Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics
Abstract
:1. Introduction
2. From Genotype to Phenotype
2.1. Protocol
2.2. Escherichia coli
2.3. Klebsiella pneumoniae
2.4. Other Enterobacteriaceae Involved in HAP
2.5. Pseudomonas aeruginosas
2.6. Acinetobacter baumannii
2.7. Stenotrophomonas maltophilia
2.8. Staphylococcus aureus
3. Discussion
4. Conclusions
Author Contributions
Conflicts of Interest
References
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Species | Escherichia Coli | Klebsiella Pneumoniae | PseudomonaS Aeruginosa | Staphylococcus Aureus | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Reference | Zankari [33] | Stoesser [34] a | Tyson [35] | Stoesser [34] a | Ruppé [40] b | Kos [41] | Köser [42] | Gordon [28] Derivation set | Gordon [28] Validation set | Bradley [43] | Lee [44] | |
N | 48 | 74 | 76 | 69 | 18 | 388 | 14 | 501 | 491 | 501 | 13 | |
Origin | Danish pigs | Bloodstream infections | Cattle | Bloodstream infections | Infection and intestinal carriage | Infections | Infections and nasal carriage | Infections and nasal carriage | Infections and nasal carriage | Infections and nasal carriage | Infections | |
ARG Database | Resfinder | In house | In house | In house | In house | In house | In house | In house | In house | In house | ARG-ANNOT | |
Mutation Analysis | None | ampC, topoisomerases | ampC, topoisomerases | Topoisomerases | Topoisomerases, porins | Topoisomerases, oprD | None | Topoisomerases | Topoisomerases | Topoisomerases | Topoisomerases | |
Ampicillin/Amoxi-Cillin/Penicillin | C | 100 | 98.6 | 100 | NR | NR | NR | 100 | 99.2 | 94.3 | 88 | NT |
ME | 0 | 1.4 | 0 | NR | NR | NR | 0 | 0.8 | 5.1 | 11.7 | NT | |
VME | 0 | 0 | 0 | NR | NR | NR | 0 | 0 | 0.6 | 0.3 | NT | |
Methicillin | C | NT | NT | NT | NT | NT | NT | 100 | 99.6 | 99.2 | 100 | 100 |
ME | NT | NT | NT | NT | NT | NT | 0 | 0.2 | 0.4 | 0 | 0 | |
VME | NT | NT | NT | NT | NT | NT | 0 | 0.2 | 0.4 | 0 | 0 | |
Co-Amoxiclav | C | NT | 100 | 100 | 98.6 | 100 | NR | NT | NT | NT | NT | NT |
ME | NT | 0 | 0 | 1.4 | 0 | NR | NT | NT | NT | NT | NT | |
VME | NT | 0 | 0 | 0 | 0 | NR | NT | NT | NT | NT | NT | |
3GC | C | 100 c | 97.2 d | 98.7 d | 97.2 d | 100 | NT | NT | NT | NT | NT | NT |
ME | 0 c | 1.4 d | 0 d | 1.4 d | 0 | NT | NT | NT | NT | NT | NT | |
VME | 0 c | 1.4 d | 1.3 d | 2.9 d | 0 | NT | NT | NT | NT | NT | NT | |
Carbapenems | C | NT | 100 e | NT | 98.6 e | 100 | 92.4 e | NT | NT | NT | NT | NT |
ME | NT | 0 e | NT | 0 e | 0 | 3.7 e | NT | NT | NT | NT | NT | |
VME | NT | 0 e | NT | 1.4 e | 0 | 3.9 e | NT | NT | NT | NT | NT | |
Fluoroquinolones | C | 97.9 | 100 f | 100 f | 91.3 f | 100 | 92.8 g | NT | 98.0 f | 98.0 f | 95.2 f | 100 |
ME | 0 | 0 f | 0 f | 2.9 f | 0 | 3.1 g | NT | 0.6 f | 0.2 f | 0.2 f | 0 | |
VME | 2.1 | 0 f | 0 f | 5.8 f | 0 | 4.1 g | NT | 1.4 f | 1.2 f | 4.6 f | 0 | |
Amikacin | C | NT | NT | NT | NT | 100 | 81.5 | 100 h | NT | NT | NT | NT |
ME | NT | NT | NT | NT | 0 | 7.7 | 0 h | NT | NT | NT | NT | |
VME | NT | NT | NT | NT | 0 | 10.8 | 0 h | NT | NT | NT | NT | |
Gentamicin | C | 100 | 100 | 100 | 98.6 | 100 | NT | 100 | 100 | 99.6 | 99.8 | 100 |
ME | 0 | 0 | 0 | 0 | 0 | NT | 0 | 0 | 0 | 0 | 0 | |
VME | 0 | 0 | 0 | 1.4 | 0 | NT | 0 | 0 | 0.4 | 0.2 | 0 | |
Tobramycin | C | NT | NT | NT | NT | NT | NT | 100 | NT | NT | NT | NT |
ME | NT | NT | NT | NT | NT | NT | 0 | NT | NT | NT | NT | |
VME | NT | NT | NT | NT | NT | NT | 0 | NT | NT | NT | NT | |
Vancomycin | C | NR | NR | NR | NR | NR | NR | NT | 100 | 100 | 100 | NT |
ME | NR | NR | NR | NR | NR | NR | NT | 0 | 0 | 0 | NT | |
VME | NR | NR | NR | NR | NR | NR | NT | 0 | 0 | 0 | NT |
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Ruppé, E.; Cherkaoui, A.; Lazarevic, V.; Emonet, S.; Schrenzel, J. Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics. Antibiotics 2017, 6, 30. https://doi.org/10.3390/antibiotics6040030
Ruppé E, Cherkaoui A, Lazarevic V, Emonet S, Schrenzel J. Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics. Antibiotics. 2017; 6(4):30. https://doi.org/10.3390/antibiotics6040030
Chicago/Turabian StyleRuppé, Etienne, Abdessalam Cherkaoui, Vladimir Lazarevic, Stéphane Emonet, and Jacques Schrenzel. 2017. "Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics" Antibiotics 6, no. 4: 30. https://doi.org/10.3390/antibiotics6040030
APA StyleRuppé, E., Cherkaoui, A., Lazarevic, V., Emonet, S., & Schrenzel, J. (2017). Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics. Antibiotics, 6(4), 30. https://doi.org/10.3390/antibiotics6040030