ORIGINAL RESEARCH

Identification of aminoglycoside phosphotransferases of clinical bacterial isolates in the microbiota of Russians

About authors

1 Laboratory of Bacterial Genetics, Department of Genetics and Biotechnology,
Vavilov Institute of General Genetics of RAS, Moscow, Russia

2 Department of biological and medical physics,
Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia

3 Scientific Research Center for Biotechnology of Antibiotics "BIOAN", Moscow

Correspondence should be addressed: Valery N. Danilenko
ul. Gubkina, d. 3, Moscow, Russia, 119991; ur.ggiv@direlav

About paper

Acknowledgements: authors thank Professor Sergey Sidorenko of North-West State Medial University for his comments on the article.

Contribution of the authors to this work: Kovtun AS — data analysis and interpretation, drafting of a manuscript; Alekseeva MG — analysis of literature, research planning, data collection and interpretation, drafting of a manuscript; Averina OV — data collection and interpretation, drafting of a manuscript; Danilenko VN — research planning, data interpretation, drafting of a manuscript. All authors participated in editing of the manuscript.

Received: 2017-03-29 Accepted: 2017-04-07 Published online: 2017-05-30
|
  1. Hossion AM, Sasaki K. Novel quercetin glycosides as potent anti- MRSA and anti-VRE agents. Recent Pat Antiinfect Drug Discov. 2013 Dec; 8 (3): 198–205.
  2. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013 Jul; 57 (7): 3348– 57.
  3. Wooldridge M. Evidence for the circulation of antimicrobial- resistant strains and genes in nature and especially between humans and animals. Rev Sci Tech. 2012 Apr; 31 (1): 231–47.
  4. Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, et al. Genomic variation landscape of the human gut microbiome. Nature. 2013 Jan 3; 493 (7430): 45–50.
  5. Elbehery AH, Aziz RK, Siam R. Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics. OMICS. 2016 Apr; 20 (4): 229–38.
  6. Blair JM, Webber MA, Baylay AJ, Ogbolu DO, Piddock LJ. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol. 2015 Jan; 13 (1): 42–51.
  7. Willmann M, El-Hadidi M, Huson DH, Schütz M, Weidenmaier C, Autenrieth IB, et al. Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics. Antimicrob Agents Chemother. 2015 Dec; 59 (12): 7335–45.
  8. Perry JA, Westman EL, Wright GD. The antibiotic resistome: what's new? Curr Opin Microbiol. 2014 Oct; 21: 45–50.
  9. Gibson MK, Forsberg KJ, Dantas G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J. 2015 Jan; 9 (1): 207–16.
  10. Shakya T, Wright GD. Nucleotide selectivity of antibiotic kinases. Antimicrob Agents Chemother. 2010 May; 54 (5): 1909–13.
  11. Wright GD. Molecular mechanisms of antibiotic resistance. Chem Commun (Camb). 2011 Apr 14; 47 (14): 4055–61.
  12. Shakya T, Stogios PJ, Waglechner N, Evdokimova E, Ejim L, Blanchard JE, et al. A small molecule discrimination map of the antibiotic resistance kinome. Chem Biol. 2011 Dec 23; 18 (12): 1591–601.
  13. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug 7; 21 (29): 8787–803.
  14. Fouhy F, Ogilvie LA, Jones BV, Ross RP, Ryan AC, Dempsey EM, et al. Identification of aminoglycoside and β-lactam resistance genes from within an infant gut functional metagenomic library. PLoS One. 2014 Sep 23; 9 (9): e108016.
  15. Forslund K, Sunagawa S, Coelho LP, Bork P. Metagenomic insights into the human gut resistome and the forces that shape it. Bioessays. 2014 Mar; 36 (3): 316–29.
  16. Emaneini M, Khoramian B, Jabalameli F, Beigverdi R, Asadollahi K, Taherikalani M, et al. Prevalence of high-level gentamicin-resistant Enterococcus faecalis and Enterococcus faecium in an Iranian hospital. J Prev Med Hyg. 2016 Dec; 57 (4): E197–E200.
  17. Mahbub Alam M, Kobayashi N, Ishino M, Sumi A, Kobayashi K, Uehara N, et al. Detection of a novel aph(2") allele (aph[2"]-Ie) conferring high-level gentamicin resistance and a spectinomycin resistance gene ant(9)-Ia (aad 9) in clinical isolates of enterococci. Microb Drug Resist. 2005 Fall; 11 (3): 239–47.
  18. Mahdiyoun SM, Kazemian H, Ahanjan M, Houri H, Goudarzi M. Frequency of Aminoglycoside-Resistance Genes in Methicillin- Resistant Staphylococcus aureus (MRSA) Isolates from Hospitalized Patients. Jundishapur J Microbiol. 2016 Jul 26; 9 (8):
  19. Standard operating procedure for fecal samples DNA extraction. The International Human Microbiome Standards (IHMS) project [Internet]. [cited 2017 Apr 3]. Available from: http://www. microbiome-standards.org/index.php#SOPS
  20. Andrews S. FastQC: A quality control tool for high throughput sequence data. Version 0.11.5 [software]. Babraham Bioinformatics group. 2016 Mar 8 [cited 2017 Apr 3]. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  21. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1; 30 (15): 2114–20.
  22. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4; 9 (4): 357–9.
  23. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012 May; 19 (5): 455–77.
  24. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015 Oct; 12 (10): 902–3.
  25. Mättö J, Suihko ML, Saarela M. Comparison of three test media for antimicrobial susceptibility testing of bifidobacteria using the Etest method. Int J Antimicrob Agents. 2006 Jul; 28 (1): 42–8.