title: Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.
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.
authors.affiliation: Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway. Theresa.Mikalsen@uit.no.
authors.forename: Theresa
authors.initials: T
authors.lastname: Mikalsen
authors.affiliation: Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway. Torunn.Annie.Pedersen@unn.no.
authors.forename: Torunn
authors.initials: T
authors.lastname: Pedersen
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands. rwillems@umcutrecht.nl.
authors.forename: Rob
authors.initials: R
authors.lastname: Willems
authors.affiliation: Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. teresacoque@gmail.com.|Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain. teresacoque@gmail.com.
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Coque
authors.affiliation: Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany. WernerG@rki.de.
authors.forename: Guido
authors.initials: G
authors.lastname: Werner
authors.affiliation: Department of Molecular Microbiology, National Medicines Institute, ul, Chełmska 30/34, 00-725, Warsaw, Poland. ewasadowy@cls.edu.pl.
authors.forename: Ewa
authors.initials: E
authors.lastname: Sadowy
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands. W.vanSchaik@umcutrecht.nl.
authors.forename: Willem
authors.initials: W
authors.lastname: van Schaik
authors.affiliation: Division of Food Microbiologyt, National Food Institute, Danish Technical University, Copenhagen V, Denmark. lboj@food.dtu.dk.
authors.forename: Lars Bogø
authors.initials: LB
authors.lastname: Jensen
authors.affiliation: Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway. arnfinn.sundsfjord@uit.no.|Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway. arnfinn.sundsfjord@uit.no.
authors.forename: Arnfinn
authors.initials: A
authors.lastname: Sundsfjord
authors.affiliation: Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway. Kristin.Hegstad@uit.no.|Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway. Kristin.Hegstad@uit.no.
authors.forename: Kristin
authors.initials: K
authors.lastname: Hegstad
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001483:Base Sequence; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics; D013293:Enterococcus faecalis / Q000235:genetics* / Q000302:isolation & purification; D016984:Enterococcus faecium / Q000235:genetics* / Q000302:isolation & purification; D022761:Gene Transfer, Horizontal / Q000235:genetics; D005798:Genes, Bacterial; D008040:Genetic Linkage; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008826:Microbial Sensitivity Tests; D009693:Nucleic Acid Hybridization; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D025341:Principal Component Analysis; D039002:Prophages / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents