Complex pathogen interactions in upper respiratory tract infections in commercial free-range layers: A cross-sectional study

The global egg industry of free-range chickens is rapidly expanding owing to perceived higher welfare standards. However, commercial free-range layers are known to be prone to a number of infections including upper respiratory tract infections (URTIs) leading to significant economic and welfare concerns. The present study explored the prevalence and diversity of respiratory tract pathogens in URTIs in free-range layers in Australia. Swabs/tissues were collected from conjunctiva, nasal cavity, infraorbital sinus, and upper trachea of birds from 15 farms across Australia with ongoing URTIs as well as two control farms which did not have a history of URTIs. These specimens were subjected to bacteriological isolation and identification, specific PCRs, strain identification using high-resolution melt curve analysis and/or whole genome sequence analysis. Clinical signs in affected flocks commonly included conjunctivitis but, sneezing, coughing, nasal discharge, sinusitis, tracheal rales, and/or laboured breathing were also observed. The morbidity ranged from 2% to 60% while mortality was often low and did not exceed 5%. Several bacterial and viral organisms were detected in different combinations from affected farms. These included Avibacterium paragallinarum (12/15 farms), Gallibacterium anatis (12/15), Ornithobacterium rhinotracheale (11/15), and Pasteurella multocida (3/15). Presence of Mycoplasma synoviae (15/15), M. gallisepticum (13/15), infectious laryngotracheitis (13/15) virus and infectious bronchitis virus (4/15) was suspected, however, their identities as vaccines or field strains were not investigated. Gallibacterium anatis, M. gallisepticum and M. synoviae were identified also in two control farms. This is the first study systematically investigated the cause/s of URTIs in commercial free-range layer chickens indicating the complex multi-pathogenic nature of URTIs.