Whole-Genome Sequencing and Molecular Analysis of Ceftazidime–Avibactam-Resistant KPC-Producing Klebsiella pneumoniae from Intestinal Colonization in Elderly Patients
Abstract
:1. Introduction
2. Results
2.1. Patients Colonized by KPC-KP Resistant to CAZ-AVI and KPC-KP Isolates
2.2. Whole-Genome Sequencing and In Silico Analysis
3. Discussion
4. Materials and Methods
4.1. Bacterial Strain Identification and Antimicrobial Susceptibility Testing (AST)
4.2. Whole-Genome Sequencing and In Silico Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Porins | MIC (mg/L) | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Patient | Isolate | ST | Carba | OmpK35 * | OmpK36 | CAZ-AVI | MEM | MVB | IMI | IMR | |||||
P1 | RM2.05.T0 | 512 | KPC-3 | AA89 stop | GD ins | 16/4 | R | >64 | R | 1/8 | S | >8 | R | 0.5/4 | S |
P2 | RM2.10.T0 | 101 | KPC-31 | AA63 stop | TD ins | >64/4 | R | 2 | S | 0.25/8 | S | ≤1 | S | 0.12/4 | S |
P3 | RM2.15.T0 | 512 | KPC-31 | AA89 stop | GD ins | 64/4 | R | 2 | S | 1/8 | S | ≤1 | S | 0.12/4 | S |
RM2.15.T4 | 512 | KPC-3 | AA89 stop | GD ins | 8/4 | S | >64 | R | 0.25/8 | S | >8 | R | 0.25/4 | S | |
P4 | RM2.21.T0 | 512 | KPC-3 | AA89 stop | GD ins | 16/4 | R | >64 | R | 8/8 | S | >8 | R | 0.25/4 | S |
RM2.21.T4 | 512 | KPC-3 | AA89 stop | GD ins | 4/4 | S | 32 | R | ≤0.06/8 | S | 4 | I | 0.12/4 | S | |
RM2.21.T8 | 512 | KPC-3 | AA89 stop | GD ins | 2/4 | S | >64 | R | 0.5/8 | S | >8 | R | 0.12/4 | S | |
P5 | RM2.31.T0 | 101 | KPC-46 | AA63 stop | TD ins | 32/4 | R | 1 | S | 0.25/8 | S | ≤1 | S | 0.12/4 | S |
RM2.31.T4 | 101 | KPC-46 | AA63 stop | TD ins | 64/4 | R | 1 | S | 0.25/8 | S | ≤1 | S | 0.12/4 | S | |
P6 | RM2.71.T0 | 101 | KPC-46 | AA63 stop | TD ins | 32/4 | R | 1 | S | 0.25/8 | S | ≤1 | S | 0.12/4 | S |
Patient | Isolate | ST | β-Lactamases | Aminoglycoside Modifying Enzyme | Fluoroquinolones | MLS | Phenicols | RIF | SUL | TET | TMT |
---|---|---|---|---|---|---|---|---|---|---|---|
P1 | RM2.05.T0 | 512 | KPC-3, TEM-1D, SHV-11 | aac(6′)-Ib, aadA2, aph(3′)-Ia | GyrA-S83I, ParC-S80I | mphA | catA1 | - | sul1 | - | dfrA12 |
P2 | RM2.10.T0 | 101 | KPC-31, SHV-1 | armA | GyrA-S83Y/D87N ParC-S80I | mphE, msrE | - | - | - | - | - |
P3 | RM2.15.T0 | 512 | KPC-31, SHV-11 | aac(6′)-Ib’,aadA2, aph(3′)-Ia | GyrA-S83I, ParC-S80I | mphA | catA1 | - | sul1 | - | dfrA12 |
RM2.15.T4 | 512 | KPC-3, SHV-11 | aac(6′)-Ib’ | GyrA-S83I, ParC-S80I | - | - | - | - | - | - | |
P4 | RM2.21.T0 | 512 | KPC-3, CMY-16, OXA-10, SHV11 | aadA1, aadA2, aac(6′)-Ib3, strA | GyrA-S83I, ParC-S80I | mphA | catA1, cmlA5, floR | arr2 | sul1, sul2 | tetA | dfrA12, dfrA14 |
RM2.21.T4 | 512 | KPC-3, CMY-16, OXA-10, SHV-11, TEM-1D | aadA1, aadA2, aac(6′)-Ib3,strA | GyrA-83I, ParC-80I | - | cmlA5, floR | arr2 | sul1, sul2 | tetA | dfrA14 | |
RM2.21.T8 | 512 | KPC-3, CMY-16, OXA-10, SHV-11, TEM-1D | aadA1, aadA2, aac(6′)-Ib3, strA | GyrA-83I, ParC-80I | - | cmlA5, floR | arr2 | sul1, sul2 | tetA | dfrA14 | |
P5 | RM2.31.T0 | 101 | KPC-46, SHV-1 | armA | GyrA-S83Y/D87N ParC-S80I | mphE, msrE | - | - | - | - | - |
RM2.31.T4 | 101 | KPC-46, SHV-1 | armA | GyrA-S83Y/D87N ParC-S80I | mphE, msrE | - | - | - | - | - | |
P6 | RM2.71.T0 | 101 | KPC-46, SHV-1 | - | GyrA-S83Y/D87NParC-S80I | mphE, msrE | - | - | - | - | - |
Patient | Isolate | ST | KLocus | Virulence Factor | Plasmid | pMLST |
---|---|---|---|---|---|---|
P1 | RM2.05.T0 | 512 | KL107 (wzi-154) | - | IncFIB, IncFII, IncX3,ColRNAI | IncF [K1:A-:B-] |
P2 | RM2.10.T0 | 101 | KL17 (wzi-137) | ybt9/ ICEKp3 | IncFIA, IncFIB, IncFII, IncR,Col440,ColRNAI | IncF [K1:A13:B-] |
P3 | RM2.15.T0 | 512 | KL107 (wzi-154) | - | IncFIB, IncFII, IncX3 | IncF [K2:A-:B-] |
RM2.15.T4 | 512 | KL107 (wzi-154) | - | IncFIB, IncFII, IncX3, ColRNAI | IncF [K2:A-:B-] | |
P4 | RM2.21.T0 | 512 | KL107 (wzi-154) | - | IncFIB, IncFII, IncC IncX3 | IncF [K2:A-:B-] IncC [C3] |
RM2.21.T4 | 512 | KL107 (wzi-154) | - | IncFIB, IncFII, IncC IncX3 | IncF [K2:A-:B-] IncC [C3] | |
RM2.21.T8 | 512 | KL107 (wzi-154) | - | IncFIB, IncFII, IncC IncX3 | IncF [K2:A-:B-] IncC [C3] | |
P5 | RM2.31.T0 | 101 | KL17 (wzi-137) | ybt9/ ICEKp3 | IncFIA, IncFIB, IncFII,IncR,Col440,ColRNAI | IncF [K2:A13:B-] |
RM2.31.T4 | 101 | KL17 (wzi-137) | ybt9/ ICEKp3 | IncFIA, IncFIB, IncFII,IncR,Col440,ColRNAI | IncF [K2:A13:B-] | |
P6 | RM2.71.T0 | 101 | KL17 (wzi-137) | ybt9/ ICEKp3 | IncFIA, IncFIB, IncFII,IncR,Col440,ColRNAI | IncF [K2:A13:B-] |
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Errico, G.; Del Grosso, M.; Pagnotta, M.; Marra, M.; Carollo, M.; Cerquetti, M.; Fogato, E.; Cesana, E.; Gentiloni Silverj, F.; Zabzuni, D.; et al. Whole-Genome Sequencing and Molecular Analysis of Ceftazidime–Avibactam-Resistant KPC-Producing Klebsiella pneumoniae from Intestinal Colonization in Elderly Patients. Antibiotics 2023, 12, 1282. https://doi.org/10.3390/antibiotics12081282
Errico G, Del Grosso M, Pagnotta M, Marra M, Carollo M, Cerquetti M, Fogato E, Cesana E, Gentiloni Silverj F, Zabzuni D, et al. Whole-Genome Sequencing and Molecular Analysis of Ceftazidime–Avibactam-Resistant KPC-Producing Klebsiella pneumoniae from Intestinal Colonization in Elderly Patients. Antibiotics. 2023; 12(8):1282. https://doi.org/10.3390/antibiotics12081282
Chicago/Turabian StyleErrico, Giulia, Maria Del Grosso, Michela Pagnotta, Manuela Marra, Maria Carollo, Marina Cerquetti, Elena Fogato, Elisabetta Cesana, Flaminia Gentiloni Silverj, Dorjan Zabzuni, and et al. 2023. "Whole-Genome Sequencing and Molecular Analysis of Ceftazidime–Avibactam-Resistant KPC-Producing Klebsiella pneumoniae from Intestinal Colonization in Elderly Patients" Antibiotics 12, no. 8: 1282. https://doi.org/10.3390/antibiotics12081282