Long-read metagenomic characterization of the microbial DNA and resistome recovered from a peracetic acid immersion chiller in a commercial poultry processing facility: a pilot study.

Peracetic acid (PAA)-based immersion chillers are a critical pathogen intervention in commercial poultry processing, yet the microbial DNA recoverable from these systems remains poorly characterized. Here, we applied long-read Oxford Nanopore Technology (ONT) metagenomics to characterize the taxonomic composition, resistance gene content and mobile element context of the microbial DNA recovered from the mid-stage immersion chiller of a commercial poultry processing facility. From 14.47 GB of sequencing data (median Q-score 19.1), we reconstructed three near-complete metagenome-assembled genomes (MAGs) assigned to the putative species Comamonas sp., Flavobacterium sp., and Pseudomonas veronii (completeness >99.5%), each encoding oxidative stress defense, mercury detoxification, and efflux gene repertoires. Assembly graph analysis revealed a high-depth Tn21-family transposon junction node shared between contigs binned to Comamonas sp. and P. veronii, indicating that the genetic determinants recovered from these two genomes occur within a common mobile-element context. In addition, forty-four circular contigs were recovered, including one classified as a near-complete Myoviridae phage genome (1.45% of assembled bases). Community-level resistome profiling identified a prevalent mercury resistance (mer) cluster spanning multiple genera, alongside the biocide resistance gene qacE and antibiotic resistance genes on reads taxonomically assigned to Salmonella and Escherichia. These findings describe the resistance gene content and genomic organization of the DNA recoverable from a single immersion chiller. Because total DNA metagenomics cannot distinguish viable from inactivated cells, no inference regarding microbial survival, selection or ongoing gene transfer is drawn. Nevertheless, these pilot findings provide a foundation for viability‑resolved and multisite investigations that can more fully define microbial dynamics in immersion chillers.