Draft genome sequencing of two Enterococcus faecium strains by pyrosequencing technology reveals niche-specific gene acquisition

Abstract number: P922

van Schaik W., Bonten M.J.M., Willems R.J.L.

Objectives:Enterococcus faecium has recently become an important cause of nosocomial infections. The rapid rise in E. faecium infections can be explained by the acquisition of antibiotic resistance mechanisms combined with the evolution of a hospital-associated E. faecium clade, termed Clonal Complex 17 (CC17). To reveal the genetic diversity in E. faecium strains from different environmental niches, we sequenced the genomes of two E. faecium strains from different clonal complexes (CC22 and CC17, respectively) using pyrosequencing technology.

Methods: The strains studied were E1071 (CC22, a vancomycin-resistant isolate that was picked up during routine hospital surveillance) and E1162 (CC17, a vancomycin-sensitive bloodstream isolate). The genomes of these two E. faecium strains were sequenced by Keygene (Wageningen, The Netherlands) using the GS FLX sequencer (454 Life Sciences, Branford CT, USA), with 20-fold coverage of the genome. Sequences were assembled using Newbler Assembler (454 Life Sciences). The draft genomes were annotated using the TIGR Annotation Engine and the encoded proteins were compared using PROMPT (Protein Mapping and Comparison Tool; http://webclu.bio.wzw.tum.de/prompt).

Results: The total number of sequence that could be assembled into contigs was 2.7 Mb for both strains, suggesting all but complete coverage of the genome. Automated and manually curated annotation of the draft genome sequences resulted in the prediction of 2716 and 2697 proteins for E1071 and E1162, respectively. More than 2200 proteins were more than 95% identical on the amino acid level between the two strains. Approximately 10% of the proteins were unique to each strain.

Using PROMPT the predicted proteins from the genomes of these two strains and the publicly available E. faecium DO strain (CC17) were compared. This revealed that the CC17 strains had genomic islands with functions in sugar uptake and metabolism that were absent in E1071. Two (partial) prophages were also specific for the CC17 strains. The presence of the TcrB copper resistance system and a specific point mutation in the vanX gene in strain E1071 strongly suggest that this strain originates from pigs.

Conclusion: Rapid draft genome sequencing has revealed the acquisition of several niche-specific genes in E. faecium and identified several genes and genetic elements that may be unique for CC17. The genome sequences contribute to ongoing functional studies into E. faecium in our laboratory.