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Non-typhoidal  Salmonella , particularly  Salmonella enterica  serovar Typhimurium ( S . Typhimurium), is the predominant endemic serovar in the Australian egg production industry and is one of the most frequently reported serovars in foodborne infections in Australia. This study was conducted to investigate the genomic characteristics of  Salmonella  isolated from retail table eggs in Western Australia and to identify the impact of production systems on genomic characteristics of  Salmonella  such as virulence and antimicrobial resistance. A total of 40 non-typhoidal  Salmonella  isolates [ S . Typhimurium isolates ( n  = 28) and  Salmonella  Infantis isolates ( n  = 12)] sourced from retail eggs produced by different production systems (barn-laid, cage, and free-range) in Western Australia were sequenced by whole-genome sequencing. The isolates were  de novo  assembled, annotated, and analyzed. The results indicated an association between  Salmonella  genomic variation and the system used to raise poultry for egg production ( p -value < 0.05). All but one of the  S . Infantis isolates were recovered from eggs collected from poultry raised under barn and cage production systems. A higher proportion (83.3%) of  S . Typhimurium isolates were recovered from the eggs produced by free-range production system as compared with those produced under barn (76.9%) and cage production systems (53.3%). Our analysis indicated that  Salmonella  isolated from the eggs produced by barn and cage production systems had more virulence genes than the isolates of the free-range produced eggs. A low carriage of antimicrobial-resistant gene was detected in the isolates of this study. We have built a  Salmonella  genomics database and characteristics-linked gene pools to facilitate future study, characterization, and tracing of  Salmonella  outbreaks.

Whole-Genome Comparative Analysis Reveals Association Between Salmonella Genomic Variation and Egg Production Systems