Table 1.
Genomic characteristics of 9 linezolid-resistant Enterococcus spp. investigated in this study
| Isolate IDa | Source/ ID | ST/ CC | No. of contigs/ Genome size (Mb) | LZDR genes in chromosome (Amino acid changes on LZDR protein) | LZDR genes in plasmids | LZD MIC (μg/ml)b | other AMR genes | Metal resistance genes | Chromosomal point mutations | Prophage | Transposons | Plasmid replicons (associated AMRa genes) | Insertion sequence | Virulence factors | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
E. casseliflavus X4962 |
Pig/Farm A -P1 | NT | 247/3.7 | cfrD (wild type) | optrA [wild type (by repUS40) | 8 | fexA, lnuB, lsaE, aph3’, dfrG, vanC3 | None | None | None | None | rep1, rep14b, repUS1, repUS41 | ISEnfa1 | None | |
|
E. faecium X3877 |
Stork/ Landfill/ | ST1739 | 136/2.6 | poxtA (wild type) | None | 8 | fexB | arsA, copA, fief, ziaA, zosA, zupT, zur, znuA | c17 mutations in PBP5 |
vB_IME197 BCJA1c |
None | rep1, rep29, repUS15 | ISSsu5 | acm, efaAfm | |
|
E. faecalis X4957 |
Pig/ farm A -P8 | ST330 | 164/3.1 | optrA (RDK: I104R, Y176D, E256K) | None | 10 | cat, fexA, lnuG, lsaA, ermA, tet(L), tet(M), aac6’-aph2″, aph3’, dfrG | cutC, tcrB, znuA | ParC (S80I), GyrA (E87G) |
phiEf11 phiFL4A phiFL2A EFC _1 LP_101 |
Tn6260 (lnuG) |
rep1, rep9a (tet(L), tet(M), cat), repUS1, repUS43 (tet(L), tet(M), cat) |
ISEnfa1 | ace, agg, cad, camE, cOB1, cCF10, ebpA, ebpC, elrA, efaAfs, fsrB, gelE, hylA, hylB, srtA, tpx | |
|
E. faecalis X5386 |
Pig/ farm B-P1 | ST330 | 137/3.0 | optrA (DP-2: Y176D, T481P) | None | 14 | cat, fexA, lnuG, lsaA, ermA, tet(L), tet(M), aac6’-aph2″, ant4’, aph3’, dfrG | cutC, znuA | ParC (S80I), GyrA (E87G) |
phiEf11 BCJA1c phiFL4A |
Tn6260 (lnuG) | rep9a (tet(L), tet(M), cat), rep9b, rep9c, repUS43 (tet(L), tet(M), cat), repUS52 (ant4’) | None | ace, agg, camE, cOB1, cCF10, dad, ebpA, ebpC, elrA, efaAfs, fsrB, gelE, hylA, hylB, SrtA, tpx | |
| X5463 | Pig farmer/ farm B- F2 | ST330 | 116/2.9 | optrA (DP-2: Y176D, T481P) | None | 10 | cat, fexA, lnuG, lsaA, ermA, tet(L), tet(M), aac6’-aph2″, ant6’, aph3’, dfrG | cutC, tcrB, znuA | ParC (S80I), GyrA (E87G) |
phiFL4A Lj928 BCJA1c |
Tn6260 (lnuG) | rep9a (tet(L), tet(M), cat), rep9b, repUS43 (tet(L), tet(M), cat) | ISS1N | ace, agg, cad, camE, cOB1, cCF10, dad, ebpA, ebpC, elrA, efaAfs, fsrB, gelE, hylA, hylB, srtA, tpx | |
|
E. faecalis X5799 |
Pig/ Farm D-P5 | ST59 | 139/ 2.9 | optrA (wild type) | None | 2 | cat, fexA, lnuB, lsaA, lsaE, ermA, tet(L), tet(M), aac6’-aph2″, aph3’, dfrG | cutC, tcrB, znuA | None | phiFL4A | Tn554 (fexA, optrA) | rep9a, rep9c, repUS43 | ISS1N, ISEnfa4 | ace, agg, camE, cOB1, cCF10, cylA, dad, ebpA, ebpC, elrA, efaAfs, fsrB, gelE, hylA, hylB, srtA, tpx | |
|
E. faecalis X5809 |
Pig/ Farm D-P10 | ST474 | 100/2.8 | optrA (EDD: K3E, Y176D, G393D) | None | 12 | cat, fexA, lnuB, lsaA, lsaE, ermA, tet(L), tet(M), aac6’-aph2″, aph3’, dfrG | cutC, tcrB, znuA | ParC (S80I), GyrA (E87G) | phiFL3A | None | rep9a (tet(L), tet(M), cat), rep9c, repUS43 (tet(L), tet(M), cat) | ISS1N | ace, agg, camE, cOB1, cCF10, cylA, dad, ebpA, ebpC, elrA, efaAfs, fsrB, gelE, hylA, hylB, srtA, tpx | |
|
E. faecalis X5445 |
Pig/ farm B-P8 | ST32 | 122/2.9 | optrA (DD_3: Y176D, G393D) | None | 10 | cat, fexA, lnuG, lsaA, ermA, ermB, tet(L), tet(M), aac6’-aph2″, ant9’, aph3’, dfrG | cutC, tcrB, znuA | None |
phiFL3A EFC_1 |
None | rep9a (tet(L), tet(M), cat), rep9c, repUS43 (tet(L), tet(M), cat) | ISS1N | ace, agg, cad, camE, cOB1, cCF10, cylA, dad, ebpA, ebpC, elrA, efaAfs, fsrB, gelE, hylA, hylB, srtA, tpx | |
|
E. faecalis X6347 |
Dog/ household 56 | ST585/ CC5 | 148/2.8 | optrA (DP-2: Y176D, T481P) | None | 12 | fexA, lnuB, lsaA, ermA, ermB, tet(L), tet(M), str | cutC, tcrB, znuA | ParC (S80I) | PHBC6A5A | None | rep7a (str), rep9a (tet(L), tet(M), cat), rep9b, repUS43 (tet(L), tet(M), cat) | None | ace, agg, cad, camE, cOB1, cCF10, cylA, cylL dad, ebpA, ebpC, elrA, efaAfs, fsrB, gelE, hylA, hylB, srtA, tpx | |
AMR Antimicrobial Resistance, F pig farmer, P pig, ST Sequence type, CC Clonal complex
aAll strains were of nasal origin, except E. faecium X3877 which was from a tracheal sample
bMIC to linezolid [7]
c17 mutations in PBP5 = S27G, A68T, A216S, T172A, V24A, 885D, K144Q, A499T, L177I, N496K, G66E, E100Q, D204G, P667S, E525D, T324A, R34Q]