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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