Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. The sample Collection
2.2. Bacterial Isolation and Identification
2.3. Real-Time PCR
2.4. MALDI-TOF Mass Spectrometry
2.5. Antimicrobial Susceptibility Testing
2.6. Next-Generation Sequencing (NGS) and Data Analysis
2.7. Typing, AMR, and Virulence Gene Profiles
2.8. Clustering Analysis
3. Results
3.1. Bacterial Detection and Identification Results
3.2. Whole Genome Sequencing and Typing Results
3.3. Antimicrobial Susceptibility Testing
3.4. AMR and Virulence Gene Profiles Results
3.5. cgMLST Analysis
4. Discussions
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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ID | Year | Host | Matrix |
---|---|---|---|
2021.TE.2 | 2020 | Wild boar | Feces |
2021.TE.3 | 2020 | Fallow deer | Feces |
2021.TE.4 | 2020 | Fallow deer | Feces |
2021.TE.5 | 2020 | Roe deer | Feces |
2021.TE.6 | 2020 | Roe deer | Feces |
2021.TE.7 | 2020 | Red deer | Feces |
2021.TE.8 | 2020 | Red deer | Feces |
2021.TE.9 | 2020 | European badger | Small intestine |
2021.TE.10 | 2020 | European badger | Feces |
2021.TE.11 | 2020 | Magpie | Small intestine |
2021.TE.12 | 2020 | Red fox | Small intestine |
2021.TE.13 | 2020 | Wolf | Feces |
2021.TE.15 | 2020 | Wild boar | Brain |
2021.TE.17 | 2020 | Wild boar | Small intestine |
2021.TE.18 | 2021 | Wild boar | Brain |
2021.TE.19 | 2021 | Wild boar | Brain |
2021.TE.20 | 2021 | Wild boar | Brain |
ID | ST | KL | O | β-Lactams | Tet | Sul | Ami | Plasmid | Ybt | Clb | Iuc | Iro | rmpA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2021.TE.2 | 133 | KL116 | O1v1 | SHV-75 | / | / | / | IncFIB(K) | ybt 9 ICEKp3 | / | unknown | / | / |
2021.TE.3 | 301 | KL116 | O2v1 | SHV-27 | / | / | / | / | / | / | / | / | / |
2021.TE.4 | 301 | KL116 | O2v1 | SHV-27 | / | / | / | / | / | / | / | / | / |
2021.TE.5 | *5670 | KL30 | O3/O3a | SHV-11 | / | / | / | / | / | / | / | / | / |
2021.TE.6 | 2217 | KL13 | O3b | SHV-1 | / | / | / | / | / | / | / | / | / |
2021.TE.7 | *ca55 | KL30 | O1v1 | SHV-65 | / | / | / | IncFIB(K) | ybt 9 ICEKp3 | / | iuc 3 | / | / |
2021.TE.8 | 200 | *KL13 | O3b | SHV-1 | / | / | / | / | / | / | / | / | / |
2021.TE.9 | 162 | KL13 | O3b | SHV-1 | / | / | / | / | ybt 16 ICEKp12 | / | / | / | / |
2021.TE.10 | 4895 | KL35 | O3/O3a | OKP-A-2 | / | / | / | IncFIB(K) | / | / | / | / | / |
2021.TE.11 | 277 | / | O3b | SHV-27 | / | / | / | IncFIB(K), Col(pHAD28) | / | / | / | / | / |
2021.TE.12 | 219 | KL121 | O1v1 | SHV-1 | / | / | / | IncFIB(AP001918) | ybt 16 ICEKp12 | / | iuc 3 | / | / |
2021.TE.13 | 116 | KL11 | O3/O3a | SHV-1 | / | / | / | / | / | / | / | / | / |
2021.TE.15 | *fc60 | KL117 | O2v2 | SHV-11 | / | / | / | IncFIB(pKPHS1) IncFIB(K)(pCAV1099-114) | / | / | / | / | / |
2021.TE.17 | 23 | KL1 | O1v2 | SHV-11 | / | / | / | repB (pK2044) | ybt 1 ICEKp1 | clb 2 | iuc 1 | iro1 | rmpA1 rmpA2 |
2021.TE.18 | 35 | KL22 | O1v1 | SHV-33 | tetA | sul2 | strA strB | IncFIB(pKPHS1) IncFIB(K) | ybt 5 ICEKp6 | / | iuc 3 | / | / |
2021.TE.19 | 3071 | KL31 | OL104 | SHV-27 | / | / | / | IncFIB(pKPHS1) IncFIB(K) | / | / | iuc 3 | / | / |
2021.TE.20 | 3071 | KL31 | O3b | SHV-27 | / | / | / | IncFIB(pKPHS1) IncFIB(K) | / | iuc 3 | / | / |
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Chiaverini, A.; Cornacchia, A.; Centorotola, G.; Tieri, E.E.; Sulli, N.; Del Matto, I.; Iannitto, G.; Petrone, D.; Petrini, A.; Pomilio, F. Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy. Animals 2022, 12, 1347. https://doi.org/10.3390/ani12111347
Chiaverini A, Cornacchia A, Centorotola G, Tieri EE, Sulli N, Del Matto I, Iannitto G, Petrone D, Petrini A, Pomilio F. Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy. Animals. 2022; 12(11):1347. https://doi.org/10.3390/ani12111347
Chicago/Turabian StyleChiaverini, Alexandra, Alessandra Cornacchia, Gabriella Centorotola, Elga Ersilia Tieri, Nadia Sulli, Ilaria Del Matto, Giorgio Iannitto, Domenico Petrone, Antonio Petrini, and Francesco Pomilio. 2022. "Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy" Animals 12, no. 11: 1347. https://doi.org/10.3390/ani12111347