Layer chicken manure as a hotspot for the dissemination of microbial communities and antimicrobial resistance genes: metagenomic insights

Abstract Manure contains a diverse range of microbial communities and antimicrobial resistant genes (ARGs), and the use of poultry manure in agricultural fields for soil enrichment may lead to environmental contamination, posing a risk to human and animal health. The current study profiled the microbiome and resistome of manure collected from poultry operations across Alberta, Canada. The sampling was conducted from 15 (cage and floor housed layer chickens) barns across Alberta from 2022–24 and processed via shotgun metagenomics. Taxonomic alignment was performed after mapping the reads via Kraken 2. The resistome of the assembled contig files was analyzed via the AMRFinderPlus database. Bacillota, Actinomycetota and Pseudomonadota were the most relatively abundant phyla in the study samples. ESPEC pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , and Pseudomonas aeruginosa ) were detected in both types of housing systems, and the relative abundances of S. aureus, P. multocida, and A. baumannii were greater in manure from cage housing, whereas E. coli and K. pneumoniae were relatively more abundant in floor-housed manure. lnu C , aad 9 , aph3-IIIa , sat 4 , and tet W ARG subtypes were found in all 15 samples. The analysis of ARGs revealed that resistance was associated mainly with the tetracycline, aminoglycoside and lincosamide classes of antibiotics. Overall, manure contains potential opportunistic pathogens and ARGs that are resistant to various classes of antibiotics. This study provides strong evidence for the need for policy change regarding the treatment of litter and manure prior to their application on agricultural land in Alberta.