Table 3 Distribution of CDSs annotated as antimicrobial resistance genes
ARDB | Number of clusters and orphans | C. bolteae 90A5 | C. bolteae 90A7 | C. bolteae 90A9 | C. bolteae 90B3 | C. bolteae 90B7 | C. bolteae 90B8 | C. clostridioforme 90A1 | C. clostridioforme 90A3 | C. clostridioforme 90A4 | C. clostridioforme 90A6 | C. clostridioforme 90A8 | C. clostridioforme 90B1 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
class A beta-lactamase | blaCLO1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
class B beta-lactamase | metallo-enzymes | 4 | 1 | 2 | 1 | 1 | 1 | 1 | 2 | 1 | 2 | 2 | 2 | 1 |
class C beta-lactamase | Amp C and Penicillin Binding Protein | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
class D beta-lactamase | Amp D (oxa type) | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 |
Teicoplanin, Vancomycin | VanRA | 4 | 2 | 1 | 1 | 1 | 1 | 3 | 1 | |||||
VanSA | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||||||
VanD | 2 | 2 | 2 | 2 | 2 | 2 | ||||||||
VanSD | 1 | 1 | 1 | 1 | 1 | 1 | ||||||||
VanXD | 1 | 1 | 1 | 1 | 1 | 1 | ||||||||
VanRD | 2 | 1 | 1 | 1 | 1 | 1 | ||||||||
Vancomycin | VanHB | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 |
VanRB | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | |
VanB | 1 | 1 | ||||||||||||
VanSB | 1 | 1 | ||||||||||||
VanWB | 1 | 1 | ||||||||||||
VanXB | 1 | 1 | ||||||||||||
VanYB | 2 | 2 | ||||||||||||
VanSC | 1 | 1 | ||||||||||||
VanRE | 1 | 1 | 1 | 1 | ||||||||||
VanG | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
VanRG | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | |
VanYG | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||||||
VanUG | 3 | 2 | 1 | |||||||||||
Teicoplanin | VanZ | 4 | 2 | 3 | 1 | 1 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 |
Lincomycin | LnuA | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 2 |
Macrolides | ErmB | 1 | 1 | 1 | ||||||||||
Macrolide-Lincosamide- Streptogramin (efflux pumps) | MacB | 1 | 6 | 8 | 7 | 7 | 6 | 6 | 6 | 6 | 6 | 6 | 5 | 6 |
MefA | 1 | 3 | 2 | 4 | 4 | 3 | 3 | 3 | 3 | 3 | 4 | 3 | 3 | |
MsrA/MsrB | 5 | 3 | 3 | 3 | 3 | 3 | ||||||||
Lsa | 1 | 1 | 1 | 1 | ||||||||||
ABC transporter (efflux pumps) | VgaA | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Tirc | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
CcmA | 6 | 2 | 2 | 3 | 3 | 2 | 4 | 3 | ||||||
Streptogramin_A Chloramphenicol | VatB | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
chloramphenicol | CAT | 3 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | ||||
linezolide | Cfr | 2 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||
Rifampicin | Arr | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
Metronidazole | Nim | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Trimethoprim | Dfra20 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Dfra | 1 | 1 | ||||||||||||
Aminoglycosides | Aac6ie | 2 | 2 | |||||||||||
Aad9ib | 1 | 1 | ||||||||||||
Ant6ia | 3 | 1 | 1 | 2 | 1 | 2 | 1 | |||||||
Aph3iiia | 1 | 2 | 1 | 1 | ||||||||||
Apha | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | |
Tetracycline | Tet40 | 1 | 1 | 1 | ||||||||||
TetO | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
TetW | 1 | 1 | 1 | 1 | 1 | |||||||||
Tet32 | 1 | 1 | 1 | |||||||||||
Bacitracin | BacA | 3 | 1 | 1 | 2 | 2 | 1 | 1 | 1 | 2 | 2 | 1 | 1 | 2 |
BcrA | 1 | 2 | 3 | 4 | 4 | 2 | 3 | 3 | 4 | 4 | 3 | 4 | 5 | |
Multidrug resistance efflux pump | Blt | 1 | 1 | |||||||||||
AcrB | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 3 | 3 | 3 | 3 | 3 | 3 |