Skip to main content
SpringerLink
Log in

Molecular Detection of Resistance and Transfer Genes in Environmental Samples

  • Chapter
  • First Online:
Environmental Protection Strategies for Sustainable Development

Part of the book series: Strategies for Sustainability ((STSU))

Abstract

Horizontal plasmid transfer is the most important means of spreading resistance to antibiotics and heavy metals, as well as virulence genes, to closely and remotely related microorganisms thereby increasing the horizontal gene pool in so diverse habitats such as soils, wastewater, aquifer recharge systems and glacier ice. An overview about the currently used molecular tools to detect and quantify the abundance of antibiotic and heavy metal resistance and transfer genes in aquatic and terrestrial environments is provided. Habitats studied range from nutrient rich environments such as manured agricultural soils to oligotrophic habitats such as drinking water or glaciers in the Antarctic. The state of the art in antibiotic and heavy metal resistance mechanisms and monitoring of conjugative transfer factors to assess the transmissibility of the resistance factors is summarized. The chapter ends with perspectives on emerging new molecular monitoring tools suited to rapid, reliable and high throughput analysis of environmental samples differing in origin and level of pollution.

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

Access this chapter

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 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover 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

Institutional subscriptions

References

  • Abou-Shanab RA, van Berkum P, Angle JS (2007) Heavy metal resistance and genotypic analysis of metal resistance genes in gram-positive and gram-negative bacteria present in Ni-rich serpentine soil and in the rhizosphere of Alyssum murale. Chemosphere 68:360–367

    CAS  Google Scholar 

  • Abriouel H, Omar NB, Molinos AC, López RL, Grande MJ, Martínez-Viedma P, Ortega E, Cañamero MM, Galvez A (2008) Comparative analysis of genetic diversity and incidence of virulence factors and antibiotic resistance among enterococcal populations from raw fruit and vegetable foods, water and soil, and clinical samples. Int J Food Microbiol 123:38–49

    CAS  Google Scholar 

  • Agersø Y, Petersen A (2007) The tetracycline resistance determinant Tet 39 and the sulphonamide resistance gene sulII are common among resistant Acinetobacter spp. isolated from integrated fish farms in Thailand. J Antimicrob Chemother 59:23–27

    Google Scholar 

  • Ahmann D, Roberts AL, Krumholz LR, Morel FM (1994) Microbe grows by reducing arsenic. Nature 371(6500):750

    CAS  Google Scholar 

  • Ahmed AM, Furuta K, Shimomura K, Kasama Y, Shimamoto T (2006) Genetic characterization of multidrug resistance in Shigella spp. from Japan. J Med Microbiol 55:1685–1691

    CAS  Google Scholar 

  • Akinbowale OL, Peng H, Barton MD (2007) Diversity of tetracycline resistance genes in bacteria from aquaculture sources in Australia. J Appl Microbiol 103:2016–2025

    CAS  Google Scholar 

  • Allen HK, Moe LA, Rodbumrer J, Gaarder A, Handelsman J (2009) Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil. ISME J 3:243–251

    CAS  Google Scholar 

  • Alvarez-Martinez CE, Christie PJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73:775–808

    CAS  Google Scholar 

  • Ansari MI, Grohmann E, Malik A (2008) Conjugative plasmids in multi-resistant bacterial isolates from Indian soil. J Appl Microbiol 104:1774–1781

    CAS  Google Scholar 

  • Antwerpen MH, Schellhase M, Ehrentreich-Foerster E, Witte W, Nuebel U (2007) DNA microarray for detection of antibiotic resistance determinants in Bacillus anthracis and closely related Bacillus cereus. Mol Cell Probes 21:152–160

    CAS  Google Scholar 

  • Auerbach EA, Seyfried EE, McMahon KD (2007) Tetracycline resistance genes in activated sludge wastewater treatment plants. Water Res 41:1143–1151

    CAS  Google Scholar 

  • Bahl MI, Burmølle M, Meisner A, Hansen LH, Sørensen SJ (2009) All IncP-1 plasmid subgroups, including the novel epsilon subgroup, are prevalent in the influent of a Danish wastewater treatment plant. Plasmid 62:134–139

    CAS  Google Scholar 

  • Barkay T, Miller SM, Summers AO (2003) Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev 27:355–384

    CAS  Google Scholar 

  • Barkay T, Liebert C, Gillman M (1989) Hybridization of DNA probes with whole-community genome for detection of genes that encode microbial responses to pollutants: mer genes and Hg2+ resistance. Appl Environ Microbiol 55:1574–1577

    CAS  Google Scholar 

  • Barker-Reid F, Fox EM, Faggian R (2010) Occurrence of antibiotic resistance genes in reclaimed water and river water in the Werribee Basin, Australia. J Water Health 8:521–531

    CAS  Google Scholar 

  • Barz M, Beimgraben C, Staller T, Germer F, Opitz F, Marquardt C, Schwarz C, Gutekunst K., Vanselow KH, Schmitz R, LaRoche J, Schulz R, Appel J 2010. Distribution analysis of hydrogenases in surface waters of marine and freshwater environments. PLoS One 5:e13846

    Google Scholar 

  • Batt AL, Snow DD, Aga DS (2006) Occurrence of sulfonamide antimicrobials in private water wells in Washington County, Idaho, USA. Chemosphere 64:1963–1971

    CAS  Google Scholar 

  • Bell JM, Paton JC, Turnidge J (1998) Emergence of vancomycin-resistant enterococci in Australia: phenotypic and genotypic characteristics of isolates. J Clin Microbiol 36:2187–2190

    CAS  Google Scholar 

  • Biddle JF, White JR, Teske AP, House CH (2011) Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes. ISME J 5(6):1038–1047. doi:10.1038/ismej.2010.199

    Google Scholar 

  • Binh CT, Heuer H, Kaupenjohann M, Smalla K (2008) Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids. FEMS Microbiol Ecol 66:25–37

    CAS  Google Scholar 

  • Böckelmann U, Dörries H-H, Ayuso-Gabella MN, Salgot de Marçay M, Tandoi V, Levantesi C, Masciopinto C, Van Houtte E, Szewzyk U, Wintgens T, Grohmann E (2009) Quantitative real-time PCR monitoring of bacterial pathogens and antibiotic resistance genes in three European artificial groundwater recharge systems. Appl Environ Microbiol 75:154–163

    Google Scholar 

  • Börjesson S, Dienues O, Jarnheimer PA, Olsen B, Matussek A, Lindgren PE (2009a) Quantification of genes encoding resistance to aminoglycosides, beta-lactams and tetracyclines in wastewater environments by real-time PCR. Int J Environ Health Res 19:219–230

    Google Scholar 

  • Börjesson S, Melin S, Matussek A, Lindgren PE (2009b) A seasonal study of the mecA gene and Staphylococcus aureus including methicillin-resistant S. aureus in a municipal wastewater treatment plant. Water Res 43:925–932

    Google Scholar 

  • Borremans B, Hobman JL, Provoost A, Brown NL, van der Lelie D (2001) Cloning and functional analysis of the pbr lead resistance determinant of Ralstonia metallidurans CH34. J Bacteriol 183:5651–5658

    CAS  Google Scholar 

  • Brochet M, Couvé E, Zouine M, Poyart C, Glaser P (2008) A naturally occurring gene amplification leading to sulfonamide and trimethoprim resistance in Streptococcus agalactiae. J Bacteriol 190:672–680

    CAS  Google Scholar 

  • Brockman FJ, Denovan BA, Hicks RJ, Fredrickson JK (1989) Isolation and characterization of quinoline-degrading bacteria from subsurface sediments. Appl Environ Microbiol 55:1029–1032

    CAS  Google Scholar 

  • Brown NL, Rouch DA, Lee BTO (1992) Copper resistance determinants in bacteria. Plasmid 27:41–51

    CAS  Google Scholar 

  • Bruce KD (1997) Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Appl Environ Microbiol 63:4914–4919

    CAS  Google Scholar 

  • Byrne-Bailey KG, Gaze WH, Kay P, Boxall AB, Hawkey PM, Wellington EM (2009) Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom. Antimicrob Agents Chemother 53:696–702

    CAS  Google Scholar 

  • Cai L, Liu G, Rensing C, Wang G (2009) Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils. BMC Microbiol 9:4

    Google Scholar 

  • Call DR (2005) Challenges and opportunities for pathogen detection using DNA microarrays. Crit Rev Microbiol 31:91–99

    CAS  Google Scholar 

  • Castiglioni S, Pomati F, Miller K, Burns BP, Zuccato E, Calamari D, Neilan BA (2008) Novel homologs of the multiple resistance regulator marA in antibiotic-contaminated environments. Water Res 42:4271–4280

    CAS  Google Scholar 

  • Chen CY, Wu KM, Chang YC, Chang CH, Tsai HC, Liao TL, Liu YM, Chen HJ, Shen AB, Li JC, Su TL, Shao CP, Lee CT, Hor LI, Tsai SF (2003) Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res 13:2577–2587

    CAS  Google Scholar 

  • Chen J, Yu Z, Michel FC Jr, Wittum T, Morrison M (2007) Development and application of real-time PCR assays for quantification of erm genes conferring resistance to macrolides-lincosamides-streptogramin B in livestock manure and manure management systems. Appl Environ Microbiol 73:4407–4416

    CAS  Google Scholar 

  • Cooksey DA (1994) Molecular mechanisms of copper resistance and accumulation in bacteria. FEMS Microbiol Rev 14:381–386

    CAS  Google Scholar 

  • Coombs JM (2009) Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface. In: Gogarten MB (ed) Horizontal gene transfer: genomes in flux, vol. 532, Humana Press, New York

    Google Scholar 

  • Cullen WR, Reimer KJ (1989) Arsenic speciation in the environment. Chem Rev 89:713–764

    CAS  Google Scholar 

  • Dang H, Zhang X, Song L, Chang Y, Yang G (2007) Molecular determination of oxytetracycline-resistant bacteria and their resistance genes from mariculture environments of China. J Appl Microbiol 103:2580–2592

    CAS  Google Scholar 

  • da Silva MF, Vaz-Moreira I, Gonzalez-Pajuelo M, Nunes OC, Manaia CM (2007) Antimicrobial resistance patterns in Enterobacteriaceae isolated from an urban wastewater treatment plant. FEMS Microbiol Ecol 60:166–176

    Google Scholar 

  • de Lipthay JR, Rasmussen LD, Oregaard G, Simonsen K, Bahl MI, Kroer N, Sørensen SJ (2008) Acclimation of subsurface microbial communities to mercury. FEMS Microbiol Ecol 65:145–155

    CAS  Google Scholar 

  • Disqué-Kochem C, Battermann A, Strätz M, Dreiseikelmann B (2001) Screening for trbB- and traG-like sequences by PCR for the detection of conjugative plasmids in bacterial soil isolates. Microbiol Res 156:159–168

    Google Scholar 

  • Ehrlich HL (1996) Geomicrobial interactions with arsenic and antimony, In: Ehrlich HL (ed) Geomicrobiology, 3rd edn. Dekker Inc., New York, NY, pp 276–293

    Google Scholar 

  • Feng L, Wang W, Cheng J, Ren Y, Zhao G, Gao C, Tang Y, Liu X, Han W, Peng X, Liu R, Wang L (2007) Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci USA 104:5602–5607

    Google Scholar 

  • Francia MV, Varsaki A, Garcillán-Barcia MP, Latorre A, Drainas C, de la Cruz F (2004) A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev 28:79–100

    CAS  Google Scholar 

  • Fredrickson JK, Hicks RJ, Li SW, Brockman FJ (1988) Plasmid incidence in bacteria from deep subsurface sediments. Appl Environ Microbiol 54:2916–2923

    CAS  Google Scholar 

  • Frye JG, Lindsey RL, Rondeau G, Porwollik S, Long F, McClelland M, Jackson CR, Englen MD, Meinersmann RJ, Berrang ME, Davis JA, Barrett JB, Turpin JB, Thitaram SN, Fedorka-Cray PJ (2010) Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information database. Microb Drug Resist 16:9–19

    CAS  Google Scholar 

  • Garcillán-Barcia MP, Francia MV, de la Cruz F (2009) The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 33:657–687. Review

    Google Scholar 

  • Gilbride KA, Lee DY, Beaudette LA (2006) Molecular techniques in wastewater: understanding microbial communities, detecting pathogens, and real-time process control. J Microbiol Methods 66:1–20

    CAS  Google Scholar 

  • Grohmann E, Muth G, Espinosa M (2003) Conjugative plasmid transfer in gram-positive bacteria. Microbiol Mol Biol Rev 67: 277–301

    CAS  Google Scholar 

  • Guardabassi L, Agersø Y (2006) Genes homologous to glycopeptide resistance vanA are widespread in soil microbial communities. FEMS Microbiol Lett 259:221–225

    CAS  Google Scholar 

  • Haferburg G, Kothe E (2007) Microbes and metals: interactions in the environment. J Basic Microbiol 47:453–467. Review

    CAS  Google Scholar 

  • Happi CT, Gbotosho GO, Folarin OA, Akinboye DO, Yusuf BO, Ebong OO, Sowunmi A, Kyle DE, Milhous W, Wirth DF, Oduola AM (2005) Polymorphisms in Plasmodium falciparum dhfr and dhps genes and age related in vivo sulfadoxine-pyrimethamine resistance in malaria-infected patients from Nigeria. Acta Trop 95:183–193

    CAS  Google Scholar 

  • Heuer H, Kopmann C, Binh CT, Top EM, Smalla K (2009) Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content. Environ Microbiol 11:937–949

    CAS  Google Scholar 

  • Hu X, Van der Auwera G, Timmery S, Zhu L, Mahillon J (2009) Distribution, diversity and potential mobility of extra-chromosomal elements related to the Bacillus anthracis pXO1- and pXO2 virulence plasmids. Appl Environ Microbiol 75: 3016–3028

    CAS  Google Scholar 

  • Iversen A, Kühn I, Rahman M, Franklin A, Burman LG, Olsson-Liljequist B, Torell E, Möllby R (2004) Evidence for transmission between humans and the environment of a nosocomial strain of Enterococcus faecium. Environ Microbiol 6:55–59

    Google Scholar 

  • Jareonmit P, Sajjaphan K, Sadowsky MJ (2010) Structure and diversity of arsenic resistant bacteria in an old tin mine area of Thailand. J Microbiol Biotechnol 20:169–178

    Google Scholar 

  • Jensen LB, Agerso Y, Sengelov G (2002) Presence of erm genes among macrolide-resistant Gram-positive bacteria isolated from Danish farm soil. Environ Int 28:487–491

    CAS  Google Scholar 

  • Jindal A, Kocherginskaya S, Mehboob A, Robert M, Mackie RI, Raski L, Zilles JL (2006) Antimicrobial use and resistance in swine waste treatment systems. Appl Environ Microbiol 72:7813–7820

    CAS  Google Scholar 

  • Kemper N (2008) Veterinary antibiotics in the aquatic and terrestrial environment. Ecol Indic 8:1–13

    CAS  Google Scholar 

  • Kim SH, Wei CI, Tzou YM, An HJ (2005) Multidrug-resistant Klebsiella pneumoniae isolated from farm environments and retail products in Oklahoma. J Food Prot 68:2022–2029

    CAS  Google Scholar 

  • Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB (2006) Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol 72:6299–6315

    CAS  Google Scholar 

  • Knapp CW, Dolfing J, Ehlert PA, Graham DW (2010) Evidence of increasing antibiotic resistance gene abundances in archived soils since (1940). Environ Sci Technol 44:580–587

    CAS  Google Scholar 

  • Koike S, Krapac IG, Oliver HD, Yannarell AC, Chee-Sanford JC, Aminov RI, Mackie RI (2007) Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period. Appl Environ Microbiol 73:4813–4823

    CAS  Google Scholar 

  • Kumar A, Schweizer HP (2005) Bacterial resistance to antibiotics: active efflux and reduced uptake. Adv Drug Deliv Rev 57:1486–1513

    CAS  Google Scholar 

  • Lachmayr KL, Kerkhof LJ, Dirienzo AG, Cavanaugh CM, Ford TE (2009) Quantifying nonspecific TEM beta-lactamase (blaTEM) genes in a wastewater stream. Appl Environ Microbiol 75:203–211

    CAS  Google Scholar 

  • Lambert PA (2005) Bacterial resistance to antibiotics: Modified target sites. Adv Drug Deliv Rev 57:1471–1485

    CAS  Google Scholar 

  • Lejon DP, Nowak V, Bouko S, Pascault N, Mougel C, Martins JM, Ranjard L (2007) Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination. FEMS Microbiol Ecol 61:424–437

    CAS  Google Scholar 

  • Levy SB (2002) Factors impacting on the problem of antibiotic resistance. J Antimicrob Chemother 49:25–30

    CAS  Google Scholar 

  • Levy SB, FitzGerald GB, Macone AB (1976) Changes in intestinal flora of farm personnel after introduction of a tetracycline-supplemented feed on a farm. N Engl J Med. 295: 583–588

    CAS  Google Scholar 

  • Levy SB, McMurry LM, Barbosa TM, Burdett V, Courvalin P, Hillen W, Roberts MC, Rood JI, Taylor DE (1999) Nomenclature for new tetracycline resistance determinants. Antimicrob Agents Chemother 43:1523–1524

    CAS  Google Scholar 

  • Levy C, Minnis D, Derrick JP (2008) Dihydropteroate synthase from Streptococcus pneumoniae: structure, ligand recognition and mechanism of sulfonamide resistance. Biochem J 412: 379–388

    CAS  Google Scholar 

  • Li XZ, Mehrotra M, Ghimire S, Adewoye L (2007) β-lactam resistance and β-lactamases in bacteria of animal origin. Vet Microbiol 121: 197–214

    CAS  Google Scholar 

  • Mackie RI, Koike S, Krapac I, Chee-Sanford J, Maxwell S, Aminov RI (2006) Tetracycline residues and tetracycline resistance genes in groundwater impacted by swine production facilities. Anim Biotechnol 17:157–176

    CAS  Google Scholar 

  • Malik A, Celik E-K, Bohn C, Boeckelmann U, Knobel K, Grohmann E (2008) Molecular detection of conjugative plasmids and antibiotic resistance genes in anthropogenic soils from Germany and India. FEMS Microbiol Lett 279:207–216

    CAS  Google Scholar 

  • Markoulatos P, Siafakas N, Moncany M (2002) Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal 16:47–51

    CAS  Google Scholar 

  • Mendez B, Tachibana C, Levy SB (1980) Heterogeneity of tetracycline resistance determinants. Plasmid 3:99–108

    CAS  Google Scholar 

  • Messi P, Guerrieri E, de Niederhäusern S, Sabia C, Bondi M (2006) Vancomycin-resistant enterococci (VRE) in meat and environmental samples. Int J Food Microbiol 107:218–222

    CAS  Google Scholar 

  • Mindlin SZ, Soina VS, Ptrova MA, Gorlenko ZhM (2008) Isolation of antibiotic resistance bacterial strains from East Siberia permafrost sediments. Genetika 44:36–44

    CAS  Google Scholar 

  • Moura A, Henriques I, Ribeiro R, Correia A (2007) Prevalence and characterization of integrons from bacteria isolated from a slaughterhouse wastewater treatment plant. J Antimicrob Chemother 60:1243–1250

    CAS  Google Scholar 

  • Moura A, Henriques I, Smalla K, Correia A (2010) Wastewater bacterial communities bring together broad-host range plasmids, integrons and a wide diversity of uncharacterized gene cassettes. Res Microbiol 161:58–66

    CAS  Google Scholar 

  • Nierman WC, Feldblyum TV, Laub MT et al (2001) Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci USA 98:4136–4141

    CAS  Google Scholar 

  • Nies DH (1999) Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51:730–750

    CAS  Google Scholar 

  • Nikolakopoulou TL, Giannoutsou EP, Karabatsou AA, Karagouni AD (2008) Prevalence of tetracycline resistance genes in Greek seawater habitats. J Microbiol 46:633–640

    CAS  Google Scholar 

  • Nriagu JO, Pacyna JM (1988) Quantitative assessment of worldwide contamination of air, water and soils by trace metals. Nature 333:134–139

    CAS  Google Scholar 

  • Ogunseitan OA, Tedford ET, Pacia D, Sirotkin KM, Sayler GS (1987) Distribution of plasmids in groundwater bacteria. J Ind Microbiol 1:311–317

    CAS  Google Scholar 

  • Oregaard G, Sørensen SJ (2007) High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA). ISME J 1:453–467

    CAS  Google Scholar 

  • Osborn AM, Bruce KD, Strike P, Ritchie DA (1997) Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon. FEMS MicrobiolRev 19:239–262

    CAS  Google Scholar 

  • Patterson AJ, Colangeli R, Spigaglia P, Scott KP (2007) Distribution of specific tetracycline and erythromycin resistance genes in environmental samples assessed by macroarray detection. Environ Microbiol 9:703–715

    CAS  Google Scholar 

  • Pechrada J, Sajjaphan K, Sadowsky MJ (2010) Structure and diversity of arsenic-resistant bacteria in an old tin mine area of Thailand. J Microbiol Biotechnol 20:169–178

    Google Scholar 

  • Pei R, Kim SC, Carlson KH, Pruden A (2006) Effect of river landscape on the sediment concentrations of antibiotics and corresponding antibiotic resistance genes (ARG). Water Res 40:2427–2435

    CAS  Google Scholar 

  • Picão RC, Poirel L, Demarta A, Silva CS, Corvaglia AR, Petrini O, Nordmann P (2008) Plasmid-mediated quinolone resistance in Aeromonas allosaccharophila recovered from a Swiss lake. J Antimicrob Chemother 62:948–950

    Google Scholar 

  • Prabhu DIG, Pandian RS, Vasan PT (2007) Pathogenicity, antibiotic susceptibility and genetic similarity of environmental and clinical isolates of Vibrio cholerae. Indian J Exp Biol 45:817–823

    CAS  Google Scholar 

  • Ramachandran D, Bhanumathi R, Singh DV (2007) Multiplex PCR for detection of antibiotic resistance genes and the SXT element: application in the characterization of Vibrio cholerae. J Med Microbiol 56:346–351

    CAS  Google Scholar 

  • Ramón-García S, Otal I, Martín C, Gómez-Lus R, Aínsa JA. (2006) Novel streptomycin resistance gene from Mycobacterium fortuitum. Antimicrob Agents Chemother 50:3920–3922

    Google Scholar 

  • Rensing C, Grass G (2003) Escherichia coli mechanisms of copper homeostasis in a changing environment. FEMS Microbiol Rev 27:197–213

    CAS  Google Scholar 

  • Roberts MC (2002) Resistance to tetracycline, macrolide-lincosamide-streptogramin, trimethoprim, and sulphonamide drug classes. Mol Biotechnol 20:261–283

    CAS  Google Scholar 

  • Roberts MC (2005) Update on acquired tetracycline resistance genes. FEMS Microbiol Lett 245:195–203

    CAS  Google Scholar 

  • Roberts MC, Kenny GE (1986) Dissemination of the tetM tetracycline resistance determinant to Ureaplasma urealyticum. Antimicrob Agents Chemother 29:350–352

    CAS  Google Scholar 

  • Roberts MC, Sutcliffe J, Courvalin P, Jensen LB, Rood J, Seppala H (1999) Nomenclature for macrolide and macrolide-lincosamide-streptogramin B resistance determinants. Antimicrob Agents Chemother 43:2823–2830

    CAS  Google Scholar 

  • Rochelle PA., Wetherbee MK, Olson BH (1991) Distribution of DNA sequences encoding narrow- and broad-spectrum mercury resistance. Appl Environ Microbiol 57:1581–1589

    CAS  Google Scholar 

  • Salanoubat M, Genin S, Artiguenave F et al (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415:497–502

    CAS  Google Scholar 

  • Samra ZQ, Naseem M, Khan SJ, Dar N, Athar MA (2009) PCR targeting of antibiotic resistant bacteria in public drinking water of Lahore metropolitan, Pakistan. Biomed Environ Sci 22:458–463

    CAS  Google Scholar 

  • Sarmah AK, Meyer MT, Boxall ABA (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

    CAS  Google Scholar 

  • Schelert J, Dixit V, Hoang V, Simbahan J, Drozda M, Blum P (2004) Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus by use of gene disruption. J Bacteriol 186:427–437

    CAS  Google Scholar 

  • Schlüter A, Krause L, Szczepanowski R, Goesmann A, Pühler A (2008) Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. J Biotechnol 136:65–76

    Google Scholar 

  • Schwarz S, Kehrenberg C, Doublet B, Cloeckaert A (2004) Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiol Rev 28:519–542

    CAS  Google Scholar 

  • Shakil S, Khan R, Zarrilli R, Khan AU (2008) Aminoglycosides versus bacteria- a description of the action, resistance mechanism, and nosocomial battleground. J Biomed Sci 15:5–14

    CAS  Google Scholar 

  • Silver S, Phung LT (1996) Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 50:753–789

    CAS  Google Scholar 

  • Sköld O (2000) Sulfonamide resistance: mechanisms and trends. Drug Resist Updat 3:155–160

    Google Scholar 

  • Sköld O (2001) Resistance to trimethoprim and sulfonamides. Vet Res 32:261–273

    Google Scholar 

  • Smalla K, Haines AS, Jones K, Krögerrecklenfort E, Heuer H, Schloter M, Thomas CM (2006) Increased abundance of IncP-1beta plasmids and mercury resistance genes in mercury-polluted river sediments: first discovery of IncP-1beta plasmids with a complex mer transposon as the sole accessory element. Appl Environ Microbiol 72:7253–7259

    CAS  Google Scholar 

  • Smith MS, Yang RK, Knapp CW, Niu Y, Peak N, Hanfelt MM, Galland JC, Graham DW (2004) Quantification of tetracycline resistance genes in feedlot lagoons by real-time PCR. Appl Environ Microbiol 70:7372–7377

    CAS  Google Scholar 

  • Sobecky PA, Hazen TH (2009) Horizontal gene transfer and mobile genetic elements in marine systems. In: Gogarten MB et al (eds) Horizontal gene transfer: genomes in flux, vol. 532. Humana Press, New York

    Google Scholar 

  • Sobecky PA, Mincer TJ, Chang MC, Helinski DR (1997) Plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups. Appl Environ Microbiol 63:888–895

    CAS  Google Scholar 

  • Srinivasan V, Nam HM, Nguyen LT, Tamilselvam B, Murinda SE, Oliver SP (2005) Prevalence of antimicrobial resistance genes in Listeria monocytogenes isolated from dairy farms. Foodborne Pathog Dis 2:201–211

    CAS  Google Scholar 

  • Stabler RA, Dawson LF, Oyston PC, Titball RW, Wade J, Hinds J, Witney AA, Wren BW (2008) Development and application of the active surveillance of pathogens microarray to monitor bacterial gene flux. BMC Microbiol 8:177

    Google Scholar 

  • Storteboom H, Arabi M, Davis JG, 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 44:1947–1953

    CAS  Google Scholar 

  • Stover CK, Pham XQ, Erwin AL et al (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959–964

    CAS  Google Scholar 

  • Swingley WD, Sadekar S, Mastrian SD, Matthies HJ, Hao J, Ramos H, Acharya CR, Conrad AL, Taylor HL, Dejesa LC, Shah MK, O’huallachain ME, Lince MT, Blankenship RE, Beatty JT, Touchman JW (2007) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 189:683–690

    CAS  Google Scholar 

  • Thompson SA., Maani EV, Lindell AH, King CJ, McArthur JV (2007) Novel tetracycline resistance determinant isolated from an environmental strain of Serratia marcescens. Appl Environ Microbiol 73:2199–2206

    CAS  Google Scholar 

  • Tom-Petersen A, Leser TD, Marsh TL, Nybroe O (2003) Effects of copper amendment on the bacterial community in agricultural soil analyzed by the T-RFLP technique. FEMS Microbiol Ecol 46:53–62

    CAS  Google Scholar 

  • Ushida K, Segawa T, Kohshima S, Takeuchi N, Fukui K, Li Z, Kanda H (2010) Application of real-time PCR array to the multiple detection of antibiotic resistant genes in glacier ice samples. J Gen Appl Microbiol 56:43–52

    CAS  Google Scholar 

  • Volkmann H, Schwartz T, Bischoff P, Kirchen S, Obst U (2004) Detection of clinically relevant antibiotic-resistance genes in municipal wastewater using real-time PCR (TaqMan). J Microbiol Methods 56:277–286

    CAS  Google Scholar 

  • Waldron PJ, Wu L, Van Nostrand JD, Schadt CW, He Z, Watson DB, Jardine PM, Palumbo AV, Hazen TC, Zhou J (2009) Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. Environ Sci Technol 43:3529–3534

    CAS  Google Scholar 

  • Wright GD (2005) Bacterial resistance to antibiotics: enzymatic degradation and modification. Adv Drug Deliv Rev 57:1451–1470

    CAS  Google Scholar 

  • Wright GD (2007) The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 5:175–186

    CAS  Google Scholar 

  • Yang S, Carlson K (2003) Evolution of antibiotic occurrence in a river through pristine, urban and agricultural landscapes. Water Res 37:4645–4656

    CAS  Google Scholar 

  • Yu Z, Michel FC Jr, Hansen G, Wittum T, Morrison M (2005) Development and application of real-time PCR assays for quantification of genes encoding tetracycline resistance. Appl Environ Microbiol 71:6926–6933

    Google Scholar 

  • Zhang T, Fang HHP (2006) Applications of real-time polymerase chain reactions for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 70:281–289

    CAS  Google Scholar 

  • Zhang X-X, Zhang T, Fang HP (2009) Antibiotic resistance genes in water environment. Appl Microbiol Biotechnol 82: 397–414

    CAS  Google Scholar 

  • Zhou Z, Raskin L, Zilles JL (2010) Effects of swine manure on macrolide, lincosamide, and streptogramin B antimicrobial resistance in soils. Appl Environ Microbiol 76:2218–2224

    CAS  Google Scholar 

  • Zhu B (2007) Abundance dynamics and sequence variation of neomycin phosphotransferase gene (nptII) homologs in river water. Aquat Microbiol Ecol 48:131–140

    Google Scholar 

Download references

Acknowledgements

We sincerely thank Miquel Salgot for critical reading of the manuscript. We regret that not all valuable contributions of colleagues in the field could have been included in this review due to space limitation.

Author information

Authors and Affiliations

  1. Department of Infectious Diseases, University Hospital Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany

    Elisabeth Grohmann

  2. Department of Environmental Microbiology, Technical University Berlin, Franklinstrasse 28/29, D-10587, Berlin, Germany

    Elisabeth Grohmann & Karsten Arends

Authors
  1. Elisabeth Grohmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Karsten Arends
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Elisabeth Grohmann .

Editor information

Editors and Affiliations

  1. Aligarh Muslim University, Aligarh, India

    Abdul Malik

  2. University Hospital Freiburg, Department of Infectious Diseases, Hugstetter Straße 55, Freiburg, 79106, Germany

    Elisabeth Grohmann

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Grohmann, E., Arends, K. (2012). Molecular Detection of Resistance and Transfer Genes in Environmental Samples. In: Malik, A., Grohmann, E. (eds) Environmental Protection Strategies for Sustainable Development. Strategies for Sustainability. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1591-2_5

Download citation

Publish with us

Policies and ethics

Search

Navigation