Evaluation of antimicrobial resistance and antimicrobial peptide-encoding genes in metagenomic samples from back-yard poultry environments

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Alonna Wright, David Coil, Guillaume Jospin and Dennett Rodriguez, Genome Center, University of California, Davis, Davis, CA, Jonathan A. Eisen, Medical Microbiology and Immunology, University of California, Davis, Davis, CA

Background/Question/Methods
Backyard poultry (BYP) ownership is a growing interest within the US, especially recently as people have been spending more time at their homes. Owning BYP presents the opportunity for the acquisition of microbes originating from BYP-associated microbiomes. Owner-administered antibiotics to BYP flocks for illnesses are currently not subject to strict regulation like commercial poultry production. Potential misuse of these antibiotics can alter the BYP-associated microbiome and potentially nurture strains of antibiotic-resistant bacteria. This study aims to use metagenomic sequencing analysis to characterize the microbial community of interior and exterior door frame surfaces of homes with BYP flocks, with a particular interest in antimicrobial resistance (AMR) and antimicrobial peptide (AMP) encoding genes. Understanding the relationship between AMR and AMP genes in environments prone to AMR-bacterial strains may aid in the development of prevention and therapeutics for these environments. To study this relationship, door frames were swabbed and submitted for shotgun metagenomic sequencing. Sequences were trimmed and filtered prior to being coassembled between samples using MEGAHIT. Coassembly contigs were analyzed for phage signals using VIBRANT and VirSorter, and taxonomically classified using Kaiju for bacteria, eukaryotic microorganisms, and viruses. Contigs were also analyzed for previously confirmed AMR genes and putative AMR genes using DeepARG, and AMP-encoding genes were predicted using Macrel. Individual contigs were analyzed across all outputs to determine contig content of AMR and/or AMP genes, as well as taxonomic origin.
Results/Conclusions
We found that although there are conflicting opinions on the role of phage in AMR transmission, only 1 contig in our dataset was identified as phage-originating and containing an AMR gene. Additionally, no phage contigs were found to contain putative AMR genes or AMP-encoding genes. However, 25 known AMR and 23 predicted AMR genes were found in bacterial contigs, as well as 29 AMP-encoding genes. Interestingly 78 known AMR, 100 predicted AMR, and 736 AMP genes were detected in contigs not assigned as bacteria or phage - implicating a vast majority of the AMR and AMP genes in this system may originate from unknown microbial members or other environmental contributors. Subsequent steps in this study will be to further characterize the origin of the non-bacterial and non-phage contigs, and to predict phage-bacteria host pairs to extrapolate potential AMR and AMP interactions that may be occurring.