A Large-Scale Sequencing-Based Survey of Plasmids in Reveals Global Dissemination of Plasmids

The food-borne pathogen is known for its capacity to cope with multiple stress conditions occurring in food and food production environments (FPEs). Plasmids can provide benefits to their host strains, and it is known that various strains contain plasmids. However, the current understanding of plasmid frequency and function in strains remains rather limited. To determine the presence of plasmids among strains and their potential contribution to stress survival, a comprehensive dataset was established based on 1,921 published genomes from strains representing 14 sequence types (STs). Our results show that an average of 54% of all strains in the dataset contained a putative plasmid. The presence of plasmids was highly variable between different STs. While some STs, such as ST1, ST2, and ST4, contained few plasmid-bearing strains (<15% of the strains per ST), other STs, such as ST121, ST5, ST8, ST3, and ST204, possessed a higher proportion of plasmid-bearing strains with plasmids found in >71% of the strains within each ST. Overall, the sizes of plasmids analyzed in this study ranged from 4 to 170 kbp with a median plasmid size of 61 kbp. We also identified two novel groups of putative plasmids based on the amino acid sequences of the plasmid replication protein, RepA. We show that highly conserved plasmids are shared among strains which have been isolated from around the world over the last few decades. To investigate the potential roles of plasmids, nine genes related to stress-response were selected for an assessment of their abundance and conservation among plasmids. The results demonstrated that these plasmid genes exhibited high sequence conservation but that their presence in plasmids was highly variable. Additionally, we identified a novel transposon, Tn, predicted to be involved in mercury-resistance. Here, we provide the largest plasmid survey of to date with a comprehensive examination of the distribution of plasmids among strains. Our results significantly increase our knowledge about the distribution, composition, and conservation of plasmids and suggest that plasmids are likely important for the survival of in food and FPEs.