern Europe. To our knowledge, this is the first report of Ca. M. haematoparvum in wolves from Italy and Portugal. In addition, a Mycoplasma sp., previously found in dogs, has been detected for the first time in wolves. Further studies are needed to fully molecularly characterise haemotropic Mycoplasma spp., which will serve as a basis for the study of its ecoepidemiology.

M1 enrichment facilitates virus detection in patients with allogeneic hematopoietic stemcell transplantation

Due to the severe consequences of viral infection in allogeneic hematopoietic stem cell transplantation (allo-HSCT) patients, the routine use of polymerase chain reaction (PCR) screening of viruses is common in clinic, while the sensitivities of molecular methods are not always sufficient for blood samples. We aimed to increase the detection efficiency of viremia in allo-HSCT patients with M1 bead enrichment. Blood samples of allo-HSCT patients with fever were collected. Simultaneously with analyses of real-time PCR without enrichment, M1 bead enrichment followed by real-time PCR was applied to detect possible viruses in these samples, and metagenomic next-generation sequencing analyses were also applied in 10 samples negative with real-time PCR without enrichment. Various species of viruses were detected with M1 enrichment method. Significantly, some viruses that had not been found by real-time PCR without M1 enrichment were also detected by those with M1 enrichment and verified by metagenomic next-generation sequencing analyses. Furthermore, blood samples enriched with M1 beads had lower Ct values of real-time PCR assay than those that had not been treated. In conclusion, M1 bead enrichment increased the detection efficiency of most viruses in hematological malignancy patients.

Development of RNA reference materials for norovirus GI and GII using digital PCR

Norovirus is a highly virulent pathogen that causes enteritis in all age groups worldwide. Owing to the diversity of noroviruses, the development of vaccines and treatments is challenging, and an early and accurate diagnosis is crucial. Reference materials (RMs) developed previously for norovirus genotypes I (GI) and II (GII) were quantified using reverse transcription quantitative PCR. In this study, we developed norovirus GI and GII RMs as in vitro transcribed RNA forms. These RMs were then assigned reference values for the RNA copy number concentration. The concentrations of GI and GII RMs determined using in-house reverse transcription digital PCR assays were (1.92±0.37)×107 and (1.20±0.27)×107 copy/mL, respectively. The homogeneity and stability of the RMs were evaluated, and their compatibility with commercial diagnostic kits was validated. These RMs can be used for the development of detection assays, as calibrants for various molecular measurement techniques, and as test materials for internal and external quality assurance.

Microfluidic purification of genomic DNA

We describe a microfluidic device to extract DNA from a cell lysate, without the need for centrifuges, magnetic beads, or gels. Instead, separation is driven by transverse migration of DNA, which occurs when a polyelectrolyte solution flowing through a microfluidic channel is subjected to an electric field. The coupling of the weak shearing with the axial electric field is highly selective for long, flexible, charged molecules, of which DNA is the sole example in a typical cell lysate. As a result of migration to the walls, DNA is held near the channel inlet by electrophoresis (there is no flow near the channel walls), while the remaining components are eluted by the much larger (at least 10-fold) convective flow. We have demonstrated the feasibility of the device by recovering up to 40 ng of purified DNA in less than 30 min from 10 μL of Escherichia coli lysate. Gel electrophoresis indicates minimal additional fragmentation during purification, up to the maximum length recorded by the gel (60 kbp). Electropherograms were also obtained for purified mammalian DNA, using a Femto Pulse system (fragment lengths up to 165 kbp). Extracted samples show strong amplification by PCR, while the original lysate does not. Mixtures of λ-DNA and BSA were used to determine the extent of the separation of DNA from a physiological concentration of proteins (30 mg/mL). The protein concentration in the extract (0.3 to 0.5 ng/µL) was reduced by five orders of magnitude from the initial mixture.

Optimized Aluminum Hydroxide Adsorption-Precipitation for Improved Viral Detection in Wastewater

Wastewater-based epidemiology (WBE) is a valuable tool for monitoring pathogen spread in communities; however, current protocols mainly target non-enveloped viruses. This study addresses the need for standardized methods to detect both enveloped and non-enveloped viruses by testing four aluminum hydroxide adsorption-precipitation techniques. Wastewater samples were spiked with an enveloped virus surrogate (Φ6 bacteriophage) and a non-enveloped virus surrogate (MS2 coliphage), and viral recovery was assessed using reverse-transcription quantitative PCR (RT-qPCR). The highest recovery for the enveloped virus was achieved with AlCl3 at pH 3.5, a 15 min flocculation time, and a 3% elution solution concentration. For the non-enveloped virus, optimal recovery was found with AlCl3 at pH 6.0, no flocculation time, and a 10% elution solution. The best method for recovering both virus types used AlCl3 at pH 6.0, 15 min flocculation, and a 3% elution solution concentration. This study shows that while optimal conditions vary between virus types, a standardized AlCl3 flocculation protocol can efficiently recover both, providing a cost-effective approach for outbreak monitoring in Grenada.

Enhancement of the Precision ID Mitochondrial DNA Whole Genome System for Challenging Unidentified Human Remains

BACKGROUND

The Precision ID mitochondrial (mt) DNA Whole Genome system is a fully automated massively parallel sequencing (MPS) solution for the whole mitochondrial genome. While extremely sensitive, the Precision ID system is susceptible to inhibitors and microbial DNA that are often co-extracted from human remains.

METHODS

DNA templates spiked with varying amounts of hematin, humic acid, and calcium, along with bones containing degraded and non-human DNA, were sequenced using the Precision ID system with and without the addition of bovine serum albumin (BSA).

RESULTS

BSA added to the initial PCR reaction successfully improved the robustness of the Precision ID system while not negatively impacting the sequencing success of uninhibited samples. The success of BSA is inhibitor-concentration dependent and is effective for templates containing at least 50 ng/μL humic acid, 50 μM hematin, and 1500 μM calcium ions. Furthermore, the presence of microbial DNA in addition to an inhibitor, results in non-specific adaptor ligation to the non-human DNA; BSA can alleviate the inhibition, allowing the human mtDNA to be amplified and sequenced.

CONCLUSIONS

The addition of BSA to the Precision ID mtDNA system can yield successful sequencing results from challenging case samples that would otherwise fail.

The Impact of Viral Concentration Method on Quantification and Long Amplicon Nanopore Sequencing of SARS-CoV-2 and Noroviruses in Wastewater

Wastewater-based surveillance has gained attention in the four years following the start of the COVID-19 pandemic. Accurate pathogen detection, quantification and characterisation rely on the selection of appropriate methodologies. Here, we explore the impact of viral concentration method on RT-qPCR inhibition and quantification of norovirus genogroups I and II (GI and GII), crAssphage, phi6 and SARS-CoV-2. Additionally, their impact on long amplicon sequencing for typing noroviruses and whole-genome sequencing (WGS) SARS-CoV-2 was explored. RT-qPCR inhibition for each viral concentration method was significantly different apart from the two ultrafiltration methods, InnovaPrep® concentrating pipette (IP) and Vivaspin® (VS) centrifugal concentrators. Using an ultrafiltration method reduced inhibition by 62.0% to 96.0% compared to the ammonium sulphate (AS) and polyethylene glycol (PEG) precipitation-based methods. Viral quantification was significantly impacted by concentration method with the highest concentrations (copies/L) observed for VS with 7.2- to 83.2-fold differences from AS depending on the target. Norovirus long amplicon sequencing showed genotype-dependent differences with IP performing best for GI and VS for GII although IP performance gains for GI were relatively small. VS outperformed AS and IP across all metrics during SARS-CoV-2 WGS. Overall, VS performed the best when considering all the areas of investigation.

Ultrasensitive detection of intact SARS-CoV-2 particles in complex biofluids using microfluidic affinity capture

Measuring virus in biofluids is complicated by confounding biomolecules coisolated with viral nucleic acids. To address this, we developed an affinity-based microfluidic device for specific capture of intact severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our approach used an engineered angiotensin-converting enzyme 2 to capture intact virus from plasma and other complex biofluids. Our device leverages a staggered herringbone pattern, nanoparticle surface coating, and processing conditions to achieve detection of as few as 3 viral copies per milliliter. We further validated our microfluidic assay on 103 plasma, 36 saliva, and 29 stool samples collected from unique patients with COVID-19, showing SARS-CoV-2 detection in 72% of plasma samples. Longitudinal monitoring in the plasma revealed our device's capacity for ultrasensitive detection of active viral infections over time. Our technology can be adapted to target other viruses using relevant cell entry molecules for affinity capture. This versatility underscores the potential for widespread application in viral load monitoring and disease management.

An optimized eDNA protocol for fish tracking in estuarine environments

Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification.

Design, validation, and implementation of multiplex digital PCR assays for simultaneous quantification of multiple targets

Quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) are applied for quantifying molecular targets in disease diagnostics, pathogen detection, and ecological monitoring. Uptake of dPCR is increasing due to its higher quantification accuracy relative to qPCR, which stems from its independence from standard curves and its increased resistance to PCR inhibitors. Throughput can be increased through multiplexing, which allows simultaneous quantification of multiple targets. However, multiplexing with dPCR faces unique challenges relative to qPCR. Here, we describe the three-phase development process of non-competing multiplex dPCR assays using target-specific fluorescently labeled hydrolysis probes. We highlight common challenges encountered, along with recommended solutions. Phase 1: In silico assay design; target-specific primers and probes are selected or designed, potential issues with primer and probe interactions are identified, and fluorophores and quenchers are chosen based on dPCR instrumentation. Phase 2: Wet-lab validation; assays are benchmarked using positive controls. Insufficient performance leads to assay redesign, as needed. Phase 3: Assay implementation; assay specificity and sensitivity are validated on relevant sample matrices. Finally, we provide recommendations on the future design and standardization of multiplexed dPCR assays, highlighting the need for better in silico predictions of assay performance, standardizing positive controls, and automating partition classification systems.

Detection of Rocahepevirus ratti in Bivalve Mollusks from São Luís Island, Maranhão, Brazil: A Potential Transmission Route of an Emerging Zoonotic Pathogen?

The attempt to investigate hepatitis E virus (HEV) contamination in naturally growing mangrove bivalve mollusks captured for local sale in a touristic area of Maranhão state in Brazil revealed the detection of rat hepatitis E virus (ratHEV). Using international standard protocols for processing and nucleic acid extraction, we analyzed 89 bivalve samples (Mytella falcata and Crassostrea rhizophorae) with two broadly reactive assays: heminested pan-Hepeviridae (ORF-1) and probe-based HEV-1 to HEV-4 (ORF-2/ORF-3). Heminested reactions presented 2 (2.2%) amplifications of the expected size. Nucleotide identities ranged from 86.6 to 89.0% with ratHEV isolates from wild rats, pigs, one human case and sewage reported in different countries. Regarding the phylogenetic tree, the sequences grouped with genotype HEV-C1. This first report of ratHEV detection in bivalve mollusks may be a starting point for further research on virus variability, distribution, host range and especially the possible role of contaminated shellfish as a vehicle for ratHEV transmission.

Multiplex one-step direct asymmetric PCR of blood and dual-labelled probe-mediated melting curve for genotyping of MTHFR and MTRR polymorphisms

Accurate, rapid, and multiplex SNP analysis holds significant clinical value. However, the inevitable nucleic acid extraction, involving centrifugation, heating, and magnetic separation, is often time-consuming. In this study, direct blood PCR was combined with dual-labelled probe-mediated melting curves to identify SNPs corresponding to MTHFR (C677T, rs#1801133 and A1298C, rs#1801131) and MTRR (A66G, rs#1801394) in a single tube. Our results indicated that nucleic acid extraction does not enhance gDNA concentrations. The results of the gDNA and whole blood samples were perfectly aligned with each other. The maximum volume tolerance for whole blood is 10%. Our method demonstrated robustness to hemolysis and temperature variations. The turnaround time of the test is <100 min with great potential value in clinical settings. Furthermore, this approach eliminates the need for complex preprocessing steps, simplifies the workflow and reduces potential sources of error. The efficiency and accuracy of this method make it a promising tool for routine clinical diagnostics and personalized medical applications. Additionally, the method's reliability and speed are crucial for effective patient management. The ability to obtain results quickly and accurately supports timely treatment decisions, which can be critical in many clinical scenarios. As a result, this technique has the potential to be widely adopted in clinical laboratories due to its practicality and effectiveness.

Improved African Swine Fever Detection for Environmental Samples in the Presence of Organic Contaminants

Geographical expansion and trans-continental transmission of the African swine fever virus (ASFV) pose a significant risk to the global swine industry due to its high impact on swine health and agro-economy. Several different modes of ASFV transmission make it difficult to predict and prevent ASFV introduction to the free area and its spread in the affected area. Indirect transmission through contaminated surfaces could be one of the possible routes to introduce ASFV to the United States due to its high resistance on environmental surfaces and the frequency of international movements. However, there is limited knowledge about environmental samples for ASFV surveillance, when compared to clinical samples from infected pigs. Therefore, the aim of this study was to develop methods for better detection of ASFV DNA in the presence of four different types of organic contaminants: soil, swine feces, feed dust, and their mixture. The presence of organic contaminants negatively affected the sensitivity of ASFV DNA detection. Centrifugation and filtration were crucial for ASFV detection in environmental samples with soil and mixture, whereas filtration reduced the sensitivity of ASFV DNA detection in samples from clean surfaces and swine feces- and feed dust-contaminated surfaces. Detection of ASFV was significantly improved when sampled by the sponge stick with DNA/RNA shield when compared to the cost-effective sampling strategy, the cotton gauze with phosphate-buffered saline. These findings highlight the effect of organic contaminants and the use of the nucleic acid stabilization buffer on ASFV diagnostic performance and provide important background for ASFV preparedness.

Considerations for the Successful Detection and Quantification of Genetically Modified Events in Grain and Food Samples Using Multiplex Digital PCR

The number of genetically modified (GMO) events for canola, corn, and soybean is steadily increasing. Some countries, including those in the EU, have regulatory requirements for the approval and use of plant ingredients containing GMOs. Multiplex digital PCR (dPCR) has been used for the simultaneous detection and quantification of various GMO events. This review covers the various factors to consider for multiplex digital PCR detection and the quantification of GMO events. DNA quality, quantity, and the presence of inhibitors are important factors to consider. Some dPCR instruments allow the use of multiple fluorescent dyes, which facilitates the setup of multiplex dPCR assays. This review focuses on the optimization of multiplex dPCR and describes the multiplex dPCR assays that have been reported for GMO detection.

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.

Variation of gene ratios in mock communities constructed with purified 16S rRNA during processing

16S ribosomal nucleic acid (16S rRNA) analysis allows to specifically target the metabolically active members of microbial communities. The stability of the ratios between target genes in the workflow, which is essential for the bioprocess-relevance of the data derived from this analysis, was investigated using synthetic mock communities constructed by mixing purified 16S rRNA from Bacillus subtilis (Bs), Staphylococcus aureus (Sa), Pseudomonas aeruginosa (Pa), Klebsiella pneumoniae (Kp) and Burkholderia cepacia (Bc) in different proportions. The RT reaction yielded one copy of cDNA per rRNA molecule for Pa, Bc and Sa but only 2/3 of the expected cDNA from 16S rRNAs of Bs and Kp. The combination of Taq DNA Platinum polymerase with subcycling PCR (scPCR) produced uniform yields of approximately 70% for second strand PCR synthesis from all target cDNAs. The proportion between templates in multicycle PCR was best preserved after 10 cycle scPCR followed by cloning. With MiSeq sequencing, correct proportions for about two thirds of templates were recovered after 10 cycle scPCR with Taq Platinum. 30 cycles standard PCR (stdPCR) or scPCR proved particularly harmful to proportion data and should be avoided.

Wastewater-based epidemiology: deriving a SARS-CoV-2 data validation method to assess data quality and to improve trend recognition

Introduction

Accurate and consistent data play a critical role in enabling health officials to make informed decisions regarding emerging trends in SARS-CoV-2 infections. Alongside traditional indicators such as the 7-day-incidence rate, wastewater-based epidemiology can provide valuable insights into SARS-CoV-2 concentration changes. However, the wastewater compositions and wastewater systems are rather complex. Multiple effects such as precipitation events or industrial discharges might affect the quantification of SARS-CoV-2 concentrations. Hence, analysing data from more than 150 wastewater treatment plants (WWTP) in Germany necessitates an automated and reliable method to evaluate data validity, identify potential extreme events, and, if possible, improve overall data quality.

Methods

We developed a method that first categorises the data quality of WWTPs and corresponding laboratories based on the number of outliers in the reproduction rate as well as the number of implausible inflection points within the SARS-CoV-2 time series. Subsequently, we scrutinised statistical outliers in several standard quality control parameters (QCP) that are routinely collected during the analysis process such as the flow rate, the electrical conductivity, or surrogate viruses like the pepper mild mottle virus. Furthermore, we investigated outliers in the ratio of the analysed gene segments that might indicate laboratory errors. To evaluate the success of our method, we measure the degree of accordance between identified QCP outliers and outliers in the SARS-CoV-2 concentration curves.

Results and discussion

Our analysis reveals that the flow and gene segment ratios are typically best at identifying outliers in the SARS-CoV-2 concentration curve albeit variations across WWTPs and laboratories. The exclusion of datapoints based on QCP plausibility checks predominantly improves data quality. Our derived data quality categories are in good accordance with visual assessments.

Conclusion

Good data quality is crucial for trend recognition, both on the WWTP level and when aggregating data from several WWTPs to regional or national trends. Our model can help to improve data quality in the context of health-related monitoring and can be optimised for each individual WWTP to account for the large diversity among WWTPs.

Evaluation of PCR-enhancing approaches to reduce inhibition in wastewater samples and enhance viral load measurements

Molecular-based assays are the most commonly used methods for the detection and quantification of viruses in wastewater. The variety of inhibitory substances present in the complex matrix of wastewater hinders downstream analysis and often leads to false negative results and underestimation of viral load. The development of robust and inhibitor-tolerant detection methods is necessary in the context of wastewater-based epidemiology, a valuable tool that has gained further importance since the emergence of the Covid-19 pandemic. Various strategies are used to mitigate inhibition in the polymerase chain reaction (PCR) with the most prevalent of all: the dilution of the sample and the inhibitor removal kits. In this study, we first indicated the presence of inhibitors in wastewater samples and the evaluation of eight different PCR enhancing strategies were further performed using reverse-transcription PCR (RT-qPCR) protocol. False negative results were eliminated through four approaches evaluated, a 10-fold dilution of the extracted sample, addition of T4 gene 32 protein (gp32), addition of Bovine Serum Albumin (BSA), and using an inhibitor removal kit. Among the methods that removed inhibition, the most significant for the removal of inhibition was the addition of gp32 (at a final concentration 0.2 μg/μl). This optimized protocol was further applied to wastewater samples tested for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and a direct comparison study was further performed with reverse-transcription droplet digital PCR (RT-ddPCR). The detection frequency of both methods was 100 % and the obtained viral concentrations were higher by RT-ddPCR; the optimized RT-qPCR assay showed a good correlation (Intraclass Correlation Coefficient: 0,713, p-value <0,007) with RT-ddPCR. This is the first study to directly compare common strategies for eliminating inhibition in wastewater and demonstrates the importance of developing robust assays to accurately assess the recovery rates and viral loads of the targets tested, in a simple, cost-effective and high-throughput manner.

One-pot MCDA-CRISPR-Cas-based detection platform for point-of-care testing of severe acute respiratory syndrome coronavirus 2

Compared to quantitative real-time PCR (q-PCR), CRISPR-Cas-mediated technology is more suitable for point-of-care testing (POCT) and has potential for wider application in the future. Generally, the operational procedure of CRISPR-Cas-mediated diagnostic method consists of two independent steps, the reaction of signal amplification and the CRISPR-Cas-mediated signal detection. Complex multi-step procedures can easily lead to cross-contamination. To develop a convenient and rapid method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, we propose a MCTOP method (Multiple cross displacement amplification-CRISPR-Cas12b-based testing in one-pot), which targets the open reading frame 1ab (ORF1ab) and nucleocapsid protein (N) gene of SARS-CoV-2. This method combines MCDA isothermal amplification and CRISPR-Cas-mediated sequence-specific detection into a one-pot reaction. The optimal reaction was achieved with isothermal amplification of 40 min and CRISPR-Cas-based detection of 15 min, both at 64°C. Then, the results can be visualized by the real-time fluorescence instrument and also lateral flow biosensor. The lowest detection limit of the proposed method is 10 copies of each of target sequences, and it has no cross-reactivity with non-SARS-CoV-2 templates. In a clinical test of 70 pharyngeal swab samples, MCTOP assay showed a specificity of 100% and sensitivities of 98 and 96% for the real-time fluorescence instrument and lateral flow biosensor, respectively. The MCTOP developed in this study is a rapid, convenient, highly sensitive, and specific method for SARS-CoV-2 nucleic acid detection. It can be used as an effective point-of-care testing (POCT) tool for clinical diagnosis and epidemiologic surveillance of SARS-CoV-2 infections, especially suitable for the basic, field and clinical laboratory.

A comprehensive review on human enteric viruses in water: Detection methods, occurrence, and microbial risk assessment

Human enteric viruses, such as norovirus, adenovirus, rotavirus, and enterovirus, are crucial targets in controlling biological contamination in water systems worldwide. Due to their small size and low concentrations in water, effective virus concentration and detection methods are essential for ensuring microbial safety. This paper reviews the typical and innovative methods for concentrating and detecting human enteric viruses, highlights viral contamination levels across different water bodies, and discusses the removal efficiencies of virus through various treatment technologies. The application and current gaps of quantitative microbial risk assessment (QMRA) for evaluating the risks of human enteric viruses is also explored. Innovative methods such as digital polymerase chain reaction and isothermal amplification show promise in sensitivity and convenience, however, distinguishing between infectious and non-infectious viruses should be a key focus of future detection techniques. The highest concentrations of human enteric viruses were detected in wastewater, ranging from 103 to 106 copies/L, while drinking water showed significantly lower concentrations, often below 102 copies/L. QMRA studies suggest that exposure to human enteric viruses, whether through contaminated drinking water, occupational contact, or accidental wastewater discharge, could result in a life expectancy of 1.96 × 10-4 to 4.53 × 10-1 days/year.