ESBL and AmpC β-Lactamases in Clinical Strains of Escherichia coli from Serra da Estrela, Portugal
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains
2.2. Phenotype Identification and Antibiotics Susceptibility
2.3. Molecular Characterization of bla Genes
3. Results
3.1. Bacterial Strains
3.2. Phenotype Identification and Antibiotic Susceptibility
3.3. Molecular Characterization of bla Genes
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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PCR Multiplex | Targeted β-lactamases | Primer’s Name | Sequence (5′-3′) | Product’s Size (bp) |
---|---|---|---|---|
PCR multiplex TSO (TEM, SHV, and OXA-1-like) | TEM variants (including TEM-1 and TEM-2) | MultiTSO-T_for | CATTTCCGTGTCGCCCTTATTC | 800 |
MultiTSO-T_rev | CGTTCATCCATAGTTGCCTGAC | |||
SHV variants (including SHV-1) | MultiTSO-S_for | AGCCGCTTGAGCAAATTAAAC | 713 | |
MultiTSO-S_rev | ATCCCGCAGATAAATCACCAC | |||
OXA-1-like variants OXA-1, OXA-4 and OXA-30 | MultiTSO-O_for | GGCACCAGATTCAACTTTCAAG | 564 | |
MultiTSO-O_rev | GACCCCAAGTTTCCTGTAAGTG | |||
PCR multiplex CTX-M (CTX-M Group 1, CTX-M Group 2, and CTX-M Group 9) | CTX-M Group 1 variants (including CTX-M-1, CTX-M-3 and CTX-M-15) | MultiCTX-MGrp1_for | TTAGGAARTGTGCCGCTGYAa | 688 |
MultiCTX-MGrp1-2_rev | CGATATCGTTGGTGGTRCCATa | |||
CTX-M Group 2 variants | MultiCTX-MGrp2_for | CGTTAACGGCACGATGAC | 404 | |
MultiCTX-MGrp1-2_rev | CGATATCGTTGGTGGTRCCATa | |||
CTX-M Group 9 variants (including CTX-M-9 and CTX-M-14) | MultiCTX-MGrp9_for | TCAAGCCTGCCGATCTGGT | 561 | |
MultiCTX-MGrp9_rev | TGATTCTCGCCGCTGAAG | |||
PCR CTX-M Group 8/25 | CTX-M Group 8/25 variants CTX-M-8, CTX-M-25, CTX-M-26, and CTX-M-39 to CTX-M-41 | CTX-MGrp8/25_for | AACRCRCAGACGCTCTACa | 326 |
CTX-MGrp8/25_rev | TCGAGCCGGAASGTGYATa | |||
PCR multiplex AmpC (ACC, FOX, MOX, DHA, CIT, and EBC) | ACC variants ACC-1 and ACC-2 | MultiACC_for | CACCTCCAGCGACTTGTTAC | 346 |
MultiACC_rev | GTTAGCCAGCATCACGATCC | |||
FOX variants FOX-1 to FOX-5 | MultiFOX_for | CTACAGTGCGGGTGGTTT | 162 | |
MultiFOX_rev | CTATTTGCGGCCAGGTGA | |||
MOX variants MOX-1, MOX-2, CMY-1, CMY-8 to CMY-11, and CMY-19 | MultiMOX_for | GCAACAACGACAATCCATCCT | 895 | |
MultiMOX_rev | GGGATAGGCGTAACTCTCCCAA | |||
DHA variants DHA-1 and DHA-2 | MultiDHA_for | TGATGGCACAGCAGGATATTC | 997 | |
MultiDHA_rev | GCTTTGACTCTTTCGGTATTCG | |||
CIT variants LAT-1 to LAT-3, BIL-1, CMY-2 to CMY-7, CMY-12 to CMY-18, and CMY-21 to CMY-23 | MultiCIT_for | CGAAGAGGCAATGACCAGAC | 538 | |
MultiCIT_rev | ACGGACAGGGTTAGGATAGYa | |||
EBC variants ACT-1 and MIR-1 | MultiEBC_for | CGGTAAAGCCGATGTTGCG | 683 | |
MultiEBC_rev | AGCCTAACCCCTGATACA |
Strain | Source | Antibiogram | Presumptive Tests | Confirmatory | ||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ESBL | AmpC | Molecular Tests | ||||||||||||||||||||||||||||||||||||
Etest | FOX | Etest | PCR | |||||||||||||||||||||||||||||||||||
AMP | AMC | TZP | CXM | CT | TZ | ERT | MEM | GEN | CIP | LVX | TIG | SXT | CT/CTL | TZ/TZL | Diameter | CN/CNI | ESBL | AmpC | ||||||||||||||||||||
MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | MIC (mg/L) | ratio | ratio | (mm) | ratio | ||||||||||||||||||||||
A1 | Urine | HAI | ≥32 | R | 4 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | >8 | + | >8 | + | 27 | <8 | N.D. | N.D. | |||||||||
A2 | Urine | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | 40 | >8 | + | >8 | + | 23 | <8 | OXA-1-like | N.D. | ||||||
A3 | Respiratory | HAI | ≥32 | R | 16 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | 1 | ≤20 | >8 | + | P.Z. | + | 24 | <8 | OXA-1-like | N.D. | |||||||||
A4 | Urine | HAI | ≥32 | R | 4 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | >8 | + | >8 | + | 25 | <8 | N.D. | N.D. | |||||||||
A5 | Urine | HAI | ≥32 | R | 16 | ≥128 | R | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | P.Z. | + | 24 | <8 | N.D. | N.D. | |||||||
A6 | Urine | HAI | ≥32 | R | 4 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | >8 | + | 24 | <8 | CTX-M Grp1 + OXA-1-like | N.D. | |||||||||
A7 | Respiratory | HAI | ≥32 | R | 16 | 8 | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | 40 | >8 | + | >8 | + | 16 | + | <8 | CTX-M Grp1 | N.D. | ||||||||
A8 | Urine | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | 40 | >8 | + | >8 | + | 24 | <8 | OXA-1-like | N.D. | ||||||
B1 | Urine | HAI | ≥32 | R | 4 | ≥128 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | >8 | + | 26 | <8 | OXA-1-like | N.D. | ||||||||
B2 | Urine | HAI | ≥32 | R | ≥32 | R | 8 | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | >8 | + | 22 | <8 | N.D. | N.D. | ||||||||
B3 | Urine | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | P.Z. | + | 24 | <8 | CTX-M Grp1 + OXA-1-like | N.D. | ||||||
B4 | Respiratory | HAI | ≥32 | R | 16 | 64 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | >8 | + | 24 | <8 | OXA-1-like | N.D. | ||||||||
B5 | Respiratory | HAI | ≥32 | R | 16 | 64 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | P.Z. | + | 24 | <8 | N.D. | N.D. | ||||||||
B6 | Urine | HAI | ≥32 | R | 16 | 16 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | P.Z. | + | 24 | <8 | OXA-1-like | N.D. | |||||||
B7 | Respiratory | HAI | ≥32 | R | 16 | 8 | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | P.Z. | + | 24 | <8 | CTX-M Grp1 + TEM | N.D. | |||||||||
B8 | Urine | HAI | ≥32 | R | ≥32 | R | 16 | R | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | P.Z. | + | 17 | + | <8 | OXA-1-like | N.D. | ||||
B9 | Urine | HAI | ≥32 | R | ≥32 | R | 8 | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | >8 | + | 26 | <8 | OXA-1-like | N.D. | ||||||
C1 | Urine | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | >8 | + | 24 | <8 | CTX-M Grp1 + OXA-1-like | N.D. | |||||
C2 | Urine | HAI | ≥32 | R | 8 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | P.Z. | + | 24 | <8 | CTX-M Grp1 + TEM + OXA-1-like | N.D. | |||||||
C3 | Urine | HAI | ≥32 | R | ≥32 | R | 32 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | P.Z. | + | 17 | + | <8 | OXA-1-like | N.D. | |||||
C4 | Urine | HAI | ≥32 | R | ≥32 | R | 16 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | >8 | + | 16 | + | <8 | OXA-1-like | N.D. | |||||
C5 | Urine | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | 40 | >8 | + | P.Z. | + | 22 | <8 | OXA-1-like | N.D. | ||||||
C6 | Urine | HAI | ≥32 | R | ≥32 | R | 64 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | >8 | + | 17 | + | <8 | OXA-1-like | N.D. | |||||
C7 | Urine | HAI | ≥32 | R | 16 | 16 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | >8 | + | 24 | <8 | OXA-1-like | N.D. | |||||||
C8 | Skin and soft tissue | HAI | ≥32 | R | ≥32 | R | 64 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | >8 | + | 15 | + | <8 | OXA-1-like | N.D. | |||||
C9 | Bloodstream | HAI | ≥32 | R | 16 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | >8 | + | 24 | <8 | CTX-M Grp1 | N.D. | ||||||||
D1 | Urine | HAI | ≥32 | R | 4 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | >8 | + | 20 | <8 | CTX-M Grp1 | N.D. | |||||||||
D2 | Skin and soft tissue | HAI | ≥32 | R | 16 | 32 | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | 1 | ≥320 | R | P.Z. | + | P.Z. | + | 15 | + | <8 | CTX-M Grp1 + OXA-1-like | N.D. | ||||||
D3 | Skin and soft tissue | HAI | ≥32 | R | 16 | 64 | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≤20 | P.Z. | + | P.Z. | + | 23 | <8 | TEM + OXA-1-like | N.D. | ||||||||
D4 | Skin and soft tissue | HAI | ≥32 | R | ≥32 | R | 16 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | P.Z. | + | 17 | + | <8 | CTX-M Grp1 + OXA-1-like | N.D. | |||||
D5 | Urine | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | >8 | + | 17 | + | <8 | CTX-M Grp1 + OXA-1-like | N.D. | ||||
D6 | Urine | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | >8 | + | 24 | <8 | OXA-1-like | N.D. | |||||
D7 | Skin and soft tissue | HAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | >8 | + | 17 | + | <8 | CTX-M Grp1 + OXA-1-like | N.D. | ||||
D8 | Urine | HAI | ≥32 | R | 8 | ≤4 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≤1 | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | P.Z. | + | 25 | <8 | CTX-M Grp1 + TEM | N.D. | ||||||||
D9 | Urine | CAI | ≥32 | R | ≥32 | R | ≥128 | R | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | >8 | + | 17 | + | <8 | CTX-M Grp1 + OXA-1-like | N.D. | ||||
E2 | Skin and soft tissue | HAI | ≥32 | R | ≥32 | R | 64 | >64 | R | >64 | R | ≥64 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | >8 | + | >8 | + | 17 | + | <8 | CTX-M Grp1 + OXA-1-like | N.D. | |||||
E3 | Urine | HAI | ≥32 | R | 16 | 16 | >64 | R | >64 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | ≥4 | R | ≥8 | R | ≤0,5 | ≥320 | R | P.Z. | + | >8 | + | 15 | + | <8 | CTX-M Grp1 + OXA-1-like | N.D. | ||||||
E4 | Skin and soft tissue | HAI | ≥32 | R | ≥32 | R | 32 | >64 | R | 8 | R | 16 | R | ≤0,5 | ≤0,25 | ≥16 | R | 0,5 | 1 | ≤0,5 | ≤20 | Inconclusive | Inconclusive | 9 | + | >8 | + | TEM | CIT |
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Oliveira, C.; Amador, P.; Prudêncio, C.; Tomaz, C.T.; Tavares-Ratado, P.; Fernandes, R. ESBL and AmpC β-Lactamases in Clinical Strains of Escherichia coli from Serra da Estrela, Portugal. Medicina 2019, 55, 272. https://doi.org/10.3390/medicina55060272
Oliveira C, Amador P, Prudêncio C, Tomaz CT, Tavares-Ratado P, Fernandes R. ESBL and AmpC β-Lactamases in Clinical Strains of Escherichia coli from Serra da Estrela, Portugal. Medicina. 2019; 55(6):272. https://doi.org/10.3390/medicina55060272
Chicago/Turabian StyleOliveira, Cátia, Paula Amador, Cristina Prudêncio, Cândida T Tomaz, Paulo Tavares-Ratado, and Rúben Fernandes. 2019. "ESBL and AmpC β-Lactamases in Clinical Strains of Escherichia coli from Serra da Estrela, Portugal" Medicina 55, no. 6: 272. https://doi.org/10.3390/medicina55060272