Champika Fernando
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View article: Using clotted, pelleted blood samples for direct molecular detection of Bartonella spp. in small mammal wildlife surveillance studies
Using clotted, pelleted blood samples for direct molecular detection of Bartonella spp. in small mammal wildlife surveillance studies Open
Objective Bartonella are emerging bacterial zoonotic pathogens. Utilization of clotted blood samples for surveillance of these bacteria in wildlife has begun to supersede the use of tissues; however, the efficacy of these samples has not b…
View article: Identification of genetic markers of resistance to macrolide class antibiotics in <i>Mannheimia haemolytica</i> isolates from a Saskatchewan feedlot
Identification of genetic markers of resistance to macrolide class antibiotics in <i>Mannheimia haemolytica</i> isolates from a Saskatchewan feedlot Open
Mannheimia haemolytica is a major contributor to bovine respiratory disease (BRD), which causes substantial economic losses to the beef industry, and there is an urgent need for rapid and accurate diagnostic tests to provide evidence for t…
View article: Tissue and cellular tropism of <i>Eptesicus fuscus gammaherpesvirus</i> in big brown bats, potential role of pulmonary intravascular macrophages
Tissue and cellular tropism of <i>Eptesicus fuscus gammaherpesvirus</i> in big brown bats, potential role of pulmonary intravascular macrophages Open
Gammaherpesviruses (γHVs) are recognized as important pathogens in humans but their relationship with other animal hosts, especially wildlife species, is less well characterized. Our objectives were to examine natural Eptesicus fuscus gamm…
View article: Investigation of expression of genes encoding glycogen degrading enzymes in<i>Gardnerella swidsinskii</i>and identification of reference genes for quantitative real-time PCR
Investigation of expression of genes encoding glycogen degrading enzymes in<i>Gardnerella swidsinskii</i>and identification of reference genes for quantitative real-time PCR Open
Gardnerella spp. express and export enzymes for the breakdown of glycogen into glucose, maltose, and malto-oligosaccharides for consumption by the vaginal microbiota but how the expression of these “public goods” is affected by substrate a…
View article: Extraction of high quality RNA from Gardnerella species
Extraction of high quality RNA from Gardnerella species Open
This protocol describes an approach for the purification of high quality RNA from Gardnerella species based on a commercially available kit (PureLink RNA Mini Kit, Invitrogen). Initial RNA extraction following the manufacturer’s protocol r…
View article: Environmental and sociodemographic factors associated with zoonotic pathogen occurrence in Norway rats (<i>Rattus norvegicus</i>) from Windsor, Ontario
Environmental and sociodemographic factors associated with zoonotic pathogen occurrence in Norway rats (<i>Rattus norvegicus</i>) from Windsor, Ontario Open
Aims Rat‐associated zoonotic pathogen transmission at the human–wildlife interface is a public health concern in urban environments where Norway rats ( Rattus norvegicus ) thrive on abundant anthropogenic resources and live in close contac…
View article: Eptesipox virus-associated lesions in naturally infected big brown bats
Eptesipox virus-associated lesions in naturally infected big brown bats Open
Bats have many unique qualities amongst mammals; one of particular importance is their reported tolerance to viruses without developing disease. Here, the authors present evidence to the contrary by describing and demonstrating viral nucle…
View article: Complete genome sequence of <i>Mannheimia bovis</i> isolated from a healthy feedlot calf in Saskatchewan, Canada
Complete genome sequence of <i>Mannheimia bovis</i> isolated from a healthy feedlot calf in Saskatchewan, Canada Open
A lack of whole genome sequences for Mannheimia spp. other than Mannheimia haemolytica complicates their identification. Here, we present the genome sequence of Mannheimia bovis 39324.S-11, isolated from a healthy calf on a feedlot in Sask…
View article: Evaluating <i>cpn60</i> for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis
Evaluating <i>cpn60</i> for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis Open
Despite being the most widely used phylogenetic marker for amplicon-based profiling of microbial communities, limited phylogenetic resolution of the 16S rRNA gene limits its use for studies of host-microbe co-evolution. In contrast, the cp…
View article: Improving the consistency of experimental swine dysentery inoculation strategies
Improving the consistency of experimental swine dysentery inoculation strategies Open
Swine dysentery (SD) caused by pathogenic Brachyspira spp. is an economic challenge for the swine industry. In research settings, experimental reproduction of swine dysentery typically relies on intragastric inoculation which has shown var…
View article: cpn60 metagenomic amplicon library preparation for the Illumina Miseq platform
cpn60 metagenomic amplicon library preparation for the Illumina Miseq platform Open
This protocol can be applied to determine the composition of a microbial community. The cpn60 gene (also known as groEL, hsp60) is present in almost all bacteria and a 552-558 bp region of the gene has been established as a barcode for spe…
View article: Additional file 5 of Improving the consistency of experimental swine dysentery inoculation strategies
Additional file 5 of Improving the consistency of experimental swine dysentery inoculation strategies Open
Additional file 5: Raw data for all trials.
View article: Combining deep sequencing and conventional molecular approaches reveals broad diversity and distribution of fleas and Bartonella in rodents and shrews from Arctic and Subarctic ecosystems
Combining deep sequencing and conventional molecular approaches reveals broad diversity and distribution of fleas and Bartonella in rodents and shrews from Arctic and Subarctic ecosystems Open
Background Bartonella are intracellular bacteria that are transmitted via animal scratches, bites and hematophagous arthropods. Rodents and their associated fleas play a key role in the maintenance of Bartonella worldwide, with > 22 specie…
View article: Experimental natural transmission (seeder pig) models for reproduction of swine dysentery
Experimental natural transmission (seeder pig) models for reproduction of swine dysentery Open
Swine dysentery is causally associated with Brachyspira hampsonii and B . hyodysenteriae infection. Given the importance of transmission models in understanding re-emergent diseases and developing control strategies such as vaccines, the o…
View article: Culling of Urban Norway Rats and Carriage of <i>Bartonella</i> spp. Bacteria, Vancouver, British Columbia, Canada
Culling of Urban Norway Rats and Carriage of <i>Bartonella</i> spp. Bacteria, Vancouver, British Columbia, Canada Open
We investigated the effects of culling on Bartonella spp. bacteria carriage among urban rats in Canada. We found that the odds of Bartonella spp. carriage increased across city blocks except those in which culling occurred. Removing rats m…
View article: Composition and Stability of the Vaginal Microbiota of Pregnant Women With Inflammatory Bowel Disease
Composition and Stability of the Vaginal Microbiota of Pregnant Women With Inflammatory Bowel Disease Open
Background Inflammatory bowel disease (IBD) is common in women of childbearing years, and active IBD during pregnancy is associated with increased rates of preterm delivery and low-birth-weight newborns. Changes in the vaginal microbiome h…
View article: cpn60 metagenomic amplicon library preparation for the Illumina Miseq platform
cpn60 metagenomic amplicon library preparation for the Illumina Miseq platform Open
This protocol can be applied to determine the composition of a microbial community. The cpn60 gene (also known as groEL, hsp60) is present in almost all bacteria and a 552-558 bp region of the gene has been established as a barcode for spe…
View article: When the Sum of the Parts Tells You More Than the Whole: The Advantage of Using Metagenomics to Characterize Bartonella spp. Infections in Norway Rats (Rattus norvegicus) and Their Fleas
When the Sum of the Parts Tells You More Than the Whole: The Advantage of Using Metagenomics to Characterize Bartonella spp. Infections in Norway Rats (Rattus norvegicus) and Their Fleas Open
Urban Norway rats (Rattus norvegicus) are a reservoir for Bartonella spp. - a genus of zoonotic bacteria transmitted by hematophagous vectors, particularly fleas. Rats and fleas may be infected with more than one Bartonella species; howeve…
View article: Infection With a Novel <i>Rickettsiella</i> Species in Emperor Scorpions (<i>Pandinus imperator</i>)
Infection With a Novel <i>Rickettsiella</i> Species in Emperor Scorpions (<i>Pandinus imperator</i>) Open
Rickettsiella infection was diagnosed in 4 adult emperor scorpions ( Pandinus imperator) from 2 different collections over a 3-year period. One case had a 2-day history of weakness, failure to lift the tail, or respond to stimulation, with…
View article: Assessment of Metagenomic Sequencing and qPCR for Detection of Influenza D Virus in Bovine Respiratory Tract Samples
Assessment of Metagenomic Sequencing and qPCR for Detection of Influenza D Virus in Bovine Respiratory Tract Samples Open
High throughput sequencing is currently revolutionizing the genomics field and providing new approaches to the detection and characterization of microorganisms. The objective of this study was to assess the detection of influenza D virus (…
View article: Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples
Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples Open
High throughput sequencing is currently revolutionizing the genomics field and providing new approaches to the detection and characterization of microorganisms. The objective of this study was to assess the detection of influenza D virus (…
View article: The pulmonary virome, bacteriological and histopathological findings in bovine respiratory disease from western Canada
The pulmonary virome, bacteriological and histopathological findings in bovine respiratory disease from western Canada Open
The aetiology and pathogenesis of bovine respiratory disease (BRD) are complex and involve the interplay of infectious agents, management and environmental factors. Previous studies of BRD focused on ante-mortem samples from the upper resp…
View article: Subclinical colitis associated with moderately hemolytic Brachyspira strains
Subclinical colitis associated with moderately hemolytic Brachyspira strains Open
Objective: Microbiological and virulence characterization of 2 moderately hemolytic Brachyspira strains. Materials and methods: Clinical isolates were obtained from diarrheic (3603-F2) and healthy (G79) pigs. Phenotypic characterization in…
View article: Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease
Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease Open
Bovine respiratory disease (BRD) causes considerable economic losses in North America. The pathogenesis involves interactions between bacteria, viruses, environment and management factors. Primary viral infection can increase the risk of s…
View article: Retrospective detection of<i>Brachyspira hampsonii</i>in archived colitis cases from western Canadian swine
Retrospective detection of<i>Brachyspira hampsonii</i>in archived colitis cases from western Canadian swine Open
Mucohaemorrhagic diarrhea associated with Brachyspira hampsonii infection has emerged as a production-limiting disease in western Canada. This pathogen was first described in North America in 2010, and reports of its detection occurred con…
View article: In vitro attenuation of a virulent swine isolate of Brachyspira hampsonii
In vitro attenuation of a virulent swine isolate of Brachyspira hampsonii Open
Brachyspira hampsonii causes dysentery-like disease in infected pigs. Serial passage of a virulent swine isolate (P13) one-hundred times in laboratory culture medium was conducted to produce an attenuated strain, and to identify genomic de…
View article: An optimized swine dysentery murine model to characterize shedding and clinical disease associated with “Brachyspira hampsonii” infection
An optimized swine dysentery murine model to characterize shedding and clinical disease associated with “Brachyspira hampsonii” infection Open
In our laboratory, CF-1 mice and the lower-zinc TD85420 diet provide a superior murine challenge model of "Brachyspira hampsonii" clade II.
View article: Infection of porcine colon explants with “Brachyspira hampsonii” leads to increased epithelial necrosis and catarrhal exudate
Infection of porcine colon explants with “Brachyspira hampsonii” leads to increased epithelial necrosis and catarrhal exudate Open
Mucohemorrhagic diarrhea in pigs caused by Brachyspira spp. has a global distribution, and an economic impact on affected farms due to poor performance of animals. Demonstrations that "Brachyspira hampsonii" is pathogenic have been achieve…
View article: Disseminated yeast <i>(</i>Order <i>Saccharomycetales)</i> infection in a Muscovy duckling <i>(Cairina moschata)</i>.
Disseminated yeast <i>(</i>Order <i>Saccharomycetales)</i> infection in a Muscovy duckling <i>(Cairina moschata)</i>. Open
A Muscovy duckling was presented for necropsy due to ongoing mortalities on a farm. Microscopic examination revealed multisystemic inflammatory lesions with intralesional and intracytoplasmic yeast-like organisms. We identified these agent…