Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis

Theresa Mikalsen, Torunn Pedersen, Rob Willems, Teresa M. Coque, Guido Werner, Ewa Sadowy, Willem van Schaik, Lars Bogø Jensen, Arnfinn Sundsfjord, Kristin Hegstad

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Abstract

Background: The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial resistance genes encoded by mobile genetic elements (MGEs). Here, we investigate this mobilome in successful hospital associated genetic lineages, E. faecium sequence type (ST) 17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) by DNA microarray analyses. Results: The hybridization patterns of 272 representative targets including plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29) and clustered regularly interspaced short palindromic repeats (CRISPR)-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. RCR-, Rep_3-, RepA_N- and Inc18-family plasmids were highly prevalent and with the exception of Rep_3, evenly distributed between the species. There was a considerable difference in the replicon profile, with rep(17/pRUM), rep(2/pRE25), rep(14/EFNP1) and rep(20/pLG1) dominating in E. faecium and rep(9/pCF10), rep(2/pRE25) and rep(7) in E. faecalis strains. We observed an overall high correlation between the presence and absence of genes coding for resistance towards antibiotics, metals, biocides and their corresponding MGEs as well as their phenotypic antimicrobial susceptibility pattern. Although most IS families were represented in both E. faecalis and E. faecium, specific IS elements within these families were distributed in only one species. The prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982- and IS4-transposases was significantly higher in E. faecium than E. faecalis, and that of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 that have only been reported in few enterococcal isolates were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. Conclusions: The targeted MGEs were highly prevalent among the selected STs, underlining their potential importance in the evolution of hospital-adapted lineages of enterococci. Although the propensity of inter-species horizontal gene transfer (HGT) must be emphasized, the considerable species-specificity of these MGEs indicates a separate vertical evolution of MGEs within each species, and for E. faecalis within each ST.
Original languageEnglish
Article number282
JournalB M C Genomics
Volume16
Issue number1
Number of pages16
ISSN1471-2164
DOIs
Publication statusPublished - 2015

Keywords

  • adaptive traits
  • mobilome
  • species evolution
  • Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Gram-Positive Cocci [07700] Enterococcus faecalis species pathogen Enterococcus faecium species pathogen
  • 03502, Genetics - General
  • 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines
  • 31000, Physiology and biochemistry of bacteria
  • 31500, Genetics of bacteria and viruses
  • DNA microarray laboratory techniques, genetic techniques
  • gene transfer laboratory techniques, genetic techniques
  • hybridization laboratory techniques
  • polymerase chain reaction PCR laboratory techniques, genetic techniques
  • Genetics
  • BIOTECHNOLOGY
  • GENETICS
  • VANCOMYCIN-RESISTANT ENTEROCOCCI
  • TOXIN-ANTITOXIN SYSTEMS
  • LEVEL GENTAMICIN RESISTANCE
  • VANB2 GENE-CLUSTER
  • CLONAL COMPLEX 2
  • INSERTION-SEQUENCE
  • GLYCOPEPTIDE RESISTANCE
  • ANTIMICROBIAL RESISTANCE
  • STAPHYLOCOCCUS-AUREUS
  • ANTIBIOTIC-RESISTANCE
  • Hospital associated/clinical enterococcus
  • Horizontal gene transfer
  • Mobile genetic elements
  • Antibiotic resistance

Cite this

Mikalsen, T., Pedersen, T., Willems, R., Coque, T. M., Werner, G., Sadowy, E., van Schaik, W., Jensen, L. B., Sundsfjord, A., & Hegstad, K. (2015). Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis. B M C Genomics, 16(1), [282]. https://doi.org/10.1186/s12864-015-1407-6