Nested PCR Method Research Articles

Optimizing the nested PCR method for Decapod iridescent virus 1 (DIV1) targeting ATPase gene by reselecting the inner primers

DIV1 has the characteristics of fast transmission and a broad host range. Its infection leads to a high mortality rate, posing a serious threat to the global crustacean aquaculture industry. In order to increase the accuracy of DIV1 detection and reduce the difficulty of result interpretation, this study modified the original nested PCR method targeting the DIV1 ATPase gene. The internal primers for the nested PCR were redesigned to produce a 338 bp amplification product in the second step PCR, effectively distinguishing the target band from primer dimers. The newly established nested PCR method exhibits strong specificity and high sensitivity, with a detection limit as low as 1.37 × 101 copies/reaction. The developed nested PCR assay provides new technical support for the accurate detection of DIV1 in global crustacean aquaculture.

Molecular detection of Epstein-Barr virus in paraffin-embedded tissue samples of patients suffering gastric cancer in Ahvaz, Iran: a case-control study.

Gastric cancer (GC) is the third most common cause of cancer-related mortality. Epstein-Barr virus (EBV) is associated with several human tumors. The present research was performed to investigate the prevalence of EBV-associated gastric cancer (EBVaGC) among Iranian patients. Seventy cases of gastric cancer and 30 cases of gastric ulcer, all preserved in formalin-fixed paraffin-embedded (FFPE), were examined in a case-control study conducted between 2011 and 2018. The specimens underwent analysis to detect the presence of the EBV genome using a Nested-PCR method targeting EBNA1. Subsequently, samples testing positive for the EBNA1 underwent further testing for the presence of the EBER gene using PCR. Finally, Positive samples were subjected to sequencing. Five out of 70 cases (7%) were found to be positive for EBV based on EBNA1 testing, while all EBNA1 positive samples were negative for EBER. Notably, EBV was not detected in patients with gastric ulcer. The mean age of EBV-positive gastric carcinomas pateints was 64.5 years. Within this group, 60% were male and 40% were female. A higher prevalence of EBV association was observed in diffuse-type cases, with 60% (3 out of 24) testing positive, compared to intestinal-type cases where 40% (2 out of 46) were EBV-positive. Most cases of EBVaGC belonged to grade Ⅰ. This research demonstrates a low prevalence of EBVaGC in Iran. Discrepancies in EBVaGC occurrence among countries could be attributed to epidemiological variables and dietary practices. A comprehensive studies will provide significant contributions to understanding of its etiology.

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.

Plasmodium falciparum transmission based on merozoite surface protein 1 (msp1) and 2 (msp2) gene diversity and antibody responses in Ibadan, Nigeria

BackgroundNigeria is a major contributor to the global malaria burden. The genetic diversity of malaria parasite populations as well as antibody responses of individuals in affected areas against antigens of the parasite can reveal the transmission intensity, a key information required to control the disease. This work was carried out to determine the allelic frequency of highly polymorphic Plasmodium falciparum genes and antibody responses against schizont crude antigens in an area of Ibadan, Nigeria. Materials and methodsBlood was collected from 147 individuals with symptoms suspected to be malaria. Malaria infection was determined using a rapid diagnostic test (RDT), and msp1 and msp2 were genotyped by a nested PCR method. In addition, levels of IgG directed against P. falciparum FCR3S1.2 schizont extract was measured in ELISA. ResultsApproximately 25% (36/147) were positive for a P. falciparum infection in RDT, but only 32 of the positive samples were successfully genotyped. MAD20 was the most prevalent and K1 the least prevalent of the msp1 alleles. For msp2, FC27 was more prevalent than 3D7. The mean multiplicities of infection (MOI) were 1.9 and 1.7 for msp1 and msp2, respectively. IgG levels correlated positively with age, however there was no difference in median antibody levels between RDT-positive and RDT-negative individuals. ConclusionLow MOI has before been correlated with low/intermediate transmission intensity, however, in this study, similar levels of P. falciparum-specific antibodies between infected and non-infected individuals point more towards a high level of exposure and a need for further measures to control the spread of malaria in this area.

Evaluation of ITS1 rDNA primers for the detection and identification of African trypanosomes in mammalian hosts and tsetse flies.

Although several primers targeted to the internal transcribed-spacer 1 (ITS1) of the ribosomal DNA (rDNA) have been designed to improve the detection of African trypanosomes, no study tried to compare their agreement level and ability to amplify different trypanosome species in tsetse flies and mammals in various epidemiological settings. This study was designed to fill this gap, by targeting tsetse-infested areas of Cameroon. For this, archived DNA samples reporting at-least one trypanosome species with species-specific PCR primers were reviewed. Ten sets of primers targeting different ITS1 rDNA sequences of trypanosomes were selected for assessment using single-round and nested-PCR method. Amplification rates (sensitivity) and agreement level of different ITS1 assays were compared using Cohen's-Kappa and McNemar's x2 statistic. Little agreement level (k = 0.05–0.52) were observed between different ITS1-primers PCRs detection of African trypanosome species despite significant (X2=54.3, p = 0.0001) high amplification rate 91.6 % (339/370). This sensitivity varied from quite low for T. simiae (11.9 %) and T. vivax (27.3 %) to fairly good for T. congolence (51.9 %), Trypanozoon (32.4 %) and T. theileri (40.3 %). Primers set targeting ITS1-A sequence of trypanosome species recorded the highest sensitivity (50.5 %) with fairly good agreement compared to 39.2 % for ITS1-C (k = 0.52), 32.4 % for ITS1-R (k = 0.47), 29.7 % for ITS1-N (k = 0.48) and 23.0 % for ITS1-KIN (k = 0.43) respectively. This study revealed a diversity in the sensitivity of different trypanosome species with different sets of ITS-primers enhancing the need to use the same sets of primers in different bio-ecological settings. The use of nested-PCR instead of single-round PCR enabled improvement of trypanosome infections detection in both tsetse and mammals. Among the sets of ITS1-primers tested, those designed by to amplify ITS1-A can be considered as the most appropriate for the detection of trypanosome infections in mammals and tsetse flies.

Identification of Cryptosporidium oocyst and Giardia cyst in of the samples of raw surface water of Kan River in Tehran

Background: Giardia and Cryptosporidium are considered the most important causal agents of non-bloody diarrhea, especially among primary school children, in many countries, including Iran. Many rivers are contaminated with Cryptosporidium oocyst and Giardia lamblia cysts due to domestic wastewater or farm wastewater and also the living of rodents on their margins. The present study aims to evaluate Kan River contamination with Cryptosporidium oocyst and Giardia cyst in Tehran by molecular method. Materials and Methods: Sampling was conducted from different parts of the Kan River in different seasons in 2019. Firstly, the smear has been prepared from sediments after filtering the water and collecting the sediment, stained with trichrome and acid-fast methods, and finally examined microscopically. Then, they were amplified with the Nested-PCR method by using the specific primers: the giardian gene from Giardia and the 18s rRNA gene from Cryptosporidium. Positive samples were sequenced, and a phylogenetic tree was drawn. Results: 12 suspected samples of Giardia cyst and 2 suspected samples of Cryptosporidium oocyst were detected, but only 4 samples infected with Giardia lamblia were molecularly found, and no Cryptosporidium infection was observed. In terms of genotype, the identified Giardia was 100% consistent with human isolates of genotype B. Conclusion: The presence of Giardia lamblia cysts in the water of the Kan River indicates the contamination of this river by human-contaminating parasites.

Bacterial pathogens in Ixodes ricinus collected from lizards Lacerta agilis and Zootoca vivipara in urban areas of Wrocław, SW Poland– preliminary study

The aim of this study was to determine the level of infection of Ixodes ricinus ticks with pathogens (Borrelia spp., Rickettsia spp., and Anaplasma spp.) collected from Lacerta agilis and Zootoca vivipara lizards in the urban areas of Wrocław (SW Poland). The study was carried out in July-August 2020. Lizards were caught by a noose attached to a pole or by bare hands, identified by species, and examined for the presence of ticks. Each lizard was then released at the site of capture. Ticks were removed with tweezers, identified by species using keys, and molecular tests were performed for the presence of pathogens. From 28 lizards (17 specimens of Z. vivipara and 11 specimens of L. agilis) a total of 445 ticks, including 321 larvae and 124 nymphs, identified as I. ricinus were collected. A larger number of ticks were obtained from L. agilis compared to Z. vivipara. Molecular tests for the presence of pathogens were performed on 445 specimens of I. ricinus. The nested PCR method for the fla gene allowed the detection of Borrelia spp. in 9.4% of ticks, and it was higher in ticks from L. agilis (12.0%) than from Z. vivipara (1.0%). The RFLP method showed the presence of three species, including two belonging to the B. burgdorferi s.l. complex (B. lusitaniae and B. afzelii), and B. miyamotoi. The overall level of infection of Rickettsia spp. was 19.3%, including 27.2% in ticks collected from Z. vivipara and 17.0% from L. agilis. Sequencing of randomly selected samples confirmed the presence of R. helvetica. DNA of Anaplasma spp. was detected only in one pool of larvae collected from L. agilis, and sample sequencing confirmed the presence of (A) phagocytophilum. The research results indicate the important role of lizards as hosts of ticks and their role in maintaining pathogens in the environment including urban agglomeration as evidenced by the first recorded presence of (B) miyamotoi and (A) phagocytophilum in I. ricinus ticks collected from L. agilis. However, confirmation of the role of sand lizards in maintaining (B) miyamotoi and A. phagocytophilum requires more studies and sampling of lizard tissue.

Molecular Survey of Leishmania Infection of Sand Flies in Karun County, Southwestern Iran.

Zoonotic cutaneous leishmaniasis (ZCL) is widely distributed in Iran and around the world. Also, Khuzestan Province is an endemic focus of ZCL. This study aims to investigate the natural infection of sand flies with the Leishmania parasite in Karun County. Sand flies were collected from Jangiyeh, Qaleh Chanan, Kut-e-Navaser, and Ghazavieh in the spring and summer in the year of 2019, by installing 60 sticky paper traps each time (30 traps outdoors and 30 traps indoors). Two hundred female sand flies with different abdominal conditions (empty, blood-fed, semi-gravid, and gravid) were examined for infection rate using the Nested-PCR method. In this study, seven species of sand flies including Phlebotomus papatasi, Ph. alexandri, Ph. sergenti, Ph. caucasicus, Sergentomyia tiberiadis, Se. sintoni, and Se. antennata were reported from Karun County, with a frequency of 79.64%, 16.96%, 1.07%, 0.18%, 0.36%, 1.61%, and 0.18%, respectively. Only eleven specimens of Ph. papatasi were found to be positive for Leishmania major, with an overall infection rate of 7.8%. The infection of Ph. papatasi was specifically reported in blood-fed, gravid, and semi-gravid specimens, with infection rates of 17.02%, 4.35%, and 14.29%, respectively. In this study, the infection of L. major from Ph. papatasi was reported. The results can be used in planning the control of ZCL in the study area.

Molecular detection and phylogenetic analysis of Borrelia Spp. In blood samples of cats and dogs by the nested-PCR method in West Azerbaijan Province, Iran.

The objective of this study was to investigate the presence and genetic attributes of Borrelia spp. in cats and dogs from the West Azerbaijan Province, located in the northwest of Iran. A total of 250 blood samples from cats and 300 blood samples from dogs were collected, and information regarding their age, sex, breed, ownership status, sampling time and region was recorded. The identification of positive samples was accomplished through nested-PCR and sequencing, with subsequent analysis of the gene sequences conducted using BioEdit software. The gene sequences for Borrelia spp. in this study showed 100% similarity to reference sequences in the GenBank® database. Phylogenetic trees were built using MEGA11. The outcomes indicated that among 250 blood samples from cats, 48 (19.2%) tested positive for Borrelia spp. gene, with a CI from 14.8 to 24.53% for cats. Similarly, out of 300 blood samples from dogs, 45 (15%) tested positive for the Borrelia spp. gene, with a CI from 11.4 to 19.48% for dogs.

Co-prevalence of Human Parvovirus 4 and Primate Erythroparvovirus 1 (B19) in Sickle Cell Disease and Healthy Populations

Background: Human Parvovirus 4 (P4) is a non-enveloped, single-stranded DNA virus belonging to the Tetraparvovirus genus within the Parvoviridae family. Epidemiologically, P4 exhibits similarities with its well-established family member, primate erythroparvovirus 1 (known as B19), a blood-borne virus implicated in causing aplastic crises in individuals with sickle cell disease (SCD). Despite the acknowledged association with B19, there is a dearth of prior investigations into the prevalence and clinical significance of P4 in SCD patients. Objectives: This study aims to ascertain the prevalence and outcomes of P4, along with exploring the co-prevalence of P4 with B19 in individuals with SCD. Methods: A total of 162 participants were enrolled, comprising 120 individuals with SCD and 45 healthy controls. The prevalence of P4 and B19 DNA was determined utilizing a nested-PCR method. Sequencing was performed on positive samples to validate the diagnosis, and a phylogenetic tree was constructed based on the sequencing results. Correlations in the data were analyzed using statistical methods. Results: The prevalence of P4 and B19, as well as the co-prevalence of these viruses, was significantly higher in SCD patients than in healthy individuals. Moreover, the prevalence of P4 did not exhibit a significant correlation with variables such as age, sex, aplastic crises, or specific complications associated with SCD. Conclusions: Sickle cell disease patients represent a susceptible population for P4 infection, as indicated by the heightened prevalence observed in this study.

Raising the bar: genus-specific nested PCR improves detection and lineage identification of avian haemosporidian parasites.

Avian haemosporidian parasites are useful model organisms to study the ecology and evolution of parasite-host interactions due to their global distribution and extensive biodiversity. Detection of these parasites has evolved from microscopic examination to PCR-based methods, with the mitochondrial cytochrome b gene serving as barcoding region. However, standard PCR protocols used for screening and identification purposes have limitations in detecting mixed infections and generating phylogenetically informative data due to short amplicon lengths. To address these issues, we developed a novel genus-specific nested PCR protocol targeting avian haemosporidian parasites. The protocol underwent rigorous testing utilizing a large dataset comprising blood samples from Malagasy birds of three distinct Passeriformes families. Furthermore, validation was done by examining smaller datasets in two other laboratories employing divergent master mixes and different bird species. Comparative analyses were conducted between the outcomes of the novel PCR protocol and those obtained through the widely used standard nested PCR method. The novel protocol enables specific identification of Plasmodium, Haemoproteus (Parahaemoproteus), and Leucocytozoon parasites. The analyses demonstrated comparable sensitivity to the standard nested PCR with notable improvements in detecting mixed infections. In addition, phylogenetic resolution is improved by amplification of longer fragments, leading to a better understanding of the haemosporidian biodiversity and evolution. Overall, the novel protocol represents a valuable addition to avian haemosporidian detection methodologies, facilitating comprehensive studies on parasite ecology, epidemiology, and evolution.

Development of a PCR-based assay for specific and sensitive detection of Fusarium buharicum from infected okra plant.

Fusarium wilt, caused by the fungus Fusarium buharicum, is an emerging disease of okra in Japan. The disease was first reported in Japan in 2015, causing significant damage to okra seedlings. Due to the potential threat in okra cultivation, the development of an accurate detection method for F. buharicum is needed for the surveillance and management of the disease. In this study, we designed a primer set and developed conventional and nested PCR assays for the specific detection of F. buharicum in infected okra plants and contaminated soil, respectively. We compared the diversity of the translation elongation factor 1 alpha (EF-1α) gene of F. buharicum with 103 other fungal species/isolates to design a species-specific primer. This primer pair successfully amplified approximately 400 bp of PCR product that was only detected in the F. buharicum isolate, not in the other fungal isolates. The developed nested PCR method was highly sensitive and could detect the fungus from a 0.01 fg DNA sample. The primer successfully detected the pathogen in artificially infected plants and soil by conventional and nested PCR, respectively. This is the first report of the development of the F. buharicum-specific primer set and detection assays, which can be used for the specific and sensitive detection of F. buharicum in field samples and for taking early control measures.

Molecular Evaluation of <i>Entamoeba gingivalis</i> and Trichomonas tenax isolated from orthodontic patients in Maysan Province, Iraq.

Entamoeba gingivalis (E. gingivalis) and Trichomonas tenax (T. tenax) are two species of parasitic protozoans that inhabit the human buccal cavity. Poor hygiene increases infection with these parasites. There has recently been a need to use orthodontics, despite its benefits, but the damage caused by orthodontics cannot be overlooked. The current study aims to assess the prevalence of oral parasites among individuals who use orthodontic appliances (fixed and mobile). The study included 200 participants, 100(76 females and 24 males) orthodontics patients, and 100(75 females and 25 males) nonorthodontics participants (control). Gathered one pair of swabs from each participant for microscopic analysis, culture, and implementation of the nested PCR method. Chi-square and Fisher’s tests were conducted to identify any statistically significant connection between parasitic infections and orthodontic treatments. The findings indicated that orthodontic patients had elevated infection rates with these parasites. Specifically, the infection rate of E. gingivalis in orthodontic patients was more infected (47%) than in non-orthodontic subjects (25%) which were the control. The prevalence of T. tenax was only 2.0% in the orthodontic patients while it was 1.0% in the control group. The prevalence rates of both parasites (E. gingivalis and T. tenax) in the orthodontic patients exhibited the highest prevalence of 19% and 16% respectively among the control subjects. The study found a significant correlation between infection and orthodontic applications at P= 0.01. The effects of other factors on oral parasite infection such as (sex, age, and orthodontic type) were also studied and compared between the two groups.

Development of a Double-Antibody Sandwich ELISA Based on a Monoclonal Antibody against the Viral NS1 Protein for the Detection of Chicken Parvovirus.

Chicken parvovirus (ChPV) infection can cause runting-stunting syndrome (RSS) in chickens. There is currently no commercially available vaccine for controlling ChPV, and ChPV infection in chickens is widespread globally. The rapid detection of ChPV is crucial for promptly capturing epidemiological data on ChPV. Two monoclonal antibodies (mAbs), 1B12 and 2B2, against the ChPV NS1 protein were generated. A double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) was developed for detecting ChPV based on the mAb 1B12 and an anti-chicken polyclonal antibody against the ChPV NS1 protein. The detection limit for the ChPV recombinant pET32a-NS1 protein was approximately 31.2 ng/mL. A total of 192 throat and cloaca swab samples were analyzed for ChPV by the established DAS-ELISA and nested PCR methods. The concordance rate between the DAS-ELISA and the nested PCR method was 89.1%. The DAS-ELISA can detect the ChPV antigen without any cross-reaction with FAdV-4, FAdV-1, NDV, AIV, MS, CIAV, aMPV, EDSV, IBV, or AGV2. The method also has high repeatability, with a coefficient of variation (CV) of less than 5%. These findings indicate that the DAS-ELISA exhibits high accuracy, good sensitivity, and specificity, making it suitable for viral detection, field surveillance, and epidemiological studies.

The Use of the Internal Transcribed Spacer Region for Phylogenetic Analysis of the Microsporidian Parasite Enterocytozoon hepatopenaei Infecting Whiteleg Shrimp (Penaeus vannamei) and for the Development of a Nested PCR as Its Diagnostic Tool.

The increasing economic losses associated with growth retardation caused by Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp, require effective monitoring. The internal transcribed spacer (ITS)-1 region, the non-coding region of ribosomal clusters between 18S and 5.8S rRNA genes, is widely used in phylogenetic studies due to its high variability. In this study, the ITS-1 region sequence (~600-bp) of EHP was first identified, and primers for a polymerase chain reaction (PCR) assay targeting that sequence were designed. A newly developed nested-PCR method successfully detected the EHP in various shrimp (Penaeus vannamei and P. monodon) and related samples, including water and feces collected from Indonesia, Thailand, South Korea, India, and Malaysia. The primers did not cross-react with other hosts and pathogens, and this PCR assay is more sensitive than existing PCR detection methods targeting the small subunit ribosomal RNA (SSU rRNA) and spore wall protein (SWP) genes. Phylogenetic analysis based on the ITS-1 sequences indicated that the Indonesian strain was distinct (86.2% nucleotide sequence identity) from other strains collected from Thailand and South Korea, and also showed the internal diversity among Thailand (N = 7, divided into four branches) and South Korean (N = 5, divided into two branches) samples. The results revealed the ability of the ITS-1 region to determine the genetic diversity of EHP from different geographical origins.

The use of the internal transcribed spacer region for phylogenetic analysis of the microsporidian parasite Enterocytozoon hepatopenaei infecting whiteleg shrimp (Penaeus vannamei) and for the development of a nested PCR as its diagnostic tool.

The increasing economic losses associated with growth retardation caused by Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp, require effective monitoring. The internal transcribed spacer (ITS)-1 region, the non-coding region of ribosomal clusters between 18S and 5.8S rRNA genes, is widely used in phylogenetic studies due to its high variability. In this study, the ITS-1 region sequence (~600-bp) of EHP was first identified, and primers for a polymerase chain reaction (PCR) assay targeting that sequence were designed. A newly developed nested-PCR method successfully detected the EHP in various shrimp (Penaeus vannamei and P. monodon) and related samples, including water and feces collected from Indonesia, Thailand, South Korea, India, and Malaysia. The primers did not cross-react with other hosts and pathogens, and this PCR assay is more sensitive than existing PCR detection methods targeting the small subunit ribosomal RNA (SSU rRNA) and spore wall protein (SWP) genes. Phylogenetic analysis based on the ITS-1 sequences indicated that the Indonesian strain was distinct (86.2%) from other strains collected from Thailand and South Korea, and also showed the internal diversity among Thailand (N = 7, divided into four branches) and South Korean (N = 5, divided into two branches) samples. The results revealed the ability of the ITS-1 region to determine the genetic diversity of EHP from different geographical origins.

High positivity rate of caprine arthritis encephalitis virus in Luzon, the Philippines revealed by nested-polymerase chain reaction assay.

Caprine arthritis encephalitis (CAE) is a worldwide economically important disease of small ruminants particularly goats. CAE has been considered to be an emerging/re-emerging disease of goats and a notifiable disease in the Philippines. In this study, a nested-PCR method to detect CAE virus (CAEv) infection was conducted between January 2021 to December 2022. A total of 1334 goat blood samples were collected from 24 goat farms throughout Luzon, the Philippines. The over-all prevalence rate was 31.41% (419/1334) in goats and 91.67% (22/24) of goat farms. These results showed high positivity rate of CAEv and the disease may be widespread in Luzon, the Philippines.

Assemblage characterization of Giardia duodenalis in South Khorasan province, eastern Iran, using HRM real-time PCR method.

Giardia duodenalis is a common parasitic protozoan causing gastrointestinal illness in humans worldwide. The genetic diversity of G. duodenalis is reflected through the identification of different assemblages. In this study, we aimed to determine the assemblages of G. duodenalis in eastern Iran using nested-PCR and high-resolution melting (HRM) real-time PCR methods. A total of 58 positive G. duodenalis, which were isolated from 1800 subjects, referred to medical center laboratories in South Khorasan province, eastern Iran, from April 2020 to March 2022, were included in this study. DNA was extracted and HRM real-time PCR was performed for assemblage characterization. HRM real-time PCR successfully characterized all samples. Accordingly, out of 58 positive samples, 53 (91.36%) and 5 (8.62%) were identified as assemblage A and B, respectively. Our findings showed that HRM real-time PCR was able to characterize the assemblages of G. duodenalis. In addition, our results suggest high prevalence of assemblage A in eastern region of Iran.

Development and application of an indirect ELISA and nested PCR for the epidemiological analysis of Klebsiella pneumoniae among pigs in China.

Klebsiella pneumoniae (K. pneumoniae) is an important opportunistic and zoonotic pathogen which is associated with many diseases in humans and animals. However, the pathogenicity of K. pneumoniae has been neglected and the prevalence of K. pneumoniae is poorly studied due to the lack of rapid and sensitive diagnosis techniques. In this study, we infected mice and pigs with K. pneumoniae strain from a human patient. An indirect ELISA was established using the KHE protein as the coating protein for the detection of K. pneumoniae specific antibody in clinical samples. A nested PCR method to detect nuclei acids of K. pneumoniae was also developed. We showed that infection with K. pneumoniae strain from a human patient led to mild lung injury of pigs. For the ELISA, the optimal coating concentration of KHE protein was 10 µg/mL. The optimal dilutions of serum samples and secondary antibody were 1:100 and 1:2500, respectively. The analytical sensitivity was 1:800, with no cross-reaction between the coated antigen and porcine serum positive for antibodies against other bacteria. The intra-assay and inter-assay reproducibility coefficients of variation are less than 10%. Detection of 920 clinical porcine serum samples revealed a high K. pneumoniae infection rate by established indirect ELISA (27.28%) and nested PCR (19.13%). Moreover, correlation analysis demonstrated infection rate is positively correlated with gross population, Gross Domestic Product (GDP), and domestic tourists. In conclusion, K. pneumoniae is highly prevalent among pigs in China. Our study highlights the role of K. pneumoniae in pig health, which provides a reference for the prevention and control of diseases associated with K. pneumoniae.

A Nested PCR Telomere Fusion Assay Highlights the Widespread End-Capping Protection of Arabidopsis CTC1.

Telomeres protect the ends of linear eukaryotic chromosomes from being recognized as DNA double-strand breaks. Two major protein complexes are involved in the protection of telomeres: shelterin and CST. The dysfunction of these complexes can challenge the function of telomeres and lead to telomere fusions, breakage-fusion-bridge cycles, and cell death. Therefore, monitoring telomere fusions helps to understand telomeres biology. Telomere fusions are often analyzed by Fluorescent In Situ Hybridization (FISH) or PCR. Usually, both methods involve hybridization with a telomeric probe, which allows the detection of fusions containing telomeric sequences, but not of those lacking them. With the aim of detecting both types of fusion events, we have developed a nested PCR method to analyze telomere fusions in Arabidopsis thaliana. This method is simple, accurate, and does not require hybridization. We have used it to analyze telomere fusions in wild-type and mutant plants altered in CTC1, one of the three components of the Arabidopsis CST telomere capping complex. Our results show that null ctc1-2 mutant plants display fusions between all telomeric regions present in Arabidopsis chromosomes 1, 3 and 5, thus highlighting the widespread end-capping protection achieved by CTC1.