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Abstract
A high-resolution sequencing approach, CRISPR-SeroSeq, has revealed the frequent occurrence of multiserovar Salmonella populations in food animals and the environment; this highlights the limitations of traditional culture-based methods, as most are reliant on isolation of a few colonies and thus underestimate serovar diversity. The work presented here relies on deep serotyping by CRISPR-SeroSeq to investigate multiserovar Salmonella population dynamics in domestic poultry production. Despite a decrease in Salmonella prevalence at broiler processing from 17% to 8% between 2016 and 2020, the rate of foodborne illnesses remains stable. This disconnect may be attributed to serovars evading detection and therefore intervention strategies. A two-year surveillance study of broiler breeder farms found 18% of Salmonella-positive environmental samples contained multiserovar populations, with serovar Kentucky often excluding others. Longitudinal sampling across two commercial complexes found 17% and 41% of samples collected from pullet and breeder flocks were Salmonella-positive, respectively, with peak prevalence around 38 weeks of age. On-farm rodents were collected and screened for Salmonella by composite gastrointestinal tract samples, revealing 35% positivity with shared serovars between the corresponding flocks and underscoring the potential for on-farm transmission. Successful Salmonella mitigation is contingent upon robust surveillance data, which in turn requires optimal sample collection and isolation methods. The combination of selective pre-enrichment with molecular enumeration in environmental breeder and broiler farm samples demonstrated comparable serovar recovery compared to traditional enrichment while reducing the isolation process by 24 hours. Additionally, PCR assays, along with retrospective bioinformatic analyses, were used to differentiate between live attenuated serovar Typhimurium vaccine and field strains found at processing. Importantly, 6% of serovar Typhimurium isolates from domestic broiler products collected in 2016 to 2022 were vaccine strains, which negatively counted towards a processing establishment’s ranking and may have dissuaded vaccination use. Collectively, these results emphasize the need to improve Salmonella detection methods while minimizing turnaround time. By leveraging high-resolution sequencing, this dissertation highlights the complexity of Salmonella populations in chickens, including serovar-specific interactions and on-farm transmission pathways. This work supports that effective control strategies require adherence to biosecurity measures, reliable monitoring, and tailored interventions, all of which are fundamental in pre-harvest poultry production.