Abstract
Antibiotic resistance is a major public health concern with growing evidence of environmental gene reservoirs, especially in freshwater. However, the presence of antibiotic resistance genes in freshwater, in addition to the wide spectrum of land use contaminants like nitrogen and phosphate, that waterways are subjected to is inconclusive. Using molecular analyses, freshwater benthic rock biofilms were screened for genes conferring resistance to antibiotics used in both humans and farmed animals (aacA-aphD to aminoglycosides; mecA to ß-lactams; ermA and ermB to macrolides; tetA, tetB, tetK, and tetM to tetracyclines; vanA and vanB to glycopeptides). We detected widespread low levels of antibiotic resistance genes from 20 waterways across southern New Zealand throughout the year (1.3 % overall detection rate; 480 samples from three rocks per site, 20 sites, eight occasions; July 2010–May 2011). Three of the ten genes, ermB, tetK, and tetM, were detected in 62 of the 4800 individual screens; representatives confirmed using Sanger sequencing. No distinction could be made between human and agricultural land use contamination sources based on gene presence distribution alone. However, land use pressures are suggested by moderate correlations between antibiotic resistance genes and high-intensity farming in winter. The detection of antibiotic resistance genes at several sites not subject to known agricultural pressures suggests human sources of resistance, like waterway contamination resulting from unsatisfactory toilet facilities at recreational sites.
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Halling-Sørensen B, Nors Nielsen S, Lanzky P, Ingerslev F, Holten Lützhøft H, Jørgensen S (1998) Occurrence, fate and effects of pharmaceutical substances in the environment—a review. Chemosphere 36(2):357–393
Kim S, Aga D (2007) Potential ecological and human health impacts of antibiotics and antibiotic-resistant bacteria from wastewater treatment plants. J Toxicol Environ Health, Part B 10:559–573
Jury K, Khan S, Vancov T, Stuetz R, Ashbolt N (2011) Are sewage treatment plants promoting antibiotic resistance? Clin Rev Environ Sci Technol 41:243–270
Wellington E, Boxall A, Cross P, Feil E, Gaze W, Hawkey P, Johnson-Rollings A, Jones D, Lee N, Otten W, Thomas C, Williams A (2013) The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria. Lancet Infect Dis 13:155–165
Sarmah A, Meyer M, Boxall A (2006) A global perspective on the use, sales, exposure pathways, occurrence, fate and effects of veterinary antibiotics (VAs) in the environment. Chemosphere 65:725–759
Hillis D, Lissemore L, Sibley P, Solomon K (2007) Effects of monensin on zooplankton communities in aquatic microcosms. Environ Sci Technol 41(18):6620–6626
Watanabe N, Harter T, Bergamaschi B (2008) Environmental occurrence and shallow ground water detection of the antibiotic monensin from dairy farms. J Environ Qual 37:S-78–S-85
Watkinson A, Murby E, Kolpin D, Costanzo S (2009) The occurrence of antibiotics in an urban watershed: from wastewater to drinking water. Sci Total Environ 407(8):2711–2723
Costanzo S, Murby J, Bates J (2005) Ecosystem response to antibiotics entering the aquatic environment. Mar Pollut Bull 51:218–223
Storteboom H, Arabi M, Davis J, Crimi B, Pruden A (2010) Identification of antibiotic resistance gene molecular signatures suitable as tracers of pristine river, urban, and agricultural sources. Environ Sci Technol 44(6):1947–1953
Chee-Sanford J, Mackie R, Koike S, Krapac I, Lin Y, Yannarell A, Maxwell S, Aminov R (2009) Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure wastes. J Environ Qual 38:1086–1108
Ding C, He J (2010) Effect of antibiotics in the environment on microbial populations. Appl Microbiol Biotechnol 87:925–941
Marti E, Variatza E, Balcazar J (2014) The role of aquatic ecosystems as reservoirs of antibiotic resistance. Trends Microbiol 22(1):36–41
Wright G (2010) Antibiotic resistance in the environment: a link to the clinic? Curr Opin Microbiol 13:589–594
Pruden A, Arabi M, Storteboom H (2012) Correlation between upstream human activities and riverine antibiotic resistance genes. Environ Sci Technol 46:11541–11549
Kümmerer K (2009) Antibiotics in the aquatic environment—a review—part II. Chemosphere 75:417–434
Pal A, Gin K, Lin A, Reinhard M (2010) Impacts of emerging organic contaminants on freshwater resources: review of recent occurrences, sources, fate and effects. Sci Total Environ 408:6062–6069
Luo Y, Mao D, Rysz M, Zhou Q, Zhang H, Xu L, Alvarez P (2010) Trends in antibiotic resistance genes occurrence in the Haihe River, China. Environ Sci Technol 44(19):7220–7225
Barker-Reid F, Fox E, Faggian R (2010) Occurrence of antibiotic resistance genes in reclaimed water and river water in the Werribee Basin. J Water Health 8:521–531
Winkworth C (2013) Antibiotic resistance genes in freshwater biofilms along a whole river. J Water Health 11(2):186–198
Knapp C, Lima L, Olivares-Rieumont S, Bowen E, Werner D, Graham D (2012) Seasonal variations in antibiotic resistance gene transport in the Almendares River, Havana, Cuba. Front Microbiol 3:396
MfE (2007) Environment New Zealand 2007. Ministry for the Environment, Wellington
PCE (2004) Growing for good: intensive farming, sustainability and New Zealand’s environment. Parliamentary commissioner for the environment. Wellington, New Zealand
Allen H, Donato J, Wang H, Cloud-Hansen K, Davies J, Handelsman J (2010) Call of the wild: antibiotic resistance genes in natural environments. Nat Rev 8:251–259
Muirhead R, Collins R, Bremer P (2006) The association of E. coli and soil particles in overland flow. Water Sci Technol 54(3):153–159
River Environmental Classification (REC Otago) (2010) MfE
Leathwick J, West D, Gerbeaux P, Kelly D, Roberston H, Brown D (2010) Freshwater ecosystems of NZ (FENZ). Department of Conservation, Wellington
Land Cover Database II (LCDB2) (2008) MfE
APHA (1998) Standard methods for the examination of water and wastewater. American Public Health Association, Washington, DC
Wagenhoff A, Townsend C, Phillips N, Matthaei C (2011) Subsidy-stress and multiple-stressor effects along gradients of deposited fine sediment and dissolved nutrients in a regional set of streams and rivers. Freshw Biol 56(9):1916–1936
Lange K, Townsend C, Matthaei C (2014) Can biological traits of stream invertebrates help disentangle the effects of multiple stressors in an agricultural catchment? Freshw Biol 59:2431–2446
Bolker B, Brooks M, Clark C, Geange S, Poulsen J, Stevens M, White J (2009) Generalized linear mixed models: a practical guide for ecology and evolution. Trends Ecol Evol 24:127–135
Johnson J, Omland K (2004) Model selection in ecology and evolution. Trends Ecol Evol 19:101–108
Grueber C, Nakagawa S, Laws R, Jamieson I (2011) Multimodel inference in ecology and evolution: challenges and solutions. J Evol Biol 24:699–711
R: A language and environment for statistical computing. Version 3.0.2 (2013) R Development Core Team
Schielzeth H (2010) Simple means to improve the interpretability of regression coefficients. Methods Ecol Evol 1:103–113
Burnham K, Anderson D (2002) Model selection and multimodel inference: a practical information-theoretic approach, 2nd edn. Springer-Verlag, New York
Nakagawa S, Schielzeth H (2013) A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods Ecol Evol 4:133–142
WHO (2000) Antimicrobial resistance: a global threat. Essent Drugs Monit 28–29
Levy S, Marshall B (2004) Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 10:S122–S129
Huijbers P, Blaak H, De Jong M, Graat E, Vandenbroucke-Grauls C, De Roda HA (2015) Role of the environment in the transmission of antimicrobial resistance to humans: a review. Environ Sci Technol 49(20):11993–12004
Leonard A, Zhang L, Balfour A, Garside R, Gaze W (2015) Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters. Environ Int 82:92–100
McArthur J, Fletcher D, Tuckfield R, Baker-Austin C (2015) Patterns of multi-antibiotic-resistant Escherichia coli from streams with no history of antimicrobial inputs. Microb Ecol. doi:10.1007/s00248-015-0678-4
Lupo A, Coyne S, Urlich Berendonk T (2012) Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies. Front Microbiol 3. doi:10.3389/fmicb.2012.00018
Gillings M, Gaze W, Pruden A, Smalla K, Tiedje J, Zhu Y (2015) Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J 9:1269–1279
D’Costa V, King C, Kalan L, Morar M, Sung W, Schwarz C, Froese D, Zazula G, Calmels F, Debruyne R, Golding G, Poinar H, Wright G (2011) Antibiotic resistance is ancient. Nature 477:457–461
Sullivan B, Karthikeyan R (2012) Occurrence and prevalence of tetracycline resistant bacteria in a rapidly urbanizing subtropical watershed. J Nat Environ Sci 2:25–31
Desjardins M, Delgaty K, Ramotar K, Seetaram C, Toye B (2004) Prevalence and mechanisms of erythromycin resistance in group A and group B Streptococcus: implications for reporting susceptibility results. J Clin Microbiol 42(12):5620–5623
Waites K, Johnson C, Gray B, Edwards K, Crain M, Benjamin W Jr (2000) Use of clindamycin disks to detect macrolide resistance mediated by ermB and mefE in Streptococcus pneumoniae isolates from adults and children. J Clin Microbiol 38(5):1731–1734
MPI (2013) Antibiotic sales analysis: 2009–2011. vol MPI Technical Paper No 2013/62. Wellington
de Klein C, Smith L, Monaghan R (2006) Restricted autumn grazing to reduce nitrous oxide emissions from dairy pastures in Southland, New Zealand. Agric Ecosyst Environ 112(2):192–199
Ledgard G (2013) Land use change in the Southland region: technical report June 2013. Environmental Southland, Invercargill
Borbone S, Lupo A, Mezzatesta M, Campanile F, Santagati M, Stefani S (2008) Evaluation of the in vitro activity of tigecycline against multiresistant Gram-positive cocci containing tetracycline resistance determinants. Int J Antimicrob Agents 31:209–215
Chee-Sanford J, Aminov R, Krapac I, Garrigues-Jeanjean N, Mackie R (2001) Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilities. Appl Environ Microbiol 67(4):1494–1502
Guay G, Rothstein D (1993) Expression of the tetK gene from Staphylococcus aureus in Escherichia coli: comparison of substrate specificities of tetA(B), tetA(C), and tetK efflux proteins. Antimicrob Agents Chemother 37(2):191–198
CVMP (2011) Reflection paper on the use of macrolides, lincosamides and streptogramins (MLS) in food-producing animals in the European Union: development of resistance and impact on human and animal health. European Medicines Agency, London
Groh J, Luo Q, Ballard J, Krumholz L (2007) Genes that enhance the ecological fitness of Shewanella oneidensis MR-1 in sediments reveal the value of antibiotic resistance. Appl Environ Microbiol 73(2):492–498
Dönhöfer A, Franckenberg S, Wickles S, Berninghausen O, Beckmann R, Wilson DN (2012) Structural basis for TetM-mediated tetracycline resistance. Proc Natl Acad Sci 109(42):16900–16905
Acknowledgments
We thank Colin Townsend and four anonymous reviewers for the editorial suggestions, Emily Nichol, Rachel, Clive, and Anne Paterson for fieldwork assistance, Nicky McHugh and Tania King for laboratory assistance, and Environment Southland for the site information. This research was funded by a New Zealand Ministry of Business, Innovation and Employment Postdoctoral Fellowship (UOOX0902) to CWL.
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Winkworth-Lawrence, C., Lange, K. Antibiotic Resistance Genes in Freshwater Biofilms May Reflect Influences from High-Intensity Agriculture. Microb Ecol 72, 763–772 (2016). https://doi.org/10.1007/s00248-016-0740-x
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DOI: https://doi.org/10.1007/s00248-016-0740-x