Identification of bacteria in the tracheal swabs of farmed ostriches and their effect on the viability of influenza A virus.

Avian influenza surveillance is a requirement for commercial trade in ostrich products, but influenza A viruses (IAVs) have proven difficult to isolate from ostrich tracheal swabs that test positive using molecular methods. We hypothesized that microbes unique to the ostrich trachea propagate in the transport medium after sampling and affect viral viability. We cultured tracheal swabs from 50 ostriches on 4 farms in South Africa, and recovered and identified 13 bacterial, 1 yeast, and 2 fungal species. sp. had not been identified previously in the oropharyngeal tract of a bird, to our knowledge. The bacteria were tested for antimicrobial susceptibility, and most aerobic species, except for sp. and sp., were sensitive to enrofloxacin; all were susceptible to sulfonamide. Virus inhibition experiments determined that ostrich-source sp., sp., and produced extracellular metabolites that caused a substantial reduction in the IAV titers of 99.9%. , , , , , and spp. similarly reduced the viability of IAV from 77.6% to 24.1%. appeared to have no effect, but , spp., and spp. slightly increased the viability of IAV by 25.9, 34.9, and 58.5%, respectively.