Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Escherichia coli Strain Phylogroup A: ST167 from a Poultry Farm in Egypt
Abstract
1. Introduction
2. Materials and Methods
2.1. Isolation and Identification of E. coli M2-13-1
2.2. Minimum Inhibitory Concentration (MIC) of Various Antimicrobial Agents Against M2-13-1
2.3. Conjugation and Transformation Experiments
2.4. Complete Genome Sequencing (WGS) and Analysis
2.5. Nucleotide Sequence Accession Numbers
3. Results and Discussion
3.1. Minimum Inhibitory Concentration (MIC) of Various Antimicrobials Against M2-13-1
3.2. Genomic Characterization of E. coli M2-13-1
3.3. Plasmidome and Resistome of E. coli M2-13-1
3.4. Identification of a blaNDM-19/IncX3 Plasmid in an Egyptian E. coli Poultry Strain
3.5. Detection of Other Multidrug-Resistant (MDR) Plasmids from E. coli M2-13-1
3.6. Analysis of the Virulome and Heavy Metal Resistance Genes
3.7. Clonal Relationship of ST167 E. coli Isolate
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Antibiotic | MIC (mg/L) a for Strain: | |||
---|---|---|---|---|
M2-13-1 (Wild type) b | M2-13-1 TS1 (E. coli DH5α + pAMS-X3-NDM-19) | M2-13-1 TC (E. coli J53 + pAMS-IncF-qnrs11) | E. coli ATCC 25922 | |
Aztreonam | <2 | <2 | <2 | <2 |
Ceftriaxone | >256 | 64 | <2 | <2 |
Meropenem | 64 | 4 | <0.5 | <2 |
Doripenem | 16 | 4 | ND | <2 |
Ertapenem | 256 | 8 | <0.5 | <2 |
Tetracycline | 64 | <2 | 64 | <2 |
Ciprofloxacin | 128 | <2 | 0.5 | <2 |
Kanamycin | >256 | <2 | >256 | <2 |
Gentamicin | 32 | <2 | ND | <2 |
Chloramphenicol | 256 | <2 | 4 | 4 |
Fosfomycin | 64 | <4 | 4 | 64 |
Colistin | <0.5 | <0.5 | <0.5 | <0.5 |
Tigecycline | 1 | 1 | <0.5 | 1 |
Sample | Size (bp) | GC% | No. of CDSs | MLST or pMLST | Incompatibility Group | Antimicrobial Resistance Genes | QRDR Point Mutations | Virulence Genes |
---|---|---|---|---|---|---|---|---|
Chromosome | 4,738,278 | 50.8 | 4557 | ST167 | NA | ND | parC: S80I, parE: S458A, gyrA: S83L, and D87N | gad, terC, hra, capU, iss, csgA, hha, hlyE, hra, nlpI, yehB, yehC, yehD |
pAMS-F-qnrs11 | 113,285 | 51.5 | 130 | F34: A-: B53 | IncFII: IncFIB | aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, qnrS11, dfrA14, sul2, tet(A), blaTEM-1B | NA | anr, traJ, traT |
pAMS-IncI1-floR | 112,645 | 51.1 | 119 | ST3 | IncI1-Iγ | aac(3)-IV, aph(4)-Ia, sul2, floR | NA | cib |
pAMS-IncY | 106,741 | 47.6 | 118 | ND | IncY | ND | NA | ND |
pAMS-X3-NDM-19 | 49,816 | 47.3 | 64 | ND | IncX3 | blaNDM-19 | NA | ND |
Chromosome | pAMS-IncI1-floR | |
---|---|---|
Adherence | E. coli common pilus (ecpABCDE) E. coli laminin-binding fimbriae (elfACD) eaeH Hemorrhagic E. coli pilus (hcpABC) Type I fimbriae (fimDF) | Type IV pili (pilQRSVW) |
Autotransporter | EhaB autotransporter protein (ehaB) | NA |
Invasion | Invasion of brain endothelial cells (ibeBC) Epithelial cell adherence (tia) | NA |
Non-LEE encoded TTSS effectors | espL1, espL4, espR1, espX1, espX4, espX5, espY1 | NA |
Secretion systems | ACE T6SS (aec15, aec16, aec17, aec18, aec19, aec22, aec24, aec25, aec26, aec27/clpV, aec28, aec29, aec30, aec31, aec32) | NA |
Toxins | Hemolysin/cytolysin A (hlyE/clyA) | NA |
Antiphagocytosis | capsule | NA |
Fimbrial adherence determinants | stjC | NA |
Immune evasion | Exopolysaccharide (galE) | NA |
Serum resistance | LPS rfb locus (rmlD) | NA |
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Soliman, A.M.; Ramadan, H.; Shimamoto, T.; Komatsu, T.; Maruyama, F.; Shimamoto, T. Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Escherichia coli Strain Phylogroup A: ST167 from a Poultry Farm in Egypt. Microorganisms 2025, 13, 1769. https://doi.org/10.3390/microorganisms13081769
Soliman AM, Ramadan H, Shimamoto T, Komatsu T, Maruyama F, Shimamoto T. Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Escherichia coli Strain Phylogroup A: ST167 from a Poultry Farm in Egypt. Microorganisms. 2025; 13(8):1769. https://doi.org/10.3390/microorganisms13081769
Chicago/Turabian StyleSoliman, Ahmed M., Hazem Ramadan, Toshi Shimamoto, Tetsuya Komatsu, Fumito Maruyama, and Tadashi Shimamoto. 2025. "Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Escherichia coli Strain Phylogroup A: ST167 from a Poultry Farm in Egypt" Microorganisms 13, no. 8: 1769. https://doi.org/10.3390/microorganisms13081769
APA StyleSoliman, A. M., Ramadan, H., Shimamoto, T., Komatsu, T., Maruyama, F., & Shimamoto, T. (2025). Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Escherichia coli Strain Phylogroup A: ST167 from a Poultry Farm in Egypt. Microorganisms, 13(8), 1769. https://doi.org/10.3390/microorganisms13081769