PCR Method Research Articles

Preliminary study of molecular identification of Mycobacterium bovis from cow’s milk in Lorestan (Iran)

Bovine tuberculosis is one of the most important common infectious diseases between humans and livestock. Cow’s milk can be investigated as one of the transmission reservoirs of the disease. Our study was conducted to investigate the presence of Mycobacterium bovis (M. bovis) DNA in cow’s milk from different regions of Lorestan province using Touch-down PCR (TD-PCR) method. So, 100 milk samples from industrial and traditional cattle farms were collected and evaluated according to the animal breed, the average age of the animal and the region where the animal was kept. Seven (26.9%) out of the 26 cow’s milk samples contaminated with Mycobacterium spp., were diagnosed as M. bovis positive. The cattle with an average age of more than 5 years were most infected with Mycobacterium. Also, the crossbred cattle with an average age of 3 to 5 years, which were kept and raised in tropical areas, showed the highest rate of M. bovis infection. Based on our knowledge, this is the first study regarding the presence of Mycobacterium in cow’s milk in Iran.

Development of a Rapid Diagnostic Method for Sporotrichosis

Introduction: Sporotrichosis, a prevalent deep fungal infection in clinical settings, currently lacks rapid and accurate diagnostic methodologies. This study explores a novel rapid diagnosis method for sporotrichosis by combining FTA cards and nested PCR with fungal fluorescence staining. Methods: The study involved skin lesion tissues from 26 patients diagnosed with sporotrichosis (Experimental Group). The Positive Control Group consisted of fungal suspensions from clinical strains of Sporothrix, while the Negative Control Group included fungal solutions of other fungi, namely Trichophyton rubrum, Trichophyton mentagrophyte, and Candida albicans. DNA was extracted from the slurry of skin lesions in the Experimental Group and from fungal suspensions in the Control Group using FTA cards, followed by nested PCR amplification. Subsequently, nested PCR amplification was performed. Histopathological examinations, including HE and fluorescence staining, were conducted on paraffin sections prepared from skin lesion tissues in the Experimental Group. Results: Among the 26 clinical skin lesion tissues in the Experimental Group, 8 cases showed a specific positive band upon nested PCR amplification, resulting in a positive rate of 30.8%. In the Control Group, the fungal solution of the clinical strain of Sporothrix showed a specific positive band upon nested PCR amplification, while all other fungi Negative Control Group tested negative. Histopathological examination revealed granulomatous inflammatory changes in most samples after HE staining. Fluorescence staining detected spores in 17 cases, resulting in a detection rate of 65.4% (17/26). Conclusion: The combination of FTA cards with nested PCR method proved to be simple and rapid but demonstrated a relatively low positive rate. Fungal fluorescence staining significantly improved the sensitivity of detecting sporotrichosis in histopathological examinations, thereby improving the speed and efficiency of diagnosis.

A rapid and visual detection assay for Senecavirus A based on recombinase-aided amplification and lateral flow dipstick.

Senecavirus A (SVA) is a newly pathogenic virus correlated with the acute death of piglets and vesicular lesions in pigs. The further prevalence of SVA will cause considerable economic damage to the global pig farming industry. Therefore, rapid and accurate diagnostic tools for SVA are crucial for preventing and controlling the disease. We designed multiple primer pairs targeting the most conserved region of the SVA 3D gene and selected those with the highest specificity. Nfo-probes were subsequently developed based on the highest specificity primer pairs. Subsequently, the recombinase-assisted amplification (RAA) reaction was completed, and the reaction temperature and duration were optimized. The RAA amplicons were detected using a lateral flow device (LFD). Finally, a rapid and intuitive RAA-LFD assay was established against SVA. The SVA RAA-LFD assay can be performed under reaction conditions of 35°C within 17 minutes, with results observable to the naked eye. We then evaluated the performance of this method. It exhibited high specificity and no cross-reaction with the other common swine pathogens. The lowest detectable limits of this method for the plasmid of pMD18-SVA-3D, DNA amplification product, and viral were 3.86×101 copies/µL, 8.76×10-7 ng/µL, and 1×100.25 TCID50/mL, respectively. A total of 44 clinical samples were then tested using the RAA-LFD, PCR, and RT-qPCR methods. The results demonstrated a consistent detection rate between the RAA-LFD and RT-qPCR assays. The SVA RAA-LFD assay developed in our study exhibits excellent specificity, sensitivity, and time-saving attributes, making it ideally suited for utilization in lack-instrumented laboratory and field settings.

Expression of AQP8 in Serum of Patients With Meniere's Disease and Its Value in Evaluating the Degree of Hydrolabyrinth and Predicting Prognosis.

This study aims to explore the role of serum aquaporin 8 (AQP8) expression in evaluating the degree of hydrolabyrinth and predicting prognosis in patients with Meniere's disease. One hundred and five patients diagnosed with Meniere's disease in our hospital were enrolled in the Meniere's disease group. Another 102 healthy subjects were enrolled as the control group. The expression of serum AQP8 mRNA was determined by the quantitative real-time PCR (qRT-PCR) method. Receiver operating characteristic (ROC) curve analysis was carried out to analyse the predictive value of serum AQP8 mRNA expression for poor prognosis in Meniere's disease patients. Multivariate logistic regression was used to analyse the influencing factors of poor prognosis in patients with Meniere's disease. The expression level of serum AQP8 mRNA in the Meniere's disease group was significantly higher than that in the control group (p < 0.05). In the severe hydrops group, serum AQP8 mRNA expression levels were higher than in the mild hydrops group and the no endolymphatic hydrops group. Additionally, the mild hydrops group had higher serum AQP8 mRNA levels than the no endolymphatic hydrops group (p < 0.05). The disease course, proportion of severe hydrops and serum AQP8 mRNA expression were all higher in the poor prognosis group compared to the good prognosis group (p < 0.05). The area under the curve (AUC) for serum AQP8 mRNA in predicting poor prognosis in Meniere's disease patients was 0.812 (95%CI: 0.702-0.922). AQP8 mRNA is associated with the degree of hydrolabyrinth in patients with Meniere's disease and plays an important role in predicting prognosis.

Efficacy of natural and synthetic inhibitors in the elimination of viruses in potato (Solanum tuberosum L.)

Background. Developing new effective plant protection methods against viruses is a vital task for seed potato production. The use of virus inhibitors (mainly synthetic ones) is the most common method in potato virus control. Products of natural origin might be a way to reduce the dependence on synthetic inhibitors. Among the former, extracts from seaweeds have high potential, producing a low or no negative impact on the environment or human health. Materials and methods. The materials of the research included potato cvs. ‘Poseidon’ and ‘Orion’ developed at the Federal Scientific Center of Agricultural Biotechnology of the Far East named after A.K. Chaika, the commercial antiviral product Ribavirin, and the sulfated polysaccharide – carrageenan – obtained from red algae at the G.B. Elyakov Pacific Institute of Bioorganic Chemistry. A highly sensitive PCR method was employed to detect viral infections in plant samples. Results. The efficacy of chemotherapy with Ribavirin (0.03%) was established at 79.8% against PVY, 77.0% against PLRV, 80.3% against PVM, and 84.5% against PVS. The most successfully eliminated viruses were PVY, PVM, and PVS. Carrageenan as an antiviral substance eliminated potato viruses at the following rates: PLRV in 74.7% of the explants, PVM in 70.2%, PVS in 69.2%, and PVY in 16.9%. Conclusion. Analyzing the antiviral activity of natural and synthetic virus inhibitors in the case study of carrageenan and Ribavirin demonstrated their high efficacy against potato viruses. Natural polysaccharides – carrageenans – were observed to have a significant antiviral effect, so their use in agricultural biotechnology might be promising for new experiments. Our approach successfully eliminated viruses in two new promising potato cultivars, ‘Poseidon’ and ‘Orion’, which were included in the system of virus-free seed production. These cultivars were submitted for patenting and official testing under the State Variety Trials.

Development and optimization of immunomagnetic bead separation-convective PCR (IMBS-CPCR) for on-site detection of four common Vibrio species in aquaculture

Foodborne infectious diseases, particularly those caused by pathogenic Vibrio species in aquaculture, are a significant concern in the field of seafood safety. They not only hinder the economic development of the industry but also pose a major threat to public health. Traditional detection methods are often too slow, insensitive, or impractical for portable use, highlighting the urgent need for a sensitive, on-site detection method for Vibrio that prioritizes convenience and speed. This study developed a visual IMBS-CPCR method for the detection of four common pathogenic Vibrio species: Vibrio alginolyticus, Vibrio anguillarum, Vibrio fluvialis, and Vibrio harveyi. The method achieved high capture rates for target bacteria (82.6%–83.3%) and low capture rates for non-target bacteria (below 11%), demonstrating good sensitivity by detecting bacteria at concentrations as low as 10 CFU/mL. Optimal amplification conditions were determined for each species, with specificity tests confirming that only target bacteria produced amplification bands. Sensitivity tests revealed detection limits of 101 CFU/mL for V. alginolyticus, V. anguillarum, and V. fluvialis, and 102 CFU/mL for V. harveyi. The combined techniques improved detection sensitivity in simulated fish samples by 10–100 fold compared to direct CPCR or PCR methods.

Analysis of the incidence of low viral load/low-level viremia and its associated factors in patients with HBV-related primary liver cancer

Objective: To retrospectively analyze the viral levels and associated factors in patients with hepatitis B virus (HBV)-related primary liver cancer (PHC) in real-world settings and further explore the correlation between low viral load (LVL) and/or low-level viremia (LLV) and PHC. Methods: Five hundred twenty-four cases with HBV-related PHC with complete pathologically confirmed data from 2013 to 2020 were included. Percentages (%) were used to express their viral load, antiviral (oral) status, patient compliance, presence or absence of cirrhosis, family history of liver cancer, and others. LVL definition: After excluding detection errors by PCR method, serum HBV DNA <50-2 000 IU/ml, and those who had received antiviral drug treatment were called LLV. Antiviral treatment (AVT) rate definition: As of the confirmed diagnosis of PHC, those who had been regularly treated using oral antiviral drugs for six months or more (≥6 months). Results: General situation: The ratio of male to female enrolled patients was 15.90:1 (493/31). Patients aged >40 years accounted for 91.98% (482 cases). Hepatitis B surface antigen (HBsAg) positivity condition: The ratio of HBsAg-positive to HBsAg-negative/anti-HBc-positive (HBsAg-/anti-HBc+) PHC patients was 5.89:1 (448/76). Among the 76 HBsAg-/anti-HBc+patients, the ratio of HBsAg-/anti-HBs+/anti-HBc+ to HBsAg-/anti-HBs-/anti-HBc+ patients was 0.95:1 (37/39). Hepatitis B e antigen (HBeA) positivity condition: The ratio of HBeAg-negative to HBeAg-positive cases was 3.23:1 (400/124). HBV DNA level condition: The medical history records of 75.00% of patients (393/524) had traceable HBV DNA test reports. Out of 393 patients, 45.04% (177/393) accounted for undetectable HBV DNA, 13.49% (53/393) accounted for LVL, 41.48% (163/393) accounted for HBV DNA exceeding the upper limit of LVL, and 4.07% (16/393) accounted for LLV. Among HBsAg-positive and HBsAg-/anti-HBc+ patients, the HBV DNA positivity rates were 59.12% (214/362) and 6.45% (2/31), respectively. Antiviral treatment condition: Among the 448 HBsAg-positive PHC patients, the total AVT rate was 18.08% (81/448), of which seven patients did not have their HBV DNA results traced back. Among them, the AVT rate of 148 patients with HBV DNA lower than the lowest detection value was 41.22% (61/148); the AVT rate of 53 patients with LVL was 18.87% (10/53); and the AVT rate of 163 patients with HBV DNA≥LVL upper limit was 1.84% (3/163). Liver cirrhosis and family history condition: 348 patients (66.41%) had liver cirrhosis. 67 patients (12.79%) had a distinct family history of HBV-related liver cirrhosis and liver cancer. Alpha-fetoprotein (AFP) condition: 514 patients underwent AFP testing, with 30.93% of the patients had normal AFP levels, and 69.07% had AFP levels exceeding the upper limit of normal values (355/514). Among them, 10 μg/L<AFP<400 μg/L and>400 μg/L accounted for 34.44% (177/514) and 34.63% (178/514), respectively. Tissue typing condition: 99.05% (519/524) were hepatocellular carcinoma, and well-differentiated and moderately differentiated cases accounted for only 8.59%. Conclusions: In the real world, comprehensive, timely screening, standardized, and effective antiviral treatment have not yet been achieved for patients with chronic hepatitis B, resulting in the persistence of HBsAg and/or HBV DNA positivity (especially LVL and/or LLV). Although LVL does not account for a high proportion among all HBV-related PHC populations, the vast majority of LVL populations have not received any antiviral treatment. In addition, some PHC populations with HBV DNA>2 000 IU/ml have not received standard antiviral treatment before the onset of the disease, which should be paid attention to. At the same time, HBsAg-/anti-HBc+ populations may have latent HBV infection and may even progress to PHC. Notably, PHC may still occur after HBeAg seronegative conversion.

Circular DNA enhanced amplification-free CRISPR/Cas12a assays for end-user friendly ultra-sensitive Porphyromonas gingivalis diagnosis

Periodontitis not only leads to tooth loss but is also associated with various systemic symptoms. Porphyromonas gingivalis (Pg) is the microorganism most closely linked to periodontitis. A rapid and accurate Pg detection method holds significant potential health benefits for patients. While several nucleic acid amplification-based diagnostic methods have been developed, there is a current lack of rapid diagnostic tools for Pg, particularly at chair-side level. Here, two detection methods for the Pg 16S gene based on the CRISPR/Cas12a system have been developed. To achieve ultra-high sensitivity in the developed CRISPR/Cas12a assays without pre-amplification, we designed a circular DNA molecule (termed as Cir-amplifier) which amplifies the signal output of the Cas12a reactions in a cascade response manner. The Cir-amplifier enhanced Fluorescence-Cas12a reaction achieved a minimum detectable limit of 0.39 CFU of Pg within 80-minute under room-temperature. In addition, the Cir-amplifier enhanced Lateral Flow Detection (LFD)-Cas12a reaction has demonstrated the ability to detect a minimum of 3.9 CFU of Pg in 90 min, with results observable by the naked eye. The potential of the two methods for Pg detection in clinical samples has been demonstrated, showing 100 % sensitivity compared to the traditional real-time PCR method. In summary, we have established two efficient detection methods for Pg that eliminate the need for pre-amplification, hence no amplicon contaminations, making them promising candidates for chair-side Pg diagnosis. Furthermore, the Cir-amplifier has been demonstrated to be adaptable to CRISPR/Cas systems producing various signal formats. The Cir-amplifier is expected to become a universal CRISPR/Cas enhancer.

Molecular Identification of Genes Resistant to Antibiotics in Staphylococcus aureus Isolated from Sub-clinical Animals Affected by Mastitis

Background and Aim: Mastitis is a prevalent and costly disease that significantly impacts the dairy industry, affecting both sheep's health and milk quality. In order to determine the bacterial causes of subclinical mastitis in Iraq and its susceptibility to antibiotics, the study aims to molecularly detect resistant Staphylococcus aureus isolated from sheep infected with mastitis. Methods: Molecular assay and phylogenetic study to detect Staph aureus isolates by using 16 Sr RNA and resistance virulence genes (aac-aph, tetk) by the conventional method of PCR. Two hundred samples were collected from the subclinical mastitis of infected ewes, Samples were reserved on an icebox and transported to the laboratories. Milk samples were cultured on Blood Agar and Mannitol Salt Agar (7.5%) plates. The culture plates were then incubated at 37°C for 24 hours. Results: The PCR assay revealed amplification of the 16S rRNA gene in all 20 isolates, amplification of the aac-aph gene in 19 isolates, and the tetK gene in all 20 isolates. The PCR products of 20 positive samples for (16 Sr RNA) target genes were sequenced, evaluated, and dropped on the Genbank-NCBI under the accession number, which became a reference to Iraq and the world. According to the current study, Staphylococcus aureus is commonly found in milk. To combat drug resistance, antimicrobial drug use should be normalized, and antimicrobial resistance surveillance should be conducted regularly. Conclusion: PCR-product of 8 positive samples for 16sr RNA target gene were sequenced, analyzed, and deposited on the Genbank-NCBI under the accession number and became a reference to Iraq and the Middle East and the world.

Molecular Identification of Genes Resistant to Antibiotics in Staphylococcus aureus Isolated from Sub-clinical Animals Affected by Mastitis

Background and Aim: Mastitis is a prevalent and costly disease that significantly impacts the dairy industry, affecting both sheep's health and milk quality. In order to determine the bacterial causes of subclinical mastitis in Iraq and its susceptibility to antibiotics, the study aims to molecularly detect resistant Staphylococcus aureus isolated from sheep infected with mastitis. Methods: Molecular assay and phylogenetic study to detect Staph aureus isolates by using 16 Sr RNA and resistance virulence genes (aac-aph, tetk) by the conventional method of PCR. Two hundred samples were collected from the subclinical mastitis of infected ewes, Samples were reserved on an icebox and transported to the laboratories. Milk samples were cultured on Blood Agar and Mannitol Salt Agar (7.5%) plates. The culture plates were then incubated at 37°C for 24 hours. Results: The PCR assay revealed amplification of the 16S rRNA gene in all 20 isolates, amplification of the aac-aph gene in 19 isolates, and the tetK gene in all 20 isolates. The PCR products of 20 positive samples for (16 Sr RNA) target genes were sequenced, evaluated, and dropped on the Genbank-NCBI under the accession number, which became a reference to Iraq and the world. According to the current study, Staphylococcus aureus is commonly found in milk. To combat drug resistance, antimicrobial drug use should be normalized, and antimicrobial resistance surveillance should be conducted regularly. Conclusion: PCR-product of 8 positive samples for 16sr RNA target gene were sequenced, analyzed, and deposited on the Genbank-NCBI under the accession number and became a reference to Iraq and the Middle East and the world.

ABCG2 Gene Expression in Non-Small Cell Lung Cancer.

Background/Objectives: ATP-binding cassette subfamily G member 2 [ABCG2/breast cancer resistance protein (BCRP)] contributes to mechanisms of multidrug resistance (MDR) and is a marker of side population (SP) cells in human cancers. The primary objective of this study was to investigate the impact of ABCG2 gene expression on the non-small cell lung cancer (NSCLC) development, course of cancer disease, and patient prognosis using publicly available data. Obtained results were supplemented with assessment of ABCG2 expression in blood of NSCLC patients. Methods: The dataset of lung cancer was analyzed utilizing the TIMER 2.0, UALCAN, TNMplot, MEXPRESS, cBioPortal, MethSurv, KM Plotter, STRING, and ShinyGO 0.80 databases. Blood samples from 50 patients were assessed using the real-time PCR method. Results: The ABCG2 gene was expressed at a low level in NSCLC, and did not correlate with clinical aggressiveness of lung cancer. Higher ABCG2 expression improved overall survival, but only in LUAD. In addition, CpG sites located on the CpG island affecting the NSCLC patient's prognosis were indicated. In the case of our own laboratory results, the study did not reveal any changes in the ABCG2 expression levels in blood collected from patients at different time points during the diagnostic-therapeutic procedure. In the in silico analysis, most ABCG2 protein interactors were associated with the development of drug resistance. Conclusions: ABCG2 appears to have a particularly significant impact on the survival of patients with lung cancer and on the effect of immunotherapy related to immune cell infiltration. Presented findings may support personalized medicine strategies based on bioinformatics findings.

Molecular Typing of Somatic Coliphage Groups and Their Occurrence and Survival in Sewage

A conventional, group-specific PCR method was developed to identify each of the four previously defined major taxa (Myoviridae, Siphoviridae, Podoviridae and Microviridae) of somatic coliphages and used to classify isolates from sewage. Somatic coliphage infectivity detection, occurrence and survival in primary human sewage effluent was observed over time to further understand the presence and behavior of the groups of somatic coliphages at two environmental temperatures (4 and 25 °C). Over time, the taxonomic composition of the somatic coliphage population in sewage changed, with the Microviridae family becoming the most prevalent family in the sewage population after several weeks. Based on their persistence and prevalence in environmental waters, phages belonging to the Microviridae family provide supporting information on sewage contamination and possibly of human enteric viruses in sewage-contaminated water.

Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds

BackgroundMutton quality is closely related to genetic variants and gene expression alterations during growth and development, resulting in differences in nutritional values, flavor, and odor.ResultsWe first evaluated and compared the composition of crude protein, crude fat, cholesterol, amino acid (AA), and fatty acid (FA) in the longissimus dorsi muscle of Guizhou black goats (GZB, n = 5) and Yunshang black goats (YBG, n = 6). The contents of cholesterol and FA related to odor in GZB were significantly lower than that in YBG, while the concentrations of umami amino acids and intramuscular fat were significantly higher in GZB. Furthermore, structural variants (SVs) in the genomes of GZB (n = 30) and YBG (n = 11) were explored. It was found that some regions in Chr 10/12/18 were densely involved with a large number of SVs in the genomes of GZB and YBG. By setting FST ≥ 0.25, we got 837 stratified SVs, of which 25 SVs (involved in 12 genes, e.g., CORO1A, CLIC6, PCSK2, and TMEM9) were limited in GZB. Functional enrichment analysis of 14 protein-coding genes (e.g., ENPEP, LIPC, ABCA5, and SLC6A15) revealed multiple terms and pathways related with metabolisms of AA, FA, and cholesterol. The SVs (n = 10) obtained by the whole genome resequencing were confirmed in percentages of 36.67 to 86.67% (n = 96) by PCR method. The SVa and SVd polymorphisms indicated a moderate negative correlation with HMGCS1 activity (n = 17).ConclusionThis study is the first to comprehensively reveal potential SVs related to mutton nutritional values, flavor, and odor based on genomic compare between two black goat breeds with closely genetic relationship. The SVs generated in this study provide a data resource for deeper studies to understand the genomic characteristics and possible evolutionary outcomes with better nutritional values, flavor and extremely light odor.

Evaluation of the relationships between physico-chemical parameters and the abundance of Vibrio spp. in blue crabs (Callinectes sapidus) and seawater from the Maryland Coastal Bays.

Fluctuations in water quality characteristics influence the productivity of blue crabs (Callinectes sapidus), and the risk of human exposure to pathogenic Vibrio species. Thus, this study assessed the prevalence of total and pathogenic/clinical markers of Vibrio parahaemolyticus and Vibrio vulnificus in blue crabs and seawater from the Maryland Coastal Bays (MCBs) and the correlation between Vibrio levels and physicochemical parameters. Three to five crabs and 1 L of seawater were collected monthly for 3 years (May 2018 to December 2020) from six sites within the MCBs. Hemolymph and crab tissue were extracted and pooled for each site. Extracted hemolymph, crab tissue, and seawater were analyzed for V. parahaemolyticus and V. vulnificus using the Most Probable Number (MPN) and real-time PCR methods. A one-way Analysis of Variance (ANOVA), correlations, and linear models were used to analyze the data. Akaike Information Criterion (AICc) was evaluated to determine the model that provides the best fit to the data relating to Vibrio concentrations and environmental factors. Results suggested that environmental factors could influence the growth of Vibrio spp. Both V. parahaemolyticus and V. vulnificus were more prevalent during the warmer months than colder months. Vibrio was more prevalent in crab samples compared to seawater. Vibrio vulnificus concentrations in seawater and hemolymph were positively correlated with temperature (p = 0.0143 seawater) and pH (p = 0.006 hemolymph). A negative correlation was observed between the concentration of V. vulnificus in whole crab (tissue) and dissolved oxygen level (p = 0.0256). The concentration of V. parahaemolyticus in seawater was positively correlated with temperature (p = 0.009) and negatively correlated with dissolved oxygen (p = 0.012). These results provide current information on the spatial and temporal distributions of Vibrio spp. in the MCBs that are useful for implementing more efficient processing and handling procedures of seafood products.

Zoonotic Pathogens Isolated from an Introduced Population of Red Swamp Crayfish (Procambarus clarkii) in Tenerife (Canary Islands, Spain)

The red swamp crayfish (Procambarus clarkii) is a widely distributed invasive species that is listed in the Delivering Alien Invasive Species Inventory for Europe. Native to North America, it has been introduced to numerous regions, such as the Canary Islands, Spain. Previous studies have confirmed the role of this crayfish in the maintenance of several foodborne pathogenic bacteria. Therefore, the aim of this study was to analyze the main zoonotic bacterial and parasitic pathogens present in a P. clarkii population introduced to the island of Tenerife, Canary Islands, and to assess the potential risk to public health and native fauna. A total of 22 crayfish from Tenerife were analyzed using Biofire FilmArray Gastrointestinal Panels and culture–PCR methods. The results show the presence of Plesiomonas shigelloides, Shigella/enteroinvasive Escherichia coli, enteropathogenic Escherichia coli, Salmonella ser. Enteritidis, Salmonella ser. Typhimurium, and Salmonella ser. Typhi. These results demonstrate the presence of a variety of pathogenic bacteria in the red swamp crayfish in Tenerife that represent a significant concern in terms of public health and conservation. Implementing educational campaigns to inform the community about the risks associated with handling and consuming contaminated crayfish, as well as initiatives for the restoration of the contaminated ecosystem, are necessary to prevent the transmission of the foodborne pathogens.

Development and application of a quadruplex real-time PCR method for Torque teno sus virus 1, Porcine circovirus type 2, pseudorabies virus, and porcine parvovirus.

In clinical diagnosis of porcine diseases, co-infection with multiple viruses often leads to similar clinical symptoms. Postweaning multisystemic wasting syndrome (PMWS) can be caused by infections with TTSuV or PCV2, while PCV2, PRV, and PPV can cause respiratory and reproductive disorders in pigs. The overlapping clinical and pathological features of these infections necessitate the development of a rapid and specific method for differentiating and detecting these four DNA viruses. In this study, four pairs of primers and TaqMan probes were designed targeting the conserved sequence of TTSuV, the Rep gene of PCV2, the gE gene of PRV, and the VP2 gene of PPV. After optimizing reaction conditions, including annealing temperature, primer concentration, and probe concentration, a quadruplex real-time PCR method was developed. This method can specifically detect TTSuV1, PCV2, PRV, and PPV simultaneously, with no cross-reactivity with ASFV, CSFV, PRRSV, PEDV, PSV, and TGEV. The minimum detection limit for each virus was 10 copies/μl, and the inter-assay and intra-assay coefficients of variation ranged from 0.33% to 1.43%. Subsequently, 150 clinical samples were tested to evaluate the practical applicability of this method. The positive rates for TTSuV1, PCV2, PRV, and PPV were 8.6% (13/150), 10.67% (16/150), 14% (21/150), and 11.33% (17/150), respectively. The results indicate that the established quadruplex real-time PCR method can assist in the accurate and rapid diagnosis of TTSuV1, PCV2, PRV, and PPV in clinical settings, providing robust support for the prevention and control of these infections.

Prevalence and Genotype Distribution of HPV in Gynecological Patients: A Cross-Sectional Study

Human papillomavirus (HPV) is a prevalent sexually transmitted virus that can lead to genital warts or cancer. Over 100 HPV strains have been discovered, some classified as high-risk and others as low-risk. This study aimed to analyze the prevalence of HPV genotypes in patients with gynecological problems and to compare the frequency of low-risk and high-risk HPV infections. A cross-sectional study was performed. Five hundred patients were recruited who attended a gynecological clinic due to various reasons such as genital warts, itching, bleeding, or even asymptomatic cases discovered during routine visits in the period extending from January 2nd, 2017 to December 31st, 2022. Genotyping was performed using the Hybrispot technique, targeting 27 different HPV genotypes. DNA flow technology, a rapid and sensitive method, was utilized for the analysis. Out of the 500 patients, 109 tested positive for HPV, indicating 21.8% incidence among those seeking gynecological care. Among the HPV-positive patients, 59% had low-risk HPV, and 41% had high-risk HPV. The most common low-risk genotypes were HPV6 and HPV11, while the most common high-risk genotypes were HPV53, HPV58, HPV18, and HPV16. Several infrequent HPV genotypes were missed by the multiplex real-time PCR method. The study revealed a higher frequency of low-risk HPV compared to high-risk HPV, with no significant difference between the two groups.

Discordant Microsatellite Instability Status in Metachronous Primary Rectal Cancer Detected During IdyllaTM Microsatellite Instability Test Validation: A Case Report

Abstract Introduction/Objective Defects in DNA mismatch repair (MMR) can be identified by immunohistochemistry (IHC) MMR, Microsatellite Instability (MSI) status testing by PCR or by MSI testing by NGS. Discrepancies may occur between the different test methods. We describe a case of a discrepancy discovered during validation of an in-house IdyllaTM MSI test (PCR method), in which repeat testing by the external reference lab led to a definitive deficient MMR/MSI-High (MSI-H) status. Methods/Case Report A 67-year-old male presented with a new rectal mass on a follow-up colonoscopy. His past surgical history included a colorectal anastomosis secondary to a low anterior resection for pT3N0 upper rectal cancer ten years ago. He had a strong family history of colorectal cancer with his father, 3 brothers, 3 paternal uncles and 2 cousins affected. Colonoscopy revealed an adenocarcinoma 3 cm distal to the anastomosis. MRI showed a plaque-like mucosal thickening along the remaining rectum below the anastomosis. He underwent a complicated redo low anterior resection. Histopathology revealed a pT1N0 invasive moderately differentiated midrectal adenocarcinoma. Test results for an external PCR-based MSI test were microsatellite stable (MSS). However, repeat testing (requested after MSI-H status was detected by the in-house IdyllaTM MSI assay) revealed a deficient MMR status (loss of expression of MSH2 and MSH6 proteins) and MSI-H by PCR analysis. These discrepant results may have been due to low tumor cellularity and tumor heterogeneity (ie, heterogeneous pattern of MSH2/MSH6 loss on IHC). Results (if a Case Study enter NA) NA Conclusion Discrepancies in deficient MMR/MSI status between and within different test methods may be attributable to intratumoral heterogeneity and low tumor cellularity. In discordant cases, pathologists must not hesitate to perform a repeat analysis using alternate methods, as a deficient MMR/MSI-H diagnosis has crucial diagnostic, prognostic and predictive implications.

Antiviral Activity of Plant-Based Additives Against African Swine Fever Virus (ASFV) in Feed Ingredients.

African swine fever (ASF) is one of the deadliest swine diseases with haemorrhagic symptoms and a high mortality rate. Plant-derived additives are potential antiviral agents against viruses due to their environmental and user-friendly properties. This study aims to evaluate the efficacy of plant-based additives (Phyto.A04 and Phyto.B) compared to an organic acid blend (OAB) in inactivating ASF virus (ASFV) in cell culture and feed. ASFV-spiked feed was treated with individual or combined additives such as OAB, Phyto.A04 and Phyto.B. The viability of ASFV after treatment of ASFV-spiked feed with additives was then confirmed by both methods, real-time PCR and cell culture. The results of the in vitro test with cell cultures showed that all three additives (OAB, Phyto.A04 and Phyto.B) exerted a strong virucidal effect on ASFV in porcine alveolar macrophage cells. OAB at a concentration of 0.3% reduced the virus concentration from 4.48 log10 HAD50/mL after 1 day of treatment (day 1) to 3.29 log10 HAD50/mL after 3 days of treatment (day 3) and remained undetected after 7 days of treatment (day 7). In Phyto.A04 with 1%, the virus was only detectable on day 1 (3.53 log10 HAD50/mL). Phyto.B with 0.01% and 0.05% both showed good efficacy in completely inhibiting virus presence on days 3 and 7. All additives, OAB, Phyto.A04 and Phyto.B, were able to inactivate ASFV in a dose-dependent manner, as confirmed by cell culture and PCR methods. The combination of additives at different concentrations consistently improved the virucidal results.

STRAIN SELECTION AND CULTIVATION OF FOOT-AND-MOUTH DISEASE VIRUSES FOR THE DEVELOPMENT OF A TRIVALENT INACTIVATED VACCINE

Foot-and-mouth disease is a well-known transboundary animal disease and has been recognised as a priority disease by the Steering Committee of the Global Framework for the Progressive Control of Transboundary Animal Diseases in Europe. The territory of the Republic of Kazakhstan is generally free of foot-and-mouth disease, however, sporadic cases of foot-and-mouth disease occur in various regions of the country as a result of importation from unfavorable countries. Epizootic safety in the Republic of Kazakhstan is maintained by vaccinating animals in the border areas of the southern and eastern regions. Inactivated vaccines against serotypes A, O, Asia produced by the All-Russian Research Institute of Animal Health (Russia) are used for vaccination. Continuous seromonitoring is carried out to maintain the level of post-vaccination antibodies at a high level, ensuring the immunity of animals to foot-and-mouth disease. However, despite all the measures taken, sporadic outbreaks of foot-and-mouth disease cause damage to livestock farming in the Republic of Kazakhstan. The effectiveness of preventive measures using vaccination depends on the strain used in the vaccine. The closer the strain used in the vaccine is genetically to the viruses circulating in that area, the more effective the preventive measures will be and the research conducted to create the most immunogenic domestic anti-foot-and-mouth disease vaccines have scientific and practical significance. This article presents the results of the selection of foot-and-mouth disease virus strains previously circulating in the territory of the Republic of Kazakhstan and studies their cultural and biological properties. Studies of the above-mentioned strains on adaptation to a transplantable cell culture line were conducted, the stability of cultural properties was studied over 10 generations and the stability was confirmed by the PCR method. Also, based on the studies, it was found that the maximum accumulation of the virus in cell culture occurs at a multiplicity of infection of 0.01-0.1 TCID50/cell. The reproductive activity of the studied isolates was within 6.5-7.25 lg TCID50/cm3 when cultivated for 16 hours.