Polymerase Chain Reaction Detection Research Articles

A-272 Evaluation of a Real-Time Multiplex Polymerase Chain Reaction Assay for Simultaneous Detection of Respiratory Pathogens in Nasopharyngeal Specimens

Abstract Background Respiratory infections present a significant challenge due to the diverse range of pathogens involved and the possibility of concurrent infections, emphasizing the importance of rapid and accurate detection for effective treatment. Advancements in molecular methods have provided cost-effective and reliable solutions for the identification of respiratory pathogens. In this study, we aimed to assess performance characteristics of the Seegene Allplex™ 2019-nCoV Assay and Seegene Novaplex™ Respiratory Panel Assays for simultaneous amplification and detection of 22 respiratory pathogens using real-time multiplex polymerase chain reaction (PCR). Methods Nucleic acid extraction was performed using the MagMAX™ Viral/Pathogen Nucleic Acid Isolation Kit (Thermo Fisher Scientific, MA) on the CyBio® FeliX liquid handler (Analytik Jena, Germany). PCR amplification and detection were performed using the Seegene Novaplex™ Respiratory Panels 1A, 2, 3, PneumoBacter Assay, and Allplex™ 2019-nCoV Assay (Seegene Inc, South Korea) on the CFX96™ System (Bio-Rad Laboratories, CA). The assays utilize Seegene MuDT™ technology that allows for the detection of multiple targets in a single channel without the need for melt curve analysis. For method validation, precision studies were performed within-run and over 4 days. The limit of detection was verified by using plasmids from Seegene containing the target sequence for each pathogen at known concentrations. Method comparison studies were carried out by extracting and analyzing a range of 41 to 79 split samples for each pathogen against the BioFire® Respiratory 2.1 Panel (bioMérieux, France), cobas® Influenza A/B & RSV Assay on the cobas® liat system (Roche Diagnostics, IN), and Lyra® SARS-CoV-2 Assay (Quidel, CA) on the CFX96™ system. Additional accuracy studies were performed by spiking negative patient samples with standards from ZeptoMetrix® (Antylia Scientific, IL) containing known concentrations of the targeted respiratory pathogens. Results Precision studies demonstrated consistent and reproducible results for all pathogens. The limit of detection was verified at 1000 copies/reaction for human parainfluenza virus 4 and human metapneumovirus, and at 100 copies/reaction for all other pathogens. Results of the spike-and-recovery studies were consistent with expected results for all targets. Patient correlation studies showed 100% agreement with expected pathogen identification for 19 pathogens, and greater than 97.9% agreement for influenza B virus, respiratory syncytial virus, human parainfluenza virus 4, and human coronavirus 229E. Conclusions The Seegene Allplex™ 2019-nCoV Assay and Novaplex™ Respiratory Panel Assays offer a rapid and reliable method for detecting respiratory pathogens in nasopharyngeal specimens. The capability of the assays to detect multiple targets in a single well enhances efficiency, cost-effectiveness, and turnaround time.

Development of a Multiplex Polymerase Chain Reaction Assay for Detecting Five Previously Unreported Papaya Viruses for Quarantine Purposes in Korea

There are concerns about the introduction and spread of plant pests and pathogens with globalization and climate change. As commercial control agents have not been developed for plant viruses, it is important to prevent virus spread. In this study, we developed a multiplex polymerase chain reaction (PCR) detection method to rapidly diagnose and control three DNA (papaya golden mosaic virus, Lindernia anagallis yellow vein virus, and melon chlorotic leaf curl virus) and two RNA (papaya leaf distortion mosaic virus and lettuce chlorosis virus) viruses that infect papaya. Specific primer sets were designed for the virus coat protein. Performing PCR, clear bands were observed with no non-specific reaction. Our multiplex PCR method can simultaneously detect small amounts of DNA/RNA to diagnose five viruses infecting papaya and prevent the spread of the virus.

Molecular detection of OXA-48 and NDM-1 carbapenemase genes among clinical isolates of Klebsiella pneumoniae recovered from patients attending a private tertiary hospital in Southwestern Nigeria

There have been increasing reports of Klebsiella pneumoniae resistant to β-lactam antibiotics. This study aimed to determine the prevalence of some selected carbapenemase genes among clinical isolates of Klebsiella pneumoniae recovered from patients attending a private tertiary hospital in Southwestern Nigeria. The study was conducted over two months (February-March 2024). A total of 50 clinical isolates of Klebsiella pneumoniae from different clinical specimens were obtained from the Medical Microbiology Department, Babcock University Teaching Hospital (BUTH). The clinical isolates were then characterized using standard microbiological procedures and were tested for susceptibility to meropenem and other classes of antibiotics according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Polymerase Chain Reaction (PCR) detection for OXA-48 and NDM-1 carbapenemase genes was performed on the 50 clinical isolates. PCR analysis showed that 9 (18%) clinical isolates were positive for the OXA-48 gene, 22 (44%) were positive for the NDM-1 gene, 4 (8%) possessed both the OXA-48 and NDM-1 genes, and 23 (46%) possessed neither the OXA-48 nor NDM-1 genes. Antibiotic Susceptibility Testing (AST) revealed that all the clinical isolates were resistant to meropenem. In conclusion, this study demonstrates the presence of OXA-48 and NDM-1 genes in clinical isolates of Klebsiella pneumoniae recovered from patients attending a private tertiary hospital in Southwestern Nigeria, highlighting the role of ESBL (extended-spectrum beta-lactamase) as a major resistance mechanism alongside other mechanisms. Population-based surveillance programs should be implemented to monitor the prevalence and epidemiology of Klebsiella pneumoniae infections at the community level, facilitating early detection of outbreaks and identification of emerging antimicrobial resistance patterns.Core TipThis study highlights the significant prevalence of NDM-1 and OXA-48 carbapenemase genes among Klebsiella pneumoniae clinical isolates in a private tertiary hospital in Southwestern Nigeria, with 44% and 18% of isolates harboring these genes, respectively. Notably, 46% of isolates were resistant to carbapenems despite lacking these genes, suggesting alternative resistance mechanisms. The findings underscore the urgent need for enhanced surveillance, infection control measures, and antibiotic stewardship programs to combat the spread of multidrug-resistant Klebsiella pneumoniae in healthcare settings.

Prevalence of trypanosomiasis caused by Trypanosoma brucei (Kinetoplastea, Trypanosomatidae) in domestic ruminants from Southern Punjab, Pakistan

Background and Aim: Trypanosomiasis, a parasitic infection caused by various Trypanosoma species, poses a significant threat to global livestock, affecting both human health and economic sectors. This study aimed to estimate the prevalence of trypanosomiasis in Southern Punjab, Pakistan, focusing on key ruminant species, including camels, cattle, buffaloes, goats, and sheep. Materials and Methods: A total of 240 blood samples, comprising 48 samples from each animal species (camel, cattle, buffaloes, goat, and sheep) were collected from three districts in Southern Punjab. The collected samples were subjected to thin smear microscopy, DNA extraction, and polymerase chain reaction (PCR) amplification. The molecular characterization was conducted using the TBR primer set, which targeted repeated satellite DNA regions and the cytochrome oxidase II gene of Trypanosoma brucei. Results: About 22.08% (53/240) of overall samples were positive for trypanosomiasis, with prevalence rates being 23.75% (19/80), 21.25% (17/80), and 21.75% (17/80) for districts Muzaffargarh, Lodhran, and Bahawalpur, respectively. 5.83% (14/240) of samples tested for T. brucei using PCR were positive in the districts of Muzaffargarh 7.50% (6/80), Lodhran 5.00% (4/80), and Bahawalpur 5.00% (4/80). Among the animals tested, camels had the highest positivity rate. The microscopic examination confirmed infection rates of 45.83% (22/48) for camels, 18.75% (9/48) for cattle, 8.33% (4/48) for buffaloes, 18.75% (9/48) for goats, and 18.75% (9/48) for sheep (p < 0.001). PCR results did not reveal substantial differences (p < 0.05) in prevalence: camels 12.50% (6/48), cattle 6.25% (3/48), buffaloes 0% (0/48), goats 8.33% (4/48), sheep 2.08% (1/48); while distinct disparities were detected district-wise: Muzaffargarh 23.75% (19/80), Lodhran 21.25% (17/80), and Bahawalpur 21.25% (17/80). The PCR results for these districts were insignificantly different: 7.50% (6/80), 5% (4/80), and 5% (4/80). The microscopic infection rate in camels from Bahawalpur was 56.30% (9/16). The microscopic analysis in Buffaloes reported a 6.30% (1/16) infection rate, but PCR results indicated no infections (0%) in any district. A significant difference (p < 0.001) in identifying Trypanosoma species was found between positively and negatively tested animals in both microscopic and PCR methods. Conclusion: This study emphasizes the necessity of regularly using PCR-based screening for its superior sensitivity and specificity over traditional microscopy. The varying occurrence of trypanosomiasis among districts reflects the intricate nature of this diseases epidemiology in the region. Reducing economic losses from trypanosomiasis in Southern Punjab, Pakistan, requires targeted interventions, such as vector control measures and farmer education. Keywords: domestic ruminants, microscopic examination, Pakistan, polymerase chain reaction detection, Trypanosoma brucei, trypanosomiasis.

Identification of a novel circovirus associated with turbot (Scophthalmus maximus) acute hemorrhage disease

Turbot (Scophthalmus maximus) is an economically important farming fish in China. However, an emerging disease named turbot acute hemorrhage disease (TAHD) has been affecting turbot farms since November 2019. TAHD is characterized by severe bleeding in the fish fins and may lead to significant mortality in one or two weeks, with accumulated mortality exceeding 90 %. The TAHD spread rapidly across the major turbot farming regions in China and resulted in significant economic losses. Virome sequencing was utilized in the diseased fish to discover a novel turbot circovirus (TCV). The TCV particle is ~30 nm in size and is located in the fish spleen and kidney. The TCV genome is 1774 bp long, with three open reading frames (ORFs) encoding the replication protein (Rep), capsid protein (Cap), and ORF3 of unknown function. The identity of the TCV Rep sequence was <53 % compared to the reported circovirus sequences. Phylogenetic analysis of the Rep and Cap protein sequences revealed that TCV is a novel circovirus. The polymerase chain reaction detection method was used to analyze the clinical TAHD samples from 2019, which were all TCV-positive. Various cell lines, including turbot kidney, epithelioma papilloma cyprinid, Chinook salmon embryo, and spotted halibut kidney, were used for TCV isolation. However, no cytopathic effect or replication was observed. The diseased fish tissue homogenate filtrate was used for experimental infection. As a result, all of the infected turbot showed signs of natural infection, with increasing numbers of cap gene copies post-infection. Based on these results, it was hypothesized that the novel circovirus TCV is closely associated with TAHD. Our research also indicated that the circovirus represents a significant threat to fish and more attention should be paid to it in aquaculture.

CAPZB mRNA is a novel biomarker for cervical high-grade squamous lesions

This study aimed to evaluate the potential of capping protein (actin filament) muscle Z-line subunit β (CAPZB) messenger ribonucleic acid (mRNA) levels as a biomarker for distinguishing low-grade squamous intraepithelial lesions of the cervix (LSIL) from high-grade squamous intraepithelial lesions of the cervix (HSIL). We collected a total of 166 cervical exfoliated cells and divided them into five groups based on histopathological results. Each sample was divided into two portions, one for fluorescence in situ hybridization (FISH) detection and the other for bisulfite sequencing polymerase chain reaction (BSP) detection. We found that FISH detection of CAPZB mRNA mean fluorescence intensity (MFI) and BSP detection of CAPZB deoxyribonucleic acid (DNA) percentage of methylation rate (PMR) performed as biomarkers for distinguishing HSIL from LSIL, with an area under the receiver operating characteristic curve (AUC), sensitivity, specificity and cut-off value of 0.893, 81.25%, 80.39% and 0.616, 0.794, 64.06%, 81.37% and 0.454, respectively. Furthermore, FISH detection of CAPZB mRNA exhibited a greater AUC (0.893) for the detection of HSIL than the CAPZB DNA methylation method (0.794), indicating the CAPZB mRNA levels can be used as a biomarker for assessing cervical lesions.

Discovery and demonstration of the temperature stress response functions of Dermatophagoides farinae proteins 1 and 2

BackgroundDermatophagoides farinae proteins (DFPs) are abundantly expressed in D. farinae; however, their functions remain unknown. Our previous transcriptome sequencing analyses revealed that the basal expression of DFP1 and DFP2 in D. farinae was high and, more importantly, upregulated under temperature stress. Therefore, DFPs were speculated to exert a temperature stress response function.ResultsReal-time quantitative polymerase chain reaction detection revealed that both DFP1 and DFP2 were significantly upregulated under temperature stress. Particularly, DFP1 was upregulated under cold stress. Electrophoresis of D. farinae total proteins revealed an increased abundance of DFP1 and DFP2 (40–55 kDa bands) under temperature stress, which was corroborated by the mass spectrometry results. After silencing DFP1 and DFP2 further, temperature stress led to decreases in gene expression and survival rates. Moreover, DFP1 was identified as the upstream regulator of DFP2.ConclusionThis study highlights the temperature stress response functions of DFP1 and DFP2 at the mRNA and protein levels. These results provide important insights for applying DFP1 and DFP2 as potential target genes for the molecular prevention and control of D. farinae to prevent allergic diseases. The newly established methods provide methodological guidance for the study of genes with unknown functions in mites.

Oral Administration of Lutein Improves Fat Graft Survival by Alleviating Oxidative Stress in Mice.

Oxidative stress induced by ischemia and hypoxia in fat transplantation is a major obstacle to graft retention. Previous studies have shown that lutein has excellent adipose tissue affinity and anti-oxidative stress ability, however, the effects of oral lutein on fat transplantation have not been studied yet. We aimed to investigate whether oral lutein can improve fat transplantation retention by regulating oxidative stress, apoptosis, and inflammatory cytokine levels in graft tissues. Nude mice were assigned to the control group (normal saline), low-dose lutein group (10 mg/kg/day) and high-dose lutein group (20 mg/kg/day) randomly. All mice were given by gavage 1 week before fat grafting and continued for 2 weeks. The grafts were collected 1, 2, and 12 weeks after treatment. By conducting histological analyses, western blotting, quantitative polymerase chain reaction and cell metabolic function detections, the regulatory effects of lutein on apoptosis and oxidative stress in grafts were demonstrated. Besides, RNA sequencing was conducted to further clarify the efficacy of lutein on fat grafting. Lutein induced superior graft retention, histological structures and more viable adipocytes than control group. It relieved tissue oxidative stress and lipid oxidative damage by decreasing reactive oxygen species, and significantly reduced inflammation and apoptosis of grafts. RNA sequencing analysis confirmed that lutein could down-regulate the genes expression of oxidative stress and related inflammation and apoptosis. Our study suggested that oral administration of lutein can improve fat graft survival by reducing the levels of oxidative stress, inflammation and apoptosis in grafted fat.

Polymorphisms in miR-17-92 cluster promoter region is associated with risk and prognosis of endometrial cancer.

Accumulating researches have reported that miR-17-92 cluster expression has strong association with tumorigenesis. In this study, we investigated the effects of 2 genetic polymorphisms in the promoter region of the miR-17-92 cluster and the risk and prognosis of endometrial cancer in northern Chinese women. Two polymorphisms (rs9588884 and rs982873) in the promoter of miR-17-92 cluster were genotyped by polymerase chain reaction and ligase detection reaction (PCR-LDR) in398 EC patients and 420 controls. The levels of miR-17-92 mRNA were investigated in 65EC tissues by real-time quantitative polymerase chain reaction (RT-qPCR). The impact of genetic features on the risk and clinical outcomes of EC was analyzed. The prognostic value of hsa-miR-17 and hsa-miR-20a in EC patients was assessed using the Kaplan-Meier plotter database. The results showed that a significant decrease in risk of EC with rs9588884 (GG vs CC: OR = 0.49, 95% CI = 0.32-0.78, P = .002; G vs C: OR = 0.75, 95% CI = 0.62-0.91, P = .005, respectively). Similarly, association was found between rs982873 and a decreased risk of EC (CC vs TT: OR = 0.53, 95% CI = 0.34-0.82, P = .004; C vs T: OR = 0.77, 95% CI = 0.63-0.94, P = .010, respectively). Moreover, survival analysis showed that the CG or GG genotype of rs9588884 may significantly increase overall survival (OS) compared with the CC genotype in the 5-year follow-up (HR = 0.49, 95% CI = 0.29-0.82 and HR = 0.36, 95% CI = 0.16-0.83, respectively). RT-qPCR results showed that the expression level of miR-17-92 mRNA in EC tissues with the rs9588884 GG genotype was significantly lower than those with the GC + CC genotype (P = .030). However, there was no significant difference in the prognosis and expression level of miR-17-92mRNA in tissues of EC patients with different genotypes of rs982873 (P = .343). In addition, analysis using Kaplan-Meier plotter database showed that high hsa-miR-20a expression was significantly correlated with poor OS in EC patients (HR = 1.63, 95% CI = 1.02-2.61, P = .039). The genetic polymorphisms rs9588884 and rs982873 in the promoter of miR-17-92 cluster decreased EC risk. Both rs9588884 and the expression level of hsa-miR-20a mRNA may be associated with its clinical outcome in EC patients.

Upconversion luminescence resonance energy transfer (LRET)-based dual-channel biosensor for rapid detection of coronavirus

Researchers recently have been working on a sensitive, accurate, and easily accessible way to detect coronaviruses. Traditional polymerase chain reaction detection technology has high sensitivity and specificity, but there are some problems, such as a complicated detection process, false negatives caused by gene mutation of coronavirus, and easy infection of operators. Antigen detection, which does not require gene amplification and other preprocessing, can be operated by non-medical staff for rapid detection. However, its detection sensitivity requires high reliability and further improvement. Accordingly, a biosensor based on luminescent resonance energy transfer (LRET) from upconversion nanoparticles (UCNPs) to gold nanoparticles (AuNPs) and antigen detection has been developed for rapid and sensitive detection of N protein of SARS-CoV-2. By adjusting the reaction conditions, LRET can be realized by making the spectral overlap between the luminescence of UCNPs and the absorption band of AuNPs, which can effectively avoid the generation of biological background light and the interference of other signals in the test process. In addition, the thiol-ene click reaction was used to link Thiol-PEG-COOH to UCNPs to improve its biocompatibility. The antigen recognition of the coronavirus based on the as-proposed detection method can be further realized on the test paper. A linear response is obtained ranging from 10 ng mL−1 to 1280 ng mL−1, and the detection limit is around 0.80 ng mL−1 with a detection time of around 10 minutes, which has a wide range of potential future. This fast and sensitive biosensor for coronavirus detection can be further reflected in the test paper and is promising for practical applications.

Simple and rapid identification of beef within 30 min using a new food nucleic acid release agent combined with direct-fast qPCR

Simple and rapid molecular detection technologies for authenticating animal species are urgently needed for food safety and authenticity. This study established a new direct-fast quantitative polymerase chain reaction (qPCR) detection technology for beef to achieve rapid and on-site nucleic acid detection in food. This technology can complete nucleic acid extraction in 4 min using a new type of food nucleic acid-releasing agent, followed by direct amplification of the DNA sample by fast qPCR in 25 min. The results indicated that direct-fast qPCR can specifically identify beef and can also identify 0.00001% of beef components in artificially simulated meat mixtures, with a detection precision variation coefficient of <4%. This method can be used to effectively identify beef in different food samples. As a simple, fast, and accurate molecular detection technology for beef, this method may provide a new tool for the on-site detection of beef components in food.

Rapid discrimination of African swine fever virus nucleic acid and virions using BenzoNuclease

African swine fever (ASF) is an acute and severe infectious disease caused by the African Swine Fever Virus (ASFV). ASFV exhibits significant resistance and stability in the environment, which, coupled with its double-stranded DNA and large genome, predisposes it to contaminate laboratory samples. This characteristic can lead to false-positive results in swine farm settings even days after disinfection, as detectable through polymerase chain reaction (PCR) or real-time fluorescent quantitative PCR (qPCR) assays. To meet the demand for efficient clinical methods capable of discriminating between ASFV nucleic acid and ASFV virions, this study aims to ascertain the efficacy of the nuclease “BenzoNuclease” in distinguishing ASFV nucleic acid (ASFV-DNA) from ASFV virions. BenzoNuclease is a versatile nucleic acid enzyme with the capacity to degrade nearly all forms of DNA and RNA. Initially, this research established a highly sensitive general PCR detection method for ASFV. Subsequently, a positive control was constructed using the M13 bacteriophage to substitute for active ASFV, facilitating the development of an improved qPCR method. It is important to note that common disinfectants have the potential to deactivate BenzoNuclease. However, in an environment simulating actual production applications, residual disinfectants do not interfere with the enzymatic efficacy of BenzoNuclease, thus not affecting the detection capabilities of this method. Positive clinical samples from pig farms, upon testing with the improved method, revealed that three samples were positive, indicating the presence of viral particles, while the remaining samples were negative, indicating the presence of nucleic acids. This provides an additional new option for sample testing in pig farms.

Molecular Identification of Mycobacterium leprae in the Leprosy Patients.

Several discoveries about leprosy indicate that Mycobacterium leprae transmission mainly occurs by inhalation, and the nose is a major port of entry and exit. Molecular probes have shown certain potential for the detection and identification of M. leprae in patients. The aim of this study was to identify M. leprae in nasal swab specimens using polymerase chain reaction (PCR)-based assays followed by gene sequencing methods. This observational study examines 64 anterior nasal swab samples taken from pretreatment leprosy patients, on-treatment and completed leprosy treatment in Bulukumba, South Sulawesi, Indonesia. samples were analyzed by molecular detection methods according to the standard methods at the Clinical Microbiology Laboratory of Hasanuddin University. Descriptive statistics were utilized to summarize patient demographics and outcomes. This study uses PCR to detect the M. leprae deoxyribonucleic acid (DNA) from nasal swab specimens. Data were collected from 64 patients with a percentage of male patients 51.54%. Based on the age category, the group 45-46 years was the most frequent (39.05%). PCR detection proline-rich antigen gene of a 531 bp DNA fragment from M. leprae, was positive in eight patients, and they were multibacillary. Furthermore, PCR was positive in 5 (31.25%) of 16 new leprosy patients, 2 (8.69%) of 23 on-treatment patients, and 1 (4%) of 25 treatment completed patients. Based on the results of the phylogenetic tree and analysis of 8 positive results detected by M. leprae from leprosy patients, almost all samples have a level of similarity, except for sample Ua7. M. leprae cannot grow in vitro, so molecular diagnostic tools were used to confirm the disease. This study predominantly of males with the age above 45 years of age being the most common. Eight M. leprae were positive from nasal swab leprosy patients. The sequencing findings provide insight into the genetic diversity of the genus M. leprae, so it is necessary to consider the detection of whole-genome sequence.

Distribution of extended-spectrum β-lactamase producing Escherichia coli genes in an integrated poultry-fish farming system in Bogor, Indonesia.

The excessive use of antimicrobials in livestock farming leads to the emergence and dissemination of antimicrobial-resistant organisms. This study aimed to detect extended-spectrum β-lactamase (ESBL)-producing Escherichia coli genes in integrated poultry-fish farms in Bogor, Indonesia. A total of 256 samples were collected from six poultry-fish farms. One hundred and seventy-five chicken cloaca swabs, 60 fish skin swabs, six pond water samples, and 15 farmer's hand swabs. ESBL-producing E. coli was confirmed through double-disk diffusion. The specific primers and probe genes for quantitative polymerase chain reaction detection of ESBL-producing E. coli targeted blaTEM, blaCTX-M, blaSHV, and blaOXA-48 genes. Among the 256 samples tested, 145 (56.6%) were positive for E. coli, and 67.6% (98/145) were identified as ESBL-producing E. coli. The most ESBL-producing E. coli isolates were obtained from chicken cloaca (78.3%, 72/92), followed by pond water (66.7%, 4/6), fish skin (47.6%, 20/42), and farmer's hand swabs (40%, 2/5). About 100% of the isolates carried the genes blaTEM and blaCTX-M, whereas 17.3% and 24.5% carried blaSHV and blaOXA-48, respectively. ESBL-producing E. coli genes were investigated in chicken cloaca, fish, pond water, and farmers' hands within an interconnected poultry-fish farming operation. The ESBL-producing E. coli in chickens can transfer resistant genes to aquatic environments. The transfer could harm other aquatic species and food chains, potentially threatening human health.

Whole Genome Sequencing to Identify Multiple Clusters of Carbapenemase-Producing Enterobacterales Cases – Colorado, 2022-2023

Background: The Colorado Department of Public Health and Environment (CDPHE) detected an increase in Klebsiella pneumoniae carbapenemase-producing carbapenem-resistant Enterobacterales (KPC-CRE) infections in October 2022. We investigated patient epidemiological links and isolate relatedness to characterize interfacility transmission of KPC-CRE in the Denver metro area and inform regional prevention strategies. Methods: We defined a case as polymerase chain reaction detection of KPC from clinical or screening specimens collected during January 2022 – January 2023. Cases were identified through statewide CRE surveillance and carbapenemase testing at the CDPHE laboratory and counted once within a 30-day period. Medical records were reviewed to identify healthcare facility admissions and patient facility overlap in the 12 months prior to sample collection. Whole genome sequencing (WGS) was performed for 34 patients with available KPC-CRE isolates using short- and long-read sequencing techniques. We performed multi-locus sequence typing, generated genome phylogenetic trees, and compared plasmid contig sequences to identify relatedness between KPC-CRE isolates. Clusters were defined as ≥2 genetically related isolates of the same organism or carbapenemase plasmid, from different patients. Results: We identified 48 cases (34 clinical and 14 screening) among 39 patients (figure). Patients had a mean age of 52 years (range 16-86) and median of three healthcare facility admissions (range 1-14). Twenty-eight patients (72%) were male. We identified 16 (41%) patients with epidemiological links to one acute care hospital (ACH), 11 (28.2%) patients to one long-term acute care hospital (LTACH), and four (10.2%) patients to each of two ventilator-capable skilled nursing facilities (vSNF). Five distinct clusters of KPC-CRE were identified by WGS among 23 patients (E. hormaechei, two distinct E. cloacae clusters, K. pneumoniae, and K. oxytoca) with linkages to ten healthcare facilities, including two vSNFs, two LTACHs, and six ACHs. Three distinct KPC genes were identified among the clusters: KPC-2, KPC-3, and KPC-4. Genomes assembled from long reads identified identical or similar KPC-gene-containing plasmids across different species or sequence types, suggesting horizontal gene transfer of KPC. Conclusions: Multiple KPC-CRE strains co-circulated and were associated with patient movement between acute and post-acute care settings. WGS allowed us to identify multi-facility clusters. Time and location of carbapenemase acquisition were challenging to determine for genetically related isolates when epidemiologic links could not be determined from medical records. This could be due to undetected cases. We notified healthcare facilities of their shared transmission risk and advocated for improved attention to infection control, carbapenemase screening, and communication upon patient transfer.

Identification, Genetic Characterization, and Pathogenicity of Three Feline Herpesvirus Type 1 Isolates from Domestic Cats in China.

(1) Background: Feline herpesvirus (FHV-1) is a significant pathogen in cats, causing respiratory and ocular diseases with consequential economic and welfare implications. (2) Methods: This study aimed to isolate and characterize FHV-1 from clinical samples and assess its pathogenicity. We collected 35 nasal and ocular swabs from cats showing symptoms of upper respiratory tract infection and FHV positivity detected by polymerase chain reaction (PCR). Viral isolation was carried out using feline kidney (F81) cell lines. Confirmation of FHV-1 presence was achieved through PCR detection, sequencing, electron microscopy, and indirect immunofluorescence assay. The isolated strains were further characterized by evaluating their titers, growth kinetics, and genetic characteristics. Additionally, we assessed the pathogenicity of the isolated strains in a feline model, monitoring clinical signs, viral shedding, and histopathological changes. (3) Results: Three strains of FHV-1 were isolated, purified, and identified. The isolated FHV-1 strains exhibited high homology among themselves and with domestic isolates and FHV-1 viruses from around the world. However, they showed varying degrees of virulence, with one strain (FHV-A1) causing severe clinical signs and histopathological lesions. (4) Conclusion: This study advances our understanding of the genetic and pathogenic characteristics of FHV-1 in China. These findings underscore FHV-A1 isolate as a potentially ideal candidate for establishing a challenge model and as a potential vaccine strain for vaccine development.

Screening and Mechanism Study of Three Antagonistic Drugs, Oxysophoridine, Rutin, and Phellodendrine, against Zearalenone-Induced Reproductive Toxicity in Ovine Oocytes.

Zearalenone (ZEN) is a common fungal toxin with reproductive toxicity in various grains. It poses a serious threat to ovine and other animal husbandry industries, as well as human reproductive health. Therefore, investigating the mechanism of toxicity and screening antagonistic drugs are of great importance. In this study, based on the natural compound library and previous Smart-seq2 results, antioxidant and anti-apoptotic drugs were selected for screening as potential antagonistic drugs. Three natural plant compounds (oxysophoridine, rutin, and phellodendrine) were screened for their ability to counteract the reproductive toxicity of ZEN on ovine oocytes in vitro using quantitative polymerase chain reaction (qPCR) and reactive oxygen species detection. The compounds exhibited varying pharmacological effects, notably impacting the expression of antioxidant (GPX, SOD1, and SOD2), autophagic (ATG3, ULK2, and LC3), and apoptotic (CAS3, CAS8, and CAS9) genes. Oxysophoridine promoted GPX, SOD1, ULK2, and LC3 expression, while inhibiting CAS3 and CAS8 expression. Rutin promoted SOD2 and ATG3 expression, and inhibited CAS3 and CAS9 expression. Phellodendrine promoted SOD2 and ATG3 expression, and inhibited CAS9 expression. However, all compounds promoted the expression of genes related to cell cycle, spindle checkpoint, oocyte maturation, and cumulus expansion factors. Although the three drugs had different regulatory mechanisms in enhancing antioxidant capacity, enhancing autophagy, and inhibiting cell apoptosis, they all maintained a stable intracellular environment and a normal cell cycle, promoted oocyte maturation and release of cumulus expansion factors, and, ultimately, counteracted ZEN reproductive toxicity to promote the in vitro maturation of ovine oocytes. This study identified three drugs that antagonize the reproductive toxicity of ZEN on ovine oocytes, and compared their mechanisms of action, providing data support and a theoretical basis for their subsequent application in the ovine breeding industry, reducing losses in the breeding industry, screening of ZEN reproductive toxicity antagonists and various toxin antagonists, improving the study of ZEN reproductive toxicity mechanisms, and even protection of human reproductive health.

Evaluation of diagnostic techniques for early detection of heartworm in experimentally infected dogs: identification of Dirofilaria immitis-derived microRNA in the initial 28 weeks post-inoculation

BackgroundDirofilaria immitis, commonly known as heartworm (HW), is a parasitic nematode transmitted by various mosquito species, leading to heartworm disease (HWD) in dogs. Diagnosis of HW typically involves antigen or microfilariae detection, or visualization of adult worms through imaging or post mortem examination. Polymerase chain reaction (PCR) and micro RNA (miRNA) detection have been explored for HW diagnosis.MethodsThree dogs, previously experimentally infected with HW, underwent blood sampling every 4 weeks for 7 months. Samples were assessed for antigen presence after heat treatment, PCR amplification, and microfilaria examination using Giemsa-stained thick smears. Additionally, whole blood aliquots underwent miRNA deep sequencing and bioinformatic analysis.ResultsHeartworm antigen was detectable after heat treatment at 20 weeks post-inoculation and via PCR at 24 weeks, with microfilariae observed in peripheral blood smears at 28 weeks. However, deep miRNA sequencing revealed that the miRNA candidate sequences are not consistently expressed before 28 weeks of infection.ConclusionsWhile ancillary molecular methods such as PCR and miRNA sequencing may be less effective than antigen detection for detecting immature larval stages in an early stage of infection, our experimental findings demonstrate that circulating miRNAs can still be detected in 28 weeks post-infection.Graphical

Metabolic response and clade variation in Accumulibacter under phosphorus deprivation stress

Two enhanced biological phosphorus removal systems (R1 and R2) fed with different carbon sources (acetic acid and propionic acid) were used to investigate the metabolic response of nitrite-type denitrifying phosphorus removal functional bacteria Accumulibacter to different phosphorus concentrations and the changes of its clade community structure. The results indicated that the systems almost lost the ability to release phosphorus after 15 d phosphorus deprivation, the contents of poly-P in the sludge of R1 and R2 decreased from 0.63 to 0.02 mgP/mgVSS and from 1.23 to 0.05 mgP/mgVSS, respectively. According to the analysis of stoichiometric parameters, the functional bacteria in both systems performed glycogen accumulating organism metabolism to survive under phosphorus-poor condition. Besides, the two systems exhibited a stronger EBPR ability even after 42 d phosphorus deprivation, and the maximum anoxic phosphorus uptake rate was 1.92 times and 2.29 times of those under phosphorus-rich conditions. Real-time quantitative Polymerase Chain Reaction detection indicated that the proportion of Accumulibacter in the two systems decreased from 16.45 % to 8.78 % and from 31.00 % to 8.43 %, respectively, as phosphorus was deprived. Clade IIC maintained its dominance in both systems, while clade IID was gradually washed out from propionic acid system, suggesting that clade IIC had a more flexible metabolic response to phosphorus deprivation stress.

Polymerase Chain Reaction Cleaner with Antibacterial Effect and Faster Elimination of Nucleic Acid Aerosol Pollution

With advancement of nucleic acid detection technology, most universities, biological testing companies, and hospitals have Polymerase Chain Reaction (PCR) laboratories. PCR detection technology is the core technology for nucleic acid detection. When nucleic acid detection is performed in a PCR laboratory, nucleic acid aerosol samples are often dispersed to the environment in the form of aerosols. At this time, there will be some nucleic acid contamination in the PCR laboratory, resulting in false positive samples. The purpose of this paper is to propose a new type of nucleic acid pollution scavenger called PCR Cleaner. Firstly, the best ratio of PCR Cleaner was obtained by a control experiment, and then the antibacterial test for the PCR Cleaner was carried by comparing the nucleic acid pollution removal efficiency of different ratios of PCR Cleaner and common nucleic acid pollution scavenger on the surface and in the air. Experiment results showed that, the removal efficiency of PCR Cleaner on the surface of nucleic acid was much higher than that of alcohol and aqueous solution. Its effect was good enough when compared to the two commonly used nucleic acid pollution scavengers (DNA/RNA-ExitusPlus and PCR clean). The antibacterial and bacteriostatic PCR Cleaner can significantly inhibit the growth of high concentration of E. coli, and can also completely inhibit the low concentration of E. coli.