Antimicrobial Susceptibility and Detection of Virulence-Associated Genes in Escherichia coli Strains Isolated from Commercial Broilers
Abstract
:1. Introduction
2. Results
2.1. Clermont’s Phylogenetic Typing
2.2. Detection of Iron-Uptake and Virulence-Associated Genes (VGs)
2.3. Antimicrobial Resistance
3. Discussion
4. Materials and Methods
4.1. Samples, Bacterial Isolation, and Identification
4.2. DNA Extraction, Clermont’s Phylogenetic Typing, and Detection of Iron Uptake and Virulence-Associated Genes
4.3. Antimicrobial Susceptibility Testing
4.4. Detection of Antimicrobial Resistance Genes
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Pathotype | Number (%) of All Samples | A | B1 | B2 | D | F | Clade I | Unknown |
---|---|---|---|---|---|---|---|---|
ExPEC | 25 (21.7) | 9 (36.0) | 2 (8.0) | 0 (0) | 9 (36.0) | 4 (16.0) | 0 (0) | 1 (4.0) |
UPEC | 8 (7.0) | 0 (0) | 0 (0) | 6 (75.0) | 2 (25.0) | 0 (0) | 0 (0) | 0 (0) |
APEC | 7 (6.1) | 0 (0) | 2 (28.6) | 0 (0) | 0 (0) | 3 (42.9) | 1 (14.3) | 1 (14.3) |
Phylogroup | Resistant Strains | |
---|---|---|
n | % | |
A | 13 | 17.1 |
B1 | 27 | 35.5 |
B2 | 5 | 6.6 |
C | 1 | 1.3 |
D | 16 | 21.1 |
F | 7 | 9.2 |
Clade I | 2 | 2.6 |
Unknown | 5 | 6.6 |
Total | 76 | 100 |
Strain Group | Mobilome | Virulence | Phenotypic Resistance | Genotypic Resistance | |
---|---|---|---|---|---|
Commensals | B-1 B1 | Int1, Tn3 | feoB | AMP, SAM, CXM, CAZ, TOB, CIP, COT | aac(6′)-Ib-cr, sul1, dfrA |
B-2 A | Int1, Tn3 | feoB | AMP, SAM, CXM, CTX, CAZ, CIP, COT | aac(6′)-Ib-cr, sul1, dfrA | |
B-13 B1 | Tn3 | feoB, sitA, iroN, iss | AMP, CXM, CTX, CIP, TET, COT | tetA, blaCTX-M-2 | |
B-23 A | feoB, sitA, iutA, iroN, tsh, iss, cvaC | AMP, SAM, CIP | qnrS | ||
UPEC | B-22 B2 | Int1, Tn3 | sitA, chuA, iutA, irp2, fyuA, papC, cvaC | AMP, CXM, CTX, CIP, TET, COT | aadA, sul2, tetB, dfrA, blaCTX-M-1 |
B-42 B2 | feoB, sitA, chuA, iutA, iroN, ibeA, irp2, fyuA, tsh, iss, cvaC | Sensitive | |||
B-21 B2 | Tn3 | feoB, sitA, chuA, iutA, irp2, fyuA, papC, cvaC | AMP, CIP, TET | aadA, sul2, tetB, dfrA | |
B-32 D | Int1, Tn3 | feoB, sitA, chuA, iutA, irp2, fyuA, kpsMTII | AMP, SAM, CIP, COT | aadA | |
APEC | B-31 F | Tn3 | feoB, sitA, chuA, iutA, iroN, irp2, tsh, iss, cvaC, kpsMTII | AMP, SAM, CIP, TET | qnrS, tetA |
B-71 clade I | Int1, Tn3 | feoB, sitA, chuA, iutA, iroN, irp2, fyuA, papC, cvaC, kpsMTII | AMP, CIP, COT | aadA, sul2, tetB | |
ExPEC | B-93 D | Int1, Tn3 | feoB, sitA, chuA, iutA, ibeA, iss, kpsMTII | AMP, GEN, TOB, CIP, TET, COT | aadA, sul1, sul2, tetA, dfrA |
Gene | Primer Sequences (5′–3′) | Product (bp) | Annealing (°C) | References |
---|---|---|---|---|
arpA | AACGCTATTCGCCAGCTTGC TCTCCCCATACCGTACGCTA | 400 | 59 | [39] |
chuA | ATGGTACCGGACGAACCAAC TGCCGCCAGTACCAAAGACA | 288 | 59 | [39] |
yjaA | CAAACGTGAAGTGTCAGGAG AATGCGTTCCTCAACCTGTG | 211 | 59 | [39] |
TspE4.C2 | CACTATTCGTAAGGTCATCC AGTTTATCGCTGCGGGTCGC | 152 | 59 | [39] |
arpA (group C) | GATTCCATCTTGTCAAAATATGCC GAAAAGAAAAAGAATTCCCAAGAG | 301 | 57 | [40] |
trpA (group E) | AGTTTTATGCCCAGTGCGAG TCTGCGCCGGTCACGCCC | 319 | 59 | [40] |
iha | CTGGCGGAGGCTCTGAGATCA TCCTTAAGCTCCCGCGGCTGA | 827 | 60 | [41] |
iroN | AAGTCAAAGCAGGGGTTGCCCG GACGCCGACATTAAGACGCAG | 655 | 60 | [41] |
fyuA | TGATTAACCCCGCGACGGGAA CGCAGTAGGCACGATGTTGTA | 880 | 55 | [42] |
ireA | TGGTCTTCAGCTATATGG ATCTATGATTGTGTTGGT | 415 | 55 | [43] |
sitA | AGGGGGCACAACTGATTCTCG TACCGGGCCGTTTTCTGTGC | 608 | 59 | [44] |
feoB | AATTGGCGTGCATGAAGATAACTG AGCTGGCGACCTGATAGAACAATG | 470 | 59 | [45] |
irp2 | AAGGATTCGCGTGAC TCGTCGGGCAGCGTTTCTTCT | 287 | 59 | [45] |
iss | ATCACATAGGATTCTGCCG ACAAAAAGTTCTATCGCTTCC | 700 | 61 | [46] |
papC | GACGGCTGTACTGCAGGGTGTGGCG ATATCCTTTCTGCAGGGATGCAATA | 328 | 61 | [47] |
iutA | GGCTGGACATGGGAACTGG CGTCGGGAACGGGTAGAATCG | 300 | 63 | [42] |
cvaC | CACACACAAACGGGAGCTGTT CACACACAAACGGGAGCTGTT | 680 | 63 | [42] |
tsh | GGTGGTGCACTGGAGTGG AGTCCAGCGTGATAGTGG | 620 | 55 | [48] |
ibeA | TGAACGTTTCGGTTGTTTTG TGTTCAAATCCTGGCTGGAA | 814 | 55 | [49] |
kps MTII | GCGCATTTGCTGATACTGTTG CATCCAGACGATAAGCATGAGCA | 272 | 63 | [42] |
qnrA | ATTTCTCACGCCAGGATTTG GATCGGCAAAGGTTAGGTCA | 516 | 53 | [50] |
qnrB | GATCGTGAAAGCCAGAAAGG ACGATGCCTGGTAGTTGTCC | 469 | 53 | [50] |
qnrS | ACGACATTCGTCAACTGCAA TAAATTGGCACCCTGTAGGC | 417 | 53 | [50] |
aac(6)-Ib-cr | GATCTCATATCGTCGAGTGGTGG GAACCATGTACACGGCTGGAC | 435 | 58 | [50] |
mcr-1 | CGGTCAGTCCGTTTGTTC CTTGGTCGGTCTGTAGGG | 309 | 58 | [51] |
mcr-2 | TGTTGCTTGTGCCGATTGGA AGATGGTATTGTTGGTTGCTG | 567 | 58 | [52] |
blaCTX-M-1 | AAAAATCACTGCGCCAGTTC AGCTTATTCATCGCCACGTT | 415 | 52 | [53] |
blaCTX-M-2 | CGACGCTACCCCTGCTATT CCAGCGTCAGATTTTTCAGG | 552 | 52 | [53] |
tetA | GGCCTCAATTTCCTGACG AAGCAGGATGTAGCCTGTGC | 372 | 55 | [54] |
tetB | GAGACGCAATCGAATTCGG TTTAGTGGCTATTCTTCCTGCC | 228 | 55 | [54] |
sul1 | CGGCGTGGGCTACCTGAACG GCCGATCGCGTGAAGTTCCG | 433 | 69 | [55] |
sul2 | GCGCTCAAGGCAGATGGCATT GCGTTTGATACCGGCACCCGT | 293 | 69 | [55] |
aadA | TGATTTGCTGGTTACGGTGAC CGCTATGTTCTCTTGCTTTTG | 284 | 60 | [56] |
dfrA | GTGAAACTATCACTAATGG TTAACCCTTTTGCCAGATTT | 474 | 55 | [57] |
drfB | GATCGCCTGCGCAAGAAATC AAGCGCAGCCACAGGATAAAT | 141 | 60 | [57] |
Int1 | GGGTCAAGGATCTGGATTTCG ACATGCGTGTAAATCATCGTCG | 483 | 62 | [58] |
Tn3 | CACGAATGAGGGCCGACAGGA ACCCACTCGTGCACCCAACTG | 500 | 58 | [59] |
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Kocúreková, T.; Karahutová, L.; Bujňáková, D. Antimicrobial Susceptibility and Detection of Virulence-Associated Genes in Escherichia coli Strains Isolated from Commercial Broilers. Antibiotics 2021, 10, 1303. https://doi.org/10.3390/antibiotics10111303
Kocúreková T, Karahutová L, Bujňáková D. Antimicrobial Susceptibility and Detection of Virulence-Associated Genes in Escherichia coli Strains Isolated from Commercial Broilers. Antibiotics. 2021; 10(11):1303. https://doi.org/10.3390/antibiotics10111303
Chicago/Turabian StyleKocúreková, Tímea, Lívia Karahutová, and Dobroslava Bujňáková. 2021. "Antimicrobial Susceptibility and Detection of Virulence-Associated Genes in Escherichia coli Strains Isolated from Commercial Broilers" Antibiotics 10, no. 11: 1303. https://doi.org/10.3390/antibiotics10111303
APA StyleKocúreková, T., Karahutová, L., & Bujňáková, D. (2021). Antimicrobial Susceptibility and Detection of Virulence-Associated Genes in Escherichia coli Strains Isolated from Commercial Broilers. Antibiotics, 10(11), 1303. https://doi.org/10.3390/antibiotics10111303