Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and High-Risk Escherichia coli CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Human Patients in Algeria
Abstract
1. Introduction
2. Results
2.1. Escherichia coli Collection
2.1.1. Antimicrobial Susceptibility Testing (AST) and Genotypic Characterization of bla Genes
2.1.2. Virulence Traits
2.1.3. Clonal Groups
Phylogroup | Clonotype (CH) a | No Isolates | UPEC Status b | ExPEC Status c | FQR |
---|---|---|---|---|---|
B2 | CH40-30 | 17 | 15 | 16 | 17 |
CH14-64 | 1 | 1 | 1 | 1 | |
CH108-Neg | 2 | 2 | 2 | 1 | |
CH1012-Neg | 1 | 0 | 0 | 1 | |
D | CH26-5 | 6 | 0 | 6 | 1 |
CH26-Neg | 3 | 0 | 3 | 0 | |
B1 | CH65-27 | 2 | 0 | 0 | 0 |
CH27-54 | 1 | 0 | 0 | 0 | |
CH65-32 | 1 | 0 | 0 | 0 | |
CH7-604 | 1 | 0 | 0 | 0 | |
A | CH11-54 | 1 | 0 | 1 | 1 |
CH11-Neg | 1 | 0 | 0 | 1 | |
CH7-94 | 1 | 0 | 0 | 0 | |
F | CH88-Neg | 2 | 0 | 0 | 2 |
Characterization of Clonal Complex (CC) 131 Isolates
In Silico Characterization of ST1193 Isolate
2.2. Klebsiella pneumoniae Collection
2.2.1. AST and Genotypic Characterization of bla Genes
2.2.2. Virulence Traits
3. Discussion
4. Materials and Methods
4.1. E. coli and K. pneumoniae Collections
4.2. Antimicrobial Susceptibility Testing (AST)
4.3. Detection and Typing of Antimicrobial Resistance Genes
4.4. Molecular Characterization of E. coli: Virulence Traits, Phylogroup, Clonotype, and Virotype Assignment
4.5. Phenotypic and Genotypic Detection of Hypervirulent K. pneumoniae
4.6. Whole Genome Sequencing (WGS) and Bioinformatics Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Isolate | UPEC Status a | ExPEC Status b | Virotype c | Phenotypic Resistance d | Virulence Genes Profile | bla Genes |
---|---|---|---|---|---|---|
Ec4 | + | + | NT | AMP, CXM, CTX, CAZ, AZT, NAL, CIP, TOB, AMI, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, papGII | CTX-M-15 |
Ec5 | + | + | NT | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, TOB, AMI, D, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, papGII | CTX-M-15 |
Ec8 | + | + | F | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB, AMI, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII | CTX-M-15 |
Ec10 | + | + | F | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII | CTX-M-15 |
Ec19 a | + | + | F | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII | CTX-M-15 |
Ec20 a | + | + | E | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII, cnfI, hlyA | CTX-M-15 |
Ec22 | + | + | F | AMP, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII | CTX-M-15 |
Ec23 | + | − | NT | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, TOB, AMI, D, NIT, TMP-SXT | fyuA, yfcV, chuA, papAH, papGII | CTX-M-15 |
Ec28 | + | + | NT | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, sat, papGII | CTX-M-15 |
Ec30 | + | + | NT | AMP, AMC, CXM, CTX, FOX, CAZ, ETP, AZT, NAL, CIP, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, sat, papGII | CTX-M-15 |
Ec31 | + | + | NT | AMP, AMC, CXM, CTX, FOX, CAZ, AZT, NAL, CIP, GEN, TOB, D, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, sat, papGII | CTX-M-15 |
Ec41 | − | + | F | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB, D, TMP-SXT | chuA, iutA, kpsMII-K5, sat, papGII | CTX-M-15 |
Ec43 | + | + | F | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB, D TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII | CTX-M-15 |
Ec45 | + | + | NT | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB, AMI, D, TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, sat, papGII | CTX-M-15 |
Ec52 | + | + | F | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB, D TMP-SXT | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII | CTX-M-15 |
Ec55 a | + | + | E | AMP, AMC, CXM, CTX, CAZ, AZT, NAL, CIP, GEN, TOB | fyuA, yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII, cnfI, hlyA | CTX-M-15 |
Ec57 | − | + | E | AMP, AMC, CXM, CTX, FOX, CAZ, AZT, NAL, CIP, GEN, TOB, D, TGC, FOS, TMP-SXT, CHL | yfcV, chuA, papAH, iutA, kpsMII-K5, sat, papGII, cnfI, hlyA | CTX-M-15 |
ID Code for Isolate/Genome a | Ec1a/LREC-468 |
---|---|
O:H antigens b | O75:H5 |
ST#1/ST#2 c | 1193/53 |
cgMLST d | 140226 |
Acquired resistance and point mutations [in brackets] e | aac(3)-IIa, aac(6′)-Ib-cr, blaCTX-M-15, blaOXA-1, catB3 [gyrA p.S83L, gyrA p.D87N, parC p.S80I, parE p.L416F] |
Plasmid content: Inc. group [pMLST] f | IncF [F-:A1:B10], IncI1-I [ST Unknown], ColBS512-like |
Virulence genes g | aslA, chuA, cia, csgA, fdeC, fimH, fyuA, gad, iha, irp2, iucC, iutA, kpsE, kpsMII_K1, neuC, nlpI, ompT, papA_F43, sat, shiA, sitA, terC, tia, usp, vat, yehA, yehB, yehC, yehD, yfcV |
Phenotypic resistance h | AMP, AMC, CXM, CAZ, CTX, ATM, NAL, CIP, GEN |
Hypermucoviscous Phenotype (HMV) a | |||||||
---|---|---|---|---|---|---|---|
Isolate | ML | MH | TSA | CA | Phenotypic Resistance b | Virulence Genes c | bla Genes |
KP6b | + | – | + | – | AMP, CXM, CTX, CAZ, AZT, CIP, FOS | terB | CTX-M-15 |
KP10c | + | + | + | + | AMP, AMC, CXM, FOX, CTX, CAZ, ETP, AZT, NAL, CIP, GEN, TOB, NIT, FOS | iucA, peg-344, rmpA | NDM, CTX-M-15 |
KP16 | + | + | + | + | AMP, AMC, CXM, FOX, CTX, CAZ, ETP, AZT, NAL, CIP, GEN, TOB, TGC, NIT, FOS, TMP-SXT, CHL | iucA, peg-344, rmpA | NDM, CTX-M-15 |
KP20a | + | + | + | – | AMP, CXM, CTX, CAZ, AZT, CIP, FOS, TMP-SXT | terB | CTX-M-15 |
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Ziadi, H.; Chougrani, F.; Cheriguene, A.; Carballeira, L.; García, V.; Mora, A. Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and High-Risk Escherichia coli CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Human Patients in Algeria. Antibiotics 2025, 14, 485. https://doi.org/10.3390/antibiotics14050485
Ziadi H, Chougrani F, Cheriguene A, Carballeira L, García V, Mora A. Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and High-Risk Escherichia coli CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Human Patients in Algeria. Antibiotics. 2025; 14(5):485. https://doi.org/10.3390/antibiotics14050485
Chicago/Turabian StyleZiadi, Hajer, Fadela Chougrani, Abderrahim Cheriguene, Leticia Carballeira, Vanesa García, and Azucena Mora. 2025. "Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and High-Risk Escherichia coli CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Human Patients in Algeria" Antibiotics 14, no. 5: 485. https://doi.org/10.3390/antibiotics14050485
APA StyleZiadi, H., Chougrani, F., Cheriguene, A., Carballeira, L., García, V., & Mora, A. (2025). Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and High-Risk Escherichia coli CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Human Patients in Algeria. Antibiotics, 14(5), 485. https://doi.org/10.3390/antibiotics14050485