Browsing by Author "Niu, Yan D."

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    Development of novel antimicrobials against avian pathogenic Escherichia coli that cause colibacillosis in laying hens
    (2021-09-29) Smith, Riley D.; Niu, Yan D.; Abdul-Careem, Mohamed F.; Wang, Yuxi
    Avian pathogenic Escherichia coli (APEC) causes colibacillosis, a poultry disease which results in losses to the Canadian egg-industry. Colibacillosis in Canada cannot be treated with antibiotics due to Canadian Food Inspection Agency regulations, necessitating novel APEC control strategies. Phage biocontrol and tannin feed inclusion have been successful in reducing APEC infection in broiler chickens. We hypothesized that phages and tannins would be effective in treating colibacillosis in laying hens. The study objectives were to isolate and characterize anti-APEC phages for use in a laying hen model, test purple prairie clover (PPC) and brown seaweed (BSW) tannin efficacy against APEC in vitro and develop a laying hen APEC infection model for assessment of phage colibacillosis control. Phages targeting APEC strains were isolated from sewage and hen feces. The host range and lytic activity of seven isolated phages were determined using microplate phage virulence assays. Tannin efficacy was assessed using minimum inhibitory concentration (MIC) assays against APEC strains, and a laying hen APEC infection model was established via air sac APEC injection. Phages were subjected to transmission electron microscopy to determine morphology and pH tolerance assays were conducted to determine pH stability. Phage genomic DNA were extracted and sequenced via the Illumina MiSeq platform. Raw sequence reads were assembled and annotated via a variety of programs. To understand the relationship between the novel phages and their relatives, comparative genomic and proteomic analysis as well as phylogenetic trees were also conducted via standard programs. Four of seven phages possessed strong lytic activity against multiple APEC strains and phages were more stable between pH = 3.5 and 9.0 than at pH = 2.5. Whole-genome sequencing data showed there are four phages of the Myoviridae, one of the Autographiviridae, and two of the Siphoviridae families. PPC and BSW tannins both inhibited APEC growth in vitro (MIC < 150 µg/mL). The air-sac infection model was unsuccessful due to an insufficient infectious dose. Results show promise for the use of phages and tannins for the control of colibacillosis in laying hens.
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    Genomic characterization and virulence gene profiling of Erysipelothrix rhusiopathiae isolated from widespread muskox mortalities in the Canadian Arctic Archipelago
    (2024-07-14) Seru, Lakshmi V.; Forde, Taya L.; Roberto-Charron, Amélie; Mavrot, Fabien; Niu, Yan D.; Kutz, Susan J.
    Abstract Background Muskoxen are important ecosystem components and provide food, economic opportunities, and cultural well-being for Indigenous communities in the Canadian Arctic. Between 2010 and 2021, Erysipelothrix rhusiopathiae was isolated from carcasses of muskoxen, caribou, a seal, and an Arctic fox during multiple large scale mortality events in the Canadian Arctic Archipelago. A single strain (‘Arctic clone’) of E. rhusiopathiae was associated with the mortalities on Banks, Victoria and Prince Patrick Islands, Northwest Territories and Nunavut, Canada (2010–2017). The objectives of this study were to (i) characterize the genomes of E. rhusiopathiae isolates obtained from more recent muskox mortalities in the Canadian Arctic in 2019 and 2021; (ii) identify and compare common virulence traits associated with the core genome and mobile genetic elements (i.e. pathogenicity islands and prophages) among Arctic clone versus other E. rhusiopathiae genomes; and iii) use pan-genome wide association studies (GWAS) to determine unique genetic contents of the Arctic clone that may encode virulence traits and that could be used for diagnostic purposes. Results Phylogenetic analyses revealed that the newly sequenced E. rhusiopathiae isolates from Ellesmere Island, Nunavut (2021) also belong to the Arctic clone. Of 17 virulence genes analysed among 28 Arctic clone isolates, four genes – adhesin, rhusiopathiae surface protein-A (rspA), choline binding protein-B (cbpB) and CDP-glycerol glycerophosphotransferase (tagF) – had amino acid sequence variants unique to this clone when compared to 31 other E. rhusiopathiae genomes. These genes encode proteins that facilitate E. rhusiopathiae to attach to the host endothelial cells and form biofilms. GWAS analyses using Scoary found several unique genes to be overrepresented in the Arctic clone. Conclusions The Arctic clone of E. rhusiopathiae was associated with multiple muskox mortalities spanning over a decade and multiple Arctic islands with distances over 1000 km, highlighting the extent of its spatiotemporal spread. This clone possesses unique gene content, as well as amino acid variants in multiple virulence genes that are distinct from the other closely related E. rhusiopathiae isolates. This study establishes an essential foundation on which to investigate whether these differences are correlated with the apparent virulence of this specific clone through in vitro and in vivo studies.