Studying genetic material from the air in layer poultry-production facilities has shed new light on potential opportunistic pathogens with antibiotic-resistance genes.
The research, led by Awais Ghaffar, PhD candidate at the University of Calgary in Canada, involved collecting air samples from nine cage-housed and six floor-housed production facilities in Alberta. He then applied an approach called shotgun metagenomics, which sequences DNA from microbes without the need to isolate or culture organisms.
Ghaffar’s work revealed differences in the airborne microbial communities in cage and floor systems. Cage systems tended to contain more live microorganisms, with some exceeding the maximum acceptable concentration in the industry.
Numerous pathogens, resistance genes
Potential opportunistic pathogens were also present in the air samples, Ghaffar told an audience at the 2025 American Association of Avian Pathologists Annual Meeting. Pasteurella multocida and Ornithobacterium rhinotracheale were found more frequently in the floor systems, while Gallibacterium anatis and Avibacterium paragallinarum were observed more commonly in cage systems.
ESKAPE pathogens — a group of multidrug-resistant bacteria that includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species — were also observed, he noted. His team observed that S. aureus, P. aeruginosa and A. baumannii were more commonly found in the floor systems, while E. faecium and K. pneumoniae were more prevalent where birds were caged.
He also identified 518 antimicrobial-resistance genes in cage houses and 183 in floor houses, with 120 unique genes and 65 genes shared between the two types of poultry facilities. The classes of antimicrobials against which resistance was found were mainly aminoglycosides, tetracyclines and lincosamides — which are used to different degrees in conventional poultry systems.
An unseen threat in the air?
“The air inside poultry farms contains a diverse range of microbial communities, the most common of which are bacteria. The continuous exposure to these microbial aerosols can impact poultry health, but it might also be a problem for the farm workers and even the surrounding environment,” Ghaffar said.
Antimicrobial resistance has been described as the “silent pandemic.” The World Health Organization, Food and Agriculture Organization and World Organization for Animal Health have an action plan, of which surveillance is a key pillar. The new work highlights the need for airborne surveillance, Ghaffar stressed.
“This is an underestimated area for dissemination of antimicrobial resistance,” he added. “We are providing a strong basis to include airborne resistance in surveillance strategies.”
