High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs). The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes. Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71. Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.

OBJECTIVE To evaluate erythema and number of CFUs on the skin of dogs with hair clipped by use of 2 sizes of clipper blades. ANIMALS 67 client-owned dogs receiving an epidural. PROCEDURES Hair was clipped with a No. 10 blade (approx hair length, 1.5 mm) on one half and a No. 40 blade (approx hair length, 0.25 mm) on the other half of each epidural site. Skin was surgically scrubbed with 2% chlorhexidine gluconate and 70% isopropyl alcohol. Samples were obtained immediately after clipping, after skin was scrubbed, and again 24 hours after clipping. Number of CFUs for both sides of the clipped areas, types of microorganisms, and growth on MacConkey agar were evaluated every 24 hours for 72 hours. Colonies were evaluated for bacterial morphology and Gram stain characteristics. Sites were evaluated 24 hours after clipping for evidence of erythema. RESULTS 24 hours after hair was clipped, there was a significantly higher incidence of erythema and higher number of Micrococcaceae bacteria for the side clipped with the No. 40 blade than the side clipped with the No. 10 blade. Number of CFUs did not differ significantly between size of clipper blades. CONCLUSIONS AND CLINICAL RELEVANCE Clipping hair with a No. 40 blade resulted in a significant increase in the incidence of erythema and higher number of Micrococcaceae bacteria, compared with results for clipping with a No. 10 blade. These results supported use of a No. 10 clipper blade to prevent erythema and reduce variation in the skin microbiome.