Core-genome multi-locus sequence types of the IncI1 plasmids identified in Salmonella enterica subsp. enterica serovars Heidelberg and Kentucky from Canadian poultry production are associated with factors related to production, year, and geographical region

The IncI1 plasmid is an important driver of antimicrobial resistance (AMR) in Salmonella enterica collected from human and poultry sources in Canada. In the present study, isolates of S. enterica subsp. enterica serovars Heidelberg (n = 1791) and Kentucky (n = 266), collected over 15 years of surveillance of Canadian poultry production, were subjected to whole-genome sequencing, from which IncI1 plasmid sequences were identified and extracted for genomic and epidemiological analyses. Extracted IncI1 sequences (n = 1123) were used to construct a novel plasmid core-genome multilocus sequence typing (pcgMLST) scheme, which was applied to a subset of plasmids specifically from chicken production (n = 940). From the pcgMLST analysis, four IncI1 genomic groups were identified, corroborated by differences in AMR potential and allelic diversity within and between groups. These groups were used to inform a multilevel multinomial model, which revealed associations with sampling year, location, and production stage. Taken together, this work demonstrates that IncI1 plasmid population dynamics in S. Heidelberg and S. Kentucky circulating in Canadian poultry production are complex and influenced by multiple factors driving dissemination across Canada.