Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats Using a Cohort Study
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Site Description and Livestock Management
2.2. Study Groups and Sampling Protocol
2.3. Fecal Sample Collection
2.4. Antimicrobial Susceptibility Screening
2.5. Characterization of Antibiotic Resistance Genes
2.6. Detection of E. coli Virulence Genes and Phylogenetic Grouping
2.7. Statistical Analysis
3. Results
3.1. Antimicrobial Resistance Proportions and Resistance Phenotypes
3.2. Proportions of Resistant E. coli Isolates and Phenotypes Among Age Groups and at Different Farm Location
3.3. Antibiotic Resistance Mechanisms
3.4. Virulence Genes and Phylogenetic Grouping of Resistant Isolates
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
Primer Name | Sequence (5’ 3’) | Target Gene(s) or Region | Amplicon Size | Ref |
---|---|---|---|---|
TEM-F | TTCTTGAAGACGAAAGGGC | blaTEM | 1150 | [48] |
TEM-R | ACGCTCAGTGGAACGAAAAC | |||
SHV-SE | ACTCAAGGATGTATTGTG | blaSHV | 747 | [57] |
SHV-AS | TTAGGGTTGCCAGTGCTCG | |||
TEM-C | ATCAGCAATAAACCAGC | blaTEM | 516 | [58] |
TEM-H | CCCCGAAGAACGTTTTC | |||
HE605 | TTTCGTGTCGCCCTTATTCC | blaTEM | 690 | [59] |
HE606 | CCGGCTCCAGATTTATCAGC | |||
TEM-164.SE | TCGCCGCATACACTATTCTCAGAATGA | blaTEM | 447 | [57] |
TEM-165.AS | ACGCTCACCGGCTCCAGATTTAT | |||
Tet A-F | GTAATTCTGAGCACTGTCGC | tetA | 937 | [48] |
Tet A-R | CTGTCCTGGACAACATTGCTT | |||
Tet B-F | CTCAGTATTCCAAGCCTTTG | tetB | 416 | [48] |
Tet B-R | CTAAGCACTTGTCTCCTGTT | |||
Tet C-F | TCTAACAATGCGCTCATCGT | tetC | 570 | [48] |
Tet C-R | GGTTGAAGGCTCTCAAGGGC | |||
Tet D-F | ATTACACTGCTGGACGCGAT | tetD | 1104 | [48] |
Tet D-R | CTGATCAGCAGACAGATTGC | |||
Tet E-F | GTGATGATGGCACTGGTCAT | tetE | 1,179 | [48] |
Tet E-R | CTCTGCTGTACATCGCTCTT | |||
Str A-R | ATGGTGGACCCTAAAACTCT | streptA/B | 893 | [13] |
Str B-F | CGTCTAGGATCGAGACAAAG | |||
strA-F | CTTGGTGATAAGGCAATTC | strept A | 548 | [40] |
strA-R | CCAATCGCAGATAGAAGGC | |||
strA-F | GTCAAGGGATTGAAACC | streptA/B | 509 | [40] |
strB-R | GGATCGTAGAACATATTGGC | |||
AadA F | GTGGATGGCGGCCTGAAGCC | aadA | 525 | [40] |
AadA R | AATGCCCAGTCGGCAGCG | |||
Sul1-F | TGGTGACGGTGTTCGGCATTC | sul1 | 789 | [48] |
Sul1-R | GCGAGGGTTTCCGAGAAGGCC | |||
Sul2-F | CGGCATCAACATAACC | sul2 | 722 | [48] |
Sul2-R | GTGTGCGGATGAAGTCAG | |||
Sul3-F | GAGCAAGATTTTTGGAATCG | sul3 | 792 | [48] |
Sul3-R. | CATCTGCAGCTAACCTAGGGCTTTGGA | |||
GyrA-F | TACACCGGTCAACATTGAGG | gyr | 648 | [48] |
Gyra-R. | TTAATGATTGCCGCCGTCGG | |||
CmlA.F | TGTCATTTACGGCATACTCG | cml | 455 | [60] |
CmlA.R | ATCAGGCATCCCATTCCCAT | |||
aac(3)IV F | TGCTGGTCCACAGCTCCTTC | aac(3)IV | 653 | [61] |
aac(3)IVR | CGGATGCAGGAAGATCAA | |||
Stx1-a | TCTCAGTGGGCGTTCTTATG | stx1 | 338 | [62] |
Stx1-b | TACCCCCTCAACTGCTAATA | |||
Stx2-a | GCGGTTTTATTTGCATTAGC | stx2 | 115 | [62] |
Stx2-b | TCCCGTCAACCTTCACTGTA | |||
EAE-a | ATGCTTAGTGCTGGTTTAGG | eae | 248 | [62] |
EAE-b | GCCTTCATCATTTCGCTTTC | |||
HlyA-a | AGCTGCAAGTGCGGGTCTG | hly | 569 | [62] |
HlyA-b | TACGGGTTATGCCTGCAAGTTCAC | |||
ChuA.1 | GACGAACCA ACGGTCAGGAT | chuA | 279 | [33] |
ChuA.2 | TGCCGCCAGTACC AAAGACA | |||
YjaA.1 | TGAAGTGTCAGGAGACGCTG | yjaA | 211 | [33] |
YjaA.2 | ATGGAGAATGCGTTCCTCAAC | |||
TspE4C2.1 | GAGTAATGTCGGGGCATTCA | tspE4.C2 | 152 | [33] |
TspE4C2.2 | CGCGCCAACAAAGTATTACG | |||
EC16S-a | CCCCCTGGACGAAGACTGAC | E. coli 16s | 401 | [62] |
EC16S-b | ACCGCTGGCAACAAAGGATA |
Appendix B
Comparison Groups | Chi Square Value | P Value |
---|---|---|
Kids vs does 3 weeks | 5.282 | P = 0.0215 |
Kids vs does 7 weeks | 2.03 | P = 0.1543 |
Kids vs does 11 weeks | 3.287 | P = 0.0698 |
Kids vs does 13 weeks | 5.151 | P = 0.0232 |
Kids 7 weeks vs kids six months | 2.611 | P = 0.1061 |
Kids 7 weeks vs kids one year | 9.734 | P = 0.0018 |
Goats on pasture vs facility | 8.968 | P = 0.0027 |
Tetracycline resistance on facility vs pasture | 57.654 | P < 0.0001 |
Ampicillin resistance on pasture vs facility | 14.742 | P = 0.0001 |
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Resistance Phenotype | Number of Isolates (n = 136) |
---|---|
Tetracycline(Tet) | 50 |
Streptomycin(Strept) | 25 |
Ampicillin(Amp) | 17 |
Nalidixic acid(Nal) | 6 |
Chloramphenicol (Chl) | 2 |
Amikacin(Ak) | 2 |
Amoxycillin/clavulanate(Amc) | 1 |
Tobramycin(Tob) | 1 |
Gentamicin(GN) | 1 |
Sulfamethoxazole-trimethoprim(Sxt) | 0 |
Meropenem | 0 |
Ciprofloxacin | 0 |
Tet/Strept | 12 |
Amp/Amc | 3 |
Tet/Amp | 1 |
Tet/Nal | 2 |
Tet/Chl | 1 |
Amp/Chl | 2 |
Tet/Amc | 1 |
Tob/Strept | 1 |
Chl/Tob | 1 |
Amp/Nal | 1 |
Ak/Tet | 1 |
Amp/strept | 1 |
Amc/Ak/Nal | 1 |
Nal/Strept/Tet | 1 |
Amp/Nal/Sxt | 1 |
Amc/Chl/Tet/Strept | 1 |
No resistance | 272 |
Antimicrobial Agent | n = 136 |
---|---|
Ampicillin | 26 |
Streptomycin | 41 |
Gentamicin | 1 |
Tetracycline | 70 |
Amikacin | 4 |
Ciprofloxacin | 0 |
Amoxycillin/Clavulanate | 7 |
Meropenem | 0 |
Choramphenicol | 7 |
Tobramycin | 3 |
Sulfamethoxazole-trimethoprim | 1 |
Nalidixic acid | 12 |
Sampling Group | Isolate Phenotype | Number of Antibiotics Resistant to: | ||||
---|---|---|---|---|---|---|
Sensitive | Resistant | Total | 1 | 2 | >2 | |
Kids 3wks (P) | 14 | 11 | 25 | 10 | 1 | 0 |
Kids 7wks (P) | 13 | 11 | 24 | 11 | 0 | 0 |
Kids 11wks (F) | 14 | 13 | 27 | 11 | 2 | 0 |
kids 13wks (F) | 33 | 25 | 58 | 24 | 1 | 0 |
Kids 14wks (F) | 11 | 11 | 22 | 9 | 2 | 0 |
Kids 6months (F/P) | 32 | 22 | 54 | 14 | 7 | 1 |
Kids 1 year (P) | 38 | 5 | 43 | 3 | 1 | 1 |
Nursing does (3wks) (P) | 16 | 2 | 18 | 2 | 0 | 0 |
Nursing does (7wks) (P) | 15 | 5 | 20 | 5 | 0 | 0 |
Nursing does (11wks) (F) | 10 | 2 | 12 | 1 | 1 | 0 |
Nursing does (13wks) (F) | 11 | 1 | 12 | 1 | 0 | 0 |
Adult does ** (P) | 32 | 12 | 44 | 8 | 4 | 0 |
Other goats * (F) | 33 | 16 | 49 | 6 | 8 | 2 |
Total | 272 | 136 | 408 | 105 | 27 | 4 |
Antimicrobial Agent | Animal Location | |||
---|---|---|---|---|
Near facility (n = 212) | % | Pasture (n = 196) | % | |
Ampicillin | 4* | 2% | 22** | 11% |
Streptomycin | 18 | 9% | 23 | 12% |
Gentamicin | 1 | 0.5% | 0 | 0% |
Tetracycline | 65* | 31% | 5** | 2.5% |
Amikacin | 4 | 2% | 0 | 0% |
Ciprofloxacin | 0 | 0% | 0 | 0% |
Amoxycillin/Clavulate | 4 | 2% | 3 | 1.5% |
Meropenem | 0 | 0% | 0 | 0% |
Choramphenical | 3 | 1.4% | 4 | 2% |
Tobramycin | 1 | 0.5% | 2 | 1% |
Sulfamethoxazole-trimethoprim | 0 | 0% | 1 | 0.5% |
Nalidixic acid | 8 | 4% | 4 | 2% |
Total resistant isolates | 85** | 40% | 51* | 26% |
Phenotype of Resistance | Number of Isolates with This Phenotype | Gene Detected | Number of Isolates |
---|---|---|---|
Ampicillin | 26 | blaTEM | 12 |
Amoxycillin/clavulanate | 7 | blaSHV | 1 |
Tetracycline | 70 | tet(B) | 69 |
Streptomycin | 41 | aadA strB/strA | 18 10 |
Sulfamethoxazole-trimethoprim | 1 | sul2 | 1 |
Chloramphenicol | 7 | - | - |
Tobramycin | 3 | aac (3)/aac (3) | 1 |
Amikacin | 4 | - | - |
Gentamicin | 1 | - | - |
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Ndegwa, E.; Almehmadi, H.; Chyer, K.; Kaseloo, P.; Ako, A.A. Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats Using a Cohort Study. Antibiotics 2019, 8, 136. https://doi.org/10.3390/antibiotics8030136
Ndegwa E, Almehmadi H, Chyer K, Kaseloo P, Ako AA. Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats Using a Cohort Study. Antibiotics. 2019; 8(3):136. https://doi.org/10.3390/antibiotics8030136
Chicago/Turabian StyleNdegwa, Eunice, Hanin Almehmadi, Kim Chyer, Paul Kaseloo, and Ankrah A. Ako. 2019. "Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats Using a Cohort Study" Antibiotics 8, no. 3: 136. https://doi.org/10.3390/antibiotics8030136
APA StyleNdegwa, E., Almehmadi, H., Chyer, K., Kaseloo, P., & Ako, A. A. (2019). Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats Using a Cohort Study. Antibiotics, 8(3), 136. https://doi.org/10.3390/antibiotics8030136