Characterization of ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a Northern Portuguese Hospital: Predominance of CTX-M-15 and High Genetic Diversity
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates
2.2. Antimicrobial Susceptibility Testing
2.3. DNA Extraction and Quantification
2.4. Detection of Antibiotic Resistance Genes
2.5. Molecular Ty** of Selected E. coli and K. pneumoniae Isolates
3. Results
3.1. Antimicrobial Resistance Phenotype in E. coli and K. pneumoniae Isolates
3.2. Genetic Characteristics of ESBL- or Carbapenemase-Producing E. coli Isolates
3.3. Genetic Characteristics of ESBL-Producing K. pneumoniae Isolates
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Origin | Date (Month Year) | Resistance Phenotype a | ESBL Production b | Β-lactamases | MLST c | Resistant Genes/Integrons d | PG e |
---|---|---|---|---|---|---|---|---|
X1068 | Blood | March 2017 | AMC, CTX, CAZ, CIP, SXT | P | CTX-M-15, TEM | ST131 | int1 | B2 |
X1080 | Blood | July 2018 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15, TEM | ST131 | int1, tetA | B2 |
X1062 | Blood | December 2016 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1063 | Blood | December 2016 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1064 | Blood | December 2016 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1 | B2 |
X1065 | Blood | June 2017 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1066 | Blood | June 2017 | AMC, CTX, CAZ, TOB, CIP, GEN | P | CTX-M-15 | ST131 | ND | B2 |
X1067 | Blood | February 2017 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1069 | Blood | March 2017 | AMC, CTX, CAZ, TOB, CIP, GEN | P | CTX-M-15 | ST131 | ND | B2 |
X1070 | Blood | March 2017 | AMC, CTX, CAZ, CIP, GEN | P | CTX-M-15 | ST131 | ND | B2 |
X1071 | Blood | April 2017 | AMC, CTX, CAZ, TET, TOB, CIP, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1072 | Blood | April 2017 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1073 | Blood | April 2017 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1074 | Blood | April 2017 | AMC, CTX, CAZ, TET, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1, tetA | B2 |
X1075 | Blood | May 2017 | AMC, CTX, CAZ, CIP | P | CTX-M-15 | ST410 | ND | A |
X1076 | Blood | May 2017 | AMC, CTX, CAZ, TET, TOB, CIP | P | CTX-M-15 | ST131 | ND | B2 |
X1105 | Blood | May 2017 | AMC, CTX, CAZ, CIP | P | CTX-M-15 | ST410 | ND | A |
X1079 | Blood | July 2018 | AMC, CTX, CAZ, TOB, CIP, GEN, SXT | P | CTX-M-15 | ST131 | int1 | B2 |
X1081 | Blood | August 2018 | AMC, CTX, CAZ, TET, TOB, CIP | P | CTX-M-15 | ST131 | tetA | B2 |
X1078 | Blood | July 2018 | CTX, TET, CIP, SXT | P | CTX-M-27 | ST131 | ND | B2 |
X3158 | Urine | February 2017 | CTX, CAZ, TET, TOB, SXT, S | P | CTX-M-15 | NT | ND | B2 |
X3159 | Urine | February 2017 | CTX, CAZ, TOB, CIP, GEN, S | P | CTX-M-15 | NT | ND | B2 |
X3160 | Urine | February 2017 | CTX, CAZ, TET, TOB, CIP, GEN, S | P | CTX-M-15 | NT | ND | B2 |
X3161 | Urine | March 2017 | CTX, CAZ, TOB, CIP, GEN, S | P | CTX-M-15 | NT | ND | B2 |
X3162 | Urine | April 2017 | CTX, CAZ, TOB, CIP, GEN, S | P | CTX-M-15 | NT | ND | D |
X3163 | Urine | May 2017 | CTX, CAZ, TET, CIP, SXT, S | P | CTX-M-15 | NT | tetA, tetB | D |
X3164 | Urine | May 2017 | CTX, CAZ, CIP, SXT, S | P | CTX-M-15 | NT | ND | B2 |
X3165 | Urine | May 2017 | CTX, CAZ, CIP, S | P | CTX-M-15 | NT | ND | B2 |
X3167 | Urine | June 2018 | CTX, CAZ, TET, TOB, CIP, GEN, SXT, S | P | CTX-M-15 | NT | tetA | B2 |
X3168 | Urine | August 2018 | CTX, CAZ, TET, TOB, CIP, GEN, SXT, S | P | CTX-M-15 | NT | tetA | B2 |
X3169 | Urine | August 2018 | CTX, CAZ, TOB, CIP, GEN, SXT, S | P | CTX-M-15 | NT | tetA | B2 |
X3170 | Urine | August 2018 | CTX, CAZ, TET, CIP, S | P | CTX-M-15 | NT | tetB | B2 |
X3173 | Urine | June 2018 | AMC, FOX, CTX, CAZ, IMP, TET, CIP, SXT, S | P | CTX-M-15, KPC2/3 | NT | tetB | A |
X3157 | Urine | February 2017 | CTX, TET, SXT, S | P | CTX-M-1 | NT | tetA | C |
X3155 | Urine | December 2016 | CTX, TOB, CIP, SXT, S | P | CTX-M-variant | NT | ND | B2 |
X3166 | Urine | May 2018 | ERT, TOB, CIP, GEN, SXT, S | P | CTX-M-variant | NT | ND | B2 |
X3171 | Urine | December 2016 | CTX, TOB, CIP, SXT, S | P | CTX-M-variant | NT | ND | NC |
X3156 | Urine | June 2017 | AMC, FOX, CTX, CAZ, IMP, TET, TOB, CIP, GEN, SXT, S | P | KPC2/3 | NT | tetA | B2 |
Sample | Origin | Date (Month Year) | Antimicrobial Resistance Phenotype a | ESBL Production b | β-lactamases | MLST c | Other Genes/Int d |
---|---|---|---|---|---|---|---|
X2175 | Urine | June 2017 | AMC, CTX, CAZ, IMP, MRP, ERT, CIP, SXT, S | P | CTX-M-15, KPC-2/3, SHV-12, TEM | ST15 | ND |
X2143 | Urine | December 2016 | AMC, FOX, CTX, CAZ, IMP, MRP, ERT, TET, CIP, GEN, SXT, S | P | CTX-M-15, KPC-2/3, SHV-27, TEM | ST280 | tetA |
X2153 | Urine | June 2017 | AMC, FOX, CTX, CAZ, IMP, MRP, ERT, TET, CIP, GEN, SXT, S | P | CTX-M-15, KPC-2/3, SHV-27, TEM | NT | tetA |
X2155 | Urine | February 2017 | AMC, CTX, CAZ, IMP, MRP, ERT, TET, CIP, GEN, SXT, S | P | CTX-M-15, KPC-2/3, SHV-27, TEM | NT | tetA |
X2166 | Urine | May 2017 | AMC, CTX, CAZ, IMP, MRP, ERT, TET, CIP, GEN, SXT, S | P | CTX-M-15, KPC-2/3, SHV-27, TEM | NT | tetA |
X3098 | Urine | December 2016 | CTX, CAZ, TET, CIP, TOB, GEN, SXT, S | P | CTX-M-15, SHV-27 | NT | tetA |
X3100 | Urine | March 2017 | CTX, CAZ, IMP, TET, CIP, TOB, SXT, S | P | CTX-M-15, SHV-27 | NT | tetA |
X3104 | Urine | May 2017 | AMC, CTX, CAZ, IMP, MRP, ERT, TET, CIP, TOB, SXT, S | P | CTX-M-15, SHV-11 | NT | ND |
X2157 | Urine | April 2017 | AMC, FOX, CTX, CAZ, IMP, MRP, ERT, CHF, CIP, GEN, SXT, S | P | CTX-M-15, KPC-2/3, SHV-28, TEM | ST15 | ND |
X3095 | Urine | December 2016 | CTX, CAZ, MRP, TET, CIP, TOB, GEN, SXT, S | P | CTX-M-15, SHV-28 | NT | tetA |
X3105 | Urine | May 2017 | AMC, CTX, CAZ, ERT, TET, CIP, TOB, GEN, SXT, S | P | CTX-M-15, SHV-28 | NT | tetA |
X3106 | Urine | May 2017 | CTX, CAZ, ERT, TET, CIP, TOB, GEN, SXT, S | P | CTX-M-55, SHV-11 | NT | tetA |
X2142 | Urine | December 2016 | AMC, FOX, CTX, CAZ, IMP, MRP, ERT, CHF, CIP, GEN, SXT, S | P | SHV-12, KPC-2/3, TEM | ST147 | ND |
X3092 | Urine | December 2016 | AMC, CTX, CAZ, IMP, TET, TOB, CIP, GEN, SXT, S | P | SHV-12 | NT | ND |
X3096 | Urine | December 2016 | CTX, CAZ, IMP, TET, CIP, SXT, S | P | SHV-12 | NT | tetA |
X3097 | Urine | December 2016 | CTX, CAZ, IMP, TET, TOB, CIP, GEN, SXT, S | P | SHV-12 | NT | tetA |
X3107 | Urine | May 2017 | AMC, FOX, ERT, CTX, CAZ, TET, CIP, SXT, S | P | SHV-12 | NT | tetA |
X2232 | Urine | January 2017 | AMC, CTX, CAZ, IMP, MRP, ERT, TET, CIP, GEN, SXT, S | P | SHV-27, KPC-2/3, TEM | ST280 | tetA |
X3085 | Bronchial secretion | December 2017 | AMC, FOX, CTX, CAZ, IMP, MRP, ERT, TOB, CIP, GEN, SXT, S | P | CTX-M-15, KPC-2/3, SHV-11 | NT | ND |
X3094 | Pus | December 2017 | CTX, CAZ, TET, TOB, GEN, SXT, S | P | CTX-M-15, SHV-11 | NT | tetA |
X3102 | Biopsy | May 2017 | AMC, CTX, CAZ, TOB, GEN, SXT, S | P | CTX-M-15, SHV-11 | NT | ND |
X3087 | Bronchial secretion | December 2016 | AMC, FOX, CTX, CAZ, IMP, MRP, ERT, TET, TOB, CIP, GEN, SXT, S | P | CTX-M-15, SHV-27 | NT | tetA |
X3088 | Bronchial secretion | June 2017 | AMC, CTX, CAZ, IMP, MRP, ERT, TOB, CIP, GEN, SXT, S | P | CTX-M-15, KPC-2/3, SHV-28 | NT | ND |
X3101 | Catheter | April 2017 | AMC, CTX, CAZ, IMP, MRP, ERT, TET, TOB, CIP, SXT, S | P | CTX-M-55, SHV-11 | NT | tetA |
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Carvalho, I.; Carvalho, J.A.; Martínez-Álvarez, S.; Sadi, M.; Capita, R.; Alonso-Calleja, C.; Rabbi, F.; Dapkevicius, M.d.L.N.E.; Igrejas, G.; Torres, C.; et al. Characterization of ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a Northern Portuguese Hospital: Predominance of CTX-M-15 and High Genetic Diversity. Microorganisms 2021, 9, 1914. https://doi.org/10.3390/microorganisms9091914
Carvalho I, Carvalho JA, Martínez-Álvarez S, Sadi M, Capita R, Alonso-Calleja C, Rabbi F, Dapkevicius MdLNE, Igrejas G, Torres C, et al. Characterization of ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a Northern Portuguese Hospital: Predominance of CTX-M-15 and High Genetic Diversity. Microorganisms. 2021; 9(9):1914. https://doi.org/10.3390/microorganisms9091914
Chicago/Turabian StyleCarvalho, Isabel, José António Carvalho, Sandra Martínez-Álvarez, Madjid Sadi, Rosa Capita, Carlos Alonso-Calleja, Fazle Rabbi, Maria de Lurdes Nunes Enes Dapkevicius, Gilberto Igrejas, Carmen Torres, and et al. 2021. "Characterization of ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a Northern Portuguese Hospital: Predominance of CTX-M-15 and High Genetic Diversity" Microorganisms 9, no. 9: 1914. https://doi.org/10.3390/microorganisms9091914