An Epidemiological Assessment of Cryptosporidium and Giardia spp. Infection in Pet Animals from Taiwan

Cryptosporidium spp. and Giardia duodenalis are enteric protozoan pathogens in humans. and animals. Companion animals infected with zoonotic species/assemblages are a matter of major public concern around the world. The objectives of the present study were to determine the prevalences of Cryptosporidium spp. and G. duodenalis infections and their co-infection statuses in dogs and cats living in Taiwan and to identify the species and assemblages. Fecal samples were collected from local animal shelters (n = 285) and a veterinary hospital (n = 108). Nested polymerase chain reaction (PCR) was performed using the SSU-rRNA, β-giardin, and glutamate dehydrogenase genes for Cryptosporidium spp. and G. duodenalis, respectively. Results showed that the overall prevalences of Cryptosporidium and G. duodenalis were 7.38% (29/393) and 10.69% (42/393). In addition, co-infection was detected in 1.02% (4/393) of all samples. Sample source, clinical sign, and breed may be risk factors that influence the infection rate. In Cryptosporidium-positive samples, C. canis and C. felis were detected most frequently. Although the canine-specific assemblages C and D (37/42) were dominant, the zoonotic human-specific assemblage A (1/42) was also found in Giardia-positive samples. Phylogenetic analysis revealed that most positive samples belonged to host-specific subtypes/assemblages, while some Cryptosporidium or Giardia-positive samples could be zoonotic. The findings suggested that pet animals could be a cause of zoonotic transmission, causing human cryptosporidiosis and giardiasis in Taiwan.

Prevalence and molecular characterization of Giardia intestinalis isolated from children and calves in Babylon province, Iraq

Background and Aim

Giardia intestinalis is one of the most prevalent intestinal parasites in humans and animals, and children in close contact with livestock are particularly at risk of infection. This study aimed to detect assemblages of G. intestinalis and determine the origin of zoonotic transmission of Giardia in children and calves in different parts of Babylon province, Iraq.

Materials and Methods

One hundred stool samples from children (68 boys and 32 girls) and 100 fecal samples from calves (46 males and 54 females) of different ages were randomly collected. Molecular techniques were used to estimate the prevalence of G. intestinalis in children and calves. A nested polymerase chain reaction (PCR) was performed by targeting the triose phosphate isomerase gene in the samples to detect G. intestinalis assemblages.

Results

The overall rates of infection with G. intestinalis in children and calves were 21% and 34%, respectively, using the conventional microscopic method. The results illustrated that 61.90% (13/21) and 38.09% (8/21) of positive samples from children were allocated to assemblages A and B, respectively (p > 0.05). In calves, assemblages A and B were detecte in 82.35% (28/34) and 17.64% (6/34) of positive samples from calves, respectively (p ≤ 0.001). Ten PCR products were sequenced and submitted to the GenBank database. Phylogenetic analysis detected five human sequences each belonging to G. intestinalis assemblages A (OM850335-OM850339) and B (OM850340-OM850344). Similarly, five calf sequences each belonged to G. intestinalis assemblages A (ON75756-ON757660) and B (ON757661-ON757665).

Conclusion

The detection of large numbers of G. intestinalis assemblage A in both humans and cattle indicated that cattle could be a main source of zoonotic G. intestinalis infection in children in Babylon province, Iraq.

Early Warning Measurement of SARS-CoV-2 Variants of Concern in Wastewaters by Mass Spectrometry

Wastewater surveillance has rapidly emerged as an early warning tool to track COVID-19. However, the early warning measurement of new SARS-CoV-2 variants of concern (VOCs) in wastewaters remains a major challenge. We herein report a rapid analytical strategy for quantitative measurement of VOCs, which couples nested polymerase chain reaction and liquid chromatography-mass spectrometry (nPCR-LC-MS). This method showed a greater selectivity than the current allele-specific quantitative PCR (AS-qPCR) for tracking new VOC and allowed the detection of multiple signature mutations in a single measurement. By measuring the Omicron variant in wastewaters across nine Ontario wastewater treatment plants serving over a three million population, the nPCR-LC-MS method demonstrated a better quantification accuracy than next-generation sequencing (NGS), particularly at the early stage of community spreading of Omicron. This work addresses a major challenge for current SARS-CoV-2 wastewater surveillance by rapidly and accurately measuring VOCs in wastewaters for early warning.

Molecular discrimination and genetic diversity of three common tick-borne pathogens in dogs in Thailand

There was little information regarding the occurrence of canine vector-borne disease (CVBDs) in shelter dogs in Thailand. This work is the first report regarding a molecular method used to determine the occurrence and genetic diversity of three canine tick-borne pathogens (TBPs) (Hepatozoon canis, Anaplasma platys and Ehrlichia canis) in blood samples from 275 shelter dogs in the north and central areas of Thailand. The PCR results based on the 18S rRNA and 16S rRNA genes showed that 71 (25.82%) dogs were positive for at least a TBP. The overall occurrence rates of H. canis, A. platys and E. canis infections were 1.81, 16.36 and 7.64%, respectively. For the phylogenetic analysis, A. platys 16S rRNA gene was genetically diverse, while H. canis 18S rRNA and E. canis 16S rRNA genes were conserved. The haplotype diversity exhibited 12 and 2 haplotypes as well as 78 and 178 polymorphic sites of A. platys and E. canis 16S rRNA genes, respectively. Our findings could be used to improve the understanding of phylogeny and genetic diversity of TBP rRNA genes and used to ameliorate the diagnosis and control programmes for the diseases in Thailand.

First report on molecular prevalence and identification of Anaplasma platys in dogs in Khon Kaen, Thailand

Background and Aim:

Anaplasma platys is a blood parasite that infects platelets, causing thrombocytopenia. Rhipicephalus sanguineus ticks are believed to transmit A. platys. To identify A. platys, nested polymerase chain reaction (PCR) has proven to be an effective diagnostic tool. In this study, the molecular prevalence of A. platys infection in dogs was investigated for the 1^st time in the Khon Kaen region of Thailand. The association between risk factors and A. platys infection was also evaluated.

Materials and Methods:

A total of 130 blood samples were collected from dogs in Khon Kaen, Thailand. DNA from the samples was extracted and nested PCR was applied for molecular analysis. Platelet count and packed cell volume (PCV) levels were measured. Platelet counts were categorized into four grades: Non-thrombocytopenia (platelets >200,000 cells/μL), mild thrombocytopenia (platelets 150,000-200,000 cells/μL), moderate thrombocytopenia (platelets 100,000-150,000 cells/μL), and severe thrombocytopenia (platelets <100,000 cells/μL). Four categories for PCV levels of >37%, 30-37%, 20-29%, and <20% were defined as no anemia, mild anemia, moderate anemia, and severe anemia, respectively. DNA sequencing was analyzed using BTSeq™ (Barcode-Tagged Sequencing; CELEMICS, Seoul, South Korea) for similarity index.

Results:

Among the 130 samples, 9 (6.9%) were positive for A. platys infection. There was an association between low platelet count and infection (p<0.05). PCV level was also associated with A. platys infection (p<0.05). DNA sequencing results of the nine positive samples showed similarity to known sequences of A. platys with 99.36-100% nucleotide identity. These results suggested low genetic diversity in A. platys infecting dogs in the Khon Kaen area.

Conclusion:

By amplifying 16S rRNA, A. platys infection was detected in the blood of Thai dogs. Further work should be performed to identify risk factors potentially associated with A. platys infection in dogs in Khon Kaen. Other related factors should also be considered, such as location and breeding, as well as the environmental characteristics of each locality. In addition, sampling a larger number of animals may reveal predictors for the positivity of A. platys in dogs in this region.

Molecular detection of Toxoplasma gondii in aborted fetuses of goats in Chattogram, Bangladesh

BACKGROUND AND AIM

Toxoplasma gondii is a protozoan parasite that is responsible for the major cause of congenital diseases, abortion, and stillbirth in humans and farm animals. Primary infection in pregnant goats due to T. gondii leads to abortion and significant economic losses in the livestock industry. Moreover, very few studies have been performed for the identification of T. gondii from aborted fetuses of goats. The study was conducted for the molecular identification of Toxoplasma gondii from aborted fetuses of goats in Chattogram, Bangladesh.

MATERIALS AND METHODS

Twenty aborted fetuses of goats were collected from 52 farms in the study area. A nested polymerase chain reaction (PCR) assay targeting the B1 gene was performed, and a positive sample yield of 197 bp amplified DNA products consistent with T. gondii.

RESULTS

The overall prevalence of toxoplasmosis in the aborted fetus of goats was 35%. Heart muscle, liver, brain, and placenta showed positive PCR results. The risk factors related to the does age, presence of cats in farms, and aborted fetus age were found to be statistically significant (p<0.05). Our results showed that T. gondii is a major possible causal factor for abortion and reproductive failure in goats. The high prevalence of T. gondii infection in aborted fetuses of goats revealed that T. gondii could be imperative in causing reproductive failure in goats.

CONCLUSION

Active or congenital toxoplasmosis was shown by the presence of T. gondii in fetal tissues, which is a matter of concern as this parasite has zoonotic significance and causes economic hazards to the livestock industry by causing various reproductive problems. Therefore, proper control measures and strategies are needed to reduce the rate of abortion in goats, ultimately saving the livestock industry.

Construction of an in-house allelic ladder for Canine Genotypes™ Panel 2.1 Kit

Dogs (Canis lupus familiaris) are among the most common companion animals in the Republic of Korea. Recently, there have been many criminal cases of dog cruelty, injury, and theft, among others. This has increased the importance of dog-related biological evidence at crime scenes. The National Forensic Service of the Republic of Korea conducts short tandem repeat (STR) analysis using the Thermo Scientific Canine Genotypes™ Panel 2.1 Kit (Canine Kit) to identify individual dogs through forensic analysis. The Canine Kit was developed as a forensic STR kit for the identification of individual dogs. However, an allelic ladder was neither developed nor included in the commercial kit, leaving an issue of accurate genotyping. Primer details for the 18 markers used in the Canine Kit are proprietary information, and thus, unavailable to end-users. In this study, an allelic ladder was constructed with 160 fragments by combining 158 fragments of STR alleles obtained by nested PCR and two fragments artificially obtained from the sex-determination marker. By including the new allelic ladder in analysis of samples amplified with the Canine Kit, the accuracy and reliability of data analysis were improved. Application of this allelic ladder would be helpful for interlaboratory data sharing and standardization of canine genotype databases.

Active equine parvovirus-hepatitis infection is most frequently detected in Austrian horses of advanced age

BACKGROUND

Equine parvovirus-hepatitis (EqPV-H) research is in its infancy. Information regarding prevalence, geographical distribution, genetic diversity, pathogenesis and risk factors enhances understanding of this potentially fatal infection.

OBJECTIVES

Determining the prevalence of EqPV-H in Austrian equids. Investigating factors increasing probability of infection, liver-associated biochemistry parameters, concurrent equine hepacivirus (EqHV) infection and phylogenetic analysis of Austrian EqPV-H variants.

STUDY DESIGN

Cross-sectional study.

METHODS

Sera from 259 horses and 13 donkeys in Austria were analysed for anti-EqPV-H VP1-specific antibodies by luciferase immunoprecipitation system (LIPS) and EqPV-H DNA by nested polymerase chain reaction (PCR). Associations between infection status, sex and age were described. Glutamate dehydrogenase (GLDH), gamma-glutamyl transferase (GGT), bile acids and albumin concentrations were compared between horses with active infection and PCR-negative horses. PCR targeting partial EqPV-H NS1 was performed and phylogenetic analysis of Austrian EqPV-H variants was conducted. Complete coding sequences (CDS) of four Austrian variants were determined by next-generation sequencing (NGS) and compared with published sequences.

RESULTS

Horses' EqPV-H seroprevalence was 30.1% and DNA prevalence was 8.9%. One horse was co-infected with EqHV. Significantly, higher probability of active EqPV-H infection was identified in 16- to 31-year-old horses, compared with 1- to 8-year-old horses (P = 0.002; OR = 8.19; 95% CI = 1.79 to 37.50) and 9- to 15-year-old horses (P = 0.03; OR = 2.96; 95% CI = 1.08 to 8.17). Liver-associated plasma parameters were not significantly different between horses with active infection and controls. Austrian EqPV-H variants revealed high similarity to sequences worldwide. No evidence of EqPV-H was detected in donkeys.

MAIN LIMITATIONS

Equids' inclusion depended upon owner consent. There was only one sampling point per animal and the sample of donkeys was small.

CONCLUSIONS

EqPV-H antibodies and DNA are frequently detected in Austrian horses, without associated hepatitis in horses with active infection. The risk of active EqPV-H infection increases with increasing age. Phylogenetic evidence supports close relation of EqPV-H variants globally, including Austrian variants.

Prevalence and molecular characterization of canine parvovirus

Background and Aim:

Canine parvovirus (CPV) belonging to family Parvoviridae causes hemorrhagic gastroenteritis in dogs and heavy mortality in young dogs. The virus has three structural (VP1, VP2 and VP3) and two non-structural proteins (NS1 and NS2), VP2 being highly immunogenic. This study aims to study molecular epidemiology of CPV by sequence analysis of VP2 gene to determine the prevailing antigenic type(s) in the northern regions of India.

Materials and Methods:

A total of 118 rectal swabs collected from dogs exhibiting clinical signs of CPV infection were processed for the isolation of DNA and subjected to polymerase chain reaction (PCR) and nested PCR (NPCR). A total of 13 NPCR products selected randomly were subjected to sequence analysis of VP2 gene.

Results:

The percent positivity of CPV was found 28% and 70% by PCR and NPCR, respectively. Dogs with vaccination history against CPV too were found positive with a percent positivity of 24.10%. Gene sequencing and phylogenetic analysis of VP2 gene from these isolates revealed that most samples formed a clade with CPV-2a isolates.

Conclusion:

Sequence analysis and phylogenetic analysis of VP2 gene in the studied regions of northern India revealed that CPV-2a was the most prevalent antigenic type.

Diagnosis of the accurate genotype of HKαα carriers in patients with thalassemia using multiplex ligation-dependent probe amplification combined with nested polymerase chain reaction

BACKGROUND

Patients carrying the HongKongαα (HKαα) allele and -α/ααα could be misdiagnosed as -α/αα by the current conventional thalassemia detection methods, leading to inaccurate genetic counseling and an incorrect prenatal diagnosis. This study was aimed to accurately analyze the genotypes of HKαα carriers and -α/ααα.

METHODS

Samples were collected in our hospital from July 2017 to October 2019. Twenty-four common types of Chinese thalassemia were screened by gap-polymerase chain reaction (Gap-PCR) and reverse dot blot (RDB). Anti-4.2 multiplex-PCR was used to confirm carriers of the ααα duplication with -α deletion. Two-round nested PCR and multiplex ligation-dependent probe amplification (MLPA) were applied to accurately identify and confirm their genotypes. For data analysis, we used descriptive statistics and Fisher's exact tests.

RESULTS

Two thousand five hundred and forty-four cases were identified as thalassemia in 5488 peripheral blood samples. The results showed that α, β, and αβ compound thalassemia were identified in 1190 (46.78%), 1286 (50.55%), and 68 (2.67%) cases, respectively. A total of 227 samples from thalassemia patients were identified as -α/αα by Gap-PCR, and the genotypes of two samples were uncertain. There was a difference between Gap-PCR and combined groups (Gap-PCR combined with nested PCR and MLPA) in detecting HKαα (P < 0.05). Among the 229 patients, 20 patients were identified as HKαα carriers and one was identified as -α/ααα by two-round nested PCR and MLPA, including 15 patients with HKαα/αα, three with HKαα/αα and β-thalassemia coinheritance, one with HKαα/--, one with HKαα/-α and β-thalassemia coinheritance, and one with -α/ααα and β-thalassemia coinheritance.

CONCLUSIONS

ααα and HKαα genotypes of patients carrying -α need to be detected to reduce the misdiagnosis rate of patients carrying HKαα and -α3.7/ααα alleles. More accurate genetic counseling can be provided in the clinic using nested PCR combined with MLPA.

Prevalence and species identification of Cryptosporidium spp. in the newborn dairy calves from Muang District, Khon Kaen Province, Thailand

Aim:

This study aims to determine the prevalence of Cryptosporidium spp. infection and to identify the species of Cryptosporidium spp. in newborn dairy calves between December 2016 and March 2017 in Muang District, Khon Kaen Province, Thailand.

Materials and Methods:

A total of 200 fecal samples from newborn dairy calves of the ages 1 day up to 28 days were collected and the presence of Cryptosporidium oocysts was examined microscopically using the modified Kinyoun’s acid-fast staining technique. Then, Cryptosporidium species were identified using nested polymerase chain reaction amplification of 18S rRNA gene and sequencing.

Results:

The modified Kinyoun’s acid-fast staining revealed the presence of Cryptosporidium oocysts in 51% (102/200). Sequence analysis of the 18S rRNA gene identified two species, namely, Cryptosporidiumbovis (n=11) and Cryptosporidiumryanae (n=11) and one isolated strain could not be identified.

Conclusion:

This study indicated that newborn dairy calves aging up to 4 weeks were highly infected with Cryptosporidium spp., and the infection mostly occurred in diarrheic dairy calves. This is the first report of Cryptosporidium in dairy calves in Khon Kaen Province and the results provide baseline information for further studies and control of Cryptosporidium infection in dairy calves in the study area.

Comparison of nested polymerase chain reaction and real-time polymerase chain reaction targeting 47kda gene for the diagnosis of scrub typhus

Introduction

Scrub typhus is a zoonotic infection caused by Orientia tsutsugamushi which is transmitted by Leptotrombidium mites. The disease manifests as a mild-to-severe illness with non-specific clinical symptoms. Rapid diagnosis and prompt treatment are essential for patient management. Both serological and molecular methods are used for the diagnosis of scrub typhus. The present study assessed the usefulness of detection of the gene encoding the 47kDa outer-membrane protein (OMP) for the laboratory diagnosis of scrub typhus.

Materials and Methods

Nested polymerase chain reaction (nPCR) and real-time PCR targeting 47 kDa OMP antigen gene of O. tsutsugamushi were performed on ethylenediaminetetraacetic acid blood samples.

Results

Six of the 103 (5.8%) patients showed the presence of 47kDa gene by nPCR. Seventy of 103 (67.9%) cases showed the presence of 47kDa gene by qPCR. Among the 70 positive cases, the majority of them were females (40/70, 57.1%). The highest number of positive cases was observed during October-February.

Conclusion

Real-time PCR targeting O. tsutsugamushi-specific 47-kDa gene is more sensitive than nPCR and may be the assay of choice for the detection of the organism in patients with suspected scrub typhus.

First report and molecular characterization of Cryptosporidium spp. in humans and animals in Khartoum state, Sudan

BACKGROUND AND AIM

Cryptosporidium is recognized to infect several mammalian species as well as humans, causing substantial economic losses and serious public health concern. Infected animals can be a source of environmental contamination and human infections. In general, the occurrence of Cryptosporidium species in animals and human in Sudan and zoonotic importance is not well documented. This study aimed to identify Cryptosporidium spp. infecting different animal species and humans and to compare between different isolates obtained.

MATERIALS AND METHODS

To provide molecular information about Cryptosporidium in animals and humans, both modified Ziehl-Neelsen (MZN) specific stain and molecular assay were used. Concentration techniques followed by three protocols of DNA extraction were carried out. After microscopic screening of 263 fecal samples (goats [n=197], cattle [n=12], sheep [n=12], and human [n=42]), 61 positive and 30 negative, randomly selected samples were used in nested polymerase chain reaction (PCR) targeting part of the 18S RNA.

RESULTS

Nested PCR amplification confirmed 91.8% (56/61) of microscopic-positive samples. 8.2% (5/61) of negative samples by PCR (positive by microscopy) were considered false negatives. Sequencing followed by alignment of the 14 isolates indicated that all samples were identical (100%) and belonged to Cryptosporidium parvum.

CONCLUSION

MZN staining procedure is reliable for the routine diagnosis of Cryptosporidium; cetyltrimethylammonium bromide extraction buffer and nested PCR targeting 18S rRNA gene are reliable and useful in epidemiological studies of this parasite.

Clinical and laboratory features of PCR-confirmed periocular tuberculosis in China

Experts lack knowledge of periocular tuberculosis (TB) in China. Nested polymerase chain reaction (PCR) shows advantages in diagnosis of extrapulmonary TB. Our study aims to explore the clinical and laboratory features of PCR-confirmed periocular TB. We retrospectively reviewed medical records of presumptive periocular TB and performed nested PCR test to confirm diagnosis. Nine cases were recruited. Clinical symptoms were chronic and insidious. Eight cases achieved favorable visual acuity, while one underwent enucleation due to fungal-TB panophthalmitis. Sensitivity of caseous necrosis, acid-fast bacilli (AFB) staining and interferon γ release assay (T-SPOT) test are 33.3%, 44.4% and 85.7% respectively. Low lymphocyte percentage (P=0.019) and high monocyte-lymphocyte ratio (P=0.042) positively correlate with AFB staining. Male gender (P=0.048) and Langhans giant cell (P=0.048) positively correlate with caseous necrosis. To conclude, traditional TB ancillary tests are not as sensitive as nested PCR technique. Several factors facilitate diagnosis including male gender, decreased lymphocytes, and typical Langhans giant cells.

Assessment of efficacy of prenatal genetic diagnosis for fragile X syndrome using nested PCR

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and the leading monogenic cause of autism spectrum disorder. It has previously been demonstrated that prenatal genetic diagnosis is efficient for the diagnosis of FXS. The present study investigated the diagnostic effects of nested polymerase chain reaction (PCR) for fragile X mental retardation 1 (FMR1) and expanded CGG repeats. It was demonstrated that the nested PCR assay rapidly measured the multi-copies of the FMR1 gene in individual samples. The nested PCR assay detected normal CGG repeat lengths and expanded CGG repeat lengths with a low occurrence of false positives. In addition, the nested PCR assay resulted in increased sensitivity and specificity for patients with FXS. Furthermore, the nested PCR assay identified the mutation and generated conclusive cases for FXS, indicating that this assay is beneficial for the diagnosis of FXS patients. In conclusion, these outcomes indicate that nested PCR assay is a reliable and easier method for diagnosis of FXS, which may be used for the diagnosis of FXS patients.

ISMap02 element targeted nested polymerase chain in the detection of Mycobacterium avium subsp. paratuberculosis in fecal samples of cattle and buffaloes

Background and Aim

Johne's disease is chronic granulomatous enteritis which affects ruminants. There are many diagnostic approaches for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) of which molecular detection methods using various elements are less time consuming and more accurate. The present study was conducted using ISMap02 element for nested polymerase chain reaction (nPCR) based detection of MAP in fecal samples. The aim was to test the sensitivity and specificity of the ISMap02 element and also to use this element for the detection of MAP in fecal samples of cattle and buffaloes.

Materials and Methods

A total of 211 fecal samples of cattle and buffaloes from different herds around Ludhiana aged between 2 and 13 years were collected, and DNA extraction was done from these samples. The nPCR was carried out for the detection of MAP in fecal samples.

Results

The ISMap02 element was specific for the detection of MAP only and showed a sensitivity of detection of 7.6 fg/µL of the standard genomic DNA. Among the 211 fecal samples of cattle and buffaloes tested for the ISMap02 element, 18 samples (8.5%) were positive for MAP.

Conclusion

The ISMap02 element is specific and sensitive for the detection of MAP in various samples, and when used in nPCR format, it can increase the sensitivity of detection.

Comparison of methods for detection of chytrid fungus (Batrachochytrium dendrobatidis) in bullfrog tadpole mouthparts

We previously reported that the tadpole of bullfrog (Lithobates catesbeiana) is a useful model for the field surveillance of the Batrachochytrium dendrobatidis (Bd) distribution. In the present study, we compared Bd detection rates in swab-scraped and resected mouthpart samples, using nested polymerase chain reaction (PCR). The resulting detection rates for swab-scraped and resected specimens were 67 and 65%, respectively, with no significant difference. Furthermore, we performed a histopathological examination for Bd distribution in the mouthparts; we found that Bd infection occurred in the tip and basement of the jaw sheaths and tooth rows. We recommend using swab-scraped samples for Bd detection. Moreover, careful attention should be paid to scraping the tip and basement of the jaw sheaths and the entire oral cavity to reduce the rates of false-negative results on nested PCR of the mouthparts of bullfrog tadpoles.

Evidence of simian retrovirus type D by polymerase chain reaction

BACKGROUND

Over the past few years, there have been reports of finding Simian retrovirus type D (SRV) in macaque colonies where some animals were characterized as antibody positive but virus negative raising questions about how SRV was transmitted or whether there is a variant strain detected by antibody but not polymerase chain reaction (PCR) in current use.

METHODS

We developed a three-round nested PCR assay using degenerate primers targeting the pol gene to detect for SRV serotypes 1-5 and applied this newly validated PCR assay to test macaque DNA samples collected in China from 2010 to 2015.

RESULTS

Using the nested PCR assay validated in this study, we found 0.15% of the samples archived on FTA^® cards were positive.

CONCLUSIONS

The source of SRV infection identified within domestic colonies might have originated from imported macaques. The multiplex nested PCR assay developed here may supplement the current assays for SRV.

Development of nested polymerase chain reaction-based diagnosis of duck enteritis virus and detection of DNA polymerase gene from non-descriptive duck breeds of West Bengal, India

AIM

The study was undertaken to detect the clinical signs, postmortem lesions of embryonated duck plague (DP) infected eggs, and histopathological changes of chorioallantoic membrane (CAM) in non-descriptive ducks of West Bengal with special reference to standardize nested polymerase chain reaction (PCR).

MATERIALS AND METHODS

After postmortem of suspected carcasses, samples were collected for virus isolation and identification through specific pathogen free (Khaki Campbell) embryonated duck eggs. PCR was also done as confirmatory test after doing postmortem of duck embryos. DP specific nested PCR was standardized for better confirmation of the disease. Sensitivity of nested primers was also tested for DP virus.

RESULTS

Gross, postmortem and histopathological changes were prominent in dead embryos. First set of primer was able to detect 602 bp fragments of DNA polymerase gene of duck enteritis virus from infected CAM. Subsequently, a DP specific nested PCR which was very much sensitive for very small amount of viral genome was successfully standardized. After NCBI blast nucleotide sequence of nested PCR product (Accession No. HG425076) showed homology with the sequences data available in GenBank.

CONCLUSION

The study concludes that PCR assay is very much helpful to diagnose DP disease and developed nested PCR is a double confirmatory diagnostic tool for DP.

Use of an Automated Nested Multiplex Respiratory Pathogen PCR Panel Postmortem in the Pediatric Forensic Setting

Respiratory pathogens have been detected in forensic investigations using multiple techniques; however, no study has examined the use of automated, nested, multiplex polymerase chain reaction (ANM-PCR), commonly used in living patients, in the forensic setting. This retrospective study assessed the utility of ANM-PCR in detecting respiratory pathogens in the pediatric forensic setting. Respiratory samples from 35 cases were tested for up to 20 respiratory pathogens. 51.4% of these cases yielded a positive ANM-PCR result, 20% of which were considered the cause of or contributory to death. The most commonly detected pathogens were rhinovirus/enterovirus and respiratory syncytial virus, and these were the only pathogens determined to play a significant role in cause of death. The sampled sites and postmortem intervals tested did not affect the likelihood of a positive or negative test. ANM-PCR panels are effective, affordable, and rapid ancillary tools in evaluating cause of death in the forensic pediatric population.

Human Papillomavirus Genotypes and Methylation of CADM1, PAX1, MAL and ADCYAP1 Genes in Epithelial Ovarian Cancer Patients

Background:

High-risk types of human papillomavirus (HR-HPV) may play a role in the development of epithelial ovarian cancer (EOC). The aim of this study was to determine any HPV genotypes and correlations to CADM1, PAX1, MAL and ADCYAP1 gene methylation in Egyptian EOC patients.

Materials and methods:

The prevalence of HR-HPV in 100 formalin fixed paraffin embedded EOC tissues was determined using nested polymerase chain reaction (PCR) with MY09/MY11 and GP5+/GP6 + primers to amplify a broad spectrum of HPV genotypes in a single reaction. DNA sequencing was applied to identify HPV genotypes for the positive samples. All samples negative for HPV were re-analyzed for HR-HPV and low-risk HPV subtypes using type specific primers.

Results:

The prevalence of HPV was 10% in our EOC cases. HPV-16 and HPV-18 were the predominant genotypes followed by HPV−33, all being associated with advanced stages. Other HR-HPV and low risk HPV genotypes were not found. CADM1 was hypermethylated in 100% of patients infected with HPV-16 and HPV-33 and in 75% of patients infected with HPV-18. Hypermethylation of PAX1 was evident in 80% and in 75% of patients infected with HPV-16 and HPV-18 while MAL was hypermethylated in 100% and ADCYAP1 was hypermethylated in 60% and in 75%, respectively.

Conclusion:

The presence of high risk HPV genotypes among epithelial ovarian carcinoma may reflect an importance of infection in the pathogenesis of EOC. In HR-HPV infected cancers, DNA methylation may be one of the mechanisms triggering the alteration in CADM1, PAX1, MAL and ADCYAP1 gene expression levels.

Diagnostic performance of rapid diagnostic tests for the diagnosis of malaria at public health facilities in north-west Ethiopia

OBJECTIVE

To assess the performance of RDTs against nested polymerase chain reaction (nPCR) for the diagnosis of malaria in public health facilities in north-western Ethiopia.

METHODS

Cross-sectional study at public health facilities in North Gondar, Ethiopia, of 359 febrile patients with signs and symptoms consistent with malaria. Finger prick blood samples were collected for testing in a P. falciparum/pan-malaria RDTs and for molecular analysis. Sensitivity, specificity and predictive values were determined for the RDTs using nPCR as reference diagnostic method. Kappa value was determined to demonstrate the consistency of the results between the diagnostic tools.

RESULTS

By RDTs, 22.28% (80/359) of patients tested positive for malaria, and by nPCR, 27.02% (97/359) did. In nPCR, 1.67% (6/359) and 0.28% (1/359) samples were positive for P. ovale and P. malariae, which had almost all tested negative in the RDTs. The sensitivity, specificity, positive and negative predictive values of RDTs for the diagnosis of malaria were 62.9%, 92.7%, 76.3% and 87.1%, respectively, with 0.589 measurement agreement between RDTs and nPCR. The sensitivity and specificity of RDTs for P. falciparum identification only were 70.8% and 95.2%, and 65.2% and 93.1% for P. vivax.

CONCLUSION

Although RDTs are commonly used at health posts in resource-limited environments, their sensitivity and specificity for the detection and species identification of Plasmodium parasites were poor compared to nPCR, suggesting caution in interpreting RDTs results. Particularly, in the light of expanded efforts to eliminate malaria in the country, more sensitive diagnostic procedures will be needed.

Cytomegalovirus Identification in Blood and Urine of Newborns by Nested Polymerase Chain Reaction

Aim

To study the frequency of congenital cytomegalovirus (CMV) infection in newborns admitted to the Division of Neonatology, using nested polymerase chain reaction (PCR) and DNA to detect differences in blood and urine specimens.

Methods

The study was carried out for eight months. Newborns (n = 520) hospitalized in five hospitals in Campo Grande, Mato Grosso do Sul, Brazil, were checked for CMV by analysing blood and urine samples.

Results

Cytomegalovirus was PCR positive in 13 urine and 10 blood samples. Of the 13 positive urine patients, three (23%) had no clinical signs suggestive of CMV, and another three (23%) patients admitted to the neonatal intensive care unit (NICU) had no definite findings of bacterial infection, with negative blood culture and some clinical signs consistent with CMV as cholestasis, hepatomegaly and eosinophilia. Three patients were on mechanical ventilation and showed improvement after prescription of ganciclovir. One CMV positive child progressed to death.

Conclusion

Cytomegalovirus detection in urine was slightly more efficient than in blood, and showed better sensitivity than in serological analysis (p < 0.01) therefore, boiled urine may be a better and easier specimen tool for CMV diagnosis in neonatal infection. The findings of the present research suggest that patients admitted to the NICU, especially premature infants, whose laboratory results are not compatible with bacterial infection, and exhibiting signs suggestive of CMV infection should have PCR done on urine for confirmation.

Sequence-based genotyping of hepatitis B virus in general population

BACKGROUND

Hepatitis B Virus (HBV) causes acute and chronic liver disease worldwide. HBV has eight genotypes (A to H) which is the reflection of its genome with their characteristic geographical distribution. Each genotype could have different pathogenic and therapeutic characteristics. There have been few records on HBV genotyping in general population from our region. This study aimed to determine hepatitis B genotypes using sequencing in the general population of Shahrekord, a Southwestern region of Iran.

METHODS

A total of 3000 serum samples (cluster sampling method) were enrolled from general population tested for HBsAg using ELISA. Using appropriate extraction kit, HBV DNA was extracted from HBsAg positive samples and each was subjected to nested PCR for detection of HBV DNA. Finally, using sequencing, the samples were used for HBV genotyping. Data were analyzed by SPSS 19 using descriptive statistics, chi square, and Fisher's exact test. P-value < 0.05 was considered as the level of significance.

RESULTS

Out of 3000 serum samples, 40 (1.3%) were positive for HBsAg. HBV DNA was detected in 10 out of 40 (25%) of the samples studied. Genotype D was the predominant HBV type found in all of these 10 HBV positive samples.

CONCLUSION

Genotype D is probably the predominant HBV type in our region.

Isolation of Canine parvovirus with a view to identify the prevalent serotype on the basis of partial sequence analysis

Aim:

The aim of this study was to isolate Canine parvovirus (CPV) from suspected dogs on madin darby canine kidney (MDCK) cell line and its confirmation by polymerase chain reaction (PCR) and nested PCR (NPCR). Further, VP2 gene of the CPV isolates was amplified and sequenced to determine prevailing antigenic type.

Materials and Methods:

A total of 60 rectal swabs were collected from dogs showing signs of gastroenteritis, processed and subjected to isolation in MDCK cell line. The samples showing cytopathic effects (CPE) were confirmed by PCR and NPCR. These samples were subjected to PCR for amplification of VP2 gene of CPV, sequenced and analyzed to study the prevailing antigenic types of CPV.

Results:

Out of the 60 samples subjected to isolation in MDCK cell line five samples showed CPE in the form of rounding of cells, clumping of cells and finally detachment of the cells. When these samples and the two commercially available vaccines were subjected to PCR for amplification of VP2 gene, a 1710 bp product was amplified. The sequence analysis revealed that the vaccines belonged to the CPV-2 type and the samples were of CPV-2b type.

Conclusion:

It can be concluded from the present study that out of a total of 60 samples 5 samples exhibited CPE as observed in MDCK cell line. Sequence analysis of the VP2 gene among the samples and vaccine strains revealed that samples belonged to CPV-2b type and vaccines belonging to CPV-2.

A Y-short tandem repeat specific DNA enhancement strategy to aid the analysis of late reported (≥ 6 days) sexual assault cases

The ability to obtain an autosomal short tandem repeat (STR) profile of the semen donor from the reproductive tract of a living victim rapidly diminishes as the post-coital interval increases. This is of concern where victims of sexual assault provide vaginal samples several days after the incident. In order to overcome the technological impediments inherent in autosomal DNA typing with extended interval samples, we previously employed the use of Y chromosome STR profiling which, by targeting only male DNA, can eliminate masking of the male profile (by the victim's alleles) or critical polymerase chain reaction reagent titration (due to excessive female DNA). Thus employing Y-STR profiling and additional enhancement strategies, we reported the ability to recover Y-STR profiles from samples collected 5 to 6 days after intercourse. However, the reproductive biology literature indicates that spermatozoa are found in the human cervix up to 7 to 10 days post coitus. Thus, even with improved extraction and profiling techniques, we failed to routinely recover profiles from samples collected ≥ 6 days after intercourse. The aim of the present work was to develop additional strategies to permit the recovery of male donor DNA profiles from ≥ 6 post-coital samples. Using nested polymerase chain reaction and DNA concentration procedures that together maximize the recovery and targeting of male DNA, we demonstrate the ability to obtain semen donor Y-STR profiles in extended interval post-coital samples collected 6 to 9 days after intercourse. This approaches the recognized time limits of sperm residence in the cervico-vaginal canal as described in the clinical literature.

Prevalence of human papillomavirus and Epstein-Barr virus in salivary gland diseases

OBJECTIVE

The roles of human papillomavirus (HPV) and Epstein-Barr virus (EBV) in head and neck neoplasms have been well reported, but little is known about their relationship with salivary gland tumours. This study investigated the presence of HPV and EBV in salivary gland diseases.

METHODS

The presence of HPV 16/18 and EBV was analysed in archival pathological specimens collected from patients who had undergone surgery for salivary gland diseases. HPV 16/18 DNA was detected using nested polymerase chain reaction (PCR) and further confirmed with immunohistochemistry. EBV DNA was detected using real-time PCR.

RESULTS

A total of 61 pathological specimens were examined: 39.5% (15/38) of pleomorphic adenomas, 33.3% (3/9) of Warthin's tumours, 33.3% (one of 3) of mucoepidermoid carcinomas, and 25.0% (one of 4) of benign lymphoepithelial lesions were positive for high-risk HPV 16/18. Only two Warthin's tumours were positive for EBV.

CONCLUSION

The infectious nature of salivary gland neoplasms was revealed by the high prevalence of HPV infection, and the specific presence of EBV in Warthin's tumours, suggesting a potential role for HPV and EBV in salivary gland diseases.

A rapid nested polymerase chain reaction method to detect circulating cancer cells in breast cancer patients using multiple marker genes

The aim of the present study was to develop a simple and rapid method for the detection of circulating cancer cells using multiple tumor markers and to investigate the clinical significance of circulating cancer cells in breast cancer patients. A novel rapid nested polymerase chain reaction (PCR) assay, with high sensitivity and specificity, was evaluated, which was considered to be suitable for clinical application. The rapid nested PCR method was used to detect the circulating cancer cells of 142 breast cancer patients, using a panel of marker genes (FAM83A, NPY1R and KRT19), which were identified by the Digital Gene Expression Displayer Tool of the National Cancer Institute-Cancer Genome Anatomy Project. In total, 79.6% of the 142 breast cancer patient blood samples were found to express at least one tumor marker. In addition, the number of positive markers was found to significantly correlate with the disease stage and presence of distant metastasis. Furthermore, positivity for more than one tumor marker appeared to predict a reduced survival time in breast cancer patients.

Distribution of cytomegalovirus gN variants and associated clinical sequelae in infants

BACKGROUND

Human cytomegalovirus (HCMV) is the most widespread cause of congenital infection. The effects of various viral strains and viral loads on the infection outcome have been under debate.

OBJECTIVES

To determine the distribution of gN variants in HCMV strains isolated from children with congenital or postnatal infection and to establish the relationship between the viral genotype, the viral load, and the sequelae.

STUDY DESIGN

The study population included congenitally HCMV-infected newborns and children with postnatal or unproven congenital HCMV infection. The genotyping was performed by RFLP analysis of PCR-amplified fragments, and the viral load was measured by quantitative real-time PCR.

RESULTS

Our results demonstrated that the HCMV genotypes gN3b, gN4b, and gN4c were prevalent in the patients examined. There were no differences in the distributions of gN genotypes in the congenitally and postnatally infected children. Multiple HCMV strains were detected in both groups of children. A significant association between the HCMV gN4 genotype and the incidence of neurological disorders was observed (p=0.045). Our results suggest that the detection of the gN2 or the gN4 genotype may be indicative of serious manifestations in children. In contrast, the gN3b and the gN1 genotypes represent less pathogenic HCMV strains. The HCMV load in urine was significantly higher in children with congenital infection compared with children with postnatal infection. No correlation was found between the viral load and the genotype.

CONCLUSION

Our results suggest that the gN genotype may be a virological marker of symptomatic HCMV infection in newborns.

Application of loop-mediated isothermal amplification for malaria diagnosis during a follow-up study in São Tomé

BACKGROUND

A reliable and simple test for the detection of malaria parasite is crucial in providing effective treatment and therapeutic follow-up, especially in malaria elimination programmes. A comparison of four methods, including nested polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) were used for the malaria diagnosis and treatment follow-up in São Tomé and Príncipe, during a successful pre-elimination campaign.

METHOD

During the period September to November 2009, blood samples from 128 children (five to 14 years old) with temperature ≥38°C (tympanic) in the District of Agua Grande were examined using four different methods, i.e., histidine-rich protein 2 (HRP-2) based rapid diagnostic tests (HRP-2-RDTs), optical microscopy, nested PCR, and LAMP. First-line treatment with artesunate-amodiaquine was given for uncomplicated malaria and intravenous quinine was given for complicated malaria. Children with persistent positivity for malaria by microscopy, or either by nested PCR, or by LAMP on day 7 were given second-line treatment with artemether-lumefantrine. Treatment follow-up was made weekly, for up to four weeks.

RESULTS

On day 0, positive results for HRP-2-RDTs, microscopy, nested PCR, and LAMP, were 68(53%), 47(37%), 64(50%), and 65(51%), respectively. When nested PCR was used as a reference standard, only LAMP was comparable; both HRP-2-RDTs and microscopy had moderate sensitivity; HRP-2-RDTs had poor positive predictive value (PPV) and a moderate negative predictive value (NPV) for the treatment follow-up. Seventy-one children with uncomplicated malaria and eight children with complicated falciparum malaria were diagnosed based on at least one positive result from the four tests as well as clinical criteria. Twelve of the 79 children receiving first-line treatment had positive results by nested PCR on day 7 (nested PCR-corrected day 7 cure rate was 85%). After the second-line treatment, nested PCR/LAMP-corrected day 28 cure rate was 83% for these 12 children.

CONCLUSIONS

HRP-2-RDTs have similar sensitivity as microscopy but less specificity. However, as compared to nested PCR, the poor sensitivity of HRP-2-RDTs indicates that low parasitaemia may not be detected after treatment, as well as the low specificity of HRP-2-RDTs indicates it cannot be applied for treatment follow-up. LAMP has similar sensitivity and specificity to nested PCR. With high PPV and NPV, LAMP is simpler and faster as compared to nested PCR with the advantage of detecting low parasitaemia becoming a potential point-of-care test for treatment follow-up.

Evaluation of MAGE-1 and MAGE-3 as tumour-specific markers to detect blood dissemination of hepatocellular carcinoma cells

The members of MAGE gene family are highly expressed in human hepatocellular carcinoma (HCC). In the present study, we tested the tumour-specific MAGE-1 and MAGE-3 transcripts in the peripheral blood of HCC patients by nested RT-PCR to detect the circulating tumour cells and evaluate their potential clinical implication. Of 30 HCC patients, the positive rate of MAGE-1 and MAGE-3 transcripts was 43.3% (13 out of 30) and 33.3% (10 out of 30) in PBMC samples, whilst the positive rate was 70% (21 out of 30) and 53.3% (16 out of 30) in the resected HCC tissue samples, respectively. The positivity for at least one MAGE gene transcript was 63.3% (19 out of 30) in PBMC samples of HCC patients and 83.3% (25 out of 30) in the resected HCC tissue samples. MAGE-1 and/or MAGE-3 mRNA were not detected in the PBMC of those patients from whom the resected HCC tissues were MAGE-1 or MAGE-3 mRNA negative, nor in the 25 PBMC samples from healthy donors. The detection of MAGE transcripts in PBMC was correlated with the advanced stages and tumour size of the HCC, being 82.4% (14 out of 17) in tumour stages III and IVa, 56.6% (five out of nine) in stage II, and null (nought out of four) in stage I. The serum alpha-FP in 33.3% (10 out of 30) of HCC patients was normal or slightly elevated (< 40 ng ml(-1)). However, six of these 10 patients (alpha-FP < 40 ng ml(-1)) were MAGE-1 and /or MAGE-3 mRNA positive in their PBMC. The follow-up survey of MAGE mRNA in PBMC was performed in 12 patients. Seven patients with persistent MAGE-1 and/or MAGE-3 mRNA positive or from negative turned to positive died because of metastasis and/or recurrence. In striking contrast, all four patients with MAGE-1 and/or MAGE-3 mRNA from positive turned to negative and one patient with persistent MAGE-3 transcript negative are alive after last test. Collectively, detection of MAGE transcripts with follow-up survey in PBMC is a feasible and reliable assay for the early prediction of the relapse and prognosis of the HCC patients.