Removal of inhibitory substances from human fecal specimens for detection of group A rotaviruses by reverse transcriptase and polymerase chain reactions

Assessment of extracellular vesicle isolation methods from human stool supernatant

Extracellular vesicles (EVs) are of growing interest due to their potential diagnostic, disease surveillance, and therapeutic applications. While several studies have evaluated EV isolation methods in various biofluids, there are few if any data on these techniques when applied to stool. The latter is an ideal biospecimen for studying EVs and colorectal cancer (CRC) because the release of tumour markers by luminal exfoliation into stool occurs earlier than vascular invasion. Since EV release is a conserved mechanism, bacteria in stool contribute to the overall EV population. In this study, we assessed five EV separation methods (ultracentrifugation [UC], precipitation [EQ‐O, EQ‐TC], size exclusion chromatography [SEC], and ultrafiltration [UF]) for total recovery, reproducibility, purity, RNA composition, and protein expression in stool supernatant. CD63, TSG101, and ompA proteins were present in EV fractions from all methods except UC. Human (18s) and bacterial (16s) rRNA was detected in stool EV preparations. Enzymatic treatment prior to extraction is necessary to avoid non‐vesicular RNA contamination. Ultrafiltration had the highest recovery, RNA, and protein yield. After assessing purity further, SEC was the isolation method of choice. These findings serve as the groundwork for future studies that use high throughput omics technologies to investigate the potential of stool‐derived EVs as a source for novel biomarkers for early CRC detection.

Development of a PCR Assay for Diagnosing Trematode (Opisthorchis and Haplorchis) Infections in Human Stools

We developed a combined conventional polymerase chain reaction (PCR) and real-time PCR (qPCR)-based assay for detecting and discriminating between Opisthorchis viverrini and Haplorchis taichui parasite infections. The first PCR amplifies the mitochondrial cytochrome c oxidase subunit I (COI) genes of parasites, and differential diagnosis is achieved by performing qPCR with specific primers and SYBR Green I. The detection limit of the assay was found to be 2.0 × 10² plasmid copies in a test in which a stool sample was spiked with a single egg, which is equivalent to 5 eggs per gram (EPG). The testing of 34 clinical stool samples that had been demonstrated to contain "Opisthorchis-like" eggs by microscopy showed that the novel assay exhibited a sensitivity of 100% for "Opisthorchis-like" parasitic infections, and 71% and 91% of these samples were found to be infected with O. viverrini and H. taichui, respectively. A further four parasitic infections were diagnosed in the 16 negative samples, and the microscopic findings of these samples were confirmed to be false negatives by sequencing analysis. The assay also displayed high specificity during the testing of 10 samples containing other common parasites. The fact that our qPCR SYBR Green I-based assay detected submicroscopic traces of parasitic DNA and was able to differentiate between parasites that produce eggs with similar morphologies indicates that it has a good potential for development of diagnostic application to use in areas where multiple parasites coexist.

Molecular epidemiology of rotavirus in children and animals and characterization of an unusual G10P[15] strain associated with bovine diarrhea in south India

Rotaviruses are enteric pathogens causing acute, watery, dehydrating diarrhea in various host species, including birds and mammals. This study collected data on the disease burden and strain prevalence of Group A rotavirus in animals and humans in Vellore and investigated interspecies transmission by comparison of circulating genotypes. Stool samples from children aged less than 5 years, admitted to the hospital between January 2003 and May 2006 for diarrhea and diarrheal samples from animals that were collected from a veterinary clinic and several dairy farms near Vellore between February 2007 and May 2008 were processed and subjected to RNA extraction and reverse-transcription PCR for genotyping of VP7 and VP4. Of 394 children with diarrhea, 158 (40%) were positive for rotavirus and the common G types identified were G1 (47, 29.7%), G2 (43, 27.2%), G9 (22, 13.9%), G10 (2, 1.2%), G12 (1, 0.6%) and mixed infections (27, 17.8%). The common P types were P[4] accounting for 57 (36%) samples, P[8] 57 (36%), P[11] 3 (1.8%) and P[6] 2 (1.2%). Of 627 animals, 35 (1 bullock, 2 goats, 32 cows) were found to be infected with rotavirus (5.5%). The common G types identified in order of frequency were G6 (17, 48.5%), G2 (10, 28%), G10 (4, 11%), G8 (2, 5.7%) and mixed infections (2, 5.7%). The common P types were P[6] accounting for 16 (46%) samples, P[4] 7 (20%), P[1] 3 (8.5%) and P[8] 3 (8.5%). An unusual P type P[15] was seen in one sample in combination with G10. The finding of G2 infections which are rarely identified in animals implies anthroponotic transmission since this genotype is predominantly associated with infection in humans.

Microbiological Quality Control for Laboratory Rodents and Lagomorphs

Mice (Mus musculus), rats (Rattus norvegicus), other rodent species, and domestic rabbits (Oryctolagus cuniculus) have been used in research for over 100 years. During the first half of the 20th century, microbiological quality control of lab animals was at best rudimentary as colonies were conventionally housed and little or no diagnostic testing was done. Hence, animal studies were often curtailed and confounded by infectious disease (Mobraaten and Sharp, 1999; Morse, 2007; Weisbroth, 1999). By the 1950s, it became apparent to veterinarians in the nascent field of comparative medicine that disease-free animals suitable for research could not be produced by standard veterinary disease control measures (e.g., improved sanitation and nutrition, antimicrobial treatments) in conventional facilities. Henry Foster, the veterinarian who founded Charles River Breeding Laboratories in 1948 and a pioneer in the large-scale production of laboratory rodents, stated in a seminar presented at the 30th anniversary of AALAS, “After a variety of frustrating health-related problems, it was decided that a major change in the company’s philosophy was required and an entirely different approach was essential”. Consequently, he and others developed innovative biosecurity systems to eliminate and exclude pathogens (Allen, 1999). In 1958, Foster reported on the Cesarean-originated barrier-sustained (COBS) process for the large-scale production of specific pathogen-free (SPF) laboratory rodents (Foster, 1958). To eliminate horizontally transmitted pathogens, a hysterectomy was performed on a near-term dam from a contaminated or conventionally housed colony. The gravid uterus was pulled through a disinfectant solution into a sterile flexible film isolator where the pups were removed from the uterus and suckled on axenic (i.e., germ-free) foster dams. After being mated to expand their number and associated with a cocktail of nonpathogenic bacteria to normalize their physiology and prime their immune system, rederived rodents were transferred to so-called barrier rooms for large-scale production. The room-level barrier to adventitious infection entailed disinfection of the room, equipment, and supplies, limiting access to trained and properly gowned personnel, and the application of new technologies such as high-efficiency particulate air-filtration of incoming air (Dubos and Schaedler, 1960; Foster, 1980; Schaedler and Orcutt, 1983; Trexler and Orcutt, 1999). The axenic and associated rodents mentioned in the COBS process are collectively classified as gnotobiotic to indicate that they have a completely known microflora. By contrast, barrier-reared rodent colonies are not gnotobiotic because they are housed in uncovered cages and thus acquire a complex microflora from the environment, supplies, personnel, and other sources. Instead, they are described as SPF to indicate that according to laboratory testing, they are free from infection with a defined list of infectious agents, commonly known as an ‘exclusion’ list.

Development of a polymerase chain reaction applicable to rapid and sensitive detection of Clonorchis sinensis eggs in human stool samples

Microscopic examination of eggs of parasitic helminths in stool samples has been the most widely used classical diagnostic method for infections, but tiny and low numbers of eggs in stool samples often hamper diagnosis of helminthic infections with classical microscopic examination. Moreover, it is also difficult to differentiate parasite eggs by the classical method, if they have similar morphological characteristics. In this study, we developed a rapid and sensitive polymerase chain reaction (PCR)-based molecular diagnostic method for detection of Clonorchis sinensis eggs in stool samples. Nine primers were designed based on the long-terminal repeat (LTR) of C. sinensis retrotransposon1 (CsRn1) gene, and seven PCR primer sets were paired. Polymerase chain reaction with each primer pair produced specific amplicons for C. sinensis, but not for other trematodes including Metagonimus yokogawai and Paragonimus westermani. Particularly, three primer sets were able to detect 10 C. sinensis eggs and were applicable to amplify specific amplicons from DNA samples purified from stool of C. sinensis-infected patients. This PCR method could be useful for diagnosis of C. sinensis infections in human stool samples with a high level of specificity and sensitivity.

Impact of milk components on recovery of viral RNA from MS2 bacteriophage

Noroviruses are responsible for approximately 44 % of outbreaks involving dairy products for which causative agents are reported. Recovery of viruses from milk and dairy products is a difficult task. The role of different components of milk in the recovery of viral RNA was evaluated in this study. Four model milk formulations (A-D) were prepared by mixing different combinations of lactose, whey protein, casein, and fat in water. Each model formulation was spiked with five concentrations of bacteriophage MS2. The phenol-guanidine thiocyanate-chloroform protocol was used for extracting viral RNA from the model milk formulations and then extracted RNA was measured by a nanodrop spectrophotometer in ng/μl. The results showed that casein and whey protein had the highest negative impact on RNA yield, especially when the number of MS2 was less than 1.3 pfu/ml. The highest RNA recovery was obtained from the model milk formulation containing all four components; lactose, whey protein, casein, and fat. The amount of extracted RNA was closely correlated with the dry matter content of each formulation and the spiked concentration of coliphage using response surface modeling (R²:0.93). It was determined that milk fat is the most effective component in facilitating RNA extraction and the highest RNA yield can be achieved via elimination of whey protein and casein from milk by centrifugation at 40,000×g for 60 min. To achieve the highest viral RNA recovery efficiency by the proposed method, milk fat must be recombined with the supernatant of the centrifuged sample and then homogenized before performing the extraction protocol.

Exposure to human and bovine noroviruses in a birth cohort in southern India from 2002 to 2006

Human and bovine norovirus virus-like particles were used to evaluate antibodies in Indian children at ages 6 and 36 months and their mothers. Antibodies to genogroup II viruses were acquired early and were more prevalent than antibodies to genogroup I. Low levels of IgG antibodies against bovine noroviruses indicate possible zoonotic transmission.

Real-time polymerase chain reaction for detection of Strongyloides stercoralis in stool

The use of real-time polymerase chain reaction (PCR) for detection of Strongyloides stercoralis in stool has recently been described. We compared five DNA extraction methods by using normal human stool spiked with Strongyloides ratti and tested by using a real-time PCR. The PowerSoil kit was found to be the best technique in terms of sensitivity and ease of use. The PCR detected DNA extracted from one spiked S. ratti larva diluted 10⁻². The PowerSoil kit was then used to extract DNA from 160 human survey samples. All culture positive specimens with a high and moderate larval load were identified by real-time PCR, but only 15% of specimens with low larval load were positive. Specificity was greater than 99%. The combination of the PowerSoil kit and real-time PCR reliably detected high to moderate larval numbers of S. stercoralis in stools but was less sensitive when the larval load was low.

Potential application of superparamagnetic nanoparticles for extraction of bacterial genomic DNA from contaminated food and environmental samples

BACKGROUND

Isolation of high-molecular-weight DNA is essential for many molecular biology applications. Owing to the presence of polymerase chain reaction (PCR) inhibitors, there is a scarcity of suitable protocols for PCR-ready DNA extraction from food and natural environments. The conventional chemical methods of DNA extraction are time consuming and laborious and the yield is very low. Thus the aim of this research was to develop a simple, rapid, cost-effective method of genomic DNA extraction from food (milk and fruit juice) and environmental (pond water) samples and to detect bacterial contaminants present in those samples.

RESULTS

This approach is efficient for both Gram-positive and Gram-negative bacteria from all the studied samples. Herein super paramagnetic bare iron oxide nanoparticles were implemented for bacterial genomic DNA isolation. The method was also compared to the conventional phenol-chloroform method in the context of quality, quantity and timing process. This method took only half an hour or less to obtain high-molecular-weight purified DNA from minimum bacterial contamination. Additionally, the method was directly compatible to PCR amplification.

CONCLUSION

The problem of availability of suitable generalized methods for DNA isolation from various samples including food and environmental has been solved by a nanobiotechnological approach that may prove to be extremely useful in biotechnological applications.

Detection of Newcastle disease virus in organs and faeces of experimentally infected chickens using RT-PCR

Newcastle disease (ND) is a highly contagious avian disease. Rapid diagnosis of ND plays an important role in controlling outbreaks. Until now, time-consuming isolation of ND virus (NDV) in embryonated chicken eggs was used for NDV detection. For rapid diagnosis, reverse transcription-polymerase chain reaction (RT-PCR) with RNA extracted from tissue samples and faeces originating from experimentally and contact-infected chickens was established. Conjunctiva, lung, caecal tonsil and kidney proved to be the most suitable organs. In infected animals, NDV was detected most frequently between day 4 and 6 post-infection. Contact-infected animals gave most positive results between day 6 and 13 after exposure. RT-PCR was also able to reproducibly detect NDV in faecal samples. The RT-PCR did not show any cross-reactivity with other avian paramyxovirus serotypes, and additionally offers the possibility of subsequent sequencing of the amplified DNA allowing pathotyping of the isolate.

PCR inhibitors - occurrence, properties and removal

The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false-negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix-specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.

Detection and species identification of Campylobacter in stool samples of children and animals from Vellore, south India

Campylobacter spp. are an important cause of bacterial gastroenteritis frequently isolated from animal, poultry and environmental samples. In this study, we investigated the zoonotic potential of Campylobacter spp. by comparing prevalence rates and species in 394 children with diarrhoea and 652 animals in Vellore using PCR-based tools. Eighteen children (4.5%) had campylobacteriosis, a majority of whom had co-pathogens (15/18) and most were infected with Campylobacter jejuni (16/18). A few C. coli and mixed infections with both species were also seen. Among the animal samples, 16/25 chicken samples (64%) were positive and all were found to be C. jejuni.

Diversity in the enteric viruses detected in outbreaks of gastroenteritis from Mumbai, Western India

Faecal specimens collected from two outbreaks of acute gastroenteritis that occurred in southern Mumbai, India in March and October, 2006 were tested for seven different enteric viruses. Among the 218 specimens tested, 95 (43.6%) were positive, 73 (76.8%) for a single virus and 22 (23.2%) for multiple viruses. Single viral infections in both, March and October showed predominance of enterovirus (EV, 33.3% and 40%) and rotavirus A (RVA, 33.3% and 25%). The other viruses detected in these months were norovirus (NoV, 12.1% and 10%), rotavirus B (RVB, 12.1% and 10%), enteric adenovirus (AdV, 6.1% and 7.5%), Aichivirus (AiV, 3% and 7.5%) and human astrovirus (HAstV, 3% and 0%). Mixed viral infections were largely represented by two viruses (84.6% and 88.9%), a small proportion showed presence of three (7.7% and 11%) and four (7.7% and 0%) viruses in the two outbreaks. Genotyping of the viruses revealed predominance of RVA G2P[4], RVB G2 (Indian Bangladeshi lineage), NoV GII.4, AdV-40, HAstV-8 and AiV B types. VP1/2A junction region based genotyping showed presence of 11 different serotypes of EVs. Although no virus was detected in the tested water samples, examination of both water and sewage pipelines in gastroenteritis affected localities indicated leakages and possibility of contamination of drinking water with sewage water. Coexistence of multiple enteric viruses during the two outbreaks of gastroenteritis emphasizes the need to expand such investigations to other parts of India.

Viral Infections of Laboratory Mice

Viral infections of laboratory mice have considerable impact on research results, and prevention of such infections is therefore of crucial importance. This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler’s murine encephalomyelitis virus. For each virus, there is a description of the agent, epizootiology, clinical symptoms, pathology, methods of diagnosis and control, and its impact on research.

Diagnosis and pharmacological management of small intestinal bacterial overgrowth in children with intestinal failure

The present article provides a general overview of the possible diagnostic procedures available for the management of small intestinal bacterial overgrowth in pediatric patients with intestinal failure. The focus is to address current diagnostic tools and understand their associated advantages and disadvantages based on a literature search. Culture of small intestinal aspirates, noninvasive breath tests and an emerging interest in quantitative bacterial DNA fingerprinting are discussed. Proper management is critical for preventing the recurrence of small intestinal bacterial overgrowth and its related complications. Antibiotic prophylaxis is one approach to the treatment of bacterial overgrowth in intestinal failure patients. Although treatment trials can be challenging in such a vulnerable population, more investigative clinical studies examining early diagnosis, more effective control of recurrence and the prevention of associated complications must be conducted.

Evaluation of PCR inhibitory effect of enrichment broths and comparison of DNA extraction methods for detection of Salmonella Enteritidis using real-time PCR assay

The best enrichment broth and DNA extraction scheme was determined for rapid and sensitive detection of Salmonella Enteritidis in steamed pork using real-time PCR. The inhibitory effect of commonly used Salmonella enrichment broths, Rappaport-Vassiliadis (RV) and Muller-Kauffmann tetrathionate with novobiocin (MKTTn), on real-time PCR was confirmed. The inhibition of PCR was statistically significant (p < 0.05) in RV and MKTTn, as compared with buffered peptone water (BPW) or phosphate-buffered saline. The inhibitory effect of the selective enrichment media was successfully removed by using a modified DNA extraction, PrepMan Ultra Reagent with an additional washing step or the DNeasy Tissue Kit. In three experiments, when applied to detection of Salmonella Enteritidis in steamed pork, the real-time PCR coupled with single 24 h enrichment with BPW performed better than double 48 h enrichment with BPW plus RV or MKTTn. The simple real-time PCR assay using BPW proved to be a rapid and sensitive test for detection of low concentrations of Salmonella Enteritidis in steamed pork samples as compared with the conventional culture method.

Characterization of group A rotavirus infections in adolescents and adults from Pune, India: 1993-1996 and 2004-2007

A total of 1,591 fecal specimens were collected in 1993-1996 and 2004-2007 from adolescents and adults with acute gastroenteritis in Pune, India for detection and characterization of rotavirus. At the two time points, group A rotavirus was detected in 8.6% and 16.2% of the adolescents and 5.2% and 17.2% of the adults, respectively. Reverse transcription-PCR with consensus primers followed by multiplex genotyping PCR detected common strains G1P[8], G2P[4], G3P[8], and G4P[8] in a total of 53.1% of the samples from 1993 to 1996, while the only prevalent strain identified in 2004-2007 was G2P[4] (23.5% of total). Uncommon rotavirus strains (G1P[4], G2P[8] G9P[6]/P[4]) increased from 7.8% (1993-1996) to 41.2% (2004-2007), while the prevalence of mixed rotavirus infections was high (39%/35%) at both time points. Mixed infections detected by multiplex PCR were confirmed by sequencing two or more individual genotype-specific PCR products of the VP7 and VP4 genes from the same sample. Phylogenetic analysis of the sequences showed circulation of a heterogeneous rotavirus strain population comprising genotypes G1 (lineages I and IIb), G2 (lineages I and IIb), G4 (lineage Ia), P[4] (lineages P[4]-5 and P[4]-1), P[8] (lineages P[8]-II and P[8]-III), and P[6] (M37-like lineage). The VP6 gene sequences of the nontypeable strains were most homologous to animal strains. This study documents the molecular epidemiology of rotavirus strains in adolescents and adults in India, and suggests that it may be important to monitor these strains over time for the potential impact on rotavirus vaccines under development for use in the Indian population. J. Med. Virol. 82:519-527, 2010. (c) 2010 Wiley-Liss, Inc.

A set of novel multiplex Taqman real-time PCRs for the detection of diarrhoeagenic Escherichia coli and its use in determining the prevalence of EPEC and EAEC in a university hospital

Background

Accurate measurement of the incidence of diarrhoeagenic E. coli in patients with diarrhoea is hindered by the current methods of detection and varies from country to country. In order to improve the diagnosis of diarrhoeagenic E. coli (DEC), we developed a set of multiplex TaqMan real-time PCRs designed to detect the respective pathogens from an overnight stool culture.

Methods

Over the period Jan. 2006 to Dec. 2006 all stool specimens (n = 1981) received were investigated for EPEC and EAEC.

Results

Of these, 371 specimens had no growth of Enterobacteriaceae. Of the remaining 1610 specimens 144 (8,9%) were positive for EPEC and 78 (4,8%) positive for EAEC. Among the EPEC positive stool specimens 28 (19,4%) were received from the tropical diseases unit, 49 (34%) from the paediatric dept. and 67 (46,5%) from the remainder of the wards. The EAEC were distributed as follows: 39 (50%) - tropical diseases, 19 (24,4%) -paediatrics and 20 (25,6%) other wards. Proportionately more EAEC and EPEC were found in children less than 3 years of age than other age groups. In only 22,2% of the detected EPEC and 23% of EAEC was the investigation requested by hospital staff.

Conclusions

This is, to our knowledge, the first study using a multiplex TaqMan PCR for the successful detection of diarrhoeagenic E. coli. In conclusion, due to the high prevalence of DEC detected, investigation of EPEC and EAEC should be recommended as a routine diagnostic test for patients with infectious diarrhoea.

Detection of spatial and temporal spread of Mycobacterium avium subsp. paratuberculosis in the environment of a cattle farm through bio-aerosols

Environmental samples were collected to investigate the spatial and temporal spread of Mycobacterium avium subsp. paratuberculosis (MAP) in a dairy cattle barn before and after the introduction of two groups of MAP-shedding animals. Samples collected off the floor of the barn reflected the moment of sampling whereas samples collected by microfiber wipes at a minimal of 3m height contained the accumulated settled dust over a 3-week period. Samples were analysed by IS900 qPCR for the presence of MAP DNA and by culture for viable MAP bacteria. MAP DNA was detected in a large number of sites both before and after introduction cattle. MAP DNA was detected inside the barn in floor and dust samples from cubicles and slatted floors and in settled dust samples located above the slatted floors and in the ventilation ridge opening. Outside the barn MAP DNA was detected by PCR in samples reflecting the walking path of the farmer despite hygiene measures. No viable MAP was detected before the introduction of shedder cattle. Three weeks later viable MAP was found inside the barn at 7/49 locations but not outside. Fifteen weeks later viable MAP was also detected in environmental samples outside the barn. In conclusion, introduction of MAP shedding cattle lead to widespread contamination of the internal and external environment of a dairy barn, including the presence of viable MAP in settled dust particles suggesting potential transmission of MAP infection through bio-aerosols.

[Predominance of G9 rotavirus in Valencia and Castellón between 2005 and 2007]

INTRODUCTION

Rotavirus is the leading cause of acute gastroenteritis in young children worldwide. Effective vaccines to prevent rotavirus infections are currently available, although their clinical use is still limited, and rotavirus still causes many episodes of infantile gastroenteritis, mainly during the winter seasons.

OBJECTIVE

To characterise G (VP7) and P (VP4) genotypes of rotaviruses causing acute gastroenteritis in children and to determine the prevalence of genotype G9 rotavirus in three public health areas in the provinces of Valencia and Castellon.

PATIENTS AND METHODS

Five-hundred and forty-one stool samples were prospectively collected from infants and children with gastroenteritis in the period between October 2005 and September 2008. They were analysed for rotavirus by ELISA or by immunochromatography. G and P genotyping was performed by reverse transcription and PCR (RT-PCR).

RESULTS

G and P rotavirus genotypes were characterised in a total of 525 faecal samples (97%), resulting in a global predominance of strains G9P[8] (56.5%) and G1P[8] (29.9%). During the period of time studied, G9P[8] was the G/P combination most frequently detected during the rotavirus seasons 2005-2006 and 2006-2007, being present in 81.2% and 64.7% of the patients, respectively. However, during the 2007-2008 season, G1P[8] strains were the most frequently found (68.8%), with a sharp decrease in G9P[8] strains to 7.2% of the samples.

CONCLUSIONS

Rotavirus G9P[8] have spread rapidly and widely during the 2005-2006 and 2006-2007 seasons, replacing other previously dominant genotypes (G1, G4) in our geographic area. Its incidence has declined sharply in 2007-2008, in which G1P[8] was again the predominating genotype.

PCR Diagnosis of Opisthorchis viverrini and Haplorchis taichui Infections in a Lao Community in an area of endemicity and comparison of diagnostic methods for parasitological field surveys

Opisthorchiasis is a major public health problem in Southeast Asia. Affected individuals often have mixed infections with the liver fluke Opisthorchis viverrini and minute intestinal flukes such as Haplorchis taichui. The usual methods of diagnosing these infections involve the demonstration of fluke eggs in stool samples under light microscopy, but sensitivity and specificity are low. We developed two PCR tests that detect and discriminate between O. viverrini and H. taichui infections. PCR tests were validated by stool samples from purged individuals. We then applied the PCR tests to estimate the prevalence of O. viverrini and H. taichui infections from a random sample of individuals selected from a community in an area of endemicity in Khong District, Laos. PCR results were compared with those from the Kato-Katz (KK) method and the formalin-ether concentration technique (FECT). When validated with purge results, PCR tests of O. viverrini and H. taichui had sensitivities of 93.7% (95% confidence interval [CI], 85.8 to 97.9%) and 73.3% (95% CI, 60.3 to 83.9%) and could detect as little as 0.75 pg DNA and 1.32 ng DNA, respectively. The PCR-determined community prevalences of O. viverrini and H. taichui infections were 63.9% (95% CI, 54.1 to 72.9%) and 30.6% (95% CI, 22.1 to 40.2%), respectively. Using PCR as the gold standard to detect O. viverrini, three KK thick smears performed comparably well, whereas one KK smear and FECT were poorer (sensitivities of 91.4% [95% CI, 81.0 to 97.1%,], 62.3% [95% CI, 49.8 to 73.7%], and 49.3% [95% CI, 37.0 to 61.6%], respectively). PCR may be a valuable and sensitive diagnostic tool, particularly for low-intensity O. viverrini and H. taichui infections.

High frequency of rotavirus viremia in children with acute gastroenteritis: discordance of strains detected in stool and sera

Recently, rotavirus antigenemia and viremia have been identified in patients with acute gastroenteritis. This study examined rotavirus viremia in children hospitalized for acute gastroenteritis in order to establish its association with fecal shedding of rotavirus, infecting genotypes and antibody marker of acute infection. Thirty-one pairs of stool-serum specimens were collected from November 2004 to February 2005 together with clinical information. All paired specimens were screened for rotavirus RNA by RT-PCR using the VP6 gene primers. All stool and serum specimens were tested for rotavirus antigen and anti-rotavirus IgM respectively by ELISA. Sixteen of 31 stool-serum pairs showed the presence of rotavirus RNA. Nine stool and two serum specimens were positive only by RT-PCR. The total positivity in rotavirus RNA was significantly higher in both stools (80.6%) and sera (58.1%) than that of stool antigen (38.7%) and anti-rotavirus IgM (25.8%) (P < 0.01). All PCR positive paired specimens were typed for the VP7 (G) and VP4 (P) genes. Five of sixteen pairs could be typed for both genes. Three of the five pairs showed concordance (G2P[4]/G2P[4]) while two showed discordance (G12P[8]/G2P[4], G8P[4]/G2P[4]) in the genotypes detected in stool and serum specimens respectively. The study documents a high frequency of rotavirus viremia in patients with acute diarrhea. The discordance of rotavirus strains at the genotypic level in the serum and stool of individual patients with diarrhea suggests the susceptibility of extra-intestinal sites for rotavirus infection and the possibility of differential dissemination of rotavirus strains from the intestine.

The first finding of Echinococcus multilocularis in dogs in Slovakia: an emerging risk for spreading of infection

Alveolar echinococcosis, caused by the metacestode Echinococcus multilocularis, is a zoonosis of public health significance. Apart from red foxes, other carnivore species can also serve as definitive hosts of this parasite. This study aimed to determine the occurrence of E. multilocularis in dogs in the Slovak Republic and identify risk factors for acquiring the infection. Out of 289 dogs examined, E. multilocularis was detected in eight samples (2.8%). Positive results were observed in shepherd dogs (12.5%), guard dogs (7.1%), hunting dogs (2.4%) and in one dog with unknown usage (2.5%). Catching rodents and feeding with raw viscera were confirmed to be the most important risk factors for E. multilocularis infection. On the contrary, the way of dog use, frequency of going to the rural areas, the age and gender of animals seem not to be risk factors for infection. No significant association was observed between the positivity of dogs coming from high endemic or non-endemic regions. This is the first report of E. multilocularis in dogs in the Slovak Republic that confirms substantial contribution of dogs to the transmission of the tapeworm in this territory and urges the necessity of prophylactic measures for dog owners.

The effect of sample type, temperature and RNAlater on the stability of avian influenza virus RNA

As a result of continuing worldwide outbreaks of highly pathogenic avian influenza (HPAI) caused by the Asian lineage of H5N1, surveillance of targeted avian species in selected regions has been implemented. In these wild bird surveys, the use of real-time reverse transcription (rRT)-PCR has proved to be an invaluable tool as a frontline screening assay for the detection of avian influenza virus (AIV) RNA. However, verification of HPAI diagnosis, particularly in a primary outbreak situation, requires confirmation by a national, community or world reference laboratory. This may necessitate freezing and thawing of samples, sub-sampling and transportation to the reference laboratory. The deleterious effects of such handling on the infectivity of virus and the yield of viral RNA have been observed. The objective of this study was to investigate the effects of freezing and thawing, time, sample type and transportation on the yield of AIV RNA. Additionally, the effect of the RNA stabilisation agent, RNAlater was investigated. It was demonstrated that the quality of AIV RNA in faecal homogenate was markedly reduced by freezing and thawing, but that treatment with RNAlater protected the viral RNA from deterioration. When using RNAlater even low titre AIV samples were protected from the detrimental effects of time and transportation conditions.

Clinical evaluation of NucliSENS magnetic extraction and NucliSENS analyte-specific reagents for real-time detection of human metapneumovirus in pediatric respiratory specimens

In this study, we evaluated the NucliSENS miniMAG (MM) and easyMAG (EM) nucleic acid extraction platforms (bioMérieux, Durham, NC) in combination with the NucliSENS EasyQ basic kit and analyte-specific reagents (ASRs) (bioMérieux) for the detection of human metapneumovirus (hMPV) in respiratory samples. Total nucleic acids from pediatric clinical samples (n = 653) and an hMPV-specific inhibition control (h-IC) were coextracted using the MM and/or the EM. Nucleic acid sequence-based amplification and real-time molecular beacon detection of hMPV were performed using a NucliSENS EasyQ analyzer (bioMérieux). Positive results were confirmed using an in-house-validated reverse transcriptase PCR ASR-based assay. The inclusion of the h-IC monitored the entire process, including the efficiency of nucleic acid extraction, amplification, and detection. The percentages of samples with inhibited amplification of the h-IC after initial NA extraction by EM and MM were 1.88% and 3.17%, respectively. After reprocessing of a new aliquot, the final h-IC inhibition rates were 0% (EM) and 1.06% (MM). The limit of detection of the assay was between 2 (EM extraction) and 10 (MM extraction) RNA copies/reaction, and specificity was 100% when testing viral respiratory isolates and clinical samples. hMPV was detected in 5.6% of pediatric samples tested and was also detected in three coinfections with respiratory syncytial virus (RSV). hMPV was the second most frequently detected respiratory virus in children of 0 to 2 years of age, after RSV. In summary, NucliSENS extraction and ASRs provided a sensitive and specific method for the detection of hMPV in respiratory samples.

Spread of infectious chronic bee paralysis virus by honeybee (Apis mellifera L.) feces

Knowledge of the spreading mechanism of honeybee pathogens within the hive is crucial to our understanding of bee disease dynamics. The aim of this study was to assess the presence of infectious chronic bee paralysis virus (CBPV) in bee excreta and evaluate its possible role as an indirect route of infection. Samples of paralyzed bees were (i) produced by experimental inoculation with purified virus and (ii) collected from hives exhibiting chronic paralysis. CBPV in bee heads or feces (crude or absorbed onto paper) was detected by reverse transcription-PCR. CBPV infectivity was assessed by intrathoracic inoculation of bees with virus extracted from feces and by placement of naive bees in cages previously occupied by contaminated individuals. CBPV RNA was systematically detected in the feces of naturally and experimentally infected bees and on the paper sheets that had been used to cover the floors of units containing bees artificially infected with CBPV or the floor of one naturally infected colony. Both intrathoracic inoculation of bees with virus extracted from feces and placement of bees in contaminated cages provoked overt disease in naive bees, thereby proving that the excreted virus was infectious and that this indirect route of infection could lead to overt chronic paralysis. This is the first experimental confirmation that infectious CBPV particles excreted in the feces of infected bees can infect naive bees and provoke overt disease by mere confinement of naive bees in a soiled environment.

Coxiella burnetiishedding by dairy cows

While shedding routes of Coxiella burnetii are identified, the characteristics of Coxiella shedding are still widely unknown, especially in dairy cattle. However, this information is crucial to assess the natural course of Coxiella burnetii infection within a herd and then to elaborate strategies to limit the risks of transmission between animals and to humans. The present study aimed at (i) describing the characteristics of Coxiella burnetii shedding by dairy cows (in milk, vaginal mucus, faeces) in five infected dairy herds, and at (ii) investigating the possible relationships between shedding patterns and serological responses. A total of 145 cows were included in a follow-up consisting of seven concomitant samplings of milk, vaginal mucus, faeces and blood (Day 0, D7, D14, D21, D28, D63, D90). Detection and quantification of Coxiella burnetii titres were performed in milk, vaginal mucus and faeces samples using real-time PCR assay, while antibodies against Coxiella were detected using an ELISA technique. For a given shedding route, and a given periodicity (weekly or monthly), cows were gathered into different shedding kinetic patterns according to the sequence of PCR responses. Distribution of estimated titres in Coxiella burnetii was described according to shedding kinetic patterns. Coxiella burnetii shedding was found scarcely and sporadically in faeces. Vaginal mucus shedding concerned almost 50% of the cows studied and was found intermittently or sporadically, depending on the periodicity considered. Almost 40% of cows were detected as milk shedders, with two predominant shedding patterns: persistent and sporadic, regardless of the sampling periodicity. Significantly higher estimated titres in Coxiella burnetii were observed in cows with persistent shedding patterns suggesting the existence of heavy shedder cows. These latter cows were mostly, persistently highly-seropositive, suggesting that repeated serological testings could be a reliable tool to screen heavy shedders, before using PCR assays.

Detection and Identification of Salmonella Typhimurium in Bovine Diarrhoeic Fecal Samples by Immunomagnetic Separation and Multiplex PCR Assay

The aim of this study was to use the immunomagnetic separation (IMS) test plus a multiplex polymerase chain reaction (m-PCR) assay to detect Salmonella at genus level and also for the identification of Salmonella enterica serovar Typhimurium in bovine diarrhoeic fecal samples. In all, 400 bovine diarrhoeic fecal specimens were examined by conventional bacterial culture, IMS, and m-PCR. For m-PCR assay, four set primers were selected: 139-141, specific for inv-A gene of Salmonella spp and the RfbJ, FliC and FljB, specific for the rfbJ, FliC and fljB genes of Salmonella Typhimurium or other Salmonella serovars with similar antigenic properties. Thirty-three (8.25%) out of the 400 fecal samples were culture positive for Salmonella serovars. Of these, 66.7% (22 of 33) were Salmonella enterica serovar Typhimurium, and 9.1% (three of 33) were serovar Dublin. In the IMS + m-PCR, four amplified product (663, 526, 284 and 183 bp) were found in all specimens that had serovar Typhimurium (4,5,12:i:1,2), they corresponded, respectively, to the rfbJ, fljB, inv-A and Flic genes of this serovar. In serovar Dublin (1,9,12:g,p:-), Georgia (6,7:b:e,n,z(15)) and, Enteritidis (1,9,12;g,m:-) only one PCR product (284 bp) was amplified from the inv-A gene. In serovars Augustenborg (6,7:i:1,2) and Lindenburg (6,8:i:1,2) three positive bands (526, 284 and 183 bp) were amplified corresponding to the fljB, inv-A and Flic genes, respectively. In serovar Virchow (6,7:r:1,2) two amplified products (284 and 526 bp) from the inv-A and FliC genes were observed. In serovar Gloucster (1,4,12(27):i:1,w) three fragments (183, 284 and 663) from the FliC, inv-A and, rfbJ genes respectively, were observed. In the positive control as expected, four PCR products were amplified corresponding to the FliC, inv-A, fljB and rfbJ genes, respectively. In conclusion, the results of this study showed that detection of Salmonella at genus level with universal ST139-141 primers and identification of Salmonella Typhimurium by using specific primers of O4, H(2):1, 2 and H(1) antigens can potentially permit to more readily evaluate fecal and other types of samples for the presence of these organisms. Compared to bacteriological culture the combination of IMS and m-PCR resulted a faster method for the detection and identification of Salmonella at genus and serovar level by using of universal and specific primers.

Characterization of VP6 genes from rotavirus strains collected in the United States from 1996–2002

We sequenced 22 VP6 genes from common rotavirus strains P[8], G1; P[4], G2; P[8], G3; P[8], G4 and P[8], G9 and uncommon type P[6], G9 collected in the US over a 6-year period. All strains defined as members of VP6 antigenic subgroup (SG) I according to reactivity patterns with monoclonal antibodies formed a genetic cluster (Genogroup I) with SG I reference strains. Similarly, all strains in antigenic SGII formed a group (Genogroup II) with corresponding standard strains of the same SG. Most US strains of each genogroup had diverged by 10-15% from the VP6 gene sequence of reference strains collected >20 years earlier and some recent isolates from other countries. Evolutionary analysis demonstrated that recently isolated US strains of both genogroups have diverged into 2-3 related clusters consistent with other recent findings. Unexpectedly, some recent isolates from other countries have diverged greatly from both older reference isolates and from the recent US isolates characterized here. This finding suggests that genetic diversity in human rotavirus VP6 genes may be greater than previously recognized. These sequences will help in the construction of a VP6 gene database to aid in the development of broadly reactive molecular assays and permit identification of regions where primers and probes for existing assays may need to be redesigned.

Development of a novel internal control for a real-time PCR for HSV DNA types 1 and 2

BACKGROUND

Detection of herpes simplex virus types 1 and 2 DNA by polymerase chain reaction (PCR) is the method of choice in many laboratories due to improved sensitivity, specificity and turnaround times compared with culture and antigen detection. However, internal controls need to be employed to ensure that inhibitors in samples do not produce false negative results.

OBJECTIVE

We have developed an internal control for our routine diagnostic HSV 1 and 2 LightCycler PCR assay that has identical primer binding sites to the HSV target DNA but an internal sequence derived from plasmid DNA and detected by a different probe and fluorophore combination.

METHODS

Production of the internal control was achieved using a straightforward two-step PCR technique in which plasmid DNA was amplified with HSV-plasmid chimeric primers, followed by amplification of the resulting amplicons with HSV primers and purification for subsequent use.

RESULTS

Both the internal control and viral DNA were amplified in initial tests with 11 tissue-culture HSV 1 and 2 positives (22 in total), with little or no inhibition of the target sequences. A high level (98%) of concordant results were obtained with 272 clinical samples assayed in parallel with and without the internal control.

CONCLUSION

These results are sufficient to justify the incorporation of the internal control into the routine LightCycler HSV DNA assay in our laboratory.

Quantitative Correlation of Helicobacter pylori Stool Antigen (HpSA) Test with the Severity of H. pylori-Related Gastritis

The Helicobacter pylori (H. pylori) load in both stomach and stool and the resulting severity of gastritis are important criteria in validating the status of H. pylori infection. We aimed to assess the reliability of the H. pylori stool antigen (HpSA) test for the primary diagnosis of H. pylori infection by calculating the best cut-off value to obtain the highest sensitivity and specificity in dyspeptic patients. We also investigated the correlation of HpSA test with the severity of gastritis and H. pylori load. The H. pylori statuses of 95 patients were evaluated by the positivity of both rapid urease test and microscopic detection of H. pylori in biopsy specimens, 88 subjects of whom were H. pylori positive. The sensitivity and specificity of the HpSA test were 51.1% (45/88) and 100% (7/7), respectively, according to the manufacturer's recommended cut-off value of 0.16. However, with the best cut-off value of 0.048, calculated by receiver operator characteristics analysis, the sensitivity of the test increased to 92.0% (81/88) with the same specificity. High values of the HpSA test were correlated with high scores of corpus H. pylori load and the severity of antrum and corpus inflammation (p < 0.05). With the best cut-off value of the HpSA test, the primary diagnosis of H. pylori infection can be made with higher sensitivity and specificity. The HpSA test is a helpful tool that evaluates the severity of H. pylori infection and the degree of gastric inflammatory activity and gastric H. pylori load.