Design and validation of real-time reverse transcription-PCR assays for detection of pandemic (H1N1) 2009 virus.

Tracking novel influenza viruses which have the potential to cause pandemics, such as the pandemic (H1N1) 2009 virus, is a public health priority. Pandemic (H1N1) 2009 virus was first identified in Mexico in April 2009 and spread worldwide over a short period of time. Well-validated diagnostic tools that are rapid, sensitive, and specific for the detection and tracking of this virus are needed. Three real-time reverse transcription PCR (RT-PCR) assays for the amplification and detection of pandemic (H1N1) 2009 virus were developed, and their performance characteristics were compared with those of other published diagnostic assays. Thirty-nine samples confirmed to be positive for pandemic (H1N1) 2009 virus from Alberta, Canada, and six additional samples that were positive for influenza A virus but that were not typeable by using published seasonal influenza H1/H3 virus assays were available for this validation. Amplification and direct sequencing of the products was considered the "gold standard" for case identification. The new assays were sensitive and able to reproducibly detect virus in a 10(-6) dilution of 4 x 10(6) 50% tissue culture infective doses/ml when 5 microl was used as the template. They showed 100% specificity and did not cross-react with other respiratory viruses or seasonal influenza A virus subtypes. The coefficient of variation in crossing cycle threshold values for the detection of different template concentrations of pandemic (H1N1) 2009 virus was < or =3.13%, showing good reproducibility. The assays had a wide dynamic range for the detection of pandemic (H1N1) 2009 virus and utilized testing platforms appropriate for high diagnostic throughput with rapid turnaround times. We developed and validated these real-time PCR procedures with the goal that they will be useful for diagnosis and surveillance of pandemic (H1N1) 2009 virus. These findings will contribute to the informed management of this novel virus.

Mycobacterium avium subspecies paratuberculosis in Bison (Bison bison) from Northern Canada.

Nested polymerase chain reaction (PCR) using the Mycobacterium avium subspecies paratuberculosis (Map)-specific region, locus 251, was used as a screening tool for the detection of Map DNA in fecal samples from northern Canadian bison herds. Further characterization of positive samples (26/835) was performed because Map DNA was found without signs of disease. Strain typing, using PCR-Restriction endonucleas assay (REA), was limited to two samples but revealed that the samples corresponded to a cattle-related strain and a sheep-related strain. Sequencing of part of the IS1311 region from the two samples revealed a unique three base-pair region, which is only found within the northern Canadian bison isolates.

Evaluation of equine papillomas, aural plaques, and sarcoids for the presence of Equine papillomavirus DNA and Papillomavirus antigen.

Immunohistochemical (IHC) testing and electron microscopy have implicated Papillomavirus (PV) as the etiologic agent for equine papillomas and aural plaques, but Equine papillomavirus (EPV) DNA has yet to be demonstrated in these lesions by polymerase chain reaction (PCR). The purpose of this study was to evaluate formalin-fixed, paraffin-embedded tissues from naturally occurring cases of equine papillomas, aural plaques, and sarcoids for the presence of EPV DNA by means of PCR and for the presence of PV antigen by means of IHC testing. We used EPV-specific primers that amplified a region of 384 base pairs (bp) spanning the E4 and L2 genes of the EPV genome and consensus PV primers that amplified a 102-bp region of the L1 gene. Group-specific PV structural antigens were detected with the use of a streptavidin-biotin-alkaline phosphatase IHC stain. With IHC testing, 23 of 38 papillomas, 4 of 9 aural plaques, and 0 of 10 sarcoids were positive for PV antigen; EPV DNA was found in 20 of the 38 papillomas and 1 of the 10 sarcoids but 0 of the 9 aural plaques. The consensus primers did not amplify novel PV DNA in any of the tissues. Nucleotide sequencing of viral DNA from 7 papillomas amplified with EPV-specific primers revealed DNA fragments that were 96% to 99% identical to known EPV sequences. Some samples had nucleotide substitutions in common, which suggests infection with related strains. Together, EPV DNA or PV antigen (or both) was demonstrated in 26 (68%) of the 38 equine papillomas. Although aural plaques contained PV antigen, they were negative for EPV DNA; therefore, we hypothesize that aural plaques contain a PV distinct from EPV.

Nested polymerase chain reaction detection and duration of porcine circovirus type 2 in semen with sperm morphological analysis from naturally infected boars.

A nested polymerase chain reaction (nPCR) protocol was applied to porcine semen to demonstrate the porcine circovirus type 2 (PCV2) shedding patterns and duration in naturally infected boars. Sperm morphology analysis was performed on a subset of samples to determine if the presence of PCV2 DNA in semen was associated with reduced semen quality. Semen was collected serially from 43 boars representing 6 breeds, aged 33.9 to 149.3 weeks. Of the 903 semen samples collected, 30 samples (3.3%) were positive for PCV2 DNA by nPCR from 13 boars. Boars shedding PCV2 DNA in semen ranged between 35.9 and 71.0 weeks of age, and shedding occurred during a period of up to 27.3 weeks. A semen nPCR test was 2.6 times more likely to be positive when collected from pigs that were < or =52 weeks of age, and 3.0 times more likely to be positive when collected from pigs that were < or =26 weeks from time of entry into the stud main unit (generalized estimating equations: P = 0.02; 95% confidence interval [CI] of the odds ratio 1.2 to 5.5, and P = 0.01; 95% CI of the odds ratio 1.3 to 6.9, respectively). These results demonstrate a sporadic and long-term shedding pattern of PCV2 DNA in semen from naturally infected boars. PCV2 DNA in semen does not appear to have detrimental effects on sperm morphology; however, boar age and, possibly, breed may contribute to the persistence of PCV2-shedding in semen.

Histological and genotypical characterization of feline cutaneous mycobacteriosis: a retrospective study of formalin-fixed paraffin-embedded tissues.

Twenty-nine cases presumptively diagnosed as feline cutaneous mycobacteriosis were evaluated microscopically with haematoxylin and eosin and modified Fite's stained sections using archived formalin-fixed paraffin-embedded tissue specimens. Lesions were characterized histologically as feline leprosy (7 cases lepromatous and 16 cases tuberculoid) or atypical mycobacteriosis (3 cases); three cases did not fit these criteria and were classified as 'miscellaneous'. Actinomycetales-specific polymerase chain reaction (PCR) of variable regions 1, 2 and 3 of the 16S ribosomal RNA (rRNA) gene and subsequent sequence analysis of the amplicons were performed to identify the species of mycobacteria associated with each case. Together, this study identified 10 different Actinomycetales organisms with greater than 98% nucleotide sequence identity to named species, nine were of the genus Mycobacterium and eight were associated with feline leprosy (both lepromatous and tuberculoid). Based on this study, we conclude that feline cutaneous mycobacteriosis should be considered as a syndrome with varied clinical and histological presentations associated with a variety of different Mycobacterium species, organisms other than Mycobacterium sp. may be associated with feline cutaneous mycobacteriosis lesions, and molecular diagnostic techniques can be an important tool for identifying agents associated with lesions of feline cutaneous mycobacteriosis.

Differential mitochondrial DNA and gene expression in inherited retinal dysplasia in miniature Schnauzer dogs.

PURPOSE: To investigate the molecular basis of inherited retinal dysplasia in miniature Schnauzers. METHODS: Retina and retinal pigment epithelial tissues were collected from canine subjects at the age of 3 weeks. Total RNA isolated from these tissues was reverse transcribed to make representative cDNA pools that were compared for differences in gene expression by using a subtractive hybridization technique referred to as representational difference analysis (RDA). Expression differences identified by RDA were confirmed and quantified by real-time reverse-transcription PCR. Mitochondrial morphology from leukocytes and skeletal muscle of normal and affected miniature Schnauzers was examined by transmission electron microscopy. RESULTS: RDA screening of retinal pigment epithelial cDNA identified differences in mRNA transcript coding for two mitochondrial (mt) proteins--cytochrome oxidase subunit 1 and NADH dehydrogenase subunit 6--in affected dogs. Contrary to expectations, these identified sequences did not contain mutations. Based on the implication of mt-DNA-encoded proteins by the RDA experiments we used real-time PCR to compare the relative amounts of mt-DNA template in white blood cells from normal and affected dogs. White blood cells of affected dogs contained less than 30% of the normal amount of two specific mtDNA sequences, compared with the content of the nuclear-encoded glyceraldehyde-3-phosphate dehydrogenase (GA-3-PDH) reference gene. Retina and RPE tissue from affected dogs had reduced mRNA transcript levels for the two mitochondrial genes detected in the RDA experiment. Transcript levels for another mtDNA-encoded gene as well as the nuclear-encoded mitochondrial Tfam transcription factor were reduced in these tissues in affected dogs. Mitochondria from affected dogs were reduced in number and size and were unusually electron dense. CONCLUSIONS: Reduced levels of nuclear and mitochondrial transcripts in the retina and RPE of miniature Schnauzers affected with retinal dysplasia suggest that the pathogenesis of the disorder may arise from a lowered energy supply to the retina and RPE.

Detection of Porcine circovirus type 2 viremia and seroconversion in naturally infected pigs in a farrow-to-finish barn.

Porcine serum was assayed by 2 polymerase chain reaction (PCR) protocols (nested PCR [nPCR] and non-nested PCR) and a competitive enzyme-linked immunosorbent assay to determine when Porcine circovirus type 2 (PCV2) viremia and a rise in the serum level of PCV2-specific antibody occurred in pigs raised in a large Canadian farrow-to-finish barn. Eight serial blood samples were collected from each of 40 pigs from 5 to 156 (+/- 1.5) d of age; 6 pigs were removed from the study for various reasons at various times. Viremia was not detected in the samples collected before 72 d of age but was detected in those collected on or after 72 d: of 33 pigs, 7 (21%) had only 1 serum sample positive for PCV2 DNA by nPCR after day 72; 11 (33%) were intermittently positive by nPCR, non-nested PCR, or both between 72 and 156 d; and the remaining 15 (45%) were repeatedly positive (in 2 to 4 samples). The level of serum antibody against PCV2 declined after weaning and increased between 72 and 107 d of age, only after PCV2 was detected in serum. Our results show that PCV2 viremia persists in the presence of elevated levels of PCV2-specific antibody.

Geographic distribution of the muscle-dwelling nematode Parelaphostrongylus odocoilei in North America, using molecular identification of first-stage larvae.

Molecular identification of dorsal-spined larvae (DSL) from fecal samples indicates that the protostrongylid parasite Parelaphostrongylus odocoilei occupies a broader geographic range in western North America than has been previously reported. We analyzed 2,124 fecal samples at 29 locations from thinhorn sheep (Ovis dalli dalli and O. d. stonei), bighorn sheep (Ovis canadensis canadensis and O. c. californiana), mountain goats (Oreamnos americanus), woodland caribou (Rangifer tarandus caribou), mule deer (Odocoileus hemionus hemionus), and black-tailed deer (O. h. columbianus). The DSL were recovered from populations of thinhorn sheep south, but not north, of the Arctic Circle, and they were not recovered from any of the bighorn sheep populations that we examined. In total, DSL were recovered from 20 locations in the United States and Canada (Alaska, Yukon Territory, Northwest Territories, British Columbia, Alberta, and California). The DSL were identified as P. odocoilei by comparing sequences of the second internal transcribed spacer (ITS2) region of ribosomal RNA among 9 protostrongylid species validated by adult comparative morphology. The ITS2 sequences were markedly different between Parelaphostrongylus and other protostrongylid genera. Smaller fixed differences served as diagnostic markers for the 3 species of Parelaphostrongylus. The ITS2 sequences (n = 60) of P. odocoilei were strongly conserved across its broad geographic range from California to Alaska. Polymorphism at 5 nucleotide positions was consistent with multiple copies of the ITS2 within individual specimens of P. odocoilei. This work combines extensive fecal surveys, comparative morphology, and molecular diagnostic techniques to describe comprehensively the host associations and geographic distribution of a parasitic helminth.

Host immune status influences the development of attaching and effacing lesions in weaned pigs.

Attaching and effacing Escherichia coli (AEEC) has been associated with naturally occurring attaching and effacing (A/E) lesions in weaned pigs, and although A/E lesions have been experimentally reproduced in newborn piglets, such lesions have been much more difficult to induce in older conventional pigs. Hence, the aim of this study was to examine the effect of oral administration of dexamethasone on the development of A/E lesions in weaned pigs challenged with a porcine enteropathogenic E. coli (PEPEC) strain and to investigate the involvement of local intestinal cytokine response. Dexamethasone, given orally at a dosage of 3 mg kg of body weight(-1), significantly enhanced both the colonization of the challenge strain and the prevalence of foci of intimately adherent bacteria, resulting in extensive A/E lesions in the ileum, cecum, and colon of challenged pigs. We also confirmed the expression of both intimin and Tir by PEPEC strain ECL1001 in A/E lesions in vivo, which is, to our knowledge, the first report of the involvement of the latter proteins in any AEEC infections in vivo. Moreover, semiquantitative reverse transcription-PCR demonstrated that interleukin 1beta (IL-1beta), IL-6, IL-8, and, to a lesser extent, IL-12p40 are significantly upregulated in the ileum following challenge with strain ECL1001, whereas dexamethasone blocks such upregulation. Taken together, our results strongly suggested that host immune status influences the development of A/E lesions in weaned pigs, and it appears that IL-1beta, IL-6, IL-8, and, to a lesser extent, IL-12p40 are expressed during infection of weaned pigs by PEPEC and may contribute to the natural resistance of the host against PEPEC infection.

An outbreak of sheep-associated malignant catarrhal fever in bison (Bison bison) after exposure to sheep at a public auction sale.

An outbreak of malignant catarrhal fever (MCF) among bison sold at an auction market was studied for an 18-month period. Forty-five of 163 bison submitted for sale from 8 different bison farms died on 7 other destination farms. The outbreak began on day 50 after the sale, peaked between days 60 and 70, and ended on day 220. Twenty-one dead bison were confirmed to be MCF cases by clinical histories, pathology, and detection of ovine herpesvirus-2 DNA in their tissues with polymerase chain reaction assays. Twenty-four dead bison were classified as suspect MCF cases from clinical histories. No cases of MCF were observed among bison remaining on originating farms or resident bison mixed with sale bison on destination farms. There were no sheep reported within 3 km of originating or destination farms, limiting bison exposure to sheep to the auction facility, where sheep were present for less than 1 day. The outbreak provides an illustration of the temporal distribution of MCF mortality expected in bison and an estimate of the time from exposure until death from MCF after a single short exposure to sheep. The study provides evidence that bison with MCF do not transmit MCF to other bison.

Mycoplasma haemofelis and Mycoplasma haemominutum detection by polymerase chain reaction in cats from Saskatchewan and Alberta.

Hemobartonellosis is caused by Mycoplasma haemofelis, previously known as Haemobartonella felis. Cats infected with this organism typically develop regenerative anemia. The related species Mycoplasma haemominutum may also cause anemia. The purposes of this study were to use polymerase chain reaction technology to determine if both organisms exist in naturally infected cats from Saskatchewan and Alberta, and to determine if disease manifestation corresponds to mycoplasma species. Thirteen of 18 cats with regenerative anemia were infected, 12 with M. haemofelis and 1 with M. haemominutum. Eight of 22 cats with nonregenerative anemia were infected, 4 with M. haemofelis and 4 with M. haemominutum. Two of 20 cats with normal complete blood (cell) counts were infected with M. haemominutum. Although both mycoplasma species were identified, ill cats were more often infected with M. haemofelis.

Comparison of synthetic tyvelose antigen with excretory-secretory antigen for the detection of trichinellosis in swine using enzyme-linked immunosorbent assay.

Two enzyme-linked immunosorbent assay (ELISA) systems, one using natural excretory-secretory (ES) antigens and the other a synthetic glycan antigen (3,6-dideoxy-D-arabinohexose [tyvelose, TY]), were evaluated for the serological diagnosis of trichinellosis in swine. Sensitivity was estimated using samples (n = 113) collected 3-21 wk PI from 15 experimentally infected pigs, and specificity was estimated using samples (n = 397) from a population of Trichinella spp.-free pigs. Results were analyzed using 2 cutoff values recommended in international guidelines (Office Internationale des Epizooties [OIE]) and by the optimal cutoff level as determined by receiver-operator characteristic (ROC) analysis. The ROC-optimized TY-ELISA consistently performed better than all other combinations. None of the combinations of test and cut-off detected infected pigs sooner than 35 days; however, the ROC-optimized TY-ELISA identified 8 of 15 pigs earlier than the ES-ELISA and detected 2 pigs missed by all other tests. At 49 days PI the sensitivity and specificity of the ROC-optimized TY-ELISA were 94.3 and 96.7%, respectively, as compared with the ROC-optimized ES-ELISA at 84.9 and 96.0%, respectively. The ROC-optimized TY-ELISA was 100% specific at OIE-recommended cut-offs. This study indicates that the TY-ELISA is as good or better than the ES-ELISA for the detection of trichinellosis in swine.

Differences in expression of retinal pigment epithelium mRNA between normal canines.

A reference database of differences in mRNA expression in normal healthy canine retinal pigment epithelium (RPE) has been established. This database identifies non-informative differences in mRNA expression that can be used in screening canine RPE for mutations associated with clinical effects on vision. Complementary DNA (cDNA) pools were prepared from mRNA harvested from RPE, amplified by PCR, and used in a subtractive hybridization protocol (representational differential analysis) to identify differences in RPE mRNA expression between canines. The effect of relatedness of the test canines on the frequency of occurrence of differences was evaluated by using 2 unrelated canines for comparison with 2 female sibling canines of blue heeler/bull terrier lineage. Differentially expressed cDNA species were cloned, sequenced, and identified by comparison to public database entries. The most frequently observed differentially expressed sequence from the unrelated canine comparison was cDNA with 21 base pairs (bp) identical to the human epithelial membrane protein 1 gene (present in 8 of 20 clones). Different clones from the same-sex sibling RPE contained repetitions of several short sequence motifs including the human epithelial membrane protein 1 (4 of 25 clones). Other prevalent differences between sibling RPE included sequences similar to a chicken genetic marker sequence motif (5 of 25), and 6 clones with homology to porcine major histocompatibility loci. In addition to identifying several repetitively occurring, noninformative, differentially expressed RPE mRNA species, the findings confirm that fewer differences occurred between siblings, highlighting the importance of using closely related subjects in representational difference analysis studies.

Expression of integrin subunits alphav and beta3 in acute lung inflammation.

Integrin subunits alphav and beta3 form a dimer, alphavbeta3, which is expressed on normal neutrophils and endothelium. We investigated the expression of integrin subunits alphav and beta3 in acute lung inflammation in Sprague-Dawley rats ( n=5 each) following intratracheal challenge with Escherichia coli or Streptococcus pneumoniae, which induce neutrophil recruitment through different mechanisms. Control rats ( n=5) were given endotoxin-free saline. Both bacterial challenges induced similar levels of recruitment of neutrophils in lungs. Western blots showed lower expression of integrin subunits alphav and beta3 in lungs challenged with E. coli compared to those given S. pneumoniae. Immunohistochemistry and immunogold electron microscopy localized both integrin subunits in neutrophils and endothelium in the control and treated rat lungs. Quantitative immunohistochemistry showed that E. coli-challenged rat lungs contained a lower percentage of neutrophils expressing integrin subunits alphav and beta3 compared to those challenged with S. pneumoniae ( P<0.05). We conclude that E. coli infection decreased the percentage of neutrophils expressing integrin subunits alphav and beta3 compared to S. pneumoniae infection. These data lay the foundation for further characterization of these integrin subunits in neutrophil migration specifically in S. pneumoniae infection that utilizes molecules other than beta2 integrins for neutrophil recruitment.

Comparison of bacterial enriched-broth culture, enzyme linked immunosorbent assay, and broth culture-polymerase chain reaction techniques for identifying asymptomatic infections with Salmonella in swine.

A polymerase chain reaction (PCR) assay was combined with a broth-culture enrichment system to detect Salmonella shed in feces from subclinically infected swine. The effectiveness of the broth culture-polymerase chain reaction (BC-PCR) assay to identify pigs shedding Salmonella in feces was compared with a microbiological culture and a commercial enzyme linked immunosorbent assay (ELISA) kit to detect Salmonella-specific serum antibody. A total of 67 pigs were tested by each of the 3 methodologies. Forty-one pigs tested positive for Salmonella by BC-PCR and ELISA identified 6 positives and 23 suspicious samples. It was shown that the BC-PCR assay is a rapid diagnostic tool for detecting of Salmonella shed by asymptomatic swine compared with current diagnostic technologies.

Histologic and genotypic characterization of a novel Mycobacterium species found in three cats.

Three cases of feline atypical mycobacteriosis from different geographical regions in North America were characterized by large clusters of filamentous bacteria visible on hematoxylin-and-eosin-stained tissue sections. PCR amplification demonstrated the presence of Mycobacterium-specific nucleic acid in samples of skin lesions from these cases. PCR-assisted cloning and DNA sequence analysis of a 541-bp length of the Mycobacterium 16S rRNA gene generated DNA sequences which were >95% identical, suggesting that the three isolates were closely related. Two of the sequences were 99% identical and may represent the same species. Alignment with comparable 16S rRNA gene sequences from 66 Mycobacterium species and partially characterized isolates highlighted similarities (>94%) with Mycobacterium bohemicum, Mycobacterium haemophilum, Mycobacterium ulcerans, Mycobacterium avium subsp. avium, and isolate IWGMT 90242. Parsimony analysis of sequence data suggested relatedness to M. leprae. Significant molecular genetic and pathobiological differences between these three similar isolates and other known species of mycobacteria suggested that the organisms may not have been described previously and that these cases may represent a new form of mycobacterial disease in cats. We suggest the term "Mycobacterium visibilis" to describe the organism from which the two nearly identical sequences were obtained.

National serologic survey for trichinellosis in sows in Canada 1996-1997.

Sera from 14,408 market sows from the Canadian domestic swine herd were tested for trichinellosis using an indirect-ELISA as a screening test and a competitive ELISA for confirmatory testing. Three sera (0.02%) gave low level reactions on the competitive ELISA. These reactions were considered nonspecific, and this designation was supported by data from previous and subsequent national surveys, in which serologic, trichinoscopic, and digestion test methodologies was used. This study provides additional evidence that Canada is free of trichinellosis in domestic swine.