Skip to main content
SpringerLink
Log in

Hierarchal clustering yields insight into multidrug-resistant bacteria isolated from a cattle feedlot wastewater treatment system

  • Published:
Environmental Monitoring and Assessment Aims and scope Submit manuscript

Abstract

Forty-two percent of Escherichia coli and 58 % of Enterococcus spp. isolated from cattle feedlot runoff and associated infiltration basin and constructed wetland treatment system were resistant to at least one antibiotic of clinical importance; a high level of multidrug resistance (22 % of E. coli and 37 % of Enterococcus spp.) was observed. Hierarchical clustering revealed a closely associated resistance cluster among drug-resistant E. coli isolates that included cephalosporins (ceftiofur, cefoxitin, and ceftriaxone), aminoglycosides (gentamycin, kanamycin, and amikacin), and quinolone nalidixic acid; antibiotics from these classes were used at the study site, and cross-resistance may be associated with transferrable multiple-resistance elements. For Enterococcus spp., co-resistance among vancomycin, linezolid, and daptomycin was common; these antibiotics are reserved for complicated clinical infections and have not been approved for animal use. Vancomycin resistance (n = 49) only occurred when isolates were resistant to linezolid, daptomycin, and all four of the MLSB (macrolide-lincosamide-streptogramin B) antibiotics tested (tylosin, erythromycin, lincomycin, and quinipristin/dalfopristin). This suggests that developing co-resistance to MLSB antibiotics along with cyclic lipopeptides and oxazolidinones may result in resistance to vancomycin as well. Effects of the treatment system on antibiotic resistance were pronounced during periods of no rainfall and low flow (long residence time). Increased hydraulic loading (short residence time) under the influence of rain caused antibiotic-resistant bacteria to be flushed through the treatment system. This presents concern for environmental discharge of multidrug-resistant organisms relevant to public health.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Abbreviations

ABC:

ATP-binding cassette

ESBL:

extended-spectrum beta-lactamases

FIB:

fecal indicator bacteria

FDA:

U.S. Food and Drug Administration

J:

Jaccard similarity

MLSB :

macrolide-lincosamide-streptogramin B

MPN:

most probable number

MRSA:

methicillin-resistant Staphylococcus aureus

UP:

undecaprenyl phosphate

UPP:

undecaprenyl pyrophosphate

USEPA:

U.S. Environmental Protection Agency

VRE:

vancomycin-resistant Enterococcus faecium

References

  • Aarestrup, F. M. (2000). Characterization of glycopeptide-resistant Enterococcus faecium (GRE) from broilers and pigs in Denmark: genetic evidence that persistence of GRE in Pig herds is associated with coselection by resistance to macrolides. Journal of Clinical Microbiology, 38(7), 2774–2777.

    CAS  Google Scholar 

  • Alexander, T. W., Yanke, L. J., Topp, E., Olson, M. E., Read, R. R., Morck, D. W., et al. (2008). Effect of subtherapeutic administration of antibiotics on the prevalence of antibiotic-resistant Escherichia coli bacteria in feedlot cattle. Applied and Environmental Microbiology, 74(14), 4405–4416.

    Article  CAS  Google Scholar 

  • Angulo, F. J., Nargund, V. N., & Chiller, T. C. (2004). Evidence of an association between use of anti-microbial agents in food animals and anti-microbial resistance among bacteria isolated from humans and the human health consequences of such resistance. Journal of Veterinary Medicine, 51, 374–379.

    Article  CAS  Google Scholar 

  • Arias, C. A., & Murray, B. E. (2008). Emergence and management of drug-resistant enterococcal infections. Expert Review of Anti-Infective Therapy, 6(5), 637–655.

    Article  CAS  Google Scholar 

  • Arias, C. A., & Murray, B. E. (2012). The rise of the Enterococcus: beyond vancomycin resistance. Nature Reviews Microbiology, 10, 266–278.

    Article  CAS  Google Scholar 

  • Arias, C. A., Panesso, D., McGrath, D. M., Qin, X., Mojica, M., Miller, C., et al. (2011). Genetic basis for in vivo daptomycin resistance in enterococci. New England Journal of Medicine, 365(10), 892–900.

    Article  CAS  Google Scholar 

  • Bozdogan, B., & Appelbaum, P. C. (2004). Oxazolidinones: activity, mode of action, and mechanism of resistance. International Journal of Antimicrobial Agents, 2004, 113–119.

    Article  Google Scholar 

  • Bradford, P. A., Petersen, P. J., Fingerman, I. M., & White, D. G. (1999). Characterization of expanded-spectrum cephalosporin resistance in E. coli isolates associated with bovine and calf diarrhoeal disease. Journal of Antimicrobial Chemotherapy, 44, 607–610.

    Article  CAS  Google Scholar 

  • Bunny, K. L., Hall, R. M., & Stokes, H. W. (1995). New mobile gene cassettes containing an aminoglycoside resistance gene, aacA7, and a chloramphenicol resistance gene, catB3, in an integron in pBWH301. Antimicrobial Agents and Chemotherapy, 39(3), 686–693.

    Article  CAS  Google Scholar 

  • Burkholder, J., Libra, B., Weyer, P., Heathcote, S., Kolpin, D., Throne, P. S., et al. (2007). Impacts of waste from concentrated animal feeding operations on water quality. Environmental Health Perspectives, 115(2), 308–312.

    Article  CAS  Google Scholar 

  • Butaye, P., Devriese, L. A., & Haesebrouck, F. (2003). Antimicrobial growth promoters used in animal feed: effects of less well known antibiotics on gram-positive bacteria. Clinical Microbiology Reviews, 16(2), 175–188.

    Article  CAS  Google Scholar 

  • Call, D. R., Davis, M. A., & Sawant, A. A. (2008). Antimicrobial resistance in beef and dairy cattle production. Animal Health Research Reviews, 9(2), 159–167.

    Article  Google Scholar 

  • Chee-Sanford, J. C., Mackie, R. I., Koike, S., Krapac, I. G., Lin, Y., Yannarell, A. C., et al. (2009). Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. Journal of Environmental Quality, 38, 1086–1108.

    Article  CAS  Google Scholar 

  • CLSI. (2013). Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Third Informational Supplement. CLSI document M100-S23, Clinical and Laboratory Standards Institute, Wayne, P.A.

  • Core Team, R. (2013). R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.

    Google Scholar 

  • Cui, L., Tominaga, E., Neoh, H., & Hiramatsu, K. (2006). Correlation between reduced daptomycin susceptibility and vancomycin resistance in vancomycin-intermediate Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 50(3), 1079–1082.

    Article  CAS  Google Scholar 

  • Dai, L., Wu, C.-M., Wang, M.-G., Wang, Y., Wang, Y., Xia, L.-N., et al. (2010). First report of the multidrug resistance gene cfr and the phenicol resistance gene fexA in a Bacillus strain from swine feces. Antimicrobial Agents and Chemotherapy, 54(9), 3953–3955.

    Article  CAS  Google Scholar 

  • Edwards, J. E., McEwan, N. R., & Wallace, R. J. (2008). Adaptation to flavomycin in the ruminal bacterium, Prevotella bryantii. Journal of Applied Microbiology, 104, 1617–1623.

    Article  CAS  Google Scholar 

  • Efron, B., & Tibshirani, R. J. (1998). An introduction to the bootstrap. Boca Raton: Chapman and Hall/CRC.

    Google Scholar 

  • FDA. (2012). Estimates of antibacterial drug sales in human medicine. U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Surveillance and Epidemiology, Silver Spring, M.D.

  • FDA. (2013). 2011 Summary report on antimicrobials sold or distributed for use in food-producing animals. U.S. Food and Drug Administration, Center for Veterinary Medicine, Rockville, M.D.

  • Feinmen, S. E. (1998). Antibiotics in animal feed: drug resistance revisited. American Society for Microbiology News, 64, 24–30.

    Google Scholar 

  • Gilchrist, M. J., Greko, C., Wallinga, D. B., Beran, G. W., Riley, D. G., & Throne, P. S. (2007). The potential role of concentrated animal feeding operations in infectious disease epidemics and antibiotic resistance. Environmental Health Perspectives, 115(2), 313–316.

    Article  Google Scholar 

  • Guerra, B., Junker, E., Schroeter, A., Malorny, B., Lehmann, S., & Helmuth, R. (2003). Phenotypic and genotypic characterization of antimicrobial resistance in German Escherichia coli isolates from cattle, swine and poultry. Journal of Antimicrobial Chemotherapy, 52, 489–492.

    Article  CAS  Google Scholar 

  • Hastie, T., Tibshirani, R., & Friedman, J. (2009). The elements of statistical learning (2nd ed.). New York: Springer.

    Book  Google Scholar 

  • Hershberger, E., Donabedian, S., Konstantinou, K., & Zervos, M. J. (2003). Quinupristin-dalfopristin resistance in gram-positive bacteria: mechanism of resistance and epidemiology. Clinical Infectious Diseases, 38(1), 92–98.

    Article  Google Scholar 

  • Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics, 6, 65–70.

    Google Scholar 

  • Holzen, C. S., Harms, K. S., Schwaiger, K., & Bauer, J. (2010). Resistance to linezolid in a porcine Clostridium perfringens strain carrying a mutation in the rplD gene encoding the ribosomal protein L4. Antimicrobial Agents and Chemotherapy, 54(3), 1351–1353.

    Article  Google Scholar 

  • Jackson, C. R., Lombard, J. E., Dargatz, D. A., & Fedorka-Cray, P. J. (2010). Prevalence, species distribution and antimicrobial resistance of enterococci isolated from US dairy cattle. Letters in Applied Microbiology, 52, 41–48.

    Article  Google Scholar 

  • Kaufman, L., & Rousseuw, P. J. (1990). Finding groups in data. New York: Wiley.

    Book  Google Scholar 

  • Khachatourians, G. G. (1998). Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria. Canadian Medical Association Journal, 159, 1129–1136.

    CAS  Google Scholar 

  • Klare, I., Konstabel, C., Badstubner, D., Werner, G., & Witte, W. (2003). Occurrence and spread of antibiotic resistances in Enterococcus faecium. International Journal of Food Microbiology, 88, 269–290.

    Article  CAS  Google Scholar 

  • Kummerer, K. (2004). Resistance in the environment. Journal of Antimicrobial Chemotherapy, 54, 311–320.

    Article  CAS  Google Scholar 

  • Lanz, R., Kuhnert, P., & Boerlin, P. (2003). Antimicrobial resistance and resistance gene determinants in clinical Escherichia coli from different animal species in Switzerland. Veterinary Microbiology, 91, 73–84.

    Article  CAS  Google Scholar 

  • Li, X.-Z. (2005). Quinolone resistance in bacteria: emphasis on plasmid-mediated mechanisms. International Journal of Antimicrobial Agents, 25, 453–463.

    Article  CAS  Google Scholar 

  • Li, X.-Z., Mehrothra, M., Ghimire, S., & Adewoye, L. (2007). Beta-lactam resistance and beta-lactamases in bacteria of animal origin. Veterinary Microbiology, 121, 197–214.

    Article  CAS  Google Scholar 

  • Li, X., Watanabe, N., Xiao, C., Harter, T., McCowan, B., Liu, Y., et al. (2014). Antibiotic-resistant E. coli in surface water and groundwater in dairy operations in Northern California. Environmental Monitoring and Assessment, 186(2), 1253–1260.

    Article  CAS  Google Scholar 

  • Lorimar, J. (2001). Soil infiltration and wetland treatment of feedlot runoff. 2001 Beef Research Report, A.S. Leaflet R1744, Iowa State University, Ames, IA.

  • Manson, J. M., Keis, S., Smith, J. M., & Cook, G. M. (2004). Acquired bacitracin resistance in Enterococcus faecalis is mediated by an ABC transporter and a novel regulatory protein, BcrR. Antimicrobial Agents and Chemotherapy, 48(10), 3743–3748.

    Article  CAS  Google Scholar 

  • McEwen, S. A., & Fedorka-Cray, P. J. (2002). Antimicrobial use and resistance in animals. Clinical Infectious Diseases, 34(Suppl 3), S93–S106.

    Article  CAS  Google Scholar 

  • Mulvey, M. R., Suskey, E., McCracken, M., Morck, D. W., & Read, R. R. (2009). Similar cefoxitin-resistance plasmids circulating in Escherichia coli from human and animal sources. Veterinary Microbiology, 134, 279–287.

    Article  CAS  Google Scholar 

  • NARMS. (2010). National Antimicrobial Resistance Monitoring System: NARMS 2010 Animal Arm Annual Report. U.S. Department of Agriculture, Agricultural Research Service, Bacterial Epidemiology and Antimicrobial Resistance Unit, Athens, G.A.

  • NARMS. (2011). National Antimicrobial Resistance Monitoring System: NARMS Retail Meat Annual Report, 2011. U.S. Food and Drug Administration, Center for Veterinary Medicine, Rockville, M.D.

  • Nikaido, H. (2009). Multidrug resistance in bacteria. Annual Review of Biochemistry, 78, 119–146.

    Article  CAS  Google Scholar 

  • Nilsson, O. (2012). Vancomycin resistant enterococci in farm animals—occurrence and importance. Infection Ecology and Epidemiology, 2, 16959.

    Article  Google Scholar 

  • Ostash, B., & Walker, S. (2010). Moenomycin family antibiotics: chemical synthesis, biosynthesis, and biological activity. Natural Product Reports, 27, 1594–1617.

    Article  CAS  Google Scholar 

  • Rodrigues-Palacios, A., Koohmaraie, M., & LeJeune, J. (2011). Prevalence, enumeration, and antimicrobial agent resistance of Clostridium difficile in cattle at harvest in the United States. Journal of Food Protection, 74(10), 1618–1624.

    Article  Google Scholar 

  • Rogers, S., Donnelly, M., Peed, L., Kelty, C., Mondal, S., Zhong, Z., et al. (2011). Decay of bacterial pathogens, fecal indicators, and real-time quantitative PCR genetic markers in manure-amended soils. Applied and Environmental Microbiology, 77(14), 4839–4848.

    Article  CAS  Google Scholar 

  • Ruzauskas, M., Virgailis, M., Siugždinienė, R., Sužiedėlienė, E., Seputienė, V., Daugelavičius, R., et al. (2009). Antimicrobial resistance of Enterococcus spp. isolated from livestock in Lithuania. Veterinarski Arhiv, 79(5), 439–449.

    Google Scholar 

  • Rysz, J., & Alvarez, P. J. J. (2004). Amplification and attenuation of tetracycline resistance in soil bacteria: aquifer column experiments. Water Research, 38, 3705–3712.

    Article  CAS  Google Scholar 

  • Sayah, R. S., Kaneene, J. B., Johnson, Y., & Miller, R. A. (2005). Patterns of antimicrobial resistance observed in Escherichia coli isolates obtained from domestic- and wild-animal fecal samples, human septage, and surface water. Applied and Environmental Microbiology, 71(3), 1394–1404.

    Article  CAS  Google Scholar 

  • Schwaber, M. J., Navon-Venezia, S., Schwartz, D., & Carmeli, Y. (2005). High levels of antimicrobial coresistance among extended-spectrum-β-lactamase-producing Enterobacteriaceae. Antimicrobial Agents and Chemotherapy, 49(5), 2137–2139.

    Article  CAS  Google Scholar 

  • Seiffert, S. N., Hilty, M., Perreten, V., & Endimiani, A. (2013). Extended-spectrum cephalosporin-resistant gram-negative organisms in livestock: an emerging problem for human health? Drug Resistance Updates, 16(1–2), 22–45.

    Article  Google Scholar 

  • Shaaly, A., Kalamorz, F., Gebhard, S., & Cook, G. M. (2013). Undecaprenyl pyrophosphate phosphatase confers low-level resistance to bacitracin in Enterococcus faecalis. Journal of Antimicrobial Chemotherapy, 68(7), 1583–1593.

    Article  CAS  Google Scholar 

  • Srinivasan, V., Gillespie, B. E., Lewis, M. J., Nguyen, L. T., Headrick, S. I., Schukken, Y. H., et al. (2007). Phenotypic and genotypic antimicrobial resistance patterns of Escherichia coli isolated from dairy cows with mastitis. Veterinary Microbiology, 124, 319–328.

    Article  CAS  Google Scholar 

  • USEPA. (2005). Detecting and mitigating the environmental impact of fecal pathogens originating from confined animal feeding operations: review. EPA/600/R-06/021, U.S. Environmental Protection Agency, Cincinnati, O.H.

  • Vilhena, C., & Bettencourt, A. (2012). Daptomycin: a review of properties, clinical use, drug delivery and resistance. Mini-Reviews in Medicinal Chemistry, 12(3), 1–8.

    Article  Google Scholar 

  • Wang, Y., Wu, C., Zhang, Q., Qi, J., Liu, H., Wang, Y., et al. (2012). Identification of New Delhi metallo-β-lactamase 1 in Acinetobacter lwoffii of food animal origin. PLoS ONE, 7(5), e37152.

    Article  CAS  Google Scholar 

  • Werner, G. (2012). Current trends of emergence and spread of vancomycin-resistant enterococci. In M. Pana (Ed.), Antibiotic resistant bacteria—a continuous challenge in the new millennium (pp. 303–354). New York: InTech.

    Google Scholar 

  • Yang, H., Dettman, B., Beam, J., Mix, C., & Jiang, X. (2006). Occurrence of ceftriaxone-resistant commensual bacteria on a dairy farm and a poultry farm. Canadian Journal of Microbiology, 52, 942–950.

    Article  CAS  Google Scholar 

  • Zhao, S., Fedorka-Cray, P. J., Friedman, S., McDermott, P. F., Walker, R. D., Qaiyumi, S., et al. (2005). Characterization of Salmonella typhimurium of animal origin obtained from the National Antimicrobial Resistance Monitoring System. Foodborne Pathogens and Disease, 2(2), 169–181.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This project was supported by the National Research Initiative of the USDA Cooperative State Research, Education, and Extension Service, grant number 2007-35102-18614. The U.S. Environmental Protection Agency, through its Office of Research and Development, also funded and collaborated in the research described herein. Any opinions expressed in this paper are those of the authors and do not necessarily reflect the official positions and policies of the USEPA. Any mention of trade names or commercial products does not constitute endorsement or recommendation for use. This material is based, in part, upon work supported by the National Science Foundation under Grant No. 0959713. The authors thank Dr. Robert Burns of Iowa State University for installation, calibration, and maintenance of the sampling equipment and collection and shipment of manure and water samples. The authors also thank the landowner who graciously allowed access and collection of samples at the study site.

Author information

Author notes

  1. Shane W. Rogers

    Present address: Department of Civil and Environmental Engineering, Clarkson University, Potsdam, NY, 13699, USA

  2. Gina Hayes

    Present address: Ohio EPA, Lazarus Government Center, 50 W. Town St., Suite 700, Columbus, OH, 43215, USA

Authors and Affiliations

  1. Institute for a Sustainable Environment, Clarkson University, Potsdam, NY, 13699, USA

    Michael A. Jahne

  2. National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, OH, 45212, USA

    Shane W. Rogers

  3. Department of Mathematics, Computer Science, and Statistics, St. Lawrence University, Canton, NY, 13617, USA

    Ivan P. Ramler

  4. Pegasus Technical Services, 46 E. Hollister St., Cincinnati, OH, 45219, USA

    Edith Holder

  5. Institute for the Environment and Sustainability, Miami University, Oxford, OH, 45056, USA

    Gina Hayes

Authors
  1. Michael A. Jahne
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shane W. Rogers
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ivan P. Ramler
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Edith Holder
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gina Hayes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shane W. Rogers.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jahne, M.A., Rogers, S.W., Ramler, I.P. et al. Hierarchal clustering yields insight into multidrug-resistant bacteria isolated from a cattle feedlot wastewater treatment system. Environ Monit Assess 187, 4168 (2015). https://doi.org/10.1007/s10661-014-4168-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10661-014-4168-9

Keywords

Search

Navigation