Table 2 Summary of metadata for farm and best BLAST hit NCBI plasmids with high similarity (≥ 95% identity and ≥ 90% alignment coverage) to a clinical plasmid. Only NCBI plasmids from environmental sources were included. The asterisk for the IncFII(S) plasmid indicates an exception where the pMLST genes were identical between the clinical and farm plasmids, but the percentage of shared gene cargo was less than 40%. Here, phylogenetic neighborhood refers to all NCBI Pathogen Detection isolates within 1000 core gene alleles of the clinical clade
Plasmid type | Number of isolates with plasmid (clinical, Holtville, Bakersfield) | Number of highly similar plasmids (clinical, Holtville, Bakersfield) | Number of best hits in NCBI Pathogen and Nucleotide databases | Geographic extent of NCBI best hits | Environmental isolation sources of NCBI best hits | Temporal range of NCBI best hits | Bacterial host range (genera) of NCBI best hits | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
IncFII(S)* | 1728 | 3 | 7 | 1728 | 3* | 7* | 30 | United States, Mexico | River water, soil, almonds, pistachios, chicken | 2010 to 2020 | Salmonella |
IncI1-I(Gamma) | 27 | 13 | 3 | 10 | 1 | 1 | 50 | United States, South Korea, Canada, United Kingdom, Denmark, Switzerland | Cow, sheep, dog, pig, chicken, catfish, horse, iguana, lettuce, soil | 2002 to 2022 | Escherichia, Salmonella, Shigella |
ColpVC | 12 | 3 | 0 | 1 | 4 | 0 | 100 | United States, Canada | Chicken, turkey, pig | 2007 to 2020 | Salmonella |
Col440I | 3 | 60 | 8 | 1 | 4 | 2 | 19 | United States, Germany, Mexico, Venezuela, Ecuador | Chicken, cow, pig, papaya, river water | 2013 to 2020 | Escherichia, Salmonella |
Unclassified | 373 | 235 | 42 | 2 | 5 | 0 | 12 | United States, Australia, United Kingdom, India, Japan | Dog, cow, pig, chicken, wastewater | 2014 to 2021 | Escherichia, Salmonella, Klebsiella |