Skip to main content
SpringerLink
Log in
Book cover

Nucleic Acids in the Environment pp 241–256Cite as

Application of the PCR for Detection of Antibiotic Resistance Genes in Environmental Samples

  • Chapter

Part of the book series: Springer Lab Manuals ((SLM))

Abstract

Extensive use of antibiotics in human or animal therapy and in husbandry has contributed significantly to an enhanced incidence of antibiotic resistant bacteria. Multiple antibiotic resistance has been recognized for a long time to represent an increasingly important problem in hospital and community (Cohen 1992; Neu 1992).

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Andersen SR (1993) Effects of waste water treatment on the species composition and antibiotic resistance ofcoliform bacteria. Curr Microbiol 26: 97–103

    Article  Google Scholar 

  • Benveniste R, Davies J (1973) Aminoglycoside antibiotic-inactivating enzymes in Actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. Proc Natl Acad Sci USA 70 (8): 2276–2280

    Article  Google Scholar 

  • Byrd JJ, Colwell RR (1990) Maintenance of plasmids pBR322 and pUC8 in noneulturable Escherichia coli in the marine environment. Appl Environ Microbiol 56 (7): 2104–2107

    Google Scholar 

  • Byrd JJ, Colwell RR (1993) Long-term survival and plasmid maintenance of Escherichia coli in marine microcosms. FEMS Microbiol Ecol 12: 9–14

    Article  Google Scholar 

  • Cohen ML (1992) Epidemiology of drug resistance: implications for a post-antimicrobial era. Science 257: 1050–1055

    Article  Google Scholar 

  • Cresswell N, Saunders VA, Wellington EMH (1991) Detection and quantification of Streptomyces violaceolatus plasmid DNA in soil. Lett Appl Microbiol 13: 193–197

    Article  Google Scholar 

  • Edwards RM, Loutit MW (1984) Chloramphenicol and tetracycline resistant bacteria of non-sewage origin in an oxidation pond. New Zealand J Sci 27: 87–91

    Google Scholar 

  • Facinelli B, Roberts MC, Giovanetti E, Casolari C, Fabio U, Varaldo PE (1993) Genetic basis of tetracycline resistance in food-borne isolates of Listeria innocua. Appl Environ Microbiol 59 (2): 614–616

    Google Scholar 

  • Flamm RK, Phillips KL, Tenover FC, Plorde JJ (1993) A survey of clinical isolates of Enterohacteriaceae using a series of DNA probes for aminoglycoside resistance genes. Mol Cell Probes 7: 139–144

    Article  Google Scholar 

  • Herrick JB, Madsen EL, Batt CA, Ghiorse WC (1993) Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Appl Environ Microbiol 59 (3): 687–694

    Google Scholar 

  • Holben WE, Jansson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54 (3): 703–711

    Google Scholar 

  • Hopkins DW, Macnaughton SJ, O’Donnell AG (1991) A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil. Soil Biol Biochem 23 (3): 217–225

    Article  Google Scholar 

  • Jacobsen CS, Rasmussen OF (1992) Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl Environ Microbiol 58 (8): 2458–2462

    Google Scholar 

  • Lee C, Langlois BE, Dawson KA (1993) Detection of tetracycline resistance determinants in pig isolates from three herds with different histories of antimicrobial agent exposure. Appl Environ Microbiol 59 (5): 1467–1472

    Google Scholar 

  • Leff LG, Dana JR, McArthur JV, Shimkets LJ (1993) Detection of Tn5-like sequences in kanamycin-resistant stream bacteria and environmental DNA. Appl Environ Microbiol 59 (2): 417–421

    Google Scholar 

  • Morgan JAW, Rhodes G, Pickup RW (1993) Survival of nonculturable Aeromonas salmonicida in lake water. Appl Environ Microbiol 59 (3): 874–880

    Google Scholar 

  • Nap J-P, Bijvoet J, Stiekema WJ (1992) Biosafety of kanamycin-resistant transgenic plants. Transgenic Res 1: 239–249

    Article  Google Scholar 

  • Neu HC (1992) The crisis in antibiotic resistance. Science 257: 1064–1072

    Article  Google Scholar 

  • Niemi M, Sibakov M, Niemela S (1983) Antibiotic resistance among different species of fecal coliforms isolated from water samples. Appl Environ Microbiol 45 (1): 79–83

    Google Scholar 

  • Ogan MT, Nwiika DE (1993) Studies on the ecology of aquatic bacteria of the lower Niger delta: multiple antibiotic resistance among the standard plate count organisms. J Appl Bacteriol 74: 595–602

    Google Scholar 

  • Ogram A, Sayler GS, Barkay TJ (1987) DNA extraction and purification from sediments. J Microbiol Meth 7: 57–66

    Article  Google Scholar 

  • Ouellette M, Bissonnette L, Roy PH (1987) Precise insertion of antibiotic resistance determinants into Tn21-like transposons: nucleotide sequence of the OXA-1 ß-laetamase gene. ProcNatl Acad Sci USA 84: 7378–7382

    Article  Google Scholar 

  • Padilla C, Vasquez C (1993) Plasmid-mediated antibiotic resistance in Psendomonas aeruginosa from well water sediments and their transformation into Escherichia coli. Lett Appl Microbiol 16: 17–20

    Article  Google Scholar 

  • Pathak SP, Bhattacheijee JW, Ray PK (1993) Seasonal variation in survival and antibiotic resistance among various bacterial populations in a tropical river. J Gen Appl Microbiol 39: 47–56

    Article  Google Scholar 

  • Piepersberg W, Distler J, Heinzel P, Perez-Gonzalez J-A (1988) Antibiotic resistance by modification: many resistance genes could be derived from cellular control genes in actinomycetes - a hypothesis. Actinomycetologica 2: 83–98

    Article  Google Scholar 

  • Pillai SD, Josephson KL, Bailey RL, Gerby CP, Pepper EL (1991) Rapid method for processing soil samples for polymerase chain reaction amplification of specific gene sequences. Appl Environ Microbiol 57: 2283–2286

    Google Scholar 

  • Porteous LA, Armstrong JL (1991) Recovery of bulk DNA from soil by a rapid, small-scale extraction method. Current Microbiol 22: 345–348

    Article  Google Scholar 

  • Porteous LA, Armstrong JL (1993) A simple mini-method to extract DNA directly from soil for use with polymerase chain reaction amplification. Curr Microbiol 27: 115–118

    Article  Google Scholar 

  • Recorbet G, Givaudan A, Steinberg C, Bally R, Normand P, Faurie G (1992) Tn5 to assess soil fate of genetically marked bacteria: screening for aminoglycoside resistance advantage and labelling specificity. FEMS Microbiol Ecol 86: 187–194

    Article  Google Scholar 

  • Sambrook J, Fritseh EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory, Cold Spring Harbor, USA

    Google Scholar 

  • Saunders JR (1984) Genetics and evolution of antibiotic resistance. Med Bull 40 (1): 54–60

    Google Scholar 

  • Sayler GS, Shields MS, Tedford ET, Breen A, Hooper SW, Sirotkin KM, Davis JW (1985) Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples. Appl Environ Microbiol 49: 1295–1303

    Google Scholar 

  • Sayler GS, Fleming JT, Applegate B, Werner C (1992) Nucleic acid extraction and analysis: detecting genes and their activity in the environment. In: Wellington EMH, Van Elsas, JD (eds) Genetic interactions among microorganisms in the natural environment. Pergamon, Oxford, pp 237–257

    Google Scholar 

  • Selenska S, Klingmüller W (1991) Direct detection of nif-gene sequences of Enterobacter agglomerans in soil. FEMS Microbiol Lett 80: 243–246

    Article  Google Scholar 

  • Shaw KJ, Rather PN, Hare RS, Miller GH (1993) Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes. Microbiol Rev 57 (1): 138–163

    Google Scholar 

  • Smalla K, Cresswell N, Mendonca-Hagler LC, Wolters A, Van Elsas JD (1993a) Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J Appl Bacteriol 74: 78–85

    Article  Google Scholar 

  • Smalla K, Prager R, Isemann M, Pukall R, Tietze E, Van Elsas JD, Tschäpe H (1993b) Distribution of streptothricin acetyltransferase encoding determinants among environmental bacteria. Mol Ecol 2: 27–33

    Article  Google Scholar 

  • Smalla K, Van Overbeek LS, Pukall R, Van Elsas JD (1993c) Prevalence of nptII and Tn5 in kanamycin-resistant bacteria from different environments. FEMS Microbiol Ecol 13: 47–58

    Article  Google Scholar 

  • Smit E, van Elsas JD (1992) Conjugal gene transfer in the soil environment: new approaches and developments. In: Gauthier MJ (ed) Gene transfers and environment. Springer, Berlin Heidelberg, New York, pp 79–94

    Google Scholar 

  • Somerville CC, Knight IT, Straube WL, Colwell RR (1989) Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol 55 (3): 548–554

    Google Scholar 

  • Stokes HW, Hall RM (1989) A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 3: 1669–1683

    Article  Google Scholar 

  • Thomson CJ, Amyes SGB (1993) Molecular epidemiology of the plasmid-encoded TEM-1 ß-lactamase in Scotland. Epidemiol Infect 110: 117–125

    Article  Google Scholar 

  • Tebbe C, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59 (8): 2657–2665

    Google Scholar 

  • Tietze E, Tschäpe H, Golubev AV (1990) DNA probes for studying streptothricin resistance evolution in enteric bacteria. J Basic Microbiol 30: 279: 287

    Google Scholar 

  • Trieu-Cuot P, Arthur M, Courvalin P (1987) Origin, evolution and dissemination of antibiotic resistance genes. Microbiol Sei 4 (9): 263–266

    Google Scholar 

  • Tsai Y-L, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57 (4): 1070–1074

    Google Scholar 

  • Tschäpe H, Tietze E, Prager R, Voigt W, Wolter E, Seitmann G (1984) Plasmid-borne streptothricin resistance in gram-negative bacteria. Plasmid 12: 189–196

    Article  Google Scholar 

  • Turpin PE, Maycroft KA, Rowlands CL, Wellington EMH (1993) Viable but non-culturable salmonellas in soil. J Appl Bacteriol 74: 421–427

    Article  Google Scholar 

  • Van Asselt GJ, Vliegenthart JS, Petit PLC, Van de Klundert JAM, Mouton RP (1992) High-level aminoglycoside resistance among enterococci and group A streptococci. J Antimicrob Chemother 30: 651–659

    Google Scholar 

  • Van Elsas JD (1992) Antibiotic resistance gene transfer in the environment: an overview. In: Wellington EMH, Van Elsas JD (eds) Genetic interactions among microorganisms in the natural environment. Pergamon, Oxford, pp 17–39

    Google Scholar 

  • Vliegenthart JS, Ketelaar-van Galen P, Van de Kundert JAM (1990) Identification of three genes coding for aminoglycoside-modifying enzymes by means of the polymerase chain reaction. J Antimicrob Chemother 25: 759–765

    Google Scholar 

  • Weichart D, Oliver JD, Kjelleberg S (1992) Low temperature induced non-eulturability and killing of Vibrio vulnificus. FEMS Microbiol Lett 100: 205–210

    Google Scholar 

  • Wendt-Potthoff K, Backhaus H, Smalla K (1994) Monitoring the fate of genetically engineered bacteria sprayed on the phylloplane of bush beans and grass. FEMS Microbiol Ecol 15: 279–290

    Article  Google Scholar 

  • Wilson K (1987) Preparation of genomic DNA from bacteria. In: Ausubel FM, Bent R, Kingston RE, Moore DD, Smith JA, Seidmann JG, Struhl K (eds) Current protocols in molecular biology. Greene and Wiley, New York

    Google Scholar 

  • Young CC, Burghoff RL, Keim LG, Minak-Bernero V, Lute JR, Hinton SM (1993) Polyvinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction- amplifiable DNA from soils. Appl Environ Microbiol 59 (6) 1972–1974

    Google Scholar 

Download references

Authors
  1. K. Smalla
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. D. van Elsas
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Environmental Biology, University of Guelph Lab. Microbial Techniques, N1G 2W1, Guelph, Ontario, Canada

    Jack T. Trevors

  2. DLO-Institute for Soil Fertility Research c/o IPO-DLO, Binnenhaven 12, P.O. Box 9060, 6700 GW, Wageningen, The Netherlands

    J. Dick van Elsas

Rights and permissions

Reprints and permissions

Copyright information

© 1995 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Smalla, K., van Elsas, J.D. (1995). Application of the PCR for Detection of Antibiotic Resistance Genes in Environmental Samples. In: Trevors, J.T., van Elsas, J.D. (eds) Nucleic Acids in the Environment. Springer Lab Manuals. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-79050-8_12

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-79050-8_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-58069-0

  • Online ISBN: 978-3-642-79050-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation