Abundant rifampin resistance genes and significant correlations of antibiotic resistance genes and plasmids in various environments revealed by metagenomic analysis

Applied Microbiology and Biotechnology

Volumn 98, Issue 11, 2014, Pages 5195-5204

  Ma, Liping ^a   Li, Bing ^a   Zhang, Tong ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Metagenomic analysis; Mobile genetic element; Plasmid; Rifampin resistance gene

Indexed keywords

ANAEROBIC DIGESTION; DNA;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC RESISTANCE GENES; GENETIC ELEMENTS; LINEAR CORRELATION; METAGENOMIC ANALYSIS; PLASMID; RESISTANCE GENES; STRONG CORRELATION;

GENES;

ACRIDINE; ACRIFLAVINE; AMINOCOUMARIN DERIVATIVE; AMINOGLYCOSIDE DERIVATIVE; CHLORAMPHENICOL; DAPTOMYCIN; DNA TOPOISOMERASE IV; DRINKING WATER; ETHAMBUTOL; FRESH WATER; MACROLIDE; QUINOLONE DERIVATIVE; RIBOSOMAL PROTEIN S12; RIBOSOME PROTEIN; RIFAMPICIN; RIVER WATER; RNA POLYMERASE BETA SUBUNIT; SULFONAMIDE; TEICOPLANIN; TETRACYCLINE; TETRACYCLINE DERIVATIVE; UNCLASSIFIED DRUG; VANCOMYCIN; ANTIINFECTIVE AGENT; BACTERIAL DNA;

ABUNDANCE; ANTIBIOTIC RESISTANCE; BIOFILM; CORRELATION; GENETIC ANALYSIS; GENOMICS; PLASMID; SPECIES DIVERSITY;

ACTIVATED SLUDGE; ANAEROBIC DIGESTION; ANTIBIOTIC RESISTANCE; AQUACULTURE; ARTICLE; BIOFILM; ENVIRONMENT; GENE POOL; GENE STRUCTURE; INTEGRON; METAGENOMICS; MOBILE GENETIC ELEMENT; MULTIDRUG RESISTANCE; NONHUMAN; PLASMID; POND; RIVER; SEDIMENT; TRANSPOSON; WASTE WATER TREATMENT PLANT; BACTERIAL GENE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY;

ANTI-BACTERIAL AGENTS; DNA, BACTERIAL; DRUG RESISTANCE, BACTERIAL; ENVIRONMENTAL MICROBIOLOGY; GENES, BACTERIAL; METAGENOMICS; PLASMIDS; RIFAMPIN;

EID: 84901653423     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-5511-3     Document Type: Article

References (40)

1. Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, Handelsman J (2010) Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 8(4):251-259
2. Boerlin P, Reid-Smith RJ (2008) Antimicrobial resistance: its emergence and transmission. Anim Health Res Rev 9(2):115-126
3. Brown MG, Balkwill DL (2009) Antibiotic resistance in bacteria isolated from the deep terrestrial subsurface. Microb Ecol 57(3):484-493
4. Budiati T, Rusul G, Wan-Abdullah WN, Arip YM, Ahmad R, Thong KL (2013) Prevalence, antibiotic resistance and plasmid profiling of Salmonella in catfish (Clarias gariepinus) and tilapia (Tilapia mossambica) obtained from wet markets and ponds in Malaysia. Aquaculture 372:127-132
5. Caoili JC, Mayorova A, Sikes D, Hickman L, Plikaytis BB, Shinnick TM (2006) Evaluation of the TB-Biochip oligonucleotide microarray system for rapid detection of rifampin resistance in Mycobacterium tuberculosis. J Clin Microbiol 44(7):2378-2381 (Pubitemid 44092401)
6. 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(16):4271-4280
7. Conseil G, Decottignies A, Jault JM, Comte G, Barron D, Goffeau A, Di Pietro A (2000) Prenyl-flavonoids as potent inhibitors of the Pdr5p multidrug ABC transporter from Saccharomyces cerevisiae. Biochemistry 39(23):6910-6917 (Pubitemid 30390384)
8. Coyne S, Guigon G, Courvalin P, Perichon B (2010) Screening and quantification of the expression of antibiotic resistance genes in Acinetobacter baumannii with a microarray. Antimicrob Agents Chemother 54(1):333-340
9. Cummings DE, Archer KF, Arriola DJ, Baker PA, Faucett KG, Laroya JB, Pfeil KL, Ryan CR, Ryan KRU, Zuill DE (2011) Broad dissemination of plasmid-mediated quinolone resistance genes in sediments of two urban coastal wetlands. Environ Sci Technol 45(2):447-454
10. Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74(3):417-425
11. Dawson RJP, Locher KP (2007) Structure of the multidrug ABC transporter Sav 1866 from Staphylococcus aureus in complex with AMPPNP. FEBS Lett 581(5):935-938 (Pubitemid 46282725)
12. Di Cesare A, Vignaroli C, Luna GM, Pasquaroli S, Biavasco F (2012) Antibiotic-resistant Enterococci in seawater and sediments from a coastal fish farm. Microb Drug Resist 18(5):502-509
13. Gomez DI, Fisher-Hoch SP, Bordt AS, Quitugua TN, Robledo J, Alvarez N, Correa N, McCormick JB, Restrepo BI (2010) Systematic interpretation of molecular beacon polymerase chain reaction for identifying rpoB mutations in Mycobacterium tuberculosis isolates with mixed resistant and susceptible bacteria. DiagnMicrobiol Infect Dis 67(1):37-46
14. Ibekwe AM, Murinda SE, Graves AK (2011) Genetic diversity and antimicrobial resistance of Escherichia coli from human and animal sources uncovers multiple resistances from human sources. PLoS One 6(6):e20819
15. Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegard B, Soderstrom H, Larsson DGJ (2011) Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS One 6(2):e17038
16. Kyselkova M, Chronakova A, Volna L, Nemec J, Ulmann V, Scharfen J, Elhottova D (2012) Tetracycline resistance and presence of tetracycline resistance determinants tet(V) and tap in rapidly growing Mycobacteria from agricultural soils and clinical isolates. Microbes Environ 27(4):413-422
17. Li B, Zhang T, Xu Z, Fang HHP (2009) Rapid analysis of 21 antibiotics of multiple classes in municipal wastewater using ultra performance liquid chromatography-tandem mass spectrometry. Anal Chim Acta 645(1-2):64-72
18. Liu B, Pop M (2009) ARDB - antibiotic resistance genes database. Nucleic Acids Res 37:D443-D447
19. Luo Y, Xu L, Rysz M, Wang YQ, Zhang H, Alvarez PJJ (2011) Occurrence and transport of tetracycline, sulfonamide, quinolone, and macrolide antibiotics in the Haihe River Basin, China. Environ Sci Technol 45(5):1827-1833
20. Mardis ER (2011) A decade's perspective on DNA sequencing technology. Nature 470(7333):198-203
21. Martínez-Martínez L, Pascual A, Jacoby GA (1998) Quinolone resistance from a transferable plasmid. LANCET 351(9105):797-799 (Pubitemid 28112342)
22. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O'Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57(7):3348-3357
23. Melamed S, Lalush C, Elad T, Yagur-Kroll S, Belkin S, Pedahzur R (2012) A bacterial reporter panel for the detection and classification of antibiotic substances. Microb Biotechnol 5(4):536-548
24. Moura A, Soares M, Pereira C, Leitao N, Henriques I, Correia A (2009) INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 25(8):1096-1098
25. Nonaka L, Ikeno K, Suzuki S (2007) Distribution of tetracycline resistance gene, tet(M), in Gram-positive and Gram-negative bacteria isolated from sediment and seawater at a coastal aquaculture site in Japan. Microbes Environ 22(4):355-364
26. Partridge SR, Tsafnat G, Coiera E, Iredell JR (2009) Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 33(4):757-784
27. Poelarends GJ, Mazurkiewicz P, Putman M, Cool RH, van Veen HW, Konings WN (2000) An ABC-type multidrug transporter of Lactococcus lactis possesses an exceptionally broad substrate specificity. Drug Resist Updat 3(6):330-334 (Pubitemid 32118399)
28. Pruden A, Arabi M, Storteboom HN (2012) Correlation between upstream human activities and riverine antibiotic resistance genes. Environ Sci Technol 46(21):11541-11549
29. Qin JJ, Li RQ, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li JH, Xu JM, Li SC, Li DF, Cao JJ, Wang B, Liang HQ, Zheng HS, Xie YL, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu HM, Yu C, Li ST, Jian M, Zhou Y, Li YR, Zhang XQ, Li SG, Qin N, Yang HM, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD,Wang J, Consortium M (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285):59-U70
30. Roy U, Nair D (2007) Biodiversity of organotin resistant Pseudomonas from west coast of India. Ecotoxicology 16(2):253-261 (Pubitemid 46295251)
31. Shi P, Jia SY, Zhang XX, Zhang T, Cheng SP, Li AM (2013) Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water. Water Res 47(1):111-120
32. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32-D36
33. Su HC, Ying GG, Tao R, Zhang RQ, Zhao JL, Liu YS (2012) Class 1 and 2 integrons, sul resistance genes and antibiotic resistance in Escherichia coli isolated from Dongjiang River, South China. Environ Pollut 169:42-49
34. Suresh N, Singh UB, Arora J, Pande JN, Seth P, Samantaray JC (2006) Rapid detection of rifampicin-resistant Mycobacterium tuberculosis by in-house, reverse line blot assay. Diagn Microbiol Infect Dis 56(2):133-140 (Pubitemid 44486626)
35. Szczepanowski R, Braun S, Riedel V, Schneiker S, Krahn I, Puhler A, Schluter A (2005) The 120 592 bp lncF plasmid pRSB107 isolated from a sewage-treatment plant encodes nine different antibiotic-resistance determinants, two iron-acquisition systems and other putative virulence-associated functions. Microbiol-Sgm 151:1095-1111 (Pubitemid 40568006)
36. Tran JH, Jacoby GA (2002) Mechanism of plasmid-mediated quinolone resistance. Proc Natl Acad Sci U S A 99(8):5638-5642 (Pubitemid 34411602)
37. Venturini C, Beatson SA, Djordjevic SP, Walker MJ (2010) Multiple antibiotic resistance gene recruitment onto the enterohemorrhagic Escherichia coli virulence plasmid. FASEB J 24(4):1160-1166
38. Xu BJ, Mao DQ, Luo Y, Xu L (2011) Sulfamethoxazole biodegradation and biotransformation in the water-sediment system of a natural river. Bioresour Technol 102(14):7069-7076
39. Yang Y, Li B, Ju F, Zhang T (2013) Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach. Environ Sci Technol 47(18):10197-10205
40. Zhang T, Zhang XX, Ye L (2011) Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One 6(10):e26041