Antibiotic Resistance Genes in Bioaerosols from Saskatchewan Livestock Operations

Antibiotic resistance is increasing, and infections with resistant microorganisms that are typically related to hospital settings are now being seen away from hospital settings. Therefore, there is a pressing need to understand the factors that contribute to the rise of antibiotic resistance. It is known that the use of antibiotics, the presence of residuals of antibiotics, high microbial density, and human activity are potential contributing sources of antibiotic resistant microorganisms. Animal operations, such as swine and poultry, are a source of antibiotic resistant bacteria. Bacteria can acquire resistance through transformation, which is the ability of the bacteria to assimilate DNA, including Antibiotic Resistance Genes, from the environment under specific conditions. Although the conditions are to be determined, Antibiotic Resistance Genes (ARG) are a piece of the puzzle to understand acquired resistance. In the environment, bioaerosols act as carriers of ARG and can be collected at the fan exhaust of animal operations. Despite ARG being detected in animal livestock operations, it is unclear the role of Saskatchewan operations in the emission and spread of bioaerosols with ARG and its overall contribution to the antimicrobial resistance emergency. We aimed to determine the role of Saskatchewan livestock operations in antibiotic resistant genes from bioaerosol emissions and spreading. The specific objectives were I) identify ARG in bioaerosols emitted from Saskatchewan swine and poultry operations; II) evaluate the abundance of ARG in bioaerosols emitted from Saskatchewan swine and poultry operations; and III) evaluate the dispersion of ARG in bioaerosols emitted from livestock operations. Two commercial swine and poultry producer barns were visited. Both swine producers managed three housing systems: finishing, gestation in stalls, and gestation in groups. Bioaerosols were collected at the fan exhaust (n=18) and 10 meters (n=15), 100 meters (n=15), and 1 kilometer (n=15) in front of the fan exhaust of swine finishing and poultry facilities, and at the fan exhaust of swine gestation in stalls (n=19) and swine gestation in groups (n=24), using a high-volume sampler with an electret filter attached to it. DNA was extracted and assessed for bacterial DNA and ARG relative abundance. In parallel to the collection of bioaerosols, the concentration of particulate matter and its fractions were measured in real-time. Overall, poultry facilities emitted more inhalable particulate matter compared with swine facilities. Regarding 16S relative abundance, significant differences were seen between poultry and both swine gestation housing types. Swine finishing and poultry operations had the highest 16S relative abundance. ARG related to quinolone, tetracycline, macrolide, iii sulfonamide, beta-lactam, vancomycin, and mobile genetic elements (MGE) were found at the exhaust of all samples at different relative abundances. Particularly, in swine finishing operations, quinolone resistance represented 34.7% of genes, whereas in swine gestation using group housing 43.25% of the genes were associated with tetracycline resistance. In swine gestation with stall housing, both tetracycline (25.38%) and beta-lactam (28.01%) resistance genes were predominant. Macrolide resistance genes accounted for 42.50% of the genes while 30.57% represented quinolone resistance in poultry operations. Many of the genes linked to tetracycline resistance were present in all facilities, and their abundance varied depending on the housing operation. Notably, tetracycline resistance genes were more diverse and abundant in swine operations where oxytetracycline was used to fight infections. Quinolone and macrolide resistance genes were detected but none of the facilities visited used quinolones or macrolides as treatment for infections. Vancomycin resistance genes were detected in some barns and in low concentrations. In poultry facilities, Bacitracin Methylene Disalicylate (BDM ®) was the only antibiotic used, and it was administered through feed and as a prophylactic measure. At swine finishing and poultry operations, a dilution pattern was observed in the abundance of 16S and ARG as the distance in front of the fan exhaust increased. However, the abundance of macrolide and beta-lactam resistance genes increased when the distance in front of the fan exhaust increased. The number of genes detected after 10 meters decreased compared to the number of genes at the fan exhaust. Mobile genetic elements were not detected beyond the fan exhaust. Livestock operations contribute to the deposition of ARG in the environment; however, it is not the only contributor. Also, after 10 meters in front of the fan exhaust the concentration and diversity of genes are low. Bioaerosols contain essential information about the microbial dynamics in the environment and can be used as tool for controlling and monitoring of prevalence of ARG. ARG related to antibiotics that have not been used in animal facilities can be found in bioaerosols at the fan exhaust. The abundance of ARG was higher in swine operations than in poultry operations.

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