Investigating the Source of Salmonella Agona Contamination in Australian Feed Mills Using Core Genome Phylogenetic Analysis.

Salmonella enterica serovar Agona is commonly detected in raw animal feed components during routine microbial monitoring of Australian commercial animal feed mills. We hypothesized that Salmonella-contaminated raw feed components originate at the rendering or oil seed crushing plant and are distributed to mills in different locations. Our objective was to investigate the source of Salmonella Agona contaminated raw feed components. Whole genome sequences of 37 Salmonella Agona isolates, 36 from raw feed components and 1 from finished feed, collected from 10 Australian feed mills located in 4 Australian states, were compared using core genome phylogenetic analysis. After DNA extraction and de novo draft assembly of the paired reads, the draft genomes were aligned using conserved signature indel phylogeny against a reference genome for Salmonella Agona, to identify single nucleotide polymorphisms in the core genome. Five distinct clades corresponding to the five different suppliers of Salmonella Agona-contaminated raw feed components were identified in the resulting phylogenetic tree. The results also provided evidence of cross-transference of Salmonella Agona between canola meal, meat meal, and finished feed within a mill. Core genome phylogenetic analysis facilitated tracing the source of Salmonella contamination in feed mills.