Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and genetic function of dairy calves
Autoři:
Carla Foditsch aff001; Richard V. V. Pereira aff002; Julie D. Siler aff001; Craig Altier aff001; Lorin D. Warnick aff001
Působiště autorů:
Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
aff001; Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
aff002
Vyšlo v časopise:
PLoS ONE 14(12)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0219635
Souhrn
The increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), a single treatment of enrofloxacin, or a single treatment of tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sequencing was conducted. The effect of antibiotic treatment on each taxon and genetic functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher relative abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other study groups. The SEED database was used for genetic functional analyses, which showed that calves in the enrofloxacin group started with a higher relative abundance of “Resistance to antibiotics and toxic compounds” function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. “Resistance to Fluoroquinolones” and “Erythromycin resistance”, of relevance given the study groups, were not statistically different in relative abundance between study groups. “Resistance to fluoroquinolones” increased during the study period regardless of study group. Despite small differences over the first weeks between study groups, at Day 112 the microbiota composition and genetic functional profile was similar among all study groups. In our study, enrofloxacin or tulathromycin had minimal impacts on the microbial composition and genetic functional microbiota of calves over the study period.
Klíčová slova:
Antimicrobials – Antibiotics – Microbiome – Veterinary diseases – Antimicrobial resistance – Antibiotic resistance – Microbial genetics – Livestock care
Zdroje
1. CDC. Antibiotic resistance threats in the United States. CDC. 2013; 22–50. CS239559-B
2. Angulo FJ, Baker NL, Olsen SJ, Anderson A, Barrett TJ. Antimicrobial use in agriculture: controlling the transfer of antimicrobial resistance to humans. 2004;15: 78–85. doi: 10.1053/j.spid.2004.01.010 15185190
3. D’Costa VM, King CE, Kalan L, Morar M, Sung WWL, Schwarz C, et al. Antibiotic resistance is ancient. Nature. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.; 2011;477: 457. Available: doi: 10.1038/nature10388 21881561
4. Martinez JL. Antibiotics and antibiotic resistance genes in natural environments. Science (80-). 2008;321: 365–367. doi: 10.1126/science.1159483 18635792
5. Tsukayama P, Boolchandani M, Patel S, Pehrsson EC, Gibson MK, Chiou KL, et al. Characterization of wild and captive baboon gut microbiota and their antibiotic resistomes. mSystems. 2018;3. doi: 10.1128/mSystems.00016-18 29963641
6. Razai M, Hussain K. Improving antimicrobial prescribing practice for sore throat symptoms in a general practice setting. 2017; 1–5. doi: 10.1136/bmjquality.u211706.w4738 28469911
7. Verraes C, Boxstael S Van, Meervenne E Van, Coillie E Van. Antimicrobial resistance in the food chain: a review. 2013; 2643–2669. doi: 10.3390/ijerph10072643 23812024
8. Tyagi A, Singh B, Billekallu NK, Niraj T. Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome. Arch Microbiol. Springer Berlin Heidelberg; 2019;0: 0. doi: 10.1007/s00203-018-1615-y 30604012
9. Windeyer MC, Leslie KE, Godden SM, Hodgins DC, Lissemore KD, LeBlanc SJ. Factors associated with morbidity, mortality, and growth of dairy heifer calves up to 3 months of age. Prev Vet Med. Elsevier B.V; 2014;113: 231–240. doi: 10.1016/j.prevetmed.2013.10.019 24269039
10. Teixeira AGV, McArt JAA, Bicalho RC. Efficacy of tildipirosin metaphylaxis for the prevention of respiratory disease, otitis and mortality in pre-weaned Holstein calves. Vet J. Elsevier Ltd; 2017;219: 44–48. doi: 10.1016/j.tvjl.2016.12.004 28093111
11. USDA-NAHMS. Dairy 2014 [Internet]. 2018. Available: https://www.aphis.usda.gov/animal_health/nahms/dairy/downloads/dairy14/Dairy14_dr_PartIII.pdf
12. Jacoby GA. Mechanisms of resistance to quinolones. Clin Infect Dis. 2005;41 Suppl 2: S120–6. doi: 10.1086/428052 15942878
13. Hooper DC, Jacoby GA. Mechanisms of drug resistance: Quinolone resistance. Ann N Y Acad Sci. 2015;1354: 12–31. doi: 10.1111/nyas.12830 26190223
14. Emmerson AM. The quinolones: decades of development and use. J Antimicrob Chemother. 2003;51: 13–20. doi: 10.1093/jac/dkg208 12702699
15. Ronald AR, Low DE. Fluoroquinolone antibiotics. Springer. 2003. doi: 10.1007/978-3-0348-8452-5
16. FDA US. Animal Drugs. In: U.S.Food & Drug Administration. Animal Drugs [Internet]. Available: https://animaldrugsatfda.fda.gov/adafda/views/#/search
17. Jelić D, Antolović R. From erythromycin to azithromycin and new potential ribosome-binding antimicrobials. Antibiotics. 2016;5: 29. doi: 10.3390/antibiotics5030029 27598215
18. Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol. Nature Publishing Group; 2005;3: 711. Available: doi: 10.1038/nrmicro1234 16138099
19. Munita JM, Arias CA. Mechanisms of antibiotic resistance. 2016;4: 1–37. doi: 10.1128/microbiolspec.VMBF-0016-2015 27227291
20. Pickering LK. Antimicrobial resistance among enteric pathogens. 2004;15: 71–77. doi: 10.1053/j.spid.2004.01.009 15185189
21. Nogueira T, David PHC, Pothier J. Antibiotics as both friends and foes of the human gut microbiome: the microbial community approach. 2018; 1–12. doi: 10.1002/ddr.21466 30370682
22. Francino MP. Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances increased susceptibility to infections. 2016;6: 1–11. doi: 10.3389/fmicb.2015.01543 26793178
23. Pereira R V, Lima S, Siler JD, Foditsch C, Warnick LD, Bicalho RC. Ingestion of milk containing very low concentration of antimicrobials: longitudinal effect on fecal microbiota composition in preweaned calves. PLoS One. 2016;11: e0147525. doi: 10.1371/journal.pone.0147525 26808865
24. Meyer F, Paarmann D, D’Souza M, Etal. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9: 386. doi: 10.1186/1471-2105-9-386 18803844
25. Pereira R V, Carroll LM, Lima S, Foditsch C, Siler JD, Bicalho RC, et al. Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota. Sci Rep. Springer US; 2018;8: 1–12. doi: 10.1038/s41598-017-17765-5
26. Pereira R V, Siler JD, Bicalho RC, Warnick LD. Multiresidue screening of milk withheld for sale at dairy farms in central New York State. J Dairy Sci. 2014;97: 1513–9. doi: 10.3168/jds.2013-7421 24440252
27. Pereira R V, Siler JD, Bicalho RC, Warnick LD. In vivo selection of resistant E. coli after ingestion of milk with added drug. PLoS One. 2014;9: 1–23. doi: 10.1371/journal.pone.0115223 25506918
28. Call DR, Matthews L, Subbiah M, Liu J. Do antibiotic residues in soils play a role in amplification and transmission of antibiotic resistant bacteria in cattle populations? Front Microbiol. 2013;4: 1–8. doi: 10.3389/fmicb.2013.00001
29. Pereira R V, Siler JD, Ng JC, Davis MA, Warnick LD, Sciences D. Effect of preweaned dairy calf housing system on antimicrobial resistance in commensal Escherichia coli. 2015;97: 7633–7643. doi: 10.3168/jds.2014-8588.Effect
30. Vikram A, Miller E, Arthur TM, Bosilevac JM, Wheeler TL, Schmidt JW. Similar Levels of Antimicrobial Resistance in U. S. Food Service Ground Beef Products with and without a ‘Raised without Antibiotics’ Claim. 2018;81: 2007–2018. doi: 10.4315/0362-028X.JFP-18-299 30476443
31. Auffret MD, Dewhurst RJ, Duthie C, Rooke JA, Wallace RJ, Freeman TC, et al. The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle. Microbiome; 2017; 1–11. doi: 10.1186/s40168-016-0209-7
32. Brown SA. Fluoroquinolones in animal health. J Vet Pharmacol Ther. 1996;19: 1–14. doi: 10.1111/j.1365-2885.1996.tb00001.x 8992019
33. Cummings KJ, Aprea VA, Altier C. Antimicrobial Resistance Trends Among Escherichia coli. 2014;11. doi: 10.1089/fpd.2013.1605 24134668
34. Muñoz-lópez M, García-pérez JL. DNA transposons: nature and applications in genomics. 2010; 115–128.
35. Heins BD, Nydam DV, Woolums AR, Berghaus RD, Overton MW. Comparative efficacy of enrofloxacin and tulathromycin for treatment of preweaning respiratory disease in dairy heifers. J Dairy Sci. Elsevier; 2014;97: 372–382. doi: 10.3168/jds.2013-6696 24183689
36. Foditsch C, Pereira R V, Ganda EK, Gomez MS, Marques EC, Santin T, et al. Oral administration of Faecalibacterium prausnitzii decreased the incidence of severe diarrhea and related mortality rate and increased weight gain in preweaned dairy heifers. PLoS One. 2015;10: 1–17. doi: 10.1371/journal.pone.0145485 26710101
37. Gomez DE, Arroyo LG, Costa MC, Viel L, Weese JS. Characterization of the fecal bacterial microbiota of healthy and diarrheic dairy calves. J Vet Intern Med. 2017;31: 928–939. doi: 10.1111/jvim.14695 28390070
38. Patrick S. Bacteroides. Molecular Medical Microbiology: Second Edition. Elsevier Ltd; 2014. doi: 10.1016/B978-0-12-397169-2.00051–2
39. Soki J. Extended role of insertion sequence elements in the antibiotic resistance of Bacteriodes. World J Clin Infect Dis. 2013;3: 1–12. doi: 10.5495/wjcid.v3.i1.1
40. Wexler HM. Bacteroides: The good, the bad, and the nitty-gritty. Clin Microbiol Rev. 2007;20: 593–621. doi: 10.1128/CMR.00008-07 17934076
41. Snydman DR, Jacobus N V., McDermott LA, Ruthazer R, Golan Y, Goldstein EJC, et al. National survey on the susceptibility of Bacteroides fragilis group: Report and analysis of trends in the United States from 1997 to 2004. Antimicrob Agents Chemother. 2007;51: 1649–1655. doi: 10.1128/AAC.01435-06 17283189
42. Betriu C, Rodríguez-Avial I, Gómez M, Culebras E, Picazo JJ. Changing patterns of fluoroquinolone resistance among Bacteroides fragilis group organisms over a 6-year period (1997–2002). Diagn Microbiol Infect Dis. 2005;53: 221–223. doi: 10.1016/j.diagmicrobio.2005.06.012 16243476
43. Singh SB, Lin HC. Hydrogen sulfide in physiology and diseases of the digestive tract. 2015; 866–889. doi: 10.3390/microorganisms3040866 27682122
44. Zhang G, Li B, Liu J, Luan M, Yue L, Jiang X, et al. The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems. 2018; 1–18.
45. Balamurugan R, Rajendiran E, George S, Samuel G V, Ramakrishna BS. Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer. J Gastroenterol Hepatol. 2008;23: 1298–1303. doi: 10.1111/j.1440-1746.2008.05490.x 18624900
46. Zhang T, Mu Y, Zhang D, Lin X, Hou Q, Wang Y, et al. Determination of microbiological characteristics in the digestive tract of different ruminant species. 2018; 1–11. doi: 10.1002/mbo3.769 30585444
47. Nakao KI, Tanaka K, Ichiishi S, Mikamo H, Shibata T, Watanabe K. Susceptibilities of 23 Desulfovibrio isolates from humans. Antimicrob Agents Chemother. 2009;53: 5308–5311. doi: 10.1128/AAC.00630-09 19786606
48. Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. 2012;7. doi: 10.1371/journal.pone.0039743 22761885
49. Song Y, Malmuthuge N, Steele MA, Guan LL. Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning. 2018; 1–15. doi: 10.1093/femsec/fix179 29267960
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