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Bioinformatics Analysis of Antimicrobial Resistance Genes and Prophages Colocalized in Human Gut Metagenomes

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Abstract

The constant increase of bacterial antibiotic-resistant strains is directly linked to a common use of antibiotics in medicine and animal breeding. It is suggested that the gut microbiota serves as a reservoir for antibiotic resistance genes that can be transferred from symbiotic bacteria to pathogenic ones, particularly due to phage transduction. In this study, using the PHASTER prophage predicting tool and CARD antibiotics resistance database we have searched for antibiotic resistance genes that are located within prophages in human gut microbiota. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA, and cpxR/cpxA genes were identified inside prophages. These genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and also multidrug resistance. Three (0.46%) of 659 putative prophages predicted in the metagenomic assemblies contained antibiotics resistance genes in their sequences.

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References

  1. van Schaik, W., Philos. Trans. R. Soc. Lond. B. Biol. Sci., 2015, vol. 370, 20140087–20140087.

  2. Martinez, J.L., Science, 2008, vol. 321, pp. 365–367.

    Article  CAS  Google Scholar 

  3. Ochman, H., Lawrence, J.G., and Groisman, E.A., Nature, 2000, vol. 405, pp. 299–304.

    Article  CAS  Google Scholar 

  4. Rolain, J.M., Fancello, L., Desnues, C., and Raoult, D., J. Antimicrob. Chemother., 2011, vol. 66, pp. 2444–2447.

    Article  CAS  PubMed  Google Scholar 

  5. Fancello, L., Desnues, C., Raoult, D., and Rolain, J.M., J. Antimicrob. Chemother., 2011, vol. 66, pp. 2448–2454.

    Article  CAS  PubMed  Google Scholar 

  6. Modi, S.R., Lee, H.H., Spina, C.S., and Collins, J.J., Nature, 2013, vol. 499, pp. 219–222.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Subirats, J., Sànchez-Melsió, A., Borrego, C.M., Balcázar, J.L., and Simonet, P., Int. J. Antimicrob. Agents, 2016, vol. 48, pp. 163–167.

    Article  CAS  PubMed  Google Scholar 

  8. Schuch, R. and Fischetti, V.A., J. Bacteriol., 2006, vol. 188, pp. 3037–3051.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Novick, R.P., Christie, G.E., and Penadés, J.R., Nat. Rev. Microbiol., 2010, vol. 8, pp. 541–551.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Zhang, Y., and LeJeune, J.T., Vet. Microbiol., 2008, vol. 129, pp. 418–425.

    Article  CAS  PubMed  Google Scholar 

  11. Appelt, S., Fancello, L., Le Bailly, M., Raoult, D., Drancourt, M., and Desnues, C.C., Appl. Environ. Microbiol., 2014, vol. 80, pp. 2648–2655.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kleinheinz, K.A., Joensen, K.G., and Larsen, M.V., Bacteriophage, 2014, vol. 4. e27943.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Enault, F., Briet, A., Bouteille, L., Roux, S., Sullivan, M.B., and Petit, M.-A., ISME J., 2017, vol. 11, pp. 237–247.

    Article  CAS  PubMed  Google Scholar 

  14. Glushchenko, O.E., Samoilov, A.E., Olekhnovich, E.I., Kovarsky, B.A., Tyakht, A.V., Pavlenko, A.V., et al., Data Brief., 2017, vol. 11, pp. 68–71.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Grazziotin, A.L., Koonin, E.V., and Kristensen, D.M., Nucleic Acids Res., 2017, vol. 45, pp. D491–D498.

    Article  CAS  PubMed  Google Scholar 

  16. Dina, J., Malbruny, B., and Leclercq, R., Antimicrob. Agents Chemother., 2003, vol. 47, pp. 2307–2309.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Miller, W.R., Munita, J.M., and Arias, C.A., Expert Rev. Anti. Infect. Ther., 2014, vol. 12, pp. 1221–1236.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Edgar, R. and Bibi, E., J. Bacteriol., 1997, vol. 179, pp. 2274–2280.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Nishino, K., Latifi, T., and Groisman, E.A., Mol. Microbiol., 2006, vol. 59, pp. 126–141.

    Article  CAS  Google Scholar 

  20. Wu Y., Li, H., Li, J., and Huang, Z.H.H., J. Microbiol., 2008, vol. 46, pp. 687–691.

    Article  CAS  PubMed  Google Scholar 

  21. Briggs, C.E. and Fratamico, P.M., Antimicrob. Agents Chemother., 1999, vol. 43, pp. 846–849.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Weatherspoon-Griffin, N., Zhao, G., Kong, W., Kong, Y., Morigen, Andrews-Polymenis, H., et al., J. Biol. Chem., 2011, vol. 286, pp. 5529–5539.

    Article  CAS  PubMed  Google Scholar 

  23. Weatherspoon-Griffin, N., Yang, D., Kong, W., Hua, Z., and Shi, Y., J. Biol. Chem., 2014, vol. 289, pp. 32571–32582.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Gal-Mor, O. and Segal, G., J. Bacteriol., 2003, vol. 185, pp. 4908–4919.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Federal Research and Clinical Center of Physical-Chemical Medicine, ul. Malaya Pirogovskaya 1a, Moscow, 119991, Russia

    E. V. Starikova, N. A. Prianichnikov & V. M. Govorun

  2. Medical School, University of Geneva, Geneva, Switzerland

    E. Zdobnov

Authors
  1. E. V. Starikova
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  2. N. A. Prianichnikov
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  3. E. Zdobnov
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  4. V. M. Govorun
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Correspondence to E. V. Starikova.

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Original Russian Text © E.V. Starikova, N.A. Prianichnikov, E. Zdobnov, V.M. Govorun, 2018, published in Biomeditsinskaya Khimiya.

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Starikova, E.V., Prianichnikov, N.A., Zdobnov, E. et al. Bioinformatics Analysis of Antimicrobial Resistance Genes and Prophages Colocalized in Human Gut Metagenomes. Biochem. Moscow Suppl. Ser. B 12, 114–118 (2018). https://doi.org/10.1134/S1990750818020129

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  • DOI: https://doi.org/10.1134/S1990750818020129

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