Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia
Abstract
:1. Introduction
2. Results
2.1. Phylogenetic Groups of E. coli Isolates
2.2. Sequence Types of E. coli Isolates
2.3. Serotypes of E. coli Isolates
2.4. Virulence-Associated Gene Profile of E. coli Isolates
2.5. Antimicrobial Resistance Genes
2.6. Co-Occurrence of Antimicrobial Resistance Genes
2.7. Plasmids and Other Mobile Genetic Elements
2.8. Determination of Conjugative Transferable Elements
3. Discussion
4. Materials and Methods
4.1. E. coli Isolates
4.2. DNA Extraction, Whole-Genome Sequencing, Raw Data Pre-Processing, De Novo Assembly, and Quality Control
4.3. Bioinformatics Analysis
4.4. Statistical 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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Characteristics | Phylogroup (N = 29) | ||||||
---|---|---|---|---|---|---|---|
A N (%) | B1 N (%) | B2 N (%) | C N (%) | D N (%) | E N (%) | G N (%) | |
Study site | |||||||
Addis Ababa (n = 11) | 7 (63.6) | 3 (27.3) | 0 | 0 | 0 | 1 (9.1) | 0 |
Hossana (n = 18) | 2 (11.1) | 10 (55.6) | 1 (5.6) | 2 (11.1) | 1 (5.6) | 1 (5.6) | 1 (5.6) |
Sex | |||||||
Female (n = 13) | 3 (23.1) | 6 (46.2) | 1 (7.7) | 1 (7.7) | 1 (7.7) | 1 (7.7) | 0 |
Male (n = 16) | 6 (37.5) | 7 (43.7) | 0 | 1 (6.3) | 0 | 1 (6.3) | 1 (6.3) |
Participants | 1 (3.7) | ||||||
Diarrheic (n = 13) | 3 (23.1) | 7 (53.8) | 0 | 1 (7.7) | 1 (7.7) | 1 (7.7) | 0 |
Non-diarrheic (n = 16) | 6 (35.7) | 6 (35.7) | 1 (6.3) | 1 (6.3) | 0 | 1 (6.3) | 1 (6.3) |
Age groups | |||||||
0–4 (n = 1) | 0 | 0 | 0 | 1 (100) | 0 | 0 | 0 |
5–9 (n = 6) | 2 (33.3) | 2 (33.3) | 0 | 0 | 1 (16.7) | 0 | 1 (16.7) |
10–14 (n = 3) | 1 (66.7) | 2 (66.7) | 0 | 0 | 0 | 0 | 0 |
15–19 (n = 2) | 1 (50) | 1 (50) | 0 | 0 | 0 | 0 | 0 |
20–45 (n = 14) | 5 (35.7) | 5 (35.7) | 1 (7.1) | 1 (7.1) | 0 | 2 (14.3) | 0 |
46–65 (n = 3) | 0 | 3 (100) | 0 | 0 | 0 | 0 | 0 |
Antimicrobial Class | Antimicrobial Resistance Genes/Mutations Detected | No (%) of ESBL-Producing Isolates Possessing the Gene/Mutation (n = 19) | No (%) of 3rd-Generation-Cephalosporin-Resistant Isolates Possessing the Gene/Mutation (n = 10) | Total No (%) of Isolates Possessing the Gene/Mutation (n = 29) |
---|---|---|---|---|
β-lactams | blaCTX-M-15 | 15 (78.9) | 7 (70) | 22 (75.9) |
blaCTX-M-3 | 4 (21.1) | 0 | 4 (13.8) | |
blaTEM-1B | 10 (52.6) | 5 (50) | 15 (51.7) | |
blaTEM-169 | 2 (10.5) | 0 | 2 (6.9) | |
blaTEM-33 | 2 (10.5) | 0 | 2 (6.9) | |
blaSHV-12 | 0 | 1 (10) | 1 (3.4) | |
blaOXA-1 | 1 (5.3) | 1 (10) | 2 (6.9) | |
Aminoglycosides | aph(6)-Id | 8 (42.1) | 3 (30) | 11 (37.9) |
aph(3″)-Ib | 8 (42.1) | 3 (30) | 11 (37.9) | |
aac(6′)-Ib-cr | 1 (5.3) | 1 (10) | 2 (6.9) | |
aac(3)-IId | 2 (10.5) | 0 | 2 (6.9) | |
aadA1 | 2 (10.5) | 0 | 2 (6.9) | |
aadA2 | 5 (26.3) | 0 | 5 (17.2) | |
aadA5 | 2 (10.5) | 2 (20) | 4 (13.8) | |
Quinolones | qnrS1 | 8 (42.1) | 5 (50) | 13 (44.8) |
qepA1 | 0 | 1 (10) | 1 (3.4) | |
qepA2 | 0 | 1 (10) | 1 (3.4) | |
qepA4 | 1 (5.3) | 1 (10) | 2 (6.9) | |
gyrA:p.S83L | 7 (36.8) | 4 (40) | 11 (37.9) | |
gyrA:p.D87N | 5 (26.3) | 3 (30) | 8 (27.6) | |
gyrA:p.S83A | 1 (5.3) | 0 | 1 (3.4) | |
gyrA:p.S83V | 1 (5.3) | 0 | 1 (3.4) | |
parC:p.S80I | 5 (26.3) | 2 (20) | 7 (24.1) | |
parC:p.E84K | 0 | 1 (10) | 1 (3.4) | |
parC:p.A56T | 1 (5.3) | 0 | 1 (3.4) | |
parE:p.S458A | 5 (26.3) | 2 (20) | 7 (24.1) | |
parE:p.L416F | 0 | 1 (10) | 1 (3.4) | |
parE:p.I529L | 0 | 1 (10) | 1 (3.4) | |
Sulfonamides | sul1 | 7 (36.8) | 3 (30) | 10 (34.4) |
sul2 | 8 (42.1) | 3 (30) | 11 (37.9) | |
Trimethoprim | dfrA1 | 2 (10.5) | 0 | 2 (6.9) |
dfrA12 | 5 (26.3) | 0 | 5 (17.2) | |
dfrA14 | 4 (21.1) | 2 (20) | 6 (20.7) | |
dfrA17 | 2 (10.5) | 2 (20) | 4 (13.8) | |
dfrB4 | 0 | 1 (10) | 1 (3.4) | |
Tetracyclines | tet(A) | 9 (47.4) | 5 (50) | 14 (48.3) |
tet(B) | 4 (21.1) | 1 (10) | 5 (17.2) | |
Macrolides | mph(A) | 5 (26.3) | 2 (20) | 7 (24.1) |
erm(B) | 1 (5.3) | 2 (20) | 3 (10.3) | |
Amphenicols | catA1 | 2 (10.5) | 1 (10) | 3 (10.3) |
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Wolde, D.; Eguale, T.; Medhin, G.; Haile, A.F.; Alemayehu, H.; Mihret, A.; Pirs, M.; Strašek Smrdel, K.; Avberšek, J.; Kušar, D.; et al. Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia. Antibiotics 2024, 13, 851. https://doi.org/10.3390/antibiotics13090851
Wolde D, Eguale T, Medhin G, Haile AF, Alemayehu H, Mihret A, Pirs M, Strašek Smrdel K, Avberšek J, Kušar D, et al. Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia. Antibiotics. 2024; 13(9):851. https://doi.org/10.3390/antibiotics13090851
Chicago/Turabian StyleWolde, Deneke, Tadesse Eguale, Girmay Medhin, Aklilu Feleke Haile, Haile Alemayehu, Adane Mihret, Mateja Pirs, Katja Strašek Smrdel, Jana Avberšek, Darja Kušar, and et al. 2024. "Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia" Antibiotics 13, no. 9: 851. https://doi.org/10.3390/antibiotics13090851