Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria
Abstract
:1. Introduction
2. Results
2.1. Demographic Characteristics
2.2. Phylogenetic Grouping
2.3. Antimicrobial Susceptibility
2.4. Extended β-Lactamase (ESBL) Production and Haemolysin Activity
2.5. Correlations between Biofilm Activity, Phylogroup, and Antibiotic Resistance
3. Discussion
4. Materials and Methods
4.1. Origin of Isolates and Bacterial Strains
4.2. Antimicrobial Susceptibility Testing
4.3. Detection of Extended Spectrum β-Lactamases Production
4.4. DNA Extraction and Phylogenetic Grouping by Quadruplex PCR
4.5. Biofilm Production
4.6. Hemolysin Production
4.7. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gender | Inpatient | Outpatient | Total | |
---|---|---|---|---|
Adult | M | 3 (3.4%) | 11 (12.7%) | 14 (16.2%) |
F | 3 (3.4%) | 38 (44.1%) | 41 (47.6%) | |
Adult Total | 6 (6.9%) | 49 (57.9%) | 55 (63.9%) | |
Children | M | 4 (4.6%) | 13 (15.1%) | 17 (19.7%) |
F | 1 (1.1%) | 5 (5.8%) | 6 (6.9%) | |
Children Total | 5 (6%) | 18 (20%) | 23 (26.7%) | |
Elderly | M | 0 | 4 (4.6%) | 4 (4.6%) |
F | 0 | 4 (4.6%) | 4 (4.6%) | |
Elderly Total | 8 (9.3%) | 8 (9.3%) | ||
Total | 11 (12.7%) | 75 (87.2%) | 86 (100%) |
R (n = 6, 7%) | MDR (n = 60, 70%) | XDR (n = 20, 23%) | Total (n = 86, 100%) | |
---|---|---|---|---|
Gender | ||||
M | 3 (3%) | 26 (30%) | 6 (7%) | 35 (41%) |
F | 3 (3%) | 34 (40%) | 14 (16%) | 51 (59%) |
Age | ||||
Adult | 3 (3%) | 37 (43%) | 16 (19%) | 56 (65%) |
Children | 2 (2%) | 18 (21%) | 2 (2%) | 22 (26%) |
Elderly | 1 (1%) | 5 (6%) | 2 (2%) | 8 (9%) |
Clinical status | ||||
Inpatient | 0 | 10 (11%) | 1 (1%) | 11 (13%) |
Outpatient | 6 (7%) | 50 (58%) | 19 (21%) | 75 (87%) |
Phylogroups | ||||
A | 1 (1%) | 4 (5%) | 2 (2%) | 7 (8%) |
B1 | 0 | 4 (5%) | 0 | 4 (5%) |
B2 | 4 (5%) | 27 (31%) | 11 (13%) | 42 (49%) |
Clade I | 0 | 0 | 1 | 1 (1%) |
Clade I or II | 0 | 1 (1%) | 0 | 1 (1%) |
D | 0 | 1 (1%) | 0 | 1 (1%) |
E | 0 | 14 (16%) | 5 (6%) | 19 (22%) |
Unknown | 1 (1%) | 9 (10%) | 1 (1%) | 11 (13%) |
ESBL production | ||||
NO | 5 (6%) | 33 (38%) | 6 (7%) | 44 (51%) |
YES | 1 (1%) | 27 (31%) | 14 (16%) | 42 (49%) |
Hemolysin activity | ||||
NO | 2 (2%) | 32 (37%) | 8 (9%) | 42 (49%) |
α-hemolysin | 1 (1%) | 9 (10%) | 9 (10%) | 19 (22%) |
β-hemolysin | 3 (3%) | 19 (22%) | 3 (3%) | 25 (29%) |
Biofilm Production | ||||||
---|---|---|---|---|---|---|
No (n = 16, 19%) | Weak (n = 61, 71%) | Moderate (n = 8, 9%) | Strong (n = 1, 1%) | |||
TOT | p Value | |||||
Phylogroup | ||||||
A | 2.3% | 4.6% | 1.1% | 0.0% | 8.1% | |
B1 | 0.0% | 4.6% | 0.0% | 0.0% | 4.6% | |
B2 | 11,6% | 31.3% | 5.8% | 0.0% | 48.8% | |
Clade I | 0.0% | 1.1% | 0.0% | 0.0% | 1.1% | |
Clade I or Clade II | 0.0% | 1.1% | 0.0% | 0.0% | 1.1% | |
D | 0.0% | 1.1% | 0.0% | 0.0% | 1.1% | |
E | 3.4% | 16.2% | 1.1% | 1.1% | 22.1% | |
Unknown | 1.1% | 10.4% | 1.1% | 0.0% | 12.7% | |
ESBL production | ||||||
ESBL- negative | 13.9% | 29.1% | 6.9% | 1.1% | 51% | p = 0.02 |
ESBL- producers | 4.7% | 41.9% | 2.4% | 0% | 49% | |
Hemolytic activity | ||||||
No hemolytic activity | 8.2% | 35% | 5.8% | 0% | 49% | |
α-hemolysin | 3.5% | 17.5% | 1% | 0% | 22% | |
β-hemolysin | 7% | 18.6% | 2.4% | 1% | 29% | |
Phenotypic resistance | ||||||
R | 3.5% | 3.5% | 0% | 0% | 7% | |
MDR | 10.5% | 50% | 8.1% | 1.2% | 70% | |
XDR | 4.7% | 17.4% | 1.2% | 0% | 23% |
Antibiotics | Biofilm Production | ||||
---|---|---|---|---|---|
Negative | Weak | Moderate | Strong | ||
Penicillins | AMX | 69% | 92% | 75% | 100% |
AMC | 50% | 61% | 50% | 100% | |
TC | 69% | 87% | 75% | 100% | |
TCC | 69% | 79% | 63% | 100% | |
PRL | 50% | 80% | 63% | 100% | |
TPZ | 25% | 16% | 25% | 0% | |
Cephalosporins | CN | 44% | 41% | 0% | 100% |
CX | 31% | 34% | 13% | 0% | |
CFM | 50% | 39% | 0% | 0% | |
CAZ | 31% | 33% | 0% | 0% | |
CTX | 13% | 25% | 0% | 0% | |
FEP | 44% | 39% | 13% | 0% | |
Carbapenem | IMP | 100% | 100% | 100% | 100% |
Aminoglycosides | GEN | 19% | 20% | 13% | 0% |
AK | 13% | 20% | 0% | 0% | |
TOB | 19% | 25% | 25% | 0% | |
Quinolones | NA | 50% | 31% | 25% | 100% |
CIP | 44% | 34% | 13% | 100% | |
OF | 44% | 31% | 25% | 100% | |
Phenicolate | C | 13% | 13% | 13% | 100% |
Monobactams | ATM | 25% | 34% | 25% | 0% |
Polymyxins | CS | 31% | 41% | 25% | 100% |
Other | NIT | 63% | 89% | 100% | 100% |
SXT | 38% | 54% | 50% | 100% | |
FF | 25% | 31% | 13% | 0% |
Antibacterial Agents | MIC Dilution Range (mg/L) | Antibacterial Agents | MIC Dilution Range (mg/L) |
---|---|---|---|
Amoxicillin | 2–32 | Gentamycin | 1–16 |
Amoxicillin + Clavulanic Acid | 16–256 | Tobramycin | 0.25–4 |
Piperacillin | 4–64 | Nalidixic Acid | 8–128 |
Piperacillin + Tazobactam | 4–64 | Ciprofloxacin | 0.125–2 |
Cephalexin | 8–128 | Ofloxacin | 0.125–2 |
Cefixime | 1–16 | Chloramphenicol | 2–32 |
Ceftazidime | 0.25–4 | Aztreonam | 0.125–2 |
Cefotaxime | 0.25–4 | Trimethoprim-Sulfamethoxazole | 2–32 |
Target Gene | Primer ID | Amplicon Size (bp) | T °C | Reference |
---|---|---|---|---|
16S rDNA | F1 R12 | 1500 | 56 | [68] |
chuA | chuA.1b chuA.2 | 288 | 59 | [69] |
yjaA | yjaA.1b yjaA.2b | 211 | 59 | [70] |
tspE4.C2 | TspE4C2. 1b TspE4C2.2b | 152 | 59 | [70] |
arpA | AceK.f ArpA1.r | 400 | 59 | [69,71] |
arpA | ArpAgpE.f ArpAgpE.r | 301 | 57 | [72] |
trpA | trpAgpC.1 trpAgpC.2 | 219 | 57 | [72] |
trpA | trpBA.f trpBA.r | 489 | 57 | [73] |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Kara, A.; Massaro, C.; Giammanco, G.M.; Alduina, R.; Boussoualim, N. Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria. Antibiotics 2024, 13, 773. https://doi.org/10.3390/antibiotics13080773
Kara A, Massaro C, Giammanco GM, Alduina R, Boussoualim N. Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria. Antibiotics. 2024; 13(8):773. https://doi.org/10.3390/antibiotics13080773
Chicago/Turabian StyleKara, Anfal, Chiara Massaro, Giovanni M. Giammanco, Rosa Alduina, and Naouel Boussoualim. 2024. "Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria" Antibiotics 13, no. 8: 773. https://doi.org/10.3390/antibiotics13080773