Plethora of Resistance Genes in Carbapenem-Resistant Gram-Negative Bacteria in Greece: No End to a Continuous Genetic Evolution
Abstract
:1. Introduction
2. Materials and Methods
2.1. Selection of the CR Gram-Negative Isolates
2.2. Molecular Characterization
3. Results
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Category of Genes | Genes and Alleles |
---|---|
Carbapenemases | blaBIC, blaDIM, blaGES, blaGIM, blaGOB, blaIMI-3 (nmcA), blaIMI-R, blaIMP, blaIMP-25 (blaSIM-1), blaIMP-35, blaIND, blaKHM, blaKPC, blaNDM, blaPAM-1, blaSFH-1, blaSMB-1, blaSME, blaSPM-1, blaTMB-1, blaVIM, blaVIM-2, blaVIM-7, blaOXA-23-like, blaOXA-40-like, blaOXA-48-like, blaOXA-51-like, ISAba1 to blaOXA-51, no ISAba1 to blaOXA-51, blaOXA-54, blaOXA-55, blaOXA-58, blaOXA-134/235/284, blaOXA-143/182/253/255, blaOXA-181/232, blaOXA-214, blaOXA-279, blaOXA-292 |
ESBL | blaCME, blaCTX-M-1/15, blaCTX-M-2, blaCTX-M-8, blaCTX-M-9, blaPER-1, blaPER-2, blaSHV, blaTEM, blaVEB, blaOXA-18, blaOXA-45 |
AmpC | blaMIR, blaACC, blaACT, blaCMY, blaDHA, blaFOX, blaMOX, blaMOX-CMY9 |
Other Beta-lactamases | blaOXA-1, blaOXA-2, blaOXA-9, blaOXA-10, blaOXA-60 |
Aminoglycoside Resistance | aac(3′), aac(3′)-Ia, aac(3′)-Ib, aac(3′)-Ic, aac(3′)-Ie, aac(3′)-Iva, aac(6′), aac(6′)-31, aac(6′)-Ib, aac(6′)-II, aac(6′)-Iia, aac(6′)-Iic, aac-aph, aadA1, aadA2, aadA4, aadB, ant2, aphA, armA, grm, npmA, rmtA, rmtB, rmtC, rmtD, strA, strB |
Quinolone Resistance | qepA, qnrA1, qnrB, qnrC, qnrD, qnrS |
Trimethoprim Resistance | dfrA1, dfrA12, dfrA13, dfrA14, dfrA15, dfrA17, dfrA19, dfrA5, dfrA7 |
Sulfonamide Resistance | sul1, sul2, sul3 |
Macrolide Resistance | mdh, mrx |
Markers for Mobile Genetic Elements | intI1, intI2, intI3, tnpISEcp1 |
Multidrug Efflux Pumps | oqxA, oqxB |
Toxin–Antitoxin Systems | higA, higB, splA, splT |
Strain | Species | MLST Typing | Carbapenemase Genes | ESBL Genes | AmpC Genes | Other Beta-Lactamase Genes | Genes Associated with Aminoglycoside Resistance | Genes Associated with Quinolone Resistance | Genes Associated with Trimethoprim Resistance | Genes Associated with Sulfonamide Resistance | Genes Associated with Macrolide Resistance | Genes Associated with Mobile Genetic Elements | Genes Associated with a Multidrug Efflux Pump | Genes Encoding a Toxin–Antitoxin System |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A114-1 | A. baumannii | ST409 | blaOXA-23-like, blaOXA-51-like | - | - | - | aac(3′)-Ia, aadA1, armA, strA, strB | - | - | sul1 | mph | intI1 | - | splA, splT |
A90-2 | A. baumannii | ST409 | blaOXA-23-like, blaOXA-51-like | blaTEM | - | - | aphA, armA, strA, strB | - | - | - | mph | - | - | splA, splT |
A261-2 | A. baumannii | ST409 | blaOXA-23-like, blaOXA-51-like | blaTEM | - | - | aphA, armA, strA, strB | - | - | - | mph | - | - | splA, splT |
A262-2 | A. baumannii | ST409 | blaOXA-23-like, blaOXA-51-like | blaTEM | - | - | aphA, armA, strA, strB | - | - | - | mph | - | - | splA, splT |
A265 | A. baumannii | ST409 | blaOXA-23-like, blaOXA-51-like | blaTEM | - | - | aphA, armA, strA, strB | - | - | sul2 | mph | - | - | splA, splT |
A268 | A. baumannii | ST409 | blaOXA-23-like | - | - | - | - | - | - | - | mph | - | - | splA, splT |
A1793 | K. oxytoca | - | blaVIM | - | - | - | aac(6′)-Ib, aac(6′)-IIc, aphA, strB | qnrS | dfrA19 | sul1 | - | intI1 | - | - |
A1829 | K. oxytoca | - | blaVIM | blaSHV | blaMOX-CMY-9 | - | aac(6′)-Ib, aac(6′)-IIc, aadA2, aphA, strA, strB | qnrS | dfrA19 | sul1, sul2 | - | intI1 | - | - |
A1846 | K. oxytoca | - | blaVIM | blaSHV | blaMOX-CMY-9 | - | aac(6′)-Ib, aac(6′)-IIc, aadA2, aphA, strA, strB | qnrS | dfrA19 | sul1, sul2 | - | intI1 | - | - |
A1795 | K. pneumoniae | ST258 | blaKPC | blaTEM | - | - | aac(6′)-Ib, aadA1, aadA2 | - | dfrA12 | sul2, sul3 | - | intI1 | - | - |
A1821 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15 | - | - | aac(3′)-Ia, aac(6′), aac(6′)-Ib, aadA1, aphA | - | - | sul1, sul2 | - | intI1, tnpISEcp1 | - | - |
A1869 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV | - | - | aac(3′)-Ia, aac(6′), aac(6′)-Ib, aadA1, aphA | - | - | sul1, sul2 | - | intI1, tnpISEcp1 | - | - |
A1833 | K. pneumoniae | ST258 | blaKPC, blaVIM | blaSHV, blaTEM, blaVEB | - | blaOXA-1 | aadA1, aadB, ant2, aphA, strA, strB | qnrS | dfrA1 | sul1, sul2 | mph | intI1 | - | - |
A1839 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV, blaTEM | - | - | aac(6′)-Ib, strA, strB | - | dfrA14 | sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A1841 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV | - | - | aac(3′)-Ia, aac(6′)-Ib, aadA1, aphA | - | - | sul1, sul2 | - | intI1, tnpISEcp1 | - | - |
A1845 | K. pneumoniae | ST258 | blaKPC, blaVIM | blaSHV | - | - | aadA1, aphA, strA, strB | qnrS | dfrA1 | sul1, sul2 | mph | intI1 | oqxA, oqxB | - |
A1847 | K. pneumoniae | ST258 | blaKPC, blaVIM | blaCTX-M-1/15 | - | blaOXA-1 | aac(6′)-Ib | - | dfrA14 | - | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A1850 | K. pneumoniae | ST258 | blaKPC, blaVIM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib | - | dfrA14 | - | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A1875 | K. pneumoniae | ST258 | blaKPC, blaVIM | blaSHV, blaTEM, blaVEB | - | blaOXA-1 | aadA1, aadB, ant2, aphA, strA, strB | qnrS | dfrA1 | sul1, sul2 | mph | intI1 | - | - |
A1881 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15 | - | - | aphA | - | dfrA1 | sul1 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A1871 | K. pneumoniae | ST258 | blaKPC | blaSHV | - | blaOXA-6 | aac(6′)-Ib | - | - | - | - | - | oqxA, oqxB | - |
A10-1 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV, blaTEM | - | blaOXA-1 | aac(6′)-Ib, strA, strB | - | dfrA14 | sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A41-1 | K. pneumoniae | ST258 | blaKPC | blaSHV, blaTEM, blaVEB | blaACT | blaOXA-1 | aadA1, aadB, ant2, rmtB, strA, strB | - | dfrA14 | sul2 | - | intI1 | oqxA, oqxB | - |
A50-1 | K. pneumoniae | ST258 | blaKPC | blaSHV | - | - | - | - | - | - | - | - | oqxA, oqxB | - |
A99-1 | K. pneumoniae | ST258 | blaKPC | blaSHV | - | - | - | - | - | - | - | - | oqxA, oqxB | - |
A55-1 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV, blaTEM | - | blaOXA-1, blaOXA-9 | aac(6′)-Ib, aadA2, aphA, strA, strB | - | dfrA12, dfrA14 | sul2 | mph, mrx | intI1, tnpISEcp1 | oqxA, oqxB | - |
A56-1 | K. pneumoniae | ST258 | blaKPC | blaSHV, blaTEM | - | blaOXA-9 | aac(6′)-Ib, aadA2, aphA | - | dfrA12 | sul1 | mph, mrx | intI1 | oqxA, oqxB | - |
A72-1 | K. pneumoniae | ST258 | blaKPC | blaSHV, blaTEM | - | - | aac(6′)-Ib, aadA1, aadA2 | - | dfrA12 | sul2, sul3 | - | intI1 | oqxA, oqxB | - |
A90-1 | K. pneumoniae | ST258 | blaKPC | blaSHV, blaTEM | - | - | aac(6′)-Ib, aadA1, aadA2 | - | dfrA12 | sul2, sul3 | - | intI1 | oqxA, oqxB | - |
A91-1 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV | - | - | aac(3′)-Ia, aac(6′)-Ib, aadA1, aphA | - | - | sul1, sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A105-1 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV | - | - | aac(3′)-Ia, aac(6′)-Ib, aadA1, aphA | - | - | sul1, sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A126-1 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV | - | - | aac(3′)-Ia, aac(6′)-Ib, aadA1, aphA | - | - | sul1, sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A264 | K. pneumoniae | ST258 | blaKPC | blaCTX-M-1/15, blaSHV | blaACT | blaOXA-1 | aadA1, aadB, ant2, rmtB, strA, strB | - | dfrA14 | sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A24-1 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib | qnrS | dfrA14 | sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A97-1 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib, aadA2, aphA | - | dfrA12, dfrA14 | sul1, sul2 | mph, mrx | intI1, tnpISEcp1 | oqxA, oqxB | - |
A100-1 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV, blaTEM | - | blaOXA-1 | aac(6′)-Ib, strA, strB | - | dfrA14 | sul2 | - | intI1 | oqxA, oqxB | - |
A102-1 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib, aadA2, aphA | - | dfrA12, dfrA14 | sul1 | mph, mrx | intI1, tnpISEcp1 | oqxA, oqxB | - |
A198 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib, strA, strB | - | dfrA14 | sul2 | - | intI1, tnpISEcp1 | oqxA, oqxB | - |
A261-1 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib, aadA2 | - | dfrA12, dfrA14 | sul1 | mph, mrx | intI1, tnpISEcp1 | oqxA, oqxB | - |
A261-3 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib, aadA2 | - | dfrA12, dfrA14 | sul1 | mph, mrx | intI1, tnpISEcp1 | oqxA, oqxB | - |
A262-1 | K. pneumoniae | ST11 | blaNDM | blaCTX-M-1/15, blaSHV | - | blaOXA-1 | aac(6′)-Ib, aadA2 | - | dfrA12, dfrA14 | sul1 | mph, mrx | intI1, tnpISEcp1 | oqxA, oqxB | - |
A84-1 | P. aeruginosa | ST235 | blaVIM-2 | - | - | blaOXA-1 | aac(6′)-Ib, aadA1, strA, strB | - | - | sul1 | - | intI1 | - | - |
A29-1 | P. aeruginosa | ST111 | blaVIM | - | - | blaOXA-1 | aac(6′)-Ib | - | - | sul1 | - | intI1 | - | - |
A102-2 | P. aeruginosa | ST111 | blaVIM | - | - | - | aac(6′)-Ilc | - | - | - | - | intI1 | - | - |
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Tsilipounidaki, K.; Athanasakopoulou, Z.; Müller, E.; Burgold-Voigt, S.; Florou, Z.; Braun, S.D.; Monecke, S.; Gatselis, N.K.; Zachou, K.; Stefos, A.; et al. Plethora of Resistance Genes in Carbapenem-Resistant Gram-Negative Bacteria in Greece: No End to a Continuous Genetic Evolution. Microorganisms 2022, 10, 159. https://doi.org/10.3390/microorganisms10010159
Tsilipounidaki K, Athanasakopoulou Z, Müller E, Burgold-Voigt S, Florou Z, Braun SD, Monecke S, Gatselis NK, Zachou K, Stefos A, et al. Plethora of Resistance Genes in Carbapenem-Resistant Gram-Negative Bacteria in Greece: No End to a Continuous Genetic Evolution. Microorganisms. 2022; 10(1):159. https://doi.org/10.3390/microorganisms10010159
Chicago/Turabian StyleTsilipounidaki, Katerina, Zoi Athanasakopoulou, Elke Müller, Sindy Burgold-Voigt, Zoi Florou, Sascha D. Braun, Stefan Monecke, Nikolaos K. Gatselis, Kalliopi Zachou, Aggelos Stefos, and et al. 2022. "Plethora of Resistance Genes in Carbapenem-Resistant Gram-Negative Bacteria in Greece: No End to a Continuous Genetic Evolution" Microorganisms 10, no. 1: 159. https://doi.org/10.3390/microorganisms10010159
APA StyleTsilipounidaki, K., Athanasakopoulou, Z., Müller, E., Burgold-Voigt, S., Florou, Z., Braun, S. D., Monecke, S., Gatselis, N. K., Zachou, K., Stefos, A., Tsagalas, I., Sofia, M., Spyrou, V., Billinis, C., Dalekos, G. N., Ehricht, R., & Petinaki, E. (2022). Plethora of Resistance Genes in Carbapenem-Resistant Gram-Negative Bacteria in Greece: No End to a Continuous Genetic Evolution. Microorganisms, 10(1), 159. https://doi.org/10.3390/microorganisms10010159