Application of real-time PCR array to the multiple detection of antibiotic resistant genes in glacier ice samples

Journal of General and Applied Microbiology

Volumn 56, Issue 1, 2010, Pages 43-52

  Ushida, Kazunari ^a   Segawa, Takahiro ^b,c   Kohshima, Shiro ^d   Takeuchi, Nozomu ^e   Fukui, Kotaro ^b   Li, Zhongqin ^f   Kanda, Hiroshi ^b  

^a KYOTO PREFECTURAL UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF POLAR RESEARCH   (Japan)

^c Transdisciplinary Research Integration Center   (Japan)

^d WILDLIFE RESEARCH CENTER OF KYOTO UNIVERSITY   (Japan)

^e CHIBA UNIVERSITY   (Japan)

^f Chinese Academy of Sciences   (China)

Author keywords

Antibiotic resistant gene; Glacier ice; Real time PCR array

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; BACTERIAL DNA; BETA LACTAM ANTIBIOTIC; CHLORAMPHENICOL; MACROLIDE; POLYPEPTIDE ANTIBIOTIC AGENT; TETRACYCLINE;

ANTARCTICA; ANTIBIOTIC RESISTANCE; ARTICLE; ASIA; BACTERIAL GENE; CONTROLLED STUDY; GENE IDENTIFICATION; GENE SEQUENCE; GLACIER; NONHUMAN; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; UNINDEXED SEQUENCE; UNITED STATES;

EID: 77950455568     PISSN: 00221260     EISSN: 13498037     Source Type: Journal    
DOI: 10.2323/jgam.56.43     Document Type: Article

References (45)

1. Aarestrup, F. M. (2006) Antimicrobial Resistance in Bacteria of Animal Origin, ASM Press, Washington DC, USA, 442 pp.
2. Agerso, Y., Bruun, M. S., Dalsgaard, I., and Larsen, J. L. (2006) The tetracycline resistance gene tet(E) is frequently occurring and present on large horizontally transferable plasmids in Aeromonas spp. from fi sh farms. Aquaculture, 266, 47-52.
3. Amato, P., Hennebelle, R., Magand, O., Sancelme, M., Delort, A. M., Barbante, C., Boutron, C., and Ferrari, C. (2007) Bacterial characterization of the snow cover at Spitzberg, Svalbard. FEMS Microbiol. Ecol., 59, 255-264.
4. Andersen, S. R. and Sandaa, R. A. (1994) Distribution of tetracycline resistance determinants among gram-negative bacteria isolated from polluted and unpolluted marine sediments. Appl. Environ. Microbiol., 60, 908-912.
5. Bauernfeind, A., Stemplinger, I., Jungwirth, R., Ernst, S., and Casellas, J. M. (1996) Sequences of β-lactamase genes encoding CTX-M-1 (MEN-1) and CTX-M-2 and relationship of their amino acid sequences with those of other β-lactamases. Antimicrob. Agents Chemother., 40, 509-513.
6. Bradford, P. A., Urban, C., Mariano, N., Projan, S. J., Rahal, J. J., and Bush, K. (1997) Imipenem resistance in Klebsiella pneumoniae is associated with the combination of ACT-1, a plasmid-mediated AmpC β-lactamase, and the foss of an outer membrane protein. Antimicrob. Agents Chemother., 41, 563-569.
7. Cabello, F. C. (2006) Heavy use of prophylactic antibiotics in aquaculture: A growing problem for human and animal health and for the environment. Environ. Microbiol., 8, 1137-1144.
8. Chee-Sanford, J. C., Aminov, R. I., Krapac, I. J., Garrigues-Jeanjean, N., and Mackie, R. I. (2001) Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilities. Appl. Environ. Microbiol., 67, 1494-1502.
9. Chopra, I. and Roberts, M. (2001) Tetracycline antibiotics: Mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol. Mol. Biol. Rev., 65, 232-260.
10. Christner, B. C., Kvitko, B. H., and Reeve, J. N. (2003) Molecular identification of bacteria and eukarya inhabiting an Antarctic cryoconite hole. Extremophiles, 7, 177-183.
11. Desomer, J., Vereecke, D., Crespi, M., and Van Montagu, M. (1992) The plasmid-encoded chloramphenicol-resistance protein of Rhodococcus fascians is homologous to the transmembrane tetracycline efflux proteins. Mol. Microbiol., 6, 2377-2385.
12. Distler, J., Bräun, C., Ebert, A., and Piepersberg, W. (1987) Gene cluster for streptomycin biosynthesis in Streptomyces griseus: Analysis of a central region including the major resistance gene. Mol. Gen. Genet., 208, 204-210.
13. Fukui, K., Sone, T., Strelin, J. A., Torielli, C. A., Mori, J., and Fujii, Y. (2008) Dynamics and GPR stratigraphy of a polar rock glacier on James Ross Island, Antarctic Peninsula. J. Glaciol., 186, 445-451.
14. Furushita, M., Shiba, T., Maeda, T., Yahata, M., Kaneoka, A., Takahashi, Y., Torii, K., Hasegawa, T., and Ohta, M. (2003) Similarity of tetracycline resistance genes isolated from fish farm bacteria to those from clinical isolates. Appl. Environ. Microbiol., 69, 5336-5342.
15. Goni-Urriza, M., Le-Capdepuy, M., Arpin, C., Raymond, N., Caumette, P., and Qentin, C. (2000) Impact of an urban effluent on antibiotic resistance of riverine Enterobacteriaceae and Aeromonas spp. Appl. Environ. Microbiol., 66, 125-132.
16. Heuer, H., Krögerrecklenfort, E., Wellington, E. M. H., Egan, S., Van Elsas, J. D., van Overbeek, L., Collard, J.-M., Guillaume, G., Karagouni, A. D., Nikolakopoulou, T. L., and Smalla, K. (2002) Gentamicin resistance genes in environmental bacteria: Prevalence and transfer. FEMS Microbiol. Ecol., 42, 289-302.
17. Jakobsen, L., Sandvang, D., Hansen, L. H., Bagger-Skjøt, L., Westh, H., Jørgensen, C., Hansen, D. S., Pedersen, B. M., Monnet, D. L., Frimodt-Møller, N., Sørensen, S. J., and Hammerum, A. M. (2007) Characterisation, dissemination and persistence of gentamicin resistant Escherichia coli from a Danish university hospital to the waste water environment. Environ. Int., 34, 108-115.
18. Koike, S., Krapac, I. G., Oliver, H. D., Yannarell, A. C., Chee-Sanford, J. C., Aminov, R. I., and Mackie, R. I. (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.
19. Lane, D. J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, ed. by Stackebrandt, E. and Goodfellow, M., John Wiley & Sons, Inc., Chichester, United Kingdom, pp.115-175.
20. Li, W., Jaroszewski, L., and Godzik, A. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 17, 282-283.
21. Malik, A., Çelik, E.-K., Bohn, C., Böckelmann, U., Knobel, K., and Grohmann, E. (2008) Detection of conjugative plasmids and antibiotic resistance genes in anthropogenic soils from Germany and India. FEMS Microbiol. Lett., 279, 207-216.
22. Matsuoka, M., Endou, K., Kobayashi, H., Inoue, M., and Nakajima, M. (1997) A dyadic plasmid that shows MLS and PMS resistance in Staphylococcus aureus. FEMS Microbiol. Lett., 148, 91-96.
23. Nagy, I., Schoofs, G., Vanderleyden, J., and De Mot, R. (1997) Transposition of the IS21-related element IS1415 in Rhodococcus erythropolis. J. Bacteriol., 179, 4635-4638.
24. Nemergut, D., Anderson, S., Cleveland, C., Martin, A., Miller, A., Seimon, A., and Schmidt, S. (2007) Microbial community succession in an unvegetated, recently deglaciated soil. Microb. Ecol., 53, 110-122.
25. Normark, S., Lindquist, S., and Lindberg, F. (1986) Chromosomal beta-lactam resistance in enterobacteria. Scand. J. Infect. Dis., 49, 38-45.
26. Pallecchi, L., Lucchetti, C., Bartoloni, A., Bartalesi, F., Mantella, A., Gamboa, H., Carattoli, A., Paradisi, F., and Rossolini, G. M. (2007) Population structure and resistance genes in antibiotic-resistant bacteria from a remote community with minimal antibiotic exposure. Antimicrob. Agents Chemother., 51, 1179-1184.
27. Perreten, V., Vorlet-Fawer, L., Slickers, P., Ehricht, R., Kuhnert, P., and Frey, J. (2005) Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J. Clin. Microbiol., 43, 2291-2302.
28. Petersen, A., Andersen, J. S., Kaewmak, T., Somsiri, T., and Dalsgaard, A. (2002). Impact of integrated fish farming on antimicrobial resistance in a pond environment. Appl. Environ. Microbiol., 68, 6036-6042.
29. Polz, M. F. and Cavanaugh, C. M. (1998) Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol., 64, 3724-3730.
30. Pruden, A., Pei, R., Storteboom, H., and Carlson, K. H. (2006) Antibiotic resistance genes as emerging contaminants: Studies in northern Colorado. Environ. Sci. Technol., 40, 7445-7450.
31. Qiu, X., Wu, L., Huang, H., McDonel, P. E., Palumbo, A. V., Tiedje, J. M., and Zhou, J. (2001) Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol., 67, 880-887.
32. Segawa, T., Miyamoto, K., Ushida, K., Agata, K., Okada, N., and Kohshima, S. (2005) Seasonal change in bacterial flora and biomass in mountain snow from the Tateyama Mountains, Japan, analyzed by 16S rRNA gene sequencing and real-time PCR. Appl. Environ. Microbiol., 71, 123-130.
33. Sengeløv, G., Agersø, Y., Halling-Sørensen, B., Baloda, S. B., Andersen, J. S., and Jensen, L. B. (2003) Bacterial antibiotic resistance levels in Danish farmland as a result of treatment with pig manure slurry. Environ. Int., 28, 587-595.
34. Sheridan, P. P., Miteva, V. I., and Brenchley, J. E. (2003) Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core. Appl. Environ. Microbiol., 69, 2153-2160.
35. Sjölund, M., Bonnedahl, J., Hernandez, J., Bengtsson, S., Cederbrant, G., Pinhassi, J., Kahlmeter, G., and Olsen, B. (2008) Dissemination of multidrug-resistant bacteria into the Arctic. Emerg. Infect. Dis., 14, 70-72.
36. Skidmore, M., Anderson, S. P., Sharp, M., Foght, J., and Lanoil, B. D. (2005) Comparison of microbial community compositions of two subglacial environments reveals a possible role for microbes in chemical weathering processes. Appl. Environ. Microbiol., 71, 6986-6997.
37. Takeuchi, N., Kohshima, S., and Seko, K. (2001) Structure, formation, darkening process of albedo reducing material (cryoconite) on a Himalayan glacier: A granular algal mat growing on the glacier. Arct. Antarct. Alpine Res., 33: 115-122.
38. Takeuchi, N. and Li, Z. (2008) Characteristics of surface dust on Ürümqi glacier No. 1 in the Tien Shan Mountains, China. Arct. Antarct. Alpine Res., 40, 744-750.
39. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
40. Van Elsas, J. D. and Bailey, M. J. (2002) The ecology of transfer of mobile genetic elements. FEMS Microbiol. Ecol., 42, 187-197.
41. Van Overbeek, L. S., Wellington, E. M. H., Egan, S., Smalla, K., Heuer, H., Collard, J.-M., Guillaume, G., Karagouni, A. D., Nikolakopoulou, T. L., and van Elsas, J. D. (2002) Prevalence of streptomycin-resistance genes in bacterial populations in European habitats. FEMS Microbiol. Ecol., 42, 277-288.
42. White, D. G., Alekshun, M. N., and Mcdermott, P. F. (2005) Frontiers in Antimicrobial Resistance: A Tribute to Stuart B. Levy, ASM Press, Washington DC, USA, 570 pp.
43. Wilson, K. H. and Blitchington, R. B. (1996) Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol., 62, 2273-2278.
44. Wohlleben, W., Arnold, W., Bissonnette, L., Pelletier, A., Tanguay, A., Roy, P. H., Gamboa, G. C., Barry, G. F., Aubert, E., Davies, J., and Kagan, S. A. (1989) On the evolution of Tn 21-like multiresistance transposons: Sequence analysis of the gene (aacC1) for gentamicin acetyltransferase-3I(AAC(3)-I), another member of the Tn 21-based expression cassette. Mol. Gen. Genet., 217, 202-208.
45. Zhang, K., Martiny, A. C., Reppas, N. B., Barry, K. W., Malek, J., Chisholm, S. W., and Church, G. M. (2006) Sequencing genomes from single cells by polymerase cloning. Nat. Biotechnol., 24, 680-686.