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

Abstract

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. Dietzia 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 Streptococcus sp. and Pseudomonas sp., were sensitive to enrofloxacin; all were susceptible to sulfonamide. Virus inhibition experiments determined that ostrich-source Streptococcus sp., Pantoea sp., and Citrobacter freundii produced extracellular metabolites that caused a substantial reduction in the IAV titers of 99.9%. Streptomyces, Corynebacterium, Staphylococcus, Arthrobacter gandavensis, Pseudomonas putida, and Acinetobacter spp. similarly reduced the viability of IAV from 77.6% to 24.1%. Dietzia appeared to have no effect, but Rothia dentocariosa, Rhodotorula spp., and Clostridium spp. slightly increased the viability of IAV by 25.9, 34.9, and 58.5%, respectively.

First isolation of influenza a subtype H5N8 in ostrich: pathological and genetic characterization

“…Respiratory affections contribute a serious hazard causing severe economic losses to the poultry industry ( Setta et al, 2018 ; Marouf et al, 2020 , 2022 ). There was no record of avian influenza infection in ostrich since the isolation of classic HPAI H5N1 2.2.1 in 2010 ( Hagag et al, 2014 ; Abolnik et al, 2019 , 2021 ). However, the new avian influenza virus isolated from ostrich belongs genetically to the HPAI H5N8 clade 2.3.4.4b viruses that have been circulated since 2016–2017 ( Kandeil et al, 2017 ; Selim et al, 2017 ).…”

Experimental infection of ostriches with H7N1 low pathogenic and H5N8 clade 2.3.4.4B highly pathogenic influenza A viruses

“…Virus isolation is still considered the "gold standard" for agent identification, where it is used primarily for diagnosis of the first clinical case and to obtain antigen for subsequent testing (OIE, 2019). Virus isolates from RT-qPCR positive ostrich field samples have been rare (Abolnik et al, 2016), but recent studies aimed at investigating the possible reasons for this determined that the standard PBS: glycerol transport medium (50 %, v/v, without antimicrobials) negatively affects AIV viability in ostrich tracheal swabs (Pieterse et al 2021) and that excluding antimicrobials from VTM encourages the growth of specific bacteria that produce metabolites with anti-viral properties (Abolnik et al, 2021). The ostrich tracheal swabs in the present study had been stored in an appropriate protein-rich VTM that included antimicrobials; therefore we used them to determine the limits of detection for virus isolation from ostrich tracheal swabs.…”

Propagation of avian influenza virus in embryonated ostrich eggs

“…Efforts at isolating ostrich-origin IAVs from RT-PCR positive specimens using ECEs have often been unsuccessful (Abolnik et al 2016 ), for various possible reasons. For example, a recent study found that bacteria present in the ostrich trachea have antiviral effects on IAV, which may partially explain the failure to isolate IAVs from RT-PCR positive tracheal swabs (Abolnik et al 2021 ). However, the possibility of a species bottleneck remains, whereby ostrich-adapted IAVs may not readily infect and replicate in chicken ECEs.…”