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

  • Environmental biotechnology
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Abstract

In the present study, a newly developed metagenomic analysis approach was applied to investigate the abundance and diversity of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in aquaculture farm sediments, activated sludge, biofilm, anaerobic digestion sludge, and river water. BLASTX analysis against the Comprehensive Antibiotic Resistance Database was conducted for the metagenomic sequence data of each sample and then the ARG-like sequences were sorted based on structured sub-database using customized scripts. The results showed that freshwater fishpond sediment had the highest abundance (196 ppm), and anaerobic digestion sludge possessed the highest diversity (133 subtypes) of ARGs among the samples in this study. Significantly, rifampin resistance genes were universal in all the diverse samples and consistently accounted for 26.9~38.6 % of the total annotated ARG sequences. Furthermore, a significant linear correlation (R 2 = 0.924) was found between diversities (number of subtypes) of ARGs and diversities of plasmids in diverse samples. This work provided a wide spectrum scan of ARGs and MGEs in different environments and revealed the prevalence of rifampin resistance genes and the strong correlation between ARG diversity and plasmid diversity for the first time.

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References

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Boerlin P, Reid-Smith RJ (2008) Antimicrobial resistance: its emergence and transmission. Anim Health Res Rev 9(2):115–126

    Article  PubMed  Google Scholar 

  • Brown MG, Balkwill DL (2009) Antibiotic resistance in bacteria isolated from the deep terrestrial subsurface. Microb Ecol 57(3):484–493

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  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(16):4271–4280

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74(3):417–425

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dawson RJP, Locher KP (2007) Structure of the multidrug ABC transporter Sav 1866 from Staphylococcus aureus in complex with AMP-PNP. FEBS Lett 581(5):935–938

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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. Diagn Microbiol Infect Dis 67(1):37–46

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Liu B, Pop M (2009) ARDB—antibiotic resistance genes database. Nucleic Acids Res 37:D443–D447

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Mardis ER (2011) A decade’s perspective on DNA sequencing technology. Nature 470(7333):198–203

    Article  CAS  PubMed  Google Scholar 

  • Martínez-Martínez L, Pascual A, Jacoby GA (1998) Quinolone resistance from a transferable plasmid. LANCET 351(9105):797–799

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Pruden A, Arabi M, Storteboom HN (2012) Correlation between upstream human activities and riverine antibiotic resistance genes. Environ Sci Technol 46(21):11541–11549

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Roy U, Nair D (2007) Biodiversity of organotin resistant Pseudomonas from west coast of India. Ecotoxicology 16(2):253–261

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Tran JH, Jacoby GA (2002) Mechanism of plasmid-mediated quinolone resistance. Proc Natl Acad Sci U S A 99(8):5638–5642

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

The authors thank the Hong Kong GRF (HKU 7201/11E) for the financial support on this study. Liping Ma thanks The University of Hong Kong for the postgraduate studentship. Dr. Bing Li thanks The University of Hong Kong for the postdoctoral fellowship. The technical assistance of Ms. Vicky Fung is also greatly appreciated.

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  1. Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, SAR, China

    Liping Ma, Bing Li & Tong Zhang

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  1. Liping Ma
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Correspondence to Tong Zhang.

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Ma, L., Li, B. & Zhang, T. Abundant rifampin resistance genes and significant correlations of antibiotic resistance genes and plasmids in various environments revealed by metagenomic analysis. Appl Microbiol Biotechnol 98, 5195–5204 (2014). https://doi.org/10.1007/s00253-014-5511-3

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