Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Study Area and Animals
2.2. Sample Collection
2.3. Bacterial Isolation
2.4. Antimicrobial Susceptibility Testing
2.5. DNA Extraction and Whole Genome Sequencing
2.6. Statistical Analysis
3. Results
3.1. Prevalence of Antimicrobial Resistance at Entry into the Feedlot
3.2. Prevalence of Antimicrobial Resistance at Slaughter
3.3. Resistance Profile Comparisons between Feedlot Entry and Slaughter
3.4. Detection of Antimicrobial Resistance Genes by Whole Genome Sequence Analysis
4. Discussion
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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Antimicrobial Agent | Tested Range | Breakpoints |
---|---|---|
Amoxicillin/Clavulanic acid | 1–32 | ≥32 |
Ampicillin | 1–32 | ≥32 |
Azithromycin | 0.12–16 | >16 |
Cefoxitin | 0.5–32 | ≥32 |
Ceftiofur | 0.12–8 | ≥8 |
Ceftriaxone | 0.25–64 | ≥4 |
Chloramphenicol | 2–32 | ≥32 |
Ciprofloxacin | 0.015–4 | ≥1 |
Gentamicin | 0.25–16 | ≥16 |
Nalidixic acid | 0.5–32 | ≥32 |
Streptomycin | 2–64 | ≥64 |
Sulfisoxazole | 16–256 | > 256 |
Tetracycline | 4–32 | ≥16 |
Trimethoprim/Sulfamethoxazole | 0.12–4 | ≥4 |
Antimicrobial Class | Antimicrobial Agent | Prevalence (95% CI) | Isolate Prevalence (%)* for Each MIC Value Tested (µg/mL) | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0.015 | 0.03 | 0.06 | 0.12 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | 128 | 256 | 512 | |||
Aminoglycosides | Gentamicin | 0.0 (0.00–2.77) | 63.7 | 35.6 | 0.7 | |||||||||||||
Streptomycin | 0.7 (0.13–4.08) | 55.6 | 43.0 | 0.7 | 0.7 | |||||||||||||
β-lactams | Ampicillin | 0.7 (0.13–4.08) | 6.7 | 46.7 | 43.7 | 0.7 | 1.5 | 0.7 | ||||||||||
Amoxicillin/Clavulanic acid | 0.7 (0.13–4.08) | 3.7 | 15.6 | 65.9 | 13.3 | 0.7 | 0.7 | |||||||||||
Cefoxitin | 0.0 (0.00–2.77) | 26.7 | 64.4 | 8.9 | ||||||||||||||
Ceftiofur | 0.0 (0.00–2.77) | 0.7 | 14.1 | 79.2 | 5.2 | 0.7 | ||||||||||||
Ceftriaxone | 0.0 (0.00–2.77) | 97 | 1.5 | 1.5 | ||||||||||||||
Folate pathway inhibitor/antagonists | Sulfisoxazole | 0.0 (0.00–2.77) | 88.1 | 11.0 | 0.7 | |||||||||||||
Trimethoprim/ Sulfamethoxazole | 0.7 (0.13–4.08) | 98.5 | 0.7 | 0.7 | ||||||||||||||
Macrolides | Azithromycin | 0.0 (0.00–2.77) | 3.0 | 15.6 | 36.3 | 44.4 | 0.7 | |||||||||||
Phenicols | Chloramphenicol | 0.0 (0.00–2.77) | 3.0 | 48.9 | 47.4 | 0.7 | ||||||||||||
Fluoroquinolones | Ciprofloxacin | 0.0 (0.00–2.77) | 97.8 | 1.5 | 0.7 | |||||||||||||
Nalidixic acid | 0.0 (0.00–2.77) | 0.7 | 13.3 | 81.5 | 4.4 | |||||||||||||
Tetracycline | Tetracycline | 0.0 (0.00–2.77) | 99.3 |
Antimicrobial Class | Antimicrobial Agent | E. coli Isolate Type | Prevalence (95% CI) | Isolate Prevalence (%) * for Each MIC Value Tested (µg/mL) | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0.015 | 0.03 | 0.06 | 0.12 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | 128 | 256 | 512 | ||||
Aminoglycosides | Gentamicin | GE | 0.0 (0.00–2.89) | 3.9 | 72.8 | 23.2 | |||||||||||||
EE | 0.0 (0.00–39.03) | 66.7 | 16.7 | 16.7 | |||||||||||||||
Streptomycin | GE | 4.7 (1.16–16.8) | 53.5 | 39.5 | 1.5 | 0.8 | 3.9 | 0.8 | |||||||||||
EE | 66.7 (53.51–75.88) | 33.3 | 33.3 | 33.3 | |||||||||||||||
β–lactams | Ampicillin | GE | 5.4 (1.34–20.02) | 15.5 | 47.3 | 28.7 | 2.3 | 0.8 | 5.4 | ||||||||||
EE | 100.0 (96.00–100.00) | 100 | |||||||||||||||||
Amoxicillin/Clavulanic acid | GE | 0.8 (0.11–5.75) | 6.2 | 35.6 | 47.3 | 10.1 | 0.8 | ||||||||||||
EE | 16.7 (8.16–31.05) | 33.3 | 50.0 | 16.7 | |||||||||||||||
Cefoxitin | GE | 0.8 (0.11–5.75) | 11.6 | 31.8 | 36.4 | 19.4 | 0.8 | ||||||||||||
EE | 16.7 (8.16–31.05) | 66.7 | 16.7 | 16.7 | |||||||||||||||
Ceftiofur | GE | 0.0 (0.00–2.89) | 12.4 | 28.7 | 52.7 | 6.2 | |||||||||||||
EE | 100.0 (96.0–100.0) | 100.0 | |||||||||||||||||
Ceftriaxone | GE | 0.0 (0.00–2.89) | 100.0 | ||||||||||||||||
EE | 100.0 (96.0–100.0) | 16.7 | 83.3 | ||||||||||||||||
Folate pathway inhibitor/antagonists | Sulfisoxazole | GE | 3.9 (1.82–8.45) | 92.2 | 3.9 | 3.9 | |||||||||||||
EE | 66.7 (53.51–75.88) | 33.3 | 66.7 | ||||||||||||||||
Trimethoprim/ Sulfamethoxazole | GE | 0.0 (0.00–2.89) | 100 | ||||||||||||||||
EE | 33.3 (23.68–45.70) | 33.3 | 33.3 | 33.3 | |||||||||||||||
Macrolides | Azithromycin | GE | 0.0 (0.00–2.89) | 10.1 | 38.7 | 51.2 | |||||||||||||
EE | 50.0 (34.83–65.64) | 33.3 | 16.7 | 50.0 | |||||||||||||||
Phenicols | Chloramphenicol | GE | 0.0 (0.00–2.89) | 0.8 | 32.6 | 65.1 | 1.5 | ||||||||||||
EE | 16.7 (8.16–31.05) | 66.7 | 16.7 | 16.7 | |||||||||||||||
Fluoroquinolones | Ciprofloxacin | GE | 0.0 (0.00–2.89) | 96.9 | 3.1 | ||||||||||||||
EE | 0.0 (0.00–39.03 | 66.7 | 16.7 | 16.7 | |||||||||||||||
Nalidixic acid | GE | 0.0 (0.00–2.89) | 11.6 | 77.5 | 10.8 | ||||||||||||||
EE | 0.0 (0.00–39.03) | 50.0 | 33.3 | 16.7 | |||||||||||||||
Tetracycline | Tetracycline | GE | 17.8 (12.66–24.43) | 81.4 | 0.8 | 2.3 | 15.5 | ||||||||||||
EE | 83.3 (67.50–93.75) | 16.7 | 83.3 |
Antimicrobial Class | Resistance Phenotype | Resistance Gene | Number of Isolates (%) |
---|---|---|---|
Aminoglycosides | STR | aph(3″)-Ib | 12 (32.4) |
Aminoglycosides | STR | aph(6)-Id | 12 (32.4) |
Aminoglycosides | STR, KAN | ant(3″)-Ia | 1 (2.7) |
Aminoglycosides | KAN | aph(3′)-Ia | 1 (2.7) |
Aminoglycosides | HYG | aph(4)-Ia | 1 (2.7) |
Aminoglycosides | GEN | aac(3)-IV | 1 (2.7) |
β-lactams | AUG, AXO, FOX, XNL | blaCMY-2 | 2 (5.4) |
β-lactams | AMP, AXO, XNL | blaCTX-M-15 | 3 (8.1) |
β-lactams | AMP, AXO, XNL | blaCTX-M-27 | 2 (5.4) |
β-lactams | AMP, AXO, XNL | blaTEM-1B | 9 (24.3) |
β-lactams | AMP | blaTEM-1C | 2 (5.4) |
Macrolides | AZI, ERY | mph(A) | 3 (8.1) |
Macrolides | AZI, ERY | mph(E) | 1 (2.7) |
Macrolides | AZI, ERY | msr(E) | 1 (2.7) |
Folate synthesis inhibitors | FIS | sul1 | 1 (2.7) |
Folate synthesis inhibitors | FIS | sul2 | 9 (24.3) |
Folate synthesis inhibitors | FIS | sul3 | 1 (2.7) |
Folate synthesis inhibitors | SXT | dfrA5 | 2 (5.4) |
Folate synthesis inhibitors | SXT | dfrA12 | 1 (2.7) |
Folate synthesis inhibitors | SXT | dfrA14 | 1 (2.7) |
Phenicols | CHL | cmlA1 | 1 (2.7) |
Fluoroquinolones | CIP | qnrS1 | 1 (2.7) |
Tetracyclines | TET | tet(A) | 12 (32.4) |
Tetracyclines | TET | tet(B) | 16 (43.2) |
Antimicrobial Classes Pattern | Total no. of Isolates (%) | Resistance Pattern (no. of Isolates) | ||
---|---|---|---|---|
Phenotypic (37) | Genotypic (37) | Phenotypic (MIC) | Genotypic (Resistance Gene) | |
All susceptible | 4 (10.8) | 5 (13.5) | 4 | 5 |
1 | 16 (43.2) | 15 (40.5) | AMP (1) | blaTEM-1B (1) |
AMP-AUG-FOX-XNL-AXO (1) | blaCMY-2 (1) | |||
FIS (1) | sul2 (1) | |||
TET (13) | tet(A)(4) | |||
tet(B) (8) | ||||
2 | 5 (13.5) | 3 (8.1) | AMP-AUG-AXO-FOX-TET-XNL (1) | blaTEM-1C, tet(A) (2) |
AMP-TET (3) | sul2, tet(B) (1) | |||
FIS-TET (1) | ||||
3 | 8 (21.6) | 10 (27.0) | AMP-STR-SXT (1) | blaCMY-2, blaTEM-1B, dfrA5, tet(A) (1) |
AMP-STR-TET (3) | blaCTX-M-15, mph(E), mph(A), msr(E), tet(A) (1) | |||
AMP-AXO-AZI-TET-XNL (1) | aph(3″)-Ib, aph(6)-Id, blaTEM-1B, tet(B) (4) | |||
FIS-STR-TET (3) | aph(3′)-Ia, aph(3″)-Ib, aph(6)-Id, blaTEM-1B, dfrA5, sul2 (1) | |||
aph(3″)-Ib, aph(6)-Id, sul2, tet(B) (3) | ||||
4 | 1 (2.7) | 1 (2.7) | AMP-AXO-FIS-STR-SXT-TET-XNL (1) | aph(3″)-Ib, aph(6)-Id, blaCTX-M-15, blaTEM-1B,dfrA14, sul2, tet(A) (1) |
5 | 3 (8.1) | 2(5.4) | AMP-AXO-AZI-FIS-STR-TET-XNL (2) | aph(3″)-Ib, aph(6)-Id, blaCTX-M-27,mph(A), sul2, tet(A) (2) |
AMP-AXO-CHL-FIS-STR-SXT-TET-XNL (1) | ||||
6 | 1 (2.7) | aac(3)-IV, ant(3″)-Ia, aph(3″)-Ib, aph(4)-Ia, aph(6)-Id, blaCTX-M-15, blaTEM-1B, cmlA1, dfrA12, qnrS1, sul1, sul3,tet(A) (1) | ||
Non-MDR | 21 (56.7) | 18 (48.6) | ||
MDR | 12 (32.4) | 14 (37.8) | ||
Resistance | 33 (89.2) | 32(86.5) |
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Messele, Y.E.; Alkhallawi, M.; Veltman, T.; Trott, D.J.; McMeniman, J.P.; Kidd, S.P.; Low, W.Y.; Petrovski, K.R. Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia. Animals 2022, 12, 2256. https://doi.org/10.3390/ani12172256
Messele YE, Alkhallawi M, Veltman T, Trott DJ, McMeniman JP, Kidd SP, Low WY, Petrovski KR. Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia. Animals. 2022; 12(17):2256. https://doi.org/10.3390/ani12172256
Chicago/Turabian StyleMessele, Yohannes E., Mauida Alkhallawi, Tania Veltman, Darren J. Trott, Joe P. McMeniman, Stephen P. Kidd, Wai Y. Low, and Kiro R. Petrovski. 2022. "Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia" Animals 12, no. 17: 2256. https://doi.org/10.3390/ani12172256
APA StyleMessele, Y. E., Alkhallawi, M., Veltman, T., Trott, D. J., McMeniman, J. P., Kidd, S. P., Low, W. Y., & Petrovski, K. R. (2022). Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia. Animals, 12(17), 2256. https://doi.org/10.3390/ani12172256