Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany
Abstract
:1. Introduction
2. Results
2.1. Bacterial Isolation
2.2. Antimicrobial Susceptibility Testing (AST)
2.3. Whole-Genome Sequencing and Analysis
2.4. Metagenomic Sequencing and Analysis of Antimicrobial Resistance Genes
2.5. Microbiome Analysis for Bacterial Species Diversity
3. Discussion
4. Materials and Methods
4.1. Sampling Areas
4.2. Bacterial Isolation
4.3. Antimicrobial Susceptibility Testing (AST)
4.4. Whole-genome Sequencing (WGS) and Analysis
4.5. Metagenomic Sequencing and Analysis of Antimicrobial Resistance Genes
4.6. Microbiome Analysis
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Designation | Species of Origin | Amikacin | Amoxicillin/Clavulanic Acid | Ampicillin | Cefotaxim | Ceftazidim | Cefepim | Colistin | Imipenem | Meropenem | Gentamicin | Tobramycin | Ciprofloxacin | Tetracycline | Trimethoprim/Sulfamethoxazol | ESBL | MDR |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
257 | WR | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
258 | WR | S | R | R | R | R | R | S | S | S | S | S | S | R | S | + | + |
259 | WR | S | R | R | R | R | R | S | S | S | S | S | S | R | S | + | + |
260 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
261 | WB | S | R | R | R | R | R | S | S | S | S | S | S | R | S | + | + |
262 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
263 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
264 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
265 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
266 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
267 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
268 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
269 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
270 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
271 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
272 | WB | S | R | R | R | R | R | S | S | S | S | S | S | S | S | + | - |
1031 | WB | S | R | R | R | R | R | S | S | S | R | R | S | R | S | + | + |
1114 | WB | S | R | R | R | R | R | S | S | S | R | R | S | R | S | + | + |
1115 | WB | S | R | R | R | R | R | S | S | S | S | S | R | R | R | + | + |
Class | Wild Boar 1 | Wild Boar 2 | Roe Deer 1 | Roe Deer 2 |
---|---|---|---|---|
Aminocoumarins | 2.0 | 1.1 | 3.0 | 1.5 |
Aminoglycosides | 10.6 | 8.3 | 15.2 | 18.3 |
Bacitracin | 0.7 | 0.0 | 0.0 | 0.0 |
Beta-lactams | 5.8 | 6.9 | 8.5 | 6.6 |
Cationic antimicrobial peptides | 1.4 | 1.3 | 0.6 | 1.2 |
Elfamycins | 1.6 | 0.8 | 1.9 | 2.7 |
Fluoroquinolones | 1.4 | 1.3 | 2.6 | 4.8 |
Fusidic acid | 0.2 | 0.0 | 0.6 | 0.9 |
Glycopeptides | 0.7 | 1.2 | 1.1 | 1.2 |
MLS | 31.1 | 39.6 | 27.6 | 28.8 |
Multi-drug resistance | 11.7 | 8.7 | 9.8 | 9.0 |
Mycobacterium tuberculosis-specific Drug | 0.1 | 0.3 | 2.0 | 1.8 |
Phenicol | 0.4 | 0.1 | 0.6 | 0.9 |
Rifampin | 2.0 | 1.5 | 4.5 | 2.4 |
Sulfonamides | 0.5 | 0.5 | 1.7 | 0.0 |
Tetracyclines | 29.2 | 28.1 | 19.3 | 18.0 |
Trimethoprim | 0.0 | 0.0 | 0.2 | 0.3 |
Fosfomycin | 0.6 | 0.1 | 0.9 | 1.5 |
Wild Boar 1 | Wild Boar 2 | Roe Deer 1 | Roe Deer 2 |
---|---|---|---|
0.049 | 0.042 | 0.033 | 0.028 |
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Homeier-Bachmann, T.; Schütz, A.K.; Dreyer, S.; Glanz, J.; Schaufler, K.; Conraths, F.J. Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany. Antibiotics 2022, 11, 123. https://doi.org/10.3390/antibiotics11020123
Homeier-Bachmann T, Schütz AK, Dreyer S, Glanz J, Schaufler K, Conraths FJ. Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany. Antibiotics. 2022; 11(2):123. https://doi.org/10.3390/antibiotics11020123
Chicago/Turabian StyleHomeier-Bachmann, Timo, Anne K. Schütz, Sylvia Dreyer, Julien Glanz, Katharina Schaufler, and Franz J. Conraths. 2022. "Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany" Antibiotics 11, no. 2: 123. https://doi.org/10.3390/antibiotics11020123