Probe qPCR Research Articles

Effects of Enterobacter cloacae insecticidal protein on the Duox-ROS system and midgut bacterial community and function of Galleria mellonella larvae

BackgroundEnterobacter cloacae insecticidal proteins have been reported to kill Galleria mellonella larvae through affecting their midgut microbiome. However, the mechanisms involved remain unclear. Here we aim to investigate how the insecticidal proteins act on the midgut Duox-ROS system and microbial community of G. mellonella larvae. MethodsReverse transcription qPCR and fluorescence probes were utilized to assess the Duox expression levels and to evaluate quantitative changes of the ROS levels. Sequencing of the 16S rRNA gene sequences of the midgut bacteria of G. mellonella larvae was conducted for further analyses of bacterial diversity, composition, and abundance. ResultsAfter the injection of the insecticidal proteins, the Duox expression levels first increased within 28 h, then dramatically peaked at 36 h, and slowly decreased thereafter. Simultaneously, the ROS levels increased significantly at 36 h, peaked at 48 h, and rapidly declined to the normal level at 60 h. Responsive to the change of the ROS levels, the structure of the midgut microbial community was altered substantially, compared to that of the untreated larvae. The relative abundance of Enterobacteriaceae and other specific pathogenic bacteria increased significantly, whereas that of Lactobacillus decreased sharply. Importantly, notable shifts were observed in the crucial midgut predicted metabolic functions, including membrane transportation, carbohydrate metabolism, and amino acid metabolism. ConclusionInsecticidal proteins of E. cloacae kill G. mellonella larvae mainly through generation of high oxidative stress, alterations of the midgut microbial community and function, and damage to the physiological functions. These findings provide insights into the inhibition mechanism of E. cloacae insecticidal proteins to G. mellonella larvae.

First Report of Xanthomonas perforans Causing Bacterial Spot of Pepper (Capsicum annuum) in North Carolina.

North Carolina (NC) is the fifth largest producer of bell pepper (Capsicum annuum) in the US with an estimated 2,400 acres in production (NASS-USDA, 2022). A survey of bacterial diseases of peppers was initiated in 2020 after numerous bacterial spot outbreaks were reported in NC. Bacterial spot is caused by a complex of four Xanthomonads: X. euvesicatoria, X. vesicatoria, X. perforans, and X. hortorum pv. gardneri (Larrahondo-Rodríguez et al., 2022). If not preemptively managed, bacterial spot can cause up to 40% yield loss (Kousik and Ritchie, 1998). During the 2020 and 2021 growing seasons, 103 yellow mucoid colonies were isolated from plants representing 51 pepper cultivars symptomatic of bacterial spot, i.e., water-soaked leaf lesions that become necrotic spots on leaves and fruits across 22 commercial fields in NC following published methods (Klein-Gordon et al., 2021). All colonies were characterized to species using the qPCR species-specific primers and probes described by Strayer et al. 2016. Of the 103 colonies, 12 isolates tested positive for X. perforans. To confirm qPCR results, a Multi-Locus Sequence Analysis (MLSA) was run using fusA, gapA, gltA, gyrB, and lacF following previously described methods (Almeida et al., 2010) on three representative isolates: AHX61, collected in September 2020 from a field with 20% disease severity in Wake County on cv. Canary Bell; AHX261, collected in July 2021 from a field with 50% disease severity in Sampson County on Jalapeño; and AHX426, collected in August 2021 from a field with 50% disease severity in Dublin County on Jalapeño. All gene sequences were deposited to NCBI (GenBank Accessions: OQ799538-OQ799552) and compared to those from X. euvesicatoria, X. hortorum pv. gardneri, X. perforans, and X. vesicatoria type strains (Almeida et al., 2010). The MLSA showed AHX61, AHX261, and AHX426 cluster with X. perforans ICMP16690T, sharing 99-100% nucleotide similarity. Koch's postulates were performed with the three strains, Xp1484T [ X. perforans type strain, (Wilson 1987)], and water as a negative control. Three 10-week-old bell pepper plants (cv. Early Cal Wonder) were dip-inoculated in 600 mL of a bacterial suspension at an OD600 of 0.3 (~5x108 CFU/mL) and 0.04% Silwet L-77 per strain or water. All 18 plants were individually incubated in a plastic bag for 48 h post-inoculation at 28°C, 80% relative humidity, and 14 h:10 h light-dark cycle in a growth chamber, after which plastic bags were removed. Water-soaking and necrotic spots characteristic of bacterial spot were first observed at six days post-inoculation (dpi). At 14 dpi, symptomatic leaves were removed from treated plants to attempt pathogen re-isolation. Yellow mucoid colonies similar in morphology to those originally inoculated were recovered from all plants and confirmed to be X. perforans through sequencing; no isolates were recovered from water-treated plants. To our knowledge, this is the first time X. perforans is isolated in commercial bell pepper and specialty pepper fields in the state. This is an indication that the Xanthomonas population on peppers in the state is more diverse than previously reported and that pathogen populations will require monitoring for possible species shifts for this crop in NC.

Liquid biopsy detection of structural variant breakpoints to monitor ovarian cancer clonal evolution.

e17538 Background: Chemotherapy is effective at inducing remission for most patients with high grade serous ovarian cancer (HGSOC), yet relapse is frequent. Methods to interrogate the clonal composition and molecular properties of minimal residual disease are needed to better understand the mechanisms of HGSOC relapse. To address this unmet need, we developed and validated a novel cfDNA-based approach for tracking on-treatment clonal evolution using tumor-informed structural variants (SVs). Methods: Genomic DNA (gDNA) was isolated from cryopreserve multisite pre-treatment HGSOC biopsies and matched germline samples and whole genome sequencing (WGS) was performed. cfDNA was isolated from contemporary pre-treatment plasma. High confidence SVs were identified from multisite WGS using a consensus method incorporating five published SV calling algorithms. Tumor-informed bespoke quantitative PCR primer/probe sets were designed to interrogate SVs breakpoints in tumor gDNA and matched cfDNA. Results: Optimization of the methodology was first performed using synthetic cfDNA generated by ultrasonication of DNA from ovarian cancer cell lines. WGS was used to identify SVs and SV breakpoint-spanning PCR assay exhibited 90% sensitivity and 89% specificity in detection of WGS-informed SVs. 11 validated SVs breakpoint-spanning PCR assays had specific amplifications in synthetic cfDNA. 8 SVs breakpoint-spanning quantitative PCR primer/probe sets were synthesized for qPCR (real-time PCR) and ddPCR (digital droplet), the custom TaqMan probe assays had significant increased sensitivity and superior specificity. When cutoff value of negative was set to “undetected” in qPCR and 0 copies/ul in ddPCR, the sensitivity and specificity of custom TaqMan probe assays can still be 100%. . After screening 18 SVs by tumor-informed SV breakpoint-spanning PCR assays, 8 SVs custom TaqMan probe qPCR assays demonstrated 100 % sensitivity and specificity in multisite biopsy samples. 3 shared and 3 private SVs custom TaqMan probe ddPCR assays were selected for absolute quantification, none of these assays had false positive or false negative when 0 copies/ul was used for cutoff value. 1 shared SV custom TaqMan probe ddPCR assay measured 0.947 copies/ul in cfDNA and 0 copies/ul in matched germline control. Altogether, our multi-layer screening approach yields the “perfect”- high sensitivity and specificity- SV breakpoint-spanning assays that are ready to apply for SVs detection in cfDNA. Conclusions: Detection of SVs from pre-treatment cfDNA using tumor-informed breakpoint-spanning ddPCR is feasible and may enable a novel and sensitive method for monitoring on-treatment disease burden. Work is ongoing to extend this method to private SVs with a goal of tracking treatment-induced tumor clonal dynamics using cfDNA.

Plasma microRNA-143 and microRNA-145 levels are elevated in patients with left ventricular dysfunction.

MicroRNA(miR)-143 and miR-145 are mainly expressed in vascular smooth muscle cells. However, the relationship between plasma miR-143 or miR-145 levels and the left ventricular (LV) function in patients with heart diseases remains unclear. Blood samples were taken from the antecubital vein in patients with heart diseases (n = 52), such as coronary artery disease, old myocardial infarction, cardiomyopathy, and valvular heart disease, and controls without heart diseases (n = 22). We measured plasma miR-143 and -145 levels by quantitative RT-PCR using TaqMan MicroRNA Assays and THUNDERBIRD Probe qPCR Mix. Plasma BNP levels were also measured. Echocardiography was performed to measure the LV ejection fraction (LVEF) and LV dilation. Plasma miR-143 and miR-145 levels were significantly higher in patients with heart diseases than in controls, respectively. Plasma miR-143 and miR-145 levels were significantly higher in patients with LVEF < 50% than in those with LVEF ≧ 50%, respectively. Plasma miR-143 and miR-145 levels were inversely correlated with LVEF, respectively. Plasma miR-143 and miR-145 levels were positively correlated with LV end-systolic dimension, respectively. Plasma miR-143 and -145 levels were positively correlated with plasma BNP levels, respectively. Plasma BNP levels were inversely correlated with LVEF. Plasma miR-143 and miR-145 levels are elevated in patients with LV dysfunction and may counteract LV dysfunction.

Rapid detection and molecular epidemiology of β-lactamase producing Enterobacteriaceae isolated from food animals and in-contact humans in Nigeria.

The emergence and spread of β-lactamase-producing Enterobacteriaceae poses a significant threat to public health, necessitating the rapid detection and investigation of the molecular epidemiology of these pathogens. We modified a multiplex real-time (RT)-PCR to concurrently detect β-lactamase genes (blaCTX-M, blaTEM, and blaSHV) and Enterobacteriaceae 16S ribosomal RNA. qPCR probes and primers were validated using control isolates, and the sensitivity and specificity assessed. The optimised multiplex qPCR was used to screen 220 non-clinical Enterobacteriaceae from food animals and in-contact humans in Southeast Nigeria selected on cefotaxime-supplemented agar plates. Binary logistic regression was used to explore factors associated with the presence of the blaTEM and blaSHV genes in these isolates, and a subset of isolates from matched sampling sites and host species were whole genome sequenced, and their antimicrobial resistance (AMR) and plasmid profiles determined. The sensitivity and specificity of the qPCR assay was 100%. All isolates (220/220) were positive for Enterobacteriaceae ribosomal 16S rRNA and blaCTX-M, while 66.4% (146/220) and 9% (20/220) were positive for blaTEM and blaSHV, respectively. The prevalence of blaTEM and blaSHV varied across different sampling sites (farm, animal market and abattoirs). Isolates from Abia state were more likely to harbour blaTEM (OR = 2.3, p = 0.04) and blaSHV (OR = 5.12,p = 0.01) than isolates from Ebonyi state; blaTEM was more likely to be detected in isolates from food animals than humans (OR = 2.34, p = 0.03), whereas the reverse was seen for blaSHV (OR = 7.23, p = 0.02). Furthermore, Klebsiella and Enterobacter isolates harboured more AMR genes than Escherichia coli, even though they were isolated from the same sample. We also identified pan resistant Klebsiella harbouring resistance to ten classes of antimicrobials and disinfectant. Therefore, we recommend ESKAPE pathogens are included in AMR surveillance in future and suggest qPCRs be utilised for rapid screening of Enterobacteriaceae from human and animal sources.

Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes.

Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered northern tidewater goby, Eucyclogobius newberryi. Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining took twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding has gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining remains the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions.

Verification Study of the Detection Method for Unauthorized Genetically Modified Papaya by Combining DNA Polymerases and Real-time PCR Instruments

In the Japanese official detection method for unauthorized genetically modified (GM) papayas, one of two types of real-time PCR reagents with DNA polymerase (TaqMan Gene Master Mix [TaqMan Gene] or FastGene QPCR Probe Mastermix w/ROX [FastGene]) is primarily used for measurement. In 2022, we conducted a laboratory performance study on the unauthorized GM papaya line PRSV-YK, and the results revealed that high threshold cycle (Cq) values for the PRSV-YK detection test were obtained using TaqMan Gene with the 7500 Fast & 7500 Real-Time PCR System (ABI7500) and QuantStudio 12K Flex (QS12K), indicating the possibility of false negatives. The possibility of similar problems with all unauthorized GM papaya lines detection tests needs to be evaluated. In this study, we performed detection tests on unauthorized GM papaya lines (PRSV-YK, PRSV-SC, and PRSV-HN), the cauliflower mosaic virus 35S promotor (CaM), and a papaya positive control (Chy), and examined how the limits of detection (LOD) for each test are affected by two types of DNA polymerases (TaqMan Gene and FastGene) and three types of real-time PCR instruments (ABI7500, QS12K, and LightCycler 480 Instrument II [LC480]). In the PRSV-YK and PRSV-SC detection tests using ABI7500 and QS12K, measurement with TaqMan Gene showed a higher LOD than FastGene. In this case, an exponential amplification curve was confirmed on the amplification plot; however, the amplification curve did not cross the ΔRn threshold line and the correct Cq value was not obtained with a threshold line=0.2. The other tests (PRSV-HN, CaM, and Chy with ABI7500 and QS12K, and all detection tests with LC480) showed no important differences in the LOD for each test using either DNA polymerase. Therefore, when performing PRSV-YK and PRSV-SC detection tests with the ABI7500 or QS12K, FastGene should be used to avoid false negatives for foods containing GM papaya lines PRSV-YK and PRSV-SC at low mixing levels.

Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between the two biomarkers has been noticed by independent studies using these methods since late 2021. The reason is presumed to be due to mutations in regions targeted by the N1 qPCR probe. In this study, we systematically investigated and unequivocally confirmed that the underlying reason for this discrepancy was mutations in the N1 probe target, and that a single mutation could cause a significant drop in signal. We first confirmed the proportion of related mutations in wastewater samples (Jan 2021-Dec 2022) using nested PCR and LC-MS. Based on relative proportions of N1 alleles, we separated the wastewater data into four time periods corresponding to different variant waves: Period I (Alpha and Delta waves with 0 mutation), Period II (BA.1/BA.2 waves with a single mutation found in all Omicron strains), Period III (BA.5.2* wave with two mutations), and Period IV (BQ.1* wave with two mutations). Significantly lower N1 copies relative to N2 copies in samples from Periods II-IV compared to those from Period I was observed in wastewater. To further pinpoint the extent to which each mutation impacted N1 quantification, we compared the qPCR response among different synthetic oligomers with corresponding mutations. This study highlighted the impact of even just one or two mutations on qPCR-based wastewater surveillance of SARS-CoV-2.

Can Multiplex SYBR Green Real-Time PCR Assay Serve as a Detection and Quantification Method Comparable to the TaqMan Method for SARS-CoV-2 Diagnosis?

The reopening of schools, business, and social sectors during the COVID-19 pandemic has caused a current increase in the number of COVID-19 cases and clusters all over the globe. While the COVID-19 pandemic is far from over, the reopening and resumption of all economic sectors are essential to recovering the world economy. Health experts all over the world have determined that the real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) method is the gold standard for diagnosing COVID-19 infections due to the test’s high sensitivity and specificity. During the past 3 years when WHO declared the COVID-19 pandemic, the cost of laboratory diagnosis of COVID-19 using a robust RT-qPCR assay is still considerably expensive, especially for low and middle-income countries. Therefore, numerous studies have reported optimized SYBR green methods which are more economical than the qPCR probe assay. Continuous diagnostic testing is vital to mitigate the spread of COVID-19. However, there is a question as to whether SYBR Green may serve as an excellent detection and quantification method for molecular diagnosis to perform SARS-CoV-2 screening. This review summarizes the numerous studies using SYBR Green RT-PCR to detect SARS-CoV-2. The reliability of SYBR Green qPCR assays for determining gene expression based on their performance is justified and the quality is comparable to the TaqMan method.

Bacterial genome-wide association study substantiates papGII of Escherichia coli as a major risk factor for urosepsis

BackgroundUrinary tract infections (UTIs) are among the most common bacterial infections worldwide, often caused by uropathogenic Escherichia coli. Multiple bacterial virulence factors or patient characteristics have been linked separately to progressive, more invasive infections. In this study, we aim to identify pathogen- and patient-specific factors that drive the progression to urosepsis by jointly analysing bacterial and host characteristics.MethodsWe analysed 1076 E. coli strains isolated from 825 clinical cases with UTI and/or bacteraemia by whole-genome sequencing (Illumina). Sequence types (STs) were determined via srst2 and capsule loci via fastKaptive. We compared the isolates from urine and blood to confirm clonality. Furthermore, we performed a bacterial genome-wide association study (bGWAS) (pyseer) using bacteraemia as the primary clinical outcome. Clinical data were collected by an electronic patient chart review. We concurrently analysed the association of the most significant bGWAS hit and important patient characteristics with the clinical endpoint bacteraemia using a generalised linear model (GLM). Finally, we designed qPCR primers and probes to detect papGII-positive E. coli strains and prospectively screened E. coli from urine samples (n = 1657) at two healthcare centres.ResultsOur patient cohort had a median age of 75.3 years (range: 18.00–103.1) and was predominantly female (574/825, 69.6%). The bacterial phylogroups B2 (60.6%; 500/825) and D (16.6%; 137/825), which are associated with extraintestinal infections, represent the majority of the strains in our collection, many of which encode a polysaccharide capsule (63.4%; 525/825). The most frequently observed STs were ST131 (12.7%; 105/825), ST69 (11.0%; 91/825), and ST73 (10.2%; 84/825). Of interest, in 12.3% (13/106) of cases, the E. coli pairs in urine and blood were only distantly related. In line with previous bGWAS studies, we identified the gene papGII (p-value < 0.001), which encodes the adhesin subunit of the E. coli P-pilus, to be associated with ‘bacteraemia’ in our bGWAS. In our GLM, correcting for patient characteristics, papGII remained highly significant (odds ratio = 5.27, 95% confidence interval = [3.48, 7.97], p-value < 0.001). An independent cohort of cases which we screened for papGII-carrying E. coli at two healthcare centres further confirmed the increased relative frequency of papGII-positive strains causing invasive infection, compared to papGII-negative strains (p-value = 0.033, chi-squared test).ConclusionsThis study builds on previous work linking papGII with invasive infection by showing that it is a major risk factor for progression from UTI to bacteraemia that has diagnostic potential.

The Fascinating Cross-Paths of Pathogenic Bacteria, Human and Animal Faecal Sources in Water-Stressed Communities of Vhembe District, South Africa.

Access to clean and safe drinking water still remains a major challenge in the developing world, causing public health risks in terms of waterborne infections, especially in rural areas of sub-Saharan Africa. This study aimed to track and detect enteric pathogens (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, Shigella flexneri, and Campylobacter jejuni subsp. jejuni) in rural water sources. It also sought to establish a correlation between these pathogens and the sources of faecal pollution. Multiplex qPCR and specific primers and probes were used for detection and tracking. The study successfully correlated the occurrence of target pathogens with sources of human and animal faecal contamination using host-specific genetic markers (BacHum and HF183 for humans, BacCow for cows, Pig-2-Bac for pigs, Cytb for chickens, and BacCan for dogs). The study revealed that enteric pathogens were found in 47.69% and 32.80% of samples during the wet and dry seasons, respectively. These pathogens were associated with human or animal faecal contamination. Correlations between pathogens and contamination sources were significant (p ≤ 0.05), with varying strengths during the wet and dry seasons. The findings emphasize the importance of identifying faecal contamination sources to protect rural communities from waterborne infections.

Development of a field-deployable qPCR assay for real-time pest monitoring in algal cultivation systems

Outdoor cultivation is commonly used to produce algal biomass for a variety of bioproducts including food, feed, fuel, pharmaceuticals, and nutraceuticals. Outdoor cultivation ponds are highly susceptible to pest pressures that may lead to periods of low productivity or even entire loss of the algal crop. Therefore, there is a need for rapid, real-time tracking of pests for early intervention to mitigate crop loss. Herein, we describe the development of a field deployable, low-cost qPCR assay for detecting both known and novel pests of a farmed eukaryotic alga species, Nannochloropsis sp. We performed a proximity guided metagenome deconvolution approach (ProxiMeta™) to discover novel pests that temporally correspond to periods of reduced pond productivity. This approach provided high-quality metagenome assemblies that were used to design qPCR probes to detect specific pests of interest. The portable qPCR assay, designed to be deployed at remote field locations, enables low-cost surveillance with a rapid (2 h) turn-around time. Frequent sampling allows for early detection and prompts intervention strategies to remedy infected ponds to minimize crop loss. The qPCR assay was used to successfully detect a known predatory bacterium within the order Bdellovibrionales both in the lab and at a remote field location. Furthermore, we assembled the genome of two novel, site-specific pests in the Saprospiraceae family and successfully designed qPCR probes that differentially detected their presence in two different pond locations. Ultimately, this assay has the potential to monitor multiple pests simultaneously and tailor targets to match likely pest infections that differ across geographical locations, helping to mitigate crop loss on a large scale.

Effect of periodontal surgery on the salivary Herpes simplex virus-1 levels-a pilot study.

Herpes simplex viruses (HSV) are one of the most important groups of human pathogenic viruses. The prominent characteristic of this virus is latency and the ability to reactivate. One of the possible factors for reactivation of this virus is dental procedures. The aim of this study was to evaluate the salivary level of Herpes simplex viruses, before and after periodontal (crown lengthening) surgery and its relation with age and sex. 30 HSV seropositive patients, who needed the crown lengthening surgery and accepted to cooperate in this research, were included as experimental group of this study. Unstimulated Saliva samples of the patients were collected in 1.5ml micro-tubes, before and 24h after the surgery, and were analyzed by Premix EX taq probe qpcr, using PCR real-time method. No significant statistical differences were observed in the salivary level of HSV before and after crown lengthening procedure (p=0.18). However, the level of HSV in saliva after surgery was significantly higher than its level before surgery in women as compared to men (p=0.003). The differences in virus level did not have any significant relationship with patients' age (p=0.9). It seems that periodontal (crown lengthening) surgery does not affect the level of HSV in saliva yet, but it could be one of the stimulators of increased HSV level after surgery in women as compared to men; but age does not play an important role in changes of level of virus before and after the surgery.

EvIPqPCR, Target Circulating Tumorous Extracellular Vesicles for Detection of Pancreatic Cancer.

Pancreatic cancer patients predominantly present with advanced disease at diagnosis, contributing to its high mortality. A noninvasive, fast screening method to detect this disease is an unmet need. Tumor-derived extracellular vesicles (tdEVs) bearing information from parental cells have emerged as a promising cancer diagnostic biomarker. However, most tdEV-based assays have impractical sample volumes and time-consuming, complex, and costly techniques. To overcome these limitations, we developed a novel diagnostic method for pancreatic cancer screening. Our approach utilizes the mitochondrial DNA to nuclear DNA ratio of EVs as a collective cell-specific characteristic. We introduce EvIPqPCR, a fast method that combines immunoprecipitation (IP) and qPCR quantification to detect tumor-derived EVs directly from serum. Importantly, our method employs DNA isolation-free and duplexing probes for qPCR, saving at least 3 h. This technique has the potential to serve as a translational assay for cancer screening with a weak correlation to prognosis biomarkers and sufficient discriminatory power among healthy controls, pancreatitis, and pancreatic cancer cases.

Evaluation of the performance of GeneSoC®, a novel rapid real-time PCR system, to detect Staphylococcus aureus and methicillin resistance in blood cultures

Staphylococcus aureus bacteremia results in substantial mortality. Rapid identification and the determination of methicillin susceptibility are crucial for immediate treatment with appropriate antibiotics. In the present study, we aimed to evaluate the basic assay performance of GeneSoC®, a novel rapid quantitative polymerase chain reaction (qPCR) method, for the detection of methicillin-susceptible (MS) or -resistant (MR) S. aureus in blood culture (BC) bottles. qPCR pimers and probes were desinged for femA and mecA genes to diagnose S. aureus and its methicilline-resistance status. GeneSoC® system can detect target genes within 12 min per sample using microfludic thermal cycling. A total of 100 BC-positive samples, showing clusters of gram-positive cocci using microscopy, were tested. The analytical sensitivity was demonstrated for the target sequence of femA and mecA genes at 10 copies/μL, respectively. The detection limit of the MRSA bacterial burden using this system was 104 and 103 CFU/mL for femA and mecA, respectively. Compared with culture-based identification and susceptibility testing, the sensitivity and specificity for the detection of femA (+)/mecA (+) MRSA using GeneSoC® were 90.9 and 98.9%, respectively, whereas the sensitivity and specificity for detection of femA (+)/mecA (-) MSSA were 96.2% and 97.3%, respectively. In conclusion, although this was a small sample and pilot study, the GeneSoC® system is beneficial for rapid, reliable, and highly sensitive real-time testing of MRSA and MSSA in BC bottles.

Development of a Real-Time Recombinase-Aided Amplification Method to Rapidly Detect Methicillin-Resistant Staphylococcus aureus.

Methicillin-resistant staphylococcus aureus (MRSA) is a major pathogen responsible for human hospital and community-onset diseases and severe invasive livestock infections. Rapid detection of MRSA is essential to control the spread of MRSA. Conventional identification methods and antibacterial susceptibility tests of MRSA are time-consuming. The commonly used qPCR assay also has the disadvantages of being complicated and expensive, restricting its application in resource-limited clinical laboratories. Here, a real-time fluorescent recombinase-assisted amplification (RAA) assay targeting the most conserved regions within the mecA gene of MRSA was developed and evaluated to detect MRSA. The detection limit of this assay was determined to be 10 copies/reaction of positive plasmids. The established RAA assay showed high specificity for MRSA detection without cross-reactivities with other clinically relevant bacteria. The diagnostic performance of real-time RAA was evaluated using 67 clinical S. aureus isolates from dairy farms, which were detected in parallel using the TaqMan probe qPCR assay. The results showed that 56 and 54 samples tested positive for MRSA by RAA and qPCR, respectively. The overall agreement between both assays was 97.01% (65/67), with a kappa value of 0.9517 (p &lt; 0.001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9012, p &lt; 0.0001), indicating that this RAA assay possesses similar detection performance to the qPCR assay. In conclusion, our newly established RAA assay is a time-saving and convenient diagnostic tool suitable for MRSA detection and screening.

Abstract 13073: Antisense Transcripts Regulate Titin Alternative Splicing and Sarcomere Function in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

The giant protein Titin is an essential structural component of the sarcomere and a key determinant of passive tension during diastole. Titin tension is regulated by alternative splicing within the spring-like domains in the I-band region of TTN pre-mRNA. The cardiac RNA-binding protein RBM20 has been shown to promote TTN exon skipping during splicing, but additional factors are likely involved. We hypothesized that a natural antisense transcript in the TTN locus ( TTN-AS1 ) could regulate TTN splicing in cis through recruitment of spliceosome components. Through single nuclei RNA-Seq and RNA fluorescence in situ hybridization (ISH) on human cardiac tissue and iPS-derived cardiomyocytes (iPS-CM), we showed that the expression of TTN-AS1 was restricted to cardiomyocyte nuclei. The percent spliced in (PSI) of each TTN exon was calculated based on RNA-Seq data from iPS-CM (n=3) and 26 exons (all in the I-band region) that are normally spliced out were included to a significantly higher extent (adjusted p&lt;0.05) upon siRNA-mediated TTN-AS1 knock down. Reduced exon skipping from TTN exon 50 was confirmed with exon-junction spanning qPCR probes (p&lt;0.05, n=3). Similar effects on splicing were seen in cells where RBM20 had been knocked down. The consequences of TTN-AS1 knock down on cardiomyocyte contractile function was assessed using sarcomere tracking. Transgenic expression of ACTN2-GFP was used to visualize z-disks in iPS-CM, sarcomeres (n=14,636) were recorded during contractions using wide-field epifluorescence microscopy and analyzed using Sarc-Graph software. The analysis revealed that in cells where TTN-AS1 had been knocked down, sarcomere length and fractional shortening, as well as contraction and relaxation time were increased (all p&lt;0.001). Again, similar effects were seen in iPS-CM where RBM20 had been knocked down. We observed co-localization of TTN-AS1 and RBM20 protein during active TTN splicing in iPS-CM nuclei using multiplex RNA ISH and immunofluorescence and confirmed interaction between TTN-AS1 and RBM20 using RNA Immunoprecipitation and qPCR. In conclusion, we show that TTN-AS1 can affect cardiomyocyte contractile properties and sarcomere dynamics through regulation of TTN alternative splicing.

Detection methods, epidemiological investigation, and host ranges of infectious precocity virus (IPV)

Giant freshwater prawn, Macrobrachium rosenbergii, is an important economically aquaculture species widely farmed in tropical and subtropical areas of the world. Infectious precocity virus (IPV) is a virus that results in slow growth and sexual precocity of farmed M. rosenbergii and causes significant economic losses. A TaqMan probe Quantitative Real-time PCR (qPCR) and a nested PCR assay for IPV detection were established in this study. IPV was detected in crustaceans M. rosenbergii, M. nipponense, Procambarus clarkii, Litopenaeus vannamei, Penaeus monodon, and Oratosquilla oratoria and insect Anisops kuroiwae. On the contrary, it was not detected in fishes Misgurnus anguillicaudatus, Carassius auratus, Oreochromis mossambicus, Micropterus salmoides, and Pangasius bocourti; crabs Eriocheir sinensis and Scylla paramamosain; and malacostraca Charybdis feriatus with nested PCR in China. TaqMan probe qPCR was used to study the tissue tropism of IPV in M. rosenbergii. IPV mainly infected the brain, abdominal nerve, integument, and gill. From July 2019 to April 2021, 260 M. rosenbergii from IPV disease (IPVD) outbreak ponds were all IPV positive in nested PCR, and 40 M. rosenbergii from normal ponds without IPVD were all IPV negative in nested PCR. These results could be beneficial to the prevention and control of IPV infection.

Abstract 1325: Naturally occurring colorectal cancer in nonhuman primates used to study human immunotherapeutic agents confirms a link between DNA methylation and mismatch repair deficiency

Abstract Background Non-human primates (NHP) such as rhesus macaques with naturally occurring cancers are a proposed model for translational cancer immunotherapy (CIT) research and have generated relevant proof-of-mechanism evidence for 3 different CIT agents. NHP spontaneously develop cancers with progression patterns, histology, and clinical symptoms similar to humans. Gene suppression by DNA hypermethylation in the promoter region is the major characteristics of the CpG-island-methylator-phenotype (CIMP) described in human CRC patients but information in rhesus macaques is scarce. To further validate these animals as translational models for CIT, we conducted a deep molecular characterization of NHP colorectal cancers and established novel qPCR panels to assess DNA methylation of marker genes published for humans. Methods Our cohort (n=16) consisted of Indian-origin rhesus macaques (Macaca mulatta) with naturally occurring CRC (n=16, female=11). Clinical examination, imaging (contrast-enhanced CT, FDG-PET) and biopsy to confirm cancer histology were performed. Molecular characterization was done by IHC for CRC-associated mismatch repair proteins MLH1, MSH2, MSH6, and PMS2 and by PCR/electrophoresis for microsatellite instability. Ultimately, we designed DNA methylation- and rhesus-specific qPCR probes (Methylight) targeting corresponding regions as published in human patients, including CACNA1G, CDKN2A, CRABP1, MLH1, and NEUROG1 as parts of the CIMP panel and BMP3, NDRG4, and SEPTIN9 as probed for human CRC-screening. Results MLH1 deficiency by IHC, in conjunction with PMS2 absence, is observed in all NHP CRC cases, clearly exceeding frequencies reported in human CRCs (ranging from 2-15%). Moreover, we have documented microsatellite instable cases in some NHP CRCs, analog to human CRCs. DNA methylation of the MLH1 promoter region was significantly elevated in CRCs (100% of CRCs &amp;gt;2-fold, p&amp;lt;0.0001) compared to healthy colon. We hypothesized that this elevation would suppress MLH1 mRNA expression. This hypothesis of epigenetic suppression is corroborated by both qPCR and RNA sequencing which demonstrate significantly downregulated levels of MLH1 mRNA. DNA methylation of the other markers is less consistent but revealed CIMP positive and CIMP negative cases in our NHP CRC cohort. Conclusions Transcriptional suppression of MLH1 by promoter hypermethylation is a major and widespread driver of genetic instability and carcinogenesis in rhesus macaque colorectal cancer. Differential DNA methylation in the promoter regions as observed in NHP CRCs can provide a screening target for liquid biopsies. This work highlights the possible translatability of naturally occurring NHP cancers for human cancer immunotherapy research and can be further explored in future tumor-bearing monkey trials. Citation Format: Simon Deycmar, Brendan Johnson, Declan Ryan, Shane Sills, David Caudell, Greg Dugan, George Schaaf, Christopher Whitlow, Kiran Kumar Solingapuram Sai, Betsy Ferguson, Benjamin Bimber, Karina Ray, Cassandra Cullin, Brandy Dozier, Armando Burgos, Michael Hettich, Bruno Gomes, Jehad Charo, Maurizio Ceppi, Mark Cline. Naturally occurring colorectal cancer in nonhuman primates used to study human immunotherapeutic agents confirms a link between DNA methylation and mismatch repair deficiency [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1325.

Development of a novel TaqMan qPCR assay for rapid detection and quantification of Gymnodinium catenatum for application to harmful algal bloom monitoring in coastal areas of Tunisia.

Gymnodinium catenatum is a dinoflagellate known to cause paralytic shellfish poisoning (PSP), commonly associated with human muscular paralysis, neurological symptoms, and, in extreme cases, death. In the present work, we developed a real-time PCR-based assay for the rapid detection of the toxic microalgal species, G. catenatum, in environmental bivalve mollusc samples as well as seawater samples. G. catenatum-specific primers and probe were designed on the ITS1-5.8S-ITS2 rDNA region. Hydrolysis probe qPCR assay was optimized. ITS1-5.8S-ITS2 rDNA region copy numbers per G. catenatum cell genome were estimated to be 122.73 ± 5.54 copies/cell, allowing cell quantification. The application of the optimized qPCR assay for G. catenatum detection and quantification in field samples has been conducted, revealing high sensitivity (detection of around 1.3105 cells/L of seawater samples. Thus, the designed hydrolysis probe qPCR assay could be considered an efficient tool for phytoplankton monitoring whilst ensuring accuracy and sensitivity and providing cost and time savings.