Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA
Abstract
:1. Introduction
2. Results
2.1. Enterococcus Isolation and Species Diversity
2.2. Antimicrobial Susceptibility Testing by Agar Dilution
2.3. PCR Screening of Antimicrobial Resistance Determinants
2.4. Antimicrobial Susceptibility Testing of optrA Positive Strains by Microdilution
2.5. Genomic Characterization of Isolates
2.5.1. Molecular Characterization of Linezolid Resistance Mechanisms
2.5.2. Genetic Environment of the optrA Gene
3. Discussion
4. Materials and Methods
4.1. Bacterial Isolation and Species Identification
4.2. Antimicrobial Susceptibility Testing
4.3. PCR Screening of Antibiotic Resistance Genes
4.4. Whole-Genome Sequencing
4.5. Statistical Analysis
4.6. Accession Numbers
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Isolate | Species | Sample Source | Geographic Location | MLST | EUVENC MDR Profile | Acquired Antimicrobial Resistance Genes and Mutations | Plasmid Replicons | Virulence Genes | Accession Number |
---|---|---|---|---|---|---|---|---|---|
INIAV004 | E. faecium | Swine | 39.2333, −8.68333 | ST22 | TET-ERY-LZD-CLO | poxtA, optrA, fex(B), tet(M), tet(L), erm(A), pbp5 (T172A), pbp5 (L177I), pbp5 (A216S), pbp5 (P667S), pbp5 (D204G), pbp5 (K144Q), pbp5 (R34Q), pbp5 (S27G), pbp5 (E100Q), pbp5 (A499T), pbp5 (G66E), pbp5 (T324A), pbp5 (A68T), pbp5 (V24A), pbp5 (N496K), pbp5 (E525D), pbp5 (E85D) | rep29, rep33, repUS43, rep1, rep2, repUS15 | acm, efaAfm | ERS6142029 |
INIAV173 | E. faecium | Swine | 38.9167, −9.2667 | ST2138 | TET-ERY-CLO | poxtA, optrA, fex(B), erm(A), ant(9)-Ia; | rep1; rep11c; rep18b; rep29; repUS15; repUS43 | acm; efaAfm | ERS11708758 |
INIAV005 | E. faecalis | Swine | 38.9485, −9.1967 | ST93 | TET-ERY- DAP | aac(6′)-aph(2″), tet(M), tet(L), erm(B) | rep9a | elrA, srtA, ace, cCf10, cOB1, cad, camE, ebpA, ebpC, efaAfs, hylA, tpx, | ERS6142031 |
INIAV168 | E. faecalis | Swine | 41.4124, −8.5206 | ST207 | TET -ERY-LZD-CLO | optrA; fex(A), tet(M), tet(L), erm(A), erm(B), clpL | repUS1; rep9b; repUS43 | elrA; srtA; ace; agg; cCF10; cOB1; cad; camE; ebpA; ebpC; efaAfs; fsrB; gelE; hylB; tpx | ERS11708754 |
INIAV169 | E. faecalis | Swine | 41.4124, −8.5206 | ST474 | TET-ERY-CIP-GEN-CLO | optrA, fex(A), cat, aac(6′)-aph(2″), aph(3′)-III, tet(M), tet(L), erm(A), erm(B), dfrG, lnu(B); gyrA (E87G), parC (S80I), lsa(E) | rep9a; repUS43 | elrA; srtA; ace; cCF10; cOB1; cad; camE; ebpA; ebpC; efaAfs; fsrB; gelE; hylA; hylB; tpx | ERS11708755 |
INIAV170 | E. faecalis | Swine | 38.7058, −8.97462 | ST474 | TET-ERY-CIP-GEN-CLO | optrA, fex(A), cat, aac(6′)-aph(2″), aph(3′)-III, tet(M), tet(L), erm(A), erm(B), dfrG, gyrA (E87G), parC (S80I), lnu(B), lsa(E) | rep9a; repUS43 | elrA; srtA; ace; cCF10; cOB1; cad; camE; ebpA; ebpC; efaAfs; fsrB; gelE; hylA; hylB; tpx | ERS11708756 |
INIAV171 | E. faecalis | Swine | 39.4598, −8.6671 | ST16 | TET-ERY-LZD-CLO | optrA, fex(A), cat, aac(6′)-aph(2″), aph(3′)-III, str, tet(M), erm(A), erm(B), str, lnu(B), lsa(E) | rep6; rep9b; repUS43 | elrA; srtA; ace; agg; cCF10; cOB1; cad; camE; cylA; cylL; cylM; ebpA; ebpC; efaAfs; hylA; tpx | ERS11708757 |
INIAV174 | E. faecalis | Swine | 38.9167, −9.2667 | ST1178 | TET-ERY-CIP-CLO | optrA, cat, ant(9)-Ia, tet(M), tet(L), erm(A), erm(B), gyrA (E87G), parC (S80I) | rep9a; repUS43 | elrA; srtA; ace; cCF10; cOB1; cad; camE; ebpA; ebpC; efaAfs; fsrB; gelE; hylA; hylB; tpx | ERS11708759 |
INIAV175 | E. faecalis | Swine | 39.4598, −8.6671 | ST58 | TET-ERY-DAP | tet (M), erm(B), ant(6)-Ia, dfrG, lnu(B), lsa(E) | repUS43 | elrA; srtA; ace; cCF10; cOB1; cad; camE; ebpA; ebpC; efaAfs; fsrB; gelE; hylA; tpx | ERS11708760 |
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Antimicrobial | Criteria (a) | E. faecalis (n = 84) | E. faecium (n = 48) | ||||
---|---|---|---|---|---|---|---|
(T)ECOFF (b) | Cattle (n = 18) | Pigs (n = 66) | (T)ECOFF (b) | Cattle (n = 12) | Pigs (n = 36) | ||
Vancomycin | MIC50 | 4 | ≤1 | ≤1 | 4 | ≤1 | ≤1 |
MIC90 | 4 | 2 | ≤1 | ≤1 | |||
% DS | 0 | 0 | 0 | 0 | |||
Teicoplanin | MIC50 | 2 | ≤0.5 | ≤0.5 | 2 | ≤0.5 | ≤0.5 |
MIC90 | ≤0.5 | ≤0.5 | 1 | ≤0.5 | |||
% DS | 0 | 0 | 0 | 0 | |||
Tetracycline | MIC50 | 4 | ≤1 | 128 | 4 | 16 | 128 |
MIC90 | 64 | 128 | 128 | >128 | |||
% DS | 44 (c) | 98 (c) | 58 | 78 | |||
Ciprofloxacin | MIC50 | 4 | 1 | 1 | 8 | 2 | 1 |
MIC90 | 2 | 4 | 4 | 2 | |||
% DS | 0 | 9 | 0 | 0 | |||
Erythromycin | MIC50 | 4 | ≤1 | >128 | 4 | ≤1 | >128 |
MIC90 | >128 | >128 | 2 | >128 | |||
% DS | 17 (c) | 86 (c) | 0 (c) | 58 (c) | |||
Linezolid | MIC50 | ND | 2 | 1 | 4 | 2 | 2 |
MIC90 | 2 | 2 | 2 | 2 | |||
% DS | - | - | 0 | 0 | |||
Gentamicin | MIC50 | 64 | ≤8 | ≤8 | 32 | ≤8 | ≤8 |
MIC90 | ≤8 | 128 | ≤8 | ≤8 | |||
% DS | 0 | 11 | 0 | 0 | |||
Ampicillin | MIC50 | 4 | ≤0.5 | 1 | 8 | 1 | 1 |
MIC90 | 2 | 2 | 1 | 8 | |||
% DS | 0 | 0 | 0 | 6 | |||
Chloramphenicol | MIC50 | 32 | ≤4 | 8 | 32 | ≤4 | ≤4 |
MIC90 | 8 | 64 | ≤4 | 16 | |||
% DS | 0 (c) | 27 (c) | 8 | 3 |
Strain | Species | Linezolid Susceptibility | OptrA Variant | ||||
---|---|---|---|---|---|---|---|
EUVENC MIC (µg/mL) | Interpretation (a) | Morroni et al. [32] | Freitas et al. [33] | Almeida et al. [34] | Amino Acid Substitutions | ||
INIAV173 | E. faecium | 4 | S | DVD (b) | OptrA_28 (b) | V12 | Y176D, A350V, G393D |
INIAV004 | E. faecium | 8 | R | WT | OptrA_1 | V19 | None |
INIAV168 | E. faecalis | 8 | R | DP | OptrA_8 | V22 | Y176D, T481P |
INIAV169 | E. faecalis | 4 | S | EDD | OptrA_7 | V34 | K3E, Y176D, G393D |
INIAV170 | E. faecalis | 4 | S | EDD | OptrA_7 | V34 | K3E, Y176D, G393D |
INIAV171 | E. faecalis | 8 | R | DP | OptrA_8 | V22 | Y176D, T481P |
INIAV174 | E. faecalis | 2 | S | EDD | OptrA_7 | V34 | K3E, Y176D, G393D |
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Gião, J.; Leão, C.; Albuquerque, T.; Clemente, L.; Amaro, A. Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA. Antibiotics 2022, 11, 615. https://doi.org/10.3390/antibiotics11050615
Gião J, Leão C, Albuquerque T, Clemente L, Amaro A. Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA. Antibiotics. 2022; 11(5):615. https://doi.org/10.3390/antibiotics11050615
Chicago/Turabian StyleGião, Joana, Célia Leão, Teresa Albuquerque, Lurdes Clemente, and Ana Amaro. 2022. "Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA" Antibiotics 11, no. 5: 615. https://doi.org/10.3390/antibiotics11050615
APA StyleGião, J., Leão, C., Albuquerque, T., Clemente, L., & Amaro, A. (2022). Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA. Antibiotics, 11(5), 615. https://doi.org/10.3390/antibiotics11050615