Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic
Abstract
:1. Introduction
2. Results
2.1. LRT ESBL-EC Isolates from Both Study Periods
2.2. Antimicrobial Resistance of ESBL-EC from Both Study Periods
2.3. Comparison of Genotype Data of ESBL-EC Isolated from LRTs from Both Study Periods
3. Discussion
4. Materials and Methods
4.1. Bacterial Strains and Patients
4.2. Antimicrobial Susceptibility Testing
4.3. Molecular Characterization of ESBL-EC Isolates
4.4. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
References
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Pre-COVID-19 N = 119 (100%) n (%) | COVID-19 N = 81 (100%) n (%) | Pearson’s Chi-Squared Value (df 1) | p Value 1 | |
---|---|---|---|---|
Average age | 67.3 | 70.8 | / | / |
0–10 years | 11 (9.2%) | 2 (2.5%) | 3.639 | 0.056 |
11–20 years | 1 (0.8%) | 0 (0%) | 0.684 | 0.408 |
21–30 years | 1 (0.8%) | 1 (1.2%) | 0.076 | 0.783 |
31–40 years | 0 (0%) | 1 (1.2%) | 1.477 | 0.224 |
41–50 years | 7 (5.9%) | 5 (6.2%) | 0.007 | 0.932 |
51–60 years | 7 (5.9%) | 5 (6.2%) | 0.007 | 0.932 |
61–70 years | 20 (16.8%) | 18 (22.2%) | 0.918 | 0.338 |
71–80 years | 28 (23.5%) | 20 (24.7%) | 0.036 | 0.85 |
81–90 years | 36 (30.3%) | 27 (33.3%) | 0.212 | 0.645 |
91+ years | 8 (6.7%) | 2 (2.5%) | 1.836 | 0.175 |
Male | 70 (58.8%) | 57 (70.4%) | 2.772 | 0.096 |
Female | 49 (41.2%) | 24 (29.6%) | 2.772 | 0.096 |
Tracheal aspirate | 87 (73.1%) | 50 (61.7%) | 2.893 | 0.089 |
Sputum | 30 (25.2%) | 21 (25.9%) | 0.013 | 0.909 |
Bronchoalveolar lavage | 2 (1.7%) | 10 (12.3%) | 9.72 | 0.002 |
Pre-COVID-19 N = 119 (100%) n (%) | COVID-19 N = 81 (100%) n (%) | Pearson’s Chi-Squared Value (df 1) | p Value 1 | |
---|---|---|---|---|
Plasmid-mediated quinolone resistance genes | ||||
qnrA | 0 (0%) | 0 (0%) | / | / |
qnrB | 0 (0%) | 0 (0%) | / | / |
qnrS | 3 (2.5%) | 4 (4.9%) | 0.834 | 0.361 |
qnrC | 0 (0%) | 0 (0%) | / | / |
qnrD | 0 (0%) | 0 (0%) | / | / |
qnrVC | 0 (0%) | 0 (0%) | / | / |
qepA | 0 (0%) | 0 (0%) | / | / |
aac(6′)-I-cr | 46 (38.7%) | 20 (24.7%) | 4.25 | 0.039 |
β-lactamase group genes | ||||
blaCTX-M-1 | 101 (84.9%) | 61 (75.3%) | 2.865 | 0.091 |
blaCTX-M-2 | 0 (0%) | 2 (2.5%) | 2.968 | 0.085 |
blaCTX-M-9 | 15 (12.6%) | 15 (18.5%) | 1.322 | 0.25 |
blaCTX-M-8 | 0 (0%) | 0 (0%) | / | / |
blaCTX-M-25 | 0 (0%) | 0 (0%) | / | / |
blaTEM | 63 (52.9%) | 26 (32.1%) | 8.477 | 0.004 |
blaSHV | 1 (0.8%) | 0 (0%) | 0.684 | 0.408 |
blaOXA | 47 (39.5%) | 24 (29.6%) | 2.049 | 0.152 |
Biocide resistance genes encoded on mobile genetic elements | ||||
qacEΔ1 | 62 (52.1%) | 24 (29.6%) | 9.929 | 0.002 |
qacE | 0 (0%) | 0 (0%) | / | / |
qacF/H/I | 0 (0%) | 1 (1.2%) | 1.477 | 0.224 |
qacG | 0 (0%) | 0 (0%) | / | / |
sugE (p) | 0 (0%) | 0 (0%) | / | / |
Chromosome-encoded biocide resistance genes | ||||
emrE | 92 (77.3%) | 65 (80.2%) | 0.246 | 0.62 |
mdfA | 119 (100%) | 81 (100%) | / | / |
sugE (c) | 119 (100%) | 81 (100%) | / | / |
ydgE | 119 (100%) | 81 (100%) | / | / |
ydgF | 119 (100%) | 81 (100%) | / | / |
Integrons | ||||
int1 | 33 (27.7%) | 37 (45.7%) | 6.824 | 0.009 |
int2 | 0 (0%) | 1 (1.2%) | 1.477 | 0.224 |
int3 | 0 (0%) | 0 (0%) | / | / |
Pre-COVID-19 N = 119 (100%) n (%) | COVID-19 N = 81 (100%) n (%) | Pearson’s Chi-Squared Value (df 1) | p Value 1 | |
---|---|---|---|---|
EP1 | 54 (45.4%) | 18 (22.2%) | 11.216 | 0.001 |
EP2 | 8 (6.7%) | 0 (0%) | 5.672 | 0.017 |
EP3 | 21 (17.6%) | 23 (28.4%) | 3.244 | 0.072 |
EP4 | 3 (2.5%) | 9 (11.1%) | 6.306 | 0.012 |
EP5 | 1 (0.8%) | 1 (1.2%) | 0.076 | 0.783 |
EP6 | 0 (0%) | 2 (2.5%) | 2.968 | 0.085 |
EPx | 32 (26.9%) | 28 (34.6%) | 1.353 | 0.245 |
Pre-COVID-19 N = 119 (100%) n (%) | COVID-19 N = 81 (100%) n (%) | Pearson’s Chi-Squared Value (df 1) | p Value 1 | |
---|---|---|---|---|
Adhesins | ||||
afa/dra | 31 (26.1%) | 13 (16%) | 2.809 | 0.094 |
fimH | 115 (96.6%) | 77 (95.1%) | 0.312 | 0.576 |
iha | 86 (72.3%) | 50 (61.7%) | 2.461 | 0.117 |
papC | 15 (12.6%) | 14 (17.3%) | 0.851 | 0.356 |
papGII | 12 (10.1%) | 11 (13.6%) | 0.579 | 0.447 |
Autotransporters | ||||
fluA | 88 (73.9%) | 64 (79%) | 0.677 | 0.411 |
sat | 26 (21.8%) | 53 (65.4%) | 38.308 | <0.001 |
tsh | 0 (0%) | 4 (4.9%) | 5.996 | 0.014 |
vat | 4 (3.4%) | 5 (6.2%) | 0.886 | 0.346 |
Protectins | ||||
iss | 12 (10.1%) | 12 (14.8%) | 1.021 | 0.312 |
kpsMTII | 81 (68.1%) | 55 (67.9%) | 0.001 | 0.98 |
ompTAPEC | 14 (11.8%) | 13 (16%) | 0.758 | 0.384 |
traT | 98 (82.4%) | 69 (85.2%) | 0.281 | 0.596 |
Iron acquisition systems | ||||
fyuA | 105 (88.2%) | 68 (84%) | 0.758 | 0.384 |
iroN | 15 (12.6%) | 13 (16%) | 0.475 | 0.491 |
irp2 | 107 (89.9%) | 69 (85.2%) | 1.021 | 0.312 |
iucD | 97 (81.5%) | 70 (86.4%) | 0.842 | 0.359 |
iutA | 98 (82.4%) | 70 (86.4%) | 0.593 | 0.441 |
Toxins | ||||
ehxA | 0 (0%) | 0 (0%) | / | / |
hlyA | 14 (11.8%) | 9 (11.1%) | 0.02 | 0.887 |
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Hrovat, K.; Seme, K.; Ambrožič Avguštin, J. Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic. Antibiotics 2024, 13, 797. https://doi.org/10.3390/antibiotics13090797
Hrovat K, Seme K, Ambrožič Avguštin J. Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic. Antibiotics. 2024; 13(9):797. https://doi.org/10.3390/antibiotics13090797
Chicago/Turabian StyleHrovat, Katja, Katja Seme, and Jerneja Ambrožič Avguštin. 2024. "Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic" Antibiotics 13, no. 9: 797. https://doi.org/10.3390/antibiotics13090797