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.; Tsagalas, I.; Sofia, M.; Spyrou, V.; Billinis, C.; Dalekos, G.N.; Ehricht, R.; Petinaki, E. 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, Tsagalas I, Sofia M, Spyrou V, Billinis C, Dalekos GN, Ehricht R, Petinaki E. 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, Ilias Tsagalas, Marina Sofia, Vassiliki Spyrou, Charalambos Billinis, George N. Dalekos, Ralf Ehricht, and Efthymia Petinaki. 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