KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Isolation of CRE
2.2. Molecular Typing and Identification
2.3. Antibiotic Susceptibility Testing and Screening of ARGs
2.4. Mating Assays and Plasmid Analysis
2.5. Whole-Genome Sequence Analysis
3. Results
3.1. Prevalence and Diversity of CRE in Urban Ponds
3.2. Antibiotic Susceptibility, ARGs and MGEs Content
3.3. CRE Clonal Relatedness
3.4. Plasmid Analysis and Transfer of Carbapenem Resistance
3.5. WGS Analysis
3.5.1. C. freundii F6
3.5.2. R. ornithinolytica N9
3.5.3. E. kobei N10
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Resistance Profile b | |||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Isolate | Sampling Site of Origin | Sampling Date | Phylogenetic Affiliation a | Typing Profiles c | Replicons | Integrase Gene | Carbapenemase Gene | PRL | TZP | FEP | CTX | CAZ | IPM | ETP | MEM | ATM | TE | TGC | AK | CIP | C | SXT | CN |
F1 | P1 | Feb/19 | Citrobacter | A-V | - | IntI1 | blaKPC | ||||||||||||||||
F2 | P1 | Citrobacter | A | - | IntI1 | blaKPC | |||||||||||||||||
F3 | P1 | Citrobacter | A-VII | IncN | IntI1 | blaKPC | |||||||||||||||||
F4 | P1 | Citrobacter | A-VI | IncL/M | IntI1 | blaKPC | |||||||||||||||||
F5 | P1 | Citrobacter | B-IX | - | IntI1 | blaKPC | |||||||||||||||||
F6 | P1 | Citrobacter | A-VIII | IncN; IncM1; IncFIA(HI1); IncFII(K); pKPC-CAV1321 | IntI1 | blaKPC | |||||||||||||||||
S1 | P1 | Sept/19 | Raoultella | D-I | - | IntI1 | blaKPC | ||||||||||||||||
S3 | P1 | Raoultella | D | - | IntI1 | blaKPC | |||||||||||||||||
S4 | P1 | Raoultella | D | - | IntI1 | blaKPC | |||||||||||||||||
S5 | P1 | Raoultella | D | - | IntI1 | blaKPC | |||||||||||||||||
O1 | P1 | Oct/19 | Raoultella | D-I | - | IntI1 | blaKPC | ||||||||||||||||
O5 | P1 | Raoultella | D-II | - | IntI1 | blaKPC | |||||||||||||||||
N1 | P1 | Nov/19 | Raoultella | E-III | IncFIA-FII | IntI1 | blaKPC; blaGES | ||||||||||||||||
N5 | P1 | Citrobacter | C-X | IncN | IntI1 | blaKPC; blaVIM | |||||||||||||||||
N6 | P1 | Citrobacter | A-V | IncN | IntI1 | blaKPC | |||||||||||||||||
N8 | P1 | Raoultella | E-III | IncL/M | IntI1; IntI3 | blaKPC; blaGES | |||||||||||||||||
N9 | P1 | Raoultella | E-III | IncFIA-FII; CoI(MGD2); CoI(pHAD28) | IntI1; IntI3 | blaKPC; blaGES | |||||||||||||||||
N10 | P1 | Enterobacter | G | CoI440I; IncFIB-FII; IncM1; IncN; IncX5; pKPC-CAV1321 | IntI1; IntI3 | blaKPC; blaGES | |||||||||||||||||
N11 | P3 | Enterobacter | H | - | - | - | |||||||||||||||||
N12 | E1 | Raoultella | E-IV | IncFIA-FII | IntI1; IntI3 | blaKPC; blaGES | |||||||||||||||||
N13 | E1 | Raoultella | E-III | - | IntI1; IntI3 | blaKPC; blaGES | |||||||||||||||||
N14 | P1 | Klebsiella | F | - | IntI3 | blaGES | |||||||||||||||||
N15 | P3 | Enterobacter | H | - | - | - |
MIC, mg/L (Susceptibility) | |||||
---|---|---|---|---|---|
ETP | MEM | IPM | CAZ | CTX | |
E. Coli J53 | 0.012 (S) | 0.016 (S) | 0.38 (S) | 0.047 (S) | 0.016 (S) |
Citrobacter F1 | >32 (R) | 16 (R) | >32 (R) | >256 (R) | 12 (R) |
E. coli J53 (F1.1t) | 0.125 (S) | 0.5 (S) | 2 (S) | 12 (R) | 3 (R) |
Citrobacter N6 | 2 (R) | 8 (IR) | >32 (R) | 64 (R) | 6 (R) |
E. coli J53 (N6.1t) | 0.75 (R) | 0.5 (S) | 8 (R) | 32 (R) | 4 (R) |
Isolates | |||
---|---|---|---|
Drug Class/Predicted Plasmids | C. freundii F6 | R. ornithinolytica N9 | E. kobei N10 |
Beta-lactam resistance | blaKPC-3 | blaKPC-3 | blaKPC-3 |
blaOXA-1 | blaGES-5 | blaGES-5 | |
blaCMY-152 | blaORN-1 | blaACT-9 | |
blaMOX-3 | |||
blaOXA-9 | |||
blaOXA-10 | |||
blaTEM-1 | |||
Chloramphenicol resistance | catB3 | ||
Aminoglycoside resistance | aac(6′)-Ib-cr | aph(6)-Id (strB) | aac(6′)-Ib9 |
aacA4 | |||
aadA1 | |||
aph(3′’)-Ib (strA) | |||
Macrolides resistance | mphA | mphE | mphA |
Quinolones resistance | qnrS1 | ||
Sulfonamides resistance | sul1 | sul2 | sul1 |
Diaminopyrimidine resistance | dfrA14 | dfrA14 | |
Tetracycline resistance | tetA-like | ||
Fosfomycin resistance | fosA | fosA | |
Resistance to other antibiotics | msr(E) | ||
Plasmid Content | IncFIA(HI1) | Col(MGD2) | CoI440I |
IncFII(K) | Col(pHAD28) | IncFIB(pECLA) | |
IncM1 | CoI440I | IncM1 | |
IncN | IncFIA/FII (pBK30683) | IncN | |
pKPC-CAV1321 | IncX5 | ||
pKPC-CAV1321 |
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Teixeira, P.; Pinto, N.; Henriques, I.; Tacão, M. KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds. Int. J. Environ. Res. Public Health 2022, 19, 5848. https://doi.org/10.3390/ijerph19105848
Teixeira P, Pinto N, Henriques I, Tacão M. KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds. International Journal of Environmental Research and Public Health. 2022; 19(10):5848. https://doi.org/10.3390/ijerph19105848
Chicago/Turabian StyleTeixeira, Pedro, Nuno Pinto, Isabel Henriques, and Marta Tacão. 2022. "KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds" International Journal of Environmental Research and Public Health 19, no. 10: 5848. https://doi.org/10.3390/ijerph19105848