Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA
Abstract
:1. Introduction
2. Results
2.1. Description of Salmonella Isolates
2.2. Nanopore Sequencing Bioinformatic Pipeline Performance
2.3. Overall Distribution of Phenotypic Antimicrobial Resistance among Salmonella Isolates
2.4. Antimicrobial Resistance Genes Detected in Salmonella Isolates
2.5. Mapping Antimicrobial Resistance Genes to Plasmids
2.6. Antimicrobial Resistance Genes Significantly Associated with Serotypes
2.7. Antimicrobial Resistance Genes Associated with Salmonella Isolates from Beef and Dairy Operations
2.8. Association between Antimicrobial Resistance Genes and Antimicrobial Susceptibility Testing
2.9. Other Associations
3. Discussion
4. Materials and Methods
4.1. Isolate Selection and Antimicrobial Susceptibility Testing
4.2. Bacteriological Culture
4.3. DNA Extraction
4.4. Whole Genome Sequencing
4.5. Bioinformatics and Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Antimicrobial | Susceptible | Intermediate | Resistant |
---|---|---|---|
Ampicillin | 39 (40) | 1 (1) | 58 (59) |
Gentamicin | 94 (96) | 1 (1) | 3 (3) |
Tetracycline | 38 (39) | 3 (3) | 57 (58) |
Trimethoprim-sulfamethoxazole | 82 (84) | 0 (0) | 16 (16) |
Serotype | N | Tetracycline | Ampicillin | Gentamicin | Trimethoprim-Sulfamethoxazole |
---|---|---|---|---|---|
Montevideo | 15 | 7 (47) | 7 (47) | 1 (7) | 2 (13) |
Typhimurium | 12 | 8 (67) | 9 (75) | 0 | 10 (83) |
Heidelberg | 11 | 11 (100) | 11 (100) | 0 | 9 (82) |
Dublin | 7 | 7 (100) | 7 (100) | 0 | 1 (14) |
Newport | 7 | 2 (29) | 2 (29) | 0 | 0 |
Muenchen | 6 | 4 (67) | 4 (67) | 0 | 1 (17) |
Muenster | 6 | 3 (50) | 2 (33) | 0 | 1 (17) |
Cerro | 4 | 4 (100) | 4 (100) | 0 | 0 |
Anatum | 4 | 1 (25) | 1 (25) | 0 | 0 |
Litchfield | 3 | 1 (33) | 1 (33) | 0 | 0 |
Cannstatt | 3 | 1 (33) | 1(33) | 1 (33) | 0 |
Infantis | 3 | 0 | 0 | 0 | 0 |
Mbandaka | 3 | 1 (33) | 1 (33) | 0 | 1 (33) |
Bredeney | 2 | 2 (100) | 2 (100) | 0 | 0 |
Brandenburg | 2 | 0 | 0 | 0 | 0 |
Kentucky | 2 | 1 (50) | 1 (50) | 0 | 0 |
Meleagridis | 2 | 2 (100) | 1 (50) | 1 (50) | 0 |
Uganda | 1 | 1 (100) | 1 (100) | 0 | 0 |
Cubana | 1 | 1 (100) | 1 (100) | 0 | 0 |
Apapa | 1 | 0 | 1 (100) | 0 | 0 |
Altona | 1 | 0 | 1 (100) | 0 | 0 |
Algona | 1 | 0 | 0 | 0 | 0 |
Bareilly | 1 | 0 | 0 | 0 | 0 |
Resistance Pattern | Serotype | Plasmid Replicon | Antimicrobial Resistance Genes |
---|---|---|---|
1 | Heidelberg | IncA/C2 | ant(3″), aph(3″), aph(3′), aph(6), blaBIL, blaCFE, blaCMY, blaLAT, dfrA, qacE, qacEdelta1, sul1, sul2, tet(A), tet(B), tet(D), tet(O) |
2 | Heidelberg | IncA/C2 | ant(3″), aph(3″), aph(3′), aph(6), blaBIL, blaCFE, blaCMY, blaLAT, dfrA, floR, qacE, qacEdelta1, sul1, sul2, tet(A), tet(B), tet(D), tet(O) |
3 | Heidelberg | IncA/C2 | aac(6′), ant(2″), ant(3″), aph(3″), aph(3′), aph(6), blaBIL, blaCARB, blaCFE, blaCMH, blaCMY, blaCTX-M, blaIMP, blaLAT, blaMOX, blaOXA, blaVEB, blaVIM, dfrA, floR, ges, qacE, qacEdelta1, sul1, sul2, tet32, tet(A), tet(B), tet(D), tet(O), tet(W) |
4 | Heidelberg | IncA/C2 | ant(3″), aph(3″), aph(6), blaBIL, blaCFE, blaCMY, blaLAT, dfrA, floR, qacE, qacEdelta1, sul1, sul2, tet(A), tet(B), tet(D), tet(O) |
5 | Heidelberg | IncA/C2 | ant(3″), aph(3″), aph(6), blaCFE, blaCMY, blaLAT, dfrA, floR, qacE, qacEdelta1, sul1, sul2, tet(A), tet(B), tet(D), tet(O) |
6 | Typhimurium | IncFIB | ant(3″), aph(3″), aph(3′), blaTEM, cmlA, cmlB, dfrA, floR, qacF, qacL, sul1, sul2, sul2, tet(M) |
7 | Typhimurium Dublin | IncA/C2 | aph(3″), aph(6), blaBIL, blaCFE, blaCMY, blaTEM, floR, sul1, sul2, tet(A) |
8 | Typhimurium | IncFIB | ant(3″), lnuF, qnrS, tet(M), tet(O), tet(S) |
9 | Dublin | IncA/C2 | aph(3″), aph(6), blaBIL, blaCFE, blaCMY, blaLAT, blaTEM, floR, sul1, sul2, tet(A) |
10 | Dublin | IncA/C2 | aph(3″), aph(3′), aph(6), blaBIL, blaCFE, blaCMY, blaLAT, blaTEM, floR, sul1, sul2, tet(A) |
11 | Meleagridis | IncHI2 | aac(3), ant(3″), aph(3″), aph(3′), qacE, qacEdelta1, rmtE, sul1, sul2, tet(A) |
12 | Bredeney Anatum | IncA/C2 IncR | aph(3″), aph(3′), aph(6), blaBIL, blaCFE, blaCMY, blaLAT, floR, sul1, sul2, tet(A) |
13 | Uganda | IncHI2 | ant(3″), aph(3″), aph(3′), blaCTX-M, blaTEM, lnuF, mphA, qacE, qacEdelta1, qacG, sul1, sul2, sul2I, tet(A), tet(M), tet(S) |
Salmonella Serotype | ARGs | Odds Ratio * |
---|---|---|
Dublin | aph(3″) | Inf |
aph(6) | Inf | |
aph(3′) | 33.4 | |
blaCMY | Inf | |
floR | Inf | |
sul2 | Inf | |
tet(A) | Inf | |
Heidelberg | ant(3″) | Inf |
aph(3″) | Inf | |
aph(6) | Inf | |
blaCMY | Inf | |
dfrA | Inf | |
floR | 56.9 | |
fosA | Inf | |
qnrB | 49.1 | |
sul1 | Inf | |
sul2 | Inf | |
tet(A) | Inf | |
tet(B) | Inf | |
tet(D) | Inf | |
tet(O) | Inf | |
Meleagridis | aac(2′) | Inf |
Montevideo | ramA | Inf |
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Chung, M.; Dudley, E.; Kittana, H.; Thompson, A.C.; Scott, M.; Norman, K.; Valeris-Chacin, R. Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA. Antibiotics 2024, 13, 843. https://doi.org/10.3390/antibiotics13090843
Chung M, Dudley E, Kittana H, Thompson AC, Scott M, Norman K, Valeris-Chacin R. Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA. Antibiotics. 2024; 13(9):843. https://doi.org/10.3390/antibiotics13090843
Chicago/Turabian StyleChung, Max, Ethan Dudley, Hatem Kittana, Alexis C. Thompson, Matthew Scott, Keri Norman, and Robert Valeris-Chacin. 2024. "Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA" Antibiotics 13, no. 9: 843. https://doi.org/10.3390/antibiotics13090843