Table 1 Comparison of antibiotics resistance genes from culture-independent and culture-enriched microbiomes to the pangenome of selected species
From: Culture-enriched human gut microbiomes reveal core and accessory resistance genes
Bacteroides uniformis | Campylobacter jejuni | Enterobacter cloacae | Enterococcus faecalis | Enterococcus faecium | Escherichia coli | Staphylococcus aureus | ||
|---|---|---|---|---|---|---|---|---|
Reference genomes | Number of genomes of species for panresistome construction | 14 | 458 | 432 | 246 | 119 | 3346 | 6632 |
Types of resistance genes found in species (total resistome) | 29 | 29 | 225 | 79 | 172 | 296 | 112 | |
Types of resistance genes present in > 95% genomes of species (core resistome) | 0 | 2 | 34 | 0 | 0 | 35 | 12 | |
Types of resistance genes present in < 95% and > 5% genomes of species (accessory resistome) | 9 | 5 | 35 | 21 | 21 | 23 | 18 | |
Types of resistance genes present in < 5% genomes of species (Rare resistome) | 20 | 22 | 156 | 58 | 151 | 238 | 82 | |
CIM and CEM | Number of CIM or CEM positive for resistance genes found in the context of species | 157 | 174 | 39 | 124 | 30 | 146 | 101 |
Types of resistance genes found in the context of the species in CIM or CEM (total resistome) | 9 | 3 | 44 | 7 | 7 | 68 | 10 | |
Types of resistance genes found in the context of the species in CIM or CEM and present in > 95% genomes of species (core resistome) | 0 | 0 | 35 | 0 | 0 | 35 | 0 | |
Types of resistance genes found in the context of the species in CIM or CEM and present in < 95% and > 5% genomes of species (accessory resistome) | 6 | 1 | 6 | 5 | 5 | 22 | 4 | |
Types of resistance genes found in the context of the species in CIM or CEM and present in < 5% genomes of species (rare resistome) | 0 | 0 | 3 | 2 | 1 | 10 | 4 | |
Types of resistance genes found in the context of the species in CIM or CEM and not found in reference genomes | 3 | 2 | 0 | 0 | 1 | 1 | 2 | |