Three-color crystal digital PCR.

Digital PCR is an exciting new field for molecular analysis, allowing unprecedented precision in the quantification of nucleic acids, as well as the fine discrimination of rare molecular events in complex samples. We here present a novel technology for digital PCR, Crystal Digital PCR™, which relies on the use of a single chip to partition samples into 2D droplet arrays, which are then subjected to thermal cycling and finally read using a three-color fluorescence scanning device. This novel technology thus allows three-color multiplexing, which entails a different approach to data analysis. In the present publication, we present this innovative workflow, which is both fast and user-friendly, and discuss associated data analysis issue, such as fluorescence spillover compensation and data representation. Lastly, we also present proof-of-concept of this three-color detection system, using a quadriplex assay for the detection of EGFR mutations L858R, L861Q and T790M.

Two outbreaks of neuropathogenic equine herpesvirus type 1 with breed-dependent clinical signs.

Equine herpesvirus type 1 (EHV-1) is a worldwide spread pathogen of horses. It can cause abortion, respiratory and neurological disease and consequentially significant economic losses in equine industries. During 2009, two outbreaks of EHV-1 were confirmed in two stud farms in Eastern Croatia. The first outbreak occurred in February following the import of 12 horses from USA, serologically negative to EHV-1 before transport. Four mares aborted in the late stage of pregnancy and one perinatal death was recorded. Other six mares showed clinical signs of myeloencephalopathy with fatal end in four. One month later, the second EHV-1 outbreak was confirmed in stud farm about 100 km further with 17 abortions, three perinatal deaths and one mild neurological case. Epidemiological data showed that the disease was probably introduced in the first stud farm during international transport. The second outbreak started with the introduction of clinically healthy stallion from the first stud farm. Molecular characterisation and phylogenetic analysis confirmed that, despite different clinical signs, the identical virus caused both outbreaks. Both horse populations were free from EHV-1 infection before the outbreak and had not been vaccinated. Significant difference in clinical signs could be explained by different breed-related risk factors.

A quantitative PCR assay for the detection and quantification of Shiga toxin-producing Escherichia coli (STEC) in minced beef and dairy products.

Shiga toxin (Stx)-producing Escherichia coli (STEC) are amongst major causes of food-borne infectious diseases and outbreaks. A new quantitative PCR (qPCR) assay was designed to detect all known stx gene subtypes in a single reaction, including the most distant variant stx2f. Performance of this assay was evaluated in combination with two different internal amplification controls (IAC), a competitive one specific for the assay and a universal IAC based on plasmid pUC19. The qPCR assay was 100% specific and showed analytical sensitivity of two STEC genome copies per reaction. The diagnostic approach proposed, combining enrichment, automated DNA extraction and qPCR detection, could reliably detect the presence of STEC in minced beef and cheese inoculated before enrichment at <4 CFU per 25 g. A comparative study performed on 240 minced beef and 113 raw milk cheese samples demonstrated that the method developed was as effective as two PCR screening assays used routinely in our laboratory to detect STEC. The new assay also proved to be appropriate for the direct quantification of STEC in milk and minced meat. It was found to be quantitative over a five log dynamic range, from 4 × 106 to 40 CFU/mL for milk and from 107 to 10² CFU/g for minced beef. In conclusion, the qPCR assay developed here represents a valuable tool for rapid detection and quantification of STEC in foods such as minced beef and dairy products as it ensures a high sensitivity and an optimal STEC diagnostic spectrum, taking into account the genetic stx variability observed in STEC population.

Duplex real-time PCR detection of type III effector tccP and tccP2 genes in pathogenic Escherichia coli and prevalence in raw milk cheeses.

AIMS: To develop a duplex real-time PCR assay targeting enterohaemorrhagic Escherichia coli (EHEC) type III effector TccP/TccP2-encoding genes which are pivotal to EHEC-mediated actin cytoskeleton reorganization in human intestinal epithelial cells. METHODS AND RESULTS: The specificity of the assay was demonstrated with DNA from EHEC reference strains and non-E. coli bacterial species. The detection limit was determined as five tccP or tccP2 copies per reaction. The assay was then evaluated on a large collection of 526 E. coli strains of human, animal, food and environmental origins. The results showed that tccP was restricted to a limited number of serotypes (i.e. O5:H(-) , O55:H7, O125:H6 and O157:H7). The tccP2 gene was present in a higher number of serotypes including the five most frequent EHEC serotypes (i.e. O26:H11, O103:H2, O111:H8, O145:H28 and O157:H7), and a few other serotypes that caused human infections (i.e. O4:H(-) , O45:H2 and O55:H7). A minority of O26:H11 and O103:H2 strains however tested negative for tccP2, though it is not known whether the lack of tccP2 affected their pathogenic potential. Real-time PCR analysis of 400 raw milk cheeses revealed the presence of tccP and/or tccP2 genes in 19·75% of the cheese enrichment suspensions. CONCLUSIONS: A highly specific and sensitive duplex real-time PCR method was developed for rapid and simultaneous detection of tccP and tccP2. Unpasteurized dairy products may be contaminated with E. coli strains carrying tccP and/or tccP2. SIGNIFICANCE AND IMPACT OF THE STUDY: The developed real-time PCR assay represents a valuable alternative to conventional PCR tests and should be useful for characterization of the virulome of pathogenic E. coli strains.

Simplex and multiplex real-time PCR assays for the detection of flagellar (H-antigen) fliC alleles and intimin (eae) variants associated with enterohaemorrhagic Escherichia coli (EHEC) serotypes O26:H11, O103:H2, O111:H8, O145:H28 and O157:H7.

AIMS: To develop real-time PCR assays targeting genes encoding the flagellar antigens (fliC) and intimin subtypes (eae) associated with the five most clinically important serotypes of enterohaemorrhagic Escherichia coli (EHEC), i.e. O26:H11, O103:H2, O111:H8, O145:H28 and O157:H7. METHODS AND RESULTS: Primers and probes specific to fliC(H2) , fliC(H7) , fliC(H8) , fliC(H11) , fliC(H28) , eae-ß1, eae-γ1, eae-ε and eae-θ were combined in simplex and multiplex 5'-nuclease PCR assays. The specificity of the assays was assessed on 201 bacterial strains and the sensitivity determined on serially diluted EHEC genomes. The developed PCR assays were found to be highly specific and detected as few as five EHEC genome equivalents per reaction. Furthermore, it was possible to detect the five major EHEC serotypes in cheese samples inoculated at concentration levels of ≤5CFU per 25g after overnight enrichment using the PCR assays. CONCLUSIONS: The PCR assays developed here were found to be sensitive and specific for the reliable detection of genes encoding the flagellar antigens and intimin variants belonging to the five most clinically relevant EHEC serotypes. SIGNIFICANCE AND IMPACT OF THE STUDY: Application of real-time PCR assays should improve the identification of foods contaminated by EHEC and facilitate the molecular typing of these organisms.

Screening of food raw materials for the presence of Shiga toxin-producing Escherichia coli O91:H21.

AIMS: To provide information on the prevalence and detection, in foods, of Shiga toxin-producing Escherichia coli (STEC) O91:H21. METHODS AND RESULTS: Seven hundred fifteen minced beef meats and 205 raw milk samples were analysed by stx-specific PCR-ELISA. Samples positive for stx were subsequently tested for the presence of wzy-O91, fliC-H21 and the adhesin-encoding gene saa. For minced meat, 16 (2.2%) and 11 (1.5%) samples were found positive for (stx, wzy-O91, fliC-H21) and (stx, wzy-O91, fliC-H21, saa) combinations, respectively. For raw milk, seven (3.4%) samples were found positive for the (stx, wzy-O91, fliC-H21) combination but none of these contained saa. Two STEC O91:H21 saa-positive strains and three STEC O91 H21- and saa-negative strains were isolated by colony hybridization. CONCLUSIONS: A low prevalence of potentially pathogenic STEC O91:H21 in food products was found using a combination of PCR assays targeting stx, wzy-O91, fliC-H21 and saa. SIGNIFICANCE AND IMPACT OF THE STUDY: The PCR-based approach described here represents a valuable method for rapid screening of food samples contaminated by STEC O91:H21.

Immune complex-based vaccine for pig protection against parvovirus.

The insoluble immune complexes (ICs) were prepared under the conditions of double immunodiffusion in gel, using the suspension of the ultrasound treated PK-15 cell-line infected with porcine parvovirus (PPV) containing both viral particles and viral proteins, as well as pig or rabbit anti-PPV polyclonal immune sera. The immunodiffusion performed in an agarose gel allows only viral subunits with a molecular mass equal to or less than 1000 kDa, rather than the viral particles, to diffuse through the gel and reach the point where the immunoprecipitate is to be formed. The immunoprecipitation under the conditions of the diffusion ensures the optimal, i.e. equimolar ratio of both immunoprecipitating components, antibody/antigen in the IC. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the Western blot analyses showed the ICs were composed of two proteins, a protein in which molecular mass corresponded to the VP2 of the PPV and a protein with a molecular mass of the IgG. This suggests that the ICs are mainly composed of the VP2 antigen and IgG class antibodies. The potency of the IC-vaccines prepared in the form of a water-in-oil-in-water emulsion was compared with that of a commercially available, inactivated oil vaccine. The vaccination of gilts, 6 weeks before mating, with the IC containing allogeneic pig antibodies, resulted in the development of high and long-lasting anti-PPV antibody titres, similar to those generated by the licenced vaccine (P > 0.01). The content of the virus material administered by the IC was twice lower than that in the licenced vaccine. Neither systemic nor local reactions were observed in the gilts during the period of the trial with the IC vaccine. The number of viable piglets per litter varied between 9 and 12 and no signs of the PPV infection were detected. Rabbits were used as one of the alternative laboratory animal models accepted for the testing of the vaccine against the PPV. The rabbit humoral immune response generated by the IC containing the allogeneic antibodies were higher than that generated by the ICs containing the xenogeneic pig antibodies. It was similar to that generated by two-times higher content of the virus material administered by a commercially available vaccine. The IC-based vaccines belong to non-replicating, subunit vaccines, which are both ecologically convenient and the safest vaccines of all.

[An acute pancreatitis in a child caused by Na-valproate]. / Akutni pankreatitis kod deteta uzrokovan Na-valproatom.

Na-valproat (Apilepsin, Eftil), is is a commonly prescribed medication approved for treatment of epilepsy, trigeminal neuralgy, migraine, and bipolar disorder. Although the common adverse effects associated with Na-valproat are usually benign, more serious and fatal complication like liver failure and acute pancreatitis (AP) can occur. Acute pancreatitis may take place in all ages, regardless of dose and serum levels of the medicine. An acute pancreatitis is relatively common after intravenous administration. The authors presented a case of acute opancreatitis in 13-years girl caused by Na-valproat.

Serological evidence of bluetongue and a preliminary entomological study in southern Croatia.

In December 2001, bluetongue (BT) was confirmed serologically by the Croatian Veterinary Institute using the competitive enzyme-linked immunosorbent assay (c-ELISA). Results of the serological testing of blood samples from ruminants in the Dubrovacko-Neretvanska County are presented (3,318 sera of ruminants from 53 herds were examined). In total, 357 bovine sera (178 or 49.9% positive), 1,268 ovine sera (174 or 13.7% positive) and 1,693 caprine sera (270 or 15.9% positive) were tested. Antibodies to BT virus serotype 9 were detected in 212 of the positive sera by serum neutralisation. A preliminary light-trap survey for midges of the Culicoides genus was also performed in the Dubrovacko-Neretvanska County. Fourteen light-trap collections from seven locations were examined and yielded a total of 4,872 Culicoides of which 4,492 (92%) belonged to the Obsoletus Complex (including C. obsoletus and C. scoticus).

Genetic typing of recent classical swine fever virus isolates from Croatia.

During a period of 5 years (1997-2001) several outbreaks of classical swine fever (CSF) were recorded in Croatia. For genetic typing, fragments of 150 nucleotides within the 5'-non-translated region (5'-NTR) and 190 nucleotides within the E2 glycoprotein coding gene of nine field isolates that were derived from domestic pigs and wild boars were used. For better epizootiological understanding, isolates from other European countries were included in the study. The results show that the isolates belong to subgroups 2.1 and 2.3 of CSF virus. Isolates from subgroup 2.1 were collected from domestic pigs during sporadic outbreaks in June 1997 and are genetically closely related. A genomic similarity between these isolates and CSF virus isolates from pigs in other European countries from the same year could also be confirmed. In contrast, the isolate from October 1997 was found to be a member of subgroup 2.3, and is closely related to European CSF virus isolates from outbreaks in the last decade in Western and Central European countries. These results show that two different sources of CSF virus caused outbreaks in Croatia during the same year. Furthermore, a close relationship was found between an isolate from a domestic pig in 1999 and isolates of subgroup 2.3 that originated from Croatian wild boars.

Comparison of antibody values in sera of pigs vaccinated with a subunit or an attenuated vaccine against classical swine fever.

Ten pigs, aged 85 days, were vaccinated with a subunit vaccine containing 32 microg of classical swine fever virus glycoprotein E2 (gp E2) (group 1), and a further 10 pigs were vaccinated with a C strain vaccine (10(4+/-0.15) TCID50/ml), produced by amplification in minipig kidney (MPK) cell culture (group 2). Nine non-vaccinated pigs served as a control group (group 3). Serum samples were collected before (day 0) and at 4, 10, 21 and 28 days after vaccination and were analysed by two commercially available enzyme immunoassays and by a neutralizing peroxidase-linked assay (NPLA). At the same times, peripheral blood was taken for determining the total leukocyte count and the body temperature was taken daily. Antibodies were not detected in serum samples collected before vaccination (day 0), and no side-effects that could be connected with vaccination were observed during the trial. Ten days after vaccination 6/10 pigs vaccinated with the subunit vaccine were seropositive. On days 21 and 28, the ratios of serologically positive to vaccinated pigs were 9/10 and 10/10, respectively. Four of the ten pigs that were vaccinated with the C strain vaccine were positive on day 21 and 9/10 on day 28. However, the results of the NPLA showed that only 4/10 pigs had an antibody titre > 1:32 at the end of the trial in both the vaccinated groups, even though the subunit vaccine initiated an earlier and higher level of neutralizing antibodies than the vaccine produced from the C strain. Challenge was performed 28 days after vaccination on four randomly selected pigs from both vaccinated groups. The pigs survived the challenge without showing any clinical signs of classical swine fever (CSF), while two nonvaccinated control pigs died on the 10th and 12th days after infection.

In vitro antimicrobial susceptibility of 183 Pseudomonas aeruginosa strains isolated from dogs to selected antipseudomonal agents.

During the years from 1993 to 2000, 183 strains of Pseudomonas aeruginosa were isolated from different pathological specimens originating from dogs. Antimicrobial susceptibility patterns against 10 antipseudomonal agents were obtained on 183 P. aeruginosa strains. In vitro antimicrobial susceptibility testing was performed using the disk diffusion method (Kirby-Bauer). Antimicrobial susceptibility profiles showed that among beta-lactam antibiotics, imipenem was the most active compound. Out of the 183 strains tested, 96.7% were sensitive to imipenem. Cefoperazone showed good in vitro activity against 86.9% of the tested strains. Against ceftazidime, 77.0% of strains showed sensitivity. An old penicillin, carbenicillin, gave only 71.6% sensitive strains. Sensitivity to amikacin was 87.4% and it was 83.1% to gentamicin. Pipimedic acid, a first-generation quinolone, was the least active compound of all those tested, 47.0% were resistant. The in vitro sensitivity against enrofloxacin showed that 71.0% strains were sensitive and 26.2% showed resistance. Almost all strains tested, 93.4%, were susceptible to ciprofloxacin and marbofloxacin. Besides imipenem, the quinolone antibiotics, marbofloxacin and ciprofloxacin were the most effective against P. aeruginosa strains isolated from dogs.

[Zoonoses caused by new viruses in the Paramyxoviridae family]. / Zoonoze uzrokovane novim virusima porodice Paramyxoviridae.

Based on the literature data, the outbreaks of new zoonoses caused by new members of the family Paramyxoviridae are briefly presented. Some characteristics of Hendra and Nipah virus, epidemiological aspects, clinical picture and pathology are described. Fruit bats are mentioned as the key to the epidemiology of Hendra virus. The virus was isolated from affected humans, horses, and from the uterine fluids of a grey-headed fruit bat (pteropus poliocephalus). New morbillivirus designated Nipah virus was isolated from pigs and humans. It caused encephalitis and pneumonia in humans.

Classical swine fever virus (C strain) distribution in organ samples of inoculated piglets.

Enzyme linked immunosorbent assays (ELISAs) and a nested polymerase chain reaction after reverse transcription (RT-PCR) were used for the detection of the Chinese strain (C strain) of classical swine fever virus (CSFV) in blood and tissue samples of experimentally inoculated piglets. One group of 10 piglets was inoculated with C strain material from rabbits and a second one with material from infected minipig kidney (MPK) cell culture. Tested blood samples were taken on the day of inoculation as well as on days 2, 4, 6, 8, 10, 13 and 16. Samples of spleen, tonsil and brain tissue were collected from piglets on days 6, 8, 10, 13 and 16 and tested for glycoprotein E(RNS) and protein NS2-3 using commercially available ELISA kits. E(RNS) and NS2-3 were detected earlier in blood samples of piglets inoculated with the C strain propagated in a cell culture. Regardless of propagation the presence of the viral E(RNS) and NS2-3 was detected in spleen and tonsil samples simultaneously. The C strain propagated in a cell culture was found in only one brain sample, whereas, the virus propagated in rabbits was detected in 70% of the brain samples. For the detection of the CSFV RNA in blood samples, a part within the 5' non-coding region was amplified. The differences in the results gained by antigen detection in blood samples decreased when nested RT-PCR was used.

Spontaneous BHV1 recombinants in which the gI/gE/US9 region is replaced by a duplication/inversion of the US1.5/US2 region.

In a bovine herpesvirus 1 (BHV1) vaccine strain, a spontaneous BHV1 mutant (Za) was found that arose from a recombination between two isomeric forms of the BHV1 genome. In this Za mutant one end of the U(S) region, containing part of the US1.5 gene, was found duplicated in an inverted orientation at the other end of the U(S) region. Concurrently, a 2.7 kb deletion was found in Za that encompasses both the US8 (gE) and US9 gene. Analysis of the in vitro growth properties of a genetically modified BHV1gE(-) mutant showed that at 11 hours post infection BHV1gE(-) viruses were secreted ten times more efficiently than wild type virus. Using this observation we developed a protocol to enrich for spontaneous gE deletion mutants in a BHV1 field isolate and found another mutant (Rof3) with similar properties as the Za mutant. Rof3 has a duplication/inversion of the US1.5 gene and part of the US2 gene and a simultaneous 3.5 kb deletion that encompasses the US7 (gI), US8 (gE) and US9 genes. The nucleotide sequences of the recombination points of both recombinants were determined and compared. No obvious sequence similarities were found, suggesting that non-homologous recombination events led to the observed recombinations. The implications for the use of BHV1 gE deletion mutants as marker or diva vaccines are discussed.

Prevalence of antibodies to IBR and BVD viruses in dairy cows with reproductive disorders.

We determined the prevalence of antibodies to infectious bovine rhinotracheitis virus (IBRV) and bovine viral diarrhea virus (BVDV) in sera of dairy cows on 4 different farms in the Republic of Croatia. A high percentage (60.8%) of cows had various reproductive disorders. The results showed that seroprevalence of infectious bovine rhinotracheitis (IBR) was 85.8% and that of bovine viral diarrhea (BVD) was 79.2% in tested cows. Antibodies to both viruses were found in 80.8% of cows with reproductive disorders but in only 46.8% of cows without reproductive disorders. This difference was statistically significant (P<0.01), and indicated a connection between reproductive disorders and simultaneous infections with IBR and BVD viruses in dairy cows.

An outbreak of abortion in mares associated with Salmonella abortusequi infection.

An abortion outbreak occurred in a herd of 38 horses, 26 of which were pregnant mares. Twenty-one mares aborted between 5-10 months of gestation. In no case were there indications of impending abortion. Pathoanatomical, histopathological, virological and bacteriological examinations were carried out on 4 aborted fetuses. Histopathology identified Gram-negative bacteria compatible with salmonella in all 4 placentae. By subsequent bacteriological examination Salmonella abortusequi was isolated as the single causative agent in each case. Nonmotile Salmonella abortusequi with antigenic formula 4,12:-:- was isolated from one of the 4 fetuses. The described episode of equine abortion clearly indicates that Salmonella abortusequi has not been eradicated from Europe as previously thought.

Susceptibility to antimicrobial agents of Streptococcus suis capsular type 2 strains isolated from pigs.

The minimal inhibitory concentrations (MICs) for thirty-three epidemiologicaly unrelated clinical isolates of Streptococcus suis capsular type 2 were determined in relation to ampicillin, ampicillin-sulbactam, amoxicillin, clavulanate-amoxicillin, penicillin G, cephalexin, gentamicin, streptomycin, erythromycin, tylosin and doxycycline, using the microtitre broth dilution procedure described by the U.S. National Committee for Clinical Laboratory Standards (NCCLS). Gentamicin was the most active compound tested, with an MIC for 90% of the strains tested (MIC(90)) of 0.4 mg/L. Overall, 70% of strains were resistant to doxycycline (MIC(90) > or = 100.0 mg/L), followed by penicillin G (51% of strains) (MIC(90) + or = 100.0 mg/L). Resistance to amoxicillin and ampicillin was 36.4% (MIC(90) 12.5 mg/L) and 33.3% (MIC(90) 50.0 mg/L), respectively. 15.2% of S. suis strains were resistant to streptomycin, tylosin and cephalexin with MIC90 values of 25.0 mg/L, 12.5 mg/L and 25.0 mg/L, respectively. A combination of ampicillin and sulbactam (MIC(90) 6.3 mg/L) and a combination of amoxicillin and clavulanate (MIC(90) 3.1 mg/L) as well as erythromycin (1.6 mg/L) were of the same efficacy, with a total of 9.1% resistant S. suis strains. This high percentage of resistance to doxycycline and penicillin G precludes the use of these antibiotics as empiric therapy of swine diseases.